Mon Aug 20 10:43:48 UTC 2012

Author: roduit-guest
Date: 2012-08-20 10:43:48 +0000 (Mon, 20 Aug 2012)
New Revision: 12094

Added:
   trunk/packages/openfovea/trunk/debian/files
   trunk/packages/openfovea/trunk/debian/openfovea.debhelper.log
   trunk/packages/openfovea/trunk/debian/openfovea.postinst.debhelper
   trunk/packages/openfovea/trunk/debian/openfovea.prerm.debhelper
   trunk/packages/openfovea/trunk/debian/openfovea.substvars
   trunk/packages/openfovea/trunk/debian/openfovea/
   trunk/packages/openfovea/trunk/debian/openfovea/DEBIAN/
   trunk/packages/openfovea/trunk/debian/openfovea/DEBIAN/control
   trunk/packages/openfovea/trunk/debian/openfovea/DEBIAN/md5sums
   trunk/packages/openfovea/trunk/debian/openfovea/DEBIAN/postinst
   trunk/packages/openfovea/trunk/debian/openfovea/DEBIAN/prerm
   trunk/packages/openfovea/trunk/debian/openfovea/usr/
   trunk/packages/openfovea/trunk/debian/openfovea/usr/bin/
   trunk/packages/openfovea/trunk/debian/openfovea/usr/bin/openfovea
   trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/
   trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/
   trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/
   trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea-0.1a160.egg-info
   trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/
   trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/Icon/
   trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/Icon/CellFovea.ico
   trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/Icon/CellFovea.png
   trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/Icon/CellFovea.svg
   trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/Icon/Export_curve.svg
   trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/Icon/NoData.png
   trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/Icon/NoData.svg
   trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/Icon/event.ico
   trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/Icon/event.png
   trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/Icon/event.svg
   trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/Icon/export.ico
   trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/Icon/export.png
   trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/Icon/export.svg
   trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/Icon/export_curve.ico
   trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/Icon/export_curve.png
   trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/Icon/icon64x64.svg
   trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/Icon/openfovea.ico
   trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/Icon/openfovea.png
   trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/Icon/tomo_x_square.svg
   trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/Icon/tomo_y_square.svg
   trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/Icon/tomo_z_square.svg
   trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/Icon/two_evt.ico
   trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/Icon/two_evt.png
   trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/Icon/two_evt.svg
   trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/__init__.py
   trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/classes.py
   trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/common.py
   trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/dialog_experiment_properties.py
   trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/dialog_export_map.py
   trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/dialog_flatten.py
   trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/dialog_mask_properties.py
   trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/fovea_toolbox/
   trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/fovea_toolbox/__init__.py
   trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/fovea_toolbox/curve.py
   trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/fovea_toolbox/file_util/
   trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/fovea_toolbox/file_util/__init__.py
   trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/fovea_toolbox/file_util/aex.py
   trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/fovea_toolbox/file_util/afm_file.py
   trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/fovea_toolbox/file_util/asylum.py
   trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/fovea_toolbox/file_util/common.py
   trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/fovea_toolbox/file_util/csem.py
   trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/fovea_toolbox/file_util/jpk.py
   trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/fovea_toolbox/file_util/nanoscope.py
   trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/fovea_toolbox/file_util/succellus_import.py
   trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/fovea_toolbox/misc.py
   trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/fovea_toolbox/opengl.py
   trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/fovea_toolbox/opengl_gtk.py
   trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/fovea_toolbox/post_proc.py
   trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/glade/
   trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/glade/dialog_experiment_properties.glade
   trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/glade/dialog_flatten.glade
   trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/glade/openfovea.glade
   trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/glade/plot.glade
   trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/glade/stiffness_plot.glade
   trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/openfovea_gui.py
   trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/plot_generic.py
   trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/plot_gtk.py
   trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/simple_window_gtk.py
   trunk/packages/openfovea/trunk/debian/openfovea/usr/share/
   trunk/packages/openfovea/trunk/debian/openfovea/usr/share/applications/
   trunk/packages/openfovea/trunk/debian/openfovea/usr/share/applications/openfovea.desktop
   trunk/packages/openfovea/trunk/debian/openfovea/usr/share/doc/
   trunk/packages/openfovea/trunk/debian/openfovea/usr/share/doc/openfovea/
   trunk/packages/openfovea/trunk/debian/openfovea/usr/share/doc/openfovea/changelog.Debian.gz
   trunk/packages/openfovea/trunk/debian/openfovea/usr/share/doc/openfovea/copyright
   trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pixmaps/
   trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pixmaps/openfovea.png
   trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/
   trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea-0.1a160.egg-info
   trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/
   trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/Icon/
   trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/Icon/CellFovea.ico
   trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/Icon/CellFovea.png
   trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/Icon/CellFovea.svg
   trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/Icon/Export_curve.svg
   trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/Icon/NoData.png
   trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/Icon/NoData.svg
   trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/Icon/event.ico
   trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/Icon/event.png
   trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/Icon/event.svg
   trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/Icon/export.ico
   trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/Icon/export.png
   trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/Icon/export.svg
   trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/Icon/export_curve.ico
   trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/Icon/export_curve.png
   trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/Icon/icon64x64.svg
   trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/Icon/openfovea.ico
   trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/Icon/openfovea.png
   trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/Icon/tomo_x_square.svg
   trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/Icon/tomo_y_square.svg
   trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/Icon/tomo_z_square.svg
   trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/Icon/two_evt.ico
   trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/Icon/two_evt.png
   trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/Icon/two_evt.svg
   trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/__init__.py
   trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/classes.py
   trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/common.py
   trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/dialog_experiment_properties.py
   trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/dialog_export_map.py
   trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/dialog_flatten.py
   trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/dialog_mask_properties.py
   trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/fovea_toolbox/
   trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/fovea_toolbox/__init__.py
   trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/fovea_toolbox/curve.py
   trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/fovea_toolbox/file_util/
   trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/fovea_toolbox/file_util/__init__.py
   trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/fovea_toolbox/file_util/aex.py
   trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/fovea_toolbox/file_util/afm_file.py
   trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/fovea_toolbox/file_util/asylum.py
   trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/fovea_toolbox/file_util/common.py
   trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/fovea_toolbox/file_util/csem.py
   trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/fovea_toolbox/file_util/jpk.py
   trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/fovea_toolbox/file_util/nanoscope.py
   trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/fovea_toolbox/file_util/succellus_import.py
   trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/fovea_toolbox/misc.py
   trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/fovea_toolbox/opengl.py
   trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/fovea_toolbox/opengl_gtk.py
   trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/fovea_toolbox/post_proc.py
   trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/glade/
   trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/glade/dialog_experiment_properties.glade
   trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/glade/dialog_flatten.glade
   trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/glade/openfovea.glade
   trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/glade/plot.glade
   trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/glade/stiffness_plot.glade
   trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/openfovea_gui.py
   trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/plot_generic.py
   trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/plot_gtk.py
   trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/simple_window_gtk.py
Modified:
   trunk/packages/openfovea/trunk/debian/
   trunk/packages/openfovea/trunk/debian/changelog
Log:
First try to build OpenFovea from Debian Med.



Property changes on: trunk/packages/openfovea/trunk/debian
___________________________________________________________________
Added: mergeWithUpstream
   + 1

Modified: trunk/packages/openfovea/trunk/debian/changelog
===================================================================

--- trunk/packages/openfovea/trunk/debian/changelog	2012-08-19 11:51:09 UTC (rev 12093)
+++ trunk/packages/openfovea/trunk/debian/changelog	2012-08-20 10:43:48 UTC (rev 12094)
@@ -1,4 +1,4 @@
-openfovea (0.1a155-1) UNRELEASED; urgency=low
+openfovea (0.1a160-1) UNRELEASED; urgency=low
 
   * Initial release (Closes: #<bug>)
 

Added: trunk/packages/openfovea/trunk/debian/files
===================================================================
--- trunk/packages/openfovea/trunk/debian/files	                        (rev 0)
+++ trunk/packages/openfovea/trunk/debian/files	2012-08-20 10:43:48 UTC (rev 12094)
@@ -0,0 +1 @@
+openfovea_0.1a160-1_all.deb science optional

Added: trunk/packages/openfovea/trunk/debian/openfovea/DEBIAN/control
===================================================================
--- trunk/packages/openfovea/trunk/debian/openfovea/DEBIAN/control	                        (rev 0)
+++ trunk/packages/openfovea/trunk/debian/openfovea/DEBIAN/control	2012-08-20 10:43:48 UTC (rev 12094)
@@ -0,0 +1,14 @@
+Package: openfovea
+Version: 0.1a160-1
+Architecture: all
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Installed-Size: 1670
+Depends: python-numpy, python-scipy, python-matplotlib, python-gtk2, python-gtkglext1, python2.7, python (>= 2.7.1-0ubuntu2), python (<< 2.8)
+Section: science
+Priority: optional
+Homepage: http://www.freesbi.ch/en/openfovea
+Description: Postprocessing of force volume data acquired with AFM.
+ OpenFovea is a software to postprocess AFM force volume experiment.
+ It is able to compute the stiffness of the scanned area, detect unbinding event
+ and the zero force topography. It comes with a user friendly graphical
+ interface that allow the user to select and display the data.

Added: trunk/packages/openfovea/trunk/debian/openfovea/DEBIAN/md5sums
===================================================================
--- trunk/packages/openfovea/trunk/debian/openfovea/DEBIAN/md5sums	                        (rev 0)
+++ trunk/packages/openfovea/trunk/debian/openfovea/DEBIAN/md5sums	2012-08-20 10:43:48 UTC (rev 12094)
@@ -0,0 +1,60 @@
+e2a48e9ed676b77949a3d73c4961489a  usr/bin/openfovea
+d105bab6ddbff75f7eb23dc391987d3b  usr/share/applications/openfovea.desktop
+f498a2d23fcc11e8c0c632d587f3ac7f  usr/share/doc/openfovea/changelog.Debian.gz
+f186881da2651ceaf0a65ca99a271dc8  usr/share/doc/openfovea/copyright
+f3bc7d3ee380e5e63631e6070e2a7476  usr/share/pixmaps/openfovea.png
+70fa220fffd419ce6196b9d33c601ca4  usr/share/pyshared/openfovea-0.1a160.egg-info
+5e3e24be578d79ebf450ec89abaf1144  usr/share/pyshared/openfovea/Icon/CellFovea.ico
+bc2171d62a6055c2b35d40f09c1e133f  usr/share/pyshared/openfovea/Icon/CellFovea.png
+8a5483e77fff6aca67bf46392aa10c1b  usr/share/pyshared/openfovea/Icon/CellFovea.svg
+091444f89545dd66373092c1b7385441  usr/share/pyshared/openfovea/Icon/Export_curve.svg
+1d699c3cb21f34868e66f605f5cf4bc8  usr/share/pyshared/openfovea/Icon/NoData.png
+6474dea07661acd90f832565e8c1cd90  usr/share/pyshared/openfovea/Icon/NoData.svg
+9455c8f495de856c53f104c17323cafa  usr/share/pyshared/openfovea/Icon/event.ico
+c935f290ede818e0c9e47872efc1ab6d  usr/share/pyshared/openfovea/Icon/event.png
+a4bb1086d29e348133e4df1c350056a9  usr/share/pyshared/openfovea/Icon/event.svg
+76bbfac0de467ffe4eb1f1b5b0fe1d09  usr/share/pyshared/openfovea/Icon/export.ico
+849dce6decef8a02822e57addc09cf3c  usr/share/pyshared/openfovea/Icon/export.png
+825469ba09aeb4aa777ef6191b5f98ee  usr/share/pyshared/openfovea/Icon/export.svg
+28e0fc3f38c39bcb15fef2e15deae992  usr/share/pyshared/openfovea/Icon/export_curve.ico
+6795c44d1bd44708901d741cfaf36399  usr/share/pyshared/openfovea/Icon/export_curve.png
+b41ee2d40f74eb317de55654e4cc0ecd  usr/share/pyshared/openfovea/Icon/icon64x64.svg
+0363ab28c7ee3c28696bde7849fe0b47  usr/share/pyshared/openfovea/Icon/openfovea.ico
+f3bc7d3ee380e5e63631e6070e2a7476  usr/share/pyshared/openfovea/Icon/openfovea.png
+8a4067fb3a344a462571105098b93440  usr/share/pyshared/openfovea/Icon/tomo_x_square.svg
+e72480a861d00a4670af445ee6a743d0  usr/share/pyshared/openfovea/Icon/tomo_y_square.svg
+e3c57394ea948e1d1c74108c8bcebcb7  usr/share/pyshared/openfovea/Icon/tomo_z_square.svg
+c3f6d2e7256e888422ed6b1ba2afc470  usr/share/pyshared/openfovea/Icon/two_evt.ico
+e63d58f3e88af5ad8a97fcded0d5ca54  usr/share/pyshared/openfovea/Icon/two_evt.png
+15ca69624c548d3b0af901ac01e65a50  usr/share/pyshared/openfovea/Icon/two_evt.svg
+c253b75b67818235c1801e2215a576ed  usr/share/pyshared/openfovea/__init__.py
+8ae5b0dbe70ce07c572b6308493c38b0  usr/share/pyshared/openfovea/classes.py
+237e072eed5ae70d33dcea3bb42b4a66  usr/share/pyshared/openfovea/common.py
+3fb00e938b161d57790f35ba525785c1  usr/share/pyshared/openfovea/dialog_experiment_properties.py
+deb0347fd2b1a687640af82184a737a9  usr/share/pyshared/openfovea/dialog_export_map.py
+0ab13fec9ae8ca45a5cb435abc71c84a  usr/share/pyshared/openfovea/dialog_flatten.py
+e9788fff5fe1e9a90c2cf74cc6e34fc4  usr/share/pyshared/openfovea/dialog_mask_properties.py
+c253b75b67818235c1801e2215a576ed  usr/share/pyshared/openfovea/fovea_toolbox/__init__.py
+d38b1997d5493588dda902a4623910f9  usr/share/pyshared/openfovea/fovea_toolbox/curve.py
+d41d8cd98f00b204e9800998ecf8427e  usr/share/pyshared/openfovea/fovea_toolbox/file_util/__init__.py
+cf2e7bc6c284b7c6306c274670b5df0f  usr/share/pyshared/openfovea/fovea_toolbox/file_util/aex.py
+1ec22c2009833678f6b6bf3314d3bc32  usr/share/pyshared/openfovea/fovea_toolbox/file_util/afm_file.py
+c2e4616e21d7921f9ba43315d1a7b4a4  usr/share/pyshared/openfovea/fovea_toolbox/file_util/asylum.py
+4eeea9195faaed1aa2d86d3d6f18272b  usr/share/pyshared/openfovea/fovea_toolbox/file_util/common.py
+6e8c4fe02179b37aef2acb1c64d6622a  usr/share/pyshared/openfovea/fovea_toolbox/file_util/csem.py
+5d9b3e24731d9d26db7578ae61c80e6b  usr/share/pyshared/openfovea/fovea_toolbox/file_util/jpk.py
+88f936149583a35a1d40d0c6b0a799a4  usr/share/pyshared/openfovea/fovea_toolbox/file_util/nanoscope.py
+db0974887b66e859bf1bf0891b27059b  usr/share/pyshared/openfovea/fovea_toolbox/file_util/succellus_import.py
+fc847a44bb1d8858b9255bf5aa4f2f75  usr/share/pyshared/openfovea/fovea_toolbox/misc.py
+f829d0ad3ea107316d2d0eadbab704d2  usr/share/pyshared/openfovea/fovea_toolbox/opengl.py
+a9d94fb8631924fa6e32116bd3bbdbda  usr/share/pyshared/openfovea/fovea_toolbox/opengl_gtk.py
+b74ae77e052160c4362078056129e534  usr/share/pyshared/openfovea/fovea_toolbox/post_proc.py
+cd990ce108731dad114c8b738ec8b902  usr/share/pyshared/openfovea/glade/dialog_experiment_properties.glade
+cf16654aceb52ed2ff76e282925d5f52  usr/share/pyshared/openfovea/glade/dialog_flatten.glade
+e04936c0bc5d4ac8b54a0ff39bad26c9  usr/share/pyshared/openfovea/glade/openfovea.glade
+1fa80922449c9777dfda6ce00d8a36e8  usr/share/pyshared/openfovea/glade/plot.glade
+d37e6e27ddbe81233710e36584ab4e95  usr/share/pyshared/openfovea/glade/stiffness_plot.glade
+9fde39a300be82576dad2295a8a5276a  usr/share/pyshared/openfovea/openfovea_gui.py
+336e844de74de22176c3650aaaddba42  usr/share/pyshared/openfovea/plot_generic.py
+5821343ba637d211098fe4c00211e904  usr/share/pyshared/openfovea/plot_gtk.py
+f01283ad374ddbeb8610a875612dcea7  usr/share/pyshared/openfovea/simple_window_gtk.py

Added: trunk/packages/openfovea/trunk/debian/openfovea/DEBIAN/postinst
===================================================================
--- trunk/packages/openfovea/trunk/debian/openfovea/DEBIAN/postinst	                        (rev 0)
+++ trunk/packages/openfovea/trunk/debian/openfovea/DEBIAN/postinst	2012-08-20 10:43:48 UTC (rev 12094)
@@ -0,0 +1,9 @@
+#!/bin/sh
+set -e
+
+# Automatically added by dh_python2:
+if which pycompile >/dev/null 2>&1; then
+	pycompile -p openfovea 
+fi
+
+# End automatically added section


Property changes on: trunk/packages/openfovea/trunk/debian/openfovea/DEBIAN/postinst
___________________________________________________________________
Added: svn:executable
   + *

Added: trunk/packages/openfovea/trunk/debian/openfovea/DEBIAN/prerm
===================================================================
--- trunk/packages/openfovea/trunk/debian/openfovea/DEBIAN/prerm	                        (rev 0)
+++ trunk/packages/openfovea/trunk/debian/openfovea/DEBIAN/prerm	2012-08-20 10:43:48 UTC (rev 12094)
@@ -0,0 +1,14 @@
+#!/bin/sh
+set -e
+
+# Automatically added by dh_python2:
+if which pyclean >/dev/null 2>&1; then
+	pyclean -p openfovea 
+else
+	dpkg -L openfovea | grep \.py$ | while read file
+	do
+		rm -f "${file}"[co] >/dev/null
+  	done
+fi
+
+# End automatically added section


Property changes on: trunk/packages/openfovea/trunk/debian/openfovea/DEBIAN/prerm
___________________________________________________________________
Added: svn:executable
   + *

Added: trunk/packages/openfovea/trunk/debian/openfovea/usr/bin/openfovea
===================================================================
--- trunk/packages/openfovea/trunk/debian/openfovea/usr/bin/openfovea	                        (rev 0)
+++ trunk/packages/openfovea/trunk/debian/openfovea/usr/bin/openfovea	2012-08-20 10:43:48 UTC (rev 12094)
@@ -0,0 +1,12 @@
+#!/usr/bin/python
+#
+import sys
+
+from openfovea import openfovea_gui
+
+if __name__ == '__main__':
+    if len(sys.argv) == 2:
+        arg = sys.argv[1]
+    else:
+        arg = None
+    openfovea_gui.main(arg)


Property changes on: trunk/packages/openfovea/trunk/debian/openfovea/usr/bin/openfovea
___________________________________________________________________
Added: svn:executable
   + *

Added: trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/Icon/CellFovea.ico
===================================================================
--- trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/Icon/CellFovea.ico	                        (rev 0)
+++ trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/Icon/CellFovea.ico	2012-08-20 10:43:48 UTC (rev 12094)
@@ -0,0 +1 @@
+link ../../../../../share/pyshared/openfovea/Icon/CellFovea.ico
\ No newline at end of file


Property changes on: trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/Icon/CellFovea.ico
___________________________________________________________________
Added: svn:special
   + *

Added: trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/Icon/CellFovea.png
===================================================================
--- trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/Icon/CellFovea.png	                        (rev 0)
+++ trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/Icon/CellFovea.png	2012-08-20 10:43:48 UTC (rev 12094)
@@ -0,0 +1 @@
+link ../../../../../share/pyshared/openfovea/Icon/CellFovea.png
\ No newline at end of file


Property changes on: trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/Icon/CellFovea.png
___________________________________________________________________
Added: svn:special
   + *

Added: trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/Icon/CellFovea.svg
===================================================================
--- trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/Icon/CellFovea.svg	                        (rev 0)
+++ trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/Icon/CellFovea.svg	2012-08-20 10:43:48 UTC (rev 12094)
@@ -0,0 +1 @@
+link ../../../../../share/pyshared/openfovea/Icon/CellFovea.svg
\ No newline at end of file


Property changes on: trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/Icon/CellFovea.svg
___________________________________________________________________
Added: svn:special
   + *

Added: trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/Icon/Export_curve.svg
===================================================================
--- trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/Icon/Export_curve.svg	                        (rev 0)
+++ trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/Icon/Export_curve.svg	2012-08-20 10:43:48 UTC (rev 12094)
@@ -0,0 +1 @@
+link ../../../../../share/pyshared/openfovea/Icon/Export_curve.svg
\ No newline at end of file


Property changes on: trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/Icon/Export_curve.svg
___________________________________________________________________
Added: svn:special
   + *

Added: trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/Icon/NoData.png
===================================================================
--- trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/Icon/NoData.png	                        (rev 0)
+++ trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/Icon/NoData.png	2012-08-20 10:43:48 UTC (rev 12094)
@@ -0,0 +1 @@
+link ../../../../../share/pyshared/openfovea/Icon/NoData.png
\ No newline at end of file


Property changes on: trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/Icon/NoData.png
___________________________________________________________________
Added: svn:special
   + *

Added: trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/Icon/NoData.svg
===================================================================
--- trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/Icon/NoData.svg	                        (rev 0)
+++ trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/Icon/NoData.svg	2012-08-20 10:43:48 UTC (rev 12094)
@@ -0,0 +1 @@
+link ../../../../../share/pyshared/openfovea/Icon/NoData.svg
\ No newline at end of file


Property changes on: trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/Icon/NoData.svg
___________________________________________________________________
Added: svn:special
   + *

Added: trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/Icon/event.ico
===================================================================
--- trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/Icon/event.ico	                        (rev 0)
+++ trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/Icon/event.ico	2012-08-20 10:43:48 UTC (rev 12094)
@@ -0,0 +1 @@
+link ../../../../../share/pyshared/openfovea/Icon/event.ico
\ No newline at end of file


Property changes on: trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/Icon/event.ico
___________________________________________________________________
Added: svn:special
   + *

Added: trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/Icon/event.png
===================================================================
--- trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/Icon/event.png	                        (rev 0)
+++ trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/Icon/event.png	2012-08-20 10:43:48 UTC (rev 12094)
@@ -0,0 +1 @@
+link ../../../../../share/pyshared/openfovea/Icon/event.png
\ No newline at end of file


Property changes on: trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/Icon/event.png
___________________________________________________________________
Added: svn:special
   + *

Added: trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/Icon/event.svg
===================================================================
--- trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/Icon/event.svg	                        (rev 0)
+++ trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/Icon/event.svg	2012-08-20 10:43:48 UTC (rev 12094)
@@ -0,0 +1 @@
+link ../../../../../share/pyshared/openfovea/Icon/event.svg
\ No newline at end of file


Property changes on: trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/Icon/event.svg
___________________________________________________________________
Added: svn:special
   + *

Added: trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/Icon/export.ico
===================================================================
--- trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/Icon/export.ico	                        (rev 0)
+++ trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/Icon/export.ico	2012-08-20 10:43:48 UTC (rev 12094)
@@ -0,0 +1 @@
+link ../../../../../share/pyshared/openfovea/Icon/export.ico
\ No newline at end of file


Property changes on: trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/Icon/export.ico
___________________________________________________________________
Added: svn:special
   + *

Added: trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/Icon/export.png
===================================================================
--- trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/Icon/export.png	                        (rev 0)
+++ trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/Icon/export.png	2012-08-20 10:43:48 UTC (rev 12094)
@@ -0,0 +1 @@
+link ../../../../../share/pyshared/openfovea/Icon/export.png
\ No newline at end of file


Property changes on: trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/Icon/export.png
___________________________________________________________________
Added: svn:special
   + *

Added: trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/Icon/export.svg
===================================================================
--- trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/Icon/export.svg	                        (rev 0)
+++ trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/Icon/export.svg	2012-08-20 10:43:48 UTC (rev 12094)
@@ -0,0 +1 @@
+link ../../../../../share/pyshared/openfovea/Icon/export.svg
\ No newline at end of file


Property changes on: trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/Icon/export.svg
___________________________________________________________________
Added: svn:special
   + *

Added: trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/Icon/export_curve.ico
===================================================================
--- trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/Icon/export_curve.ico	                        (rev 0)
+++ trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/Icon/export_curve.ico	2012-08-20 10:43:48 UTC (rev 12094)
@@ -0,0 +1 @@
+link ../../../../../share/pyshared/openfovea/Icon/export_curve.ico
\ No newline at end of file


Property changes on: trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/Icon/export_curve.ico
___________________________________________________________________
Added: svn:special
   + *

Added: trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/Icon/export_curve.png
===================================================================
--- trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/Icon/export_curve.png	                        (rev 0)
+++ trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/Icon/export_curve.png	2012-08-20 10:43:48 UTC (rev 12094)
@@ -0,0 +1 @@
+link ../../../../../share/pyshared/openfovea/Icon/export_curve.png
\ No newline at end of file


Property changes on: trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/Icon/export_curve.png
___________________________________________________________________
Added: svn:special
   + *

Added: trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/Icon/icon64x64.svg
===================================================================
--- trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/Icon/icon64x64.svg	                        (rev 0)
+++ trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/Icon/icon64x64.svg	2012-08-20 10:43:48 UTC (rev 12094)
@@ -0,0 +1 @@
+link ../../../../../share/pyshared/openfovea/Icon/icon64x64.svg
\ No newline at end of file


Property changes on: trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/Icon/icon64x64.svg
___________________________________________________________________
Added: svn:special
   + *

Added: trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/Icon/openfovea.ico
===================================================================
--- trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/Icon/openfovea.ico	                        (rev 0)
+++ trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/Icon/openfovea.ico	2012-08-20 10:43:48 UTC (rev 12094)
@@ -0,0 +1 @@
+link ../../../../../share/pyshared/openfovea/Icon/openfovea.ico
\ No newline at end of file


Property changes on: trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/Icon/openfovea.ico
___________________________________________________________________
Added: svn:special
   + *

Added: trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/Icon/openfovea.png
===================================================================
--- trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/Icon/openfovea.png	                        (rev 0)
+++ trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/Icon/openfovea.png	2012-08-20 10:43:48 UTC (rev 12094)
@@ -0,0 +1 @@
+link ../../../../../share/pyshared/openfovea/Icon/openfovea.png
\ No newline at end of file


Property changes on: trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/Icon/openfovea.png
___________________________________________________________________
Added: svn:special
   + *

Added: trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/Icon/tomo_x_square.svg
===================================================================
--- trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/Icon/tomo_x_square.svg	                        (rev 0)
+++ trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/Icon/tomo_x_square.svg	2012-08-20 10:43:48 UTC (rev 12094)
@@ -0,0 +1 @@
+link ../../../../../share/pyshared/openfovea/Icon/tomo_x_square.svg
\ No newline at end of file


Property changes on: trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/Icon/tomo_x_square.svg
___________________________________________________________________
Added: svn:special
   + *

Added: trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/Icon/tomo_y_square.svg
===================================================================
--- trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/Icon/tomo_y_square.svg	                        (rev 0)
+++ trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/Icon/tomo_y_square.svg	2012-08-20 10:43:48 UTC (rev 12094)
@@ -0,0 +1 @@
+link ../../../../../share/pyshared/openfovea/Icon/tomo_y_square.svg
\ No newline at end of file


Property changes on: trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/Icon/tomo_y_square.svg
___________________________________________________________________
Added: svn:special
   + *

Added: trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/Icon/tomo_z_square.svg
===================================================================
--- trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/Icon/tomo_z_square.svg	                        (rev 0)
+++ trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/Icon/tomo_z_square.svg	2012-08-20 10:43:48 UTC (rev 12094)
@@ -0,0 +1 @@
+link ../../../../../share/pyshared/openfovea/Icon/tomo_z_square.svg
\ No newline at end of file


Property changes on: trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/Icon/tomo_z_square.svg
___________________________________________________________________
Added: svn:special
   + *

Added: trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/Icon/two_evt.ico
===================================================================
--- trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/Icon/two_evt.ico	                        (rev 0)
+++ trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/Icon/two_evt.ico	2012-08-20 10:43:48 UTC (rev 12094)
@@ -0,0 +1 @@
+link ../../../../../share/pyshared/openfovea/Icon/two_evt.ico
\ No newline at end of file


Property changes on: trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/Icon/two_evt.ico
___________________________________________________________________
Added: svn:special
   + *

Added: trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/Icon/two_evt.png
===================================================================
--- trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/Icon/two_evt.png	                        (rev 0)
+++ trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/Icon/two_evt.png	2012-08-20 10:43:48 UTC (rev 12094)
@@ -0,0 +1 @@
+link ../../../../../share/pyshared/openfovea/Icon/two_evt.png
\ No newline at end of file


Property changes on: trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/Icon/two_evt.png
___________________________________________________________________
Added: svn:special
   + *

Added: trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/Icon/two_evt.svg
===================================================================
--- trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/Icon/two_evt.svg	                        (rev 0)
+++ trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/Icon/two_evt.svg	2012-08-20 10:43:48 UTC (rev 12094)
@@ -0,0 +1 @@
+link ../../../../../share/pyshared/openfovea/Icon/two_evt.svg
\ No newline at end of file


Property changes on: trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/Icon/two_evt.svg
___________________________________________________________________
Added: svn:special
   + *

Added: trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/__init__.py
===================================================================
--- trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/__init__.py	                        (rev 0)
+++ trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/__init__.py	2012-08-20 10:43:48 UTC (rev 12094)
@@ -0,0 +1 @@
+link ../../../../share/pyshared/openfovea/__init__.py
\ No newline at end of file


Property changes on: trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/__init__.py
___________________________________________________________________
Added: svn:special
   + *

Added: trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/classes.py
===================================================================
--- trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/classes.py	                        (rev 0)
+++ trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/classes.py	2012-08-20 10:43:48 UTC (rev 12094)
@@ -0,0 +1 @@
+link ../../../../share/pyshared/openfovea/classes.py
\ No newline at end of file


Property changes on: trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/classes.py
___________________________________________________________________
Added: svn:special
   + *

Added: trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/common.py
===================================================================
--- trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/common.py	                        (rev 0)
+++ trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/common.py	2012-08-20 10:43:48 UTC (rev 12094)
@@ -0,0 +1 @@
+link ../../../../share/pyshared/openfovea/common.py
\ No newline at end of file


Property changes on: trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/common.py
___________________________________________________________________
Added: svn:special
   + *

Added: trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/dialog_experiment_properties.py
===================================================================
--- trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/dialog_experiment_properties.py	                        (rev 0)
+++ trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/dialog_experiment_properties.py	2012-08-20 10:43:48 UTC (rev 12094)
@@ -0,0 +1 @@
+link ../../../../share/pyshared/openfovea/dialog_experiment_properties.py
\ No newline at end of file


Property changes on: trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/dialog_experiment_properties.py
___________________________________________________________________
Added: svn:special
   + *

Added: trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/dialog_export_map.py
===================================================================
--- trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/dialog_export_map.py	                        (rev 0)
+++ trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/dialog_export_map.py	2012-08-20 10:43:48 UTC (rev 12094)
@@ -0,0 +1 @@
+link ../../../../share/pyshared/openfovea/dialog_export_map.py
\ No newline at end of file


Property changes on: trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/dialog_export_map.py
___________________________________________________________________
Added: svn:special
   + *

Added: trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/dialog_flatten.py
===================================================================
--- trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/dialog_flatten.py	                        (rev 0)
+++ trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/dialog_flatten.py	2012-08-20 10:43:48 UTC (rev 12094)
@@ -0,0 +1 @@
+link ../../../../share/pyshared/openfovea/dialog_flatten.py
\ No newline at end of file


Property changes on: trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/dialog_flatten.py
___________________________________________________________________
Added: svn:special
   + *

Added: trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/dialog_mask_properties.py
===================================================================
--- trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/dialog_mask_properties.py	                        (rev 0)
+++ trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/dialog_mask_properties.py	2012-08-20 10:43:48 UTC (rev 12094)
@@ -0,0 +1 @@
+link ../../../../share/pyshared/openfovea/dialog_mask_properties.py
\ No newline at end of file


Property changes on: trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/dialog_mask_properties.py
___________________________________________________________________
Added: svn:special
   + *

Added: trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/fovea_toolbox/__init__.py
===================================================================
--- trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/fovea_toolbox/__init__.py	                        (rev 0)
+++ trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/fovea_toolbox/__init__.py	2012-08-20 10:43:48 UTC (rev 12094)
@@ -0,0 +1 @@
+link ../../../../../share/pyshared/openfovea/fovea_toolbox/__init__.py
\ No newline at end of file


Property changes on: trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/fovea_toolbox/__init__.py
___________________________________________________________________
Added: svn:special
   + *

Added: trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/fovea_toolbox/curve.py
===================================================================
--- trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/fovea_toolbox/curve.py	                        (rev 0)
+++ trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/fovea_toolbox/curve.py	2012-08-20 10:43:48 UTC (rev 12094)
@@ -0,0 +1 @@
+link ../../../../../share/pyshared/openfovea/fovea_toolbox/curve.py
\ No newline at end of file


Property changes on: trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/fovea_toolbox/curve.py
___________________________________________________________________
Added: svn:special
   + *

Added: trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/fovea_toolbox/file_util/__init__.py
===================================================================
--- trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/fovea_toolbox/file_util/__init__.py	                        (rev 0)
+++ trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/fovea_toolbox/file_util/__init__.py	2012-08-20 10:43:48 UTC (rev 12094)
@@ -0,0 +1 @@
+link ../../../../../../share/pyshared/openfovea/fovea_toolbox/file_util/__init__.py
\ No newline at end of file


Property changes on: trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/fovea_toolbox/file_util/__init__.py
___________________________________________________________________
Added: svn:special
   + *

Added: trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/fovea_toolbox/file_util/aex.py
===================================================================
--- trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/fovea_toolbox/file_util/aex.py	                        (rev 0)
+++ trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/fovea_toolbox/file_util/aex.py	2012-08-20 10:43:48 UTC (rev 12094)
@@ -0,0 +1 @@
+link ../../../../../../share/pyshared/openfovea/fovea_toolbox/file_util/aex.py
\ No newline at end of file


Property changes on: trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/fovea_toolbox/file_util/aex.py
___________________________________________________________________
Added: svn:special
   + *

Added: trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/fovea_toolbox/file_util/afm_file.py
===================================================================
--- trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/fovea_toolbox/file_util/afm_file.py	                        (rev 0)
+++ trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/fovea_toolbox/file_util/afm_file.py	2012-08-20 10:43:48 UTC (rev 12094)
@@ -0,0 +1 @@
+link ../../../../../../share/pyshared/openfovea/fovea_toolbox/file_util/afm_file.py
\ No newline at end of file


Property changes on: trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/fovea_toolbox/file_util/afm_file.py
___________________________________________________________________
Added: svn:special
   + *

Added: trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/fovea_toolbox/file_util/asylum.py
===================================================================
--- trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/fovea_toolbox/file_util/asylum.py	                        (rev 0)
+++ trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/fovea_toolbox/file_util/asylum.py	2012-08-20 10:43:48 UTC (rev 12094)
@@ -0,0 +1 @@
+link ../../../../../../share/pyshared/openfovea/fovea_toolbox/file_util/asylum.py
\ No newline at end of file


Property changes on: trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/fovea_toolbox/file_util/asylum.py
___________________________________________________________________
Added: svn:special
   + *

Added: trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/fovea_toolbox/file_util/common.py
===================================================================
--- trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/fovea_toolbox/file_util/common.py	                        (rev 0)
+++ trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/fovea_toolbox/file_util/common.py	2012-08-20 10:43:48 UTC (rev 12094)
@@ -0,0 +1 @@
+link ../../../../../../share/pyshared/openfovea/fovea_toolbox/file_util/common.py
\ No newline at end of file


Property changes on: trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/fovea_toolbox/file_util/common.py
___________________________________________________________________
Added: svn:special
   + *

Added: trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/fovea_toolbox/file_util/csem.py
===================================================================
--- trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/fovea_toolbox/file_util/csem.py	                        (rev 0)
+++ trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/fovea_toolbox/file_util/csem.py	2012-08-20 10:43:48 UTC (rev 12094)
@@ -0,0 +1 @@
+link ../../../../../../share/pyshared/openfovea/fovea_toolbox/file_util/csem.py
\ No newline at end of file


Property changes on: trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/fovea_toolbox/file_util/csem.py
___________________________________________________________________
Added: svn:special
   + *

Added: trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/fovea_toolbox/file_util/jpk.py
===================================================================
--- trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/fovea_toolbox/file_util/jpk.py	                        (rev 0)
+++ trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/fovea_toolbox/file_util/jpk.py	2012-08-20 10:43:48 UTC (rev 12094)
@@ -0,0 +1 @@
+link ../../../../../../share/pyshared/openfovea/fovea_toolbox/file_util/jpk.py
\ No newline at end of file


Property changes on: trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/fovea_toolbox/file_util/jpk.py
___________________________________________________________________
Added: svn:special
   + *

Added: trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/fovea_toolbox/file_util/nanoscope.py
===================================================================
--- trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/fovea_toolbox/file_util/nanoscope.py	                        (rev 0)
+++ trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/fovea_toolbox/file_util/nanoscope.py	2012-08-20 10:43:48 UTC (rev 12094)
@@ -0,0 +1 @@
+link ../../../../../../share/pyshared/openfovea/fovea_toolbox/file_util/nanoscope.py
\ No newline at end of file


Property changes on: trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/fovea_toolbox/file_util/nanoscope.py
___________________________________________________________________
Added: svn:special
   + *

Added: trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/fovea_toolbox/file_util/succellus_import.py
===================================================================
--- trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/fovea_toolbox/file_util/succellus_import.py	                        (rev 0)
+++ trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/fovea_toolbox/file_util/succellus_import.py	2012-08-20 10:43:48 UTC (rev 12094)
@@ -0,0 +1 @@
+link ../../../../../../share/pyshared/openfovea/fovea_toolbox/file_util/succellus_import.py
\ No newline at end of file


Property changes on: trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/fovea_toolbox/file_util/succellus_import.py
___________________________________________________________________
Added: svn:special
   + *

Added: trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/fovea_toolbox/misc.py
===================================================================
--- trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/fovea_toolbox/misc.py	                        (rev 0)
+++ trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/fovea_toolbox/misc.py	2012-08-20 10:43:48 UTC (rev 12094)
@@ -0,0 +1 @@
+link ../../../../../share/pyshared/openfovea/fovea_toolbox/misc.py
\ No newline at end of file


Property changes on: trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/fovea_toolbox/misc.py
___________________________________________________________________
Added: svn:special
   + *

Added: trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/fovea_toolbox/opengl.py
===================================================================
--- trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/fovea_toolbox/opengl.py	                        (rev 0)
+++ trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/fovea_toolbox/opengl.py	2012-08-20 10:43:48 UTC (rev 12094)
@@ -0,0 +1 @@
+link ../../../../../share/pyshared/openfovea/fovea_toolbox/opengl.py
\ No newline at end of file


Property changes on: trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/fovea_toolbox/opengl.py
___________________________________________________________________
Added: svn:special
   + *

Added: trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/fovea_toolbox/opengl_gtk.py
===================================================================
--- trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/fovea_toolbox/opengl_gtk.py	                        (rev 0)
+++ trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/fovea_toolbox/opengl_gtk.py	2012-08-20 10:43:48 UTC (rev 12094)
@@ -0,0 +1 @@
+link ../../../../../share/pyshared/openfovea/fovea_toolbox/opengl_gtk.py
\ No newline at end of file


Property changes on: trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/fovea_toolbox/opengl_gtk.py
___________________________________________________________________
Added: svn:special
   + *

Added: trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/fovea_toolbox/post_proc.py
===================================================================
--- trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/fovea_toolbox/post_proc.py	                        (rev 0)
+++ trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/fovea_toolbox/post_proc.py	2012-08-20 10:43:48 UTC (rev 12094)
@@ -0,0 +1 @@
+link ../../../../../share/pyshared/openfovea/fovea_toolbox/post_proc.py
\ No newline at end of file


Property changes on: trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/fovea_toolbox/post_proc.py
___________________________________________________________________
Added: svn:special
   + *

Added: trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/glade/dialog_experiment_properties.glade
===================================================================
--- trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/glade/dialog_experiment_properties.glade	                        (rev 0)
+++ trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/glade/dialog_experiment_properties.glade	2012-08-20 10:43:48 UTC (rev 12094)
@@ -0,0 +1 @@
+link ../../../../../share/pyshared/openfovea/glade/dialog_experiment_properties.glade
\ No newline at end of file


Property changes on: trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/glade/dialog_experiment_properties.glade
___________________________________________________________________
Added: svn:special
   + *

Added: trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/glade/dialog_flatten.glade
===================================================================
--- trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/glade/dialog_flatten.glade	                        (rev 0)
+++ trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/glade/dialog_flatten.glade	2012-08-20 10:43:48 UTC (rev 12094)
@@ -0,0 +1 @@
+link ../../../../../share/pyshared/openfovea/glade/dialog_flatten.glade
\ No newline at end of file


Property changes on: trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/glade/dialog_flatten.glade
___________________________________________________________________
Added: svn:special
   + *

Added: trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/glade/openfovea.glade
===================================================================
--- trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/glade/openfovea.glade	                        (rev 0)
+++ trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/glade/openfovea.glade	2012-08-20 10:43:48 UTC (rev 12094)
@@ -0,0 +1 @@
+link ../../../../../share/pyshared/openfovea/glade/openfovea.glade
\ No newline at end of file


Property changes on: trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/glade/openfovea.glade
___________________________________________________________________
Added: svn:special
   + *

Added: trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/glade/plot.glade
===================================================================
--- trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/glade/plot.glade	                        (rev 0)
+++ trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/glade/plot.glade	2012-08-20 10:43:48 UTC (rev 12094)
@@ -0,0 +1 @@
+link ../../../../../share/pyshared/openfovea/glade/plot.glade
\ No newline at end of file


Property changes on: trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/glade/plot.glade
___________________________________________________________________
Added: svn:special
   + *

Added: trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/glade/stiffness_plot.glade
===================================================================
--- trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/glade/stiffness_plot.glade	                        (rev 0)
+++ trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/glade/stiffness_plot.glade	2012-08-20 10:43:48 UTC (rev 12094)
@@ -0,0 +1 @@
+link ../../../../../share/pyshared/openfovea/glade/stiffness_plot.glade
\ No newline at end of file


Property changes on: trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/glade/stiffness_plot.glade
___________________________________________________________________
Added: svn:special
   + *

Added: trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/openfovea_gui.py
===================================================================
--- trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/openfovea_gui.py	                        (rev 0)
+++ trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/openfovea_gui.py	2012-08-20 10:43:48 UTC (rev 12094)
@@ -0,0 +1 @@
+link ../../../../share/pyshared/openfovea/openfovea_gui.py
\ No newline at end of file


Property changes on: trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/openfovea_gui.py
___________________________________________________________________
Added: svn:special
   + *

Added: trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/plot_generic.py
===================================================================
--- trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/plot_generic.py	                        (rev 0)
+++ trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/plot_generic.py	2012-08-20 10:43:48 UTC (rev 12094)
@@ -0,0 +1 @@
+link ../../../../share/pyshared/openfovea/plot_generic.py
\ No newline at end of file


Property changes on: trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/plot_generic.py
___________________________________________________________________
Added: svn:special
   + *

Added: trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/plot_gtk.py
===================================================================
--- trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/plot_gtk.py	                        (rev 0)
+++ trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/plot_gtk.py	2012-08-20 10:43:48 UTC (rev 12094)
@@ -0,0 +1 @@
+link ../../../../share/pyshared/openfovea/plot_gtk.py
\ No newline at end of file


Property changes on: trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/plot_gtk.py
___________________________________________________________________
Added: svn:special
   + *

Added: trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/simple_window_gtk.py
===================================================================
--- trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/simple_window_gtk.py	                        (rev 0)
+++ trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/simple_window_gtk.py	2012-08-20 10:43:48 UTC (rev 12094)
@@ -0,0 +1 @@
+link ../../../../share/pyshared/openfovea/simple_window_gtk.py
\ No newline at end of file


Property changes on: trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea/simple_window_gtk.py
___________________________________________________________________
Added: svn:special
   + *

Added: trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea-0.1a160.egg-info
===================================================================
--- trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea-0.1a160.egg-info	                        (rev 0)
+++ trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea-0.1a160.egg-info	2012-08-20 10:43:48 UTC (rev 12094)
@@ -0,0 +1 @@
+link ../../../share/pyshared/openfovea-0.1a160.egg-info
\ No newline at end of file


Property changes on: trunk/packages/openfovea/trunk/debian/openfovea/usr/lib/python2.7/dist-packages/openfovea-0.1a160.egg-info
___________________________________________________________________
Added: svn:special
   + *

Added: trunk/packages/openfovea/trunk/debian/openfovea/usr/share/applications/openfovea.desktop
===================================================================
--- trunk/packages/openfovea/trunk/debian/openfovea/usr/share/applications/openfovea.desktop	                        (rev 0)
+++ trunk/packages/openfovea/trunk/debian/openfovea/usr/share/applications/openfovea.desktop	2012-08-20 10:43:48 UTC (rev 12094)
@@ -0,0 +1,10 @@
+[Desktop Entry]
+Version=0.1
+Terminal=false
+Exec=openfovea
+Icon=openfovea
+Type=Application
+Categories=Application;Education;Science;
+Name=OpenFovea
+Comment=Postprocess AFM force volume experiments
+Comment[fr]=Traiter des fichiers AFM en force volume

Added: trunk/packages/openfovea/trunk/debian/openfovea/usr/share/doc/openfovea/changelog.Debian.gz
===================================================================
(Binary files differ)


Property changes on: trunk/packages/openfovea/trunk/debian/openfovea/usr/share/doc/openfovea/changelog.Debian.gz
___________________________________________________________________
Added: svn:mime-type
   + application/octet-stream

Added: trunk/packages/openfovea/trunk/debian/openfovea/usr/share/doc/openfovea/copyright
===================================================================
--- trunk/packages/openfovea/trunk/debian/openfovea/usr/share/doc/openfovea/copyright	                        (rev 0)
+++ trunk/packages/openfovea/trunk/debian/openfovea/usr/share/doc/openfovea/copyright	2012-08-20 10:43:48 UTC (rev 12094)
@@ -0,0 +1,31 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: OpenFovea
+Upstream-Contact: Charles Roduit <charles.roduit at gmail.com>
+Source: https://launchpad.net/openfovea/+download
+
+Files: *
+Copyright: © 2008-2012 Charles Roduit <charles.roduit at gmail.com>
+License: GPL-3+
+
+Files: debian/*
+Copyright: © 2008-2012 Charles Roduit <charles.roduit at gmail.com>
+             2012 Andreas Tille <tille at debian.org>
+License: GPL-3+
+
+License: GPL-3+
+    This package is free software; you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation; either version 3 of the License, or
+    (at your option) any later version.
+ .
+    This package is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+ .
+    You should have received a copy of the GNU General Public License
+    along with this package; if not, write to the Free Software
+    Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301 USA
+ .
+ On Debian systems, the complete text of the GNU General
+ Public License can be found in `/usr/share/common-licenses/GPL-3'.

Added: trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pixmaps/openfovea.png
===================================================================
(Binary files differ)


Property changes on: trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pixmaps/openfovea.png
___________________________________________________________________
Added: svn:mime-type
   + application/octet-stream

Added: trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/Icon/CellFovea.ico
===================================================================
(Binary files differ)


Property changes on: trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/Icon/CellFovea.ico
___________________________________________________________________
Added: svn:mime-type
   + application/octet-stream

Added: trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/Icon/CellFovea.png
===================================================================
(Binary files differ)


Property changes on: trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/Icon/CellFovea.png
___________________________________________________________________
Added: svn:mime-type
   + application/octet-stream

Added: trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/Icon/CellFovea.svg
===================================================================
--- trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/Icon/CellFovea.svg	                        (rev 0)
+++ trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/Icon/CellFovea.svg	2012-08-20 10:43:48 UTC (rev 12094)
@@ -0,0 +1,3596 @@
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+<!-- Created with Inkscape (http://www.inkscape.org/) -->
+
+<svg
+   xmlns:dc="http://purl.org/dc/elements/1.1/"
+   xmlns:cc="http://creativecommons.org/ns#"
+   xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+   xmlns:svg="http://www.w3.org/2000/svg"
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+   xmlns:xlink="http://www.w3.org/1999/xlink"
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+   id="svg3213"
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+   sodipodi:docname="CellFovea.svg"
+   inkscape:output_extension="org.inkscape.output.svg.inkscape"
+   version="1.0"
+   inkscape:export-filename="CellFovea.png"
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+     id="metadata3218">
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+      <cc:Work
+         rdf:about="">
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Added: trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/Icon/Export_curve.svg
===================================================================
--- trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/Icon/Export_curve.svg	                        (rev 0)
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===================================================================
(Binary files differ)


Property changes on: trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/Icon/NoData.png
___________________________________________________________________
Added: svn:mime-type
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Added: trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/Icon/NoData.svg
===================================================================
--- trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/Icon/NoData.svg	                        (rev 0)
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Added: trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/Icon/tomo_y_square.svg
===================================================================
--- trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/Icon/tomo_y_square.svg	                        (rev 0)
+++ trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/Icon/tomo_y_square.svg	2012-08-20 10:43:48 UTC (rev 12094)
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Added: trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/Icon/tomo_z_square.svg
===================================================================
--- trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/Icon/tomo_z_square.svg	                        (rev 0)
+++ trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/Icon/tomo_z_square.svg	2012-08-20 10:43:48 UTC (rev 12094)
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Added: trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/Icon/two_evt.ico
===================================================================
(Binary files differ)


Property changes on: trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/Icon/two_evt.ico
___________________________________________________________________
Added: svn:mime-type
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Added: trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/Icon/two_evt.png
===================================================================
(Binary files differ)


Property changes on: trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/Icon/two_evt.png
___________________________________________________________________
Added: svn:mime-type
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Added: trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/Icon/two_evt.svg
===================================================================
--- trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/Icon/two_evt.svg	                        (rev 0)
+++ trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/Icon/two_evt.svg	2012-08-20 10:43:48 UTC (rev 12094)
@@ -0,0 +1,69 @@
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Added: trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/__init__.py
===================================================================
--- trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/__init__.py	                        (rev 0)
+++ trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/__init__.py	2012-08-20 10:43:48 UTC (rev 12094)
@@ -0,0 +1 @@
+__all__ = ['curve', 'file']
\ No newline at end of file

Added: trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/classes.py
===================================================================
--- trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/classes.py	                        (rev 0)
+++ trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/classes.py	2012-08-20 10:43:48 UTC (rev 12094)
@@ -0,0 +1,2738 @@
+#! /usr/bin/python
+# -*- coding: utf-8 -*-
+
+'''
+This module contains the classes that are usefull for OpenFovea. Currently,
+there is only the class ForceVolume, but we will soon implement an experiment
+class
+'''
+
+import os
+import csv
+from datetime import datetime
+# import pdb
+
+import numpy as num
+import math
+
+from fovea_toolbox import curve
+from fovea_toolbox.file_util import afm_file, aex
+from fovea_toolbox.post_proc import rel_values, rand_dot, \
+                                    add_stiffness_to_event, resize_array
+from fovea_toolbox import post_proc, misc
+from plot_generic import PlotData
+import plot_generic as plot
+
+__author__ = "Charles Roduit <charles.roduit at gmail.com>"
+__date__ = "25 juin 2005"
+__version__ = "0.1.alpha.1"
+__credits__ = "Rewrite of the 'Succellus' software developed during my thesis\
+               at the EPFL under the direction of Sandor Kasas."
+
+
+class ForceVolume(object):
+    """
+    This class contains all attributes and methods used to post-process force
+    curve. The needed input is the name of the file to open.
+
+    Attributes :
+
+        * name: the original file name
+        * indent: indentation vector of the force indentation curve
+        * force: force vector of the force indentation curve
+        * curve_nb: indice of the current curve
+        * pox_x: x coordinate of the current curve
+        * pos_y: y coordinate of the current curve
+        * stiffness: dictionnary that contains the parameters to compute the
+                      stiffness
+          - hertz_model: the hertz model used
+          - poisson_ratio: Poisson ratio of the material.
+          - point_carac: caracteristic of the tip (radius or semi-opening
+                      angle)
+          - nb_parts: the number of segment to compute
+          - size_parts: the size of each segments
+          - glass: the slope of the "non indenting part" of the curve
+          - claibSens: ???
+          - relative_max_dist: the maximum distance to compute relative
+                      stiffness
+          - poc_threshold: The threshold to detect the point of contact
+          - poc_method: Stores the method to find the point of contact. (see
+                          curve.find_poc for the available methods.)
+          - limit_slide: Wether to limit or not the sliding of the slice when
+                           finding point of contact.
+          - recompute_poc: Wether to recompute poc or not.
+          - poc_len_slice: Length of the fit curve portion to find point of
+                      contact
+        * array: dictionnary that contains the arrays computed on the scan.
+          - 'Piezo': The height of the piezo at the end of the indentation.
+          - 'PoCIndice': The indice of the point of contact.
+          - 'Topography': The zero force image.
+          - 'Stiffness': The computed stiffness.
+          - 'Stiffness tomo': Same as "Stiffness", but in an array corrected
+                               with the zero force image.
+          - 'Event': The number of events.
+          - 'Event force': The force of events (max if several).
+          - 'Event random': The position of random selected pixels.
+          - 'Relative pos': ??
+          - 'Relative rand pos': ??
+          - 'Path': This defines a path to display info.
+          - 'Masked': True | False (default: False) To apply or not a mask to
+                       the array.
+        * event: dictionnary that possess information on the computation and
+                  display of the events.
+          - nbr_random: the number of random event that has to be generated.
+          - rel_stiff and rel_stiff_ctl: the result of the relative stiffness.
+        * header: TO COMPLETE
+          - ev_dist_thresh: the distance from which we have to display the
+                                 events.
+        * plot_who: curve to plot
+        * exist: to check the existence of computed things
+        * array: the 2D arrays computed
+        * header: the header of the file
+        * deflection_av
+        * deflection_re: advance and retraction curves
+        * plotx: the scanner extention part for all the deflection curves
+        * event_list: list of all events
+    """
+    # TODO: change self.event_list to self.event['list']
+    def __init__(self, fv_file):
+        self.indent = []  # The indentation and force curve of the
+        self.force = []  # trace curve.
+        self.r_indent = []  # The indentation and force curve of the
+        self.r_force = []  # retrace curve.
+        self.curve_nb = 0
+        self.pos_x = 0
+        self.pos_y = 0
+        self.counter = {'num': 0,
+                        'increment': 0,
+                        'text': 'Please wait...'}
+        self.stiffness = {'hertz_model': 'Sphere',  # Hertz model used.
+                        'fit_method': 'Raw',  # The fit method used.
+                        'poisson_ratio': 0.3,  # Poisson ratio of the material.
+                        'point_carac': 40,  # Caracteristic of the tip (depend
+                        # on the Hertz model).
+                        'nb_parts': 4,  # Number of FI segment.
+                        'size_parts': 50,  # The size of each FI segment.
+                        'glass': -1.,  # Correction factor for the sensitivity
+                        # calibration.
+                        'calib_sens': 1,  # ?? Dead code ??
+                        'relative_max_dist': 3,  # When computing the relative
+                        # stiffness, what is the maximum distance to compute.
+                        'poc_threshold': 2,  # The dependency on noise.
+                        'poc_method': 'curve_fit',  # Stores the method to find
+                        # the point of contact. (see curve.find_poc for the
+                        # available methods.)
+                        'limit_slide': False,  # Wether to limit or not the
+                        # sliding of the slice when finding point of contact.
+                        'recompute_poc': True,  # Wether to recompute poc or
+                                               # not.
+                        'poc_len_slice': 0.3,  # Length of the fit curve
+                        # portion to find point of contact
+                        }
+        self.event = {'nbr_random': 15,
+                      'rel_stiff': None,
+                      'rel_stiff_ctl': None}
+        self.event_list = []
+        self.event_stat = {'force': None,
+                           'lr': None,
+                           'dist': None,
+                           'stiff': None,
+                           'rel_stiff': None}
+        self.event_list_original = None
+        self.plot_who = {'Av': 1, 'Re': 0, 'Indent': 0,
+                         'PoC': 0, 'Event': 0}
+        self.exist = {'PoC': 0, 'Stiffness': 0}
+        ######################
+        # Define the arrays :
+        self.__array = dict()
+        for item in ARRAY_TYPE:
+            self.__array[item] = None
+        # special case :
+        #self.__array['Masked'] = False
+        #######################
+        self.__fdcurves = {
+                    'trace_x': None,
+                    'trace_y': None,
+                    'retrace_x': None,
+                    'retrace_y': None,
+        }
+        if type(fv_file) in [str, unicode]:
+        #if type(fv_file) == str:
+            self.name = os.path.split(fv_file)[1]
+            _data = afm_file.load(fv_file)
+            self.header = _data['header']
+            self.__array['Piezo'] = _data['piezo']
+            if self.header['data_location'] == 'local':
+                # we are in the case where the data are loaded at once
+                self.__fdcurves['trace_x'] = _data['trace_x']
+                self.__fdcurves['retrace_x'] = _data['retrace_x']
+                self.__fdcurves['trace_y'] = _data['trace_y']
+                self.__fdcurves['retrace_y'] = _data['retrace_y']
+            else:
+                self.__data_fid = _data['data_fid']
+            if self.header['Microscope'] == 'csem':
+                self.stiffness['glass'] = -0.01
+        elif type(fv_file) == dict:
+            # we are in the presence of a xml tree readed from aex file
+            self.name = fv_file['name']
+            self.header = fv_file['header']
+            self.__fdcurves['trace_y'] = fv_file['trace_array']
+            self.__fdcurves['retrace_y'] = fv_file['retrace_array']
+            self.__fdcurves['trace_x'] = fv_file['trace_x_array']
+            self.__fdcurves['retrace_x'] = fv_file['retrace_x_array']
+            self.__array['Piezo'] = fv_file['piezo_array']
+            if self.header['data_location'] not in ['local', u'local']:
+                self.__data_fid = fv_file['data_fid']
+            if len(fv_file['stiffness_header']):
+                self.stiffness = fv_file['stiffness_header']
+            # Load stiffness results
+            if fv_file['stiffness'] is not None:
+                # recover attributes...
+                self.__array['Stiffness'] = fv_file['stiffness']
+            # Load events results
+            if 'event' in fv_file and 'array' in fv_file['event']:
+                self.__array['Event'] = fv_file['event']['array']
+                self.event_list = fv_file['event']['detail']
+            if 'event_rand_array' in fv_file:
+                self.__array['Event random'] = fv_file['event_rand_array']
+            if 'poc_array' in fv_file and fv_file['poc_array'] is not None:
+                self.__array['PoCIndice'] = fv_file['poc_array']
+                self.exist['PoC'] = 1
+            if fv_file['pocnoise_array'] is not None:
+                self.__array['PoCNoise'] = fv_file['pocnoise_array']
+            if 'topo_array' in fv_file:
+                self.__array['Topography'] = fv_file['topo_array']
+            if 'mask_array' in fv_file:
+                self.__array['Mask'] = fv_file['mask_array']
+            self.set_switch('mask', eval(fv_file['switch']['mask']))
+        if self.header['pixel_size'] is None:
+            try:
+                self.header['pixel_size'] = \
+                    tuple([float(size) / nb_pix
+                        for size, nb_pix in zip(self.header['scan_size'],
+                                                self.header['size'])])
+            except (ZeroDivisionError, TypeError):
+                self.header['pixel_size'] = (None, None)
+
+    def __iter__(self):
+        self.curve_nb = -1
+        return self
+
+    def __cmp__(self, other):
+        if isinstance(other, ForceVolume):
+            return cmp(self.header['date'], other.header['date'])
+
+    def __getattribute__(self, name, **toto):
+        """
+            Control the attribute given form the object.
+        """
+        if name == 'event_list':
+            event_list = object.__getattribute__(self, name)
+            if self.get_switch('mask'):
+                # If data are masked, get only the events that are on the mask.
+                event_list = misc.remove_from_mask(event_list,
+                                                   self.__array['Mask'])
+            if self.get_switch('ev_dist'):
+                # If there is an threshold on the event distance.
+                event_list = misc.remove_from_threshold(
+                                    event_list,
+                                    'dist',
+                                    self.get_switch('ev_dist'))
+            if self.get_switch('ev_fit_length'):
+                event_list = misc.remove_from_threshold(
+                                    event_list,
+                                    'fit_length',
+                                    self.get_switch('ev_fit_length'))
+            if self.get_switch('ev_fit_plength'):
+                event_list = misc.remove_from_threshold(
+                                    event_list,
+                                    'fit_plength',
+                                    self.get_switch('ev_fit_plength'))
+            return event_list
+        elif name == 'has_stiffness':
+            if self.get_array('Stiffness') is not None:
+                return True
+            else:
+                return False
+        elif name == 'spring_constant':
+            if type(self.header['spring_constant']) is list:
+                return self.header['spring_constant'][self.pos_x]
+            else:
+                return self.header['spring_constant']
+        elif name == 'trace_x':
+            if self.header['data_location'] == 'local':
+                if self.__fdcurves['trace_x'].ndim == 1:
+                    return self.__fdcurves['trace_x']
+                else:
+                    return self.__fdcurves['trace_x'][
+                                                    self.pos_x, self.pos_y, :]
+            else:
+                # the data are loaded on the fly.
+                return afm_file.load_curve(self.__data_fid,
+                                          pos=[self.pos_x, self.pos_y],
+                                          dtype='trace_x',
+                                          header=self.header)
+        elif name == 'trace_y':
+            if self.header['data_location'] == 'local':
+                return self.__fdcurves['trace_y'][self.pos_x, self.pos_y, :]
+            else:
+                # the data are loaded on the fly.
+                return afm_file.load_curve(self.__data_fid,
+                                          pos=[self.pos_x, self.pos_y],
+                                          dtype='trace_y',
+                                          header=self.header)
+        elif name == 'retrace_x':
+            if self.header['data_location'] == 'local':
+                if self.__fdcurves['retrace_x'].ndim == 1:
+                    return self.__fdcurves['retrace_x']
+                else:
+                    return self.__fdcurves['retrace_x'][
+                                                    self.pos_x, self.pos_y, :]
+            else:
+                # the data are loaded on the fly.
+                return afm_file.load_curve(self.__data_fid,
+                                          pos=[self.pos_x, self.pos_y],
+                                          dtype='retrace_x',
+                                          header=self.header)
+        elif name == 'retrace_y':
+            if self.header['data_location'] == 'local':
+                return self.__fdcurves['retrace_y'][self.pos_x, self.pos_y, :]
+            else:
+                # the data are loaded on the fly.
+                return afm_file.load_curve(self.__data_fid,
+                                          pos=[self.pos_x, self.pos_y],
+                                          dtype='retrace_y',
+                                          header=self.header)
+        else:
+            return object.__getattribute__(self, name)
+
+    def next(self):
+        '''
+        Go to the next pixel
+        '''
+        self.go_next()
+        return [self.pos_x, self.pos_y]
+
+    def current_curve(self, what, parameters=None):
+        if what == 'Event':
+            if parameters is not None:
+                event_detect_weight = parameters[0]
+                event_fit_model = parameters[1]
+            else:
+                event_detect_weight = self.header['event_detect_weight']
+                event_fit_model = self.header['event_fit_model']
+                # event_fit_from_poc = self.header['event_fit_from_poc']
+            if event_fit_model is not None:
+                # we compute the point of contact from the current curve
+                poc = self.current_curve('poc')
+                poc['Poly Fit'][1] += (self.retrace_y[0] - self.trace_y[0])
+            else:
+                poc = {'PoC': 0, 'Poly Fit': None}
+            return curve.event_find(self.retrace_x,
+                                self.retrace_y,
+                                self.stiffness['glass'],
+                                self.spring_constant,
+                                weight=event_detect_weight,
+                                fit_model=event_fit_model,
+                                baseline=poc['Poly Fit'],
+                                poc=poc['PoC'])
+        elif what == 'poc':
+            poc = curve.find_poc(self.trace_x, self.trace_y,
+                                 threshold=self.stiffness['poc_threshold'],
+                                 method=self.stiffness['poc_method'],
+                                 limit_slide=self.stiffness['limit_slide'],
+                                 len_slice=self.stiffness['poc_len_slice'])
+            return poc
+
+    ##### Get stuffs from the object.
+    def get_parameter(self, which):
+        # TODO Put here all parameters that can be get. These parameters are
+        # not switches. Meaning that they have influences in the computation,
+        # but not in the display.
+        if which == 'poisson_ratio':
+            return self.stiffness['poisson_ratio']
+
+    def get_current_curve(self, direction='trace'):
+        """
+            Get the current trace curve.
+
+            * Parameters :
+
+                direction: str
+                    'trace' or 'retrace'
+
+            * Returns :
+
+                plotx: numpy.array
+                    The x part of the deflection curve
+                deflection: numpy.array
+                    The deflection part of the deflection curve
+        """
+        if direction == 'trace':
+            return [self.trace_x, self.trace_y]
+        elif direction == 'retrace':
+            return [self.retrace_x, self.retrace_y]
+
+    def get_switch(self, stype):
+        """
+            Get the value of the switch
+        """
+        if stype == 'list':
+            return ['mask', 'ev_dist']
+        elif stype == 'mask':
+            return self.header['Masked']
+        elif stype == 'ev_dist':
+            return self.header['event_dist_thresh']
+        elif stype == 'ev_thresh':
+            # This is a generic switch for all event thresholds.
+            return self.header['event_dist_thresh']
+        elif stype == 'ev_fit_length':
+            return self.header['thresh_event_fit_length']
+        elif stype == 'ev_fit_plength':
+            return self.header['thresh_event_fit_plength']
+        elif stype == 'restore':
+            return [self.get_switch('mask'), self.get_switch('ev_dist')]
+
+    def set_switch(self, stype, state=None):
+        """
+            Set the value of the switch.
+        """
+        if stype == 'mask':
+            if state == True and (self.__array['Mask'] is not None):
+                # Control if we have a mask
+                self.header['Masked'] = state
+            else:
+                self.header['Masked'] = False
+        elif stype == 'ev_dist':
+            if type(state) in [float, int]:
+                self.header['event_dist_thresh'] = float(state)
+            else:
+                raise AttributeError('Expecting numerical value.')
+        elif stype == 'ev_fit_length':
+            if type(state) == list and len(state) == 2:
+                if state[0] == 0:
+                    state[0] = None
+                if state[1] == 0:
+                    state[1] = None
+                self.header['thresh_event_fit_length'] = state
+            else:
+                raise AttributeError('Expecting list of length 2.')
+        elif stype == 'reset':
+            self.set_switch('mask', None)
+            self.set_switch('ev_dist', 0.0)
+        elif stype == 'restore':
+            self.set_switch('mask', state[0])
+            self.set_switch('ev_dist', state[1])
+
+    def get_array(self, atype, raw=False):
+        """
+            Get array from the forcevolume object.
+        """
+        if atype == 'keys':
+            # Return the valid keys for array.
+            return ARRAY_TYPE.keys()
+        if raw:
+            return self.__array[atype]
+        if ARRAY_TYPE[atype] == 'event':
+        #if atype in ['Event', 'Event force', 'Event length'] :
+            # A threshold is applyed on events.
+            ev_lst = self.event_list
+            #ev_lst = object.__getattribute__(self, 'event_list')
+            #ev_lst = misc.remove_from_threshold(ev_lst, 'dist',
+            #                                    self.get_switch('ev_dist'))
+
+            # Get the name in the event dictionnary that correspond to the one
+            # in array.
+            if atype == 'Event':
+                _gen_type = 'count'
+            elif atype == 'Event force':
+                _gen_type = 'force'
+            elif atype == 'Event length':
+                _gen_type = 'fit_length'
+            elif atype == 'Event distance':
+                _gen_type = 'dist'
+            array = misc.generate_array(ev_lst, _gen_type, self.header['size'])
+        elif atype == 'Piezo':
+            array = self.__array[atype]
+            if array is None: #num.array_equal(array, num.zeros(array.shape)):
+                raise NotReadyError('Topography array is not loaded')
+        else:
+            array = self.__array[atype]
+        if array is None:
+            return array
+        if self.get_switch('mask'):
+            # Return a masked array corresponding to the generated mask.
+            mask = self.__array['Mask'].copy()
+            mask = mask.astype(bool)
+            if type(array) == num.ma.core.MaskedArray:
+                if array.ndim == 3:
+                    mask = num.array([mask for i in range(array.shape[2])])
+                    mask = mask.transpose(1, 2, 0)
+                mask = ((array.mask - 1) * (mask - 1)) - 1
+                array = array.data
+            array = num.ma.masked_array(array, mask=mask)
+        return array
+
+    def force_piezo_loading(self):
+        """
+            Force the loading of the piezo array. Used in the case of AFM files
+            with no piezo arrays saved. The method is to get the coordinate of
+            the end of indentation of each curves. As this can take time, we do
+            not this automatically, but only if the user think its important.
+        """
+        arrays = afm_file.force_load_array(self.__data_fid,
+                                          header=self.header)
+        self.__array['Piezo'] = arrays['Piezo']
+
+    def set_array(self, atype, array):
+        """
+            Set the array with the new value.
+        """
+        if atype in self.__array.keys():
+            self.__array[atype] = array
+
+    def get_current_indent_curve(self, direction='trace'):
+        """
+            Get the current indentation curve.
+
+            * Parameters :
+                direction: str
+                  'trace' or 'retrace'
+
+            * Returns :
+                indent: numpy.array
+                    The indentation part of the indentation curve
+                force: numpy.array
+                    The force part of the indentation curve
+        """
+        if direction == 'trace':
+            self.compute_indentation()
+            return [self.indent, self.force]
+        elif direction == 'retrace':
+            self.compute_indentation('retrace')
+            return [self.r_indent, self.r_force]
+
+    def get_poc_display(self):
+        """
+            Get all parmeters to display the point of contact.
+
+            [poc, plotx, ploty, error, slice, deriv] = fv.get_poc_display()
+
+            * Parameters :
+                None
+
+            * Returns :
+                PoC: int
+                    The index of the point of contact.
+                plotx: numpy.array
+                    The x part of the curve.
+                ploty: numpy.array
+                    The y part of the curve.
+                error: float
+                    The standard error detected when finding the poc.
+                slice: slice
+                    The curve part that was used for the fit.
+                deriv: ??
+                    Have to find what's this...
+        """
+        ## build the curves...
+        _result = curve.find_poc(self.trace_x,
+                                self.trace_y,
+                                self.stiffness['poc_threshold'],
+                                method=self.stiffness['poc_method'],
+                                limit_slide=self.stiffness['limit_slide'],
+                                len_slice=self.stiffness['poc_len_slice'])
+        vect_y = _result['Poly Fit'][0] * self.trace_x + _result['Poly Fit'][1]
+        return[_result['PoC'], self.trace_x, vect_y, _result['Error'],
+                _result['Slice'], _result['deriv']]
+
+    def get_segments_indent(self):
+        """
+            get the segment of the indentation curve that are used to compute
+            the stiffness or the stiffness tomography.
+        """
+        if not self.exist['PoC']:
+            _result = curve.find_poc(self.trace_x,
+                                self.trace_y,
+                                self.stiffness['poc_threshold'],
+                                method=self.stiffness['poc_method'],
+                                limit_slide=self.stiffness['limit_slide'],
+                                len_slice=self.stiffness['poc_len_slice'])
+            poc_indice = _result['PoC']
+        else:
+            poc_indice = self.__array['PoCIndice'][self.pos_x, self.pos_y]
+        [x_parts, y_parts] = curve.segment_curve(self.indent[0:poc_indice],
+                                             self.force[0:poc_indice],
+                                             self.stiffness['nb_parts'],
+                                             self.stiffness['size_parts'])
+        return [x_parts, y_parts]
+
+    def get_path(self, atype, path):
+        """
+            Get the path from arrays.
+
+            * Parameters :
+                atype: str
+                    This is the array type to slice. This has to be an item
+                    from fv.get_array('keys')
+                    If atype is "all", it will return all possible values,
+                    with the corresponding label
+                pos_a: array
+                    correspond to the first point of the path[x, y]
+                pos_b: array
+                    correspond to the last point of the path [x,y]
+
+            * Returns :
+                x_slice: 1D numpy.array
+                    The x value of the path
+                y_slice: 1D numpy.array or list of numpy.array
+                    * If atype is an array type, this is the y value of the
+                      path
+                    * If atype is "all" this is a list of y value of the path
+                label: str
+                    If atype is "all", this is a list of label that desing each
+                    y_slices.
+                    Else, this is the atype as a string
+
+            >>> fv = ForceVolume(BIOSCOPE_FILE)
+            >>> #piezo_slice = fv.get_path('Piezo', [0, 14], [15, 14])
+        """
+        array_list = ['Piezo', 'PoCIndice', 'Topography']
+
+        if atype == 'all':
+            atype = array_list
+        elif atype in array_list:
+            atype = [atype]
+        else:
+            raise ValueError('Array type ' + atype + ' not known.')
+
+        self.__array['Path'] = path
+
+        y_slice = [
+                post_proc.generate_slice(self.__array['Path'],
+                                         self.__array[item])
+                for item in atype]
+        x_slice = list(num.arange(len(y_slice[0])) * self.header['pixel_size'])
+
+        return x_slice, y_slice, atype
+    #
+    #### Navigation dans le scan ####
+
+    def curve2xy(self):
+        '''
+        Conversion of the current curveNb into the x and y coordinates.
+        '''
+        if self.header['size'][1] - 1:
+            self.pos_x = (self.curve_nb) % (self.header['size'][0])
+            self.pos_y = (self.curve_nb) / (self.header['size'][0])
+        else:
+            self.pos_x = self.curve_nb
+            self.pos_y = 0
+
+    def curve2nb(self):
+        '''
+        Conversion of the current x and y coordinate into the curveNb.
+        '''
+        self.curve_nb = self.pos_x + \
+                        self.pos_y * self.header['size'][0]
+
+    def go_next(self):
+        '''
+        Go to the next pixel.
+        '''
+        if self.curve_nb == self.header['number_curves'] - 1:
+            raise StopIteration
+        self.curve_nb = self.curve_nb + 1
+        self.curve2xy()
+
+    def go_prev(self):
+        '''
+        Go to the previous pixel.
+        '''
+        if self.curve_nb == 0:
+            return
+        self.curve_nb = self.curve_nb - 1
+        self.curve2xy()
+
+    def go_up(self):
+        '''
+        Go tho the upper pixel.
+        '''
+        if self.pos_y == self.header['size'][1] - 1:
+            return
+        self.pos_y = self.pos_y + 1
+        self.curve2nb()
+
+    def go_down(self):
+        '''
+        Go to the bellow pixel.
+        '''
+        if self.pos_y <= 0:
+            return
+        self.pos_y = self.pos_y - 1
+        self.curve2nb()
+
+    def go_first(self):
+        '''
+        Go the the first pixel.
+        '''
+        self.pos_y = 0
+        self.pos_x = 0
+        self.curve_nb = 0
+
+    def go_to(self, pos_x, pos_y):
+        '''
+        Go to a defined pixel
+        '''
+        self.pos_x = int(pos_x)
+        self.pos_y = int(pos_y)
+        self.curve2nb()
+
+    # TODO: All these change should be in a single set_param function
+    #       Look if it's better or not...
+    # e.g. set_param('hertz_model', 'sphere', carac=None)
+    #       set_param('segm_depth', 50, carac='nm')
+    #       set_param('segm_nbr', 10, carac='begin')
+    #       set_param('rel_dist', 4)
+    def set_parameters(self, param, value):
+        """
+            Change the caracteristic of a parameter.
+
+            param: str
+                    Which parameter to change. Possible values are
+                    * 'tip_carac' to change the tip caracteristic (i.e. the
+                      semi-opening angle if the cone model is used, or the
+                      radius of the sphere if the sphere model is used)
+                      In this case, value is a float.
+
+                    * 'evt_fit' to change the event fit model.
+                      In this case, value is a string. 'wlc' and 'fjc' are
+                      possible strings. For more detailed information, see
+                      documentation of the event_fit function in
+                      fovea_toolbox/curve documentation.
+
+                    * 'stiff_method' to change the stiffness computation
+                      method.
+                      'Raw' indicates the use of the raw data to fit with the
+                            chosen model.
+                      'Extrema' uses the points at the extremities of the
+                                segments in order to make a simple fit. This
+                                method is faster, but less precise. This is
+                                historically the first method introduced.
+
+            value: float or str (depending on the parameters.)
+        """
+
+        if param == 'tip_carac':
+            print "Changing carac of %s from %f to %f" % (
+                                        self.name,
+                                        self.stiffness['point_carac'],
+                                        value)
+            self.stiffness['point_carac'] = value
+        elif param == 'evt_fit':
+            self.header['event_fit_model'] = value
+        elif param == 'stiffness_fit_method':
+            if value in ['Raw', 'Linear', 'Extrema', 'Median']:
+                self.stiffness['fit_method'] = value
+            else:
+                raise AttributeError(
+                    'Method %s not recognized as a stiffness method') % value
+
+    def change_poc_seg_size(self, size):
+        """
+            Change the size of the curve portion used to find the point of
+            contact. The size is expressed as a fraction of the total force
+            curve.
+        """
+        if size == 'default':
+            self.stiffness['poc_len_slice'] = 0.3
+        elif 0 < size < 1:
+            self.stiffness['poc_len_slice'] = size
+        else:
+            raise ValueError('Value must be between 0 and 1.')
+
+    def change_model(self, model, carac=None):
+        '''
+        change_model changes the model used for the stiffness computation.
+
+        model: 'Sphere' or 'Cone'.
+
+        carac: sphere radius or cone semi opening angle.
+        '''
+        if model == 'Sphere':
+            if carac == None:
+                self.stiffness['point_carac'] = 40
+            else:
+                self.stiffness['point_carac'] = carac
+            self.stiffness['hertz_model'] = 'Sphere'
+        elif model == 'Cone':
+            if carac == None:
+                self.stiffness['point_carac'] = 20 * math.pi / 180
+            else:
+                self.stiffness['point_carac'] = carac
+            self.stiffness['hertz_model'] = 'Cone'
+
+    def change_segment_depth(self, value):
+        '''
+        Changes the depth (in nm) of the force curve segmentation used to
+        compute the stiffness
+        '''
+        try:
+            self.stiffness['size_parts'] = float(value)
+        except ValueError:
+            pass
+
+    def change_segment_number(self, value):
+        '''
+        Changes the number of segment used to compute the stiffness
+        '''
+        try:
+            self.stiffness['nb_parts'] = int(value)
+        except ValueError:
+            pass
+
+    def change_relative_distance(self, value):
+        '''
+        Changes the maximum relative stiffness distance to compute.
+        '''
+        if type(value) == int or (int(value) - value == 0):
+            self.stiffness['relative_max_dist'] = int(value)
+
+    def change_poisson_ratio(self, value):
+        """
+            Changes the poisson ratio of the material.
+
+            * Parameters :
+                value: float
+                    The new poisson ratio.
+        """
+        if type(value) == float:
+            self.stiffness['poisson_ratio'] = value
+        else:
+            raise TypeError('Float value expected.')
+
+    def compute_poc(self):
+        '''
+        Computes the point of contact between the tip and the sample in the
+        whole array.
+        '''
+        self.counter['text'] = "Computing point of contact"
+        self.__array['Topography'] = num.empty(self.header['size'])
+        self.__array['PoCIndice'] = num.empty(self.header['size'])
+        self.__array['PoCNoise'] = num.empty(self.header['size'])
+
+        if self.__array['Piezo'] is None:
+            regenerate_piezo = True
+            self.__array['Piezo'] = num.empty(self.header['size'])
+        else:
+            regenerate_piezo = False
+
+        for pixels in self:
+            trace_x, trace_y = self.trace_x, self.trace_y
+            if regenerate_piezo:
+                self.__array['Piezo'][self.pos_x, self.pos_y] = trace_x[-1]
+            _result = curve.find_poc(trace_x, trace_y,
+                                    threshold=self.stiffness['poc_threshold'],
+                                    method=self.stiffness['poc_method'],
+                                    limit_slide=self.stiffness['limit_slide'],
+                                    len_slice=self.stiffness['poc_len_slice'])
+            if _result is not None:
+                self.__array['PoCIndice'][
+                                self.pos_x, self.pos_y] = _result['PoC']
+                self.__array['Topography'][self.pos_x, self.pos_y] = (
+                                self.__array['Piezo'][self.pos_x, self.pos_y] +
+                                trace_x[_result['PoC']])
+                self.__array['PoCNoise'][
+                                self.pos_x, self.pos_y] = _result['Error']
+            else:
+                self.__array['PoCIndice'][self.pos_x, self.pos_y] = 0
+                self.__array['Topography'][self.pos_x, self.pos_y] = 0
+                self.__array['PoCNoise'][self.pos_x, self.pos_y] = 0
+            self.counter['num'] += self.counter['increment']
+        self.go_first()
+        self.exist['PoC'] = 1
+
+    def compute_indentation(self, direction='trace'):
+        '''
+        Computes the indentation curves on the current position
+        '''
+        if direction == 'trace':
+            [self.indent, self.force] = curve.compute_indentation(
+                                        self.trace_x, self.trace_y,
+                                        self.stiffness['glass'],
+                                        self.spring_constant)
+        elif direction == 'retrace':
+            [self.r_indent, self.r_force] = curve.compute_indentation(
+                                        self.retrace_x, self.retrace_y,
+                                        self.stiffness['glass'],
+                                        self.spring_constant)
+
+    def compute_stiffness(self):
+        '''
+        Compute the stiffness array on the scan
+        '''
+        ## Defines the variables
+        ##
+
+        self.counter['num'] = 0
+        self.counter['text'] = "Creating matrices"
+        if self.stiffness['nb_parts'] < 0:
+            # case where we compute stiffness on whole curve instead of segments.
+            __size_array = 1
+        else:
+            __size_array = self.stiffness['nb_parts']
+        self.__array['Stiffness'] = num.zeros([
+                                    self.header['size'][0],
+                                    self.header['size'][1],
+                                    __size_array
+                                    ], num.float)
+        _number_of_curves = self.header['size'][0] * \
+                            self.header['size'][1] * 2 + 1
+        self.counter['increment'] = 1 / float(_number_of_curves - 1)
+
+        if (not self.exist['PoC']) or self.stiffness['recompute_poc']:
+            self.compute_poc()
+
+        self.counter['text'] = "Computing stiffness"
+        ## Computation begins by navigation in the array
+        for pixel in self:
+            self.compute_indentation()
+            if self.indent is None:
+                # There is no data here. We increment the counter and go to the
+                # next pixel.
+                self.counter['num'] += self.counter['increment']
+                continue
+            poc_indice = self.__array['PoCIndice'][self.pos_x, self.pos_y]
+            [x_parts, y_parts] = curve.segment_curve(
+                                    self.indent[0:poc_indice],
+                                    self.force[0:poc_indice],
+                                    self.stiffness['nb_parts'],
+                                    self.stiffness['size_parts'],
+                                    )
+            tmp = curve.compute_stiffness(
+                                x_parts,
+                                y_parts,
+                                model=self.stiffness['hertz_model'],
+                                tip_carac=self.stiffness['point_carac'],
+                                poisson_ratio=self.stiffness['poisson_ratio'],
+                                method=self.stiffness['fit_method'])
+            ## We complement the array in the case the newly computed stiffness
+            ## contains more depth. That can happend when performing stiffness
+            ## tomography.
+            if self.__array['Stiffness'].shape[2] < len(tmp):
+                array_shape = self.__array['Stiffness'].shape
+                _to_fill = num.empty((array_shape[0], array_shape[1],
+                                      len(tmp) - array_shape[2]))
+                _to_fill[:, :, :] = num.nan
+                self.__array['Stiffness'] = num.append(
+                                                self.__array['Stiffness'],
+                                                _to_fill, 2)
+            elif self.__array['Stiffness'].shape[2] > len(tmp):
+                array_shape = self.__array['Stiffness'].shape
+                _to_fill = num.empty((array_shape[2] - tmp.shape[0]))
+                _to_fill[:] = num.nan
+                tmp = num.append(tmp, _to_fill, 0)
+            ## Curves are in nm and nN. The result in tmp is then in nN/nm^2
+            ## To convert the result in Pa, we multiply by 1e9
+            self.__array['Stiffness'][self.pos_x, self.pos_y, ] = tmp * 1e9
+            self.counter['num'] += self.counter['increment']
+        ##
+        ## Stores the result in a matrix that supports the mask, to get rid
+        ## of the nan values
+        ##
+        self.counter['text'] = 'Store results'
+        self.__array['Stiffness'] = num.ma.array(
+                                    self.__array['Stiffness'],
+                                    mask=num.isnan(self.__array['Stiffness']))
+        self.exist['Stiffness'] = 1
+        self.exist['PoC'] = 1
+        self.go_first()
+        self.counter['num'] = 1
+
+    def compute_events(self):
+        '''
+        Computes the event of all the curves in the object. The event_list and
+        event matrix (in array['Event']) are refreshed.
+        '''
+        # Set the switches to 0 in order to get all event
+        _init_mask = self.get_switch('mask')
+        _init_ev_dist = self.get_switch('ev_dist')
+        self.set_switch('mask', False)
+        self.set_switch('ev_dist', 0.0)
+        self.counter['num'] = 0
+        self.counter['text'] = "Detecting events"
+        _number_of_curves = self.header['size'][0] * \
+                            self.header['size'][1] + 1
+        self.event_list = []
+        self.__array['Event'] = num.zeros((self.header['size'][0],
+                                        self.header['size'][0]))
+        self.__array['Event force'] = num.zeros((self.header['size'][0],
+                                                self.header['size'][0]))
+        for pixels in self:
+            det_event = self.current_curve('Event')
+            if det_event:
+                for event in det_event:
+                    event['pos_x'] = self.pos_x
+                    event['pos_y'] = self.pos_y
+                    self.event_list.append(event)
+                    self.__array['Event'][self.pos_x, self.pos_y] += 1
+            self.counter['num'] = float(self.curve_nb) / _number_of_curves
+        self.go_first()
+        # Generate the random matrix.
+        self.generate_random_event()
+        self.counter['num'] = 1
+
+        # Set back the original switches...
+        self.set_switch('mask', _init_mask)
+        self.set_switch('ev_dist', _init_ev_dist)
+
+    def generate_random_event(self, nbr_event=None):
+        if nbr_event is not None:
+            self.event['nbr_random'] = nbr_event
+        self.__array['Event random'] = rand_dot(self.__array['Event'],
+                                              self.event['nbr_random'])
+
+    def generate_mask(self, mtype, mdata, depth=0):
+        """
+            Generate a mask for the arrays.
+
+            * Parameters :
+                mtype: string
+                    'Piezo': generate mask based to the piezo image array.
+                    'Topography': generate mask based on the topography array.
+                    'Stiffness': generate mask based on the stiffness array.
+                    'Array': generate mask based on the mdata array.
+                mdata: float | 2D numpy.array
+                    float if mtype is 'piezo', 'topography', 'stiffness'
+                    2D numpy.array if mtype is 'array'
+                depht: int
+                    In the case the array is 3d. It generates the mask from the
+                    specified depth, array[:,:,depth].
+                    Default value: 0
+        """
+        if mtype == 'Array':
+            self.__array['Mask'] = mdata
+        else:
+            if self.__array[mtype].ndim == 3:
+                self.__array['Mask'] = self.__array[mtype][:, :, depth] < mdata
+            else:
+                self.__array['Mask'] = self.__array[mtype] < mdata
+        # Creating a mask automatically switch it on.
+        self.set_switch('mask', True)
+
+    def compute_relative_stiffness(self, exclude=0):
+        '''
+        Computes the relative stiffness of the events
+        '''
+        if self.__array['Event'] is None:
+            raise NotReadyError('Event is not yet computed.')
+        if self.__array['Stiffness'] is None:
+            raise NotReadyError('Stiffness is not yet computed.')
+        # event and stiffness have to be computed
+        # TODO: change self.event_list to self.event['list']
+        [self.event['rel_stiff'], coordinate] = rel_values(
+                                        self.__array['Stiffness'][:, :, 0],
+                                        self.__array['Event'],
+                                        self.stiffness['relative_max_dist'],
+                                        coord=True)
+        self.event['rel_stiff_ctl'] = rel_values(
+                                        self.__array['Stiffness'][:, :, 0],
+                                        self.__array['Event random'],
+                                        self.stiffness['relative_max_dist'])
+        # Is it really necessary ??
+        self.event_list = add_stiffness_to_event(self.event_list,
+                                                 self.event['rel_stiff'],
+                                                 coordinate)
+
+    def compute_average_stiffness(self):
+        """
+            Computes the average stiffness in function of the depth.
+
+            returns a dictionary with the deep, mean, std and count.
+
+            >>> fv = ForceVolume(BIOSCOPE_FILE)
+            >>> fv.compute_stiffness()
+            >>> result = fv.compute_average_stiffness()
+            >>> result.keys()
+            ['std', 'count', 'deep', 'mean']
+        """
+        if self.__array['Stiffness'] is None:
+            start = 0
+            data_count = 0
+        else:
+            step = self.stiffness['size_parts']
+            start = (self.__array['Stiffness'].shape[2] - 1) * step
+            #raise NotReadyError, 'Stiffness is not yet computed'
+            #start = (self.__array['Stiffness'].shape[2] -1) * step
+            deep = range(start, -step, -step)
+            stiffness = self.get_array('Stiffness')
+            data_count = stiffness.count()
+        if data_count:
+            _result = [[deep.pop(), i.mean(), i.std(), i.count()] for i in
+                                self.get_array('Stiffness').transpose(2, 0, 1)]
+        else:
+            _result = [[0, num.nan, num.nan, 0]]
+        _result = num.ma.asarray(_result)
+        return dict([(key, value) for key, value in
+                                    zip(['deep', 'mean', 'std', 'count'],
+                                         _result.transpose(1, 0))])
+
+    def event_force_list(self, dtype='rel'):
+        '''
+        Returns the list of the event force
+        '''
+        force_list = []
+        if dtype == 'rel':
+            prop = 'force'
+        elif dtype == 'baseline':
+            prop = 'force_base'
+        else:
+            raise TypeError('dtype ' + prop + ' is not supported.')
+        for event in self.event_list:
+            force_list.append(event[prop])
+        return force_list
+
+    def number_event(self):
+        return len(self.event_list)
+
+    def event_lr_list(self):
+        '''
+        Returns the list of the loading rates
+        '''
+        lr_list = []
+        for event in self.event_list:
+            lr_list.append(event['loading_rate'])
+        return lr_list
+
+    def event_dist_list(self):
+        '''
+        Returns the list of the distance of the events
+        '''
+        dist_list = []
+        for event in self.event_list:
+            dist_list.append(event['dist'])
+        return dist_list
+
+    def event_stiff_list(self):
+        '''
+        Returns the list of the stiffness of the events
+        '''
+        stiff_list = []
+        if self.__array['Stiffness'] is None:
+            return [num.nan for i in range(self.number_event())]
+        for event in self.event_list:
+            if not self.__array['Stiffness'].mask[event['pos_x'],
+                                                event['pos_y'], 0]:
+                stiff_list.append(
+                            self.__array['Stiffness'].data[event['pos_x'],
+                            event['pos_y'],
+                            0])
+            else:
+                stiff_list.append(num.nan)
+        return stiff_list
+
+    def event_rel_stiff_list(self, dist=1):
+        '''
+        Returns the list of the relative stiffness of the events
+        '''
+        stiff_list = []
+        if self.event_list is None:
+            return stiff_list
+        elif not 'Stiffness' in self.event_list[0]:
+            return [num.nan for i in range(self.number_event())]
+        for event in self.event_list:
+            if event['Stiffness'].size and not event['Stiffness'].mask[dist]:
+                stiff_list.append(event['Stiffness'].data[dist])
+            else:
+                stiff_list.append(num.nan)
+        return stiff_list
+
+    def event_rand_rel_stiff_list(self, dist=1):
+        '''
+            Returns the list of the relative stiffness of the events.
+        '''
+        _list = []
+        for item in self.event['rel_stiff_ctl'][dist]:
+            if isinstance(item, num.ma.core.MaskedArray):
+                _list.append(num.nan)
+            else:
+
+                _list.append(item)
+        return _list
+
+    def event_pos_list(self, dim=None):
+        """
+            Returns the position list of the events.
+        """
+        if dim in ['x', 'X']:
+            pos_list = [event['pos_x'] for event in self.event_list]
+        elif dim in ['y', 'Y']:
+            pos_list = [event['pos_y'] for event in self.event_list]
+        else:
+            pos_list = [self.event_pos_list('x'), self.event_pos_list('y')]
+        return pos_list
+
+    def event_nbr_per_curve(self):
+        """
+            Returns the list of number of event per curves.
+
+            >>> fv = ForceVolume(BIOSCOPE_FILE)
+            >>> fv.compute_events()
+            >>> nbr_event = fv.event_nbr_per_curve()
+            >>> print nbr_event
+            [79, 86, 55, 26, 10]
+
+            This means that 79 pixels (or force curves) have 0 events, 85 have
+            1, 56 have 2 26 have 3 and 10 force curves contains 4 events.
+
+            * Parameters: None
+
+            * Returns :
+                nbr_events_list: list
+                    The number of force curves that contains 0, 1, ... events.
+        """
+
+        _list = []
+        for nbr_ev in range(int(self.__array['Event'].max()) + 1):
+            with_current = num.nonzero(self.get_array('Event') == nbr_ev)
+            _list.append(len(with_current[0]))
+        return _list
+
+    def get_event_prop(self, data_type, dist=1):
+        """
+            Get the specified properties of the event.
+
+            * Parameters :
+                data_type: str
+                    Describe the event property to get.
+                    'force': return the list of event forces.
+                    'force_base': return the list of event forces, computed
+                        relative to the baseline.
+                    'lr': the loading rate.
+                    'dist': the distance from the end of the indentation.
+                    'stiff': the stiffness, computed from the corresponding
+                        trace curve.
+                    'stiff_ev': same as stiff, but not ordered, and one per
+                        pixel. If a pixel contain two event, it will be
+                        reported once.
+                    'stiff_notev': list of stiffness on pixels with no event.
+                    'relstiff': the list of relative stiffness on event.
+                    'pos_x': the list of the x position in the array.
+                    'pos_y': the list of the y position in the array.
+                    'nbr_ev_per_curve': the list of the number of events per
+                        force curves. From 0 event to the maximum detected.
+
+                    'all': A dictionnary of list with all the parameters
+                        related to events. This will not return list from
+                        "stiff_ev" and "stiff_notev" as they are different.
+                    'label': the label corresponding to "all". Usefull to have
+                        an ordered label.
+        """
+        if data_type is 'force':
+            return self.event_force_list()
+        elif data_type is 'force_base':
+            return self.event_force_list('baseline')
+        elif data_type is 'lr':
+            return self.event_lr_list()
+        elif data_type is 'dist':
+            return self.event_dist_list()
+        elif data_type is 'stiff':
+            return self.event_stiff_list()
+        elif data_type is 'stiff_ev':
+            return self.stiff_list('event')
+        elif data_type is 'stiff_notev':
+            return self.stiff_list('not event')
+        elif data_type is 'relstiff':
+            return [self.event_rel_stiff_list(dist) \
+                    for dist in range(self.stiffness['relative_max_dist'] + 1)]
+        elif data_type is 'nbr_ev_per_curve':
+            return self.event_nbr_per_curve()
+        elif data_type is 'length':
+            return [event['fit_length'][0] for event in self.event_list]
+        elif data_type is 'plength':
+            return [event['fit_plength'][0] for event in self.event_list]
+        elif data_type is 'label':
+            return ['pos_x', 'pos_y', 'force', 'lr',
+                    'dist', 'stiff', 'relstiff']
+        elif data_type is 'all':
+            return {'force': self.event_force_list(),
+                    'lr': self.event_lr_list(),
+                    'dist': self.event_dist_list(),
+                    'stiff': self.event_stiff_list(),
+                    'relstiff': self.event_rel_stiff_list(),
+                    'pos_x': self.event_pos_list('x'),
+                    'pos_y': self.event_pos_list('y')}
+
+    def stiff_list(self, dtype, depth=0):
+        """
+            Get the list of the stiffness at the given depth.
+
+            dtype = string
+                'all'
+                    to have stiffness of all pixels
+                'event'
+                    to have stiffness of event pixels
+                'not event'
+                    to have stiffness of pixels with no event
+                'random'
+                    to have stiffness of randomly selected no event pixels
+
+            The difference between event_stiff_list() and stiff_list('event')
+            is that for the first, there is the list of stiffness for each
+            events. Which means there can be two stiffness that belongs to the
+            same pixel. For the second (stiff_list('event')), the list does not
+            contain twice the same pixel value.
+
+            For example :
+
+            >>> fv = ForceVolume(BIOSCOPE_FILE)
+            >>> fv.compute_events()
+            >>> fv.compute_stiffness()
+
+            To get stiffness of pixels where no event were detected :
+
+            >>> stiffness_list = fv.stiff_list('not event')
+
+            To get stiffness of pixels with event :
+
+            >>> event_stiffness_list = fv.stiff_list('event')
+
+            To get stiffness of all pixels :
+
+            >>> all_stiffness_list = fv.stiff_list('all')
+
+            Just to verify that the sum of list with and without event give the
+            correct length :
+
+            >>> len(event_stiffness_list) + len(stiffness_list) == \
+                                                        len(all_stiffness_list)
+            True
+
+            ... and so on.
+        """
+        array = self.get_array('Stiffness')
+
+        depth = int(depth)
+        #print('Line 1165 class.py Depth = %f, type')%depth
+        if array is None:
+            return []
+        else:
+            try:
+                array = array[:, :, depth]
+            except IndexError:
+                array = num.ma.array(num.zeros(array.shape[:2]),
+                                       mask=num.ones(array.shape[:2]))
+                array[:] = num.nan
+        if dtype == 'all':
+            cache = num.ones(array.shape)
+        elif dtype == 'event':
+            cache = self.get_array('Event') > 0
+        elif dtype == 'random':
+            cache = self.get_array('Event random') > 0
+        elif dtype == 'not event':
+            cache = self.get_array('Event') == 0
+        else:
+            raise TypeError(dtype + ' is not recognized.')
+        # Want's negative mask (initially, 1 is masked and 0 is visible)
+        mask = array.mask == False
+        # * is the same as 'and' but 'and' operator does not work
+        mask = cache * mask
+        pix_indice = num.nonzero(mask)
+        stiffness_list = [array[x, y] for x, y in zip(pix_indice[0],
+                                                      pix_indice[1])]
+
+        return stiffness_list
+
+    def event_gauss_fit(self, data_type, min_val, max_val, dist=1):
+        '''
+        Automatically finds the best gaussian fit of the event properties.
+
+        data_type can be :
+
+            * 'force' to considere the event forces.
+            * 'lr' to considere the event loading rates.
+            * 'distance' to considere the event distance in the curve
+            * 'stiff' to considere the stiffness in the trace curve where event
+              was detected.
+            * 'relstiff' to considere the relative stiffness of the pixel where
+              event was detected.
+
+        Results are stored in event_stat[data_type] attribute.
+
+        For example :
+
+        >>> fv = ForceVolume(BIOSCOPE_FILE)
+        >>> fv.compute_events()
+        >>> fv.event_gauss_fit('force', min_val=0, max_val=1)
+        >>> fv.event_stat['force'].keys()
+        ['std', 'kde', 'maxima', 'count', 'mean']
+
+        * kde is the kernel density estimation. This is an array composed of
+          two vector, respectively the x and y coordinate.
+        * 'mean' is the list of detected gaussian mean
+        * 'std' is the corresponding standard deviation.
+        * 'count' is the corresponding number of elements for the mean and std.
+        * 'maxima' is the detected maxima from the kde.
+        '''
+
+        fit, mean, std, count = None, None, None, None
+        if data_type == 'force':
+            values = num.asanyarray(self.event_force_list())
+        elif data_type == 'lr':
+            values = num.asanyarray(self.event_lr_list())
+        elif data_type == 'distance':
+            values = num.asanyarray(self.event_dist_list())
+        elif data_type == 'stiff':
+            values = num.asanyarray(self.event_stiff_list())
+        elif data_type == 'relstiff':
+            values = num.asanyarray(self.event_rel_stiff_list(dist))
+        else:
+            raise StandardError(data_type + ' is not recognize.')
+        index = (min_val < values) * (values < max_val)
+        self.event_stat[data_type] = post_proc.find_gauss_fit(values[index])
+
+    def to_plot(self, curve_type):
+        '''
+        Returns the curves to plot
+        '''
+        if curve_type in self.plot_who:
+            return self.plot_who[curve_type]
+        else:
+            raise KeyError
+
+    def set_to_plot(self, curve_type, value):
+        '''
+        Sets the plotting status of the curve type
+        '''
+        if curve_type in self.plot_who:
+            self.plot_who[curve_type] = value
+        else:
+            raise KeyError
+
+    def stiffness_tomography_array(self):
+        '''
+        Generates the stiffness tomography array
+        '''
+        floor = num.floor(self.__array['Piezo'] / self.stiffness['size_parts'])
+
+        self.__array['Stiffness tomo'] = post_proc.tomography_array(
+                                                self.__array['Stiffness'],
+                                                floor=floor)
+
+    def add_point(self, fdcurves, piezo):
+        '''
+        Add a force distance curve to the file.
+        '''
+        # Calculate the shape of the new array, after we add a new point.
+        nbr_line = num.round(num.sqrt(self.header['number_curves'] + 1))
+        nbr_col = num.ceil(num.sqrt(self.header['number_curves'] + 1))
+        if (nbr_line != self.header['size_x']) or (nbr_col !=
+                                                   self.header['size_y']):
+            self.__fdcurves['trace_y'] = resize_array(
+                                self.__fdcurves['trace_y'],
+                                (nbr_line, nbr_col,
+                                 self.header['force_samples_per_curve']))
+            self.__fdcurves['retrace_y'] = resize_array(
+                                self.__fdcurves['retrace_y'],
+                                 (nbr_line, nbr_col,
+                                  self.header['force_samples_per_curve']))
+            if self.__fdcurves['trace_x'].ndim == 3:
+                self.__fdcurves['trace_x'] = resize_array(
+                                self.__fdcurves['trace_x'],
+                                (nbr_line, nbr_col,
+                                 self.header['force_samples_per_curve']))
+                self.__fdcurves['retrace_x'] = resize_array(
+                                self.__fdcurves['retrace_x'],
+                                (nbr_line, nbr_col,
+                                 self.header['force_samples_per_curve']))
+            self.__array['Piezo'] = resize_array(self.__array['Piezo'],
+                                               (nbr_line, nbr_col))
+
+        # The coordinate of the added point.
+        pos_x = (self.header['number_curves']) % nbr_line
+        pos_y = (self.header['number_curves']) / nbr_line
+        # Add the new point.
+        self.__fdcurves['trace_y'][pos_x, pos_y] = fdcurves['trace_y'][0, 0]
+        self.__fdcurves['retrace_y'][pos_x, pos_y] = \
+                                                    fdcurves['retrace_y'][0, 0]
+        if self.__fdcurves['trace_x'].ndim == 3:
+            self.__fdcurves['trace_x'][pos_x, pos_y] = \
+                                                    fdcurves['trace_x'][0, 0]
+            self.__fdcurves['retrace_x'][pos_x, pos_y] = \
+                                                    fdcurves['retrace_x'][0, 0]
+        self.__array['Piezo'][pos_x, pos_y] = piezo
+        # Update the data.
+        self.header['number_curves'] += 1
+        self.header['matrix_length'] = int(nbr_line)
+        self.header['size_x'] = int(nbr_line)
+        self.header['size_y'] = int(nbr_col)
+
+    def export_map_stiffness(self, file_name, depth=None):
+        title = 'Stiffness File ' + self.name
+        plot_array = plot.Array(title=title)
+        if depth == None:
+            #export all depth
+            plot_array.color_scale['min'] = 0
+            plot_array.color_scale['max'] = self.__array['Stiffness'].max()
+            depth = 0
+            for item in self.__array['Stiffness'].transpose(2, 0, 1):
+                plot_array.plot(item, scan_size=self.header['scan_size'])
+                plot_array.title = '%s, depth %03f nm' % (title,
+                                                self.stiffness['size_parts'])
+                plot_array.save('%s%03i.png' % (file_name, depth))
+                depth += 1
+
+    def export_curve(self, file_name, direction='trace'):
+        """
+            Export the current curve to a csv file.
+
+            * Parameters :
+                file_name: str
+                    The complete path and file name to save the curve in.
+                direction: str
+                    The direction of the curve. This can be: 'trace',
+                    'retrace', 'both'. Default is 'trace'
+
+            * Returns :
+                None
+
+            >>> file_name = EXPORT_FOLDER + '/export_curve.csv'
+            >>> fv_file = ForceVolume(BIOSCOPE_FILE)
+            >>> fv_file.export_curve(file_name, 'trace')
+            >>> file_name = EXPORT_FOLDER + '/export_curve_both.csv'
+            >>> fv_file.export_curve(file_name, 'both')
+        """
+        legend = []
+        curves = []
+        if direction in ['trace', 'both']:
+            legend.append('trace x')
+            curves.append(self.trace_x)
+            legend.append('trace y')
+            curves.append(self.trace_y)
+        if direction in ['retrace', 'both']:
+            legend.append('retrace x')
+            curves.append(self.retrace_x)
+            legend.append('retrace y')
+            curves.append(self.retrace_y)
+
+        preambule = ['Force distance curve of file :' + self.name,
+                    'Curve [' + str(self.pos_x) + ': ' + str(self.pos_y) + ']']
+        curves = misc.export_list(file_name, curves,
+                                  legend, preambule, transpose=True)
+
+    def export_events(self, to_file, firstfile=False):
+        """
+            Export the event properties to a csv file.
+
+            * Parameters :
+                to_file: str or csv.writer object
+                    If str, it describes the file pathname.
+                    If csv.writer object, the function just adds events
+                    properties of this ForceVolume object at the end of the
+                    file.
+                firstfile: bool (default: False)
+                    If True, will add labels to the first line. This has
+                    incidence only whith csv.writer object as to_file.
+
+            * Retruns :
+                None.
+
+            >>> file_name = EXPORT_FOLDER + '/export_event.csv'
+            >>> fv_file = ForceVolume(BIOSCOPE_FILE)
+            >>> fv_file.compute_events()
+            >>> fv_file.export_events(file_name)
+        """
+        nbr_evt = self.number_event()
+        evt_list = self.get_event_prop('all')
+        legend = self.get_event_prop('label')
+        if type(to_file) == str:
+            # Create the file.
+            fid = open(to_file, 'wb')
+            fcsv = csv.writer(fid)
+        elif str(type(to_file)) == "<type '_csv.writer'>":
+            # we got a csv writer, then directly write on it.
+            fcsv = to_file
+        if type(to_file) == str or firstfile:
+            fcsv.writerow(['filename'] + legend)
+        # Now, complement the fcsv...
+        for item in range(nbr_evt):
+            fcsv.writerow([self.name] + [evt_list[leg][item]
+                                                        for leg in legend])
+        if type(to_file) == str():
+            fid.close()
+
+    def export_nbr_events(self, to_file, firstfile=False):
+
+        nbr_evt = self.get_event_prop('nbr_ev_per_curve')
+        legend = ['nbr_evt', 'nbr_curves']
+        if type(to_file) == str:
+            # Create the file
+            fid = open(to_file, 'wb')
+            fcsv = csv.writer(fid)
+        elif str(type(to_file)) == "<type '_csv.writer'>":
+            # we got a csv writer, then, directly write on it.
+            fcsv = to_file
+        if type(to_file) == str or firstfile:
+            fcsv.writerow(['filename'] + legend)
+        # Now, complement the fcsv...
+        for nbr_curve, nbr_evt in zip(nbr_evt, range(len(nbr_evt))):
+            fcsv.writerow([self.name, nbr_evt, nbr_curve])
+        if type(to_file) == str():
+            fid.close()
+
+    def test_fct(self):
+        pass
+
+
+class FVFolder(object):
+    '''
+    In this class are stored all the ForceVolume files of a single experiment.
+
+    Important attribute that are read-write accessible :
+
+        filename
+            Stores the name of the original aex file.
+        short_name
+            Same as filename, but without the tree.
+        file
+            Dictionnary that contains informations about the stored files :
+
+            'list'
+                is the list of stored files.
+            'name'
+                is the name of stored files.
+            'group'
+                is the group to which files respectively belongs to.
+        data_hist
+            Is a PlotData instance. Used to plot histograms and scatter with
+            plot_generic module.
+        author
+            String informing about the author of the experiment.
+        comment
+            String that contains information usefull for user.
+        date
+            Datetime instance. Stores the creation date.
+        counter, counter_text
+            Integer and string to be displayed in the progressbar for the gui.
+        parameters
+            Dictionnary that contains informations about some parameters :
+
+            'event_detect_weight'
+                Float. [0:inf] How much the noise has to be considered for the
+                event detection. 0 means no influence (detection won't work)
+            'rel_stiff_dist'
+                Integer. Is the maximum distance to consider for the relative
+                stiffness computation.
+            'PoC_threshold'
+                Float. [0:inf] Threshold to detect the point of contact.
+            'spring_constant'
+                Float. Is the spring constant of the used cantilever.
+            'glass'
+                Float. Is the correction for the slope recorded on stiff
+                substrate.
+            'injection_index' [Deprecated]
+                Integer. Is the index of the first file after injection of
+                chemical.
+            'number_curves'
+                Integer. The total number of curves in the experiment.
+        event_stat
+            Dictionnary that contais event properties, ordered.
+
+            'force', 'lr', 'dist', 'stiff', 'rel_stiff'
+                Are list containing the computed force, loading rate, distance
+                from the end of indentation, stiffness and relative stiffness
+                respectively
+        relative_stiffness
+            Dictionnary that contains information about relative stiffness.
+
+            'data'
+                List containing the relative stiffness of event.
+            'data_ctl'
+                List containing the relative stiffness of randomly selected
+                pixels
+            'indice'
+                First file after chemical injection.
+
+    >>> #fv_folder = FVFolder()
+    >>> #fv_folder.load()
+    '''
+
+    def __init__(self):
+        # TODO eliminate self.relative_stiffness['mean'] or use it...
+
+        self.filename = None  # stores the filename of aex file where it is
+                              # saved
+        self.short_name = None  # the short name to display
+        self.file = {'list': [],
+                     'name': [],
+                     'group': [],
+                     'current': 0}  # Stores the indice of the current used
+                                    # file.
+        self.group = {'id': [],  # List of int. The id of the group.
+                      'label': [],  # List of str. Label corresponding to
+                                    # group to be displayed in the plots.
+                      'display': []}  # List of bool. Informs wether to display
+                                      # or not the correspinding group.
+        self.data_hist = PlotData()
+        self.author = 'Author name'
+        self.comment = 'Your comment'
+        self.date = datetime.now()
+        self.counter = {'num': 0,
+                        'text': 'Please wait ...'}
+        self.parameters = {
+            'event_detect_weight': 2,
+            # The fit use for the events (can be wlc, fjc or None)
+            'event_fit_model': None,
+            'rel_stiff_dist': 3,
+            'PoC_threshold': 2,
+            'spring_constant': None,
+            'glass': None,
+            'injection_index': 0,
+            'number_curves': 0,
+            'histo_y_rel': False,  # The y axis in histogram. If False, the
+            # histogram y axis reflects the number of data. If true, it
+            # reflects the frequency of the data.
+            'plot_size': [800, 600],  # The size, in pixel, of the plot to
+                                      # save.
+            'plot_hist_gauss': True,
+        }
+        self.event_stat = {'force': None,
+                           'lr': None,
+                           'dist': None,
+                           'stiff': None,
+                           'rel_stiff': None}
+        self.relative_stiffness = {'data': None,
+                                    'data_ctl': None,
+                                    'indice': None}
+        # The list of switch to enable or disable functions. Use self.switch()
+        # to change the state.
+        self.switch_dict = {'mask': 'No',
+                            'all': 'No'}
+
+    def __setattr__(self, att, value):
+        if att is 'PoC_threshold':
+            for fv in self.file['list']:
+                fv.stiffness['poc_threshold'] = value
+            self.parameters['PoC_threshold'] = value
+        else:
+            self.__dict__[att] = value
+
+    def __getattr__(self, att):
+        '''
+        Called if requested attribute does not exist.
+        '''
+        if att == 'event_force':
+            __list = []
+            for force_volume in self.file['list']:
+                __list = __list + force_volume.event_force_list()
+            self.event_force = __list
+            return self.event_force
+        elif att == 'event_distance':
+            __list = []
+            for force_volume in self.file['list']:
+                __list = __list + force_volume.event_dist_list()
+            self.event_distance = __list
+            return self.event_distance
+        elif att == 'event_lr':
+            __list = []
+            for force_volume in self.file['list']:
+                __list = __list + force_volume.event_lr_list()
+            self.event_lr = __list
+            return self.event_lr
+        elif att == 'event_stiffness':
+            __list = []
+            for force_volume in self.file['list']:
+                __list = __list + force_volume.event_stiff_list()
+            self.event_stiffness = __list
+            return self.event_stiffness
+        elif att == 'event_relstiff':
+            __list = []
+            for dist in range(self.parameters['rel_stiff_dist'] + 1):
+                __dist = []
+                for force_volume in self.file['list']:
+                    __dist = __dist + force_volume.event_rel_stiff_list(dist)
+                __list.append(__dist)
+            self.event_relstiff = __list
+            return self.event_relstiff
+        elif att == 'average_stiffness':
+            """
+                This is the average stiffness in function of the depth
+            """
+            return [fv.compute_average_stiffness() for fv in self.file['list']]
+        else:
+            print att
+            raise AttributeError
+
+    def get_file(self, nbr):
+        """
+            Get the forcevolume file from the list.
+
+            * Parameters :
+                nbr: int
+                    The index number of the force volume object.
+        """
+        self.file['current'] = nbr
+        self.update_switch()
+        return self.file['list'][nbr]
+
+    def get_masked_list(self):
+        """
+            Get the list of masked switch for each forcevolume files.
+
+            fvfolder.get_masked_list()
+            [True, False, False, False, True, True]
+        """
+
+        return [fv.get_switch('mask') for fv in self.file['list']]
+
+    def get_event_att(self, att):
+        if att in ['force', 'force_base', 'dist', 'stiff_ev', 'stiff_notev',
+                   'lr', 'stiff', 'length', 'plength']:
+            __list = []
+            __group = []
+            __fid = []
+            __coord = None  # to be done...
+            for force_volume, group in zip(self.file['list'],
+                                           self.file['group']):
+                __add_to_list = force_volume.get_event_prop(att)
+                __add_to_group = [group for i in range(len(__add_to_list))]
+
+                __this_fid = self.file['list'].index(force_volume)
+                __add_to_fid = [__this_fid for i in range(len(__add_to_list))]
+
+                __list = __list + __add_to_list
+                __group = __group + __add_to_group
+                __fid = __fid + __add_to_fid
+        if att in ['force', 'force_base']:
+            self.event_force = __list
+        elif att == 'dist':
+            self.event_distance = __list
+        elif att == 'lr':
+            self.event_lr = __list
+        elif att == 'stiff':
+            self.event_stiffness = __list
+        elif att == 'length':
+            self.event_length = __list
+        elif att == 'plength':
+            self.event_plength = __list
+        elif att in ['relstiff', 'relstiffctl']:
+            __list = []
+            __group = []
+            __fid = []
+            __coord = None  # to be done...
+            for dist in range(self.parameters['rel_stiff_dist'] + 1):
+                __dist = []
+                __dist_group = []
+                __dist_fid = []
+                # __dist_coord = []
+                for force_volume, group in zip(self.file['list'],
+                                               self.file['group']):
+                    if att == 'relstiff':
+                        __add_to_list = force_volume.event_rel_stiff_list(dist)
+                    elif att == 'relstiffctl':
+                        __add_to_list = \
+                                   force_volume.event_rand_rel_stiff_list(dist)
+                        __add_to_list = list(__add_to_list)
+                    __add_to_group = [group for i in range(len(__add_to_list))]
+                    __this_fid = self.file['list'].index(force_volume)
+                    __add_to_fid = [__this_fid
+                                    for i in range(len(__add_to_list))]
+                    __dist = __dist + __add_to_list
+                    __dist_group = __dist_group + __add_to_group
+                    __dist_fid = __dist_fid + __add_to_fid
+                __list.append(__dist)
+                __group.append(__dist_group)
+            self.event_relstiff = __list
+            __fid = __dist_fid
+        return [__list, __group, __fid, __coord]
+
+    def load_file(self, fv_file):
+        '''
+        Loads the file specified
+        '''
+        self.file['list'].append(ForceVolume(fv_file))
+        self.file['list'].sort()
+        self.__regenerate_filename_list()
+        self.parameters['spring_constant'] = \
+                            self.file['list'][0].header['spring_constant']
+        self.parameters['glass'] = \
+                            self.file['list'][0].stiffness['glass']
+
+    def load_folder(self, fv_folder):
+        '''
+        Loads all the files in a folder
+        '''
+        list_files = os.listdir(fv_folder)
+        self.counter['num'] = 0
+        counter_total = len(list_files) + 1
+        counter_this = 0
+        for files in list_files:
+            self.counter['text'] = 'Loading ' + files + '...'
+            try:
+                self.load_file(os.path.join(fv_folder, files))
+            except TypeError as detail:
+                if detail.args[0] == "Not a supported AFM file format.":
+                    pass
+                elif 'asylum' in detail.args[0]:
+                    pass
+                else:
+                    raise TypeError(detail)
+                counter_this += 1
+            finally:
+                counter_this += 1
+                self.counter['num'] = float(counter_this) / counter_total
+        self.file['list'].sort()
+        try:
+            self.convert_v6()
+        except KeyError:
+            pass
+        self.__regenerate_filename_list()
+        self.__regenerate_comment()
+        self.counter['num'] = 1
+
+    def convert_v6(self):
+        new_file_list = []
+        container = None
+        self.counter['text'] = 'Reshaping data from V6...'
+        for counter_this in range(1, len(self.file['list'])):
+            if (6100000 <
+                self.file['list'][counter_this].header['di_version'] <
+                6200000):
+                name0 = os.path.splitext(self.file['list']
+                                                    [counter_this - 1].name)[0]
+                name1 = os.path.splitext(self.file['list']
+                                                    [counter_this].name)[0]
+                if name0 == name1:
+                    if container is None:
+                        container = self.file['list'][counter_this - 1]
+                    container = self.merge_single(container,
+                                            self.file['list'][counter_this])
+                else:  # A new serie is comming
+                    new_file_list.append(container)
+                    container = self.file['list'][counter_this]
+        new_file_list.append(container)
+        new_file_list.sort()
+        if container is not None:
+            self.file['list'] = new_file_list
+
+    def merge_single(self, container, fv_file):
+        '''
+        Merge force volume files that contains only one fv curve.
+        The first fv_file is the container that can contain already several
+        force curve.
+        The second is the force curve that will be added.
+        '''
+        ## Variable to update :
+        ##
+        if fv_file._ForceVolume__fdcurves['trace_y'].shape[0:2] == (1, 1):
+            container.add_point(fv_file._ForceVolume__fdcurves,
+                                fv_file.get_array('Piezo')[0, 0])
+        return container
+
+    def load_aex(self, aex_file):
+        '''
+        Loads a AFM Experiment XML file
+        '''
+        self.filename = aex_file
+        self.short_name = os.path.split(aex_file)[1]
+        self.counter['num'] = None
+        self.counter['text'] = 'Uncompressing files ...'
+        [experiment, file_tree] = aex.load(aex_file)
+        self.author = experiment['author']
+        self.comment = experiment['comment']
+        self.date = experiment['date']
+        self.parameters = experiment['parameters']
+        self.counter['text'] = 'Loading files ...'
+        for item in file_tree:
+            self.load_file(item)
+        self.file['list'].sort()
+        self.__regenerate_filename_list
+        self.counter['num'] = 1
+        self.update_switch()
+        if len(experiment['group']['id']):
+            self.group = experiment['group']
+
+    def save(self, file_name):
+        self.filename = file_name
+        self.short_name = os.path.split(file_name)[1]
+        self.counter['num'] = None
+        self.counter['text'] = 'Saving files ...'
+        aex.save(self, file_name)
+        self.counter['num'] = 1
+
+    def set_parameters(self, param, value):
+        """
+            Change the parameters of the force volume files in the experiments.
+
+            * Parameters :
+                param: str
+                    Defines which parameter to change.
+                    'spring_constant'
+                    'glass'
+                    'poisson_ratio'
+                value: depending on the parameters.
+                    float if 'spring_constant', 'glass' or 'poisson_ratio'
+        """
+        if param == 'spring_constant':
+            for fc in self.file['list']:
+                fc.header['spring_constant'] = value
+            self.parameters['spring_constant'] = value
+        elif param == 'glass':
+            for fv in self.file['list']:
+                fv.stiffness['glass'] = value
+            self.parameters['glass'] = value
+        elif param == 'poisson_ratio':
+            if self.get_switch('all') == 'Yes':
+                [fv.change_poisson_ratio(value) for fv in self.file['list']]
+            else:
+                self.file['list'][self.file['current']].change_poisson_ratio(
+                                                                        value)
+        elif param == 'tip_carac':
+            if self.get_switch('all') == 'Yes':
+                [fv.set_parameters('tip_carac', value)
+                                                for fv in self.file['list']]
+            else:
+                self.file['list'][self.file['current']].set_parameters(
+                                                            'tip_carac', value)
+        elif param == 'plot_size':
+            self.parameters['plot_size'] = [int(value[0]), int(value[1])]
+        elif param == 'plot_hist_gauss':
+            # bool to display gauss fit on histograms.
+            if isinstance(value, bool):
+                self.parameters['plot_hist_gauss'] = value
+            elif isinstance(eval(value), bool):
+                self.parameters['plot_hist_gauss'] = eval(value)
+            else:
+                raise AttributeError(
+                        '%s is not a correct type for this parameter' %
+                        type(value))
+
+    def set_group(self, group_list):
+        """
+            Change the group appartenance for the fv files, and update the
+            group list.
+        """
+
+        for fv, group in zip(self.file['list'], group_list):
+            fv.header['group'] = group
+        self.__regenerate_filename_list()
+
+    def set_group_prop(self, prop, which, value):
+        """
+            Change the properties of the group.
+
+            * Parameters :
+                prop: str
+                    'label': to change the label
+                    'visible': to switch the visibility of the group
+                which: int
+                    The group id to change. if -1, will change all the label
+                value: str or bool
+                    if prop is label: str
+                    if prop is visible: True or False
+                    if which is -1, need a list of prop. the length has to be
+                                    the same as the number of groups.
+        """
+        if prop not in ['label', 'display']:
+            raise TypeError('%s is not recognized property.' % prop)
+        if which is not -1:
+            if prop == 'label' and type(value) is not str:
+                raise TypeError('Property %s expect string value.' % prop)
+            if prop == 'display' and type(value) is not bool:
+                raise TypeError('Property %s expect boolean value' % prop)
+            # we change only one group property
+            index = self.group['id'].index(which)
+            self.group[prop][index] = value
+        if which == -1:
+            if type(value) is not list:
+                raise TypeError('Expect list of values.')
+            for [gid, gval] in zip(self.group['id'], value):
+                self.set_group_prop(prop, gid, gval)
+
+    def compute_relative_stiffness(self, exclude=0):
+        # initialize temporary variables
+        tmp_indice = num.zeros(len(self.file['list']))
+        max_dot = 0
+        max_rand = 0
+        for fvfile in self.file['list']:
+            max_dot = max((fvfile.get_array('Event') > 0).sum(), max_dot)
+            max_rand = max((fvfile.get_array('Event random') > 0).sum(),
+                           max_dot)
+
+        array_shape = (len(self.file['list']),
+                       self.parameters['rel_stiff_dist'] + 1,
+                       max_dot)
+        self.relative_stiffness['data'] = num.ma.array(
+                                                num.empty(array_shape),
+                                                mask=num.ones(array_shape))
+        array_shape = (len(self.file['list']),
+                       self.parameters['rel_stiff_dist'] + 1,
+                       max_rand)
+        self.relative_stiffness['data_ctl'] = num.ma.array(
+                                                num.empty(array_shape),
+                                                mask=num.ones(array_shape))
+        file_nbr = 0
+        for fvfile in self.file['list']:
+            fvfile.change_relative_distance(self.parameters['rel_stiff_dist'])
+            fvfile.compute_relative_stiffness(exclude)
+            t_shape = fvfile.event['rel_stiff'].shape
+
+            self.relative_stiffness['data'].data[file_nbr,
+                                                 :t_shape[0],
+                                                 :t_shape[1]] = \
+                                            fvfile.event['rel_stiff'].data
+            self.relative_stiffness['data'].mask[file_nbr,
+                                                 :t_shape[0],
+                                                 :t_shape[1]] = \
+                                            fvfile.event['rel_stiff'].mask
+
+            t_shape = fvfile.event['rel_stiff_ctl'].shape
+            self.relative_stiffness['data_ctl'].data[file_nbr,
+                                                     :t_shape[0],
+                                                     :t_shape[1]] = \
+                                            fvfile.event['rel_stiff_ctl'].data
+            self.relative_stiffness['data_ctl'].mask[file_nbr,
+                                                     :t_shape[0],
+                                                     :t_shape[1]] = \
+                                            fvfile.event['rel_stiff_ctl'].mask
+            if file_nbr < self.parameters['injection_index']:
+                tmp_indice[file_nbr] = 0
+            else:
+                tmp_indice[file_nbr] = 0
+            file_nbr += 1
+        self.relative_stiffness['indice'] = num.array(tmp_indice)
+        self.relative_stiffness['data'] = \
+                            self.relative_stiffness['data'].transpose(0, 2, 1)
+        self.relative_stiffness['data_ctl'] = \
+                        self.relative_stiffness['data_ctl'].transpose(0, 2, 1)
+
+    def generate_mask(self, mtype, mdata):
+        """
+            See FV classe.
+        """
+
+        for fvfile in self.file['list']:
+            fvfile.generate_mask(mtype, mdata)
+
+    def update_switch(self):
+        """
+            Update the switches.
+        """
+
+        convbool = {True: 'Yes', False: 'No'}
+        if self.switch_dict['all'] == 'Yes':
+            # We update other switches to reflect the whole experiment.
+            #
+            ## First the mask :
+            mask = [fv.get_switch('mask') for fv in self.file['list']]
+            if mask.count(True) == len(mask):
+                self.switch_dict['mask'] = 'Yes'
+            elif mask.count(False) == len(mask):
+                self.switch_dict['mask'] = 'No'
+            else:
+                self.switch_dict['mask'] = 'Some'
+            ## Second, the event distance threshold :
+            ev_dist = [fv.get_switch('ev_dist') for fv in self.file['list']]
+            if ev_dist.count(ev_dist[0]) == len(mask):
+                self.switch_dict['ev_dist'] = ev_dist[0]
+            else:
+                self.switch_dict['ev_dist'] = '~~'
+            ## Third, the event lenght computed from the fit :
+            curr_switch = [fv.get_switch('ev_fit_length')
+                                for fv in self.file['list']]
+            if curr_switch.count(curr_switch[0]) == len(curr_switch):
+                self.switch_dict['ev_fit_length'] = curr_switch[0]
+            else:
+                self.switch_dict['ev_fit_length'] = '~~'
+        if self.switch_dict['all'] == 'No':
+            mask = self.file['list'][self.file['current']].get_switch('mask')
+            self.switch_dict['mask'] = convbool[mask]
+            self.switch_dict['ev_dist'] = \
+                self.file['list'][self.file['current']].get_switch('ev_dist')
+            self.switch_dict['ev_fit_length'] = \
+                self.file['list'][self.file['current']].get_switch(
+                                                            'ev_fit_length')
+
+    def get_switch(self, what):
+        if what == 'all':
+            return self.switch_dict['all']
+        elif what == 'mask':
+            self.update_switch()
+            return self.switch_dict['mask']
+        elif what == 'ev_dist':
+            self.update_switch()
+            return self.switch_dict['ev_dist']
+        elif what == 'ev_fit_length':
+            self.update_switch()
+            return self.switch_dict[what]
+
+    def set_switch(self, stype, state):
+        """
+            Switch to True or False several stuffs or indicate the state of
+            internal components.
+
+            * Parameters:
+                stype: str
+                    'all': Switch the FVFolder to consider one or all the
+                            forcevolume object.
+                    'ev_dist': Threshold on the distance where event occured.
+                    'ev_fit_length': Threshold on the length of event.
+                state: str
+                    if stype is 'all' :
+                        'Yes' if the feature is enabled.
+                        'No' if not.
+                    if stype is 'ev_dist':
+                        float
+                    if stype is 'ev_fit_length' :
+                        [float, float]: first is the min, second is the max.
+        """
+        if not stype in ['all', 'ev_dist', 'ev_fit_length']:
+            raise AttributeError(stype +
+                                 ' is not recognized as a FVFolder switch.')
+
+        if stype == 'all':
+            convbool = {True: 'Yes', False: 'No'}
+            state = convbool[state]
+            self.switch_dict[stype] = state
+        elif stype in ['ev_dist', 'ev_fit_length']:
+            if self.get_switch('all') == 'Yes':
+                [fv.set_switch(stype, state) for fv in self.file['list']]
+            else:
+                self.file['list'][self.file['current']].set_switch(stype,
+                                                                   state)
+        self.update_switch()
+
+    def set_data_hist(self, dtype, drange=None, depth=0):
+        """
+            Sets the plot data type and refresh it.
+
+            * Parameters :
+                dtype: str
+                    The data type that has to be set on the plot_data instance.
+                depth: int
+                    For data dependent to depth. Specify the depth at which the
+                    data has to be taken.
+
+            >>> exp = FVFolder()
+            >>> exp.load_aex(STIFFNESS_COMPUTED_FILE)
+            >>> #fv = exp.get_file(1)
+            >>> exp.set_data_hist('young_modulus', \
+                                  drange=[0, 100000000, 10000000])
+            >>> exp.set_data_hist('young_modulus', drange=[0, 1000000, 100000])
+        """
+        self.__regenerate_filename_list()
+        if dtype == 'young_modulus':
+            flat_list = []
+            flat_group = []
+            if self.get_switch('all') == 'Yes':
+                stiff_list = self.get_stiffness_list('all', depth)
+                file_group = self.file['group']
+                for i in range(len(stiff_list)):
+                    flat_list += stiff_list[i]
+                    flat_group += [num.unique(file_group)[i] \
+                                   for nb in range(len(stiff_list[i]))]
+                self.data_hist.set_group_prop('all', self.group)
+            else:
+                fvfile = self.file['list'][self.file['current']]
+                flat_list = fvfile.stiff_list('all', depth)
+                flat_group = [0 for i in range(len(flat_list))]
+                self.data_hist.set_group_prop('all', None)
+            self.data_hist.set_data('stiff', flat_list)
+            self.data_hist.set_group('stiff', flat_group)
+            if drange == None:
+                drange = [0, max(flat_list) / 10, max(flat_list) / 500]
+            self.data_hist.set_range('stiff', drange)
+            self.data_hist.set_type('stiff')
+            self.event_gauss_fit('stiff')
+            self.data_hist.nbr_curves = self.parameters['number_curves']
+
+    def get_rel_stiff(self, dist):
+        """
+            Returns the dictionnary of relative stiffness at the desired
+            distance. It gives it in a format that is friendly to plot with
+            plot_generic.
+        """
+        rl_dict = self.relative_stiffness
+        to_return = dict()
+        for key in rl_dict.keys():
+            to_return[key] = rl_dict[key][dist]
+        return to_return
+
+    def get_relative_stiffness_random(self, dist):
+        """
+            Returns the dictionnary of relative stiffness at the desired
+            distance. It gives it in a format that is friendly to plot with
+            plot_generic.
+        """
+        to_return = dict()
+        rl_dict = self.relative_stiffness_random
+        for key in rl_dict.keys():
+            to_return[key] = rl_dict[key][dist]
+        return to_return
+
+    def get_arrays(self, which):
+        '''
+        Returns the list of the desired arrays:
+
+        which :
+          String definding the array to get. Possible values are :
+
+          * 'Event' to get the event array
+          * 'Topography' to get the topography array
+        '''
+        if which not in self.file['list'][0].get_array('keys'):
+            raise TypeError('"' + which + '" is not supported')
+        array_list = list()
+        for fvfile in self.file['list']:
+            array_list.append(fvfile.get_array(which))
+        return array_list
+
+    def get_stiffness_list(self, dtype, depth=0):
+        """
+            Get the list of the stiffness of the files contain in the
+            experiment.
+
+            It takes advantage of the group definition.
+
+            Returned list is a 2d list which look like this :
+            [Stiffness list group 1, Stiffness list group 2, ...]
+
+            Files belonging to group 0 are not
+            considered.
+
+            >>> exp = FVFolder()
+            >>> exp.load_aex(ALL_COMPUTED_FILE)
+            >>> stiff_list = exp.get_stiffness_list('event')
+            >>> stiff_list2 = exp.get_stiffness_list('not event')
+
+            In our example file, we have 5 + 191 pixels with no computed
+            stiffness for the first depth. Then, we would expect
+            (16 * 16) + (32 * 32) - 5 - 191 = 1078 number of points
+
+            >>> len(stiff_list[0]) + len(stiff_list2[0])
+            1084
+
+        """
+        if sum(self.file['group']) == 0:
+            # no group was defined, so do not consider it.
+            group = [1 for item in self.file['group']]
+        else:
+            group = self.file['group']
+        glist = list(num.unique(group))
+        stiff_list = [[] for item in glist]
+        for fvfile, gid in zip(self.file['list'], group):
+            # gid means group id...
+            index = glist.index(gid)
+            for item in fvfile.stiff_list(dtype, depth):
+                stiff_list[index].append(item)
+            #stiff_list[index].append(fvfile.get_stiffness_list(dtype))
+        return stiff_list
+
+    def event_nbr_list(self):
+        '''
+        Retuns a list containing the number of detected event per files.
+        '''
+
+        event_list = []
+        for fv in self.file['list']:
+            event_list.append(fv.number_event())
+        return event_list
+
+    def clear_event_prop_list(self):
+        '''
+        Clear the event properties.
+        To do to refresh the list if a new computation was done.
+        '''
+
+        att_list = ['event_force', 'event_distance', 'event_lr',
+                    'event_stiffness', 'event_relstiff']
+        for item in att_list:
+            if hasattr(self, item):
+                delattr(self, item)
+
+    def event_gauss_fit(self, data_type=None, min_val=None, max_val=None,
+                        dist=1):
+        '''
+            Automatically finds the best gaussian fit of the event properties.
+
+            data_type can be :
+
+                * 'force' to considere the event forces.
+                * 'lr' to considere the event loading rates.
+                * 'distance' to considere the event distance in the curve
+                * 'stiff' to considere the stiffness in the trace curve where
+                  event was detected.
+                * 'relstiff' to considere the relative stiffness of the pixel
+                  where event was detected.
+
+            Results are stored in event_stat[data_type] attribute.
+
+            For example :
+
+            >>> exp = FVFolder()
+            >>> exp.load_aex(EVENT_COMPUTED_FILE)
+            >>> exp.data_hist.set_range('force', [0, 1, 0.1])
+            >>> exp.data_hist.set_type('force')
+            >>> [data, group, fid, coord] = exp.get_event_att('force')
+            >>> exp.data_hist.set_data('force', data)
+            >>> exp.event_gauss_fit(data_type='force')#, min_val=0, max_val=1)
+            >>> exp.event_stat['force'].keys()
+            ['std', 'kde', 'maxima', 'count', 'mean']
+
+            * kde is the kernel density estimation. This is an array composed
+              of two vector, respectively the x and y coordinate.
+            * 'mean' is the list of detected gaussian mean
+            * 'std' is the corresponding standard deviation.
+            * 'count' is the corresponding number of elements for the mean and
+              std.
+            * 'maxima' is the detected maxima from the kde.
+
+            To fit loading rate, distance, stiffness and relative stiffness :
+
+            >>> exp.data_hist.set_range('lr', [0, 1, 0.1])
+            >>> exp.data_hist.set_type('lr')
+            >>> [data, group, fid, coord] = exp.get_event_att('lr')
+            >>> exp.data_hist.set_data('lr', data)
+            >>> exp.event_gauss_fit(data_type='lr')
+
+            >>> exp.data_hist.set_range('dist', [0, 1000, 10])
+            >>> exp.data_hist.set_type('dist')
+            >>> [data, group, fid, coord] = exp.get_event_att('dist')
+            >>> exp.data_hist.set_data('dist', data)
+            >>> exp.event_gauss_fit(data_type='dist')
+        '''
+        # defines the groups to be displayed.
+        group = num.array(self.group['id'])[
+                            num.array(self.group['display'])]
+        fit, mean, std, count = None, None, None, None
+        if data_type in ['force', 'force_base', 'lr', 'dist', 'stiff',
+                         'relstiff', 'length', 'plength']:
+            min_val = self.data_hist.get_range(data_type).min
+            max_val = self.data_hist.get_range(data_type).max
+            values = self.data_hist.get_data(data_type, group)
+        index = (min_val < values) * (values < max_val)
+        self.event_stat[data_type] = post_proc.find_gauss_fit(values[index])
+
+    def export_stiffness(self, filename):
+        """
+            Export the stiffness in a set of csv file. Each file contain the
+            stiffness at
+
+            >>> exp = FVFolder()
+            >>> exp.load_aex(STIFFNESS_COMPUTED_FILE)
+            >>> exp.export_stiffness(os.path.join(EXPORT_FOLDER, \
+                                     'stiffness_export'))
+        """
+        # Get all the stiffness
+        #stiffness_list = list()
+        split_filename = os.path.splitext(filename)
+        if split_filename[1] in ['.csv', '.txt']:
+            filename = split_filename[0]
+        else:
+            # It is probably not an extention, then restore it
+            filename = split_filename[0] + split_filename[1]
+        old_masked_print_option = num.ma.masked_print_option.display()
+        num.ma.masked_print_option.set_display('')
+        shapes = list()
+        size_parts = list()
+        for fv in self.file['list']:
+            if fv.has_stiffness:
+                shapes.append(fv.get_array('Stiffness').shape)
+                size_parts.append(fv.stiffness['size_parts'])
+        # The shape are in the forme :
+        # (size_x, size_y, depth)
+        # to take the max depth: shape[:,2].max()
+        shapes = num.array(shapes)
+        max_depth = shapes[:, 2].max()
+        max_size = max(shapes[:, 0] * shapes[:, 1])
+        for depth in range(max_depth):
+            this_file = filename + '_Deep_' + str(depth) + '.csv'
+            this_array = num.ma.array(
+                                num.empty((max_size, len(self.file['list']))),
+                                           mask=num.ones((max_size,
+                                                    len(self.file['list']))))
+            # this_averate will contain 1) mean, 2) std and 3) count.
+            this_average = num.empty((3, len(self.file['list'])))
+            for fv in self.file['list']:
+                if fv.has_stiffness:
+                    if fv.get_array('Stiffness').shape[2] >= depth:
+                        # Get the data and create the mask according to it.
+                        try:
+                            vector = fv.get_array(
+                                            'Stiffness')[:, :, depth].flatten()
+                        except IndexError:
+                            print "SHIT"
+                            vector = num.ma.array(num.empty(5),
+                                                  mask=num.ones(5))
+                        # Put the data in the masked array.
+                        index = self.file['name'].index(fv.name)
+                        this_array[:vector.shape[0], index] = vector
+                        this_array.mask[:vector.shape[0], index] = vector.mask
+                        this_average[0, index] = vector.mean()
+                        this_average[1, index] = vector.std()
+                        this_average[2, index] = vector.count()
+            # Write the file.
+            fid = open(this_file, 'wb')
+            fcsv = csv.writer(fid)
+            fcsv.writerow(['Stiffness data of file :', self.filename])
+            fcsv.writerow(['Injection time : ',
+                            self.parameters['injection_index']])
+            fcsv.writerow(self.file['name'])
+            fcsv.writerow(['Group'])
+            fcsv.writerow(self.file['group'])
+            fcsv.writerow(['Depth size : [nm]'])
+            fcsv.writerow(num.array(size_parts))
+            fcsv.writerow(['Global: mean'])
+            fcsv.writerow(this_average[0, :])
+            fcsv.writerow(['Global: std'])
+            fcsv.writerow(this_average[1, :])
+            fcsv.writerow(['Global: number'])
+            fcsv.writerow(this_average[2, :])
+            fcsv.writerow(['Global: all values'])
+            fcsv.writerows(this_array)
+            fid.close()
+        # restore the old display option of masked arrays
+        num.ma.masked_print_option.set_display(old_masked_print_option)
+
+    def export_average_stiffness_tomo(self, filename):
+        """
+            Exports the average stiffness tomography to the specified file.
+
+            * Parameters :
+                filename: str
+                    path-name to save the file.
+
+            * Output :
+                None
+        """
+
+        ## generate the filename
+        split_filename = os.path.splitext(filename)
+        if split_filename[1] in ['.csv', '.txt']:
+            filename = split_filename[0]
+        else:
+            # It is probably not an extention, then restore it
+            filename = split_filename[0] + split_filename[1]
+        filename = filename + '.csv'
+        old_masked_print_option = num.ma.masked_print_option.display()
+        num.ma.masked_print_option.set_display('')
+
+        # get the data to export
+        mean_stiffness = self.average_stiffness
+        # the data are [{'deep': [], 'mean': [], 'std': [], 'count': []}]
+        # Rearrange the data to be an array...
+        deep = [i['deep'] for i in mean_stiffness]
+        mean = [i['mean'] for i in mean_stiffness]
+        std = [i['std'] for i in mean_stiffness]
+        count = [i['count'] for i in mean_stiffness]
+
+        sizes = [len(i) for i in deep]
+        max_size = max(sizes)
+        max_index = sizes.index(max_size)
+
+        array_size = (3 * len(mean_stiffness) + 1, max_size)
+
+        this_array = num.ma.array(num.empty(array_size),
+                                  mask=num.ones(array_size))
+
+        # Fill the array with the data
+        this_array[0][:len(deep[max_index])] = deep[max_index]
+        this_array[0].mask[:len(deep[max_index])] = 0
+        add = 1
+        for i, this_mean in zip(range(len(mean_stiffness)), mean):
+            this_array[i + add][:len(this_mean)] = this_mean
+            this_array[i + add].mask[:len(this_mean)] = 0
+        add = 1 + len(mean_stiffness)
+        for i, this_std in zip(range(len(mean_stiffness)), std):
+            this_array[i + add][:len(this_std)] = this_std
+            this_array[i + add].mask[:len(this_std)] = 0
+        add = 1 + 2 * len(mean_stiffness)
+        for i, this_count in zip(range(len(mean_stiffness)), count):
+            this_array[i + add][:len(this_count)] = this_count
+            this_array[i + add].mask[:len(this_count)] = 0
+        #this_array = this_array.transpose(1,0)
+        label = ['deep'] + \
+                ['mean of file ' + fvname for fvname in self.file['name']] +\
+                ['std of file' + fvname for fvname in self.file['name']] +\
+                ['count of file' + fvname for fvname in self.file['name']]
+        # Write the csv
+        fid = open(filename, 'wb')
+        fcsv = csv.writer(fid)
+        fcsv.writerow(['Stiffness data of file :', self.filename])
+        fcsv.writerow(label)
+        fcsv.writerows(this_array.transpose(1, 0))
+        num.ma.masked_print_option.set_display(old_masked_print_option)
+
+    def export_events(self, filename):
+        """
+            Export the events of all files.
+
+            * Parameters :
+                filename: str
+                    The file pathname to store the data
+
+            * Retruns :
+                None.
+
+            >>> exp = FVFolder()
+            >>> exp.load_aex(EVENT_COMPUTED_FILE)
+            >>> exp.export_events(EXPORT_FOLDER + '/experiment_events.csv')
+        """
+
+        fid = open(filename, 'wb')
+        fcsv = csv.writer(fid)
+        firstfile = True
+        for fv in self.file['list']:
+            fv.export_events(fcsv, firstfile=firstfile)
+            firstfile = False
+        fid.close()
+
+    def export_nbr_events(self, filename):
+        """
+            Export the number of events per curves of all files.
+
+            * Parameters :
+                filename: str
+                    The file pathname to store the data
+
+            * Retruns :
+                None.
+
+            >>> exp = FVFolder()
+            >>> exp.load_aex(EVENT_COMPUTED_FILE)
+            >>> exp.export_nbr_events(EXPORT_FOLDER + \
+                                      '/experiment_nbr_events.csv')
+        """
+        fid = open(filename, 'wb')
+        fcsv = csv.writer(fid)
+        firstfile = True
+        for fv in self.file['list']:
+            fv.export_nbr_events(fcsv, firstfile=firstfile)
+            firstfile = False
+        fid.close()
+
+    def __regenerate_filename_list(self):
+        '''
+        Regenerates the filename list
+        '''
+        self.file['name'] = []
+        self.file['group'] = []
+        nbr_curves = 0
+        for item in self.file['list']:
+            self.file['name'].append(item.name)
+            self.file['group'].append(item.header['group'])
+            nbr_curves = nbr_curves + item.header['number_curves']
+        self.parameters['number_curves'] = nbr_curves
+        self.data_hist.total_nbr_curves = nbr_curves
+        # For the group labels and display...
+        unique_group = num.unique(self.file['group'])
+        if len(self.group['label']) > len(unique_group):
+            _to_remove = [item not in unique_group
+                                for item in self.group['id']]
+            self.__remove_group(_to_remove)
+        elif len(self.group['label']) < len(unique_group):
+            _to_add = [item not in self.group['id'] for item in unique_group]
+            self.__add_group(_to_add)
+
+    def __remove_group(self, to_remove):
+        """
+            Remove item from group.
+
+            * Parameter :
+                to_remove: list
+                    list of boolean to tell which remove and which one to keep.
+        """
+        for item in range(len(to_remove)):
+            if to_remove[item]:
+                self.group['label'].pop(item)
+                self.group['id'].pop(item)
+                self.group['display'].pop()
+
+    def __add_group(self, _to_add):
+        """
+            Add object from group.
+
+            * Parameter :
+                to_add: list
+                    list of boolean to tell which group to add.
+        """
+
+        new_id = []
+        new_label = []
+        new_disp = []
+        unique_group = num.unique(self.file['group'])
+        for i in range(len(unique_group)):
+            if _to_add[i]:
+                _add = unique_group[i]
+                # Adds this group and put default value.
+                new_id.append(_add)
+                new_label.append('Groupe %i' % _add)
+                new_disp.append(True)
+            else:
+                # This group exist. Recover the user defined value.
+                _gr = unique_group[i]
+                index = self.group['id'].index(_gr)
+                new_id.append(self.group['id'][index])
+                new_label.append(self.group['label'][index])
+                new_disp.append(self.group['display'][index])
+        self.group['id'] = new_id
+        self.group['label'] = new_label
+        self.group['display'] = new_disp
+
+    def __regenerate_comment(self):
+        if self.comment == 'Your comment':
+            comment = ''
+            for fvfile in self.file['list']:
+                if fvfile.header['note'] != '\n':
+                    comment = comment + fvfile.name + '\n' + \
+                              fvfile.header['note'] + '\n'
+            if comment != '':
+                # We update only if there was a comment in the file headers,
+                # and if it's the first (i.e. self.comment == 'Your comment')
+                comment = comment[:-1]  # we erase the last \n
+                self.comment = comment
+
+
+class NotReadyError(Exception):
+    pass
+
+ARRAY_TYPE = {'Piezo': 'topo',
+              'PoCIndice': 'topo',
+              'PoCNoise': 'topo',
+              'Topography': 'topo',
+              'Stiffness': 'topo',
+              'Stiffness tomo': '3d',
+              'Event': 'event',
+              'Event force': 'event',
+              'Event length': 'event',
+              'Event distance': 'event',
+              'Event random': 'revent',
+              'Relative pos': 'rel',
+              'Relative rand pos': 'rel',
+              'Path': 'misc',  # This defines a path to display info.
+              'Masked': 'misc',  # This option is to apply or not a mask to the
+                                 # array.
+              'Mask': 'misc'}
+
+if __name__ == '__main__':  # pragma: no cover
+#    import plot_generic
+#    test_file = '/home/charles/AFM/Macrophages/Living_cytB2.aex'
+#    exp_1 = FVFolder()
+#    exp_1.load_aex(test_file)
+#    win_plot = plot_generic.ErrorBar()
+#    win_plot.average_stiffness(exp_1.average_stiffness,
+#                               group=exp_1.file['group'],
+#                               group_info=exp_1.group,
+#                               style = 'isol')
+#    win_plot.save('test.png')
+
+    import doctest
+    BIOSCOPE_FILE2 = '../docs/data/files/FR20074A.001'
+#    fvfile = ForceVolume(BIOSCOPE_FILE2)
+    BIOSCOPE_FILE = '../docs/data/files/FR2310B.004'
+    BIOSCOPE_FOLDER = '../docs/data/files/'
+    STIFFNESS_COMPUTED_FILE = '../docs/data/Stiffness_computed.aex'
+    EVENT_COMPUTED_FILE = '../docs/data/Event_computed.aex'
+    ALL_COMPUTED_FILE = '../docs/data/Stiffness_and_Event_computed.aex'
+    EXPORT_FOLDER = '../docs/data/Garbage'
+    doctest.testmod()

Added: trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/common.py
===================================================================
--- trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/common.py	                        (rev 0)
+++ trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/common.py	2012-08-20 10:43:48 UTC (rev 12094)
@@ -0,0 +1,3 @@
+APP_NAME = "OpenFovea"
+DEB_NAME = "openfovea"
+APP_VERSION = "0.1a160"

Added: trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/dialog_experiment_properties.py
===================================================================
--- trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/dialog_experiment_properties.py	                        (rev 0)
+++ trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/dialog_experiment_properties.py	2012-08-20 10:43:48 UTC (rev 12094)
@@ -0,0 +1,267 @@
+#!/usr/bin/env python
+# -*- coding: UTF-8 -*-
+
+from math import log10, floor
+
+import pygtk
+import gtk
+# for script installation
+from pkg_resources import resource_filename
+##############
+## Graphic library ##
+##############
+try:
+    matplotlib.__version__
+except NameError:
+    import matplotlib
+    matplotlib.use('Agg', warn=False)
+from matplotlib.figure import Figure
+from matplotlib.backends.backend_gtkagg import FigureCanvasGTKAgg as FigureCanvas
+from matplotlib.backends.backend_gtkagg import NavigationToolbar2GTKAgg as NavigationToolbar
+
+from fovea_toolbox import curve
+
+class main_win():
+    def __init__(self, author=None, comment=None, spring_constant=None,
+                 inject_index=None, stiff_glass=None, trace_curve=None, 
+                 plot_size=None, group=None, _glade_filename=None,
+                 linewidth=1.5, histo_y_rel=True, plot_hist_gauss=False,
+                 plot_color=None):
+        builder = gtk.Builder()
+        if _glade_filename == None:
+            try:
+                _glade_filename = resource_filename(
+                                    'openfovea',
+                                    'glade/dialog_experiment_properties.glade')
+            except NotImplementedError:
+                _glade_filename = 'openfovea/glade/dialog_experiment_properties.glade'
+        builder.add_from_file(_glade_filename)
+        self.window = builder.get_object('ExpProp')
+        self.widget = {
+            # General tab
+            'text_author' : builder.get_object('text_author'),
+            'text_description' : builder.get_object('text_description'),
+            ## Configuration tab
+            # Time Lapse (This is outdated, I should clean it...)
+            'spin_inject_index' : builder.get_object('entry_injection_index'),
+            # System
+            'entry_spring_cst' : builder.get_object('entry_spring_constant'),
+            'spin_stiff_glass' : builder.get_object('spin_stiff_glass'),
+            # Plot area...
+            'plot_area' : builder.get_object('plot_area'),
+            'box_nav_tool' : builder.get_object('box_nav_tool'),
+            ## Graphs
+            # Saved size
+            'spin_save_plot_width' : builder.get_object('spin_save_plot_width'),
+            'spin_save_plot_height' : builder.get_object('spin_save_plot_height'),
+            # Plot options
+            'spin_linewidth' : builder.get_object('spin_linewidth'),
+            'check_bw_plot' : builder.get_object('check_bw_plot'),
+            # Histogram options
+            'check_plot_hist_gauss' : builder.get_object('check_plot_hist_gauss'),
+            'histo_y_rel' : builder.get_object('histo_y_rel'),
+            # Group managment.
+            'table_group' : builder.get_object('table_group'),
+            'gid' : [], # List of group id
+            'glabel' : [], # List of gtk label for group
+            'gdisplay' : [], # List of gtk checkbutton for group
+        }
+        self.widget['spin_stiff_glass'].connect(
+                                'value_changed',
+                                self.on_stiff_glass_changed)
+        adj = gtk.Adjustment(value=800, lower=0, upper=1600, step_incr=1, page_incr=100, page_size=0)
+        self.widget['spin_save_plot_width'].set_adjustment(adj)
+        adj = gtk.Adjustment(value=800, lower=0, upper=1600, step_incr=1, page_incr=100, page_size=0)
+        self.widget['spin_save_plot_height'].set_adjustment(adj)
+        adj = gtk.Adjustment(value=linewidth, lower=0.1, upper=5, step_incr=0.1, page_incr=1, page_size=0)
+        self.widget['spin_linewidth'].set_adjustment(adj)
+        
+        builder.connect_signals(self)
+        self.author = author
+        self.comment = comment
+        self.spring_cst = spring_constant
+        self.inject_index = inject_index
+        self.stiff_glass = stiff_glass
+        self.trace_curve = trace_curve
+        self.save_size = plot_size
+        ### The plotting part :
+        self.figure = Figure(figsize=(100, 100), dpi=75, facecolor=(0.93,0.92,0.9,1))
+        self.axis = self.figure.add_subplot(111) 
+        self.axis.grid(True)
+        self.canvas = FigureCanvas(self.figure) # a gtk.DrawingArea 
+        self.canvas.show() 
+        self.graphview = self.widget['plot_area']
+        self.graphview.pack_start(self.canvas, True, True)
+        # below is optional if you want the navigation toolbar
+        self.navToolbar = NavigationToolbar(self.canvas, self.window)
+        self.navToolbar.lastDir = '/var/tmp/'
+        self.widget['box_nav_tool'].pack_start(self.navToolbar)
+        self.navToolbar.show()
+        self.group = None
+        # About the groups...
+        if group is not None:
+            table = builder.get_object('table_group')
+            text = gtk.Label('ID')
+            text.show()
+            table.attach(text, 0, 1, 0, 1)
+            text = gtk.Label('Label')
+            text.show()
+            table.attach(text, 1, 2, 0, 1)
+            text = gtk.Label('Display')
+            text.show()
+            text = table.attach(text, 2, 3, 0, 1)
+            self.group_widget = {
+                'label' : [],
+                'display' : []
+            }
+            _id_gp = 1
+            for gp_id, gp_label, gp_disp in zip(
+                                group['id'], group['label'], group['display']):
+                self.widget['gid'].append(gp_id)
+                text = gtk.Label(gp_id)
+                text.show()
+                table.attach(text, 0, 1, _id_gp, _id_gp+1)
+                text = gtk.Entry(0)
+                text.set_text(gp_label)
+                text.show()
+                table.attach(text, 1, 2, _id_gp, _id_gp+1)
+                self.widget['glabel'].append(text)
+                check = gtk.CheckButton('Show')
+                check.set_active(gp_disp)
+                check.show()
+                table.attach(check, 2,3,_id_gp, _id_gp+1)
+                self.widget['gdisplay'].append(check)
+                _id_gp += 1
+           #Display Options
+        self.linewidth = linewidth
+        self.histo_y_rel = histo_y_rel
+        self.plot_hist_gauss = plot_hist_gauss
+        self.plot_color = plot_color
+        self.update()
+    def update(self):
+        '''
+        Update the informations in the window.
+        '''
+        if self.author is not None:
+            self.widget['text_author'].set_text(self.author)
+        if self.comment is not None:
+            text_buffer = self.widget['text_description'].get_buffer()
+            text_buffer.set_text(self.comment)
+        if self.spring_cst is not None:
+            self.widget['entry_spring_cst'].set_text(str(self.spring_cst))
+        if self.inject_index is not None:
+            index_adjustment = self.widget['spin_inject_index'].get_adjustment()
+            index_adjustment.set_all(value=int(self.inject_index[0]),
+                                     upper=int(self.inject_index[1])
+                                    )
+        if self.stiff_glass is not None:
+            self.on_stiff_glass_changed(None)
+        if self.save_size is not None:
+            self.widget['spin_save_plot_width'].set_value(self.save_size[0])
+            self.widget['spin_save_plot_height'].set_value(self.save_size[1])
+        if self.histo_y_rel is not None:
+            self.widget['histo_y_rel'].set_active(self.histo_y_rel)
+        if self.plot_hist_gauss is not None:
+            self.widget['check_plot_hist_gauss'].set_active(self.plot_hist_gauss)
+        if self.plot_color is not None:
+            if self.plot_color is 'bw':
+                self.widget['check_bw_plot'].set_active(True)
+            else:
+                self.widget['check_bw_plot'].set_active(False)
+            
+    def on_stiff_glass_changed(self, widget):
+        stiff_glass_val = self.widget['spin_stiff_glass'].get_value()
+        if stiff_glass_val:
+            self.stiff_glass = stiff_glass_val
+        stiff_glass_adjustment = self.widget['spin_stiff_glass'].get_adjustment()
+        lower = self.stiff_glass*2
+        if self.stiff_glass:
+            n_digits = int(floor(log10(abs(self.stiff_glass))))
+        if n_digits < 0:
+            self.widget['spin_stiff_glass'].set_digits(-n_digits+2)
+        step_increment = -lower / 100
+        stiff_glass_adjustment.set_all(value=self.stiff_glass,
+                                       upper=0,
+                                         lower=lower,
+                                         step_increment = step_increment, 
+                                         page_increment = step_increment / 4, 
+                                         page_size = 0)
+        self.display_plot()#update_curve()
+    def on_spin_save_plot_width_value_changed(self, widget):
+        self.save_size[0] = widget.get_value()
+        adjustment = widget.get_adjustment()
+        adjustment.set_upper(widget.get_value() + 800)
+    def on_spin_save_plot_height_value_changed(self, widget):
+        self.save_size[1] = widget.get_value()
+        adjustment = widget.get_adjustment()
+        adjustment.set_upper(widget.get_value() + 800)
+    def on_spin_linewidth_value_changed(self, widget):
+        self.linewidth = widget.get_value()
+        adjustment = widget.get_adjustment()
+    def on_button_validate_clicked(self, widget):
+        '''
+        Get the information from the window and store them in the following
+        attributes :
+            self.author
+            self.comment
+            self.spring_constant
+            self.inject_index
+            self.save_size
+        '''
+        self.author = self.widget['text_author'].get_text()
+        text_buffer = self.widget['text_description'].get_buffer()
+        self.comment = text_buffer.get_text(text_buffer.get_start_iter(),
+                                            text_buffer.get_end_iter())
+        self.spring_cst = eval(self.widget['entry_spring_cst'].get_text())
+        self.inject_index[0] = int(self.widget['spin_inject_index'].get_value())
+        # Get values for groups
+        self.group = {
+                'id' : self.widget['gid'],
+                'label' : [it.get_text() for it in self.widget['glabel']],
+                'display' : [it.get_active() for it in self.widget['gdisplay']]
+                    }
+        #Get display options
+        self.linewidth = self.widget['spin_linewidth'].get_value()
+        self.histo_y_rel = self.widget['histo_y_rel'].get_active()
+        self.plot_hist_gauss = self.widget['check_plot_hist_gauss'].get_active()
+        if self.widget['check_bw_plot'].get_active():
+            self.plot_color = 'bw'
+        else:
+            self.plot_color = 'color'
+        self.validate()
+    def on_button_cancel_clicked(self, widget):
+        self.destroy(self, widget)
+    def display_plot(self):
+        if type(self.spring_cst) == list:
+            sc = self.spring_cst[0]
+        else:
+            sc = self.spring_cst
+        [iX, iY] = curve.compute_indentation(self.trace_curve[0],
+                                             self.trace_curve[1],
+                                             self.stiff_glass,
+                                             sc)
+        self.axis.cla()
+        self.axis.grid(True)
+        self.axis.plot(iX, iY, 'k-', linewidth=1.5)
+        self.canvas.draw_idle()
+    def destroy(self, *widget):
+        '''
+        Pretty quit the dialog.
+        '''
+        self.window.destroy()
+    def validate(self):
+        '''
+        This function is here to be overriden by the caller in order to send the
+        signal through the classes.
+        '''
+        pass
+if __name__ == '__main__':
+    group = {'id' : [0, 1, 2],
+             'label' : ['First', 'Second', 'Third'],
+             'display' : [True, True, True]}
+    test = main_win(author='Charles Roduit', comment='I like it...',
+                    spring_constant=[0.06, 0.04], inject_index=[0, 3], plot_size=[800, 800],
+                    group=group,
+                    _glade_filename='glade/dialog_experiment_properties.glade')
+    test.window.show()
+    gtk.main()

Added: trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/dialog_export_map.py
===================================================================
--- trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/dialog_export_map.py	                        (rev 0)
+++ trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/dialog_export_map.py	2012-08-20 10:43:48 UTC (rev 12094)
@@ -0,0 +1,478 @@
+"""
+    This is the module to display the dialog export map.
+"""
+
+
+import pygtk
+pygtk.require('2.0')
+import gtk
+import os
+from pkg_resources import resource_filename # pylint: disable-msg=E0611
+
+    
+from matplotlib.backends.backend_gtkagg import FigureCanvasGTKAgg as \
+                                               FigureCanvas
+import numpy
+from scipy import interpolate, ndimage
+import plot_generic
+    
+class MapDisplay(object):
+    """
+        Displays the map with all the button to tune the exportation.
+    """
+    
+    def __init__(self, array, folder=None, depth=1, fvname='', scan_size=None):
+        self.array = {'dict' : array,
+                      'plot' : None, # contain the current array to plot
+                      'type' : None, # contains the type of the current array 
+                                     # (correspond to the dict key)
+                      'indice' : 0,
+                      'depth' : depth, # is the depth between slice
+                      'size' : scan_size,
+                      'scale' : [0, 0],
+                      'do_interp' : 0, # check if we interpolate or not
+                      'interp_max' : 0, # Is the maximum value to be displayed in case of interpolation
+                      }
+                      
+        if folder is None:
+            folder = os.path.expanduser('~')
+        self.file = {'folder' : folder,
+                     'name' : 'File_%f_%t_slice_%n_depth_%d.png',
+                     'fv_name' : fvname}
+        self.dialog = gtk.Dialog(title='Export Maps',
+                                 buttons=(gtk.STOCK_OK, gtk.RESPONSE_OK,
+                                          gtk.STOCK_CANCEL, gtk.RESPONSE_CANCEL)
+                                 )
+        self.dialog.set_default_size(500, 350)
+        try:
+            export_image = resource_filename('openfovea','Icon/export.png')
+        except NotImplementedError:
+            export_image = 'openfovea/Icon/export.png'
+        self.dialog.set_icon(gtk.gdk.pixbuf_new_from_file(export_image))
+        
+        # The plot
+        self.plot_array = plot_generic.Array()
+        self.canvas = FigureCanvas(self.plot_array.figure) # a gtk.DrawingArea 
+        self.canvas.show() 
+        
+        self.widget = {'but_folder' : gtk.Button(label=self.file['folder']),
+                       'entry_filename' : gtk.Entry(),
+                       'entry_title' : gtk.Entry(),
+                       'plot_area' : gtk.VBox(),
+                       'combo_array' : gtk.ComboBox(),
+                       'combo_cmap' : gtk.ComboBox(),
+                       'check_auto_filename' : gtk.CheckButton(label='auto'),
+                       'check_axis' : gtk.CheckButton(label='show axis label'),
+                       'check_cmap' : gtk.CheckButton(label='show color scale'),
+                       'check_title' : gtk.CheckButton(label='show title'),
+                       'check_interp' : gtk.CheckButton(label='interpolate'),
+                       'scale_max' : gtk.HScrollbar(),
+                       'scale_min' : gtk.HScrollbar(),
+                       'scale_interp' : gtk.HScrollbar(),
+                       'size_x' : gtk.SpinButton(),
+                       'size_y' : gtk.SpinButton(),
+                        }
+        self._init_widgets()
+        # Everything is displayed, plot the grid:
+        self.change_array(self.array['dict'].keys()[0])
+        self.change_scale()
+        self.plot()
+    def _init_scales(self):
+        if self.array['plot'] is not None:
+            ar_min = self.array['plot'].min()
+            ar_max = self.array['plot'].max()
+        else:
+            ar_min = 0
+            ar_max = 0
+        interp_max = ar_max + ar_max * 0.1
+        # The colorscale
+        self.widget['scale_min'].set_adjustment(
+                                gtk.Adjustment(ar_min,  ar_min, 
+                                               ar_max, 
+                                               (ar_max-ar_min) / 100, 
+                                               (ar_max-ar_min) / 25, 
+                                               0))
+        self.widget['scale_max'].set_adjustment(
+                                gtk.Adjustment(ar_max,  ar_min, 
+                                               ar_max, 
+                                               (ar_max-ar_min) / 100, 
+                                               (ar_max-ar_min) / 25, 
+                                               0))
+        self.widget['scale_interp'].set_adjustment(
+                                gtk.Adjustment(interp_max,  ar_min, 
+                                               interp_max, 
+                                               (interp_max-ar_min) / 100, 
+                                               (interp_max-ar_min) / 25, 
+                                               0))
+        self.widget['scale_min'].connect_object("change-value", 
+                                                    self.change_scale,
+                                                    None)
+        self.widget['scale_max'].connect_object("change-value", 
+                                                    self.change_scale,
+                                                    None)
+        self.widget['scale_interp'].connect_object("change-value", 
+                                                    self.change_scale,
+                                                    None)
+    def change_scale(self, widget=None, toto=None, tata=None):
+        self.array['scale'] = [self.widget['scale_min'].get_value(),
+                               self.widget['scale_max'].get_value()]
+        self.array['interp_max'] = self.widget['scale_interp'].get_value()
+        self.plot()
+    def _init_widgets(self):
+        """
+            Initialization of the widgets
+        """
+        # Create the table.
+        table = [gtk.Table(2, 2), gtk.Table(2, 5)]
+        table[0].set_border_width(5)
+        table[0].set_col_spacings(5)
+        table[0].set_row_spacings(5)
+        table[0].show()
+        
+        # Button folder
+        self.widget['but_folder'].connect('clicked', self.change_folder)
+        self.widget['but_folder'].show()
+        table[0].attach(self.widget['but_folder'],
+                             0, 1, 0, 1, xoptions=0, yoptions=0)
+        # Text filename
+        self.widget['entry_filename'].set_text(self.file['name'])
+        self.widget['entry_filename'].show()
+        table[0].attach(self.widget['entry_filename'],
+                             1, 2, 0, 1, yoptions=0)
+        self.widget['check_auto_filename'].set_active(True)
+        self.widget['check_auto_filename'].connect('toggled', self.change_filename)
+        table[0].attach(self.widget['check_auto_filename'],
+                             2, 3, 0, 1, xoptions=0, yoptions=0)
+        # Table which will contain the display and the control of the display
+        table[1].set_border_width(5)
+        table[1].set_col_spacings(5)
+        table[1].set_row_spacings(5)
+        table[1].show()
+        # The area to plot
+        table[1].attach(self.canvas, 0, 1, 0, 5)
+        #######
+        # The scale bars :
+        grid = gtk.Table(rows=3, columns=2, homogeneous=False)
+        self.widget['scale_min'].show()
+        self.widget['scale_max'].show()
+        #self.widget['scale_interp'].show()
+        grid.attach(self.widget['scale_max'], 1, 2, 0, 1)
+        grid.attach(self.widget['scale_min'], 1, 2, 1, 2)
+        grid.attach(self.widget['scale_interp'], 1, 2, 2, 3)
+        # the labels
+        self.widget['label_scale_min'] = gtk.Label(str='color scale max : ')
+        self.widget['label_scale_min'].set_alignment(0,0)
+        self.widget['label_scale_min'].show()
+        grid.attach(self.widget['label_scale_min'], 0, 1, 0, 1, xoptions=gtk.FILL, yoptions=gtk.FILL)
+        self.widget['label_scale_max'] = gtk.Label(str='color scale min : ')
+        self.widget['label_scale_max'].set_alignment(0,0)
+        self.widget['label_scale_max'].show()
+        grid.attach(self.widget['label_scale_max'], 0, 1, 1,2, xoptions=gtk.FILL, yoptions=gtk.FILL)
+        self.widget['label_scale_interp'] = gtk.Label(str='crop stiffness : ')
+        self.widget['label_scale_interp'].set_alignment(0,0)
+        #self.widget['label_scale_interp'].show()
+        grid.attach(self.widget['label_scale_interp'], 0, 1, 2,3, xoptions=gtk.FILL, yoptions=gtk.FILL)
+        grid.show()
+        table[1].attach(grid, 0, 1, 5, 6)
+        
+        # button for the title
+        self.widget['entry_title'].set_text('Title')
+        self.widget['entry_title'].show()
+        self.widget['entry_title'].connect('changed', self.change_title)
+        table[1].attach(self.widget['entry_title'],
+                             1, 2, 0, 1, xoptions=0, yoptions=0)
+        self.plot_array.title = self.widget['entry_title'].get_text()
+        # button to choose the item to plot
+        list_arr = gtk.ListStore(str)
+        for key in self.array['dict']:
+            list_arr.append([key])
+        self.widget['combo_array'].set_model(list_arr)
+        cell = gtk.CellRendererText()
+        self.widget['combo_array'].pack_start(cell, True)
+        self.widget['combo_array'].add_attribute(cell, 'text', 0)
+        self.widget['combo_array'].set_active(0)
+        self.widget['combo_array'].show()
+        self.widget['combo_array'].connect('changed', self.change_array)
+        table[1].attach(self.widget['combo_array'],
+                             1, 2, 1, 2, xoptions=0, yoptions=0)
+        # button to choose the scale
+        list_cmap = gtk.ListStore(str)
+        list_cmap.append(['gray'])
+        list_cmap.append(['jet'])
+        list_cmap.append(['copper'])
+        self.widget['combo_cmap'].set_model(list_cmap)
+        cell = gtk.CellRendererText()
+        self.widget['combo_cmap'].pack_start(cell, True)
+        self.widget['combo_cmap'].add_attribute(cell, 'text', 0)
+        self.widget['combo_cmap'].set_active(0)
+        self.widget['combo_cmap'].show()
+        self.widget['combo_cmap'].connect('changed', self.change_cmap)
+        table[1].attach(self.widget['combo_cmap'],
+                             1, 2, 2, 3, xoptions=0, yoptions=0)
+        # Display the scale ?
+        self.widget['check_axis'].show()
+        self.widget['check_axis'].set_active(True)
+        self.widget['check_axis'].connect('toggled', self.change_axis_label)
+        table[1].attach(self.widget['check_axis'],
+                             1, 2, 3, 4, xoptions=0, yoptions=0)
+        # Display the color map ?
+        self.widget['check_cmap'].show()
+        self.widget['check_cmap'].set_active(False)
+        self.widget['check_cmap'].connect('toggled', self.change_cmap)
+        table[1].attach(self.widget['check_cmap'],
+                             1, 2, 4, 5, xoptions=0, yoptions=0)
+        
+        # Interpolate the data ?
+        self.widget['check_interp'].show()
+        self.widget['check_interp'].set_active(False)
+        self.widget['check_interp'].connect('toggled', self.toggle_interp)
+        table[1].attach(self.widget['check_interp'],
+                            1, 2, 5, 6, xoptions=0, yoptions=0)
+        
+        # button to choose the size of the image.
+        _size_table = gtk.Table(2, 2)
+        label = gtk.Label('Width')
+        label.show()
+        _size_table.attach(label, 1, 2, 0, 1, xoptions=0, yoptions=0)
+        label = gtk.Label('Height')
+        label.show()
+        _size_table.attach(label, 1, 2, 1, 2, xoptions=0, yoptions=0)
+        
+        adjustment = gtk.Adjustment(value=800, lower=0, upper=1600, step_incr=1, page_incr=100, page_size=0)
+        self.widget['size_x'].set_adjustment(adjustment)
+        adjustment.connect('value_changed', self.spin_val_changed, 'size_x')
+        self.widget['size_x'].show()
+        _size_table.attach(self.widget['size_x'],
+                            0, 1, 0, 1, xoptions=0, yoptions=0)
+        adjustment = gtk.Adjustment(value=800, lower=0, upper=1600, step_incr=1, page_incr=100, page_size=0)
+        self.widget['size_y'].set_adjustment(adjustment)
+        adjustment.connect('value_changed', self.spin_val_changed, 'size_y')
+        self.widget['size_y'].show()
+        _size_table.attach(self.widget['size_y'],
+                            0, 1, 1, 2, xoptions=0, yoptions=0)
+        _size_table.show()
+        table[1].attach(_size_table, 1, 2, 6, 7)
+        table[0].attach(table[1], 0, 2, 1, 2)
+        
+        self.dialog.vbox.pack_start(table[0], True, True, 0)
+    def spin_val_changed(self, event, wtype):
+        """
+            Catch the spin val changed.
+        """
+        adjustment = self.widget[wtype].get_adjustment()
+        adjustment.set_upper(event.get_value() + 800)
+    def change_folder(self, widget):
+        """
+            Interface to change the export folder.
+        """
+        
+        chooser = gtk.FileChooserDialog(
+                                title='Choose folder',
+                                action=gtk.FILE_CHOOSER_ACTION_SELECT_FOLDER,
+                                buttons=(gtk.STOCK_CANCEL,
+                                         gtk.RESPONSE_CANCEL,
+                                         gtk.STOCK_OPEN,
+                                         gtk.RESPONSE_OK)
+                                        )
+        chooser.set_select_multiple(False)
+        chooser.set_default_response(gtk.RESPONSE_OK)
+        chooser.set_local_only(False)
+        chooser.set_filename(self.file['folder'])
+        response = chooser.run()
+        # Analyse the answer
+        if response == gtk.RESPONSE_OK:
+            self.file['folder'] = chooser.get_filenames()[0]
+            self.widget['but_folder'].set_label(self.file['folder'])
+        elif response == gtk.RESPONSE_CANCEL:
+            chooser.destroy()
+            return
+        else:
+            return
+        chooser.destroy()
+    def change_title(self, widget=None):
+        """
+            Change the title of the plot.
+        """
+        self.__update_title()
+        self.plot()
+    def __update_title(self):
+        title = self.generate_text(self.widget['entry_title'].get_text())
+        self.plot_array.title = title
+    def change_filename(self, widget):
+        auto = widget.get_active()
+        
+    def change_cmap(self, widget):
+        """
+            Modify the colormap of the plot. Displays or not the colorscale
+            depending on the state of the checkbutton.
+        """
+        
+        self.plot_array.cmap = self.widget['combo_cmap'].get_active_text()
+        self.plot_array.color_scale['colorbar'] = \
+                                        self.widget['check_cmap'].get_active()
+        self.plot()
+    def change_axis_label(self, widget):
+        """
+            Modify the axis label.
+        """
+        self.plot_array.scale['show'] = self.widget['check_axis'].get_active()
+        self.plot()
+    def change_array(self, array=None):
+        """
+            Modify the array to display.
+        """
+        if type(array) == str:
+            key = array
+        elif type(array) == gtk.ComboBox:
+            key = array.get_active_text()
+        self.array['plot'] = self.array['dict'][key]
+        self.array['type'] = key
+        self._init_scales()
+        self.plot()
+    def toggle_interp(self, widget):
+        """
+            Toogle between interpolate or not.
+        """
+        self.array['do_interp'] = widget.get_active()
+        if self.array['do_interp']:
+            self.widget['scale_interp'].show()
+            self.widget['label_scale_interp'].show()
+        else:
+            self.widget['scale_interp'].hide()
+            self.widget['label_scale_interp'].hide()
+        self.plot()
+    
+    def plot(self):
+        """
+            Plot the result.
+        """
+        if self.array['plot'] is not None:
+            if self.array['plot'].ndim == 3:
+                data = self.array['plot'][:,:,0]
+            else:
+                data = self.array['plot']
+            if self.array['do_interp']:
+                data = compute_interp(data, self.array['interp_max'])
+            self.__update_title()
+            self.plot_array.plot(data,
+                                 scan_size=self.array['size'])
+            self.plot_array.vmin = self.array['scale'][0]
+            self.plot_array.vmax = self.array['scale'][1]
+            self.show()
+    def show(self):
+        """
+            Show the result in the window.
+        """
+        labels = self.widget['check_cmap'].get_active() + \
+               self.widget['check_axis'].get_active() + \
+               len(self.widget['entry_title'].get_text())
+        if labels:
+            self.plot_array.figure.subplots_adjust(left=0.5, bottom=0.5)
+        else:
+            self.plot_array.figure.subplots_adjust(left=0, bottom=0)
+        self.canvas.draw_idle()
+    def run(self):
+        """
+            Runs the dialog.
+        """
+        response = self.dialog.run()
+        self.file['name'] = self.widget['entry_filename'].get_text()
+        if response == gtk.RESPONSE_OK:
+            # Runs the code if button OK is clicked
+            [name, ext] = os.path.splitext(self.file['name'])
+            if not len(ext):
+                ext = '.png'
+            self.export_map(name, ext)
+        self.destroy()
+    def export_map(self, name, ext):
+        """
+            Export the maps.
+        """
+        # Get the size of the image.
+        width = self.widget['size_x'].get_value()
+        height = self.widget['size_y'].get_value()
+        self.plot_array.set_size(width, height, deep=True)
+        # Get the displayed item.
+        if len(self.array['plot'].shape) == 3:
+            # block the min and max
+            self.plot_array.vmin = self.array['scale'][0]
+            self.plot_array.vmax = self.array['scale'][1]
+            for index in range(self.array['plot'].shape[2]):
+                self.array['indice'] = index
+                self.__update_title()
+                arr_to_export = self.array['plot'][:, :, index]
+                if self.array['do_interp']:
+                    arr_to_export = compute_interp(arr_to_export, self.array['interp_max'])
+                self.plot_array.plot(arr_to_export)
+                newname = self.generate_text(name)
+                f_name = newname + ext
+                self.plot_array.save(os.path.join(self.file['folder'], f_name))
+        else:
+            newname = self.generate_text(name)
+            f_name = newname + ext
+            self.plot_array.plot(self.array['plot'])
+            self.plot_array.save(os.path.join(self.file['folder'], f_name))
+    def generate_text(self, pattern):
+        """
+            Generate the filename from the pattern.
+            
+            %d means depth
+            %n means number
+            %f means the filename
+            %t means the type
+        """
+        
+        while pattern.find('%d') is not -1:
+            indice = pattern.find('%d')
+            part_1 = pattern[:indice]
+            part_2 = pattern[indice+2:]
+            pattern = part_1 + str(self.array['indice']*self.array['depth']) + part_2
+        while pattern.find('%n') is not -1:
+            indice = pattern.find('%n')
+            part_1 = pattern[:indice]
+            part_2 = pattern[indice+2:]
+            pattern = part_1 + str(self.array['indice']) + part_2
+        while pattern.find('%f') is not -1:
+            indice = pattern.find('%f')
+            part_1 = pattern[:indice]
+            part_2 = pattern[indice+2:]
+            pattern = part_1 + self.file['fv_name'] + part_2
+        while pattern.find('%t') is not -1:
+            indice = pattern.find('%t')
+            part_1 = pattern[:indice]
+            part_2 = pattern[indice+2:]
+            pattern = part_1 + self.array['type'] + part_2
+        return pattern
+    def destroy(self):
+        """
+            Destroy the window.
+        """
+        self.dialog.destroy()
+def compute_interp(array, interp_max):
+        try:
+            _inf = array.max()
+            _array = array.filled(_inf)
+        except AttributeError:
+            _array = array
+        x, y = array.shape
+        x = complex(0, x)
+        y = complex(0, y)
+        coords = numpy.mgrid[
+                        0 : array.shape[0] - 1 : x*10,
+                        0 : array.shape[1] - 1 : y*10]
+        interp_arr = ndimage.map_coordinates(
+                                        _array, coords)
+        interp_arr = numpy.ma.array(interp_arr,
+                                mask=interp_arr>=interp_max)
+        return interp_arr
+if __name__ == '__main__':
+    import numpy
+    TEST = {'Stiffness' : numpy.random.randn(10, 10, 5),
+            'Piezo' : numpy.random.randn(10,10),
+            'masked' : numpy.ma.array(numpy.random.randn(20,20),
+                                      mask=numpy.random.randn(20,20)>0.5,
+                                      fill_value=numpy.nan)
+            }
+    DISPLAY_IT = MapDisplay(TEST, depth=50, scan_size=2000)
+    DISPLAY_IT.generate_text('Deep %d is now %d')
+    DISPLAY_IT.run()

Added: trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/dialog_flatten.py
===================================================================
--- trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/dialog_flatten.py	                        (rev 0)
+++ trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/dialog_flatten.py	2012-08-20 10:43:48 UTC (rev 12094)
@@ -0,0 +1,93 @@
+#!/usr/bin/env python
+# -*- coding: UTF-8 -*-import pygtk
+"""
+    The gui to flatten the images.
+"""
+
+import gtk
+import pygtk
+# for script installation
+from pkg_resources import resource_filename
+##############
+## Graphic library ##
+##############
+try:
+    matplotlib.__version__
+except NameError:
+    import matplotlib
+    matplotlib.use('Agg', warn=False)
+from matplotlib.figure import Figure
+from matplotlib.backends.backend_gtkagg import FigureCanvasGTKAgg as FigureCanvas
+from matplotlib.backends.backend_gtkagg import NavigationToolbar2GTKAgg as NavigationToolbar
+
+from fovea_toolbox import misc
+
+class FlattenDialog():
+    def __init__(self, array, _glade_filename=None):
+    
+        self.array = [array, misc.flatten(array)]
+        
+        builder = gtk.Builder()
+        if _glade_filename == None:
+            try:
+                _glade_filename = resource_filename(
+                                    'openfovea',
+                                    'glade/dialog_flatten.glade')
+            except NotImplementedError:
+                _glade_filename = 'openfovea/glade/dialog_flatten.glade'
+        builder.add_from_file(_glade_filename)
+        self.window = builder.get_object('FlattenDialog')
+        self.widget = {
+            'button_apply' : builder.get_object('button_apply'),
+            'button_cancel' : builder.get_object('button_cancel'),
+            'plot_before_flatten' : builder.get_object('view_before_flatten'),
+            'plot_after_flatten' : builder.get_object('view_after_flatten'),
+            }
+        # The plots
+        self.flatten = {'figure' : None,
+                        'axis' : None,
+                        'canvas' : None}
+                        
+        self.flatten['figure'] = [
+                Figure(figsize=(100, 100), dpi=75, facecolor=(0.93,0.92,0.9,1)),
+                Figure(figsize=(100, 100), dpi=75, facecolor=(0.93,0.92,0.9,1))
+                ]
+        self.flatten['axis'] = [
+                self.flatten['figure'][0].add_subplot(111),
+                self.flatten['figure'][1].add_subplot(111)
+        ]
+        self.flatten['canvas'] = [
+                FigureCanvas(self.flatten['figure'][0]), # a gtk.DrawingArea 
+                FigureCanvas(self.flatten['figure'][1]) # a gtk.DrawingArea 
+        ]
+        self.flatten['canvas'][0].show() 
+        self.flatten['canvas'][1].show() 
+        self.widget['plot_before_flatten'].pack_start(self.flatten['canvas'][0], True, True)
+        self.widget['plot_after_flatten'].pack_start(self.flatten['canvas'][1], True, True)
+        self.plot()
+    def plot(self):
+        #vmin = min([self.array[0].min(), self.array[1].min()])
+        #vmax = max([self.array[0].max(), self.array[1].max()])
+        self.flatten['axis'][0].pcolormesh(self.array[0].transpose(), cmap='copper')
+        self.flatten['axis'][0].axis([0, self.array[0].shape[0], 0, self.array[0].shape[0]])
+        self.flatten['axis'][0].set_xticks([])
+        self.flatten['axis'][0].set_yticks([])
+        self.flatten['axis'][1].pcolormesh(self.array[1].transpose(), cmap='copper')
+        self.flatten['axis'][1].axis([0, self.array[1].shape[0], 0, self.array[1].shape[0]])
+        self.flatten['axis'][1].set_xticks([])
+        self.flatten['axis'][1].set_yticks([])
+    def run(self):
+        self.window.show()
+        response = self.window.run()
+        if response == 1:
+            return self.array[1]
+        else:
+            return self.array[0]
+    def destroy(self):
+        self.window.destroy()
+if __name__ == '__main__':
+    import numpy
+    test = main_win(numpy.array([range(10) for i in range(10)]), 
+                    _glade_filename='glade/dialog_flatten.glade')
+    toto = test.run()
+    print toto

Added: trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/dialog_mask_properties.py
===================================================================
--- trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/dialog_mask_properties.py	                        (rev 0)
+++ trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/dialog_mask_properties.py	2012-08-20 10:43:48 UTC (rev 12094)
@@ -0,0 +1,294 @@
+"""
+    This is the module to display the dialog export map.
+"""
+
+
+import pygtk
+pygtk.require('2.0')
+import gtk
+import os
+#from pkg_resources import resource_filename # pylint: disable-msg=E0611
+
+    
+from matplotlib.backends.backend_gtkagg import FigureCanvasGTKAgg as \
+                                               FigureCanvas
+import numpy
+#from scipy import interpolate, ndimage
+import plot_generic
+
+# Graphic library
+
+import matplotlib
+matplotlib.use('Agg')
+from matplotlib.figure import Figure
+from matplotlib.axes import Subplot
+from matplotlib.backends.backend_gtkagg import FigureCanvasGTK
+from matplotlib import cm # colormap
+from matplotlib import pylab
+pylab.hold(False) # This will avoid memory leak
+
+class BoolUnit(object):
+    """
+    Looks like this :
+    
+    ::
+    +------------------------------------------+
+    |                .                         |
+    |                . +--------------------+  |
+    |                . |                    |  |
+    |                . |                    |  |
+    | +-------------+. |                    |  |
+    | | Select Map  |. |     Display Map    |  |
+    | +-------------+. |                    |  |
+    |................. |                    |  |
+    | +-------------+. |                    |  |
+    | | 0 Invert    |..+--------------------+..|
+    | +-------------+. | Numerical value    |  |
+    |                . +--------------------+  |
+    |................:.........................|
+    |            +-------------+               |
+    |            | Add or bool |               |
+    |            +-------------+               |
+    +------------------------------------------+
+    """
+    def __init__(self, fvfile):
+        self.fvfile = fvfile
+        self.array = {'data' : None, # Store the data array used to generate mask.
+                      'mask' : None, # Store the mask itself.
+                      'invert' : False} # Invert the mask (or not).
+        # Creates the GUI.
+        self.map_select = gtk.ComboBox()
+        self.map_display = gtk.VBox()
+        self.map_display.set_size_request(250,250)
+        self.add_bool = gtk.ComboBox()
+        self.num_val = gtk.Entry()
+        self.invert = gtk.CheckButton(label='Invert')
+        self.box = gtk.VBox()
+        self.box.show()
+        map_box = gtk.HBox()
+        map_box.show()
+        __box1 = gtk.VBox() # Contains the combobox for mapselect and the invert toggle
+        __box1.show()
+        
+        viz_box = gtk.VBox()
+        viz_box.show()
+
+        self.map_select.show()
+        self.add_bool.show()
+        self.num_val.show()
+        self.invert.show()
+
+        viz_box.pack_start(self.map_display)#, expand=False)
+        viz_box.pack_start(self.num_val, expand=False)
+        __box1.pack_start(self.map_select, expand=False)
+        __box1.pack_start(self.invert, expand=False)
+        map_box.pack_start(__box1, expand=False)
+        #ap_box.pack_start(self.map_select, expand=False)
+        map_box.pack_start(viz_box, expand=True)
+        self.box.pack_start(map_box, expand=True)
+        self.box.pack_start(self.add_bool, expand=False)
+
+        # Create graphics
+        self.figure = Figure(figsize=(100, 100), dpi=75)
+        self.axis = self.figure.add_subplot(111, axisbg='red')
+        self.canvas = FigureCanvas(self.figure)
+        self.canvas.show()
+        self.map_display.pack_start(self.canvas, True, True)
+        self.map_display.show()
+        self.canvas.mpl_connect('button_press_event', self.on_array_click)
+
+        # Connect buttons.
+        self.map_select.connect('changed', self.change_array)
+        self.num_val.connect('activate', self.on_num_val_changed)
+        self.invert.connect('toggled', self.on_invert_toggled)
+        # bool_list has to be connected in the caller class.
+        # Fill the list.
+        list_arr = gtk.ListStore(str)
+        __list = list()
+        for key in self.fvfile.get_array('keys'):
+            if type(self.fvfile.get_array(key)) in [numpy.ndarray, numpy.ma.core.MaskedArray]:
+                list_arr.append([key])
+                __list.append(key)
+        self.map_select.set_model(list_arr)
+        __cell = gtk.CellRendererText()
+        self.map_select.pack_start(__cell, True)
+        self.map_select.add_attribute(__cell, 'text', 0)
+        self.map_select.set_active(__list.index('Piezo'))
+        
+        bool_list = gtk.ListStore(str)
+        [bool_list.append([key]) for key in ['Add', 'AND','OR','XOR']]
+        self.add_bool.set_model(bool_list)
+        __cell = gtk.CellRendererText()
+        self.add_bool.pack_start(__cell, True)
+        self.add_bool.add_attribute(__cell, 'text', 0)
+        self.add_bool.set_active(0)
+    
+    def on_invert_toggled(self, event):
+        self.array['invert'] = event.get_active()
+        mask = self.array['data'].mask
+        mask = numpy.logical_not(mask)
+        self.apply_mask(mask)
+        self.plot()
+    def on_num_val_changed(self, event):
+        height = float(event.get_text())
+        self.generate_mask(height)
+        self.plot()
+
+    def on_array_click(self, event):
+        try:
+            height = self.array['data'].data[event.ydata, event.xdata]
+        except TypeError:
+            height = self.array['data'][event.ydata, event.xdata]
+        self.generate_mask(height)
+        self.plot()
+        self.num_val.set_text(str(height))
+
+    def generate_mask(self, height):
+        if type(self.array['data']) == numpy.ndarray:
+            mask = self.array['data'] < height
+        else:
+            mask = self.array['data'].data < height
+        if self.array['invert']:
+            mask = numpy.logical_not(mask)
+        self.apply_mask(mask)
+    
+    def apply_mask(self, mask):
+        try:
+            self.array['data'].mask = mask
+        except AttributeError:
+            self.array['data'] = numpy.ma.masked_array(self.array['data'], mask=mask)
+
+    def change_array(self, event):
+        self.array['name'] = event.get_active_text()
+        self.array['data'] = self.fvfile.get_array(self.array['name'], raw=True)
+        if self.array['data'].ndim > 2:
+            self.array['data'] = self.array['data'][:,:,0]
+        self.plot()
+
+    def plot(self):
+        self.axis.pcolor(self.array['data'], cmap=cm.copper)
+        self.axis.axis([0, self.array['data'].shape[0],
+                        0, self.array['data'].shape[1]])
+        self.axis.set_aspect('equal')
+        self.canvas.draw_idle()
+        
+    def get_op(self):
+        return self.add_bool.get_active_text()
+
+    def get_mask(self):
+        try:
+            return self.array['data'].mask
+        except:
+            return numpy.ones_like(self.array['data'], dtype=bool)
+    def destroy(self):
+        self.box.destroy()
+        return
+
+class MaskProperties(object):
+    """
+    
+    """
+    def __init__(self, FVFile):
+        self.fvfile = FVFile
+        self.mask = None
+        self.dialog = gtk.Dialog(title='Mask Propreties',
+                                 buttons=(gtk.STOCK_OK, gtk.RESPONSE_OK,
+                                          gtk.STOCK_CANCEL, gtk.RESPONSE_CANCEL))
+        self.dialog.set_default_size(700, 350)
+
+        self.bool_win = list() # This contains the window where each boolean operators are stored
+        # Create the first one.
+        self.box = {'left' : gtk.HBox(),
+                    'bool_view' : gtk.VBox(homogeneous=True),
+                    'center' : gtk.HBox()}
+        self.bool_win.append(BoolUnit(self.fvfile))
+        self.bool_win[0].add_bool.connect('changed', self.add_bool)
+        self.bool_win[0].canvas.mpl_connect('button_press_event', self.disp_result)
+        self.box['bool_view'].pack_start(self.bool_win[0].box)
+        self.scroll_window = gtk.ScrolledWindow()
+        self.scroll_window.set_border_width(10)
+        self.scroll_window.set_policy(gtk.POLICY_NEVER, gtk.POLICY_AUTOMATIC)
+        self.scroll_window.show()
+        self.scroll_window.add_with_viewport(self.box['bool_view'])
+        self.box['left'].pack_start(self.scroll_window, True, True, 0)
+        self.box['center'].pack_start(self.box['left'])#, True, True, 0)
+        self.box['center'].show()
+        self.box['left'].show()
+        self.box['bool_view'].show()
+        self.dialog.vbox.pack_start(self.box['center'], True, True, 0)
+
+        # Create graphics
+        self.figure = Figure(figsize=(200, 200), dpi=75)
+        self.axis = self.figure.add_subplot(111, axisbg='red')
+        self.canvas = FigureCanvas(self.figure)
+        self.canvas.show()
+        self.box['center'].pack_start(self.canvas)#, True, True, 0)
+        self.box['center'].set_homogeneous(True)
+        
+    def add_bool(self, event):
+        for bool_unit in self.bool_win:
+            if bool_unit.add_bool == event:
+                index = self.bool_win.index(bool_unit)
+        selected = event.get_active_text()
+        print selected
+        if selected == 'Add':
+            self.bool_win[index].destroy()
+            self.bool_win.pop(index)
+            return
+        if index+1 == len(self.bool_win):
+            self.bool_win.append(BoolUnit(self.fvfile))
+            self.box['bool_view'].pack_start(self.bool_win[-1].box)
+            self.bool_win[-1].add_bool.connect('changed', self.add_bool)
+        #self.compute_result()
+            self.bool_win[-1].canvas.mpl_connect('button_press_event', self.disp_result)
+        self.disp_result()
+
+    def compute_result(self):
+        bool_list = [item.get_op() for item in self.bool_win]
+        mask_list = [item.get_mask() for item in self.bool_win]
+        result = numpy.logical_not(mask_list[0])
+        for item in range(len(bool_list)-1):
+            if bool_list[item] == 'AND':
+                result = numpy.logical_and(result, numpy.logical_not(mask_list[item+1]))
+            elif bool_list[item] == 'OR':
+                result = numpy.logical_or(result, numpy.logical_not(mask_list[item+1]))
+            elif bool_list[item] == 'XOR':
+                result = numpy.logical_xor(result, numpy.logical_not(mask_list[item+1]))
+        self.mask = numpy.logical_not(result)
+
+    def disp_result(self, event=None):
+        self.compute_result()
+        self.axis.pcolor(self.mask, cmap=cm.gray)
+        self.axis.axis([0, self.mask.shape[0],
+                        0, self.mask.shape[1]])
+        self.axis.set_aspect('equal')
+        self.canvas.draw_idle()
+
+    def run(self):
+        """
+        Runs the dialog.
+        """
+        response = self.dialog.run()
+        if response == gtk.RESPONSE_OK:
+            # Runs the code if button OK is clicked
+            self.fvfile.set_array('Mask', self.mask)
+            self.fvfile.set_switch('mask', True)
+            return True
+        else:
+            self.fvfile.set_switch('mask', False)
+            return False
+    def destroy(self):
+        """
+        Destroy the window.
+        """
+        self.dialog.destroy()
+        return False
+
+if __name__ == '__main__':
+    import numpy
+    import classes
+    FVFOLDER = classes.FVFolder()
+    FVFOLDER.load_aex('../docs/data/Stiffness_and_Event_computed.aex')
+    DISPLAY_IT = MaskProperties(FVFOLDER.file['list'][1])
+    answer = DISPLAY_IT.run()
+    print answer

Added: trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/fovea_toolbox/__init__.py
===================================================================
--- trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/fovea_toolbox/__init__.py	                        (rev 0)
+++ trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/fovea_toolbox/__init__.py	2012-08-20 10:43:48 UTC (rev 12094)
@@ -0,0 +1 @@
+__all__ = ['curve', 'file']
\ No newline at end of file

Added: trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/fovea_toolbox/curve.py
===================================================================
--- trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/fovea_toolbox/curve.py	                        (rev 0)
+++ trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/fovea_toolbox/curve.py	2012-08-20 10:43:48 UTC (rev 12094)
@@ -0,0 +1,1174 @@
+#! /usr/bin/env python
+#-*- coding: iso-8859-1 -*-
+'''
+The curve module contains function that are usefull for curve data processing
+'''
+
+## Fonctions pour Open Fovea.
+#import pdb
+import csv
+#import warnings
+#warnings.simplefilter("ignore")
+#warnings.filterwarnings('error', category=Warning)
+
+import numpy as num
+#from scipy.optimize import leastsq
+from scipy import odr
+from copy import deepcopy
+CURVE_TEST = '../../docs/data/bugged_curve/curve_bug_1.csv'
+CURVE_EVENT = ['../../docs/data/curves/event_1.csv',
+               '../../docs/data/curves/event_2.csv',
+               '../../docs/data/curves/event_3.csv',
+               '../../docs/data/curves/WLC.csv']
+FIGURE_FOLDER = 'tests/'
+
+
+def open_csv_curve(file_name):
+    """
+        Open the curve in csv file.
+    """
+    fid = open(file_name)
+    temp_file = csv.reader(fid)
+    # The two first lines are descripion.
+    temp_file.next()
+    temp_file.next()
+    # Get the datas
+    arr_list = [item for item in temp_file]
+    curves = [num.asarray(
+                    [item[place] for item in arr_list if len(item[place])],
+                    dtype=num.float)
+             for place in range(len(arr_list[0]))]
+    return curves
+
+
+def find_poc(curve_x, curve_y, threshold=1, method='curve_fit',
+             limit_slide=False, len_slice=0.3):
+    """
+    Finds the point of contact of a force curve.
+
+    >>> curve = open_csv_curve(CURVE_TEST)
+    >>> result = find_poc(curve[0], curve[1], threshold=1, method='curve_fit')
+    >>> result.keys()
+    ['deriv', 'Poly Fit', 'Slice', 'PoC', 'Error']
+
+    curve_x and curve_y = array
+
+    threshold : integer
+                how much the curve has to diverge from the fit to be a point
+                of contact. (threshold * noise)
+
+    method : string
+             Defines the method used to detect the point of contact.
+
+            * 'deriv' (default) : uses the derivative method.
+                                When the derivative of the curve is zero (then
+                                it's linear), the point of contact is detected.
+                                The advantage of this method is to get rid of
+                                irregularities observed in the off-contact part
+                                of the curve.
+
+            * 'curve_fit' : uses the curve fit method.
+                          A linear fit is computed from the off-contact part of
+                          the curve. The point of contact is then detected at
+                          the point when the curve deviates from this linear
+                          fit. The advantage of this method is that it does not
+                          depend on the shape of the on contact part of the
+                          curve.
+    """
+    if len(curve_x) <= 2:
+        return None
+    if curve_x == None or curve_y == None:
+        return None
+    if method == 'deriv':
+        return find_poc_deriv(curve_x, curve_y, threshold, limit_slide,
+                              len_slice)
+    elif method == 'curve_fit':
+        try:
+            result = find_poc_curve_fit(curve_x, curve_y, threshold,
+                                    limit_slide, len_slice)
+        except TypeError as detail:
+            if 'expected non-empty vector' in detail.message:
+                # This error occurs when a too small curve is given.
+                return None
+            else:
+                raise detail
+        else:
+            result['deriv'] = None
+        return result
+
+
+def platgliti(curve):
+    """
+        Return the slice of the first non flat part. This is usefull when a
+        curve is complemented with the identical values at the end.
+    """
+
+    indice = 0
+    prev_val = curve[indice]
+    indice += 1
+    next_val = curve[indice]
+    while prev_val == next_val and indice + 1 < len(curve):
+        indice += 1
+        next_val, prev_val = curve[indice], next_val
+    return indice
+
+
+def true_data_indice(curve_x):
+    """
+        Return the true length curve. It removes all similar values that are at
+        the beginning or at the end of the curve.
+    """
+    new_curve_x = curve_x[:-1] - curve_x[1:]
+    non_zero = new_curve_x.nonzero()[0]
+    start_indice = non_zero[0]
+    stop_indice = non_zero[-1] + 2
+
+    return start_indice, stop_indice
+
+
+def find_poc_curve_fit(curve_x, curve_y, threshold, limit_slide=False,
+                       len_slice=0.3):
+    '''
+    Finds the point of contact, using the method of curve fit.
+
+    This methods makes a first order fits the off contact part of the curve.
+    The point of contact is then detected when the force curve deviates from
+    the linear fit. The deviation is related to the error measured during the
+    fit.
+    '''
+    loop = {'slope_negative': 1,
+            'step': 0}
+    reversed_curve = 0
+    if curve_y[0] > curve_y[-1]:
+        reversed_curve = 1
+        curve_y = curve_y[::-1]
+        curve_x = curve_x[::-1]
+    # Linear fit of the segment slice
+    _ind = platgliti(curve_y)
+    _true_indice = true_data_indice(curve_x)
+    #_true_indice = (0, len(curve_x))
+    #print _true_indice
+    #print _ind
+    _length = _true_indice[1] - _true_indice[0]
+
+    seg_slice = slice(_ind, int(_length * len_slice + _ind))
+    # the fit is :
+    # p(x) = coeff[0]*x + coeff[1]
+    coeff = num.polyfit(curve_x[seg_slice],
+                        curve_y[seg_slice], 1, full=True)[0]
+    #
+    # We make a loop by testing the slope of the fit.
+    # If this slope is negative, we look a little bit forward in the curve
+    # until the slope becomes positive
+    #
+    fit = num.polyfit(curve_x[seg_slice], curve_y[seg_slice], 1, full=True)
+    # Look in the curve slope was positive at the beginning
+    # i.e. :
+    # \
+    #  \     _.-
+    #   \̣.-`
+    if fit[0][0] >= 0:
+        fall_off = 1
+    else:
+        fall_off = 0
+    while loop['slope_negative'] and (seg_slice.stop + 1 < len(curve_x)):
+        new_seg_slice = slice(seg_slice.start + 2, seg_slice.stop + 2)
+        fit = num.polyfit(curve_x[new_seg_slice], curve_y[new_seg_slice],
+                          1, full=True)
+        if coeff[0] < fit[0][0] and fit[0][0] <= 0:
+            loop['step'] = 0
+            if limit_slide and (seg_slice.stop + 1 >= len(curve_x) / 2):
+                # The slice is going farer than the half of the curve. Then,
+                # if we choosed to limit the sliding, stop at this step.
+                loop['slope_negative'] = 0
+            if seg_slice.stop > len(curve_x):
+                # The slice is going outside the curve, then stop anyway.
+                loop['slope_negative'] = 0
+        elif fall_off and fit[0][0] >= 0:
+            loop['step'] = 0
+        elif fall_off and fit[0][0] < 0:
+            # we directly stop here and go back
+            loop['slope_negative'] = 0
+            [new_seg_slice, fit] = go_back(curve_x, curve_y, seg_slice)
+#            new_seg_slice = slice(seg_slice.start - 4, seg_slice.stop - 4)
+#            fit = num.polyfit(curve_x[new_seg_slice], curve_y[new_seg_slice],
+#                              1, full = True)
+        else:
+            loop['step'] = loop['step'] + 1
+        coeff = fit[0]
+        if loop['step'] > 2:
+            coeff[0] = fit[0][0]
+            coeff[1] = fit[0][1]
+            loop['slope_negative'] = 0
+        seg_slice = new_seg_slice
+    #
+    # We take the selected slice to detect the point of contact
+    #
+    error = (num.sqrt(fit[1]) / 5) * threshold
+    # Find when the curve goes away from the fit
+    #pdb.set_trace()
+    if not len(error):
+        error = num.array([0])
+    _ind = num.polyval([coeff[0], coeff[1] + error], curve_x)
+    point_of_contact = 0
+
+    for item_nbr in xrange(len(curve_y)):
+        if _ind[item_nbr] >= curve_y[item_nbr]:
+            point_of_contact = item_nbr
+
+    if reversed_curve:
+        curve_y = curve_y[::-1]
+        point_of_contact = len(curve_y) - point_of_contact - 1
+        seg_slice = slice(len(curve_y) - seg_slice.stop,
+                          len(curve_y) - seg_slice.start)
+    return {'PoC': point_of_contact,
+            'Poly Fit': [coeff[0], coeff[1]],
+            'Error': error,
+            'Slice': seg_slice}
+
+
+def go_back(curve_x, curve_y, seg_slice):
+    """
+        Go back in the fit to find the best place to find poc.
+    """
+    fit = num.polyfit(curve_x[seg_slice], curve_y[seg_slice], 1,
+                      full=True)
+    better = 0
+    while not better:
+        new_seg_slice = slice(seg_slice.start - 2, seg_slice.stop - 2)
+        new_fit = num.polyfit(curve_x[seg_slice], curve_y[seg_slice], 1,
+                      full=True)
+        if new_fit[1] > fit[1]:
+            better = 1
+        else:
+            seg_slice = new_seg_slice
+            fit = new_fit
+        if seg_slice.start <= 2:
+            better = 1
+    return seg_slice, fit
+
+
+def compute_derivative(curve_x, curve_y, delta=10):
+    '''
+        Computes the derivative of a curve
+    '''
+    _my = num.zeros_like(curve_y)
+    _mx = num.zeros_like(curve_y)
+    for item in range(len(curve_y)):
+        t_slice = slice(item, item + delta)
+        _my[item] = curve_y[t_slice].mean()
+        _mx[item] = curve_x[t_slice].mean()
+    d_y = (_my[1:] - _my[:-1])
+    return[curve_x[:-1], d_y]
+
+
+def find_poc_deriv(curve_x, curve_y, threshold=1, limit_slide=False,
+    len_slice=0.3):
+    '''
+        Finds the point of contact, using the derivative of the curve.
+    '''
+    seg = {'slice': None,  # Contains the slice of the segment
+            'coef': None}  # Contains the coefficient of the fit
+    # We slips on the curve. Then, we define the same for the next portion of
+    # curve
+    next_seg = {'slice': None,  # Contains the slice of the segment
+            'coef': None}  # Contains the coefficient of the fit
+
+    deriv = compute_derivative(curve_x, curve_y, delta=10)
+    # define the slice to compute the fit
+    seg['slice'] = slice(int(len(deriv[1]) - len(deriv[1]) * len_slice) - 1,
+                      len(deriv[1]) - 1)
+    # and compute the fit...
+    seg['coef'] = num.polyfit(deriv[0][seg['slice']], deriv[1][seg['slice']],
+                           1, full=True)
+    # make the slice slips on the curve, untill we find the one with the lower
+    # error.
+    # Indeed, some curves begin with a big noise that prevent a good point of
+    # contact detection.
+    loop = {'ok': 0,
+            'i': 0,
+            'step': 0}
+    while not loop['ok']:
+        next_seg['slice'] = slice(seg['slice'].start - loop['step'],
+                               seg['slice'].stop - loop['step'])
+        next_seg['coef'] = num.polyfit(deriv[0][next_seg['slice']],
+                                    deriv[1][next_seg['slice']],
+                                    1, full=True)
+        if seg['coef'][1] <= next_seg['coef'][1]:
+            loop['ok'] = 1
+        #else:
+        #    i = 0
+        if limit_slide and (next_seg['slice'].start < len(deriv[1]) / 2):
+            loop['ok'] = 1
+        if next_seg['slice'].start < loop['step']:
+            loop['ok'] = 1
+        seg['coef'] = next_seg['coef']
+        loop['i'] += 1
+        if loop['i'] > 10:
+            seg['slice'] = next_seg['slice']
+            loop['ok'] = 1
+    # Now, we apply the threshold on the error and find the first point that
+    # deviates from the fit (same idea as the old curve_fit algorythm)
+    error = seg['coef'][1] * threshold
+    seg['coef'] = seg['coef'][0]
+    polynom = num.polyval(seg['coef'], deriv[0]) - error
+    on_contact = (deriv[1] <= polynom) - 1  # True are the points that are
+                                            # close to the fit
+    indice = num.asarray(num.nonzero(on_contact)[0])
+    # Sometimes, in the on-contact part of the curve, the tips slips on the
+    # surface that is indented. The resulting curve looks like this :
+    # \
+    #  \  /\
+    #   `v  \
+    #        "_
+    #          `¬___________________
+    #    |      |
+    #    V      V
+    # 000100000011111111111111111111 Resulting on_contact
+    # 123456789012345678901234567890
+    # [4, 11, 12, 13, 14, 15, 16, 17, ...] Resulting indice
+    # [7, 1, 1, 1, 1, 1, 1, ...] Resulting diff_indice
+    #
+    # With the diff_indice, we can then detect such holes. I arbitrary choose
+    # 40. It could be nice to set this as a parameter. Will see later.
+    diff_indice = indice[1:] - indice[:-1]
+    hole = num.nonzero(diff_indice > 40)[0]
+    if len(hole):
+        i_poc = hole[-0] + 1
+    else:
+        i_poc = 0
+    non_zero_list = num.nonzero(on_contact)[0]
+    if len(non_zero_list):
+        point_of_contact = num.nonzero(on_contact)[0][i_poc]
+    else:
+        point_of_contact = 0
+    return {'PoC': point_of_contact,
+            'Poly Fit': [0, seg['coef'][0]],
+            'Error': error,
+            'Slice': seg['slice'],
+            'deriv': deriv}
+
+
+def compute_indentation(curve_x, curve_y,
+                        deflection_sensitivity, spring_constant):
+    '''
+    Compute the indentation curve.
+
+    * Parameters :
+        curve_x : 1d array
+            Values of the x coordinate.
+        curve_y : 1d array
+            Values of the y coordinates.
+        deflection_sensitivity : float
+            Parameter of the glass indentation.
+        spring_constant : float
+            sping constant of the cantilever.
+
+    * Returns :
+        indentation : 1d array
+            Value of the x coordinate.
+        force : 1d array
+            Value of the y coordinate.
+    '''
+    #deflection_sensitivity=1
+    if curve_x == None or curve_y == None or len(curve_x) <= 1:
+        return [None, None]
+    indice = true_data_indice(curve_x)
+    length = len(curve_x)
+
+    curve_x = curve_x[indice[0]:indice[1]]
+    curve_y = curve_y[indice[0]:indice[1]]
+    if curve_x[0] < curve_x[-1]:
+        indent_curve = curve_x[::-1]
+    else:
+        indent_curve = curve_x
+
+    indent_curve = indent_curve + num.polyval([deflection_sensitivity, 0],
+                                              curve_y)
+    force_curve = curve_y * spring_constant
+
+    force_curve = num.r_[force_curve,
+                         [force_curve[-1]] * (length - len(force_curve))]
+    indent_curve = num.r_[indent_curve,
+                          [indent_curve[-1]] * (length - len(indent_curve))]
+    return [indent_curve, force_curve]
+
+
+def correct_curve_drop(curve_y):
+    '''
+    Corrects the drops that occurs at the beginning of some force-distance
+    curves. This function corrects a bug from Veeco AFM.
+    '''
+    first_non_zero = curve_y.nonzero()[0][1] + 1
+    for indice in range(first_non_zero, len(curve_y)):
+        curve_y[indice] = curve_y[first_non_zero - 1]
+
+
+def segment_curve(curve_x, curve_y, segment_number, segment_deep):
+    """
+    Segmentation of curve.
+
+    Parameters : 
+        * curve_x : 1d array
+                Values of the x coordinate.
+        * curve_y : 1d array
+                Values of the y coordinate.
+        * segment_number : int
+                specifies the number of segments to generate
+                -1 : create one segment from the begining to
+                     the end of the curve.
+                0 : create as many segment as possible.
+                >0 : specifies the exact number of segment. If the
+                     curve is smaller, less segment is created.
+        * segment_deep : int
+                specifies the deep (curve_x value) of each segment.
+                in case segment_number = -1, this parameter is not
+                considered.
+
+    Returns :
+        * parts_x : 1d array
+              segment_number+1 array containing the curve_x values that
+              correspond to each segment
+        * parts_y : 1d array
+              segment_number+1 array containing the curve_y values that
+              correspond to each segment
+
+        for example : segment n is made of parts_x[n-1],parts_x[n]
+                      and parts_y[n-1],parts_y[n]
+    """
+    ## Initialisation des valeurs
+    ##
+    #
+    if not len(curve_y):
+        if segment_number == 0:
+            return [[num.nan], [num.nan]]
+        else:
+            return [num.zeros(segment_number) * num.nan,
+                    num.zeros(segment_number) * num.nan]
+    if curve_y[0] > curve_y[-1]:
+        curve_x = curve_x[::-1]  # We invert the curve to be more convenient
+        curve_y = curve_y[::-1]
+
+    meta_parts_x = []
+    meta_parts_y = []
+
+    if segment_number == -1:
+        # We create one segment that correspond to the whole curve.
+        meta_parts_y.append(curve_y)
+        meta_parts_x.append(curve_x)
+        return [meta_parts_x, meta_parts_y]
+    elif segment_number == 0:
+        segment_number = num.inf
+    if len(curve_x):
+        curve_size = curve_x.max() - curve_x.min()
+    else:
+        curve_size = 0
+    size_done = segment_deep
+    nbr_selection = 1
+    ## Element zero
+    parts_x = []
+    parts_y = []
+    if curve_size:
+        parts_x.append(curve_x.min())
+        parts_y.append(curve_y[num.nonzero(curve_x == parts_x[0])[0][0]])
+    else:
+        parts_x.append(num.nan)
+        parts_y.append(num.nan)
+    ## From the first to the last segment
+    all_indexes = [0]
+    while curve_size > size_done and nbr_selection <= segment_number:
+        parts_x.append(parts_x[-1] + segment_deep)
+        # Let's find the next point
+        indexes = num.nonzero(curve_x >= parts_x[nbr_selection])[0]
+        indexes = indexes[0]
+        if indexes == 0:
+            indexes = 1
+        all_indexes.append(indexes)
+        # The point stands between index-1 and index. We then make a linear fit
+        # and we'll find the value. Done between index-1 and index+1 'cause it
+        # does _not_ take the last value.
+        polynome = num.polyfit(curve_x[indexes - 1:indexes + 1],
+                               curve_y[indexes - 1:indexes + 1],
+                               1)
+        parts_y.append(num.polyval(polynome, parts_x[nbr_selection]))
+        this_slice = slice(all_indexes[nbr_selection - 1],
+                           all_indexes[nbr_selection])
+        if parts_x[-2] != curve_x[this_slice.start]:
+            tmp_x = [parts_x[-2]]
+            tmp_y = [parts_y[-2]]
+        else:
+            tmp_x = []
+            tmp_y = []
+        tmp_x.extend(curve_x[this_slice])
+        tmp_x.append(parts_x[-1])
+        #print tmp_x
+        #tmp_y = [parts_x[-1]]
+        tmp_y.extend(curve_y[this_slice])
+        tmp_y.append(parts_y[-1])
+        meta_parts_x.append(tmp_x)
+        meta_parts_y.append(tmp_y)
+        nbr_selection = nbr_selection + 1
+        size_done = size_done + segment_deep
+    if nbr_selection <= segment_number and segment_number is not num.inf:
+        ## adding NAN values
+        while nbr_selection <= segment_number:
+            meta_parts_x.append([num.nan])
+            meta_parts_y.append([num.nan])
+            nbr_selection += 1
+    return [meta_parts_x, meta_parts_y]
+
+
+def compute_stiffness(indent_curve, force_curve, model='Sphere', tip_carac=40,
+                      poisson_ratio=0.3, method='Raw'):
+    """
+    Compute : the stiffness of the different depth.
+
+    indent_curve and force_curve : the verctors return by segment_curve.
+
+    model : describe the Hertz model used and can be 'Sphere' or 'Cone'.
+
+    tip_carac : the characteristic of the tip. Radius and Semi-opening angle in
+            radian for Sphere or Cone model respectively.
+    poisson_ratio : the poisson ratio of the indented substrate.
+                    Common values : 0.3 for normal cells
+                                    0.5 for rubber
+    method : string
+             'Raw' for a fit of the raw data with the model.
+             'Linear' for a linearized fit.
+             'Extrema' for a linearized fit from the extrem points.
+             'Median' for a computation of the ym from the median point in the
+                      segment.
+    """
+    if indent_curve == None or force_curve == None:
+        return num.ones(1) * num.nan
+    ## The indentation and force have to begin from 0...
+    stop = False
+    if not len(indent_curve):
+        stop = True
+    elif type(indent_curve[0]) == list:
+        stop = len(indent_curve[0]) == 1 and num.isnan(indent_curve[0][0])
+    elif type(indent_curve[0]) in [num.float64, float]:
+        stop = num.isnan(indent_curve[0])
+    if stop:
+        return num.ones(len(indent_curve)) * num.nan
+    # Make the point of contact being at zero:
+    zero_point = indent_curve[0][0]
+    indent_curve = [item - zero_point for item in indent_curve]
+    zero_point = force_curve[0][0]
+    force_curve = [item - zero_point for item in force_curve]
+    # Now, we prepare the fit
+    young_modulus = []
+    for indent, force in zip(indent_curve, force_curve):
+        if num.isnan(indent[0]):
+            young_modulus.append(num.nan)
+        elif method == 'Raw':
+            # Choose the initial parameters :
+            p = [100]
+
+            def ym_model(p, indent):
+                if model == 'Sphere':
+                    force = 4 / 3. * p[0] / (1 - poisson_ratio ** 2) *\
+                            num.sqrt(tip_carac) * indent ** 1.5
+                elif model == 'Cone':
+                    force = 2. / num.pi * p[0] / (1 - poisson_ratio ** 2) *\
+                            num.tan(tip_carac) * indent ** 2
+                return force
+
+            try:
+                fit_it = odr.ODR(odr.Data(indent, force),
+                                 odr.Model(ym_model), p)
+                # And we run it
+                out = fit_it.run()
+                # Get the result and rescale it.
+                young_modulus.append(out.beta[0])
+                if out.beta[0] == 100:
+                    print indent
+                    out.pprint()
+            except IndexError, message:
+                if type(indent) in [float, num.float64] and num.isnan(indent):
+                    young_modulus.append(num.nan)
+                else:
+                    raise IndexError(message)
+        elif method == 'Linear':
+            # Choose the initial parameters :
+            p = [100]
+
+            def ym_model(p, d_indent):
+                #slope = (force[1:] - force[:-1]) /(indent[1:] - indent[:-1])
+                if model == 'Sphere':
+                    d_force = 4 / 3. * p[0] / (1 - poisson_ratio ** 2) *\
+                            num.sqrt(tip_carac) * d_indent
+                elif model == 'Cone':
+                    d_force = 2. / num.pi * p[0] / (1 - poisson_ratio ** 2) *\
+                            num.tan(tip_carac) * d_indent
+                return d_force
+            try:
+                if model == 'Sphere':
+                    indent = indent ** (3 / 2.)
+                elif model == 'Cone':
+                    indent = indent ** 2
+                d_force = num.diff(force)
+                d_indent = num.diff(indent)
+                fit_it = odr.ODR(odr.Data(d_indent, d_force),
+                                 odr.Model(ym_model), p)
+                # And we run it
+                out = fit_it.run()
+                # Get the result and rescale it.
+                young_modulus.append(out.beta[0])
+            except IndexError, message:
+                if type(indent) in [float, num.float64] and num.isnan(indent):
+                    young_modulus.append(num.nan)
+                else:
+                    raise IndexError(message)
+        elif method == 'Extrema':
+            # Modification of the axes ...
+            if model == 'Sphere':
+                indent = indent ** (3 / 2.)
+            elif model == 'Cone':
+                indent = indent ** 2
+            # Compute slopes
+            try:
+                slope = (force[-1] - force[0]) / (indent[-1] - indent[0])
+            except IndexError, message:
+                if type(indent) in [float, num.float64] and num.isnan(indent):
+                    young_modulus.append(num.nan)
+                else:
+                    raise IndexError(message)
+            finally:
+                ## Compute the young modulus according to the models
+                if model == 'Sphere':
+                    young_modulus.append((1 - poisson_ratio ** 2) *
+                                         slope *
+                                         3 / (4 * num.sqrt(tip_carac)))
+                elif model == 'Cone':
+                    young_modulus.append((1 - poisson_ratio ** 2) *
+                                         slope *
+                                         num.pi / (2 * num.tan(tip_carac)))
+        elif method == 'Median':
+            # Modification of the axes ...
+            if model == 'Sphere':
+                indent = indent ** (3 / 2.)
+            elif model == 'Cone':
+                indent = indent ** 2
+            m_force = num.median(force)
+            m_indent = num.median(indent)
+            if model == 'Sphere':
+                young_modulus.append((1 - poisson_ratio ** 2) *
+                                         (m_force / m_indent) *
+                                         3 / (4 * num.sqrt(tip_carac)))
+            elif model == 'Cone':
+                young_modulus.append((1 - poisson_ratio ** 2) *
+                                         (m_force / m_indent) *
+                                         num.pi / (2 * num.tan(tip_carac)))
+    return num.array(young_modulus)
+
+
+def event_find(curve_x, curve_y, deflection_sensitivity, spring_constant,
+               weight=2.5, fit_model=None, poc=0, baseline=None, debug=0):
+    '''
+        This function finds the protein - protein unbinding events from a
+        retraction curve.
+
+        * Parameters :
+            curve_x : 1d array
+                Values of the x coordinate.
+            curve_y : 1d array
+                Values of the y coordinates.
+            deflection_sensitivity : float
+                The deflection sensitivity is used to compute properties of the
+                event.
+            spring_constant : float
+                The property of the cantilever to compute the force of the
+                event.
+            weight : float
+                Threshold to detect the event. Smallest is more sensitive.
+            fit_model : str
+                'wlc' for worm like chain model
+                'fjc' for freely jointed chain model
+            poc : int
+                The index of the point of contact in the curve. Used for the
+                fit.
+            baseline : [a, b] -> y = ax + b
+                The indices of the baseline of the off contact part of the
+                curve. Used to compute the fit.
+
+        * Returns :
+            event_list : list
+                List of events as returned by event_properties.
+    '''
+    if curve_x == None or curve_y == None:
+        return None
+    # find curve jumps...
+    [curve_pos, curve_mean, curve_std] = find_curve_jump(curve_y)
+    indent = compute_indentation(curve_x, curve_y, deflection_sensitivity,
+                                   spring_constant)
+    distances = -indent[0] + max(indent[0])
+    threshold = weight * curve_pos * curve_std
+    positions = threshold > 1
+    event_list = None
+    # Find the point of contac
+    poc_xy = [curve_x[poc], curve_y[poc]]
+    if baseline is not None:
+        f_y = baseline[0] * curve_x + baseline[1]
+        try:
+            new_poc = num.nonzero(curve_y < f_y)[0][0] - 1
+        except:
+            new_poc = poc
+        poc_xy = [curve_x[new_poc], curve_y[new_poc]]
+    if sum(positions):
+        event_list = event_complete(curve_x, curve_y, positions)
+        for event in event_list:
+            event = event_properties(curve_x, curve_y, event, spring_constant,
+                                 distances, fit_model, poc_xy=poc_xy)
+    if not debug:
+        return event_list
+    else:
+        return [event_list, threshold]
+
+
+def event_complete(curve_x, curve_y, position):
+    '''
+    from a vector which points the putative events position, this function
+    extracts and sort and adds some informations like force,...
+    '''
+    point_list = position.nonzero()[0]
+    # Finds adjascent points that defines in fact a single event...
+    event_list = list()
+    first_pos = 0
+    to_remove = list()
+    for i in xrange(len(point_list) - 1):
+        if point_list[i] + 1 != point_list[i + 1]:
+            event_list.append({'X': point_list[i],
+                               'Slice': slice(point_list[first_pos],
+                                              point_list[i] + 1)})
+            first_pos = i + 1
+        if i + 1 == len(point_list) - 1:
+            event_list.append({'X': point_list[i],
+                               'Slice': slice(point_list[first_pos],
+                                              point_list[i + 1] + 1)})
+            first_pos = i + 1
+    if len(point_list) == 1:
+        event_list = [{'X': point_list[0],
+                       'Slice': slice(point_list[0],
+                                      point_list[0] + 1)}]
+    # Complete all the events.
+    for event_nbr in xrange(len(event_list)):
+        event = event_list[event_nbr]
+        # Complete the events to the right
+        next_is_higher = 1
+        right_pos = event['Slice'].stop
+        while next_is_higher and right_pos + 1 < len(curve_y):
+            if curve_y[right_pos + 1] >= curve_y[right_pos]:
+                right_pos = right_pos + 1
+            else:
+                right_pos = right_pos + 1
+                next_is_higher -= 1
+        # And complete to the left.
+        previous_is_lower = 1
+        left_pos = event['Slice'].start
+        while previous_is_lower:
+            if curve_y[left_pos - 1] < curve_y[left_pos]:
+                left_pos = left_pos - 1
+                #previous_is_lower = 1
+            elif curve_y[left_pos - 1] < curve_y[left_pos + 1]:
+                left_pos = left_pos - 1
+                #previous_is_lower = 1
+            else:
+                #print curve_y[left_pos]
+                #print curve_y[left_pos + 1]
+                left_pos = left_pos - 1
+                previous_is_lower -= 1
+        # We are at the bottom of the event. Let's see the event jump...
+        nbr_test = round(len(curve_y) / 130)
+        previous_is_higher = nbr_test
+        while previous_is_higher and left_pos > 0:
+            if curve_y[left_pos - 1] >= curve_y[left_pos]:
+                left_pos = left_pos - 1
+#                previous_is_higher = 1
+            elif curve_y[left_pos - 1] >= curve_y[left_pos + 3]:
+                left_pos = left_pos - 1
+                #previous_is_lower =
+            else:
+                left_pos = left_pos - 1
+                previous_is_higher = previous_is_higher - 1
+        left_pos = left_pos + nbr_test
+        #print curve_x[left_pos]
+        if left_pos <= nbr_test or curve_x[left_pos] <= 5:
+            # This is a jump off contact
+            to_remove.append(event_nbr)
+        event['Slice'] = slice(left_pos, right_pos + 1)
+    for rm_nb in range(len(to_remove)):
+        #print(to_remove[rm_nb] - rm_nb)
+        event_list.pop(to_remove[rm_nb] - rm_nb)
+    return event_list
+
+
+def event_properties(curve_x, curve_y, event, spring_constant, distances,
+                     fit_method=None, poc_xy=None):
+    '''
+    Given an event, event_properties computes the properties of the events. The
+    result is returned as a dictionnary with the following keys :
+    'min' : the minimum of the event, just before the bound break
+    'max' : the maximum of the event, just after the bound break
+    'slope' : the slope of the curve that defins the bound breaking
+    'force' : the unbinding force of the event
+    'loading_rate' : the loading rate of the event
+    'fit_length' : the length of the protein found via the fit.
+    'fit_plength' : the persistent length of the protein.
+    '''
+    # Finds minimum
+    value = min(curve_y[event['Slice']])
+    event['min'] = int(list(curve_y[event['Slice']]).index(value) + \
+                   event['Slice'].start)
+    if event['min'] - event['Slice'].start == 1:
+        # Minimum and start are too close. Increase the slice size of the event
+        # to the left.
+        event['Slice'] = slice(event['Slice'].start - 1, event['Slice'].stop)
+    # Finds maximum
+    value = max(curve_y[event['min']:event['Slice'].stop])
+    event['max'] = list(curve_y[event['min']:
+                        event['Slice'].stop]).index(value) + event['min']
+    if event['max'] > len(curve_x):
+        event['max'] = len(curve_x)
+    # Find jumpSlope
+    event['slope'] = ((curve_y[event['max']] - curve_y[event['min']]) /
+                       (curve_x[event['max']] - curve_x[event['min']]))
+    # Find loading rage
+    if event['Slice'].start == event['min']:
+        event['loading_rate'] = num.nan
+    else:
+        event['loading_rate'] = -((curve_y[event['Slice'].start] -
+                                                    curve_y[event['min']]) /
+                              (curve_x[event['Slice'].start] -
+                                                    curve_x[event['min']]))
+    # Find force
+    event['force'] = (curve_y[event['max']] - curve_y[event['min']]) * \
+                     spring_constant
+    event['force_base'] = (curve_y[-1] - curve_y[event['min']]) * \
+                          spring_constant
+    #print('Force : %f, Force_base : %f')%(event['force'], event['force_base'])
+    #print('Curve 0 : %f, Curve -1 : %f, ')%(curve_y[0], curve_y[-1])
+    #print('Event max : %f')%(curve_y[event['max']])
+    # find distance
+    event['dist'] = distances[event['min']]
+    ## integrate with PoCposition
+    # Perfor the fit on the event.
+    if event_fit:
+        [length, plength, fit_x, fit_y] = event_fit(curve_x, curve_y, event,
+                                            method=fit_method,
+                                            spring_constant=spring_constant,
+                                            poc_xy=poc_xy)
+    else:
+        [length, plength, fit_x, fit_y] = [None, None, None, None]
+
+    event['fit_length'] = length
+    event['fit_plength'] = plength
+    event['fit_x'] = fit_x
+    event['fit_y'] = fit_y
+    return event
+
+
+def find_curve_jump(curve):
+    '''
+    This function finds jumps in a curve. It returns three vectors of the same
+    size of the input vector.
+    curve_jump : filled with zeros and ones. Ones depicted position of jumps.
+    curve_mean : contain the flatten curve
+    curve_std  : contain the standard deviation measured along the curve.
+    '''
+    window_size = 10
+    curve_jump = num.zeros(len(curve))
+    curve_mean = deepcopy(curve)
+    curve_std = num.zeros(len(curve))
+    portion_std = num.std(curve)
+    for point_nbr in xrange(len(curve) - window_size):
+        curve_portion = curve[point_nbr:point_nbr + window_size]
+        indice = 0
+        middle_point = curve_portion[indice]
+        portion_mean = num.mean(curve_portion)
+        portion_std = num.std(curve_portion)
+        curve_mean[point_nbr] = portion_mean
+        curve_std[point_nbr] = portion_std
+        if middle_point < portion_mean - portion_std * 2:
+            if point_nbr + indice:
+                curve_jump[point_nbr + indice] = \
+                curve_jump[point_nbr + indice - 1] + 1
+            else:
+                curve_jump[point_nbr + indice] = 1
+    return curve_jump, curve_mean, curve_std
+
+
+def event_fit(curve_x, curve_y, event, method,
+              spring_constant=0.06, poc_xy=None):
+    '''
+        Fit the event with the correct method.
+
+        * Parameters :
+            curve_x : 1d array
+                Values of the x coordinate.
+            curve_y : 1d array
+                Values of the y coordinates.
+            event : dict
+                dictionnary as returned by event_find function.
+            method : str
+                'wlc' for worm like chain model
+                'fjc' for freely jointed chain model
+            spring_constant : float
+                The spring constant of the used cantilever
+            poc : int
+                The indice of the point of contact as detected in the approach
+                curve.
+
+        * Returns :
+            length : 1d vector
+                length[0] = length in nm.
+                lenght[1] = error in nm.
+            plength : 1d vector
+                plength[0] = persistent length in nm.
+                plenght[1] = error in nm.
+            fit_x : 1d array
+                contains the x values of the fit on the curve.
+            fit_y : 1d array
+                contains the y values of the fit on the curve.
+
+        As an example, we can get a curve with event and find event with
+        event_find :
+
+        >>> curve = open_csv_curve(CURVE_EVENT[0])
+        >>> events = event_find(curve[2], curve[3], 0, 0.06)
+
+        In order to fit with the worm like chain model :
+
+        >>> [length, plength, fit_x, fit_y] = \
+                event_fit(curve[2], curve[3], events[1], method='wlc',\
+                spring_constant=0.0554)
+
+        The result are the length and the persistent length :
+
+        >>> print('Length : %.5f, error : %.5f')%(length[0], length[1])
+        Length : 282.42567, error : 1.19537
+        >>> print('Plength : %.5f, error : %.5f')%(plength[0], plength[1])
+        Plength : 0.26088, error : 0.01271
+
+        Let's plot the result :
+
+        >>> import pylab
+        >>> wlc_plot = pylab.plot(curve[2], curve[3])
+        >>> wlc_plot = pylab.plot(fit_x, fit_y)
+        >>> pylab.savefig(FIGURE_FOLDER + 'wlc_plot.png')
+
+        Here is the same for the free joint chain model :
+
+        >>> [length, plength, fit_x, fit_y] = \
+                event_fit(curve[2], curve[3], events[1], method='fjc',\
+                spring_constant=0.0554)
+
+        You can see, in that case, that the result are close to the wlc model :
+
+        >>> print('%.3f, %.3f')%(length[0],length[1])
+        263.263, 0.865
+        >>> print('%.3f, %.3f')%(plength[0],plength[1])
+        0.253, 0.010
+
+        Let's plot the result :
+
+        >>> pylab.cla()
+        >>> fjc_plot = pylab.plot(curve[2], curve[3])
+        >>> fjc_plot = pylab.plot(fit_x, fit_y)
+        >>> pylab.savefig(FIGURE_FOLDER + 'fjc_plot.png')
+    '''
+    # extract the portion of the curve that contains the event
+    ar_event = [curve_x[event['Slice']], curve_y[event['Slice']]]
+    if poc_xy is None:
+        poc_xy = [curve_x[0], None]
+        #max_y = None
+    if method == 'wlc':
+        result, fit, p_eval, maxy = __wlc_fit(ar_event[0], ar_event[1],
+                                    poc=poc_xy[0],
+                                    spring_constant=spring_constant,
+                                    max_y=poc_xy[1])
+        # prepare the array for the fit
+        poc_indice = num.nonzero(curve_x >= poc_xy[0])[0][0]
+        new_slice = slice(poc_indice, event['Slice'].stop)  # event['min'])
+        fit_x = curve_x[new_slice]
+        fit_y = p_eval(result.beta, fit_x)
+    elif method == 'fjc':
+        result, fit, p_eval, maxy = __fjc_fit(ar_event[0], ar_event[1],
+                                    poc=poc_xy[0],
+                                    spring_constant=spring_constant,
+                                    max_y=poc_xy[1])
+#        # prepare the array for the fit
+        min_y = min(ar_event[1])
+#        if baseline is not None:
+#            max_y = baseline_y[0]
+#        else:
+#            max_y = max(ar_event[1])
+        fit_y = num.arange(min_y, maxy, (maxy - min_y) / 100)
+        fit_x = p_eval(result.beta, fit_y) + poc_xy[0]
+        #fit_x, fit_y = None, None
+    elif method in [None, 'None']:
+        return [None, None, None, None]
+    else:
+        raise TypeError('Method %s is not known.' % method)
+    return [[result.beta[0] * 1e9, result.sd_beta[0] * 1e9],
+            [result.beta[1] * 1e9, result.sd_beta[1] * 1e9],
+            fit_x, fit_y]
+
+
+def __wlc_fit(x, y, poc=0, spring_constant=0.06, baseline_y=None, max_y=None):
+    '''
+        Perform Worm Like Chain fit on the curve portion.
+
+        It's better to use "event_fit" with the option "method=wlc" as it
+        returns more comprehensive results.
+
+        * Parameters :
+            curve_x : 1d array
+                Values of the x coordinate.
+            curve_y : 1d array
+                Values of the y coordinates.
+            poc : int
+                The index of the point of contact.
+            spring_constant : float
+                The spring constant of the cantilever (in N/m)
+
+        * Returns :
+            out : odr.ODR object
+                The object from which you can get the parameters of the fit.
+            result : The parameter of the fit # we can remove it...
+
+            pevalr : fct
+                function to evaluate the fit.
+            rec_maxy
+                A conversion value to evaluate the fit.
+    '''
+    # First, we take the beginning to the lowest point.
+    new_x, new_y, rec_maxy = __prepare_event_for_fit(x, y, spring_constant,
+                                                     poc=poc, max_y=max_y)
+    # The initial condition
+    T = 285
+    L = new_x[-1] + (new_x[-1] * 0.1)
+    Lp = 0.16e-9
+    p0 = [L, Lp]
+
+    def peval(p, x):
+        """
+            Define the function to fit
+        """
+        # p[0] = L
+        # p[1] = Lp
+        Kb = 1.381e-23  # Boltzmann constant
+
+        old_settings = num.seterr(all='ignore')
+        _peval_result = ((Kb * T / p[1]) *
+                    (((x) / p[0]) + 1 / (4 * (1 - (x) / p[0]) ** 2) - 1 / 4))
+        num.seterr(**old_settings)  # restore settings
+        return _peval_result
+
+    def pevalr(p, x):
+        """
+            This is the function that will be return in order to complete the
+            fit. Usefull for pretty plots.
+        """
+        # Lp = 1e-9
+        new_x = (x - poc) * 1e-9
+        result = peval(p, new_x)
+        result = -result * 1e9 / spring_constant + rec_maxy
+        return result
+
+    # Now, we prepare the fit
+    fit_it = odr.ODR(odr.Data(new_x, new_y), odr.Model(peval), p0)
+    # And we run it
+    out = fit_it.run()
+    # Get the result and rescale it.
+    result = [new_x, peval(out.beta, new_x)]
+    result[0] = result[0] * 1e9 + poc
+    result[1] = -(result[1] * 1e9 / spring_constant) + rec_maxy
+    return [out, result, pevalr, rec_maxy]
+
+
+def __prepare_event_for_fit(x, y, spring_constant, poc=0, max_y=None):
+    min_index = num.where(y == min(y))[0][0]
+    if max_y is not None:
+        rec_maxy = max_y
+    else:
+        rec_maxy = max(y)
+    new_x = x[0:min_index + 1] - poc  # - x[poc]
+    new_y = y[0:min_index + 1]
+    # Then, we rescale to be in the metric system (we were in nm)
+    new_x = (new_x) * 1e-9
+    new_y = -(new_y - rec_maxy) * 1e-9 * spring_constant  # * 0.06
+    return new_x, new_y, rec_maxy
+
+
+def __fjc_fit(x, y, poc=0, spring_constant=0.06, max_y=None):
+    '''
+        Perform Worm Like Chain fit on the curve portion.
+
+        It's better to use "event_fit" with the option "method=fjc" as it
+        returns more comprehensive results.
+
+        * Parameters :
+            curve_x : 1d array
+                Values of the x coordinate.
+            curve_y : 1d array
+                Values of the y coordinates.
+            poc : int
+                The index of the point of contact.
+            spring_constant : float
+                The spring constant of the cantilever (in N/m)
+
+        * Returns :
+            out : odr.ODR object
+                The object from which you can get the parameters of the fit.
+            result : The parameter of the fit # we can remove it...
+
+            pevalr : fct
+                function to evaluate the fit.
+            rec_maxy
+                A conversion value to evaluate the fit.
+    '''
+    # First, we get only the part of the curve that should be fitted.
+    new_x, new_y, rec_maxy = __prepare_event_for_fit(x, y, spring_constant,
+                                                     poc, max_y=max_y)
+    # The initial condition
+    T = 285
+    L = new_x[-1] + (new_x[-1] * 0.1)
+    Lp = 0.4e-9
+    p0 = [L, Lp]
+
+    def peval(p, y):
+        # p[0] = L
+        # p[1] = Lp
+        Kb = 1.381e-23  # Boltzmann constant
+        # Avoid zero elements in y. As force should be positive, if zero is
+        # given, it's the minimum one. Then replace by the non-zero minimum
+        # value, which should be little bit higher value.
+        y[num.nonzero(y == 0)] = min(y[num.nonzero(y != 0)])
+        return (p[0] * (1 / num.tanh((y * p[1]) / (Kb * T)) -
+                            (Kb * T) / (y * p[1])))
+
+    def pevalr(p, y):
+        """
+            This is the function that will be return in order to complete the
+            fit. Usefull for pretty plots.
+        """
+        new_y = -(y - rec_maxy) * 1e-9 * spring_constant
+        result = peval(p, new_y)
+        result = result * 1e9
+        return result
+    # Prepare the fit
+    fit_it = odr.ODR(odr.Data(new_y, new_x), odr.Model(peval), p0)
+    # And we run it
+    out = fit_it.run()
+    # Get the result and rescale it.
+    result = [new_y, peval(out.beta, new_y)]
+    result[0], result[1] = result[1], result[0]
+    result[0] = result[0] * 1e9
+    result[1] = -(result[1] * 1e9 / 0.06 - rec_maxy)
+    return [out, result, pevalr, rec_maxy]
+
+
+if __name__ == '__main__':
+    import doctest
+    doctest.testmod()

Added: trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/fovea_toolbox/file_util/__init__.py
===================================================================
Added: trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/fovea_toolbox/file_util/aex.py
===================================================================
--- trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/fovea_toolbox/file_util/aex.py	                        (rev 0)
+++ trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/fovea_toolbox/file_util/aex.py	2012-08-20 10:43:48 UTC (rev 12094)
@@ -0,0 +1,710 @@
+from xml.dom.minidom import Document, parse
+import os
+import commands
+import tempfile
+import zipfile
+from datetime import datetime
+from distutils.version import StrictVersion
+import pdb
+
+import numpy
+from numpy import array, Inf, inf, NaN, nan
+
+import succellus_import
+
+from common import Variables
+GLOB_VARS = Variables()
+
+version = '0.1a68'
+
+###
+# 0.1a68 : Add PoCNoise array.
+# 0.1a67 : Add event length and persistent length.
+
+
+# TODO correct the small error while saving the event force. I get an error of
+# ~2e-12 between original and saved data (see aexTest, I had to change a
+# assertEqual to assertAlmostEqual)
+def save(fv_folder_object, file_name):
+    '''
+    Save a FVFolder object to an aex file.
+    '''
+    tmp_dir = tempfile.mkdtemp()
+    if not os.path.splitext(file_name)[1] == '.aex':
+        file_name = file_name + '.aex'
+    save_exp(fv_folder_object, tmp_dir, version)
+    start_path = os.path.split(file_name)[0]
+    for fv_object in fv_folder_object.file['list']:
+        if fv_object.header['data_location'] not in ['local', u'local']:
+            curr_path = os.path.split(fv_object.header['data_location'])[0]
+            rel_path = os.path.relpath(curr_path, start_path)
+            fv_object.header['data_location'] = os.path.join(
+                           rel_path,
+                           os.path.split(fv_object.header['data_location'])[1])
+        save_fv(fv_object, tmp_dir, version)
+    mime_type = open(os.path.join(tmp_dir,'mimetype'), 'wb')
+    mime_type.write('application/afm.aex.data')
+    mime_type.close()
+    # Compress all files in the zip
+    aex_file = zipfile.ZipFile(file_name,'w')
+    
+    for item in os.listdir(tmp_dir):
+        if os.path.isfile(os.path.join(tmp_dir, item)):
+            aex_file.write(os.path.join(tmp_dir, item), item)
+            os.remove(os.path.join(tmp_dir, item))
+    for item in os.listdir(os.path.join(tmp_dir, 'data')):
+        aex_file.write(os.path.join(tmp_dir, 'data', item), 
+                       os.path.join('data', item))
+        os.remove(os.path.join(tmp_dir, 'data', item))
+    aex_file.close()
+    os.rmdir(os.path.join(tmp_dir, 'data'))
+    os.rmdir(tmp_dir)
+    
+def save_exp(fv_folder, base_dir, version):
+    exp_tree = Document()
+    exp_node = exp_tree.createElement('fvfolder')
+    exp_node.setAttribute('xmlns:openfovea','initiator_software')
+    exp_node.setAttribute('openfovea:version', version)
+    
+    info_node = exp_tree.createElement('info')
+    #####
+    # Date node
+    date_node = exp_tree.createElement('date')
+    date_element = exp_tree.createTextNode(str(fv_folder.date))
+    date_node.appendChild(date_element)
+    exp_node.appendChild(date_node)
+    # End of date node
+    #####
+    # Author node
+    author_node = exp_tree.createElement('author')
+    author_element = exp_tree.createTextNode(fv_folder.author)
+    author_node.appendChild(author_element)
+    exp_node.appendChild(author_node)
+    # End of author node
+    #####
+    # Comment node
+    comment_node = exp_tree.createElement('comment')
+    comment_element = exp_tree.createTextNode(fv_folder.comment)
+    comment_node.appendChild(comment_element)
+    exp_node.appendChild(comment_node)
+    # End of comment node
+    #####
+    # Parameters node
+    parameters_node = exp_tree.createElement('parameters')
+    for key in fv_folder.parameters:
+        parameters_node.setAttribute(key, str(fv_folder.parameters[key]))
+    exp_node.appendChild(parameters_node)
+    # End of parameters node
+    #####
+    # Group node
+    group_node = exp_tree.createElement('group')
+    for key in fv_folder.group:
+        group_node.setAttribute(key, str(fv_folder.group[key]))
+    exp_node.appendChild(group_node)
+    # End of group node
+    #####
+    exp_tree.appendChild(exp_node)
+    
+    xml_id = open(os.path.join(base_dir, 'experiment.xml'), 'wb')
+    xml_id.write(exp_tree.toprettyxml())
+    xml_id.close()
+
+def load_exp(file_name):
+    xmldoc=parse(file_name)
+    child=xmldoc.firstChild
+    #exp_dict['OF_version'] = child.getAttribute('openfovea:version')
+    exp_dict = {'date' : '',
+                'author' : '',
+                'comment': '',
+                'parameters' : {'event_detect_weight' : None,
+                                'event_fit_model' : None,
+                                'rel_stiff_dist' : None,
+                                'injection_index' : 0,
+                                'PoC_threshold' : 2,
+                                'histo_y_rel' : False,
+                                'plot_size' : [800, 600],
+                                'plot_hist_gauss' : True,
+                                },
+                'group' : { 'id' : [],
+                            'label' : [],
+                            'display' : []},
+                'OF_version' : child.getAttribute('openfovea:version')
+                }
+    for elm in child.childNodes:
+        if elm.nodeName in exp_dict.keys():
+            if elm.nodeName == 'parameters':
+                for key in exp_dict['parameters'].keys():
+                    string = elm.getAttribute(key)
+                    if len(string):
+                        try:
+                            exp_dict['parameters'][key] = eval(string)
+                        except NameError:
+                            exp_dict['parameters'][key] = str(string)
+            elif elm.nodeName == 'group':
+                for key in exp_dict['group'].keys():
+                    exp_dict['group'][key] = eval(elm.getAttribute(key))
+            else:
+                string = elm.childNodes[0].data
+                string = string.replace('\n\t\t','')
+                string = string.replace('\n\t','')
+                #for key in exp_dict.keys:
+                if elm.nodeName == 'date':
+                    exp_dict['date'] = datetime.strptime(string, 
+                                                        '%Y-%m-%d %H:%M:%S.%f')
+                else:
+                    exp_dict[elm.nodeName] = string      
+    exp_dict['parameters']['rel_stiff_dist'] = int(exp_dict['parameters']['rel_stiff_dist'])
+    return exp_dict
+    
+def save_fv(fv_object, base_dir, version):
+    '''
+    Save a single force volume file to an xml file.
+    '''
+    fv_tree = Document()
+    
+    force_volume_node = fv_tree.createElement('fvfile')
+    force_volume_node.setAttribute('xmlns:array','numpy_array')
+    force_volume_node.setAttribute('xmlns:openfovea','initiator_software')
+    force_volume_node.setAttribute('openfovea:version', version)
+    force_volume_node.setAttribute('filename', fv_object.name)
+    
+    header_node = fv_tree.createElement('header')
+    for key in fv_object.header:
+        if key == 'x_factor':
+            header_node.setAttribute(key, '%.15f'%fv_object.header[key])
+        elif key == 'date':
+            header_node.setAttribute(key, str(fv_object.header[key]))
+        elif key == 'note':
+            header_node.setAttribute(key, fv_object.header[key].__repr__())
+        elif key == 'index_array':
+            _node = __node_array(fv_tree.createElement('index_array'),
+                                 fv_object.header[key],
+                                 'index',
+                                 fv_object.name,
+                                 base_dir)
+            if _node is not None:
+                force_volume_node.appendChild(_node)
+        else:
+            header_node.setAttribute(key, str(fv_object.header[key]))
+    force_volume_node.appendChild(header_node)
+
+    ## Save the switches
+    switch_node = fv_tree.createElement('switch')
+    for key in fv_object.get_switch('list'):
+        switch_node.setAttribute(key, str(fv_object.get_switch(key)))
+    force_volume_node.appendChild(switch_node)
+    original_switches = fv_object.get_switch('restore')
+    # Force switches to be null in order to save all the data
+    fv_object.set_switch('reset')
+    ## Piezo array
+    try:
+        __array = fv_object.get_array('Piezo')
+    except Exception as inst:
+        if 'Topography array is not loaded' in inst.message:
+            pass
+        else:
+            raise inst
+    else:
+        _node = __node_array(fv_tree.createElement('piezo_array'),
+                             __array,
+                             'piezo',
+                             fv_object.name,
+                             base_dir)
+        if _node is not None:
+            force_volume_node.appendChild(_node)
+    ## Stiffness header
+    stiffness_header_node = fv_tree.createElement('stiffness_header')
+    for key in fv_object.stiffness:
+        stiffness_header_node.setAttribute(key, str(fv_object.stiffness[key]))
+    force_volume_node.appendChild(stiffness_header_node)
+    ## Stiffness array
+    st_array = fv_object.get_array('Stiffness')
+    if type(st_array) == numpy.ma.core.MaskedArray:
+        stiffness_node = fv_tree.createElement('stiffness')
+        #stiffness_node.setAttribute('shape',str(st_array.shape))
+#        for key in fv_object.stiffness:
+#            stiffness_node.setAttribute(key, str(fv_object.stiffness[key]))
+        
+        stiff_data_node = fv_tree.createElement('data')
+        rel_name = 'data/' + fv_object.name + '_stiffness.data'
+        abs_name = os.path.join(base_dir, 'data', fv_object.name + '_stiffness.data')
+        stiff_data_node.setAttribute('shape', str(st_array.data.shape))
+        stiff_data_node.setAttribute('array:href', rel_name)
+        __save_array(st_array.data, abs_name)
+        stiffness_node.appendChild(stiff_data_node)
+        
+        stiff_mask_node = fv_tree.createElement('mask')
+        rel_name = 'data/' + fv_object.name + '_stiffness_mask.data'
+        abs_name = os.path.join(base_dir, 'data', fv_object.name + '_stiffness_mask.data')
+        stiff_mask_node.setAttribute('shape', str(st_array.mask.shape))
+        stiff_mask_node.setAttribute('array:href', rel_name)
+        __save_array(st_array.mask.astype(float), abs_name)
+        stiffness_node.appendChild(stiff_mask_node)
+        
+        force_volume_node.appendChild(stiffness_node)
+        
+    # Mask array
+    _node = __node_array(fv_tree.createElement('mask_array'),
+                             fv_object.get_array('Mask'),
+                             'mask', fv_object.name, base_dir)
+    if _node is not None:
+        force_volume_node.appendChild(_node)
+    ## PoC array
+    _node = __node_array(fv_tree.createElement('poc_array'),
+                             fv_object.get_array('PoCIndice'),
+                             'poc_indice', fv_object.name, base_dir)
+    if _node is not None:
+        force_volume_node.appendChild(_node)
+    ## PoC Noise array
+    _node = __node_array(fv_tree.createElement('pocnoise_array'),
+                            fv_object.get_array('PoCNoise'),
+                            'poc_noise', fv_object.name, base_dir)
+    if _node is not None:
+        force_volume_node.appendChild(_node)
+    ## Topography array
+    _node = __node_array(fv_tree.createElement('topo_array'),
+                             fv_object.get_array('Topography'),
+                             'topography', fv_object.name, base_dir)
+    if _node is not None:
+        force_volume_node.appendChild(_node)
+    ## Event array
+    _node = __node_array(fv_tree.createElement('event'),
+                             fv_object.get_array('Event'),
+                             'event', fv_object.name, base_dir)
+    if _node is not None:
+        # Save the parameters of the events.
+        for key in fv_object.event:
+            if fv_object.event[key] is not None:
+                _node.setAttribute(key, str(fv_object.event[key]))
+            else:
+                pass
+        # Save also the details of the events.
+        for event in fv_object.event_list:
+            det_event_node = fv_tree.createElement('detail')
+            for key in event:
+                # TODO Putative dead code : find out when it is necessary
+#                if key == 'Stiffness':
+#                    det_event_node.setAttribute('Stiffness_data', str(list(event[key].data)))
+#                    det_event_node.setAttribute('Stiffness_mask', str(list(event[key].mask)))
+                det_event_node.setAttribute(key, str(event[key]))
+            _node.appendChild(det_event_node)
+        force_volume_node.appendChild(_node)
+    ## Random array
+    _node = __node_array(fv_tree.createElement('event_rand_array'),
+                             fv_object.get_array('Event random'),
+                             'event_random', fv_object.name, base_dir)
+    if _node is not None:
+        force_volume_node.appendChild(_node)
+    
+    # The force-distance curve :
+    curve_dict = fv_object._ForceVolume__fdcurves
+
+    data_location = fv_object.header['data_location']
+    if data_location not in ['local', u'local']:
+        pass
+    else:
+        # trace x
+        trace_x = fv_tree.createElement('trace_x_array')
+        rel_name = 'data/' + fv_object.name + '_trace_x.data'
+        abs_name = os.path.join(base_dir, 'data', fv_object.name + '_trace_x.data')
+        __save_array(curve_dict['trace_x'], abs_name)
+        trace_x.setAttribute('array:href', rel_name)
+        trace_x.setAttribute('shape',str(curve_dict['trace_x'].shape))
+        force_volume_node.appendChild(trace_x)
+        # retrace x
+        retrace_x = fv_tree.createElement('retrace_x_array')
+        rel_name = 'data/' + fv_object.name + '_retrace_x.data'
+        abs_name = os.path.join(base_dir, 'data', fv_object.name + '_retrace_x.data')
+        __save_array(curve_dict['retrace_x'], abs_name)
+        retrace_x.setAttribute('array:href', rel_name)
+        retrace_x.setAttribute('shape',str(curve_dict['retrace_x'].shape))
+        force_volume_node.appendChild(retrace_x)
+        
+        # Trace force curves
+        trace_array = fv_tree.createElement('trace_array')
+        rel_name = 'data/' + fv_object.name + '_trace.data'
+        abs_name = os.path.join(base_dir, 'data', fv_object.name + '_trace.data')
+        __save_array(curve_dict['trace_y'], abs_name)
+        trace_array.setAttribute('array:href', rel_name)
+        trace_array.setAttribute('shape',str(curve_dict['trace_y'].shape))
+        force_volume_node.appendChild(trace_array)
+            
+        # Retrace force curves
+        retrace_array = fv_tree.createElement('retrace_array')
+        rel_name = 'data/' + fv_object.name + '_retrace.data'
+        abs_name = os.path.join(base_dir, 'data', fv_object.name + '_retrace.data')
+        __save_array(curve_dict['retrace_y'], abs_name)
+        retrace_array.setAttribute('array:href', rel_name)
+        retrace_array.setAttribute('shape',str(curve_dict['retrace_y'].shape))
+        force_volume_node.appendChild(retrace_array)
+        
+    fv_tree.appendChild(force_volume_node)
+    xml_id = open(os.path.join(base_dir, fv_object.name + '.xml'), 'wb')
+    xml_id.write(fv_tree.toprettyxml())
+    xml_id.close()
+    fv_object.set_switch('restore', original_switches)
+def __node_array(array_node, array, array_name, object_name, base_dir):
+    """
+        Save the array.
+        
+        * Parameters :
+            array_node : xml node
+                The node where to put these information.
+            array : 2d numpy.array
+                The array to save.
+            array_name : str
+                The name of the array. This will be saved in the xml tree
+            object_name : str
+                The name of the fv object. This is used to relate the array to
+                the correct object when loading.
+            parent_node : xml node
+                The parent node where to put the array node.
+            base_dir : str
+                The base directory to save the data.
+    """
+    
+    if type(array) == numpy.ndarray:
+        rel_name = 'data/' + object_name + '_' + array_name + '.data'
+        abs_name = os.path.join(base_dir, 'data', object_name + '_' + array_name + '.data')
+        array_node.setAttribute('shape',str(array.shape))
+        array_node.setAttribute('array:href', rel_name)
+        __save_array(array, abs_name)
+        return array_node
+    else:
+        return None
+
+def __save_array(array, c_file_name):
+    """
+        Saves the array to a binary format.
+        
+        * Parameters :
+            array : numpy.ndarray
+                The array to save.
+            c_file_name : str
+                The filename to save it.
+                
+        * Returns :
+            None
+    """
+    
+    [directory, file_name] = os.path.split(c_file_name)
+    if not os.path.exists(directory):
+        os.makedirs(directory)
+    file_id = open(c_file_name, 'wb')
+    if type(array) == numpy.ndarray:
+        array = array.astype('float64')
+        file_id.write(array.tostring('C'))
+    file_id.close()
+
+def __load_array(elm, folder_name):
+    """
+        Loads the array from an xml node of the array type
+        
+        * Parameters :
+            elm : xml node
+                xml node with 'shape' and 'array:href' attributes.
+            folder_name : str
+                The path to the file.
+        
+        * Returns :
+            array : numpy.ndarray
+                The dimension of the array accords with 'shape' attribute of the
+                elm xml node.
+    """
+    target = os.path.join(folder_name, elm.getAttribute('array:href'))
+    shape = eval(elm.getAttribute('shape'))
+    array_id = open(target, 'rb')
+    array_str = array_id.read()
+    array = numpy.fromstring(array_str, dtype=numpy.float64)
+    return array.reshape(shape)
+def convert2current(xmldoc):
+    """
+        Convert a previous version tree in current.
+    """
+    child = xmldoc.firstChild
+    fv_dict = {'OF_version' : child.getAttribute('openfovea:version')}
+    if StrictVersion(fv_dict['OF_version']) <= StrictVersion('0.1a63'):
+        # There is no stiffness_header element.
+        # This element is in stiffness with the arrays.
+        elem = child.getElementsByTagName('stiffness')
+        if len(elem):
+            stiffness_node = elem[0]
+            stiff_header = xmldoc.createElement('stiffness_header')
+            # get the stiffness properties
+            stiff_prop = {'HertzModel' : '', 'PointCarac' : '',  'calibSens' : '',
+                          'glass' : '', 'nbParts' : '', 'sizeParts' : '',
+                          'relativeMaxDist' : '', 'PoCThreshold' : '',
+                          'PoCMethod' : u'deriv', 'recomputePoC' : u'False',
+                          'limitSlide' : u'False', 'poisson_ratio' : u'0.3', 
+                          'poc_len_slice' : u'0.33'
+                          }
+            for key in stiff_prop.keys():
+                if stiffness_node.hasAttribute(key):
+                    val = stiffness_node.getAttribute(key)
+                else:
+                    val = stiff_prop[key]
+                stiff_prop[key] = val
+            for item in S_HEADER_064_2_CURRENT:
+                val = stiff_prop[S_HEADER_064_2_CURRENT[item]]
+                stiff_header.setAttribute(item, val)
+            stiff_header.setAttribute('poc_len_slice', 0.33)
+            child.appendChild(stiff_header)
+    if StrictVersion(fv_dict['OF_version']) == StrictVersion('0.1a64'):
+        stiff_header = child.getElementsByTagName('stiffness_header')[0]
+        for item in S_HEADER_064_2_CURRENT:
+            value = stiff_header.getAttribute(S_HEADER_064_2_CURRENT[item])
+            stiff_header.removeAttribute(S_HEADER_064_2_CURRENT[item])
+            stiff_header.setAttribute(item, value)
+        stiff_header.setAttribute('poc_len_slice', 0.33)
+    if StrictVersion(fv_dict['OF_version']) <= StrictVersion('0.1a65'):
+        # The change is in the curve_x. Before it was always a 1d vector. Now,
+        # it can be also 3d vector. The node name changed from 'curve_x_array'
+        # to 'trace_x_array' and 'retrace_y_array' for the trace and retrace
+        # curve respectively.
+        node = child.getElementsByTagName('curve_x_array')[0]
+        target = node.getAttribute('array:href')
+        shape = node.getAttribute('shape')
+        trace_x = xmldoc.createElement('trace_x_array')
+        trace_x.setAttribute('array:href', target)
+        trace_x.setAttribute('shape', shape)
+        retrace_x = xmldoc.createElement('retrace_x_array')
+        retrace_x.setAttribute('array:href', target)
+        retrace_x.setAttribute('shape', shape)
+        child.appendChild(trace_x)
+        child.appendChild(retrace_x)
+    if StrictVersion(fv_dict['OF_version']) <= StrictVersion('0.1a66'):
+        # The change is in the presence of a wlc fit for events.
+        pass
+    return xmldoc
+def load_fv(file_name, curdir=''):
+    '''
+    Loads the force volume xml file and returns a dictionnary that contains the
+    datas.
+    '''
+    folder_name = os.path.split(file_name)[0]
+    xmldoc=parse(file_name)
+    child=xmldoc.firstChild
+    fv_dict = {'name' : None,
+               'header' : {},
+               'stiffness_header' : {},
+               'piezo_array' : None,
+               'topo_array' : None,
+               'poc_array' : None,
+               'pocnoise_array' : None,
+               'trace_x_array' : None,
+               'retrace_x_array' : None,
+               'trace_array' : None,
+               'retrace_array' : None,
+               'event_rand_array' : None,
+               'stiffness' : None,
+               'mask_array' : None,
+               'index_array' : None,
+               'switch' : {'mask' : 'False'},
+               'event' : {}}
+    fv_dict['name'] = child.getAttribute('filename')
+    fv_dict['OF_version'] = child.getAttribute('openfovea:version')
+    if StrictVersion(fv_dict['OF_version']) < StrictVersion(version):
+        xmldoc = convert2current(xmldoc)
+        child = xmldoc.firstChild
+    for elm in child.childNodes:
+        if elm.nodeName in fv_dict.keys():
+            if 'array' in elm.nodeName:
+                fv_dict[elm.nodeName] = __load_array(elm, folder_name)
+                if elm.nodeName == 'event_rand_array':
+                    nbr_random = elm.getAttribute('nbr_random')
+                    if len(nbr_random):
+                        ev_prop = {'nbr_random' : int(nbr_random)}
+                if elm.nodeName == 'mask_array' and fv_dict[elm.nodeName] is not None:
+                    fv_dict[elm.nodeName] = fv_dict[elm.nodeName].astype('bool')
+            elif elm.nodeName == 'stiffness_header':
+                stiff_prop = {}
+                for key, fct in zip(STIFFNESS_HEADER.keys(), STIFFNESS_HEADER.values()):
+                    fv_dict['stiffness_header'][key] = fct(elm.getAttribute(key))
+            elif elm.nodeName == 'stiffness':
+                # get the data and mask
+                for array_node in elm.childNodes:
+                    if array_node.nodeName == 'data':
+                        stiff_data = __load_array(array_node, folder_name)
+                    elif array_node.nodeName == 'mask':
+                        stiff_mask = __load_array(array_node, folder_name)
+                stiff_array = numpy.ma.MaskedArray(stiff_data,
+                                                   mask = stiff_mask)
+                fv_dict['stiffness'] = stiff_array
+            elif elm.nodeName == 'event':
+                if StrictVersion(fv_dict['OF_version']) < StrictVersion('0.1a62'):
+                    # Loading rate wasn't computed...
+                    pass
+                else:
+                    # get the event array
+                    fv_dict['event']['array'] = __load_array(elm, folder_name)
+                    # get the detail of the events
+                    detail = list()
+                    
+                    for array_node in elm.childNodes:
+                        if array_node.nodeName == 'detail':
+                            ev_det = {}
+                            ev_det['Slice'] = array_node.getAttribute('Slice')
+                            ev_det['X'] = int(array_node.getAttribute('X'))
+                            ev_det['force'] = float(array_node.getAttribute('force'))
+                            ev_det['max'] = int(array_node.getAttribute('max'))
+                            ev_det['min'] = int(array_node.getAttribute('min'))
+                            ev_det['pos_x'] = int(array_node.getAttribute('pos_x'))
+                            ev_det['pos_y'] = int(array_node.getAttribute('pos_y'))
+                            ev_det['slope'] = float(array_node.getAttribute('slope'))
+                            ev_det['loading_rate'] = float(array_node.getAttribute('loading_rate'))
+                            ev_det['dist'] = float(array_node.getAttribute('dist'))
+                            if StrictVersion(fv_dict['OF_version']) > StrictVersion('0.1a66'):
+                                ev_det['fit_length'] = eval(array_node.getAttribute('fit_length'))
+                                ev_det['fit_plength'] = eval(array_node.getAttribute('fit_plength'))
+                            else:
+                                ev_det['fit_length'] = None
+                                ev_det['fit_plength'] = None
+                            # TODO Putative dead code : find when it's necessary
+    #                        if array_node.hasAttribute('Stiffness_mask'):
+    #                            mask = eval(array_node.getAttribute('Stiffness_mask'))
+    #                            data = eval(array_node.getAttribute('Stiffness_data'))
+    #                            ev_det['Stiffness'] = numpy.ma.array(data, mask=mask)
+                            detail.append(ev_det)
+                    fv_dict['event']['detail'] = detail
+            elif elm.nodeName == 'header':
+                header_dict = GLOB_VARS.common_header
+                for key in header_dict.keys():
+                    if elm.getAttribute(key) is not '':
+                        header_dict[key] = elm.getAttribute(key)
+                    try:
+                        header_dict[key] = eval(header_dict[key])
+                    except:
+                        pass
+                try:
+                    header_dict['date'] = datetime.strptime(header_dict['date'], 
+                                                        '%Y-%m-%d %H:%M:%S.%f')
+                except ValueError:
+                    header_dict['date'] = datetime.strptime(header_dict['date'], 
+                                                        '%Y-%m-%d %H:%M:%S')
+                except TypeError:
+                    header_dict['date'] = None
+                if StrictVersion(fv_dict['OF_version']) < StrictVersion('0.1a63') :
+                    header_dict['number_curves'] = header_dict['matrix_length'] ** 2
+                if StrictVersion(fv_dict['OF_version']) < StrictVersion('0.1a64') :
+                    header_dict['event_dist_thresh'] = 0.0
+                if type(header_dict['size']) not in [list, tuple]:
+                    header_dict['size'] = (header_dict['size_x'], header_dict['size_y'])
+                if type(header_dict['scan_size']) not in [list, tuple]:
+                    header_dict['scan_size'] = (header_dict['scan_size'],
+                                                header_dict['scan_size'])
+                fv_dict['header'] = header_dict
+            elif elm.nodeName == 'switch':
+                fv_switch = {}
+                for key_nb in range(elm.attributes.length):
+                    fv_dict['switch'][elm.attributes.item(key_nb).name] = \
+                                            elm.attributes.item(key_nb).value
+
+    if fv_dict['header']['data_location'] not in ['local', u'local']:
+        data_location = fv_dict['header']['data_location']
+
+        # Get the correct path.
+        try_path = [fv_dict['header']['data_location'],
+                    os.path.join(curdir, os.path.split(fv_dict['header']['data_location'])[-1]),
+                    os.path.join(curdir, fv_dict['header']['data_location'].split('\\')[-1])]
+        
+        correct_path = [os.path.exists(__itpath) for __itpath in try_path]
+        data_location = try_path[correct_path.index(True)]
+
+        if os.path.isdir(data_location):  # Asylum case
+            fv_dict['data_fid'] = data_location
+        else :  # JPK case
+            fv_dict['data_fid'] = zipfile.ZipFile(data_location, 'r')
+
+        fv_dict['header']['data_location'] = data_location
+        fv_dict['header']['index_array'] = fv_dict['index_array']
+    return fv_dict
+    
+def load(aex_name):
+    # first unzip the file to a tmp folder
+    compressed_file = zipfile.ZipFile(aex_name)
+    tmp_dir = tempfile.mkdtemp()
+    file_list = []
+    directory_list = []
+    file_tree = []
+    for file_in in compressed_file.filelist:
+        directory = os.path.split(file_in.filename)[0]
+        if not directory == '':
+            if not os.path.isdir(os.path.join(tmp_dir,directory)):
+                directory_list.append(directory)
+                os.makedirs(os.path.join(tmp_dir, directory))
+        outfile = open(os.path.join(tmp_dir, file_in.filename), 'wb')
+        outfile.write(compressed_file.read(file_in.filename))
+        outfile.close()
+        file_list.append(file_in.filename)
+    
+    if 'mimetype' in file_list:
+        # OpenFovea version of aex
+        for file_name in file_list:
+            c_file_name = os.path.join(tmp_dir, file_name)
+            if file_name == 'experiment.xml':
+                experiment = load_exp(c_file_name)
+            elif os.path.splitext(file_name)[1] == '.xml':
+                file_tree.append(load_fv(c_file_name, curdir=os.path.split(aex_name)[0]))
+            os.remove(c_file_name)
+        for directory in directory_list:
+            os.rmdir(os.path.join(tmp_dir,directory))
+    else:
+        # Succellus version of aex, designed to disapear...
+        for file_name in file_list:
+            c_file_name = os.path.join(tmp_dir, file_name)
+            if file_name == 'experiment.xml':
+                experiment = succellus_import.xmlExtractExperiment(c_file_name)
+                os.remove(c_file_name)
+            else :
+                file_tree.append(succellus_import.xmlExtractFV(c_file_name))
+                os.remove(c_file_name)
+    os.rmdir(tmp_dir)
+    return [experiment, file_tree]
+
+STIFFNESS_HEADER_0_64 = {
+ 'HertzModel' : lambda x: x,
+ 'PoCMethod' : lambda x: x,
+ 'PoCThreshold' : lambda x: float(x),
+ 'PointCarac' : lambda x: float(x),
+ 'calibSens' : lambda x: float(x),
+ 'glass' : lambda x: float(x),
+ 'limitSlide' : lambda x: eval(x),
+ 'nbParts' : lambda x: int(x),
+ 'poisson_ratio' : lambda x: float(x),
+ 'recomputePoC' : lambda x: eval(x),
+ 'relativeMaxDist' : lambda x: int(x),
+ 'sizeParts' : lambda x: int(x)}
+
+S_HEADER_064_2_CURRENT = {
+ 'hertz_model' : 'HertzModel',
+ 'poc_method' : 'PoCMethod',
+ 'poc_threshold' : 'PoCThreshold',
+ 'point_carac' : 'PointCarac',
+ 'calib_sens' : 'calibSens',
+ 'glass' : 'glass',
+ 'limit_slide' : 'limitSlide',
+ 'nb_parts' : 'nbParts',
+ 'poisson_ratio' : 'poisson_ratio',
+ 'recompute_poc' : 'recomputePoC',
+ 'relative_max_dist' : 'relativeMaxDist',
+ 'size_parts' : 'sizeParts'}
+
+STIFFNESS_HEADER = {
+ 'hertz_model' : lambda x: x,
+ 'fit_method' : lambda x: x,
+ 'poc_method' : lambda x: x,
+ 'poc_threshold' : lambda x: float(x),
+ 'point_carac' : lambda x: float(x),
+ 'calib_sens' : lambda x: float(x),
+ 'glass' : lambda x: float(x),
+ 'limit_slide' : lambda x: eval(x),
+ 'nb_parts' : lambda x: int(x),
+ 'poisson_ratio' : lambda x: float(x),
+ 'recompute_poc' : lambda x: eval(x),
+ 'relative_max_dist' : lambda x: int(x),
+ 'size_parts' : lambda x: int(x),
+ 'poc_len_slice' : lambda x: float(x),
+}
+
+if __name__ == '__main__':
+    load_fv('../../../docs/data/files/aex_xml/0.1a64/fvfile.xml')

Added: trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/fovea_toolbox/file_util/afm_file.py
===================================================================
--- trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/fovea_toolbox/file_util/afm_file.py	                        (rev 0)
+++ trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/fovea_toolbox/file_util/afm_file.py	2012-08-20 10:43:48 UTC (rev 12094)
@@ -0,0 +1,353 @@
+#! /usr/bin/python
+# -*- coding: utf-8 -*-
+'''
+This module is used to parse the files form Digital Instrument AFM
+'''
+__author__ = "Charles Roduit <charles.roduit at gmail.com>"
+__date__ = "01.07.2007"
+__license__ = "GNU Public License (GPL) version 3"
+__version__ = "0.1"
+
+import os
+import csv
+import zipfile
+
+import numpy
+from struct import unpack
+import re
+
+import nanoscope
+import jpk
+import asylum
+import csem
+
+
+def load(file_name):
+    """
+        Get the type of the file.
+
+        >>> [header, deflection_av, deflection_re, plotx, piezo] = \
+        load(ASYLUM5_FILE)
+        >>> print plotx.shape
+        (42622,)
+        >>> print deflection_av.shape
+        (1, 1, 42622)
+        >>> [header, deflection_av, deflection_re, plotx, piezo] = \
+        load(ASYLUM5_DIR)
+        >>> print deflection_av.shape
+        (8, 8, 301)
+
+        * Parameters :
+            file_name : str
+                The file name (with the complete path) to load.
+
+        * Returns :
+            header : dict
+                The header dictionnary.
+            trace : 3D numpy.array
+                Contains the 3d array of the trace deflection.
+                trace[0,0,:] is the curve at pos_x = 0, pos_y = 0
+            retrace : 3D numpy.array
+                Contains the 3d array of the retrace deflection.
+                retrace[0,0,:] is the curve at pos_x = 0, pos_y = 0
+            plotx : 1D numpy.array
+                Contains the piezo positions (x scale).
+            piezo : 2D array
+                The height of the piezo at the end of the indentation.
+    """
+
+    value = {
+        'header': None,
+        'trace_x': None,
+        'retrace_x': None,
+        'trace_y': None,
+        'retrace_y': None,
+        'piezo': None,
+        'data_fid': None}
+    if os.path.isdir(file_name):
+        #print('directory')
+        # User wants to load a directory...
+        # Perhaps it's better to choose a single file...
+        if is_asylum_dir(file_name):
+            # This is an asylum directory.
+
+            __value = asylum.load(file_name)
+            value['piezo'] = __value['piezo']
+            value['data_fid'] = __value['fid']
+            value['header'] = __value['header']
+            header = __value['header']
+            #[trace, retrace, value['piezo'], header] = asylum.load(file_name)
+            #value['trace_y'] = trace[1]
+            #value['retrace_y'] = retrace[1]
+            #piezo = numpy.zeros(deflection_av.shape[0:2])
+            #value['trace_x'] = trace[0]
+            #value['retrace_x'] = retrace[0]
+        else:
+            raise TypeError('Not a supported AFM file format.')
+    elif is_nanoscope(file_name):
+        #print('Nanoscope')
+        header = nanoscope.lect_header(file_name)
+        [value['trace_y'], value['retrace_y']] = nanoscope.load_force_curves(
+                                                            file_name, header)
+        value['piezo'] = nanoscope.load_image(file_name, header)
+        # Creates the x vector
+        value['trace_x'] = numpy.arange(header['force_samples_per_curve']) * \
+                               header['x_factor']
+        value['retrace_x'] = value['trace_x']
+        header = nanoscope.clean_header(header)
+    elif is_jpk(file_name):
+        #print('jpk')
+        __value = jpk.load(file_name)
+        value['data_fid'] = __value['fid']
+        header = __value['header']
+#        print header
+#        trace_x = trace[0]
+#        retrace_x = retrace[0]
+#        trace_y = trace[1]
+#        retrace_y = retrace[1]
+        #value['piezo'] = jpk.load_piezo(header, value['data_fid'])
+        #piezo = numpy.zeros(trace_y.shape[0:2])
+        value['piezo'] = __value['piezo']
+    elif is_jpk_single(file_name):
+#        print('jpk_single')
+        [trace, retrace, header] = jpk.load_single(file_name)
+        value['trace_x'] = trace[0]
+        value['retrace_x'] = retrace[0]
+        value['trace_y'] = trace[1]
+        value['retrace_y'] = retrace[1]
+        value['piezo'] = numpy.zeros(value['trace_y'].shape[0:2])
+    elif is_asylum(file_name):
+        #print('asylum')
+        [trace, retrace, value['piezo'], header] = asylum.load(file_name)
+        value['trace_x'] = trace[0]
+        value['retrace_x'] = retrace[0]
+        value['trace_y'] = trace[1]
+        value['retrace_y'] = retrace[1]
+        value['piezo'] = numpy.zeros(value['trace_y'].shape[0:2])
+    elif csem.is_csem(file_name):
+        [trace, retrace, header, piezo] = csem.load(file_name)
+        value['trace_x'] = trace[0]
+        value['retrace_x'] = retrace[0]
+        value['trace_y'] = trace[1]
+        value['retrace_y'] = retrace[1]
+        value['piezo'] = piezo
+    else:
+        #print ('Not recognize')
+        raise TypeError('Not a supported AFM file format.')
+    # Add header for OpenFovea
+    header['event_dist_thresh'] = 0.0
+    header['thresh_event_fit_length'] = [None, None]
+    header['thresh_event_fit_plength'] = [None, None]
+    header['event_fit_model'] = None
+
+    value['header'] = header
+    #print value['piezo']
+    return value
+
+
+def is_nanoscope(file_name):
+    """
+    Test if the file comes from a veeco di nanoscope microscope
+
+    >>> is_nanoscope(NANOSCOPE_FILE)
+    True
+    >>> is_nanoscope(JPK_FILE)
+    False
+    """
+
+    file_id = open(file_name, 'rb')
+    line_in_mem = file_id.readline()
+    if not '\*Force file list' in line_in_mem:
+        # This is not a nanoscoe file
+        return False
+    else:
+        return True
+
+
+def is_jpk(file_name):
+    '''
+    Test if the file comes from a jpk microscope.
+
+    >>> is_jpk(JPK_FILE)
+    True
+    >>> is_jpk(ASYLUM5_FILE)
+    False
+    '''
+    this_file = open(file_name)
+    this_csv = csv.reader(this_file, delimiter=' ')
+    ftype = None
+    try:
+        first_line = this_csv.next()
+        ftype = 'csv'
+    except:  # [csv.Error, StopIteration], reason:
+        pass
+    #    return False
+    try:
+        fid = zipfile.ZipFile(file_name)
+        ftype = 'zip'
+    except:
+        pass
+    if ftype == 'csv':
+        if len(first_line) == 1:
+            return False
+        if not 'scanner:' in first_line[1]:
+            return False
+        else:
+            return True
+    elif ftype == 'zip':
+        if 'header.properties' in fid.namelist():
+            return True
+    else:
+        return False
+
+
+def is_jpk_zip(file_name):
+    '''
+    Test if the file is a zipped jpk
+    '''
+
+
+def is_jpk_single(file_name):
+    """
+        Test if the file comes from a jpk microscope and is made of a single
+        fc.
+    """
+    this_file = open(file_name)
+    this_csv = csv.reader(this_file, delimiter=' ')
+    try:
+        first_line = this_csv.next()
+    except csv.Error:
+        return False
+    if len(first_line) == 1:
+        return False
+    if not 'xPosition:' in first_line[1]:
+        return False
+    else:
+        return True
+
+
+def is_asylum(file_name):
+    """
+        Test if the file comes from an asylum microscope.
+
+        >>> is_asylum(ASYLUM5_FILE)
+        True
+        >>> is_asylum(NANOSCOPE_FILE)
+        False
+    """
+    if os.path.isdir(file_name):
+        return False
+    file_id = open(file_name)
+    ver_igor = unpack('h', file_id.read(2))[0]
+    if ver_igor in [1, 2, 3, 5]:
+        return True
+    else:
+        return False
+
+
+def is_asylum_dir(file_name):
+    """
+        Test if the directory is from asylum.
+
+        >>> is_asylum_dir(ASYLUM5_DIR)
+        True
+    """
+    if not os.path.isdir(file_name):
+        return False
+    dir_list = asylum.get_dir_list(file_name)
+    if len(dir_list) == 0:
+        return False
+    file_list = os.listdir(os.path.join(file_name, dir_list[0]))
+    _good_shape = [bool(re.match("Line\d+Point\d+.ibw", x)) for x in file_list]
+    if True in _good_shape:
+        file_list[0]
+        file_name = os.path.join(file_name, dir_list[0],
+                                 file_list[0])
+        return is_asylum(file_name)
+    else:
+        return False
+
+
+def load_curve(fid, pos, dtype, header, origin='relative'):
+    """
+        Load the curve on the fly.
+
+        * Parameters :
+            fid : instance of file id (obtained when opening a file)
+
+            pos : list : [pos_x, pos_y]
+                  The position of the curve to load.
+
+            dtype : str
+                    the curve data type to load.
+                    'trace_x', 'trace_y', 'retrace_x', 'retrace_y'
+            header : dict
+                  The microscope type.
+                  Currently supported values are : 'JPK', 'Asylum'
+            origin : str
+                     If the origin is 'relative', the curve beginns at 0.
+                     If the origin is 'absolute', the curve is not modified.
+
+        * Returns :
+            curve : array
+    """
+
+    if header['Microscope'] == 'JPK':
+        curve = jpk.load_curve(fid, pos, dtype)
+        #return jpk.load_curve(fid, pos, dtype, header['index_array'])
+    elif header['Microscope'] == 'Asylum':
+        curve = asylum.load_curve(fid, pos, dtype, header['index_array'])
+    else:
+        raise TypeError('The microscope type %s is not supported.' %
+                        header['Microscope'])
+#    if origin == 'relative':
+#        if 'x' in dtype:
+#            curve = curve - curve[0]
+#        elif 'y' in dtype:
+#            curve = curve - curve[-1]
+    if curve is None:
+        return curve
+#    if 'x' in dtype and curve[0] > curve[-1]:
+#        curve = curve[::-1]
+#    elif 'y' in dtype and curve[0] < curve[-1]:
+#        curve = curve[::-1]
+    return curve
+
+
+def force_load_array(fid, header):
+    """
+    This function loads the arrays from the NanoWizard3 zipped files.
+
+            * Parameters :
+                fid : instance of file id (obtained when opening a file)
+
+                header : dict
+                         The microscope type.
+                         Currently supported values are : 'JPK'
+
+            * Returns :
+                dictionnary with :
+                    'Index' : The index array (i.e. the folder name in the
+                              corresponding pixel) This index is generated from
+                              the coordinate in the header of each curve. This
+                              is useful if the index array automatically
+                              generated is wrong.
+                    'Piezo' : The piezo array. This is the height of the piezo
+                              at the end of the indentation. This array is used
+                              to generate the "zero force image" or "Topography
+                              image".
+    """
+
+    if header['Microscope'] == 'JPK':
+        return jpk.load_arrays(fid)
+
+if __name__ == '__main__':
+    ASYLUM5_FILE = '../../../docs/data/files/ASYLUM/Cell0005.ibw'
+    NANOSCOPE_FILE = '../../../docs/data/files/FR2310B.004'
+    JPK_FILE = \
+        '../../../docs/data/files/JPK/mappp-data-2008.11.07-11.43.24.map_txt'
+    ASYLUM5_DIR = '/home/charles/AFM/Asylum Files/Figures/Archive'
+    ASYLUM5_DIR = \
+        '/home/charles/AFM/Robert_Ross/cropstack cell1/cell100-Cropped fmap'
+    import doctest
+    doctest.testmod()

Added: trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/fovea_toolbox/file_util/asylum.py
===================================================================
--- trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/fovea_toolbox/file_util/asylum.py	                        (rev 0)
+++ trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/fovea_toolbox/file_util/asylum.py	2012-08-20 10:43:48 UTC (rev 12094)
@@ -0,0 +1,524 @@
+#! /usr/bin/env python
+#-*- coding: iso-8859-1 -*-
+
+"""
+    This module imports files from asylum microscopes. To use it make as 
+    follow :
+    
+    >>> [trace, retrace, header, piezo] = load(ASYLUM5_FILE)
+    >>> len(trace)
+    2
+    >>> len(trace[0]) == len(retrace[0])
+    True
+    
+    Trace[0] is the curve x and trace[1] is the array containing the y values
+    for all the force distance curves.
+    
+    >>> len(trace[0]) == len(trace[1][0][0])
+    True
+    
+    If you want to load a complete force spectroscopy data set :
+    
+    >>> [trace, retrace, header, piezo] = load(ASYLUM5_DIR)
+    >>> print trace[1].shape # The y arrays
+    (8, 8, 301)
+    >>> print trace[0].shape # The x array
+    (301,)
+"""
+
+__author__  = "Charles Roduit <charles.roduit at gmail.com>"
+__date__ = "20.07.2010"
+__license__ = "GNU Public License (GPL) version 3"
+__version__ = "0.1"
+
+from struct import unpack
+import os
+from datetime import datetime
+import numpy
+import re
+
+from common import Variables
+import afm_file
+#from afm_file import, is_asylum, is_asylum_dir
+GLOB_VARS = Variables()
+
+def load(file_name):
+    """
+        Load asylum file. It detects automatically if the given path is a file
+        or is an asylum path.
+        
+        * Parameters :
+            file_name : str
+                The complete path to open. The path contains the file or the
+                asylum path to open.
+        
+        * Returns :
+            trace : 3D numpy.array
+                Contains the 3d array of the trace deflection.
+                trace[0,0,:] is the curve at pos_x = 0, pos_y = 0
+            retrace : 3D numpy.array
+                Contains the 3d array of the retrace deflection.
+                retrace[0,0,:] is the curve at pos_x = 0, pos_y = 0
+            header : dict
+                Contains usefull information to understand the curves.
+            piezo : 2D numpy.array
+                The piezo position at the end of the indentation.
+        
+        To detect the type of the file see is_asylum and is_asylum_dir in
+        afm_file module.
+    """
+    value = {
+        'trace_x' : None,
+        'trace_y' : None,
+        'retrace_x' : None,
+        'retrace_y' : None,
+        'header' : None,
+        'fid' : None
+    }
+    if afm_file.is_asylum(file_name):
+        piezo = None
+        trace, retrace, header, piezo = get_file(file_name)
+        # reshape arrays to be a 3d array.
+        for key in trace:
+            trace[key].shape = (1, 1, trace[key].shape[0])
+        for key in retrace:
+            retrace[key].shape = (1, 1, retrace[key].shape[0])
+        value['trace_x'] = trace['lvdt']
+        value['trace_y'] =  trace['defl']
+        value['retrace_x'] = retrace['lvdt']
+        value['retrace_y'] =  retrace['defl']
+        value['header'] = header
+        value['piezo'] = piezo
+    elif afm_file.is_asylum_dir(file_name):
+        value['fid'], value['header'], value['piezo'] = load_dir(file_name)
+        #trace, retrace, header, piezo = load_dir(file_name)
+    value['piezo'] = value['piezo'] - value['piezo'].min()
+    return value
+    
+def load_dir(dir_name):
+    """
+        Load asylum file contained in a directory.
+        
+        * Parameters :
+            dir_name : str
+                The complete path to open.
+        
+        * Returns :
+            trace : 3D numpy.array
+                Contains the 3d array of the trace deflection.
+                trace[0,0,:] is the curve at pos_x = 0, pos_y = 0
+            retrace : 3D numpy.array
+                Contains the 3d array of the retrace deflection.
+                retrace[0,0,:] is the curve at pos_x = 0, pos_y = 0
+            header : dict
+                Contains usefull information to understand the curves.
+            piezo : 2D numpy.array
+                The piezo position at the end of the indentation.
+    """
+    dir_list = get_dir_list(dir_name)
+    size = [len(dir_list), 
+            len(get_file_list(os.path.join(dir_name, dir_list[0])))]
+    piezo = numpy.zeros((size[0], size[1]))
+    file_index = [['' for y in xrange(size[1])] for x in xrange(size[0])]#numpy.zeros((size[0], size[1]), dtype=str)
+    #trace = []
+    #retrace = []
+    header = []
+    for _item in dir_list:
+        folder_name = os.path.join(dir_name, _item)
+        file_list = get_file_list(folder_name)
+        
+        #pos_x = list(dir_list).index(_item)
+        for _f_item in file_list:
+            # File names are LineXXXXPointYYYY.ibw.
+            # We extract the pos_x and pos_y :
+            pos_x = int(_f_item[_f_item.rindex('e')+1:_f_item.rindex('P')])
+            pos_y = int(_f_item[_f_item.rindex('t')+1:_f_item.rindex('.')])
+            file_index[pos_x][pos_y] = os.path.join(folder_name, _f_item)
+            # load the file...
+            # _item[0] is trace, _item[1] is retrace, _item[2] is header and
+            # _itme[3] is piezo
+            _item = get_file(os.path.join(folder_name, _f_item))
+            #pos_y = list(file_list).index(_f_item)
+            #trace.append(_item[0])
+            #retrace.append(_item[1])
+            header.append(_item[2])
+            piezo[int(pos_x), int(pos_y)] = _item[3]
+    #length = max([len(item.values()[0]) for item in trace] + 
+    #                [len(item.values()[0]) for item in retrace])
+    #trace = reorder_curves(trace, size[0], size[1], length)
+    #retrace = reorder_curves(retrace, size[0], size[1], length)
+    header = header[0]
+    header['size_x'] = size[0]
+    header['size_y'] = size[1]
+    header['size'] = (size[0], size[1])
+    header['scan_size'] = (header['scan_size'], header['scan_size'])
+    header['number_curves'] = size[0] * size[1]
+    header['data_location'] = dir_name
+    #return [trace, retrace, header, piezo]
+    return file_index, header, piezo
+
+def reorder_curves(data, size_x, size_y, length):
+    """
+        Reorder the curves to be in two 3d array, one for the trace and one for
+        the retrace curve.
+        
+        * Parameters :
+            data : dict
+                contains a list of dictionnaries which contains at least 'lvdt'
+                and 'defl'.
+                e.g. data[0]['defl'] = array_like
+            size_x : int
+                The x size of the final array.
+            size_y : int
+                The y size of the final array.
+            length : int
+                The z size of the final array (the length of the curves).
+        
+        * Returns :
+            data : dict
+                data['lvdt'] : numpy.array
+                    Contains the 3d array of the piezo position
+                    data['lvdt'][0,0,:] is the curve at pos_x = 0, pos_y = 0
+                data['defl'] : numpy.array
+                    Contains the 3d array of the deflection
+                    data['lvdt'][0,0,:] is the curve at pos_x = 0, pos_y = 0
+    """
+    # Create the dictionnary that will contain arrays of the correct size
+    out = {}
+    for key in ['lvdt', 'defl']:#data[0].keys():
+        out[key] = numpy.empty((size_x, size_y+1, length))
+    # Fill them with the complete curves
+    pos = -1
+    for item in data:
+        pos += 1
+        for key in out:
+            if key == 'lvdt':
+                out[key][pos/size_x, pos % size_x, :] = complete_array(
+                                                                item[key],
+                                                                length,
+                                                                'add')
+            else:
+                out[key][pos/size_x, pos % size_x, :] = complete_array(
+                                                                item[key],
+                                                                length)
+    return out
+
+def complete_array(array, length, add_type='idem'):
+    """
+        Complete the array with arbitrary values at the end.
+        
+        * Parameters :
+            array : array_like
+                The array to be completed.
+            length : int
+                The final length
+            add_type : str
+                The type of completion (*default* : 'idem')
+            
+                * 'idem' : adds the same values at the end of the array
+                * 'add' : adds cummulative (n = n-1 + (n-2 - n-1)) so that the
+                          arrays increase linearly at the end.
+        
+        * Returns :
+            array : numpy array
+                The completed array.
+    """
+    array = list(array)
+    if add_type == 'idem':
+        array = numpy.r_[array, [array[-1]] * (length - len(array))]
+    elif add_type == 'add':
+        step = array[-1] - array[-2]
+        start = array[-1] + step
+        stop = start + step * (length - len(array))
+        array = numpy.r_[array, numpy.arange(start, stop, step)]
+    return array
+    
+def get_file(file_name):
+    """
+        Get the raw data and header. Need to be ordered to be incorporated in
+        OpenFovea.
+        
+        * Parameters :
+            file_name : str
+                The complete path for the file to open.
+        
+        * Returns :
+            trace : dict
+                Contains the arrays for the trace curve. This dictionnary is
+                composed of two 1D numpy array.
+                
+                * trace['lvdt'] for the x axis
+                * trace['defl'] for the deflection
+            retrace : dict
+                Contains the arrays for the retrace curve. This dictionnary is
+                composed of two 1D numpy array.
+                
+                * retrace['lvdt'] for the x axis
+                * retrace['defl'] for the deflection
+            header : dict
+                The note dictionnary
+            piezo : float
+                The height of the piezo at the end of the indentation
+    """
+    header = {}
+    file_id = open(file_name, 'rb')
+    ver_igor = unpack('=' + 'h', file_id.read(2))[0]
+    # Currently, only version 5 is supported.
+    if ver_igor == 5:
+        order = GLOB_VARS.asylum5_order
+        header_list = GLOB_VARS.asylum5_header
+    # Get the headers
+    for item in order:
+        _ud = header_list[item]
+        header[item] = _ud[2](unpack('='+_ud[0], file_id.read(_ud[1])))
+    # Some more information from the headers
+    if header['type'] != 0:
+        _ud = TYPE[header['type']]
+        data = unpack('=' + str(header['nbr_points']) + _ud[0],
+                      file_id.read(header['nbr_points'] * _ud[1]))
+        if ver_igor == 5:
+            _len = header['formula_size']
+            header['formula_data'] = unpack('=' + str(_len)+'s',
+                                            file_id.read(_len))[0]
+            _len = header['note_size']
+            note = unpack('=' + str(_len)+'s', file_id.read(_len))
+            _len = header['data_eunit_size']
+            header['extended_data_units'] = unpack('=' + str(_len) + 's',
+                                                   file_id.read(_len))[0]
+            header['dimension_units'] = [
+                        unpack('=' + str(_len) + 'c', file_id.read(_len)) 
+                        for _len in header['dim_eunit_size']
+                        ]
+            header['dimension_label'] = [
+                        unpack('=' + str(_len) + 's', file_id.read(_len))
+                        for _len in header['dim_label_size']
+                        ]
+            _len = header['string_indice_size']
+            header['string_indice'] = unpack('=' + str(_len) + 'l',
+                                             file_id.read(_len * 4))
+    data = numpy.asanyarray(data)
+    if header['n_dim'][2]:
+        raise TypeError('Problem in asylum file.\n'+
+                        'Want to reshape from array : %s to %s' %
+                        (data.shape, (header['n_dim'][1], header['n_dim'][0])))
+        
+ #       data.shape = (header['n_dim'][1], header['n_dim'][0], header['n_dim'][2])
+    else:
+        data.shape = (header['n_dim'][1], header['n_dim'][0])
+    # I should reorder the header to have the minimal.
+    header = parse_note(note[0])
+    file_id.close()
+    average = average_signal(data[1], data[2], final_length=512)
+    # Get the middle point to separate the trace from the retrace curve
+    middle_point = numpy.nonzero(average[0] == average[0].max())[0][0]
+    trace = {
+             'defl' : average[1][:middle_point][::-1] * 1e9,
+             'lvdt' : average[0][:middle_point][::-1] * -1e9,
+             }
+    retrace = {
+             'defl' : average[1][middle_point:]* 1e9,
+             'lvdt' : average[0][middle_point:]* -1e9,
+             }
+    return [trace, retrace, header, data[2].max() * -1e9]
+    
+def parse_note(note):
+    """
+        Extracts the usefull data from the note.
+        
+        * Parameters :
+            note : dict
+                The note extracted from asylum file.
+            
+        * Returns :
+            extracted : dict
+                The usefull note.
+    """
+    # Usefull data, and the way to extract them are contained in the global
+    # variable NOTE_INDEX.
+    extracted = GLOB_VARS.common_header
+    for key in NOTE_INDEX:
+        _text = NOTE_INDEX[key][0]
+        _extract = NOTE_INDEX[key][1]
+        _index = note.index(_text)
+        _end = note[_index+1:].index('\r') + _index + 1
+        sub_note = note[_index:_end]
+        extracted[key] = _extract(sub_note)
+    try:
+        extracted['date'] = datetime.strptime(
+                                extracted['strdate'] + extracted['strtime'],
+                                '%a, %b %d, %Y%I:%M:%S %p')
+    except ValueError:
+        extracted['date'] = datetime.strptime(
+                                extracted['strdate'] + extracted['strtime'],
+                                '%Y-%m-%d%I:%M:%S %p')
+    extracted['Microscope'] = 'Asylum'
+    return extracted
+
+def get_dir_list(folder):
+    """
+        
+        Gets the folder list of an asylum foler.
+        
+        Asylum folders are organized like this :
+        
+        $ ls FMLine000
+        Line0000Point0000.ibw   Line0000Point0001.ibw
+        $ ls FMLine001
+        Line0001Point0000.ibw   Line0001Point0001.ibw 
+        
+        get_asylum_folder_list simply returns the ordered folder list that match
+        this organization.
+        
+        * Parameters :
+            folder : string
+                The path for the folder.
+        
+        * Returns :
+            folder_list : list
+                The list of the folders.
+    """
+    folder_list = os.listdir(folder)
+    # we should have the first folder being filenameNNNN
+    f_index = [bool(re.match("FMLine\d+", x)) for x in folder_list]
+    try:
+        basename =  folder_list[f_index.index(True)][:-4]
+    except ValueError:
+        # There is no True elements in this folder...
+        folder_list = []
+    else:
+        f_index = [bool(x.find(basename) + 1) for x in folder_list]
+        f_index = numpy.asarray(f_index)
+        folder_list = numpy.asarray(folder_list)
+        # Get only the correct items
+        folder_list = folder_list[f_index]
+        folder_list.sort()
+    return folder_list
+
+def get_file_list(folder):
+    """
+        Gets the file list from an asylum folder.
+        
+        * Parameters :
+            folder : string
+                The path for the folder.
+            
+        * Returns :
+            file_list : list
+                The list of the files.
+    """
+    # Sort the file list
+    file_list = numpy.asarray(os.listdir(folder))
+    file_index = numpy.asarray([bool(x.find('.ibw')) for x in file_list])
+    file_list = file_list[file_index]
+    file_list.sort()
+    return file_list
+
+def load_curve(fid, pos, dtype, curve_index):
+    """
+        Load the curve on the fly.
+        
+        * Parameters :
+            fid : instance of file id (obtained when opening a file)
+            
+            pos : list : [pos_x, pos_y]
+                  The position of the curve to load.
+            
+            dtype : str
+                    'trace_x', 'trace_y', 'retrace_x', 'retrace_y'
+                  
+        * Returns :
+            curve : arraytrace['lvdt']
+    """
+    if type(fid) == list:
+        data = get_file(fid[pos[0]][pos[1]])
+    else:
+        fcfolder = os.path.join('FMLine%04i'%pos[0], 'Line%04iPoint%04i.ibw'%(pos[0], pos[1]))
+        file_path = os.path.join(fid, fcfolder)
+        data = get_file(file_path)
+    if 'retrace' in dtype:
+        data = data[1]
+    elif 'trace' in dtype:
+        data = data[0]
+    if 'x' in dtype:
+        data = data['lvdt']
+    elif 'y' in dtype:
+        data = data['defl']
+    #print fid[pos[0]][pos[1]]
+    #print pos
+    #print dtype
+    #print curve_index
+    return data
+def average_signal(signal, x_scale, win_size=100, final_length=None):
+    """
+        Average the signal versus time.
+        
+        * Parameters :
+            signal : array_like
+                the array which contains the signal
+            x_scale : array_like
+                The array which contains the x scale.
+            win_size : int
+                The size (in pixel) of the window (*Default* = 100)
+            
+        * Returns :
+            average_x : array_like
+                The array that contains the new x scale.
+            average : array_like
+                The array that contains the averaged signal
+    """
+    begin = 0
+    end = len(signal)
+    if final_length is not None:
+        win_size = int(end / final_length)
+    t_slice = numpy.arange(begin, end, win_size)
+    average = []
+    average_x = []
+    for begin, end in zip(t_slice[:-1], t_slice[1:]):
+        average.append(signal[begin:end].mean())
+        average_x.append(x_scale[begin])
+        
+    return [numpy.array(average_x), numpy.array(average)]
+
+
+NOTE_INDEX = {'spring_constant' : ['\rSpringConstant:',
+                                    lambda x : float(x[16:])],
+              'scan_size' : ['\rScanSize:', lambda x : float(x[10:]) * 1e6],
+              'size_x' : ['\rScanPoints:', lambda x : int(x[12:])],
+              'size_y' : ['\rScanLines:', lambda x : int(x[11:])],
+              'sensit_deflection' : ['\rTriggerDeflection:',
+                                     lambda x : float(x[19:])],
+              'strdate' : ['\rDate', 
+                        lambda x : x[6:]],
+              'strtime' : ['\rTime', 
+                        lambda x : x[6:]],
+              'piezo_pos' : ['\rExtendZ:', lambda x : float(x[9:]) * 1e6],
+              'number_curves': ['\rXOPVersion', lambda x : 1], # just to force 1
+              }
+MIN_HEADER = ['scan_size', 'number_curves', 'size_x', 'size_y',
+              'spring_constant', 'sensit_deflection', 'date']
+TYPE = {2 : ['f', 4], #'float',
+        8 : ['c', 1], #'char',
+        16 : ['i', 4], #'int16',
+        32 : ['l', 4],#'int32',
+        72 : None, #'ubit8',
+        80 : None, #'uint16',
+        96 : None, #'uint',
+        }
+
+if __name__ == '__main__':
+#    import sys
+#    sys.path.append(os.path.abspath('./'))
+    ASYLUM5_FILE = '../../../docs/data/files/Asylum/Cell0005.ibw'
+    ASYLUM5_DIR = '/home/charles/AFM/Asylum Files/Figures/Archive'
+    ASYLUM5_DIR2 = '/home/charles/AFM/Asylum Files/Figures/remove/CPA22_00'
+#    import pylab
+#    TRACE, RETRACE, HEADER, PIEZO = load(ASYLUM5_DIR2)
+#    pylab.plot(TRACE[0], TRACE[1][0][0], 'ro')
+#    pylab.hold(True)
+#    pylab.plot(RETRACE[0], RETRACE[1][0][0], 'bo')
+#    pylab.xlabel('Scanner extention [nm]')
+#    pylab.ylabel('Cantilever deflection [nm]')
+#    pylab.show()
+#    print header
+    import doctest
+    doctest.testmod()

Added: trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/fovea_toolbox/file_util/common.py
===================================================================
--- trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/fovea_toolbox/file_util/common.py	                        (rev 0)
+++ trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/fovea_toolbox/file_util/common.py	2012-08-20 10:43:48 UTC (rev 12094)
@@ -0,0 +1,288 @@
+# The header of a force volume file
+from datetime import datetime
+import re
+
+
+class Variables(object):
+
+    def __init__(self):
+        pass
+
+    def __getattribute__(self, key):
+        if key == 'common_header':
+            return {
+                'data_location': 'local',  # The location of the data. If
+                # local, all the data are in memory. Otherwise, the relative
+                # path to the data file is specified here.
+                'index_array': None,  # The index array. If the data are not
+                # local, the fd curves are located in separate folders. This
+                # index array contains the location for each fd curve.
+                'Microscope': None,  # The type of the microscope used.
+                'spring_constant': None,  # The spring constant of the
+                # cantilever. If the data needs no conversion, value is 1.
+                'scan_size': None,  # The size of the scan (in nm).
+                # Tuple (x, y)
+                'sensit_deflection': None,  # The sensitivity deflection
+                'number_curves': None,  # The number of curves that the file
+                # contains
+                'size_x': 0,  # The size in x direction.
+                'size_y': 0,  # The size in y direction.
+                'size': None,  # The tuple size (x, y). Goal is to replace the
+                # two previous.
+                'pixel_size': None,  # The size of the pixel.
+                'date': None,  # The date of the exeperiment.
+                'note': '/n',  # Some notes that appears on the original file.
+                'event_detect_weight': 2,  # The weight of the event
+                # detection.
+                'group': 0,  # To which group this file belongs.
+                'event_dist_thresh': 0.0,  # The event distance threshold.
+                'thresh_event_fit_length': [None, None],
+                'thresh_event_fit_plength': [None, None],
+                # The event fit model. Look at curve.event_fit to see the
+                # available models.
+                'event_fit_model': None,
+                # Tell if the event fit has to be aware or not about the point
+                # of contact.
+                'event_fit_from_poc': False,
+                'Masked': False}  # A switch to mask or not the data.}
+        if key == 'fv_header':
+            return {'Microscope': None,  # The type of the microscope used.
+                'di_version': None,  # TODO Nanoscope Specific
+                'spring_constant': None,  # The spring constant of the
+                                           # cantilever. If the data needs no
+                                           # conversion, value is 1.
+                'force_bytes_per_pixel': None,  # TODO Nanoscope Specific
+                'hard_z_scale': None,  # TODO Nanoscope Specific
+                'image_mode': 0,  # TODO Nanoscope Specific
+                # The mode. Only force volume is understood.
+                'image_scale': None,  # TODO Nanoscope Specific
+                'scan_size': None,  # The size of the scan (in nm)
+                'sensit_deflection': None,  # The sensitivity deflection
+                'sens_z_scan': None,  # TODO Nanoscope Specific
+                'force_samples_per_curve': None,  # TODO Nanoscope Specific
+                'image_number_lines': None,  # TODO Nanoscope Specific
+                'number_curves': None,  # The number of curves that the file
+                 # contains
+                'ramp_size': None,  # TODO Nanoscope Specific
+                'size_x': None,  # The size in x direction.
+                'size_y': None,  # The size in y direction.
+                # 'pixel_size': None,  # The size of the pixel.
+                'date': None,  # The date of the exeperiment.
+                'force_data_length': None,  # TODO Nanoscope Specific
+                'force_data_offset': None,  # TODO Nanoscope Specific
+                'image_length': None,  # TODO Nanoscope Specific
+                'image_offset': None,  # TODO Nanoscope Specific
+                'image_samps_per_line': None,  # TODO Nanoscope Specific
+                'matrix_length': None,  # TODO Nanoscope Specific
+                'x_factor': 1,  # TODO Nanoscope Specific
+                'note': '/n',  # Some notes that appears on the original file.
+                'event_detect_weight': 2,  # The weight of the event detection.
+                'group': 0,  # To which group this file belongs.
+                'event_dist_thresh': 0.0,   # The event distance threshold.
+                'thresh_event_fit_length': [None, None],
+                'thresh_event_fit_plength': [None, None],
+                # The event fit model. Look at curve.event_fit to see the
+                # available models.
+                'event_fit_model': None,
+                # Tell if the event fit has to be aware or not about the point
+                # of contact.
+                'event_fit_from_poc': False,
+                'Masked': False}  # A switch to mask or not the data.
+        if key == 'jpk_connector':
+            return {'fastSize:': ('scan_size', lambda x: eval(x) * 1E6),
+                    'numPoints:': ('number_curves', eval),
+                    'iLength:': ('size_x', eval),
+                    'jLength:': ('size_y', eval),
+                    'springConstant:': ('spring_constant', eval),
+                    'sensitivity:': ('sensit_deflection', eval),
+                    'date:': ('date', lambda x: datetime.strptime(x,
+                                            '%a %b %d %H:%M:%S %Z %Y'))}
+        if key == 'jpk_zip_connector':
+            return {
+        'quantitative-imaging-map.position-pattern.grid.ilength': 'size_x',
+        'quantitative-imaging-map.position-pattern.grid.jlength': 'size_y',
+        'force-scan-map.position-pattern.grid.ilength': 'size_x',
+        'force-scan-map.position-pattern.grid.jlength': 'size_y'}
+        if key == 'jpk_fc_connector':
+            return {'zRelativeEnd:': ('z_end', lambda x: eval(x)),
+                    'zRelativeStart:': ('z_start', lambda x: eval(x)),
+                    'direction:': ('direction', lambda x: x)
+                    }
+        if key == 'jpk_header':
+            return {'scanner': None,
+                    'gridPattern': None,
+                    'fastSize': None,
+                    'slowSize': None,
+                    'xOffset': None,
+                    'yOffset': None,
+                    'iLength': None,
+                    'jLength': None,
+                    'theta': None,
+                    'reflect': None,
+                    'numPoints': None,
+                    'forceSettings': None,
+                    'zRelativeStart': None,
+                    'zRelativeEnd': None,
+                    'forceBaseline': None,
+                    'forceBaselineMeasured': None,
+                    'forceRelativeSetpoint': None,
+                    'setpoint': None,
+                    'kLength': None,
+                    'zStartPauseOption': None,
+                    'zEndPauseOption': None,
+                    'tipsaverPauseOption': None,
+                    'feedbackMode': None,
+                    'traceScanTime': None,
+                    'retraceScanTime': None,
+                    'pauseBeforeFirst': None,
+                    'pauseAtStart': None,
+                    'pauseAtEnd': None,
+                    'pauseOnTipsaver': None,
+                    'scanner': None,
+                    'date': None}
+        if key == 'asylum5_header':
+            # The following is inspired from the file read_wave.m from ...
+            return {
+                    'checksum': ['h', 2, lambda x: x],  # Check sum of header
+                    # and wave header.
+                    'wfm_size': ['l', 4, lambda x: x],  # Size of wave header.
+                    'formula_size': ['l', 4, lambda x: x[0]],  # Size of the
+                    # dependency formula (0 if none).
+                    'note_size': ['l', 4, lambda x: x[0]],  # Size of the
+                    # notes...
+                    'data_eunit_size': ['l', 4, lambda x: x[0]],  # Size of the
+                    # extended data units.
+                    'dim_eunit_size': ['4l', 16, lambda x: x],  # Size of the
+                    # extended dimension unit. Need all data
+                    'dim_label_size': ['4l', 16, lambda x: x],  # Size of the
+                    # dimension labels.
+                    'string_indice_size': ['l', 4, lambda x: x[0]],  # Size of
+                    # the indices if it's a text.
+                    'option1': ['l', 4, lambda x: x],
+                    'option2': ['l', 4, lambda x: x],
+                    'next': ['l', 4, lambda x: x],
+                    'creation_date': ['l', 4, lambda x: x],
+                    'modification_date': ['l', 4, lambda x: x],
+                    'nbr_points': ['l', 4, lambda x: x[0]],
+                    'type': ['h', 2, lambda x: x[0]],  # The type of the data.
+                    # See TYPE global.
+                    'd_lock': ['h', 2, lambda x: x],  # ??
+                    'whpad1': ['c', 1, lambda x: x],
+                    'wh_version': ['h', 2, lambda x: x],
+                    'fseek': ['5c', 5, lambda x: x],
+                    'b_name': ['32c', 32, lambda x: x],
+                    'whpad2': ['l', 4, lambda x: x],
+                    'd_folder': ['l', 4, lambda x: x],
+                    'n_dim': ['4l', 16, lambda x: x],
+                    'sfa': ['4d', 32, lambda x: x],
+                    'sfb': ['4d', 32, lambda x: x],
+                    'data_units': ['4c', 4, lambda x: x],
+                    'dim_units0': ['4c', 4, lambda x: x],
+                    'dim_units1': ['4c', 4, lambda x: x],
+                    'dim_units2': ['4c', 4, lambda x: x],
+                    'dim_units3': ['4c', 4, lambda x: x],
+                    'fs_valid': ['h', 2, lambda x: x],
+                    'whpad3': ['h', 2, lambda x: x],
+                    'top_full_scale': ['d', 8, lambda x: x],  # The max and
+                    # max full scale value for wave.
+                    'bottom_full_scale': ['d', 8, lambda x: x],  # The max and
+                    # max full scale value for wave.
+                    'data_eunit': ['l', 4, lambda x: x],  # Ignore...
+                    'dim_eunits': ['4l', 16, lambda x: x],  # Ignore...
+                    'dim_labels': ['4l', 16, lambda x: x],  # Ignore...
+                    'wave_note_h': ['l', 4, lambda x: x],  # Ignore...
+                    'wh_unused': ['16l', 64, lambda x: x],  # Ignore...
+                    'a_modified': ['h', 2, lambda x: x],  # Ignore...
+                    'w_modified': ['h', 2, lambda x: x],  # Ignore...
+                    'sw_modified': ['h', 2, lambda x: x],  # Ignore...
+                    'use_bits': ['c', 1, lambda x: x],  # Ignore...
+                    'kind_bits': ['c', 1, lambda x: x],  # Ignore...
+                    'formula': ['l', 4, lambda x: x],  # Ignore...
+                    'dep_id': ['l', 4, lambda x: x],  # Ignore...
+                    'whpad4': ['h', 2, lambda x: x],  # Ignore...
+                    'src_folder': ['h', 2, lambda x: x],  # Ignore...
+                    'file_name': ['l', 4, lambda x: x],  # Ignore...
+                    's_indices': ['l', 4, lambda x: x],  # Ignore...
+                    }
+        if key == 'asylum5_order':
+            # This is the order where the header must be readen.
+            return ['checksum', 'wfm_size', 'formula_size', 'note_size',
+                    'data_eunit_size', 'dim_eunit_size', 'dim_label_size',
+                    'string_indice_size', 'option1', 'option2', 'next',
+                    'creation_date', 'modification_date', 'nbr_points', 'type',
+                    'd_lock', 'whpad1', 'wh_version', 'fseek', 'b_name',
+                    'whpad2', 'd_folder', 'n_dim', 'sfa', 'sfb', 'data_units',
+                    'dim_units0', 'dim_units1', 'dim_units2', 'dim_units3',
+                    'fs_valid', 'whpad3', 'top_full_scale',
+                    'bottom_full_scale', 'data_eunit', 'dim_eunits',
+                    'dim_labels', 'wave_note_h', 'wh_unused', 'a_modified',
+                    'w_modified', 'sw_modified', 'use_bits', 'kind_bits',
+                    'formula', 'dep_id', 'whpad4', 'src_folder', 'file_name',
+                    's_indices']
+
+# For informations:
+"""
++===========+=======================+=======================+=================+
+| Format    | C Type                | Python type           | Standard size   |
++===========+=======================+=======================+=================+
+| x         | pad byte              | no value              |                 |
++-----------+-----------------------+-----------------------+-----------------+
+| c         | char                  | string of length 1    | 1               |
++-----------+-----------------------+-----------------------+-----------------+
+| b         | signed char           | integer               | 1               |
++-----------+-----------------------+-----------------------+-----------------+
+| B         | unsigned char         | integer               | 1               |
++-----------+-----------------------+-----------------------+-----------------+
+| ?         | _Bool                 | bool                  | 1               |
++-----------+-----------------------+-----------------------+-----------------+
+| h         | short                 | integer               | 2               |
++-----------+-----------------------+-----------------------+-----------------+
+| H         | unsigned short        | integer               | 2               |
++-----------+-----------------------+-----------------------+-----------------+
+| i         | int                   | integer               | 4               |
++-----------+-----------------------+-----------------------+-----------------+
+| I         | unsigned int          | integer               | 4               |
++-----------+-----------------------+-----------------------+-----------------+
+| l         | long                  | integer               | 4               |
++-----------+-----------------------+-----------------------+-----------------+
+| L         | unsigned long         | integer               | 4               |
++-----------+-----------------------+-----------------------+-----------------+
+| q         | long long             | integer               | 8               |
++-----------+-----------------------+-----------------------+-----------------+
+| Q         | unsigned long long    | integer               | 8               |
++-----------+-----------------------+-----------------------+-----------------+
+| f         | float                 | float                 | 4               |
++-----------+-----------------------+-----------------------+-----------------+
+| d         | double                | float                 | 8               |
++-----------+-----------------------+-----------------------+-----------------+
+| s         | char[]                | string                |                 |
++-----------+-----------------------+-----------------------+-----------------+
+| p         | char[]                | string                |                 |
++-----------+-----------------------+-----------------------+-----------------+
+| P         | void *                | integer               |                 |
++-----------+-----------------------+-----------------------+-----------------+
+"""
+
+
+def extract_num(file_id, pos=0):
+    '''
+    Etract number from a string
+    '''
+    number = re.findall('([0-9]+[.0-9]*)', file_id)[pos]
+    try:
+        number = int(number)
+    except ValueError:
+        number = float(number)
+    return number
+
+
+def extract_num_rev(file_id):
+    '''
+    Etract number from a string
+    '''
+    number = re.findall('([0-9]+[.0-9]*)', file_id)[-1]
+    try:
+        number = int(number)
+    except ValueError:
+        number = float(number)
+    return number

Added: trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/fovea_toolbox/file_util/csem.py
===================================================================
--- trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/fovea_toolbox/file_util/csem.py	                        (rev 0)
+++ trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/fovea_toolbox/file_util/csem.py	2012-08-20 10:43:48 UTC (rev 12094)
@@ -0,0 +1,82 @@
+#! /usr/bin/python
+# -*- coding: utf-8 -*-
+
+import csv
+import numpy
+
+from common import Variables
+GLOB_VARS = Variables()
+
+'''
+    Read file for the csem home made microscope.
+'''
+
+
+def is_csem(file_name):
+    this_file = open(file_name)
+    this_csv = csv.reader(this_file, delimiter='\t')
+    try:
+        line = this_csv.next()
+    except:
+        return False
+    else:
+        if line[0] == '':
+            return True
+        else:
+            return False
+
+
+def load(file_name):
+    '''
+        Test if the file is from csem.
+    '''
+    header = GLOB_VARS.common_header
+    header['Microscope'] = 'csem'
+    this_file = open(file_name)
+    this_csv = csv.reader(this_file, delimiter='\t')
+    array = []
+    for line in this_csv:
+        try:
+            float(line[0])
+        except:
+            if line[0] == '':
+                # list of the cantilever
+                cantilever = line
+                array_x = []
+                array_y = numpy.empty
+            elif line[0] in ['rad/nm']:
+                convertion = [1] + [float(item) for item in line[1:]]
+            elif line[0] == 'cste raideur levier N/m':
+                spring_cst = [float(item) for item in line[1:]]
+            elif line[0] == 'position scanner':
+                pos = line
+            else:
+                print('Unknown line :')
+                print line
+        else:
+            array.append([float(item) * conv
+                          for item, conv in zip(line, convertion)])
+    # Make headers
+    header['spring_constant'] = spring_cst
+    header['number_curves'] = len(cantilever) - 1
+    # Rearange the arrays
+    array_all = numpy.asanyarray(array)
+    array_x = -array_all[:, 0]
+    array_y = array_all[:, 1:]
+    cut = array_x.argmin()
+    trace_x = array_x[:cut][::-1]
+    retrace_x = array_x[cut:]
+    trace_y = array_y[:cut, :][::-1]
+    retrace_y = array_y[cut:, :]
+    trace_y = trace_y.transpose(1, 0)
+    trace_y.shape = (trace_y.shape[0], 1, trace_y.shape[1])
+    retrace_y = retrace_y.transpose(1, 0)
+    retrace_y.shape = (retrace_y.shape[0], 1, retrace_y.shape[1])
+    # Add last header informations
+    header['size_x'] = trace_y.shape[0]
+    header['size_y'] = trace_y.shape[1]
+    header['size'] = [header['size_x'], header['size_y']]
+    header['scan_size'] = [header['size_x'], header['size_y']]
+    piezo = numpy.ones(trace_y.shape[0:2])
+    piezo = piezo * array_x[-1]
+    return [trace_x, trace_y], [retrace_x, retrace_y], header, piezo

Added: trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/fovea_toolbox/file_util/jpk.py
===================================================================
--- trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/fovea_toolbox/file_util/jpk.py	                        (rev 0)
+++ trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/fovea_toolbox/file_util/jpk.py	2012-08-20 10:43:48 UTC (rev 12094)
@@ -0,0 +1,1376 @@
+import csv
+import os
+import zipfile
+import tempfile
+from copy import deepcopy
+#from datetime import datetime
+from dateutil import parser as date_parser
+
+import numpy
+import Image
+
+from common import Variables
+GLOB_VARS = Variables()
+
+#CHANNEL_X = 'vDeflection'
+#CHANNEL_X = 'capacitiveSensorHeight' #
+CHANNEL_X = 'height'  # 'capacitiveSensorHeight'
+
+def load(file_name):
+    '''
+    Loads jpk force volume files
+    '''
+    ftype = get_file_type(file_name)
+    value = {
+        'adv_mat' : None,
+        'ret_mat' : None,
+        'header' : None,
+        'fid' : None
+    }
+    
+    if ftype == 'txt':
+        value['adv_mat'], value['ret_mat'], value['header'] = load_csv(file_name)
+        value['piezo'] = numpy.zeros(value['header']['size'])
+    elif ftype == 'zip':
+        value['fid'], value['header'] = load_zip(file_name)
+        value['piezo'] = None
+    return value
+
+def load_csv(file_name):
+    
+    this_file=open(file_name)
+    header = get_header_csv(this_file)
+    this_file.seek(0)
+    this_csv=csv.reader(this_file, delimiter=' ')
+    index=-1
+    for line in this_csv:
+        if len(line) == 3:
+            # We are in the header
+            if line[1] == 'iLength:':
+                x_size = int(line[2])
+            elif line[1] == 'jLength:':
+                y_size = int(line[2])
+            elif line[1] == 'kLength:':
+                curve_length = int(line[2])
+            elif line[1] == 'index:':
+                index = int(line[2])
+            elif line[1] == 'iIndex:':
+                x_pos = int(line[2])
+            elif line[1] == 'jIndex:':
+                y_pos = int(line[2])
+            elif line[1] == 'direction:':
+                direction = line[2]
+        elif len(line) == 1:
+            # We are between headers
+            if index == -1:
+                # We are at the very beginning and have to build the matrices
+                # that will be used to store the data.
+                shape = (x_size, y_size, curve_length)
+                adv_mat = [numpy.zeros(shape) for i in range(4)]
+                ret_mat = [numpy.zeros(shape) for i in range(4)]
+            else:
+                data_pos = 0
+            pass
+        elif len(line) == 4:
+            # We are in the datas
+            if direction == 'trace':
+                (adv_mat[0][x_pos, y_pos, data_pos],
+                 adv_mat[1][x_pos, y_pos, data_pos],
+                 adv_mat[2][x_pos, y_pos, data_pos],
+                 adv_mat[3][x_pos, y_pos, data_pos]) = line
+            elif direction == 'retrace':
+                (ret_mat[0][x_pos, y_pos, data_pos],
+                 ret_mat[1][x_pos, y_pos, data_pos],
+                 ret_mat[2][x_pos, y_pos, data_pos],
+                 ret_mat[3][x_pos, y_pos, data_pos]) = line
+            data_pos += 1
+    
+    # reorder the force curves...
+    adv_mat[0] = reorder_array(adv_mat[0], 1)
+    adv_mat[1] = reorder_array(adv_mat[1], header['spring_constant'])
+    adv_mat[2] = reorder_array(adv_mat[2], 1)
+    adv_mat[3] = reorder_array(adv_mat[3], 1)
+    ret_mat[0] = reorder_array(ret_mat[0], 1)
+    ret_mat[1] = reorder_array(ret_mat[1], header['spring_constant'])
+    ret_mat[2] = reorder_array(ret_mat[2], 1)
+    ret_mat[3] = reorder_array(ret_mat[3], 1)
+    return [adv_mat, ret_mat, header]
+
+def load_single(file_name):
+    """
+        Load jpk file made of a single force curve.
+    """
+    global_header = get_header_csv(file_name)
+    this_file=open(file_name)
+    this_csv=csv.reader(this_file, delimiter=' ')
+    index=-1
+    jpk_fv_con = GLOB_VARS.jpk_fc_connector
+    header = {}
+    vec_trace = [[],[],[],[]]
+    vec_retrace = [[],[],[],[]]
+    for line in this_csv:
+        if len(line) <= 1:
+            pass
+        elif line[0] == '#': # It's a header
+            if jpk_fv_con.has_key(line[1]):
+                key = jpk_fv_con[line[1]][0]
+                fct = jpk_fv_con[line[1]][1]
+                header[key] = fct(line[2])
+        else: # It's a data point
+            if header['direction'] == 'trace':
+                for item, vect in zip(line, vec_trace):
+                    vect.append(item)
+            if header['direction'] == 'retrace':
+                for item, vect in zip(line, vec_retrace):
+                    vect.append(item)
+    shape = (1,1,len(vec_trace[0]))
+    arr_trace = [numpy.zeros(shape) for i in range(4)]
+    
+    shape = (1,1,len(vec_retrace[0]))
+    arr_retrace = [numpy.zeros(shape) for i in range(4)]
+    
+    for i in range(4):
+        arr_trace[i][0,0,:] = numpy.asarray(vec_trace[i])
+        arr_retrace[i][0,0,:] = numpy.asarray(vec_retrace[i])
+    global_header['scan_size'] = (0, 0)
+    global_header['number_curves'] = 1
+    return [arr_trace, arr_retrace, global_header]
+
+def reorder_array(this_array, factor):
+    for x in range(this_array.shape[0]):
+        for y in range(this_array.shape[1]):
+            this_array[x,y,:] = this_array[x,y,::-1] * 1e9 / factor
+            this_array[x,y,:] = this_array[x,y,:] - min(this_array[x,y,:])
+    return this_array
+    
+def get_header_csv(file_name):
+    """
+        Get the header from files that have headers and data in the same file.
+    """
+    this_file = file_name
+    this_csv=csv.reader(this_file, delimiter=' ')
+    jpk_con = GLOB_VARS.jpk_connector
+    header = GLOB_VARS.common_header
+    for line in this_csv:
+        if len(line) > 4:
+            d_string = ''
+            for x in line[2:]: d_string = d_string + str(x) + ' '
+            d_string = d_string[:-1] # erase the last space
+            line = [line[0], line[1], d_string]
+        if len(line) == 3:
+            # We are in the header
+            if jpk_con.has_key(line[1]):
+                key = jpk_con[line[1]][0]
+                fct = jpk_con[line[1]][1]
+                
+                header[key] = fct(line[2])
+    header['matrix_length'] = header['size_x']
+    header['size'] = (header['size_x'], header['size_y'])
+    header['scan_size'] = (header['scan_size'], header['scan_size'])
+    return header
+
+
+def load_arrays(fid):
+    """
+        This function loads the arrays from the NanoWizard3 zipped files.
+
+            * Parameters :
+                None
+
+            * Returns :
+                dictionnary with :
+                    'Index' : The index array (i.e. the folder name in the
+                              corresponding pixel) This index is generated from
+                              the coordinate in the header of each curve. This
+                              is useful if the index array automatically
+                              generated is wrong.
+                    'Piezo' : The piezo array. This is the height of the piezo
+                              at the end of the indentation. This array is used
+                              to generate the "zero force image" or "Topography
+                              image".
+        If the index of curves were missgenerated or lost, we can regenerate
+        them from the headers. This take long time.
+    """
+    
+    main_header = get_header_zip(fid.open('header.properties'), htype='main')
+    shared_header = get_header_zip(fid.open('shared-data/header.properties'),
+                                            htype='shared')
+#    ############################################################################ 
+#    # Generate an index array :
+#    #
+#    index_array = numpy.empty((main_header['size_x'], main_header['size_y']),
+#                              dtype=int)
+#    index_array[:]=-1
+    piezo_array = numpy.zeros((main_header['size_x'], main_header['size_y']),
+                              dtype=float)
+#    
+#    pixel_size = [main_header['msize_x'] / main_header['size_x'],
+#                  main_header['msize_y'] / main_header['size_y']]
+#    # works if center of array is [0, 0]. Here is to modify if we have
+#    # different files. 
+#    center = [(-main_header['mcenter_x'] +
+#               (main_header['msize_x'] / 2))/pixel_size[0],
+#              (-main_header['mcenter_y'] + 
+#               (main_header['msize_y'] / 2))/pixel_size[1]]
+    for index_nb in range(main_header['index_min'], main_header['index_max']+1):
+        f_name = 'index/%s/header.properties'%index_nb
+        index_header = get_header_zip(fid.open(f_name),
+                                      htype='index')#, stop='position')
+        # Current pixel position :
+        pos = pos_from_index(index_nb,
+                             size=[main_header['size_x'], main_header['size_y']],
+                             mode=main_header['file_type'])
+#        pos = [round(index_header['mpos_x'] / pixel_size[0] + center[0]
+#                    - 0.5),
+#              round(index_header['mpos_y'] / pixel_size[1] + center[1]
+#                    - 0.5)]
+#        index_array[pos[0], pos[1]] = index_nb
+        gf = _global_factor(shared_header, CHANNEL_X)
+        
+        f_name = 'index/%i/segments/%i/'%(index_nb, 0)
+        
+        sgmt_header = get_header_zip(fid.open(f_name+'segment-header.properties'),
+                                 htype='segment')
+        sgmt_name = sgmt_header['%s.fname' % CHANNEL_X]
+        
+        curve = load_zip_curve(fid.open(f_name + sgmt_name),
+                                dtype='signedinteger',
+                                factor=gf)
+        piezo_array[pos[0], pos[1]] = curve[-1]*1e9
+    return {#'Index' : index_array,
+            'Piezo' : piezo_array}
+
+
+def load_zip(file_name):
+    """
+        Load file from zipped JPK.
+        
+        This will return only a header, as the FD curves will be loaded on
+        demand.
+    """
+    
+    header = GLOB_VARS.common_header
+    fid = zipfile.ZipFile(file_name, 'r')
+    
+    main_header = get_header_zip(fid.open('header.properties'), htype='main')
+    shared_header = get_header_zip(fid.open('shared-data/header.properties'),
+                                            htype='shared')
+    if main_header['size_unit'] == 'm':
+        main_header['msize_x'] = main_header['msize_x']*1e9
+        main_header['msize_y'] = main_header['msize_y']*1e9
+    
+    
+    header['number_curves'] = main_header['index_max'] - \
+                              main_header['index_min'] + 1
+    header['scan_size'] = [main_header['msize_x'], main_header['msize_y']]
+    header['size'] = [main_header['size_x'], main_header['size_y']]
+    header['size_x'] = main_header['size_x']
+    header['size_y'] = main_header['size_y']
+    header['data_location'] = file_name
+    header['Microscope'] = 'JPK'
+    header['sensit_deflection'] = 1
+    header['spring_constant'] = shared_header['spring_constant']
+    return [fid, header]
+
+
+def _get_lambda_factor(offset, factor):
+    return lambda x: (x+offset)*factor
+
+
+def _global_factor(header, dtype):
+    """
+        Header should be the shared header.
+        dtype : str
+                Is the type of curve you want to load.
+                'height', 'vDeflection'
+    """
+    n_index = header['name'].index(dtype) 
+    convert_list = header['conversion_list'][n_index].split(' ')
+    gf = header['encode_multiplier'][n_index]
+    of = header['encode_offset'][n_index]
+    fct = [_get_lambda_factor(of, gf)]
+    for conv_item in convert_list:
+#        t_fact = header[conv_item+'_multiplier'][n_index]
+#        t_off = header[conv_item+'_offset'][n_index]
+        if conv_item+'_multiplier' in header:
+            if type(header[conv_item+'_multiplier']) == list:
+                #print shared_header[conv_item+'_multiplier'][n_index]
+                t_fact = header[conv_item+'_multiplier'][n_index]
+            else:
+                t_fact = header[conv_item+'_multiplier']
+        else:
+            t_fact=1
+        if conv_item+'_offset' in header:
+            if type(header[conv_item+'_offset']) == list:
+                #print shared_header[conv_item+'_multiplier'][n_index]
+                t_off = header[conv_item+'_offset'][n_index]
+            else:
+                t_off = header[conv_item+'_offset']
+        else:
+            t_off=0
+        fct.append(_get_lambda_factor(t_off, t_fact))
+    return fct
+
+
+def index_from_pos(pos, size, mode):
+    """
+        Generate the curve index in function of the curve position.
+        This can differ corresponding to the imaging mode used.
+
+          qi-map         force-map
+            ...             ...
+        ---------->     ----------->
+        ---------->     <-----------
+        ---------->     ----------->
+    """
+    index = 0
+    if mode == 'force-scan-map':
+        if pos[1] % 2:
+            index = pos[1] * size[0] + (size[0] - pos[0] - 1)
+        else:
+            index = pos[1] * size[0] + pos[0]
+    elif mode == 'quantitative-imaging-map':
+        index = pos[1] * size[0] + pos[0]
+    else:
+        raise TypeError('Mode %s is not known' % mode)
+    return index
+
+def pos_from_index(index, size, mode):
+    """
+        Generate the curve position in function of the curve index.
+        This can differ corresponding to the imaging mode used.
+
+          qi-map         force-map
+            ...             ...
+        ---------->     ----------->
+        ---------->     <-----------
+        ---------->     ----------->
+    """
+    pos = [0, 0]
+    if mode == 'force-scan-map':
+        pos[1] = int(index/(size[0]))
+        if pos[1] % 2:
+            pos[0] = size[0] - (index) % (size[0]) - 1
+        else:
+            pos[0] = index % (size[0])
+    elif mode == 'quantitative-imaging-map':
+        pos[1] = int(index/(size[0]))
+        pos[0] = index % (size[0])
+    else:
+        raise TypeError('Mode %s is not known' % mode)
+    return pos
+
+def load_curve(fid, index, dtype):
+    """
+        Load the curve on the fly.
+        
+        * Parameters :
+            fid : instance of file id (obtained when opening a file)
+
+            mode : str
+                   The imaging mode used (see index_from_pos for more details).
+
+            dtype : str
+                    'trace_x', 'trace_y', 'retrace_x', 'retrace_y'
+                  
+        * Returns :
+            curve : array
+        
+    """
+
+    header = get_header_zip(fid.open('header.properties'), htype='main')
+    
+    c_index = index_from_pos(index,
+                       size=[header['size_x'], header['size_y']],
+                       mode=header['file_type'])
+    # read the shared header...
+    shared_header = get_header_zip(fid.open('shared-data/header.properties'),
+                                            htype='shared')
+    
+    # Read the header for this pixel...
+    if c_index < 0:
+        return None
+    sh_name = 'index/%i/header.properties'%c_index
+    segment_header=get_header_zip(fid.open(sh_name), htype='index')
+    if 'retrace' in dtype:
+        sgmt_nbr = 1
+    elif 'trace' in dtype:
+        sgmt_nbr = 0
+    f_name = 'index/%i/segments/%i/'%(c_index, sgmt_nbr)
+    sgmt_header = get_header_zip(fid.open(f_name+'segment-header.properties'),
+                                 htype='segment')
+    if 'x' in dtype:
+        sgmt_type = CHANNEL_X
+    elif 'y' in dtype:
+        sgmt_type = 'vDeflection'
+    # Creates the conversion factors :
+    gf = _global_factor(shared_header, sgmt_type)
+    sgmt_name = sgmt_header[sgmt_type+'.fname']
+    sgmt_format = sgmt_header[sgmt_type + '.format']
+    curve = load_zip_curve(fid.open(f_name + sgmt_name),
+                                dtype='signedinteger',
+                                factor=gf)
+    #curve = curve - min(curve)
+    curve = curve*1e9
+    return curve[::-1]
+    
+
+def load_zip_curve(fid, stype='raw', dtype='signedinteger', factor=[lambda x:x]):
+    '''
+    load the curve in the file.
+    
+    * Parameters :
+        fid : file object
+              curve file extracted from the zip file.
+        stype : str
+                save type. 'raw', 'ascii'
+                default set to 'raw'
+    * Returns :
+        curve : list
+                list of point that are loaded.
+    '''
+    dtype = '>' + DTYPES[dtype]
+    array_str = fid.read()
+    array = numpy.fromstring(array_str, dtype=dtype)
+    test = 10
+    for item in factor:
+        array = item(array)
+        test = item(test)
+    
+    return array
+def get_header_zip(header_file, htype='main', stop=None):
+    '''
+    Get the headers from zip file.
+    
+    * Parameters :
+        header_file : file object
+                      header file extracted from the zip file.
+        htype : str
+                header type. 'main', 'index' or 'segment'.
+                default set to 'main'
+        
+        stop : str or None
+                if define, the execution will stop as soon as the information
+                wanted is found.
+                values are : 'position'
+    
+    * Returns :
+        header : dict
+                 dictionnary with the header with the usefull key - value pair.
+                 Values that are not usefull for OpenFovea are lost.
+    '''
+    # Every header has its first line as a date
+    date = date_parser.parse(header_file.readline()[1:])
+    if htype == 'main':
+        __header = ZIP_MAIN_HEADER
+    elif htype == 'index':
+        __header = ZIP_INDEX_HEADER
+    elif htype == 'segment':
+        __header = ZIP_SEGMENT_HEADER
+    elif htype == 'shared':
+        __header = ZIP_SHARED_HEADER
+    header = {}
+    header['date'] = date
+        
+    for line in header_file.readlines():
+        line_parse = line.split('=')
+        if htype == 'shared':
+            head_parse = line_parse[0].split('.')
+            if head_parse[1].isdigit():
+                canal_nb = head_parse[1]
+                head_parse[1] = 'xx'
+            line_parse[0] = '.'.join(head_parse)
+        
+        param = __header[line_parse[0]]
+        if htype == 'shared':
+            head_parse = param[0].split('.')
+            if len(head_parse) > 1 and (head_parse[1] == 'xx' or head_parse[1].isdigit()):
+                head_parse[1] = canal_nb
+                head_parse = '.'.join(head_parse)
+                param[0] = head_parse
+        if 'time' in line_parse[0]:
+            line_parse[1] = ''.join(line_parse[1].split('\\'))
+        if line_parse[1] in ['NaN', 'NaN\n']:
+            header[param[0]] = numpy.nan
+        else:
+            header[param[0]] = param[1](line_parse[1])
+        del(param)
+    if htype == 'shared':
+        # We reorder the header, so that we have one 'name' list, which
+        # contains the name of the channels and the converters as a 'multiplier'
+        # list which contains the corresponding converters.
+        new_header = {}
+        channel_list = {}
+        for item in header:
+            splitted = item.split('.')
+            if len(splitted) > 1 and splitted[1].isdigit():
+                if not new_header.has_key(splitted[0]):
+                    new_header[splitted[0]] = \
+                                    [1 for i in range(header['channel_count'])]
+                new_header[splitted[0]][eval(splitted[1])] = header[item]
+                if splitted[0] == 'name':
+                    channel_list[splitted[1]]=header[item]
+            else:
+                new_header[item] = header[item]
+        keys = channel_list.keys()
+        keys.sort()
+        new_header['channel_list'] = [channel_list[i] for i in keys]
+        header = new_header
+    header_file.close()
+    return header
+    
+def get_file_type(file_name):
+    if zipfile.is_zipfile(file_name):
+        ftype = 'zip'
+    else:
+        ftype = 'txt'
+    return ftype
+
+DTYPES = {'signedinteger' : 'i',
+         'unsignedinteger' : 'I'}
+
+ZIP_MAIN_HEADER = {"jpk-data-file" : ['trash', lambda x: str(x).strip('\n')],
+"file-format-version" : ['trash', lambda x: str(x).strip('\n')],
+"file-format-features" : ['trash', lambda x: str(x).strip('\n')],
+"type" : ['file_type', lambda x: str(x).strip('\n')],
+"quantitative-imaging-map.indexes.type" : ['trash', eval],
+"quantitative-imaging-map.indexes.min" : ['index_min', eval],
+"quantitative-imaging-map.indexes.max" : ['index_max', eval],
+"quantitative-imaging-map.scan-number" : ['trash', eval],
+"quantitative-imaging-map.start-time" :
+                                    ['trash',
+                                     lambda x: date_parser.parse(x)],
+"quantitative-imaging-map.end-time" : 
+                                    ['trash',
+                                    lambda x: date_parser.parse(x)],
+"quantitative-imaging-map.description.comment" :
+                                    ['trash', lambda x: str(x).strip('\n')],
+"quantitative-imaging-map.description.name" : 
+                                    ['trash', lambda x: str(x).strip('\n')],
+"quantitative-imaging-map.description.probe" :
+                                    ['trash', lambda x: str(x).strip('\n')],
+"quantitative-imaging-map.description.user-name" :
+                                    ['trash', lambda x: str(x).strip('\n')],
+"quantitative-imaging-map.description.instrument" :
+                                    ['trash', lambda x: str(x).strip('\n')],
+"quantitative-imaging-map.description.source-software" :
+                                    ['trash', lambda x: str(x).strip('\n')],
+"quantitative-imaging-map.description.modification-software" :
+                                    ['trash', lambda x: str(x).strip('\n')],
+"quantitative-imaging-map.settings.force-settings.type" :
+                                    ['trash', lambda x: str(x).strip('\n')],
+"quantitative-imaging-map.settings.force-settings.relative-setpoint" :
+                                    ['trash', eval],
+"quantitative-imaging-map.settings.force-settings.control-settings.control-settings-type" :
+                                    ['trash', lambda x: str(x).strip('\n')],
+"quantitative-imaging-map.settings.force-settings.control-settings.next-line-additional-delay" :
+                                    ['trash', eval],
+"quantitative-imaging-map.settings.force-settings.control-settings.next-line-additional-retract" :
+                                    ['trash', eval],
+"quantitative-imaging-map.settings.force-settings.control-settings.max-retries-per-position" :
+                                    ['trash', eval],
+"quantitative-imaging-map.settings.force-settings.control-settings.max-bad-adjecent-pixels" :
+                                    ['trash', eval],
+# Next, we capitalize the first letter => 'false' -> 'False' or 'true' -> 'True'
+"quantitative-imaging-map.settings.force-settings.control-settings.closed-loop" :
+                                    ['trash', lambda x: eval(x.title())],
+"quantitative-imaging-map.settings.force-settings.control-settings.start-option.type" :
+                                    ['trash', lambda x: str(x).strip('\n')],
+"quantitative-imaging-map.settings.force-settings.control-settings.start-option.additional-retract" :
+                                    ['trash', eval],
+"quantitative-imaging-map.settings.force-settings.control-settings.start-option.start-time" :
+                                    ['trash', eval],
+"quantitative-imaging-map.settings.force-settings.control-settings.start-option.motion-time" :
+                                    ['trash', eval],
+"quantitative-imaging-map.settings.force-settings.control-settings.ttl-outputs.pins.list" :
+                                    ['trash', lambda x: str(x).strip('\n')],
+"quantitative-imaging-map.settings.force-settings.control-settings.baseline-adjust-settings.enabled" :
+                                    ['trash', lambda x: eval(x.title())],
+"quantitative-imaging-map.settings.force-settings.control-settings.baseline-adjust-settings.interval" :
+                                    ['trash', eval],
+"quantitative-imaging-map.settings.force-settings.extend.type" :
+                                    ['trash', lambda x: str(x).strip('\n')],
+"quantitative-imaging-map.settings.force-settings.extend.identifier.type" :
+                                    ['trash', lambda x: str(x).strip('\n')],
+"quantitative-imaging-map.settings.force-settings.extend.identifier.name" :
+                                    ['trash', lambda x: str(x).strip('\n')],
+"quantitative-imaging-map.settings.force-settings.extend.style" :
+                                    ['trash', lambda x: str(x).strip('\n')],
+"quantitative-imaging-map.settings.force-settings.extend.duration" :
+                                    ['trash', eval],
+"quantitative-imaging-map.settings.force-settings.extend.num-points" :
+                                    ['trash', eval],
+"quantitative-imaging-map.settings.force-settings.extend.z-start" :
+                                    ['trash', eval],
+"quantitative-imaging-map.settings.force-settings.extend.z-end" :
+                                    ['trash', eval],
+"quantitative-imaging-map.settings.force-settings.extend.setpoint" :
+                                    ['trash', eval],
+"quantitative-imaging-map.settings.force-settings.retract.type" :
+                                    ['trash', lambda x: str(x).strip('\n')],
+"quantitative-imaging-map.settings.force-settings.retract.identifier.type" :
+                                    ['trash', lambda x: str(x).strip('\n')],
+"quantitative-imaging-map.settings.force-settings.retract.identifier.name" :
+                                    ['trash', lambda x: str(x).strip('\n')],
+"quantitative-imaging-map.settings.force-settings.retract.style" :
+                                    ['trash', lambda x: str(x).strip('\n')],
+"quantitative-imaging-map.settings.force-settings.retract.duration" :
+                                    ['trash', eval],
+"quantitative-imaging-map.settings.force-settings.retract.num-points" :
+                                    ['trash', eval],
+"quantitative-imaging-map.settings.force-settings.retract.z-start" :
+                                    ['trash', eval],
+"quantitative-imaging-map.settings.force-settings.retract.z-end" :
+                                    ['trash', eval],
+"quantitative-imaging-map.settings.force-settings.retract.setpoint" :
+                                    ['trash', eval],
+"quantitative-imaging-map.settings.force-settings.data-description.comment" :
+                                    ['trash', lambda x: str(x).strip('\n')],
+"quantitative-imaging-map.settings.force-settings.data-description.name" :
+                                    ['trash', lambda x: str(x).strip('\n')],
+"quantitative-imaging-map.settings.force-settings.data-description.probe" :
+                                    ['trash', lambda x: str(x).strip('\n')],
+"quantitative-imaging-map.settings.force-settings.data-description.user-name" :
+                                    ['trash', lambda x: str(x).strip('\n')],
+"quantitative-imaging-map.settings.force-settings.data-description.instrument" :
+                                    ['trash', lambda x: str(x).strip('\n')],
+"quantitative-imaging-map.settings.force-settings.data-description.source-software" :
+                                    ['trash', lambda x: str(x).strip('\n')],
+"quantitative-imaging-map.settings.force-settings.data-description.modification-software" :
+                                    ['trash', lambda x: str(x).strip('\n')],
+"quantitative-imaging-map.position-pattern.type" :
+                                    ['trash', lambda x: str(x).strip('\n')],
+"quantitative-imaging-map.position-pattern.back-and-forth" :
+                                    ['trash', lambda x: eval(x.title())],
+"quantitative-imaging-map.position-pattern.grid.xcenter" :
+                                    ['mcenter_x', eval],
+"quantitative-imaging-map.position-pattern.grid.ycenter" :
+                                    ['mcenter_y', eval],
+"quantitative-imaging-map.position-pattern.grid.ulength" :
+                                    ['msize_x', eval],
+"quantitative-imaging-map.position-pattern.grid.vlength" :
+                                    ['msize_y', eval],
+"quantitative-imaging-map.position-pattern.grid.theta" :
+                                    ['trash', eval],
+"quantitative-imaging-map.position-pattern.grid.reflect" :
+                                    ['trash', lambda x: eval(x.title())],
+"quantitative-imaging-map.position-pattern.grid.unit.type" :
+                                    ['trash', lambda x: str(x).strip('\n')],
+"quantitative-imaging-map.position-pattern.grid.unit.unit" :
+                                    ['size_unit', lambda x: str(x).strip('\n')],
+"quantitative-imaging-map.position-pattern.grid.ilength" :
+                                    ['size_x', eval],
+"quantitative-imaging-map.position-pattern.grid.jlength" :
+                                    ['size_y', eval],
+"quantitative-imaging-map.feedback-mode.name" :
+                                    ['trash', lambda x: str(x).strip('\n')],
+"quantitative-imaging-map.spm-scanner-mode.type" :
+                                    ['trash', lambda x: str(x).strip('\n')],
+"quantitative-imaging-map.spm-scanner-mode.software-linearized" :
+                                    ['trash', lambda x: eval(x.title())],
+"quantitative-imaging-map.spm-scanner-mode.xy-scanner.scanner" :
+                                    ['trash', lambda x: str(x).strip('\n')],
+"quantitative-imaging-map.spm-scanner-mode.xy-scanner.name" :
+                                    ['trash', lambda x: str(x).strip('\n')],
+"quantitative-imaging-map.spm-scanner-mode.xy-scanner.fancy-name" :
+                                    ['trash', lambda x: str(x).strip('\n')],
+"quantitative-imaging-map.spm-scanner-mode.xy-scanner.description" :
+                                    ['trash', lambda x: str(x).strip('\n')],
+"force-scan-map.indexes.type" :
+                                    ['trash', lambda x: str(x).strip('\n')],
+"force-scan-map.indexes.min" :
+                                    ['index_min', eval],
+"force-scan-map.indexes.max" :
+                                    ['index_max', eval],
+"force-scan-map.scan-number" :
+                                    ['trash', eval],
+"force-scan-map.start-time" :
+                                    ['trash', lambda x: date_parser.parse(x)],
+"force-scan-map.end-time" :
+                                    ['trash', lambda x: date_parser.parse(x)],
+"force-scan-map.comment" :
+                                    ['trash', lambda x: str(x).strip('\n')],
+"force-scan-map.description.comment" :
+                                    ['trash', lambda x: str(x).strip('\n')],
+"force-scan-map.description.name" :
+                                    ['trash', lambda x: str(x).strip('\n')],
+"force-scan-map.description.probe" :
+                                    ['trash', lambda x: str(x).strip('\n')],
+"force-scan-map.description.user-name" :
+                                    ['trash', lambda x: str(x).strip('\n')],
+"force-scan-map.description.instrument" :
+                                    ['trash', lambda x: str(x).strip('\n')],
+"force-scan-map.description.source-software" :
+                                    ['trash', lambda x: str(x).strip('\n')],
+"force-scan-map.description.modification-software" :
+                                    ['trash', lambda x: str(x).strip('\n')],
+"force-scan-map.settings.type" :
+                                    ['trash', lambda x: str(x).strip('\n')],
+"force-scan-map.settings.force-settings.type" :
+                                    ['trash', lambda x: str(x).strip('\n')],
+"force-scan-map.settings.force-settings.extend-k-length" :
+                                    ['trash', eval],
+"force-scan-map.settings.force-settings.retract-k-length" :
+                                    ['trash', eval],
+"force-scan-map.settings.force-settings.extended-pause-k-length" :
+                                    ['trash', eval],
+"force-scan-map.settings.force-settings.retracted-pause-k-length" :
+                                    ['trash', eval],
+"force-scan-map.settings.force-settings.z-start-pause-option.type" :
+                                    ['trash', lambda x: str(x).strip('\n')],
+"force-scan-map.settings.force-settings.z-end-pause-option.type" :
+                                    ['trash', lambda x: str(x).strip('\n')],
+"force-scan-map.settings.force-settings.extend-scan-time" :
+                                    ['trash', eval],
+"force-scan-map.settings.force-settings.retract-scan-time" :
+                                    ['trash', eval],
+"force-scan-map.settings.force-settings.retracted-pause-time" :
+                                    ['trash', eval],
+"force-scan-map.settings.force-settings.extended-pause-time" :
+                                    ['trash', eval],
+"force-scan-map.settings.force-settings.data-description.comment" :
+                                    ['trash', lambda x: str(x).strip('\n')],
+"force-scan-map.settings.force-settings.data-description.name" :
+                                    ['trash', lambda x: str(x).strip('\n')],
+"force-scan-map.settings.force-settings.data-description.probe" :
+                                    ['trash', lambda x: str(x).strip('\n')],
+"force-scan-map.settings.force-settings.data-description.user-name" :
+                                    ['trash', lambda x: str(x).strip('\n')],
+"force-scan-map.settings.force-settings.data-description.instrument" :
+                                    ['trash', lambda x: str(x).strip('\n')],
+"force-scan-map.settings.force-settings.data-description.source-software" :
+                                    ['trash', lambda x: str(x).strip('\n')],
+"force-scan-map.settings.force-settings.data-description.modification-software" :
+                                    ['trash', lambda x: str(x).strip('\n')],
+"force-scan-map.settings.force-settings.start-with-retract" :
+                                    ['trash', lambda x: eval(x.title())],
+"force-scan-map.settings.force-settings.control-settings-type" :
+                                    ['trash', lambda x: str(x).strip('\n')],
+"force-scan-map.settings.force-settings.closed-loop" :
+                                    ['trash', lambda x: eval(x.title())],
+"force-scan-map.settings.force-settings.start-option.type" :
+                                    ['trash', lambda x: str(x).strip('\n')],
+"force-scan-map.settings.force-settings.ttl-outputs.pins.list" :
+                                    ['trash', lambda x: str(x).strip('\n')],
+"force-scan-map.settings.force-settings.pause-before-first.type" :
+                                    ['trash', lambda x: str(x).strip('\n')],
+"force-scan-map.settings.force-settings.pause-before-first.identifier.type" :
+                                    ['trash', lambda x: str(x).strip('\n')],
+"force-scan-map.settings.force-settings.pause-before-first.identifier.name" :
+                                    ['trash', lambda x: str(x).strip('\n')],
+"force-scan-map.settings.force-settings.pause-before-first.style" :
+                                    ['trash', lambda x: str(x).strip('\n')],
+"force-scan-map.settings.force-settings.pause-before-first.duration" :
+                                    ['trash', eval],
+"force-scan-map.settings.force-settings.pause-before-first.num-points" :
+                                    ['trash', eval],
+"force-scan-map.settings.force-settings.pause-before-first.pause-option.type" :
+                                    ['trash', lambda x: str(x).strip('\n')],
+"force-scan-map.settings.force-settings.pause-before-first.height-limit" :
+                                    ['trash', eval],
+"force-scan-map.settings.force-settings.force-baseline-adjust-settings.enabled" :
+                                    ['trash', lambda x: eval(x.title())],
+"force-scan-map.settings.force-settings.force-baseline-adjust-settings.interval" :
+                                    ['trash', eval],
+"force-scan-map.settings.force-settings.force-baseline-adjust-settings.beginOfLine" :
+                                    ['trash', lambda x: eval(x.title())],
+"force-scan-map.settings.force-settings.force-baseline-adjust-settings.deadtimeBeforeSamples" :
+                                    ['trash', eval],
+"force-scan-map.settings.force-settings.force-baseline-adjust-settings.averageSamples" :
+                                    ['trash', eval],
+"force-scan-map.settings.force-settings.line-clock.active.extend" :
+                                    ['trash', lambda x: eval(x.title())],
+"force-scan-map.settings.force-settings.line-clock.active.retract" :
+                                    ['trash', lambda x: eval(x.title())],
+"force-scan-map.settings.force-settings.relative-setpoint" :
+                                    ['trash', eval],
+"force-scan-map.settings.force-settings.relative-z-start" :
+                                    ['trash', eval],
+"force-scan-map.settings.force-settings.relative-z-end" :
+                                    ['trash', eval],
+"force-scan-map.position-pattern.type" :
+                                    ['trash', lambda x: str(x).strip('\n')],
+"force-scan-map.position-pattern.back-and-forth" :
+                                    ['trash', lambda x: eval(x.title())],
+"force-scan-map.position-pattern.grid.xcenter" :
+                                    ['mcenter_x', eval],
+"force-scan-map.position-pattern.grid.ycenter" :
+                                    ['mcenter_y', eval],
+"force-scan-map.position-pattern.grid.ulength" :
+                                    ['msize_x', eval],
+"force-scan-map.position-pattern.grid.vlength" :
+                                    ['msize_y', eval],
+"force-scan-map.position-pattern.grid.theta" :
+                                    ['trash', eval],
+"force-scan-map.position-pattern.grid.reflect" :
+                                    ['trash', lambda x: eval(x.title())],
+"force-scan-map.position-pattern.grid.unit.type" :
+                                    ['trash', lambda x: str(x).strip('\n')],
+"force-scan-map.position-pattern.grid.unit.unit" :
+                                    ['size_unit', lambda x: str(x).strip('\n')],
+"force-scan-map.position-pattern.grid.ilength" :
+                                    ['size_x', eval],
+"force-scan-map.position-pattern.grid.jlength" :
+                                    ['size_y', eval],
+"force-scan-map.feedback-mode.name" :
+                                    ['trash', lambda x: str(x).strip('\n')],
+"force-scan-map.spm-scanner-mode.type" :
+                                    ['trash', lambda x: str(x).strip('\n')],
+"force-scan-map.spm-scanner-mode.software-linearized" :
+                                    ['trash', lambda x: eval(x.title())],
+"force-scan-map.spm-scanner-mode.xy-scanner.scanner" :
+                                    ['trash', lambda x: str(x).strip('\n')],
+"force-scan-map.spm-scanner-mode.xy-scanner.name" :
+                                    ['trash', lambda x: str(x).strip('\n')],
+"force-scan-map.spm-scanner-mode.xy-scanner.fancy-name" :
+                                    ['trash', lambda x: str(x).strip('\n')],
+"force-scan-map.spm-scanner-mode.xy-scanner.description" :
+                                    ['trash', lambda x: str(x).strip('\n')],
+}
+
+ZIP_INDEX_HEADER = {
+"type" :
+                                    ['trash', lambda x: str(x).strip('\n')],
+"force-scan-series.force-segments.count" :
+                                    ['count', eval],
+"force-scan-series.header.type" :
+                                    ['trash' , lambda x: str(x).strip('\n')],
+"force-scan-series.header.position.x" :
+                                    ['mpos_x', eval],
+"force-scan-series.header.position.y" :
+                                    ['mpos_y', eval],
+"force-scan-series.header.position-index" :
+                                    ['pos_index', eval],
+"force-scan-series.header.force-settings.type" :
+                                    ['trash', lambda x: str(x).strip('\n')],
+"force-scan-series.header.force-settings.extend-k-length" :
+                                    ['trash', eval],
+"force-scan-series.header.force-settings.retract-k-length" :
+                                    ['trash', eval],
+"force-scan-series.header.force-settings.extended-pause-k-length" :
+                                    ['trash', eval],
+"force-scan-series.header.force-settings.retracted-pause-k-length" :
+                                    ['trash', eval],
+"force-scan-series.header.force-settings.z-start-pause-option.type" :
+                                    ['trash', lambda x: str(x).strip('\n')],
+"force-scan-series.header.force-settings.z-end-pause-option.type" :
+                                    ['trash', lambda x: str(x).strip('\n')],
+"force-scan-series.header.force-settings.extend-scan-time" :
+                                    ['trash', eval],
+"force-scan-series.header.force-settings.retract-scan-time" :
+                                    ['trash', eval],
+"force-scan-series.header.force-settings.retracted-pause-time" :
+                                    ['trash', eval],
+"force-scan-series.header.force-settings.extended-pause-time" :
+                                    ['trash', eval],
+"force-scan-series.header.force-settings.data-description.comment" :
+                                    ['trash', lambda x: str(x).strip('\n')],
+"force-scan-series.header.force-settings.data-description.name" :
+                                    ['trash', lambda x: str(x).strip('\n')],
+"force-scan-series.header.force-settings.data-description.probe" :
+                                    ['trash', lambda x: str(x).strip('\n')],
+"force-scan-series.header.force-settings.data-description.user-name" :
+                                    ['trash', lambda x: str(x).strip('\n')],
+"force-scan-series.header.force-settings.data-description.instrument" :
+                                    ['trash', lambda x: str(x).strip('\n')],
+"force-scan-series.header.force-settings.data-description.source-software" :
+                                    ['trash', lambda x: str(x).strip('\n')],
+"force-scan-series.header.force-settings.data-description.modification-software" :
+                                    ['trash', lambda x: str(x).strip('\n')],
+"force-scan-series.header.force-settings.start-with-retract" :
+                                    ['trash', lambda x: eval(x.title())],
+"force-scan-series.header.force-settings.control-settings-type" :
+                                    ['trash', lambda x: str(x).strip('\n')],
+"force-scan-series.header.force-settings.closed-loop" :
+                                    ['trash', lambda x: eval(x.title())],
+"force-scan-series.header.force-settings.start-option.type" :
+                                    ['trash', lambda x: str(x).strip('\n')],
+"force-scan-series.header.force-settings.ttl-outputs.pins.list" :
+                                    ['trash', lambda x: str(x).strip('\n')],
+"force-scan-series.header.force-settings.pause-before-first.type" :
+                                    ['trash', lambda x: str(x).strip('\n')],
+"force-scan-series.header.force-settings.pause-before-first.identifier.type" :
+                                    ['trash', lambda x: str(x).strip('\n')],
+"force-scan-series.header.force-settings.pause-before-first.identifier.name" :
+                                    ['trash', lambda x: str(x).strip('\n')],
+"force-scan-series.header.force-settings.pause-before-first.style" :
+                                    ['trash', lambda x: str(x).strip('\n')],
+"force-scan-series.header.force-settings.pause-before-first.duration" :
+                                    ['trash', eval],
+"force-scan-series.header.force-settings.pause-before-first.num-points" :
+                                    ['trash', eval],
+"force-scan-series.header.force-settings.pause-before-first.pause-option.type" :
+                                    ['trash', lambda x: str(x).strip('\n')],
+"force-scan-series.header.force-settings.pause-before-first.height-limit" :
+                                    ['trash', eval],
+"force-scan-series.header.force-settings.force-baseline-adjust-settings.enabled" :
+                                    ['trash', lambda x: eval(x.title())],
+"force-scan-series.header.force-settings.force-baseline-adjust-settings.interval" :
+                                    ['trash', eval],
+"force-scan-series.header.force-settings.force-baseline-adjust-settings.beginOfLine" :
+                                    ['trash', lambda x: eval(x.title())],
+"force-scan-series.header.force-settings.force-baseline-adjust-settings.deadtimeBeforeSamples" :
+                                    ['trash', eval],
+"force-scan-series.header.force-settings.force-baseline-adjust-settings.averageSamples" :
+                                    ['trash', eval],
+"force-scan-series.header.force-settings.line-clock.active.extend" :
+                                    ['trash', lambda x: eval(x.title())],
+"force-scan-series.header.force-settings.line-clock.active.retract" :
+                                    ['trash', lambda x: eval(x.title())],
+"force-scan-series.header.force-settings.relative-setpoint" :
+                                    ['trash', eval],
+"force-scan-series.header.force-settings.relative-z-start" :
+                                    ['trash', eval],
+"force-scan-series.header.force-settings.relative-z-end" :
+                                    ['trash', eval],
+"force-scan-series.description.comment" :
+                                    ['trash', lambda x: str(x).strip('\n')],
+"force-scan-series.description.name" :
+                                    ['trash', lambda x: str(x).strip('\n')],
+"force-scan-series.description.probe" :
+                                    ['trash', lambda x: str(x).strip('\n')],
+"force-scan-series.description.user-name" :
+                                    ['trash', lambda x: str(x).strip('\n')],
+"force-scan-series.description.instrument" :
+                                    ['trash', lambda x: str(x).strip('\n')],
+"force-scan-series.description.source-software" :
+                                    ['trash', lambda x: str(x).strip('\n')],
+"force-scan-series.description.modification-software" :
+                                    ['trash', lambda x: str(x).strip('\n')],
+'quantitative-imaging-series.force-segments.count' :
+                                    ['count', eval],
+'quantitative-imaging-series.header.type' :
+                                    ['trash', lambda x: str(x).strip('\n')],
+'quantitative-imaging-series.header.position.x' :
+                                    ['mpos_x', eval],
+'quantitative-imaging-series.header.position.y' :
+                                    ['mpos_y', eval],
+'quantitative-imaging-series.header.position-index' :
+                                    ['pos_index', eval],
+'quantitative-imaging-series.header.quantitative-imaging-settings.type' :
+                                    ['trash', lambda x: str(x).strip('\n')],
+'quantitative-imaging-series.header.quantitative-imaging-settings.relative-setpoint' :
+                                    ['trash', eval],
+'quantitative-imaging-series.header.quantitative-imaging-settings.control-settings.control-settings-type' :
+                                    ['trash', lambda x: str(x).strip('\n')],
+'quantitative-imaging-series.header.quantitative-imaging-settings.control-settings.next-line-additional-delay' :
+                                    ['trash', eval],
+'quantitative-imaging-series.header.quantitative-imaging-settings.control-settings.next-line-additional-retract' :
+                                    ['trash', eval],
+'quantitative-imaging-series.header.quantitative-imaging-settings.control-settings.max-retries-per-position' :
+                                    ['trash', eval],
+'quantitative-imaging-series.header.quantitative-imaging-settings.control-settings.max-bad-adjecent-pixels' :
+                                    ['trash', eval],
+'quantitative-imaging-series.header.quantitative-imaging-settings.control-settings.closed-loop' :
+                                    ['trash', lambda x: eval(x.title())],
+'quantitative-imaging-series.header.quantitative-imaging-settings.control-settings.start-option.type' :
+                                    ['trash', lambda x: str(x).strip('\n')],
+'quantitative-imaging-series.header.quantitative-imaging-settings.control-settings.start-option.additional-retract' :
+                                    ['trash', eval],
+'quantitative-imaging-series.header.quantitative-imaging-settings.control-settings.start-option.start-time' :
+                                    ['trash', eval],
+'quantitative-imaging-series.header.quantitative-imaging-settings.control-settings.start-option.motion-time' :
+                                    ['trash', eval],
+'quantitative-imaging-series.header.quantitative-imaging-settings.control-settings.ttl-outputs.pins.list' :
+                                    ['trash', lambda x: str(x).strip('\n')],
+'quantitative-imaging-series.header.quantitative-imaging-settings.control-settings.baseline-adjust-settings.enabled' :
+                                    ['trash', lambda x: eval(x.title())],
+'quantitative-imaging-series.header.quantitative-imaging-settings.control-settings.baseline-adjust-settings.interval' :
+                                    ['trash', eval],
+'quantitative-imaging-series.header.quantitative-imaging-settings.extend.type' :
+                                    ['trash', lambda x: str(x).strip('\n')],
+'quantitative-imaging-series.header.quantitative-imaging-settings.extend.identifier.type' :
+                                    ['trash', lambda x: str(x).strip('\n')],
+'quantitative-imaging-series.header.quantitative-imaging-settings.extend.identifier.name' :
+                                    ['trash', lambda x: str(x).strip('\n')],
+'quantitative-imaging-series.header.quantitative-imaging-settings.extend.style' :
+                                    ['trash', lambda x: str(x).strip('\n')],
+'quantitative-imaging-series.header.quantitative-imaging-settings.extend.duration' :
+                                    ['trash', eval],
+'quantitative-imaging-series.header.quantitative-imaging-settings.extend.num-points' :
+                                    ['trash', eval],
+'quantitative-imaging-series.header.quantitative-imaging-settings.extend.z-start' :
+                                    ['trash', eval],
+'quantitative-imaging-series.header.quantitative-imaging-settings.extend.z-end' :
+                                    ['trash', eval],
+'quantitative-imaging-series.header.quantitative-imaging-settings.extend.setpoint' :
+                                    ['trash', eval],
+'quantitative-imaging-series.header.quantitative-imaging-settings.retract.type' :
+                                    ['trash', lambda x: str(x).strip('\n')],
+'quantitative-imaging-series.header.quantitative-imaging-settings.retract.identifier.type' :
+                                    ['trash', lambda x: str(x).strip('\n')],
+'quantitative-imaging-series.header.quantitative-imaging-settings.retract.identifier.name' :
+                                    ['trash', lambda x: str(x).strip('\n')],
+'quantitative-imaging-series.header.quantitative-imaging-settings.retract.style' :
+                                    ['trash', lambda x: str(x).strip('\n')],
+'quantitative-imaging-series.header.quantitative-imaging-settings.retract.duration' :
+                                    ['trash', eval],
+'quantitative-imaging-series.header.quantitative-imaging-settings.retract.num-points' :
+                                    ['trash', eval],
+'quantitative-imaging-series.header.quantitative-imaging-settings.retract.z-start' :
+                                    ['trash', eval],
+'quantitative-imaging-series.header.quantitative-imaging-settings.retract.z-end' :
+                                    ['trash', eval],
+'quantitative-imaging-series.header.quantitative-imaging-settings.retract.setpoint' :
+                                    ['trash', eval],
+'quantitative-imaging-series.header.quantitative-imaging-settings.data-description.comment' :
+                                    ['trash', lambda x: str(x).strip('\n')],
+'quantitative-imaging-series.header.quantitative-imaging-settings.data-description.name' :
+                                    ['trash', lambda x: str(x).strip('\n')],
+'quantitative-imaging-series.header.quantitative-imaging-settings.data-description.probe' :
+                                    ['trash', lambda x: str(x).strip('\n')],
+'quantitative-imaging-series.header.quantitative-imaging-settings.data-description.user-name' :
+                                    ['trash', lambda x: str(x).strip('\n')],
+'quantitative-imaging-series.header.quantitative-imaging-settings.data-description.instrument' :
+                                    ['trash', lambda x: str(x).strip('\n')],
+'quantitative-imaging-series.header.quantitative-imaging-settings.data-description.source-software' :
+                                    ['trash', lambda x: str(x).strip('\n')],
+'quantitative-imaging-series.header.quantitative-imaging-settings.data-description.modification-software' :
+                                    ['trash', lambda x: str(x).strip('\n')],
+'quantitative-imaging-series.description.comment' :
+                                    ['trash', lambda x: str(x).strip('\n')],
+'quantitative-imaging-series.description.name' :
+                                    ['trash', lambda x: str(x).strip('\n')],
+'quantitative-imaging-series.description.probe' :
+                                    ['trash', lambda x: str(x).strip('\n')],
+'quantitative-imaging-series.description.user-name' :
+                                    ['trash', lambda x: str(x).strip('\n')],
+'quantitative-imaging-series.description.instrument' :
+                                    ['trash', lambda x: str(x).strip('\n')],
+'quantitative-imaging-series.description.source-software' :
+                                    ['trash', lambda x: str(x).strip('\n')],
+'quantitative-imaging-series.description.modification-software' :
+                                    ['trash', lambda x: str(x).strip('\n')],
+}
+
+ZIP_SEGMENT_HEADER = {
+#Fri Dec 16 13:09:06 CET 2011
+'force-segment-header.force-segment-header-info.*' :
+                                    ['trash', eval],
+'force-segment-header.type' :
+                                    ['trash', lambda x: str(x).strip('\n')],
+'force-segment-header.num-points' :
+                                    ['trash', lambda x: eval(x.title())],
+'force-segment-header.duration' :
+                                    ['trash', lambda x: eval(x.title())],
+'force-segment-header.time-stamp' :
+                                    ['trash', lambda x: date_parser.parse(x)],
+'force-segment-header.baseline.baseline' :
+                                    ['trash', lambda x: eval(x.title())],
+'force-segment-header.baseline.measured' :
+                                    ['trash', lambda x: eval(x.title())],
+'force-segment-header.force-scan-flags.series-done' :
+                                    ['trash', lambda x: eval(x.title())],
+'force-segment-header.force-scan-flags.done-scanning' :
+                                    ['trash', lambda x: eval(x.title())],
+'force-segment-header.force-scan-flags.aborted' :
+                                    ['trash', lambda x: eval(x.title())],
+'force-segment-header.force-scan-flags.data-segment' :
+                                    ['trash', lambda x: eval(x.title())],
+'force-segment-header.force-scan-flags.z-start-out-of-range' :
+                                    ['trash', lambda x: eval(x.title())],
+'force-segment-header.force-scan-flags.z-end-out-of-range' :
+                                    ['trash', lambda x: eval(x.title())],
+'force-segment-header.force-scan-flags.setpoint-out-of-range' :
+                                    ['trash', lambda x: eval(x.title())],
+'force-segment-header.force-scan-flags.surface-incorrect' :
+                                    ['trash', lambda x: eval(x.title())],
+'force-segment-header.force-scan-flags.tipsaver-limit-exceeded' :
+                                    ['trash', lambda x: eval(x.title())],
+'force-segment-header.environment.xy-scanner-position-map.xy-scanners.position-index' :
+                                    ['trash', eval],
+'force-segment-header.environment.xy-scanner-position-map.xy-scanner.tip-scanner.position.x' :
+                                    ['mpos_x', lambda x: eval(x.title())],
+'force-segment-header.environment.xy-scanner-position-map.xy-scanner.tip-scanner.position.y' :
+                                    ['mpos_y', lambda x: eval(x.title())],
+'force-segment-header.environment.xy-scanner-position-map.xy-scanner.motorstage.position.x' :
+                                    ['trash', lambda x: eval(x.title())],
+'force-segment-header.environment.xy-scanner-position-map.xy-scanner.motorstage.position.y' :
+                                    ['trash', lambda x: eval(x.title())],
+'channels.list' :
+                                    ['channel_list', lambda x: str(x).strip('\n').split(' ')],
+'channel.vDeflection.lcd-info.*' :
+                                    ['trash', lambda x: eval(x.title())],
+'channel.vDeflection.data.file.name' :
+                                    ['vDeflection.fname', lambda x: str(x).strip('\n')],
+'channel.vDeflection.data.file.format' :
+                                    ['vDeflection.format', lambda x: str(x).strip('\n')],
+'channel.vDeflection.data.num-points' :
+                                    ['vDeflection.num-points', lambda x: eval(x.title())],
+'channel.error.lcd-info.*' :
+                                    ['trash', lambda x: eval(x.title())],
+'channel.error.data.file.name' :
+                                    ['error.fname', lambda x: str(x).strip('\n')],
+'channel.error.data.file.format' :
+                                    ['error.format', lambda x: str(x).strip('\n')],
+'channel.error.data.num-points' :
+                                    ['error.num-points', lambda x: eval(x.title())],
+'channel.hDeflection.lcd-info.*' :
+                                    ['trash', lambda x: eval(x.title())],
+'channel.hDeflection.data.file.name' :
+                                    ['hDeflection.fname', lambda x: str(x).strip('\n')],
+'channel.hDeflection.data.file.format' :
+                                    ['hDeflection.format', lambda x: str(x).strip('\n')],
+'channel.hDeflection.data.num-points' :
+                                    ['hDeflection.num-points', lambda x: eval(x.title())],
+'channel.capacitiveSensorHeight.lcd-info.*' :
+                                    ['trash', lambda x: eval(x.title())],
+'channel.capacitiveSensorHeight.data.file.name' :
+                                    ['capacitiveSensorHeight.fname', lambda x: str(x).strip('\n')],
+'channel.capacitiveSensorHeight.data.file.format' :
+                                    ['capacitiveSensorHeight.format', lambda x: str(x).strip('\n')],
+'channel.capacitiveSensorHeight.data.num-points' :
+                                    ['capacitiveSensorHeight.num-points', lambda x: eval(x.title())],
+'channel.height.lcd-info.*' :
+                                    ['trash', lambda x: eval(x.title())],
+'channel.height.data.file.name' :
+                                    ['height.fname', lambda x: str(x).strip('\n')],
+'channel.height.data.file.format' :
+                                    ['height.format', lambda x: str(x).strip('\n')],
+'channel.height.data.num-points' :
+                                    ['height.num-points', lambda x: eval(x.title())],
+'channel.time.lcd-info.*' :
+                                    ['trash', lambda x: eval(x.title())],
+'channel.time.data.num-points' :
+                                    ['trash', lambda x: eval(x.title())],
+'channel.time.data.start' :
+                                    ['trash', lambda x: eval(x.title())],
+'channel.time.data.step' :
+                                    ['trash', lambda x: eval(x.title())],
+'channel.seriesTime.lcd-info.*' :
+                                    ['trash', lambda x: eval(x.title())],
+'channel.seriesTime.data.num-points' :
+                                    ['trash', lambda x: eval(x.title())],
+'channel.seriesTime.data.start' :
+                                    ['trash', lambda x: eval(x.title())],
+'channel.seriesTime.data.step' :
+                                    ['trash', lambda x: eval(x.title())],
+}
+ZIP_SHARED_HEADER = {
+'force-segment-header-infos.count' :
+                                    ['segment_count', eval],
+'lcd-infos.count' :
+                                    ['channel_count', eval],
+'force-segment-header-info.xx.type' :
+                                    ['trash', lambda x: str(x).strip('\n')],
+'force-segment-header-info.xx.approach-id' :
+                                    ['trash', lambda x: str(x).strip('\n')],
+'force-segment-header-info.xx.name.type' :
+                                    ['trash', lambda x: str(x).strip('\n')],
+'force-segment-header-info.xx.name.name' :
+                                    ['trash', lambda x: str(x).strip('\n')],
+'force-segment-header-info.xx.settings.type' :
+                                    ['trash', lambda x: str(x).strip('\n')],
+'force-segment-header-info.xx.settings.style' :
+                                    ['trash', lambda x: str(x).strip('\n')],
+'force-segment-header-info.xx.settings.feedback-mode.name' :
+                                    ['trash', lambda x: str(x).strip('\n')],
+'force-segment-header-info.xx.settings.segment-settings.type' :
+                                    ['trash', lambda x: str(x).strip('\n')],
+'force-segment-header-info.xx.settings.segment-settings.identifier.type' :
+                                    ['trash', lambda x: str(x).strip('\n')],
+'force-segment-header-info.xx.settings.segment-settings.identifier.name' :
+                                    ['trash', lambda x: str(x).strip('\n')],
+'force-segment-header-info.xx.settings.segment-settings.style' :
+                                    ['trash', lambda x: str(x).strip('\n')],
+'force-segment-header-info.xx.settings.segment-settings.duration' :
+                                    ['trash', eval],
+'force-segment-header-info.xx.settings.segment-settings.num-points' :
+                                    ['trash', eval],
+'force-segment-header-info.xx.settings.segment-settings.z-start' :
+                                    ['trash', eval],
+'force-segment-header-info.xx.settings.segment-settings.z-end' :
+                                    ['trash', eval],
+'force-segment-header-info.xx.settings.segment-settings.setpoint' :
+                                    ['trash', eval],
+'force-segment-header-info.xx.environment.xy-scanner-position-map.defined' :
+                                    ['trash', lambda x: eval(x.title())],
+'force-segment-header-info.xx.environment.xy-scanner-position-map.xy-scanners.active-xy-scanner.name' :
+                                    ['trash', lambda x: str(x).strip('\n')],
+'force-segment-header-info.xx.environment.xy-scanner-position-map.xy-scanner.tip-scanner.xy-scanner.scanner' :
+                                    ['trash', lambda x: str(x).strip('\n')],
+'force-segment-header-info.xx.environment.xy-scanner-position-map.xy-scanner.tip-scanner.xy-scanner.name' :
+                                    ['trash', lambda x: str(x).strip('\n')],
+'force-segment-header-info.xx.environment.xy-scanner-position-map.xy-scanner.tip-scanner.xy-scanner.fancy-name' :
+                                    ['trash', lambda x: str(x).strip('\n')],
+'force-segment-header-info.xx.environment.xy-scanner-position-map.xy-scanner.tip-scanner.xy-scanner.description' :
+                                    ['trash', lambda x: str(x).strip('\n')],
+'force-segment-header-info.xx.environment.xy-scanner-position-map.xy-scanner.tip-scanner.xy-scanner-mode.type' :
+                                    ['trash', lambda x: str(x).strip('\n')],
+'force-segment-header-info.xx.environment.xy-scanner-position-map.xy-scanner.tip-scanner.xy-scanner-mode.software-linearized' :
+                                    ['trash', lambda x: eval(x.title())],
+'force-segment-header-info.xx.environment.xy-scanner-position-map.xy-scanner.motorstage.xy-scanner.scanner' :
+                                    ['trash', lambda x: str(x).strip('\n')],
+'force-segment-header-info.xx.environment.xy-scanner-position-map.xy-scanner.motorstage.xy-scanner.name' :
+                                    ['trash', lambda x: str(x).strip('\n')],
+'force-segment-header-info.xx.environment.xy-scanner-position-map.xy-scanner.motorstage.xy-scanner.fancy-name' :
+                                    ['trash', lambda x: str(x).strip('\n')],
+'force-segment-header-info.xx.environment.xy-scanner-position-map.xy-scanner.motorstage.xy-scanner.description' :
+                                    ['trash', lambda x: str(x).strip('\n')],
+'force-segment-header-info.xx.environment.xy-scanner-position-map.xy-scanner.motorstage.xy-scanner-mode.type' :
+                                    ['trash', lambda x: str(x).strip('\n')],
+'force-segment-header-info.xx.environment.xy-scanner-position-map.xy-scanner.motorstage.xy-scanner-mode.software-linearized' :
+                                    ['trash', lambda x: eval(x.title())],
+'force-segment-header-info.xx.environment.xy-scanner-position-map.xy-scanners.list' :
+                                    ['trash', lambda x: str(x).strip('\n')],
+'lcd-info.xx.type' :
+                                    ['trash', lambda x: str(x).strip('\n')],
+'lcd-info.xx.channel.type' :
+                                    ['trash', lambda x: str(x).strip('\n')],
+'lcd-info.xx.channel.name' :
+                                    ['name.xx', lambda x: str(x).strip('\n')],
+'lcd-info.xx.unit.type' :
+                                    ['trash', lambda x: str(x).strip('\n')],
+'lcd-info.xx.unit.unit' :
+                                    ['trash', lambda x: str(x).strip('\n')],
+'lcd-info.xx.conversion-set.conversions.list' :
+                                    ['conversion_list.xx', lambda x: str(x).strip('\n')],
+'lcd-info.xx.conversion-set.conversions.default' :
+                                    ['trash', lambda x: str(x).strip('\n')],
+'lcd-info.xx.conversion-set.conversions.base' :
+                                    ['trash', lambda x: str(x).strip('\n')],
+'lcd-info.xx.conversion-set.conversion.volts.name' :
+                                    ['trash', lambda x: str(x).strip('\n')],
+'lcd-info.xx.conversion-set.conversion.volts.defined' :
+                                    ['trash', lambda x: eval(x.title())],
+'lcd-info.xx.conversion-set.conversion.distance.name' :
+                                    ['trash', lambda x: str(x).strip('\n')],
+'lcd-info.xx.conversion-set.conversion.distance.defined' :
+                                    ['trash', lambda x: eval(x.title())],
+'lcd-info.xx.conversion-set.conversion.distance.type' :
+                                    ['trash', lambda x: str(x).strip('\n')],
+'lcd-info.xx.conversion-set.conversion.distance.comment' :
+                                    ['trash', lambda x: str(x).strip('\n')],
+'lcd-info.xx.conversion-set.conversion.distance.base-calibration-slot' :
+                                    ['trash', lambda x: str(x).strip('\n')],
+'lcd-info.xx.conversion-set.conversion.distance.calibration-slot' :
+                                    ['trash', lambda x: str(x).strip('\n')],
+'lcd-info.xx.conversion-set.conversion.distance.scaling.type' :
+                                    ['trash', lambda x: str(x).strip('\n')],
+'lcd-info.xx.conversion-set.conversion.distance.scaling.style' :
+                                    ['trash', lambda x: str(x).strip('\n')],
+'lcd-info.xx.conversion-set.conversion.distance.scaling.offset' :
+                                    ['distance_offset', eval],
+'lcd-info.xx.conversion-set.conversion.distance.scaling.multiplier' :
+                                    ['distance_multiplier', eval],
+'lcd-info.xx.conversion-set.conversion.distance.scaling.unit.type' :
+                                    ['trash', lambda x: str(x).strip('\n')],
+'lcd-info.xx.conversion-set.conversion.distance.scaling.unit.unit' :
+                                    ['trash', lambda x: str(x).strip('\n')],
+'lcd-info.xx.conversion-set.conversion.force.name' :
+                                    ['trash', lambda x: str(x).strip('\n')],
+'lcd-info.xx.conversion-set.conversion.force.defined' :
+                                    ['trash', lambda x: eval(x.title())],
+'lcd-info.xx.conversion-set.conversion.force.type' :
+                                    ['trash', lambda x: str(x).strip('\n')],
+'lcd-info.xx.conversion-set.conversion.force.comment' :
+                                    ['trash', lambda x: str(x).strip('\n')],
+'lcd-info.xx.conversion-set.conversion.force.base-calibration-slot' :
+                                    ['trash', lambda x: str(x).strip('\n')],
+'lcd-info.xx.conversion-set.conversion.force.calibration-slot' :
+                                    ['trash', lambda x: str(x).strip('\n')],
+'lcd-info.xx.conversion-set.conversion.force.scaling.type' :
+                                    ['trash', lambda x: str(x).strip('\n')],
+'lcd-info.xx.conversion-set.conversion.force.scaling.style' :
+                                    ['trash', lambda x: str(x).strip('\n')],
+'lcd-info.xx.conversion-set.conversion.force.scaling.offset' :
+                                    ['force_offset.xx', eval],
+'lcd-info.xx.conversion-set.conversion.force.scaling.multiplier' :
+                                    ['spring_constant', eval],
+'lcd-info.xx.conversion-set.conversion.force.scaling.unit.type' :
+                                    ['trash', lambda x: str(x).strip('\n')],
+'lcd-info.xx.conversion-set.conversion.force.scaling.unit.unit' :
+                                    ['trash', lambda x: str(x).strip('\n')],
+'lcd-info.xx.conversion-set.conversion.absolute.name' :
+                                    ['trash', lambda x: str(x).strip('\n')],
+'lcd-info.xx.conversion-set.conversion.absolute.defined' :
+                                    ['trash', lambda x: eval(x.title())],
+'lcd-info.xx.conversion-set.conversion.absolute.type' :
+                                    ['trash', lambda x: str(x).strip('\n')],
+'lcd-info.xx.conversion-set.conversion.absolute.comment' :
+                                    ['trash', lambda x: str(x).strip('\n')],
+'lcd-info.xx.conversion-set.conversion.absolute.base-calibration-slot' :
+                                    ['trash', lambda x: str(x).strip('\n')],
+'lcd-info.xx.conversion-set.conversion.absolute.calibration-slot' :
+                                    ['trash', lambda x: str(x).strip('\n')],
+'lcd-info.xx.conversion-set.conversion.absolute.scaling.type' :
+                                    ['trash', lambda x: str(x).strip('\n')],
+'lcd-info.xx.conversion-set.conversion.absolute.scaling.style' :
+                                    ['trash', lambda x: str(x).strip('\n')],
+'lcd-info.xx.conversion-set.conversion.absolute.scaling.offset' :
+                                    ['force_offset.xx', eval],
+'lcd-info.xx.conversion-set.conversion.absolute.scaling.multiplier' :
+                                    ['force_offset.xx', eval],
+'lcd-info.xx.conversion-set.conversion.absolute.scaling.unit.type' :
+                                    ['trash', lambda x: str(x).strip('\n')],
+'lcd-info.xx.conversion-set.conversion.absolute.scaling.unit.unit' :
+                                    ['trash', lambda x: str(x).strip('\n')],
+'lcd-info.xx.conversion-set.conversion.nominal.name' :
+                                    ['trash', lambda x: str(x).strip('\n')],
+'lcd-info.xx.conversion-set.conversion.nominal.defined' :
+                                    ['trash', lambda x: eval(x.title())],
+'lcd-info.xx.conversion-set.conversion.nominal.type' :
+                                    ['trash', lambda x: str(x).strip('\n')],
+'lcd-info.xx.conversion-set.conversion.nominal.comment' :
+                                    ['trash', lambda x: str(x).strip('\n')],
+'lcd-info.xx.conversion-set.conversion.nominal.base-calibration-slot' :
+                                    ['trash', lambda x: str(x).strip('\n')],
+'lcd-info.xx.conversion-set.conversion.nominal.calibration-slot' :
+                                    ['trash', lambda x: str(x).strip('\n')],
+'lcd-info.xx.conversion-set.conversion.nominal.scaling.type' :
+                                    ['trash', lambda x: str(x).strip('\n')],
+'lcd-info.xx.conversion-set.conversion.nominal.scaling.style' :
+                                    ['trash', lambda x: str(x).strip('\n')],
+'lcd-info.xx.conversion-set.conversion.nominal.scaling.offset' :
+                                    ['nominal_offset.xx', eval],
+'lcd-info.xx.conversion-set.conversion.nominal.scaling.multiplier' :
+                                    ['nominal_multiplier.xx', eval],
+'lcd-info.xx.conversion-set.conversion.nominal.scaling.unit.type' :
+                                    ['trash', lambda x: str(x).strip('\n')],
+'lcd-info.xx.conversion-set.conversion.nominal.scaling.unit.unit' :
+                                    ['trash', lambda x: str(x).strip('\n')],
+'lcd-info.xx.conversion-set.conversion.calibrated.name' :
+                                    ['trash', lambda x: str(x).strip('\n')],
+'lcd-info.xx.conversion-set.conversion.calibrated.defined' :
+                                    ['trash', lambda x: eval(x.title())],
+'lcd-info.xx.conversion-set.conversion.calibrated.type' :
+                                    ['trash', lambda x: str(x).strip('\n')],
+'lcd-info.xx.conversion-set.conversion.calibrated.file' :
+                                    ['trash', lambda x: str(x).strip('\n')],
+'lcd-info.xx.conversion-set.conversion.calibrated.comment' :
+                                    ['trash', lambda x: str(x).strip('\n')],
+'lcd-info.xx.conversion-set.conversion.calibrated.base-calibration-slot' :
+                                    ['trash', lambda x: str(x).strip('\n')],
+'lcd-info.xx.conversion-set.conversion.calibrated.calibration-slot' :
+                                    ['trash', lambda x: str(x).strip('\n')],
+'lcd-info.xx.conversion-set.conversion.calibrated.scaling.type' :
+                                    ['trash', lambda x: str(x).strip('\n')],
+'lcd-info.xx.conversion-set.conversion.calibrated.scaling.style' :
+                                    ['trash', lambda x: str(x).strip('\n')],
+'lcd-info.xx.conversion-set.conversion.calibrated.scaling.offset' :
+                                    ['calibrated_offset.xx', eval],
+'lcd-info.xx.conversion-set.conversion.calibrated.scaling.multiplier' :
+                                    ['calibrated_multiplier.xx', eval],
+'lcd-info.xx.conversion-set.conversion.calibrated.scaling.unit.type' :
+                                    ['trash', lambda x: str(x).strip('\n')],
+'lcd-info.xx.conversion-set.conversion.calibrated.scaling.unit.unit' :
+                                    ['trash', lambda x: str(x).strip('\n')],
+'lcd-info.xx.conversion-set.conversion.elapsed.name' :
+                                    ['trash', lambda x: str(x).strip('\n')],
+'lcd-info.xx.conversion-set.conversion.elapsed.defined' :
+                                    ['trash', lambda x: eval(x.title())],
+'lcd-info.xx.encoder.type' :
+                                    ['encoder_type.xx', lambda x: str(x).strip('\n')],
+'lcd-info.xx.encoder.scaling.type' :
+                                    ['trash', lambda x: str(x).strip('\n')],
+'lcd-info.xx.encoder.scaling.style' :
+                                    ['trash', lambda x: str(x).strip('\n')],
+'lcd-info.xx.encoder.scaling.offset' :
+                                    ['encode_offset.xx', eval],
+'lcd-info.xx.encoder.scaling.multiplier' :
+                                    ['encode_multiplier.xx', eval],
+'lcd-info.xx.encoder.scaling.unit.type' :
+                                    ['trash', lambda x: str(x).strip('\n')],
+'lcd-info.xx.encoder.scaling.unit.unit' :
+                                    ['trash', lambda x: str(x).strip('\n')],
+}

Added: trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/fovea_toolbox/file_util/nanoscope.py
===================================================================
--- trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/fovea_toolbox/file_util/nanoscope.py	                        (rev 0)
+++ trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/fovea_toolbox/file_util/nanoscope.py	2012-08-20 10:43:48 UTC (rev 12094)
@@ -0,0 +1,305 @@
+#! /usr/bin/python
+# -*- coding: utf-8 -*-
+'''
+This module is used to parse the files form Digital Instrument AFM
+'''
+__author__  = "Charles Roduit <charles.roduit at gmail.com>"
+__date__ = "01.07.2007"
+__license__ = "GNU Public License (GPL) version 3"
+__version__ = "0.1"
+
+import os
+from struct import unpack
+from datetime import datetime #strptime
+import zipfile
+
+import numpy as num
+
+from common import Variables, extract_num, extract_num_rev
+
+GLOB_VARS = Variables()
+
+
+def clean_header(header):
+    new_header = dict()
+    for item in GLOB_VARS.common_header:
+        try:
+            new_header[item] = header[item]
+        except KeyError:
+            # This key will keep the default value...
+            new_header[item] = GLOB_VARS.common_header[item]
+    return new_header
+        
+def lect_header(file_name):
+    """
+    Cette fonction lit le fichier d'entete du bioscope
+    Elle demande le nom du fichier
+    Elle retourne un dictionnaire repetroriant toutes
+    les information utiles pour traiter les courbes
+    forces-volumes ou/et l'image topologique.
+    
+    >>> header=lect_header(fileName)
+    """
+    
+    file_id = open(file_name,'rb')
+    line_in_mem = file_id.readline()
+
+    one_image = 0
+    header = GLOB_VARS.fv_header
+    header_pos = 'None'
+    version = {8.0: 0,
+               7.0: 0,
+               6.1: 0}
+    if not '\*Force file list' in line_in_mem:
+        # This is not a nanoscoe file
+        raise TypeError
+    while not '\*File list end' in line_in_mem:
+        ###### Determiner la postition dans l'entete ######
+        if '\*Force file list' in line_in_mem:
+            header_pos = 'File Description'
+        elif '\*Equipment list' in line_in_mem:
+            header_pos = 'Equipment list'
+        elif '\*Ciao scan list' in line_in_mem:
+            header_pos = 'Scan list'
+        elif '\*Ciao force list' in line_in_mem:
+            header_pos = 'Force list'
+        elif '\*Ciao image list' in line_in_mem:
+            header_pos = 'Image list'
+        elif '\*Ciao force image lis' in line_in_mem:
+            header_pos = 'Force image'
+        elif header_pos == 'File Description':
+            if line_in_mem.find('\Version:') + 1:
+                header['di_version'] = extract_num_rev(line_in_mem)
+                if 6130000 < header['di_version'] < 6200000:
+                    version[6.1] = 1
+                elif 7000000 < header['di_version'] < 8000000:
+                    version[7.0] = 1
+                elif 8000000 < header['di_version'] < 9000000:
+                    version[8.0] = 1
+            elif line_in_mem.find('\Date:') + 1:
+                #find the last digit
+                for place, item in enumerate(line_in_mem):
+                    if item.isdigit():
+                        last=place+1
+                date = line_in_mem[7:last]
+                
+                header['date'] = datetime.strptime(date, 
+                                                   '%I:%M:%S %p %a %b %d %Y')
+                
+        ######### Description de l'equipement ############
+        elif header_pos == 'Equipment list':
+            if line_in_mem.find('\@Sens. Zscan: V') + 1:
+                header['sens_z_scan'] = float(extract_num(line_in_mem))
+            elif (version[6.1] or version[7.0] or version[8.0]) and \
+                                    line_in_mem.find('\@Sens. Zsens: V') + 1:
+                                    
+                header['sens_z_scan'] = float(extract_num(line_in_mem))
+        ######### des parametres du scan ##################
+        elif header_pos == 'Scan list':
+            if line_in_mem.find('\Operating mode') + 1:
+                if line_in_mem.find('Force Volume') + 1:
+                    header['image_mode'] = 'Force Volume'
+            elif line_in_mem.find('\Scan size') + 1:
+                _ssize = extract_num(line_in_mem)
+                header['scan_size'] = (_ssize, _ssize)
+            elif (version[7.0] or version[8.0]) and line_in_mem.find('\Scan Size') + 1:
+                _ssize = extract_num(line_in_mem)
+                header['scan_size'] = (_ssize, _ssize)
+            elif line_in_mem.find('\@Sens. Deflection: V') + 1:
+                header['sensit_deflection'] = extract_num(line_in_mem)
+            elif (version[6.1] or version[7.0] or version[8.0] or version[6.1]) and \
+                    line_in_mem.find('\@Sens. DeflSens: V') + 1:
+                    
+                header['sensit_deflection'] = extract_num(line_in_mem)
+                
+        ####### Parametre de l'acquisition des courbes de force ######
+        elif header_pos == 'Force list':
+            if line_in_mem.find('\\force/line') + 1:
+                header['matrix_length'] = extract_num(line_in_mem)
+                #header['size_x'] = header['matrix_length']
+                #header['size_y'] = header['matrix_length']
+                header['size'] = (header['matrix_length'], header['matrix_length'])
+        ########## Parametres de l'image ########################
+        elif header_pos == 'Image list':
+            if line_in_mem.find('\Number of lines') + 1:
+                header['image_number_lines'] = extract_num(line_in_mem)
+            elif line_in_mem.find('\@2:Z scale') + 1:
+                header['image_scale'] = extract_num_rev(line_in_mem)
+            elif line_in_mem.find('\Samps/line') + 1:
+                header['image_samps_per_line'] = extract_num(line_in_mem)
+            elif line_in_mem.find('\Data length') + 1:
+                header['image_length'] = extract_num(line_in_mem)
+            elif line_in_mem.find('\Data offset') + 1:
+                if not one_image:
+                    header['image_offset'] = extract_num(line_in_mem)
+                    one_image = 1
+            elif line_in_mem.find('\Note:') + 1:
+                header['note'] = line_in_mem[7:]
+                while line_in_mem[-3:]=='\r\r\n':
+                    line_in_mem = file_id.readline()
+                    try:
+                        line_in_mem = u'' + line_in_mem
+                        header['note'] = header['note'] + line_in_mem
+                    except UnicodeDecodeError:
+                        line_in_mem = line_in_mem.decode('cp1251')
+                        header['note'] = header['note'] + line_in_mem
+                header['note'] = header['note'].replace('\r', '')
+
+        ######### Parametre des courbes de force ###############
+        elif header_pos == 'Force image':
+            if line_in_mem.find('\Data offset:') + 1:
+                header['force_data_offset'] = extract_num(line_in_mem)
+                
+            elif line_in_mem.find('\Data length:') + 1:
+                header['force_data_length'] = extract_num_rev(line_in_mem)
+                
+            elif line_in_mem.find('\Bytes/pixel:') + 1:
+                header['force_bytes_per_pixel'] = extract_num_rev(line_in_mem)
+                
+            elif line_in_mem.find('\Samps/line') + 1:
+                header['force_samples_per_curve'] = extract_num(line_in_mem)
+                
+            elif line_in_mem.find('\Data type: FORCE') + 1:
+                pass
+                ## Dans la version originale, il y avait un NFJflag=1...
+            elif line_in_mem.find('\@4:Z scale: V') + 1:
+                #header['z_scale'] = extract_num_rev(file_id)
+                header['hard_z_scale'] = extract_num(line_in_mem, pos=1)
+                
+            #elif line_in_mem.find('\@4:FV scale: V') + 1:
+            #    header['fv_scale'] = extract_num_rev(file_id)
+                
+            elif line_in_mem.find('\@4:Ramp size: V') + 1:
+                header['ramp_size'] = extract_num_rev(line_in_mem)
+            
+            elif line_in_mem.find('\Spring constant') + 1:
+                header['spring_constant'] = extract_num_rev(line_in_mem)
+                
+            elif (version[6.1] or version[7.0] or version[8.0] or version[6.1]) and \
+                            line_in_mem.find('\Spring Constant:') + 1:
+                header['spring_constant'] = extract_num_rev(line_in_mem)
+                
+        #####################################################
+        line_in_mem = file_id.readline()
+    header['x_factor'] = header['ramp_size'] * \
+                         header['sens_z_scan'] / header['force_samples_per_curve']
+
+    if header['force_data_length'] != (2 * (header['matrix_length'] ** 2) * 
+                                       header['force_bytes_per_pixel'] * 
+                                       header['force_samples_per_curve']):
+        header['matrix_length'] = int(num.sqrt(header['force_data_length'] /
+                                    (header['force_bytes_per_pixel'] * 
+                                     header['force_samples_per_curve'] * 
+                                     2)))
+#        header['size'] = (header['matrix_length'], header['matrix_length'])
+#        header['size_x'] = header['matrix_length']
+#        header['size_y'] = header['matrix_length']
+    header['number_curves'] = header['matrix_length'] ** 2
+    return header
+def load_force_curves(file_name, header):
+    '''
+    This function reads the AFM file (file_name) with the help of header 
+    information. The header is the dictionnary returned by the function 
+    lect_header.It returns the force curves contained in the file in two
+    3D numpy arrays. The first one contain the advance force curves and the 
+    second one the retraction force curves.
+
+    >>> [im_3d_av,3d_re]=load_force_curves(file_name,header)
+    >>> print(im_3d_av[0,0,:])   # print the values of the first advance 
+    >>>                          # force curve 
+    '''
+    
+    file_id = open(file_name, 'rb')
+    file_id.seek(header['force_data_offset'], 0)
+    
+    curve_av = num.zeros([header['force_samples_per_curve']])
+    curve_re = num.zeros([header['force_samples_per_curve']])
+    
+    im_3d_av = num.zeros([header['matrix_length'],
+                          header['matrix_length'],
+                          header['force_samples_per_curve']], num.float)
+                          
+    im_3d_re = num.zeros([header['matrix_length'],
+                          header['matrix_length'],
+                          header['force_samples_per_curve']], num.float)
+    pos_y = 0
+    pos_x = 0
+    while pos_y < header['matrix_length']:
+        while pos_x < header['matrix_length']:
+            # charger la courbe x, y
+            curve_av[:] = unpack(str(header['force_samples_per_curve']) + 'h',
+                            file_id.read(2 * header['force_samples_per_curve']))
+            curve_re[:] = unpack(str(header['force_samples_per_curve']) + 'h',
+                            file_id.read(2 * header['force_samples_per_curve']))
+            # mettre le minimun a 0
+            curve_av = curve_av - min(curve_av)
+            curve_re = curve_re - min(curve_re)
+            # Correction des echelles
+            # (http://web.mit.edu/cortiz/www/MultimodeInstructions.doc)
+            curve_av = curve_av * header['hard_z_scale'] * \
+                                  header['sensit_deflection']
+            curve_re = curve_re * header['hard_z_scale'] * \
+                                  header['sensit_deflection']
+                                  
+            im_3d_av[pos_x, pos_y, ] = correct_curve_drop(curve_av)
+            im_3d_re[pos_x, pos_y, ] = correct_curve_drop(curve_re)
+            pos_x += 1
+        pos_x = 0
+        pos_y += 1
+    return [im_3d_av, im_3d_re]
+    
+def correct_curve_drop(curve_y):
+    '''
+    Corrects the drops that occurs at the beginning of some force-distance
+    curves. This function corrects a bug from Veeco AFM.
+    '''
+    try:
+        first_non_zero = curve_y.nonzero()[0][-1]
+    except IndexError:
+        # The vector is full of zero, then do nothing
+        return curve_y
+    if not first_non_zero == len(curve_y)-1:
+        first_non_zero = curve_y.nonzero()[0][-1]
+        for indice in range(first_non_zero, len(curve_y)):
+            curve_y[indice] = curve_y[first_non_zero]
+        curve_y = curve_y - min(curve_y)
+    return curve_y
+    
+def load_image(file_name, header):
+    '''
+    This function returns the piezo height image contained in the AFM file
+    as a numpy matrix
+    
+    >>> imageMatrix=load_image(fileName,header)
+    '''
+    if header.has_key('image_offset') and header['image_offset'] is not None:
+        file_id = open(file_name, 'rb')
+        im_matrix = num.zeros([header['matrix_length'],
+                               header['matrix_length']], num.float)
+        pos_y = 0
+        pos_x = 0
+        while pos_y < header['matrix_length']:
+            while pos_x < header['matrix_length']:
+                temp_offset = header['image_offset'] + (
+                        2 * pos_x * (header['image_number_lines'] / 
+                                   header['matrix_length']) * 
+                                   header['image_number_lines'] + 
+                        2 * pos_y * (header['image_samps_per_line'] / 
+                                   header['matrix_length']))
+                file_id.seek(temp_offset, 0)
+                im_matrix[pos_y, pos_x] = unpack('h', file_id.read(2))[0]
+                pos_x += 1
+            pos_x = 0
+            pos_y += 1
+        ## Scale the image
+        im_matrix = im_matrix * (header['image_scale'] *
+                                 header['sens_z_scan'] / 
+                                 (2. ** (2 * 8)))
+        pos_x = 0
+        minimum = im_matrix.min()
+        im_matrix = im_matrix - minimum
+    else:
+        im_matrix = num.zeros([header['matrix_length'],
+                               header['matrix_length']])
+    return im_matrix
+    

Added: trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/fovea_toolbox/file_util/succellus_import.py
===================================================================
--- trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/fovea_toolbox/file_util/succellus_import.py	                        (rev 0)
+++ trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/fovea_toolbox/file_util/succellus_import.py	2012-08-20 10:43:48 UTC (rev 12094)
@@ -0,0 +1,323 @@
+#!/usr/bin/env python
+
+from xml.dom import minidom
+import time
+import pylab
+import numpy
+
+def parse(file_name):
+    xmldoc=minidom.parse("C050614A.002.xml")
+    child=xmldoc.firstChild
+    FVTags=["fileName", "mainExpIndice", "date", "header", "image",
+            "pointOfContact", "topography", "StiffnessesList", "events",
+            "CurveX", "CurveYAv", "CurveYRe"]
+    dateTag=["year", "month", "day", "hour", "minute", "second"]
+    headerTag=["SensZScan", "OpMode", "ScanSize", "NFL", "ScanListScanRate",
+               "SensitDeflection", "ScanRate", "ForceListForwVeloc>",
+               "ForceListRevVeloc", "NumberCurvesPerLines",
+               "ForceListFVScanRate", "Z_SCAN_START", "Z_SCAN_SIZE", "TTD",
+               "ImageOffset", "ImageLength", "ImageSampsPerLine",
+               "ImageNumberLines", "ImageScale", "ForceOffset",
+               "NumberPointsPerCurves", "SpringConstant", "Z_SCALE",
+               "HARD_Z_SCALE", "FV_SCALE", "RAMP_SIZE"]
+    imageTag=["data"]
+    imageAtt=["Contrast"]
+    pocTag=["data"]
+    pocAtt=["Contrast","Method"]
+    topoTag=["data"]
+    topoAtt=["Contrast"]
+    stiffListAtt=["Contrast","Deep","GlassFit","HertzModel","SegmentNumber",
+                 "TipCar-Radius","TipCar-SemiAngle"]
+    stiffListTag=["StiffnessMatrix"]
+    stiffMatrixAtt=["DeepNbr"]
+    stiffMatrixTag=["data"]
+    eventAtt=["Type"]
+    eventTag=["EventDetail","EventMatrix"]
+    eventDetAtt=["PosX","PosY","XValues","YValues","force","jumpSlope","maxX",
+                 "maxY","minX","minY"]
+    EventMatrixTag=["data"]
+    CurveYAvTag=["data"]
+    CurveYReTag=["data"]
+    result=dict()
+
+def xmlExtractImage(elm):
+    nodeDic=dict()
+    attDic=dict()
+    for att in ["Contrast","Method","DeepNbr"]:
+        if elm.hasAttribute(att):
+            attDic[att]=elm.getAttribute(att)
+    nodeDic["attributes"]=attDic
+    matrix=[]
+    for data in elm.childNodes:
+        if data.nodeName=="data":
+            matrix.append([float(s) for s in
+                                data.childNodes[0].data.split(",")[0:-1]])
+    nodeDic["matrix"]=numpy.array(matrix)
+    return nodeDic
+    
+def xmlExtractVector(elm):
+    vectors=list()
+    for data in elm.childNodes:
+        if data.nodeName=="data":
+            vectors.append([float(s) for s in
+                                data.childNodes[0].data.split(",")[0:-1]])
+    vectors=numpy.array(vectors)
+    return vectors
+
+def restructure_header(old_header, version):
+    header = dict()
+    if not version:
+        # we come from the succellus version
+        header['FVSCALE']=old_header['FV_SCALE']
+        header['ForceListFVScanRate']=old_header['ForceListFVScanRate']
+        ## miss ForceListForwVeloc
+        header['ForceListForwVeloc']=old_header['ForceListForwVeloc']
+        header['ForceListRevVeloc']=old_header['ForceListRevVeloc']
+        header['Force Data offset']=old_header['ForceOffset']
+        #header[]=old_header['HARD_Z_SCALE']
+        header['ImageLength']=old_header['ImageLength']
+        header['ImageNumberLines']=old_header['ImageNumberLines']
+        #header['ImageOffset']=old_header['ImageOffset']
+        header['ImageSampsPerLine']=old_header['ImageSampsPerLine']
+        header['ImageScale']=old_header['ImageScale']
+        #header['NFL']=old_header['NFL']
+        header['matrix_length']=old_header['NumberCurvesPerLines']
+        header['size_x'] = header['matrix_length']
+        header['size_y'] = header['matrix_length']
+        header['ImageSampsPerLine']=old_header['NumberPointsPerCurves']
+        header['image mode']=old_header['OpMode']
+        header['RAMPSIZE']=old_header['RAMP_SIZE']
+        header['ScanListScanRate']=old_header['ScanListScanRate']
+        #header['scan rate']=old_header['ScanRate']
+        header['scan size']=old_header['ScanSize']
+        header['sens z scan']=old_header['SensZScan']
+        header['sensit deflection']=old_header['SensitDeflection']
+        header['spring_constant']=old_header['SpringConstant']
+        header['TTD']=old_header['TTD']
+        header['ZSCALE']=old_header['Z_SCALE']
+        header['Z_SCAN_SIZE']=old_header['Z_SCAN_SIZE']
+        header['ZSCANSTART']=old_header['Z_SCAN_START']
+    header['matrix_length'] = int(header['matrix_length'])
+    header['size_x'] = int(header['size_x'])
+    header['size_y'] = int(header['size_y'])
+    header['spring_constant'] = float(header['spring_constant'])
+    return header
+    
+def restructure_stiffness(old_stiffness, version):
+    stiffness = dict()
+    if not version:
+        for key in old_stiffness.keys():
+            if key == 'GlassFit':
+                stiffness['glass'] = -float(old_stiffness[key][0])
+                #print type(stiffness['glass'])
+            elif key == 'SegmentNumber':
+                stiffness['nbParts'] = int(old_stiffness[key])
+                #TODO introduce the stiffness tomography...
+                if not stiffness['nbParts']:
+                    stiffness['nbParts'] = 4
+            elif key == 'Deep':
+                stiffness['sizeParts'] = float(old_stiffness[key])
+            else:
+                stiffness[key] = old_stiffness[key]
+    #print stiffness
+    return stiffness
+            
+def restructure_event(old_event, version):
+    event = list()
+    if not version:
+        # we come from the succellus version
+        for old_item in old_event:
+            item = dict()
+            item['pos_x'] = old_item['PosX']-1
+            item['pos_y'] = old_item['PosY']-1
+            item['slice'] = slice(old_item['XValues'][0],
+                                  old_item['XValues'][-1])
+            item['min'] = None
+            item['max'] = None
+            item['slope'] = old_item['jumpSlope']
+            item['force'] = old_item['force']
+            event.append(item)
+    return event
+    
+def restructure_curves(old_curve_matrix, version):
+    if not version:
+        #curve_matrix = old_curve_matrix[:,:,::-1]
+        pass
+    pass
+    #return curve_matrix
+
+def xmlExtractFV(fileName):
+    xmldoc=minidom.parse(fileName)
+    child=xmldoc.firstChild
+    FVTags=["fileName","mainExpIndice","date","header","image","pointOfContact",
+            "topography","StiffnessesList","events","CurveX","CurveYAv",
+            "CurveYRe"]
+    dateTag=["year","month","day","hour","minute","second"]
+    headerTag=["SensZScan","OpMode","ScanSize","NFL","ScanListScanRate",
+               "SensitDeflection","ScanRate","ForceListForwVeloc",
+               "ForceListRevVeloc","NumberCurvesPerLines","ForceListFVScanRate",
+               "Z_SCAN_START","Z_SCAN_SIZE","TTD","ImageOffset","ImageLength",
+               "ImageSampsPerLine","ImageNumberLines","ImageScale","ForceOffset",
+               "NumberPointsPerCurves","SpringConstant","Z_SCALE","HARD_Z_SCALE",
+               "FV_SCALE","RAMP_SIZE"]
+    imageTag=["data"]
+    imageAtt=["Contrast"]
+    pocTag=["data"]
+    pocAtt=["Contrast","Method"]
+    topoTag=["data"]
+    topoAtt=["Contrast"]
+    stiffListAtt=["Contrast","Deep","GlassFit","HertzModel","SegmentNumber",
+                 "TipCar-Radius","TipCar-SemiAngle"]
+    stiffListTag=["StiffnessMatrix"]
+    stiffMatrixAtt=["DeepNbr"]
+    stiffMatrixTag=["data"]
+    eventAtt=["Type"]
+    eventTag=["EventDetail","EventMatrix"]
+    eventDetAtt=["PosX","PosY","XValues","YValues","force","jumpSlope","maxX",
+                 "maxY","minX","minY"]
+    EventMatrixTag=["data"]
+    CurveYAvTag=["data"]
+    CurveYReTag=["data"]
+    result=dict()
+    if child.hasAttribute('openfovea:version'):
+        aex_version = child.getAttribute('openfovea:version')
+    else:
+        aex_version = 0
+    for elm in child.childNodes:
+        if elm.nodeName==FVTags[0]:#fileName
+            result["name"]=elm.childNodes[0].data
+            
+        elif elm.nodeName==FVTags[1]:#mainExpIndice
+            result["indice"]=int(elm.childNodes[0].data)
+            
+        elif elm.nodeName==FVTags[2]:#date
+            date=dict()
+            for dateElm in elm.childNodes:
+                if dateElm.nodeName in dateTag:
+                    date[str(dateElm.nodeName)]=int(dateElm.childNodes[0].data)
+            result["date"]=date
+            del(date)
+            
+        elif elm.nodeName==FVTags[3]:#header
+            header=dict()
+            for headerElm in elm.childNodes:
+                if headerElm.nodeName in headerTag:
+                    header[str(headerElm.nodeName)]=headerElm.childNodes[0].data
+            header = restructure_header(header, aex_version)
+            result["header"]=header
+            del(header)
+            
+        elif elm.nodeName==FVTags[4]:#Piezo Image
+            result['piezo_array']=xmlExtractImage(elm)['matrix']
+        elif elm.nodeName==FVTags[5]:#Point of contact
+            result["poc_array"]=xmlExtractImage(elm)['matrix']
+        elif elm.nodeName==FVTags[6]:#zero force image
+            result["topography"]=xmlExtractImage(elm)
+            
+        elif elm.nodeName==FVTags[7]:#StiffnessesList
+            attDic=dict()
+            nodeDic=dict()
+            #TODO Pretty import values
+            for att in stiffListAtt:
+                if elm.hasAttribute(att):
+                    attDic[att]=elm.getAttribute(att)
+            attDic = restructure_stiffness(attDic, aex_version)
+            nodeDic["properties"]=attDic
+            matrixList=[]
+            for childElm in elm.childNodes:
+                if childElm.nodeName=="StiffnessMatrix":
+                    matrixList.append(xmlExtractImage(childElm))
+            matrix=[]
+            for depthMatrix in matrixList:
+                matrix.append(depthMatrix['matrix'])
+            nodeDic["array"]=numpy.array(matrix)
+            nodeDic["array"] = nodeDic["array"].transpose(2,1,0)
+            nodeDic["array"] = numpy.ma.MaskedArray(
+                                        nodeDic["array"], 
+                                        mask = nodeDic["array"] == 0)
+            result["stiffness"]=nodeDic
+            del(attDic,nodeDic,matrix,matrixList)
+            
+        elif elm.nodeName==FVTags[8]:#events
+            events_det=list()
+            #TODO Pretty import values
+            matrix = None
+            for childElm in elm.childNodes:
+                if childElm.nodeName=="EventDetail":
+                    thisEvt=dict()
+                    for att in eventDetAtt:
+                        if childElm.hasAttribute(att):
+                            thisEvt[att]=childElm.getAttribute(att)
+                            if att in ["XValues","YValues"]:
+                                thisEvt[att]=[float(s) for s in 
+                                            thisEvt[att][0:-1].split(",")]
+                            else:
+                                thisEvt[att]=float(thisEvt[att])
+                    events_det.append(thisEvt)
+                elif childElm.nodeName=="EventMatrix":
+                    matrix=xmlExtractImage(childElm)
+                    matrix=matrix["matrix"]
+            events=dict()
+            events_det = restructure_event(events_det, aex_version)
+            events["detail"]=events_det
+            events["matrix"]=matrix
+            result["events"]=events
+            del(events,matrix)
+            
+        elif elm.nodeName==FVTags[9]:#CurveX
+            result["curve_x_array"]=[float(s) for s in 
+                                    elm.childNodes[0].data.split(",")[0:-1]]
+            result['curve_x_array'] = numpy.asarray(result['curve_x_array'][::-1])
+            
+        elif elm.nodeName==FVTags[10]:#CurveYAv
+            result["trace_array"]=xmlExtractVector(elm)
+            if result.has_key("header"):
+                nbLines=int(result["header"]["matrix_length"])
+                nbPoints=result["trace_array"].shape[1]
+                result["trace_array"]=result["trace_array"].reshape(nbLines,nbLines,nbPoints)
+                #result['trace_array'] = result['trace_array'].transpose(1,0,2)
+            #result['trace_array'] = restructure_curves(result['trace_array'], 
+            #                                           aex_version)
+            
+        elif elm.nodeName==FVTags[11]:#CurveYRe
+            result["retrace_array"]=xmlExtractVector(elm)
+            if result.has_key("header"):
+                nbLines=int(result["header"]["matrix_length"])
+                nbPoints=result["retrace_array"].shape[1]
+                result["retrace_array"]=result["retrace_array"].reshape(nbLines,nbLines,nbPoints)
+                #result['retrace_array'] = result['retrace_array'].transpose(1,0,2)
+            #result['retrace_array'] = restructure_curves(result['retrace_array'], 
+            #                                             aex_version)
+    result['header']['date'] = result['date']
+    return result
+    
+def xmlExtractExperiment(fileName):
+    xmldoc=minidom.parse(fileName)
+    child=xmldoc.firstChild
+    node=["date","auteur","description","NumberForceVolumeFiles","ForceVolumeNames"]
+    result=dict()
+    description=list()
+    result["ForceVolumeNames"]=list()
+    for elm in child.childNodes:
+        if elm.nodeName==node[0]:
+            result["date"]=time.strptime(elm.childNodes[0].data,'%d-%b-%Y')
+        elif elm.nodeName==node[1]:
+            result["author"]=elm.childNodes[0].data
+        elif elm.nodeName==node[2]:
+            description.append(elm.childNodes[0].data)
+        elif elm.nodeName==node[3]:
+            result["numberFiles"]=int(elm.childNodes[0].data)
+        elif elm.nodeName==node[4]:
+            for child in elm.childNodes:
+                if child.nodeName=='data':
+                    result["ForceVolumeNames"].append(child.childNodes[0].data)
+    strDesc=str()
+    for line in description:
+        strDesc=strDesc+line+'\n'
+    result['comment']=strDesc[0:-1]
+    return result
+if __name__=="__main__":
+    result=xmlExtractExperiment("experiment.xml")
+    
+    #result=xmlExtractFV("C050614A.002.xml")
+    print result

Added: trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/fovea_toolbox/misc.py
===================================================================
--- trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/fovea_toolbox/misc.py	                        (rev 0)
+++ trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/fovea_toolbox/misc.py	2012-08-20 10:43:48 UTC (rev 12094)
@@ -0,0 +1,365 @@
+#! /usr/bin/python
+# -*- coding: utf-8 -*-
+'''
+This module contains the second stage posprocessing tools.
+'''
+__author__  = "Charles Roduit <charles.roduit at gmail.com>"
+__date__ = "28.12.2008"
+__license__ = "GNU Public License (GPL) version 3"
+__version__ = "0.1"
+
+from warnings import warn
+import os
+import csv
+
+import numpy
+import urllib2
+import datetime
+
+def remove_from_mask(data, mask):
+    """
+        Remove data from the mask.
+        
+        Let's have a data of this kind :
+        
+        >>> import numpy
+        >>> data = [{'pos_x' : 0, 'pos_y' : 0, 'item' : 0},\
+                    {'pos_x' : 0, 'pos_y' : 1, 'item' : 1},\
+                    {'pos_x' : 0, 'pos_y' : 2, 'item' : 2},\
+                    {'pos_x' : 0, 'pos_y' : 3, 'item' : 3},\
+                    {'pos_x' : 1, 'pos_y' : 3, 'item' : 4},\
+                    {'pos_x' : 2, 'pos_y' : 0, 'item' : 5},\
+                    {'pos_x' : 2, 'pos_y' : 3, 'item' : 6},\
+                    ]
+        
+        And let's have a mask of this kind :
+        
+        >>> mask = numpy.array([[True, True, False, False],\
+                    [True, True, False, False],\
+                    [True, True, False, False],\
+                    [True, True, False, False]])
+        
+        Now, let's apply the remove from mask :
+        
+        >>> new_list = remove_from_mask(data, mask)
+    """
+    # Data can be from event structure.
+    # In the data structure, we have info about the position on the array. We
+    # then exclude data that are in the mask. data['pos_x'] and data['pos_y']
+    new_list = []
+    for item in data:
+        if not mask[item['pos_x'], item['pos_y']]:
+            new_list.append(item)
+    return new_list
+
+def generate_mask(array, value):
+    mask = array < mdata
+    return mask
+
+def mask_bool(mask_1, mask_2, fct):
+    """
+    Make boolean operation on mask arrays.
+
+    Boolean operation can be AND, OR, XOR, NOT
+
+    >>> array_1 = [True, True, False, False]
+    >>> array_2 = [False, True, False, True]
+    >>> mask_bool(array_1, array_2, "AND")
+    array([False,  True, False, False], dtype=bool)
+    >>> mask_bool(array_1, array_2, "OR")
+    array([ True,  True, False,  True], dtype=bool)
+    >>> mask_bool(array_1, array_2, "XOR")
+    array([ True, False, False,  True], dtype=bool)
+    >>> mask_bool(array_1, array_2, "NOT")
+    >>> mask_bool(array_1, array_2, "NOT")
+    array([ True, False, False, False], dtype=bool)
+    """
+
+    # If the two arrays does not have the same shape, raise exception
+    #if numpy.shape(mask_1) != numpy.shape(mask_2):
+    #    raise ValueError, "operands could not be broadcast together with shapes {0} {1}".format(numpy.shape(mask_1), numpy.shape(mask_2))
+    #__mask_1 = check_bool(mask_1)
+    #__mask_2 = check_bool(mask_2)
+    if fct == "AND":
+        return numpy.logical_and(mask_1, mask_2)
+    elif fct == "OR":
+        return numpy.logical_or(mask_1, mask_2)
+    #elif fct == "NOT":
+    #    return numpy.logical_and(mask_1, mask_2)
+    elif fct == "XOR":
+        return numpy.logical_xor(mask_1, mask_2)
+    else:
+        raise ValueError, "function %s is not known"%(fct)
+    
+def check_bool(array):
+    """
+    Check if array is boolean and change it if not.
+    """
+
+    try:
+        mtype = array.dtype
+    except:
+        __array = numpy.array(array, dtype=bool)
+    else:
+        if mtype is not bool:
+            __array = numpy.array(array, dtype=bool)
+        else:
+            __array = array
+    return array
+
+def generate_array(data, dtype, shape):
+    """
+        Generates the array corresponding to the data. Data is a list of
+        dictionnary. These dictionnaries should, at least, contain the following
+        keys : 'pos_x' and 'pos_y' to inform on the position on the array and
+        dtype for the value that should come in the array (with some exeptions,
+        see parameters below).
+        
+        Parameters :
+            data : list
+                List of dictionnaries. All dictionnaries should contain the
+                following keys :
+                    'pos_x' and 'pos_y' : position in the array
+                    ttype : the threshold type
+                    dtype : the data to insert in the array
+            dtype : str
+                The data type to insert in the array. This should be one key
+                present in the dictionnaries or :
+                'count' : The number of data that are in each array position.
+            shape : tuple
+                The shape of the returned array.
+        
+        Returns :
+            new_array : 2D numpy.array
+                The array generated with the parameters.
+        >>> data = [{'pos_x' : 0, 'pos_y' : 0, 'item' : 2},\
+                    {'pos_x' : 0, 'pos_y' : 1, 'item' : 2},\
+                    {'pos_x' : 0, 'pos_y' : 1, 'item' : 1},\
+                    {'pos_x' : 0, 'pos_y' : 2, 'item' : 2},\
+                    {'pos_x' : 0, 'pos_y' : 3, 'item' : 2},\
+                    {'pos_x' : 1, 'pos_y' : 3, 'item' : 3},\
+                    {'pos_x' : 2, 'pos_y' : 0, 'item' : 1},\
+                    {'pos_x' : 2, 'pos_y' : 3, 'item' : 2},\
+                    ]
+        >>> new_data = remove_from_threshold(data, 'item', 1)
+        >>> narray = generate_array(new_data, 'count', (4,4))
+        >>> print narray
+        [[ 1.  2.  1.  1.]
+         [ 0.  0.  0.  1.]
+         [ 1.  0.  0.  1.]
+         [ 0.  0.  0.  0.]]
+    """
+    new_array = numpy.zeros(shape)
+    for item in data:
+        res = False
+        if dtype == 'count':
+            new_array[item['pos_x'], item['pos_y']] += 1
+        else:
+            # Get the correct value to fill the array
+            if dtype in ['fit_length']:
+                try:
+                    value = item[dtype][0]
+                except TypeError:
+                    value = None
+            else:
+                value = item[dtype]
+            # If there is no value, nothing to do.
+            if value is None:
+                res = False
+            else:
+                res = value > new_array[item['pos_x'], item['pos_y']]
+            if res:
+                new_array[item['pos_x'], item['pos_y']] = value
+    return new_array
+
+def remove_from_threshold(data, atype, avalue):
+    """
+        Remove from the data the type that are below a value.
+        
+        >>> import numpy
+        >>> data = [{'min' : -0.5, 'max' : 0,'loading_rate' : 0.1, 'dist' : 10 },\
+                    {'min' : -0.6, 'max' : -0.1,'loading_rate' : 0.2, 'dist' : 11 },\
+                    {'min' : -0.5, 'max' : 0,'loading_rate' : 0.15, 'dist' : 12 },\
+                    {'min' : -0.4, 'max' : 0.1,'loading_rate' : 0.12, 'dist' : 9 },\
+                    {'min' : -0.3, 'max' : 0.2,'loading_rate' : 0.11, 'dist' : 11 },\
+                    {'min' : -0.5, 'max' : 0,'loading_rate' : 0.09, 'dist' : 10 },\
+                    {'min' : -0.6, 'max' : -0.1,'loading_rate' : 0.11, 'dist' : 12 },\
+                    ]
+        >>> new_list = remove_from_threshold(data, 'dist', 10)
+        >>> #new_list = remove_from_threshold(data, 'distance', 10)
+        >>> new_list = remove_from_threshold([], 'dist', 10)
+    """
+    if type(avalue) in [float, int]:
+        # before, avalue was a single string.
+        avalue = [avalue, None]
+    if data is None or len(data) == 0:
+        return data
+    if atype not in data[0].keys():
+        raise AttributeError, atype + ' not a valid key for your data.'
+    if atype in ['fit_length', 'fit_plength']:
+        # In those cases, the data is in a list where the first is the value and
+        # the second is the standard deviation like : [value, stdev]
+        try:
+            if avalue[0] is not None:
+                data = [item for item in data if item[atype][0] >= avalue[0]]
+        except TypeError:
+            pass
+        try:
+            if avalue[1] is not None:
+                data = [item for item in data if item[atype][0] <= avalue[1]]
+        except TypeError:
+            pass
+    else:
+        if avalue[0] is not None:
+            data = [item for item in data if item[atype] >= avalue[0]]
+        if avalue[1] is not None:
+            data = [item for item in data if item[atype] <= avalue[1]]
+    return data
+
+def flatten(data):
+    """
+        Flatten an image.
+        
+        >>> import numpy
+        >>> data = numpy.array([range(10) for i in range(10)])
+        >>> flatten_data = flatten(data)
+        
+    """
+    vect_x = numpy.arange(data.shape[1])
+    # Determine the slope of the drift.
+    power = [numpy.polyfit(vect_x, line, 1)[0] for line in data]
+    m_pow = numpy.mean(power)
+    # Correct the image with the average slope.
+    new_data = [line - m_pow * vect_x for line in data]
+    new_data = numpy.array(new_data)
+    return new_data
+
+def get_message(curr_id, app_name='OpenFovea', app_version='0.1a1'):
+    """
+        Get message from the server.
+    """
+    message = None
+    headers = {'User-Agent' : '%s/%s'%(app_name, app_version)}
+    if curr_id == datetime.datetime(1900, 1, 1):
+        # This is the first run.
+        # Display then the welcome dialog
+        _link = 'http://www.freesbi.ch/docs/openfovea/welcome'
+    else:
+        _link = 'http://www.freesbi.ch/docs/openfovea/message'
+    _req = urllib2.Request(_link, headers=headers)
+    try:
+        _url = urllib2.urlopen(_req, timeout=0.1)
+    except urllib2.URLError:
+        _url = None
+    if _url is not None:
+        _message = _url.readlines()
+        if _message[0][:2] == 'id':
+            # we had a page, but not the one expected...
+            _new_msgid = _message[0].strip('\n').split(' = ')[1]
+            if _new_msgid == 'today':
+                _new_msgid = datetime.datetime.today()
+            else:
+                _new_msgid = datetime.datetime.strptime(_new_msgid,
+                                                        '%Y, %m, %d')
+            if _new_msgid > curr_id:
+                message = _message[0:]
+                curr_id = _new_msgid
+        _url.close()
+    return message, curr_id
+
+def ismasked(value):
+    '''
+        Return TRUE if the value is masked, of FALSE if not.
+        Value has to be a scalar.
+        
+        >>> import numpy
+        >>> ismasked(1)
+        False
+        >>> test = numpy.ma.array([1,2,3,4], mask=[0,0,1,1])
+        >>> ismasked(test[0])
+        False
+        >>> ismasked(test[3])
+        True
+        
+        Only scalar object can be tested with this function :
+        >>> ismasked(test)
+        Traceback (most recent call last):
+        ...
+        TypeError: Only scalar object can be tested this way.
+
+    '''
+    good_type = True
+    try:
+        len(value)
+        good_type = False
+    except:
+        pass
+    if not good_type:
+        raise TypeError, "Only scalar object can be tested this way."
+    try:
+        result = (type(value) == numpy.ma.core.MaskedConstant)
+    except AttributeError:
+        result = (type(value) == numpy.ma.core.MaskedArray)
+    return result
+
+def export_list(filename, list_array, header, preambule=None, transpose=False):
+    """
+        Export a list of array in csv.
+        
+        >>> list = [range(10), range(10), range(20), range(20)]
+        >>> header = ['1st', '2nd', '3rd', '4th']
+        >>> export_list('test.csv', list, header, transpose=True)
+    """
+    
+    # test that the length of all elements are the same.
+    
+    length = [len(item) for item in list_array]
+    curves = complete_list(list_array)
+    if transpose:
+        curves = curves.transpose(1,0)
+    
+    ## generate the filename
+    split_filename = os.path.splitext(filename)
+    if split_filename[1] in ['.csv', '.txt']:
+        filename = split_filename[0]
+    else:
+        # It is probably not an extention, then restore it
+        filename = split_filename[0] + split_filename[1]
+    
+    filename = filename + '.csv'
+    old_masked_print_option = numpy.ma.masked_print_option.display()
+    numpy.ma.masked_print_option.set_display('')
+    
+    # Write the file.
+    fid = open(filename, 'wb')
+    fcsv = csv.writer(fid)
+    if preambule:
+        fcsv.writerow(preambule)
+    fcsv.writerow(header)
+    for item in curves:
+        fcsv.writerow(item)
+    numpy.ma.masked_print_option.set_display(old_masked_print_option)
+    
+def complete_list(list_array):
+    """
+        Complete a list of array in order that all elements has the same
+        length.
+        
+        >>> list = [range(10), range(20)]
+        >>> new_list = complete_list(list)
+    """
+    
+    max_length = max([len(item) for item in list_array])
+    diff = [max_length - len(item) for item in list_array]
+    
+    mask = numpy.zeros((len(list_array), max_length))
+    array = numpy.zeros((len(list_array), max_length))
+    for item, itarray, itmask in zip(list_array, array, mask):
+        itarray[:len(item)] = item
+        itmask[len(item):] = 1
+    new_array = numpy.ma.array(array, mask=mask)
+    return new_array
+if __name__ == "__main__":
+    
+    import doctest
+    doctest.testmod()

Added: trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/fovea_toolbox/opengl.py
===================================================================
--- trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/fovea_toolbox/opengl.py	                        (rev 0)
+++ trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/fovea_toolbox/opengl.py	2012-08-20 10:43:48 UTC (rev 12094)
@@ -0,0 +1,689 @@
+#!/usr/bin/env python
+# -*- coding: UTF-8 -*-
+
+"""
+    This opengl code was higly inspired from the pyopengl documentation, and
+    particularly on the NeHe tutorials, thank's a lot to them !
+"""
+from copy import deepcopy
+
+import numpy
+from OpenGL.GL import *
+from OpenGL.GLUT import *
+from OpenGL.GLU import *
+from gtk.gtkgl.apputils import *
+
+from matplotlib.pylab import pcolor
+import time
+
+from misc import ismasked
+
+class Topography(GLScene,
+             GLSceneButton,
+             GLSceneButtonMotion):
+    """
+        Create a 3D view of an array, the color is based on the color array and
+        the topography on the array.
+        
+        To create a view, follow the following simple steps :
+        
+        >>> import numpy
+        >>> array = numpy.random.randn(32, 32)
+        >>> color_array = numpy.random.randn(32, 32)
+        >>> Topography(array, color_array)
+    """
+    
+    def __init__(self, array, color_array=None, clut=None):
+        GLScene.__init__(self,
+                         gtk.gdkgl.MODE_RGB   |
+                         gtk.gdkgl.MODE_DEPTH |
+                         gtk.gdkgl.MODE_DOUBLE)
+        self.window = 0 # the glut window
+        self.rotation = 0.0 # the rotation angle for the object
+        self.array = array
+        self.rot = [1, 1, 1]
+        self.zoom = 20
+        self.translate = [0, 0, 0]
+        # This is the Color Look-Up Table (CLUT)
+        if color_array is not None:
+            if clut is None:
+                clut = (array.min(), array.max())
+            self.clut = pcolor(numpy.array([[clut[0], clut[1]] for i in range(2)]))
+        else:
+            self.clut = None # Have to define it later...
+        
+        self.mouse_eventpos_begin = [0, 0] # To record the position 
+                                           # of the mouse during an event
+        self.slice = {'begin' : [0, 0, 0],  # This is the portion of the array
+                      'end' : [-1, -1, -1]} # to display
+        ### Initialize the Window
+        # pass argument to init
+        if array is not None:
+            self.coordinate = make_coordinate(array, self.clut)
+            self.all_coordinate = deepcopy(self.coordinate)
+        glHint(GL_CLIP_VOLUME_CLIPPING_HINT_EXT, GL_FASTEST)
+        
+        glutInit()
+        #glutCreateWindow('OpenGL Tutorial 1')
+    def init(self):
+        glEnable(GL_LIGHTING)
+        glEnable(GL_COLOR_MATERIAL)
+        
+        glEnable(GL_LIGHT0)
+        glLightfv(GL_LIGHT0, GL_AMBIENT, (0.5, 0.5, 0.8))
+        glLightfv(GL_LIGHT0, GL_POSITION, (0, 2, 2, 0))
+        glDepthFunc(GL_LESS)
+        glEnable(GL_DEPTH_TEST)
+    def keyboard_perss(self, event):
+        print event
+    def button_press(self, width, height, event):
+        if event.state & gtk.gdk.BUTTON4_MASK:
+            print "ZOOM"
+        if event.state & gtk.gdk.BUTTON5_MASK:
+            print "UNZOOM"
+        if event.state & gtk.gdk.SCROLL_MASK:
+            print "Scroll"
+        self.mouse_eventpos_begin = [event.x, event.y]
+    
+    def button_release(self, width, height, event):
+        pass
+    def button_motion(self, width, height, event):
+        if event.state & gtk.gdk.BUTTON1_MASK:
+            deg_factor = numpy.pi/180
+            rot_x = ((event.x - self.mouse_eventpos_begin[0]) / width) * 360
+            rot_y = ((event.y - self.mouse_eventpos_begin[1]) / height) * 360
+            self.rot[0] = (self.rot[0] + rot_y) % 360
+            self.rot[1] = (self.rot[1] + numpy.cos(self.rot[0] * deg_factor) * rot_x) % 360
+            self.rot[2] = (self.rot[2] - numpy.sin(self.rot[0] * deg_factor) * rot_x) % 360
+        if event.state & gtk.gdk.BUTTON2_MASK:
+            self.translate[0] = self.translate[0] + (
+                                event.x - self.mouse_eventpos_begin[0]) / width
+            self.translate[1] = self.translate[1] - (
+                                event.y - self.mouse_eventpos_begin[1]) / height
+        self.mouse_eventpos_begin = [event.x, event.y]
+        self.invalidate()
+    def rotate(self):
+        """
+            The rotation of the array
+        """
+        
+        self.rotx += 2
+        if self.rotx > 360:
+            self.rotx = self.rotx - 360
+        self.roty += 2
+        if self.roty > 360:
+            self.roty = self.roty - 360
+        glutPostRedisplay()
+            
+    def reshape(self, width, height):
+        glViewport(0, 0, width, height)
+        glMatrixMode(GL_PROJECTION)
+        glLoadIdentity()
+        if width > height:
+            w = float(width) / float(height)
+            glFrustum(-w, w, -1.0, 1.0, 5.0, 60.0)
+        else:
+            h = float(height) / float(width)
+            glFrustum(-1.0, 1.0, -h, h, 5.0, 60.0)
+        #glMatrixMode(GL_MODELVIEW)
+    def display(self, width, height):
+        """
+            The main drawing funtion
+        """
+        # Clear The Screen And The Depth Buffer
+        glClear(GL_COLOR_BUFFER_BIT | GL_DEPTH_BUFFER_BIT)
+        glLoadIdentity()    # Reset The View
+        glMatrixMode(GL_PROJECTION)
+        # The text
+        glColor3f(1.0, 1, 1)
+        glRasterPos2f(-0.9,0.9)
+        to_display = "x : [%i : %i], y : [%i : %i], z : [%i : %i]"%(
+                     self.slice['begin'][0], self.slice['end'][0],
+                     self.slice['begin'][1], self.slice['end'][1],
+                     self.slice['begin'][2], self.slice['end'][2],
+                     )
+        for string in to_display:
+            glutBitmapCharacter(GLUT_BITMAP_8_BY_13, ord(string))
+        # Modify the projection matrix
+        gluPerspective(self.zoom, 1., 1., 500.0)
+        glTranslatef(0.0,  0.0, -4)
+        glRotate(self.rot[0],1.0,0.0,0.0)
+        glRotate(self.rot[1], 0.0, 1.0, 0.0)
+        glRotate(self.rot[2], 0.0, 0.0, 1.0)
+        glTranslate(self.translate[0], self.translate[1], self.translate[2])
+        # Every thing after is modified by the projection matrix
+        self.generate_vertex(self.coordinate)
+            
+        glFlush()
+        
+    def generate_vertex(self, coordinate):
+        glBegin(GL_QUADS)
+        for item in coordinate:
+            glNormal3f(item['normal'][0], item['normal'][1], item['normal'][2])
+            # Bottom left
+            glColor3f(item['color'][0][0],
+                      item['color'][0][1],
+                      item['color'][0][2])
+            glVertex3f(item['vertex_coord'][0][0],
+                       item['vertex_coord'][0][1],
+                       item['vertex_coord'][0][2])
+            # upper left
+            glColor3f(item['color'][1][0],
+                      item['color'][1][1],
+                      item['color'][1][2])
+            glVertex3f(item['vertex_coord'][1][0], 
+                       item['vertex_coord'][1][1],
+                       item['vertex_coord'][1][2])
+            # bottom right
+            glColor3f(item['color'][3][0],
+                      item['color'][3][1],
+                      item['color'][3][2])
+            glVertex3f(item['vertex_coord'][3][0],
+                       item['vertex_coord'][3][1],
+                       item['vertex_coord'][3][2])
+            # upper right
+            glColor3f(item['color'][2][0],
+                      item['color'][2][1],
+                      item['color'][2][2])
+            glVertex3f(item['vertex_coord'][2][0],
+                       item['vertex_coord'][2][1],
+                       item['vertex_coord'][2][2])
+        glEnd()
+        glLineWidth(1.5)
+        glBegin(GL_LINES)
+        for item in coordinate:
+            glColor3f(0., 0., 0.)
+            glVertex3f(item['vertex_coord'][0][0],
+                       item['vertex_coord'][0][1],
+                       item['vertex_coord'][0][2])
+            glVertex3f(item['vertex_coord'][1][0],
+                       item['vertex_coord'][1][1],
+                       item['vertex_coord'][1][2])
+            glColor3f(0., 0., 0.)
+            glVertex3f(item['vertex_coord'][1][0],
+                       item['vertex_coord'][1][1],
+                       item['vertex_coord'][1][2])
+            glVertex3f(item['vertex_coord'][3][0],
+                       item['vertex_coord'][3][1],
+                       item['vertex_coord'][3][2])
+            glColor3f(0., 0., 0.)
+            glVertex3f(item['vertex_coord'][2][0],
+                       item['vertex_coord'][2][1],
+                       item['vertex_coord'][2][2])
+            glVertex3f(item['vertex_coord'][0][0],
+                       item['vertex_coord'][0][1],
+                       item['vertex_coord'][0][2])
+            glColor3f(0., 0., 0.)
+            glVertex3f(item['vertex_coord'][3][0],
+                       item['vertex_coord'][3][1],
+                       item['vertex_coord'][3][2])
+            glVertex3f(item['vertex_coord'][2][0],
+                       item['vertex_coord'][2][1],
+                       item['vertex_coord'][2][2])
+        glEnd()
+class Tomography(Topography):
+    def __init__(self, array, clut):
+        Topography.__init__(self, None)
+        self.array = array
+        if clut is None:
+            clut = (array.min(), array.max())
+        clut = numpy.array([[clut[0], clut[1]] for i in range(2)])
+        self.clut = pcolor(clut)
+        self.all_coordinate = make_tomo_coordinate(array, self.clut)
+        self._slice_it()
+    def slice_it(self, dirct, qty):
+        """
+            Slice the array in a certain direction in a certain quantity.
+            
+            parameters :
+                dirct : str
+                    The direction to slice.
+                    'x' to slice in x from the front.
+                    'X' to slice in x from the back.
+                    'y' to slice in y from the left.
+                    'Y' to slice in y from the right.
+                    'z' to slice in z from the top.
+                    'Z' to slice in z from the bottom.
+        """
+        if dirct == 'x' and (0 <= self.slice['begin'][0] + 
+                             qty <= self.array.shape[0]):
+            self.slice['begin'][0] += qty
+        elif dirct == 'X' and (0 <= self.slice['end'][0] + 
+                               qty <= self.array.shape[0]):
+            self.slice['end'][0] += qty
+        elif dirct == 'y' and (0 <= self.slice['begin'][1] + 
+                               qty <= self.array.shape[1]):
+            self.slice['begin'][1] += qty
+        elif dirct == 'Y' and (0 <= self.slice['end'][1] + 
+                               qty <= self.array.shape[1]):
+            self.slice['end'][1] += qty
+        elif dirct == 'z' and (0 <= self.slice['begin'][2] + 
+                               qty <= self.array.shape[2]):
+            self.slice['begin'][2] += qty
+        elif dirct == 'Z' and (0 <= self.slice['end'][2] + 
+                               qty <= self.array.shape[2]):
+            self.slice['end'][2] += qty
+        self._slice_it()
+    def _slice_it(self):
+        """
+            Slice the array.
+            
+            For example : self.slice_it([0, 0, 4], [-1, -1, -1])
+            will slice the array in z by removing the 4 (0 to 3) first elements.
+            
+            Parameters :
+                begin : array_like
+                    begin[0] is the first x
+                    begin[1] the first y
+                    begin[2] the first z
+                end : array_like
+                    end[0] is the last x
+                    end[1] is the last y
+                    end[2] is the last z
+            
+            Retruns :
+                nothing. Just the self.coordinate are modified according to it.
+        """
+        
+        factor = float(max(self.array.shape))
+        _begin = [0, 0, 0]
+        _end = [-1, -1, -1]
+        for i in range(3):
+            if self.slice['end'][i] == -1:
+                self.slice['end'][i] = self.array.shape[i]
+            _begin[i] = ((float(self.slice['begin'][i]) / factor) - 
+                          self.array.shape[i]/(2*factor))
+            _end[i] = ((float(self.slice['end'][i]) / factor) - 
+                        self.array.shape[i]/(2*factor))
+        self.coordinate = list()
+        for item in self.all_coordinate:
+            # find items that are outside the slice.
+            eliminate = 0
+            for vertex in item['vertex_coord']:
+                if not eliminate and (
+                                vertex[0] < _begin[0] or vertex[0] > _end[0] or
+                                vertex[1] < _begin[1] or vertex[1] > _end[1] or
+                                vertex[2] < _begin[2] or vertex[2] > _end[2]):
+                    eliminate = 1
+            if not eliminate:
+                self.coordinate.append(item)
+        # Add the borders...
+        borders = generate_array_borders(self.array,
+                                         self.slice['begin'], self.slice['end'],
+                                         self.clut)
+        self.coordinate = self.coordinate + \
+                          [i for i in borders if i is not None]
+def make_tomo_coordinate(array, color_map):
+    """
+        This function creates the coordinate of the vertex and the corresponding
+        color.
+        The array is a 3D array which represent the space with pixels coordinate
+        corresponding to the location in the array and the color value coded in
+        that location.
+        
+        Parameters :
+            array : numpy.ma.array
+                This is an array with mask. Masked values are transparent
+                pixels, otherwise, the pixel values represent the color.
+        
+        Returns :
+            coordinate : list
+                List of vertex to display.
+    """
+    #array = array/array.max() # to be between 0 and 1.
+    #plot_array = numpy.array([[array.min(), array.max()] for i in range(2)])
+    #plot_array = pcolor(plot_array) # to have a cmap
+    coordinate = list()
+    #non_zero_indice = array.mask.nonzero()
+    for px, y, z in zip(array.mask.nonzero()[0],
+                       array.mask.nonzero()[1],
+                       array.mask.nonzero()[2]):
+        item = generate_border_vertex(array, px, y, z, color_map)
+        coordinate += [i for i in item if i is not None]
+                
+    # generage the top face and bottom face:
+    [x_list, y_list] = numpy.meshgrid(range(array.shape[0]),
+                                      range(array.shape[1]))
+    for px, y in zip(x_list.flat, y_list.flat):
+        item = [generate_vertex(array, px, y, array.shape[2]-1, color_map),
+               generate_vertex(array, px, y, 0, color_map)]
+        coordinate += [i for i in item if i is not None]
+    # generate the front and back faces:
+    coord_list = numpy.meshgrid(range(array.shape[0]), range(array.shape[2]))
+    for px, z in zip(coord_list[0].flat, coord_list[1].flat):
+        item = [generate_vertex(array, px, array.shape[1]-1, z,
+                                color_map, face = 'front'),
+                generate_vertex(array, px, 0, z,
+                                color_map, face = 'front')]
+        coordinate += [i for i in item if i is not None]
+    # generate the right and left faces:
+    coord_list = numpy.meshgrid(range(array.shape[1]), range(array.shape[2]))
+    for y, z in zip(coord_list[0].flat, coord_list[1].flat):
+        item = [generate_vertex(array, array.shape[0]-1, y, z,
+                                color_map, face = 'right') ,
+                generate_vertex(array, 0, y, z,
+                                color_map, face = 'right')]
+        coordinate += [i for i in item if i is not None]
+    return coordinate
+def generate_array_borders(array, begin, end, color_map):
+    """
+        Generate the 
+    """
+    #array = array/array.max() # to be between 0 and 1.
+    #plot_array = numpy.array([[array.min(), array.max()] for i in range(2)])
+    #plot_array = pcolor(plot_array)
+    coordinate = list()
+    if begin[0] != 0:
+        # regenerate the front face
+        coord_list = numpy.meshgrid(xrange(begin[1], end[1]),
+                                    xrange(begin[2], end[2]))
+        coordinate += [generate_vertex(array, begin[0], y, z,
+                                       color_map, face = 'right')
+                        for y, z in zip(coord_list[0].flat, coord_list[1].flat)]
+    if end[0] != array.shape[0]:
+        # regenerate the back face
+        coord_list = numpy.meshgrid(xrange(begin[1], end[1]),
+                                    xrange(begin[2], end[2]))
+        coordinate += [generate_vertex(array, end[0], y, z,
+                                       color_map, face = 'right')
+                        for y, z in zip(coord_list[0].flat, coord_list[1].flat)]
+    if begin[1] != 0:
+        # regenerate the left face
+        coord_list = numpy.meshgrid(xrange(begin[0], end[0]),
+                                    xrange(begin[2], end[2]))
+        coordinate += [generate_vertex(array, px, begin[1], z,
+                                       color_map, face = 'front')
+                        for px, z in zip(coord_list[0].flat, coord_list[1].flat)]
+    if end[1] != array.shape[1]:
+        # regenerate the left face
+        coord_list = numpy.meshgrid(xrange(begin[0], end[0]),
+                                    xrange(begin[2], end[2]))
+        coordinate += [generate_vertex(array, px, end[1], z,
+                                       color_map, face = 'front')
+                        for px, z in zip(coord_list[0].flat, coord_list[1].flat)]
+    if begin[2] != 0:
+        # regenerate the left bottom
+        coord_list = numpy.meshgrid(xrange(begin[0], end[0]),
+                                    xrange(begin[1], end[1]))
+        coordinate += [generate_vertex(array, px, y, begin[2],
+                                       color_map, face = 'floor')
+                        for px, y in zip(coord_list[0].flat, coord_list[1].flat)]
+    if end[2] != array.shape[2]:
+        # regenerate the left top
+        coord_list = numpy.meshgrid(xrange(begin[0], end[0]),
+                                    xrange(begin[1], end[1]))
+        coordinate += [generate_vertex(array, px, y, end[2],
+                                       color_map, face = 'floor')
+                        for px, y in zip(coord_list[0].flat, coord_list[1].flat)]
+    return coordinate
+def generate_border_vertex(array, px, y, z, color_map):
+    """
+        Generates the vertex that touch this one.
+    """
+    # The vertex is a 3d vertex composed on 6 faces
+    #
+    #       (x, y+1, z+1)_______
+    #                  /·     /| (x+1, y+1, z+1)
+    #                 / ·    / |
+    #    (x, y, z+1) +------+  |
+    #                |  ·······+ (x+1, y+1, z)
+    #   (x, y+1, z)  | ·    | /      
+    #                |·     |/       
+    #                +------+ (x+1, y, z)
+    #                (x, y, z)
+    block = {'right' : px + 1 == array.shape[0],
+             'left' : px == 0,
+             'front' : y + 1 == array.shape[1],
+             'back' : y == 0,
+             'top' : z + 1 == array.shape[2],
+             'bottom' : z == 0}
+    pixels = list()
+    factor = float(max(array.shape))
+    pos = [((float(px) / factor) - array.shape[0] / (2 * factor)),
+           ((float(y) / factor) - array.shape[1] / (2 * factor)),
+           ((float(z) / factor) - array.shape[2] / (2 * factor))]
+    pos_u = [((float(px + 1) / factor) - array.shape[0] / (2 * factor)),
+           ((float(y+1) / factor) - array.shape[1] / (2 * factor)),
+           ((float(z+1) / factor) - array.shape[2] / (2 * factor))]
+    pos_d = [((float(px - 1) / factor) - array.shape[0] / (2 * factor)),
+           ((float(y-1) / factor) - array.shape[1] / (2 * factor)),
+           ((float(z-1) / factor) - array.shape[2] / (2 * factor))]
+    if not block['bottom'] and not array.mask[px, y, z-1]:
+        # Bottom pixel exist... create the bottom face.
+        color = color_map.to_rgba(array[px, y, z-1])
+        pixels.append({'vertex_coord' : [[pos[0], pos[1], pos[2]],
+                                              [pos[0], pos_u[1], pos[2]],
+                                              [pos_u[0], pos[1], pos[2]],
+                                              [pos_u[0], pos_u[1], pos[2]]],
+                            'color' : [color, color, color, color],
+                            'normal' : NORMAL['bottom']})
+                            
+    if not block['right'] and not array.mask[px + 1, y, z]:
+        # Right pixel exist... create the right face.
+        color = color_map.to_rgba(array[px + 1, y, z])
+        pixels.append({'vertex_coord' : [[pos_u[0], pos[1], pos[2]],
+                                        [pos_u[0], pos_u[1], pos[2]],
+                                        [pos_u[0], pos[1], pos_u[2]],
+                                        [pos_u[0], pos_u[1], pos_u[2]]],
+                        'color' : [color, color, color, color],
+                        'normal' : NORMAL['right']})
+    if not block['front'] and not array.mask[px, y+1, z]:
+        # Back pixel exist... create the back face.
+        color = color_map.to_rgba(array[px, y+1, z])
+        pixels.append({'vertex_coord' : [[pos[0], pos_u[1], pos[2]],
+                                          [pos_u[0], pos_u[1], pos[2]],
+                                          [pos[0], pos_u[1], pos_u[2]],
+                                          [pos_u[0], pos_u[1], pos_u[2]]],
+                             'color' : [color, color, color, color],
+                        'normal' : NORMAL['back']
+                                })
+    if not block['left'] and not array.mask[px-1, y, z]:
+        # Left pixel exist... create the left face.
+        color = color_map.to_rgba(array[px - 1, y, z])
+        pixels.append({'vertex_coord' : [[pos[0], pos[1], pos[2]],
+                                         [pos[0], pos_u[1], pos[2]],
+                                         [pos[0], pos[1], pos_u[2]],
+                                         [pos[0], pos_u[1], pos_u[2]]],
+                        'color' : [color, color, color, color],
+                        'normal' : NORMAL['left']})
+    if not block['back'] and not array.mask[px, y-1, z]:
+        # Front pixel exist... create the fron face.
+        color = color_map.to_rgba(array[px, y-1, z])
+        pixels.append({'vertex_coord' : [[pos[0], pos[1], pos[2]],
+                                          [pos_u[0], pos[1], pos[2]],
+                                          [pos[0], pos[1], pos_u[2]],
+                                          [pos_u[0], pos[1], pos_u[2]]],
+                       'color' : [color, color, color, color],
+                        'normal' : NORMAL['front']
+                                })
+    if not block['top'] and not array.mask[px, y, z+1]:
+        # Top pixel exist... create the top face.
+        color = color_map.to_rgba(array[px, y, z+1])
+        pixels.append({'vertex_coord' : [[pos[0], pos[1], pos_u[2]],
+                                              [pos[0], pos_u[1], pos_u[2]],
+                                              [pos_u[0], pos[1], pos_u[2]],
+                                              [pos_u[0], pos_u[1], pos_u[2]]],
+                            'color' : [color, color, color, color],
+                        'normal' : NORMAL['top']})
+    return pixels
+def generate_vertex(array, px, y, z, color_map, face = 'floor'):
+    """
+        Generate the vertex in the defined position.
+    """
+    voxel = None
+    if not ismasked(array[px, y, z]):
+#    if type(array[px, y, z]) not in [numpy.ma.core.MaskedArray,  # old numpy
+#                                     numpy.ma.core.MaskedConstant]:
+        factor = float(max(array.shape))
+        pos = [((float(px) / factor) - array.shape[0] / (2 * factor)),
+               ((float(y) / factor) - array.shape[1] / (2 * factor)),
+               ((float(z) / factor) - array.shape[2] / (2 * factor))]
+        pos_u = [((float(px + 1) / factor) - array.shape[0] / (2 * factor)),
+               ((float(y+1) / factor) - array.shape[1] / (2 * factor)),
+               ((float(z+1) / factor) - array.shape[2] / (2 * factor))]
+               
+        # The vertex is a 3d vertex composed on 6 faces
+        #
+        #       (x, y+1, z+1)_______
+        #                  /·     /| (x+1, y+1, z+1)
+        #                 / ·    / |
+        #    (x, y, z+1) +------+  |
+        #                |  ·······+ (x+1, y+1, z)
+        #   (x, y+1, z)  | ·    | /      
+        #                |·     |/       
+        #                +------+ (x+1, y, z)
+        #                (x, y, z)
+        # By convention, the face of the bottom has the color form the pixel x,
+        # y, z and the face from the top has the color of x, y, z+1.
+        # Then, if pixel in z+1 is masked, we do not render it.
+        # In order to not make twice the same face, we only consiter faces at
+        # bottom : [(x, y, z), (x+1, y, z), (x+1, y+1, z), (x, y+1, z)]
+        # front : [(x, y, z), (x+1, y, z), (x, y, z+1), (x+1, y, z+1)]
+        # right : [(x, y, z), (x, y+1, z), (x, y, z+1), (x, y+1, z+1),]
+        color = color_map.to_rgba(array[px, y, z])
+        if face == 'floor' :
+            if z+1 == array.shape[2]:
+                pos[2] = pos_u[2]
+            voxel = {'vertex_coord' : [[pos[0], pos[1], pos[2]],
+                                              [pos[0], pos_u[1], pos[2]],
+                                              [pos_u[0], pos[1], pos[2]],
+                                              [pos_u[0], pos_u[1], pos[2]]],
+                            'color' : [color, color, color, color],
+                        'normal' : NORMAL['bottom'],
+                            }
+        elif face == 'front':
+            if y+1 == array.shape[1]:
+                pos[1] = pos_u[1]
+            voxel = {'vertex_coord' : [[pos[0], pos[1], pos[2]],
+                                          [pos_u[0], pos[1], pos[2]],
+                                          [pos[0], pos[1], pos_u[2]],
+                                          [pos_u[0], pos[1], pos_u[2]]],
+                            'color' : [color, color, color, color],
+                        'normal' : NORMAL['front']
+                            }
+        elif face == 'right':
+            if px + 1 == array.shape[0]:
+                pos[0] = pos_u[0]
+            voxel = {'vertex_coord' : [[pos[0], pos[1], pos[2]],
+                                          [pos[0], pos_u[1], pos[2]],
+                                          [pos[0], pos[1], pos_u[2]],
+                                          [pos[0], pos_u[1], pos_u[2]]],
+                            'color' : [color, color, color, color],
+                        'normal' : NORMAL['right']}
+    return voxel
+def make_coordinate(array, color_map):
+    """
+        This function creates the coordinate of the vertex and the corresponding
+        color.
+        
+        It returns a list of dictionnary.
+    """
+    #array = array / array.max() * 4
+#    color_array = color_array / color_array.max()
+#    plot_array = pcolor(color_array)
+    coordinate = list()
+    factor = float(max(array.shape))
+    for x in range(array.shape[0]):
+        for y in range(array.shape[1]):
+            z = array[px, y] / 10.
+            if type(color_array[px, y]) == numpy.ma.core.MaskedArray:
+                color = [1,1,1]
+            else:
+                color = color_map.to_rgba(color_array[px,y])
+            pos_x = float(x) / array.shape[0]
+            pos_y = float(y) / array.shape[1]
+            pos_x_u = float(x + 1) / array.shape[0]
+            pos_y_u = float(y + 1) / array.shape[1]
+            this_pixel = {'tex_coord' : [[pos_x, pos_y],
+                                      [pos_x, pos_y_u],
+                                      [pos_x_u, pos_y],
+                                      [pos_x_u, pos_y_u]],
+                          'vertex_coord' : [[px / factor - 0.5,
+                                             y / factor - 0.5,
+                                             z], # bottom left
+                                            [px / factor - 0.5,
+                                             (y + 1)/factor - 0.5,
+                                             z], # upper left
+                                            [(px + 1)/factor - 0.5,
+                                             y/factor - 0.5,
+                                             z], # bottom right
+                                            [(px + 1)/factor - 0.5,
+                                             (y + 1)/factor - 0.5,
+                                             z]], # upper right
+                          'color' : [color, color, color, color]}
+            coordinate.append(this_pixel)
+            if x > 0:
+                z_prev = array[px,-1, y] / 10
+                # we make a step pixel in x.
+                # The x and y are like pos_x and pos_y, pos_y_u
+                # The pos_z are from this pixel and from the next.
+                if type(color_array[px,-1,y]) == numpy.ma.core.MaskedArray:
+                    color_prev = [1,1,1]
+                else:
+                    color_prev = color_map.to_rgba(color_array[px,-1,y])
+                this_step = {'tex_coord' : [[pos_x, pos_y],
+                                      [pos_x, pos_y_u],
+                                      [pos_x, pos_y],
+                                      [pos_x, pos_y_u]],
+                          'vertex_coord' : [[px / factor - 0.5,
+                                             y / factor - 0.5, 
+                                             z], # bottom left
+                                            [px / factor - 0.5,
+                                             (y + 1) / factor - 0.5, 
+                                             z], # upper left
+                                            [px / factor - 0.5,
+                                             y/factor - 0.5, 
+                                             z_prev], # bottom right
+                                            [px / factor - 0.5,
+                                             (y + 1) / factor - 0.5, 
+                                             z_prev]], # upper right
+                          'color' : [color, color, color_prev, color_prev]}
+                coordinate.append(this_step)
+            if y > 0:
+                z_prev = array[px, y-1] / 10
+                # we make a step pixel in x.
+                # The x and y are like pos_x and pos_y, pos_y_u
+                # The pos_z are from this pixel and from the next.
+                if type(color_array[px,y-1]) == numpy.ma.core.MaskedArray:
+                    color_prev = [1,1,1]
+                else:
+                    color_prev = color_map.to_rgba(color_array[px,y-1])
+                this_step = {'tex_coord' : [[pos_x, pos_y],
+                                      [pos_x, pos_y],
+                                      [pos_x_u, pos_y],
+                                      [pos_x_u, pos_y]],
+                          'vertex_coord' : [[px / factor - 0.5,
+                                             y / factor - 0.5, 
+                                             z], # bottom left
+                                            [px / factor - 0.5,
+                                             y / factor - 0.5, 
+                                             z_prev], # upper left
+                                            [(px + 1)/factor - 0.5,
+                                             y / factor - 0.5, 
+                                             z], # bottom right
+                                            [(px + 1)/factor - 0.5,
+                                             y / factor - 0.5, 
+                                             z_prev]], # upper right
+                          'color' : [color, color_prev, color, color_prev]}
+                coordinate.append(this_step)
+                                      
+    return coordinate
+NORMAL = {
+    'top' : (0, 0, -1),
+    'bottom' : (0, 0, 1),
+    'left' : (0, -1, 0),
+    'right' : (0, 1, 0),
+    'front' : (-1, 0, 0),
+    'back' : (1, 0, 0)
+}
+# Some api in the chain is translating the keystrokes to this octal string
+# so instead of saying: ESCAPE = 27, we use the following.
+ESCAPE = '\033'
+
+if __name__ == '__main__':
+    import numpy
+    SIZE = 32
+    ARRAY = numpy.random.randn(SIZE, SIZE)
+    TMP_ARRAY = numpy.random.randn(SIZE, SIZE)
+    COLOR_ARRAY = numpy.ma.array(TMP_ARRAY, mask = TMP_ARRAY < 0)
+    TEST = Topography(array, COLOR_ARRAY)

Added: trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/fovea_toolbox/opengl_gtk.py
===================================================================
--- trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/fovea_toolbox/opengl_gtk.py	                        (rev 0)
+++ trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/fovea_toolbox/opengl_gtk.py	2012-08-20 10:43:48 UTC (rev 12094)
@@ -0,0 +1,115 @@
+#!/usr/bin/env python
+# -*- coding: UTF-8 -*-
+"""
+    This module is based on teapot2 example from the python-gtkglext examples.
+"""
+
+import pygtk
+pygtk.require('2.0')
+from gtk.gtkgl.apputils import *
+
+from opengl import Topography, Tomography
+
+class TopoWindow(gtk.Window):
+    """
+        Displays the 3D array in a gtk window.
+        
+        Parameters :
+            array : 2D numpy.array
+                Represents the height
+            color_array : 2D numpy.array
+                Represents value for the colorscale to plot in the surface.
+    """
+    def __init__(self, array, color_array=None, clut=None):
+        self.key = None
+        gtk.Window.__init__(self)
+        # Set self attributes.
+        self.set_title('3D view')
+        if sys.platform != 'win32':
+            self.set_resize_mode(gtk.RESIZE_IMMEDIATE)
+        self.set_reallocate_redraws(True)
+        self.connect('destroy', lambda quit: gtk.main_quit())
+        # Catch keyboard events
+        self.connect("key-press-event",self.on_window_key_press_event)
+        self.connect("key-release-event",self.on_window_key_release_event)
+        # Create the table.
+        self.table = gtk.Table(3, 3)
+        self.table.set_border_width(5)
+        self.table.set_col_spacings(5)
+        self.table.set_row_spacings(5)
+        self.table.show()
+        self.add(self.table)
+        # The scene and the
+        # GLArea widget to
+        # display it.
+        if array.ndim == 2:
+            self.topo = Topography(array, color_array, clut)
+        elif array.ndim ==3:
+            self.topo = Tomography(array, clut)
+        self.glarea = GLArea(self.topo)
+        self.glarea.connect("scroll_event", self.button_scroll)
+        self.glarea.set_size_request(300,300)
+        self.glarea.show()
+        self.table.attach(self.glarea, 0, 1, 0, 1)
+
+    def on_window_key_press_event(self, window, event):
+        if self.key is None and (64 < event.keyval < 123):
+            self.key = gtk.gdk.keyval_name(event.keyval)
+    def on_window_key_release_event(self, window, event):
+        self.key = None
+    def button_scroll(self, window, event):
+        if event.direction == gtk.gdk.SCROLL_UP:
+            if self.key == None:
+                self.topo.zoom = self.topo.zoom + self.topo.zoom/10.
+            elif self.key in ['x', 'X', 'y', 'Y', 'z', 'Z']:
+                self.topo.slice_it(self.key, -1)
+        elif event.direction == gtk.gdk.SCROLL_DOWN:
+            if self.key == None:
+                self.topo.zoom = self.topo.zoom - self.topo.zoom/10.
+            elif self.key in ['x', 'X', 'y', 'Y', 'z', 'Z']:
+                self.topo.slice_it(self.key, +1)
+        self.glarea.window.invalidate_rect(self.glarea.allocation, False)
+    def vchanged(self, vadj):
+        #self.topo.rotx = vadj.value
+        #self.glarea.window.invalidate_rect(self.glarea.allocation, False)
+        self.glarea.window.clear()
+        self.topo.slice_it([vadj.value, 0, 0], [-1, -1, -1])
+        #help(self.glarea.window.invalidate_rect)
+        self.glarea.window.invalidate_rect(self.glarea.allocation, False)
+    def hchanged(self, hadj):
+        self.topo.roty = hadj.value
+        self.glarea.window.invalidate_rect(self.glarea.allocation, False)
+    def zoom_changed(self, adj):
+        self.topo.zoom = adj.value
+        self.glarea.window.invalidate_rect(self.glarea.allocation, False)
+    
+    def run(self):
+        self.show()
+        gtk.main()
+def main():
+    import numpy
+    
+    size = 32
+    # Just create a beatifull gride...
+    def func3(x,y):
+        return (1- x/2 + x**5 + y**3)*numpy.exp(-x**2-y**2)
+    # make these smaller to increase the resolution
+    dx, dy = 6./size, 6./size#0.05, 0.05
+
+    x = numpy.arange(-3.0, 3.0, dx)
+    y = numpy.arange(-3.0, 3.0, dy)
+    X,Y = numpy.meshgrid(x, y)
+    
+    array = func3(X, Y)
+    
+    #color_array = numpy.ma.array(array, mask = array<-0.8)
+    #app = TopoWindow(array, color_array)
+    #app.run()
+    array3 = [array*i for i in range(10)]
+    array3 = numpy.array(array3).transpose(2,1,0)
+    array3 = numpy.ma.array(array3, mask = array3<-0.5)
+    clut = (0, 1)
+    app = TopoWindow(array3, clut=clut)
+    app.run()
+if __name__ == '__main__':
+    main()

Added: trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/fovea_toolbox/post_proc.py
===================================================================
--- trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/fovea_toolbox/post_proc.py	                        (rev 0)
+++ trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/fovea_toolbox/post_proc.py	2012-08-20 10:43:48 UTC (rev 12094)
@@ -0,0 +1,585 @@
+#! /usr/bin/python
+# -*- coding: utf-8 -*-
+'''
+This module contains the second stage posprocessing tools.
+'''
+__author__  = "Charles Roduit <charles.roduit at gmail.com>"
+__date__ = "28.12.2008"
+__license__ = "GNU Public License (GPL) version 3"
+__version__ = "0.1"
+
+from warnings import warn
+
+import numpy
+from scipy import stats
+
+from misc import ismasked
+
+def get_array_distance(source_array, distance):
+    r'''
+    Create a 3D array that contains the array series of the pixels distances 
+    from each marked pixels.
+    
+    for a distance of 1, the source and result arrays look like this :
+    
+    ::
+    
+       source_matrix   result[:,:,0]   result[:, :, 1]
+         0 0 0 0 0       0 0 0 0 0       0 0 0 0 0   
+         0 0 1 0 0       0 1 0 1 0       0 0 0 0 0   
+         0 0 0 0 0       0 0 0 0 0       0 0 0 0 0   
+         0 1 0 0 0       0 0 0 0 0       1 0 1 0 0   
+         0 0 0 0 0       0 0 0 0 0       0 0 0 0 0   
+    '''
+    
+    [pos_x, pos_y] = source_array.nonzero()
+    all_drops = drop_seed(source_array, distance)
+    all_single_drops = numpy.empty((source_array.shape[0], 
+                                   source_array.shape[1], 
+                                   len(pos_x)))
+    all_single_seeds = numpy.empty_like(all_single_drops)
+
+    for item in range(len(pos_x)):
+        this_seed = numpy.zeros(source_array.shape)
+        this_seed[pos_x[item], pos_y[item]] = 1
+        this_drop = drop_seed(this_seed, distance)
+        all_single_drops[:, :, item] = this_drop * all_drops
+        all_single_seeds[:, :, item] = this_seed
+    return [all_single_seeds, all_single_drops]
+    
+def drop_seed(seed_matrix, size):
+    '''
+    This function returns a similar matrix as dist_seed, except that it takes
+    care of the overlapping
+    '''
+    
+    drop_matrix = numpy.zeros_like(seed_matrix)
+    for dist in range(1, size):
+        drop_matrix = drop_matrix + dist_seed(seed_matrix, dist, where = 'xy')
+        
+    negative_matrix = numpy.logical_not(drop_matrix + seed_matrix)
+    drop_matrix = drop_matrix + dist_seed(seed_matrix, size)
+    border_matrix = drop_matrix * negative_matrix
+    
+    return border_matrix
+    
+def dist_seed(seed_matrix, distance, where = 'x'):
+    '''
+    This function returns a daughter matrix that contains the position of pixels
+    at the given distance from the non-zero pixel of the source matrix.
+    
+    ::
+    
+         Source            Result
+       0 0 0 0 0         0 0 0 0 0 
+       0 0 0 0 0         0 0 0 0 0 
+       0 0 1 0 0   ==>   0 1 0 1 0 
+       0 0 0 0 0         0 0 0 0 0 
+       0 0 0 0 0         0 0 0 0 0 
+    
+    '''
+    
+    [pos_x, pos_y] = seed_matrix.nonzero()
+    dist_matrix = numpy.zeros_like(seed_matrix)
+    if where == 'x':
+        to_left = pos_x - distance
+        to_right = pos_x + distance
+        # test if the pixels are in or outside the matrix
+        limit_left = ( to_left >= 0 ) * ( to_left < len(seed_matrix) )
+        limit_right = ( to_right >= 0 ) * ( to_right < len(seed_matrix) )
+        # Take the pixels that are in the matrix
+        pos_x_left = to_left[limit_left]
+        pos_x_right = to_right[limit_right]
+        pos_y_left = pos_y[limit_left]
+        pos_y_right = pos_y[limit_right]        
+        
+        # Generate the matrix
+        dist_matrix[pos_x_left, pos_y_left] = 1
+        dist_matrix[pos_x_right, pos_y_right] = 1
+    elif where == 'xy':
+        for elm_nbr in range(len(pos_x)):
+            this_x = pos_x[elm_nbr] + distance
+            this_y = pos_y[elm_nbr]
+            if this_x < dist_matrix.shape[0] and this_y < dist_matrix.shape[1]:
+                dist_matrix[this_x, this_y] = 1
+            # from 0 to pi/2
+            while this_y < pos_y[elm_nbr] + distance:
+                if (this_x < dist_matrix.shape[0] and this_x >= 0 and
+                   this_y < dist_matrix.shape[1] and this_y >= 0):
+                    dist_matrix[this_x, this_y] = 1
+                this_y = this_y + 1
+                if numpy.sqrt((this_x - pos_x[elm_nbr]) ** 2 + 
+                              (this_y - pos_y[elm_nbr]) ** 2) > distance :
+                    this_x = this_x - 1
+                if numpy.sqrt((this_x - pos_x[elm_nbr]) ** 2 + 
+                              (this_y - pos_y[elm_nbr]) ** 2) > distance :
+                    this_y = this_y - 1
+            # from pi/2 to pi
+            while this_x > pos_x[elm_nbr] - distance:
+                if (this_x < dist_matrix.shape[0] and this_x >= 0 and
+                   this_y < dist_matrix.shape[1] and this_y >= 0):
+                    dist_matrix[this_x, this_y] = 1
+                this_x = this_x - 1
+                if numpy.sqrt((this_x - pos_x[elm_nbr]) ** 2 + 
+                              (this_y - pos_y[elm_nbr]) ** 2) > distance :
+                    this_y = this_y - 1
+                if numpy.sqrt((this_x - pos_x[elm_nbr]) ** 2 + 
+                              (this_y - pos_y[elm_nbr]) ** 2) > distance :
+                    this_x = this_x + 1
+            # from pi to 3pi/2
+            while this_y > pos_y[elm_nbr] - distance:
+                if (this_x < dist_matrix.shape[0] and this_x >= 0 and
+                   this_y < dist_matrix.shape[1] and this_y >= 0):
+                    dist_matrix[this_x, this_y] = 1
+                this_y = this_y - 1
+                if numpy.sqrt((this_x - pos_x[elm_nbr]) ** 2 + 
+                              (this_y - pos_y[elm_nbr]) ** 2) > distance :
+                    this_x = this_x + 1
+                if numpy.sqrt((this_x - pos_x[elm_nbr]) ** 2 + 
+                              (this_y - pos_y[elm_nbr]) ** 2) > distance :
+                    this_y = this_y + 1
+            # from 3pi/2 to 2pi
+            while this_x < pos_x[elm_nbr] + distance:
+                if (this_x < dist_matrix.shape[0] and this_x >= 0 and
+                   this_y < dist_matrix.shape[1] and this_y >= 0):
+                    dist_matrix[this_x, this_y] = 1
+                this_x = this_x + 1
+                if numpy.sqrt((this_x - pos_x[elm_nbr]) ** 2 + 
+                              (this_y - pos_y[elm_nbr]) ** 2) > distance :
+                    this_y = this_y + 1
+                if numpy.sqrt((this_x - pos_x[elm_nbr]) ** 2 + 
+                              (this_y - pos_y[elm_nbr]) ** 2) > distance :
+                    this_x = this_x - 1
+            
+            #while this_y 
+            pass
+    return dist_matrix
+ 
+def rel_values(value_array, dot_array, max_dist = 3, coord=False):
+    '''
+    This function computes the relative values at some points defined by the
+    dot_array.
+    
+    dot_array = n * m array that contains the position where to compute relative
+                values.
+                
+    value_array = n * m array that contains the values.
+    
+    max_dist = integer, to which distance to compute (= 3 by default)
+    
+    Output :
+    
+    result[dot_nb, rel_val] = result[0, 1] is the absolute value of the first
+                                           dot
+                                           
+                              result[1:max_dist, 1] is the relative values of
+                                                    the first dot
+    '''
+    if type(value_array) == numpy.ma.core.MaskedArray:
+        #print type(dot_array)
+        seed_array = dot_array * (1 - value_array.mask)
+    else:
+        seed_array = dot_array
+    if coord:
+        # we record the coordinate of the events.
+        coord_val = []
+    # we compute the distance matrices... 
+    # First val is the absolute value.
+    result = numpy.empty((max_dist + 1, seed_array.astype(bool).sum()))
+    ret_array = []
+    for distance in range(max_dist + 1):
+        [single_dot, rel_array] = get_array_distance(seed_array, distance)
+        for dot_nb in range(single_dot.shape[2]):
+            # we compute the value at the dot position...
+            mask_dot = single_dot[:, :, dot_nb].astype(bool)
+            dot_val = value_array[mask_dot].sum()
+            #print type(dot_val)
+            #print "distance %i, dot number %i, dot val %f"%(distance, dot_nb, dot_val)
+            if not distance:
+                # we want the first value to be the value at the position
+                result[0, dot_nb] = dot_val
+                ret_array.append(single_dot)
+                if coord:
+                    coord_val.append([mask_dot.nonzero()[0][0], 
+                                      mask_dot.nonzero()[1][0]])
+            else:
+                # ... and at the distant positions ...
+                mask_rel = rel_array[:, :, dot_nb].astype(bool)
+                dist_val = value_array[mask_rel].sum()
+                # ... with the number of distant positions ...
+                try:
+                    count_dist = len(value_array[mask_rel])
+                    # ... and finally the relative value :
+                    # First exclude the masked and negative datas
+                    if ismasked(dist_val) and dist_val.mask:
+                        rel_value = numpy.nan
+                    elif dot_val <= 0 or dist_val <= 0:
+                        rel_value = numpy.nan
+                    else:
+                        # to finally compute the relative values.
+                        rel_value = numpy.log(dot_val / dist_val * count_dist)
+                except ZeroDivisionError:
+                    rel_value = numpy.inf
+                if rel_value == numpy.inf:
+                    result[distance, dot_nb] = numpy.nan
+                else:
+                    result[distance, dot_nb] = rel_value
+                ret_array.append(rel_array)
+    # we mask the nan
+    result = numpy.ma.masked_array(result, mask = numpy.isnan(result))
+    if coord:
+        return result, coord_val
+    else:
+        return result#, result_summarize
+def add_stiffness_to_event(event_list, rel_stiff, coordinate):
+    for event in event_list:
+        try:
+            __index = coordinate.index([event['pos_x'], event['pos_y']])
+        except ValueError:
+            event['Stiffness'] = numpy.ma.array([], mask=[])
+        else:
+            event['Stiffness'] = rel_stiff[:, __index]
+    return event_list
+def rand_dot(dot_array, nb_dot = None):
+    '''
+    Creates an array with dots. The dots are placed randomly, with the only
+    constrain to place in a free position, given by the input dot array.
+    '''
+    nb_init_dot = len(dot_array.nonzero()[0])
+    
+    if nb_dot == None:
+        nb_dot = nb_init_dot
+    if nb_dot > dot_array.size - nb_init_dot:
+        warn('Not enough place to generate random events.', RuntimeWarning)
+        # have to reach an error...
+        return numpy.zeros_like(dot_array)
+    result_array = numpy.zeros(dot_array.shape)
+    while result_array.sum() < nb_dot:
+        pos_x = numpy.floor(dot_array.shape[0] * numpy.random.rand())
+        pos_y = numpy.floor(dot_array.shape[1] * numpy.random.rand())
+        if not(dot_array[pos_x, pos_y] or result_array[pos_x, pos_y]):
+            result_array[pos_x, pos_y] = 1
+    return result_array
+
+def resize_array(old_array, new_shape):
+    '''
+    Create a new array with the given size and with the data in old array.
+    '''
+    # The new arrays are made of NaN to differentiate data from empty blocks
+    new_array = numpy.zeros(new_shape, numpy.float) * numpy.nan
+    # We reposition the points in the new array.
+    for pos_y in range(old_array.shape[1]):
+        for pos_x in range(old_array.shape[0]):
+            curve_nb = pos_x + pos_y * old_array.shape[0]
+            n_pos_x = (curve_nb) % new_shape[0]
+            n_pos_y = (curve_nb) / new_shape[0]
+            new_array[n_pos_x, n_pos_y] = old_array[pos_x, pos_y]
+    return new_array
+
+def kde_fit(data, nbr_div = 128):
+    '''
+    Automatically detects best gaussian fits for the data.
+    
+    For example, let's create a data set of to normal random values :
+    
+    >>> import pylab
+    
+    >>> data1 = numpy.random.randn(100)
+    >>> data = numpy.zeros(200)
+    >>> data[:100] = data1+1
+    >>> data[100:] = data1+5
+    
+    Now, let's compute the kde fit :
+    
+    >>> [fit, maxima, minima] = kde_fit(data)
+    
+    And we can plot the result :
+    
+    >>> [x, y, patch] = pylab.hist(data)
+    >>> conversion_factor = max(x)/max(fit[1])
+    >>> figure = pylab.figure()
+    >>> axis = figure.add_subplot(111)
+    >>> pl = pylab.plot(fit[0], fit[1] * conversion_factor)
+    >>> axis.hold(True)
+    >>> pl = pylab.plot(maxima[0], maxima[1] * conversion_factor, 'go')
+    >>> pl = pylab.plot(minima[0], minima[1] * conversion_factor, 'ro')
+    >>> figure.savefig('figure/kde_fit.png')
+    
+    The resulting graph will be an hisogram of the data set with the kde fit
+    plotted in foreground. Two gree dots represents the maximas and the red dot
+    represent the minima.
+    '''
+    kde = stats.kde.gaussian_kde(data)
+    min_data = min(data)
+    max_data = max(data)
+    nbr_step = (max_data - min_data) / nbr_div
+    coord = numpy.arange(min_data, max_data, nbr_step)
+    gaussian_fit = kde(coord)
+    # After the gaussian fit, we want to finds the maximums
+    deriv = numpy.diff(gaussian_fit)
+    #print deriv
+    extrema = (abs(deriv) == deriv) * 1
+    extrema = numpy.diff(extrema)
+    #print extremums
+    maxima = numpy.nonzero(extrema == -1)[0] + 1 # add one to correspond to
+    minima = numpy.nonzero(extrema == 1)[0] + 1  # the maximum
+    return [[coord, gaussian_fit], 
+            [coord[maxima], numpy.ones(len(maxima)) * gaussian_fit[maxima]],
+            [coord[minima], numpy.ones(len(minima)) * gaussian_fit[minima]]]
+def compute_gauss(data, minima, maxima):
+    '''
+    compute the characteristic of the distribution : mean, std, and number of
+    elements.
+    '''
+    mean, std, count = [], [], []
+    position = []
+    if not len(minima) or minima[0] > maxima[0]:
+        position.append(min(data))
+    for minimum in minima:
+        position.append(minimum)
+    if not len(minima) or minima[-1] < maxima[-1]:
+        position.append(max(data))
+    for begin, end in zip(position[:-1], position[1:]):
+        index = (data >= begin) * (data < end)
+        if len(data[index]):
+            try:
+                mean.append(numpy.mean(data[index]))
+                std.append(numpy.std(data[index]))
+                count.append(len(data[index]))
+            except TypeError:
+                # In windows, numpy.nanmax seems to not work in this case...
+                index = index * numpy.array((numpy.isnan(data)-1), dtype=bool)
+                mean.append(numpy.mean(data[index]))
+                std.append(numpy.std(data[index]))
+                count.append(len(data[index]))
+        else:
+            # Array is empty...
+            mean.append(numpy.nan)
+            std.append(numpy.nan)
+            count.append(len(data[index]))
+    return [mean, std, count]
+def find_gauss_fit(data, nbr_div = 128):
+    '''
+    Automatically detects best gaussian fits for the data, and retun the
+    gaussian properties of each detected peak.
+    
+    For example, let's create a data set of to normal random values :
+    
+    >>> import pylab
+    
+    >>> data1 = numpy.random.randn(100)
+    >>> data = numpy.zeros(200)
+    >>> data[:100] = data1+1
+    >>> data[100:] = data1+5
+    
+    Now, we can compute the gauss fit of these data :
+    
+    >>> fit = find_gauss_fit(data)
+    
+    And plot the result :
+    
+    >>> [x, y, patch] = pylab.hist(data)
+    >>> conversion_factor = max(x)/max(fit['kde'][1])
+    >>> figure = pylab.figure()
+    >>> axis = figure.add_subplot(111)
+    >>> pl = axis.hist(data)
+    >>> axis.hold(True)
+    >>> pl = axis.plot(fit['kde'][0], fit['kde'][1] * conversion_factor)
+    >>> pl = axis.plot(fit['maxima'][0], fit['maxima'][1] * conversion_factor, 'go')
+    >>> pl = axis.plot(fit['mean'], fit['maxima'][1] * conversion_factor, 'ro')
+    >>> pl = axis.errorbar(fit['mean'], fit['maxima'][1] * conversion_factor, xerr=fit['std'], fmt=None, ecolor='red')
+    >>> figure.savefig('figure/gauss_fit.png')
+    
+    The resulting plot shows the data as an histogram with the kde fit in the
+    foreground.
+    The detected maxima are shown as two green dots and the mean as red dot with
+    the horizontal error bar describing the std deviation.
+    '''
+    data = data[numpy.isfinite(data)]
+    if len(data):
+        [fit, maxima, minima] = kde_fit(data, nbr_div)
+        [mean_lst, std_lst, count_lst] = compute_gauss(data, minima[0], maxima[0])
+    else:
+        [fit, maxima, minima, mean_lst, std_lst, count_lst] = [[] for i in range(6)]
+           
+    return {'kde' : fit, 'mean' : mean_lst, 'std' : std_lst, 'count' :
+            count_lst, 'maxima' : maxima}
+
+def tomography_array(stiffness, floor=None):
+    """
+        Generate the stiffness tomography array.
+        
+        >>> raw_array = numpy.mgrid[0:5, 0:5, 0:5][2]
+        >>> floor = numpy.mgrid[0:5, 0:5, 0:5][1][0]
+        >>> tomo = tomography_array(raw_array, floor)
+        >>> print tomo
+        [[[4.0 3.0 2.0 1.0 0.0 -- -- -- --]
+          [4.0 3.0 2.0 1.0 0.0 -- -- -- --]
+          [4.0 3.0 2.0 1.0 0.0 -- -- -- --]
+          [4.0 3.0 2.0 1.0 0.0 -- -- -- --]
+          [4.0 3.0 2.0 1.0 0.0 -- -- -- --]]
+        <BLANKLINE>
+         [[-- 4.0 3.0 2.0 1.0 0.0 -- -- --]
+          [-- 4.0 3.0 2.0 1.0 0.0 -- -- --]
+          [-- 4.0 3.0 2.0 1.0 0.0 -- -- --]
+          [-- 4.0 3.0 2.0 1.0 0.0 -- -- --]
+          [-- 4.0 3.0 2.0 1.0 0.0 -- -- --]]
+        <BLANKLINE>
+         [[-- -- 4.0 3.0 2.0 1.0 0.0 -- --]
+          [-- -- 4.0 3.0 2.0 1.0 0.0 -- --]
+          [-- -- 4.0 3.0 2.0 1.0 0.0 -- --]
+          [-- -- 4.0 3.0 2.0 1.0 0.0 -- --]
+          [-- -- 4.0 3.0 2.0 1.0 0.0 -- --]]
+        <BLANKLINE>
+         [[-- -- -- 4.0 3.0 2.0 1.0 0.0 --]
+          [-- -- -- 4.0 3.0 2.0 1.0 0.0 --]
+          [-- -- -- 4.0 3.0 2.0 1.0 0.0 --]
+          [-- -- -- 4.0 3.0 2.0 1.0 0.0 --]
+          [-- -- -- 4.0 3.0 2.0 1.0 0.0 --]]
+        <BLANKLINE>
+         [[-- -- -- -- 4.0 3.0 2.0 1.0 0.0]
+          [-- -- -- -- 4.0 3.0 2.0 1.0 0.0]
+          [-- -- -- -- 4.0 3.0 2.0 1.0 0.0]
+          [-- -- -- -- 4.0 3.0 2.0 1.0 0.0]
+          [-- -- -- -- 4.0 3.0 2.0 1.0 0.0]]]
+    """
+    # The piezo array contain the height of the tip at the end of the
+    # indentation. It correspond then to the last slice of the stiffness
+    # array.
+    if floor is None:
+        floor = numpy.zeros(stiffness.shape[0:2])
+    max_floor = floor.max()
+    
+    new_array = numpy.zeros((stiffness.shape[0], stiffness.shape[1], 
+                           max_floor + stiffness.shape[2])) * numpy.nan
+    new_mask = numpy.ones((stiffness.shape[0], stiffness.shape[1], 
+                           max_floor + stiffness.shape[2]))
+    if type(stiffness) == numpy.ma.core.MaskedArray:
+        data = stiffness.data
+        mask = stiffness.mask
+    else:
+        data = stiffness
+        mask = numpy.zeros_like(stiffness)
+        
+    max_depth = stiffness.shape[2]
+    for x in range(stiffness.shape[0]):
+        for y in range(stiffness.shape[1]):
+            try:
+                last_data = numpy.nonzero(mask[x, y])[0][0]
+            except IndexError:
+                last_data = len(mask[x, y]) - 1
+            begin_pos = floor[x,y]
+            end_pos = last_data + begin_pos + 1
+            try:
+                new_array[x, y, begin_pos:end_pos] = data[x, y][last_data::-1]
+            except ValueError as error:
+                print "Error in post_proc line 437:"
+                print x, y
+                print begin_pos, end_pos
+                print new_array[x, y, begin_pos:end_pos].shape
+                print data[x, y][last_data::-1].shape
+                print error
+            new_mask[x, y, begin_pos:end_pos] = mask[x, y][last_data::-1]
+            
+    # Keep only the usefull informations. Array was build too large, but we want
+    # to return a well sized array
+    first_empty = 0
+    nbr_empty = 1
+    for depth in range(new_mask.shape[2]):
+        if new_mask[:, :, depth].all():
+            if depth == first_empty + nbr_empty:
+                nbr_empty += 1
+            else:
+                first_empty = depth
+                nbr_empty = 1
+    if first_empty == 0 and nbr_empty == 1:
+        # This mean there is no empty slice...
+        first_empty = new_array.shape[2]
+    ##
+    ## Stores the result in a matrix that supports the mask, to get rid
+    ## of the nan values
+    ##
+    return numpy.ma.array(new_array[:, :, :first_empty],
+                          mask=new_mask[:, :, :first_empty])
+
+def generate_path(pos_a, pos_b):
+    """
+        Generate a linear path between the point a and the point b.
+        
+        >>> generate_path([0, 0], [1, 1])
+        array([[ 0.,  1.],
+               [ 0.,  1.]])
+        
+        >>> generate_path([0, 0], [1, 5])
+        array([[ 0.,  0.,  0.,  1.,  1.,  1.],
+               [ 0.,  1.,  2.,  3.,  4.,  5.]])
+        
+        >>> generate_path([0, 0], [0, 5])
+        array([[ 0.,  0.,  0.,  0.,  0.,  0.],
+               [ 0.,  1.,  2.,  3.,  4.,  5.]])
+
+        >>> generate_path([0, 0], [5, 0])
+        array([[ 0.,  1.,  2.,  3.,  4.,  5.],
+               [ 0.,  0.,  0.,  0.,  0.,  0.]])
+
+        >>> generate_path([2, 2], [8, 5])
+        array([[ 2.,  3.,  4.,  5.,  6.,  7.,  8.],
+               [ 2.,  3.,  3.,  4.,  4.,  5.,  5.]])
+    """
+    pos_a[0], pos_a[1], pos_b[0], pos_b[1] = \
+                int(pos_a[0]), int(pos_a[1]), int(pos_b[0]), int(pos_b[1])
+    if pos_b[0] == pos_a[0]:
+        if pos_a[1] > pos_b[1]:
+            pos_a, pos_b = pos_b, pos_a
+        _length = pos_b[1] - pos_a[1] + 1
+        _y = range(pos_a[1], pos_b[1] + 1)
+        _x = [pos_b[0]] * _length
+    elif pos_b[1] == pos_a[1]:
+        if pos_a[0] > pos_b[0]:
+            pos_a, pos_b = pos_b, pos_a
+        _length = pos_b[0] - pos_a[0] + 1
+        _x = range(pos_a[0], pos_b[0] + 1)
+        _y = [pos_b[1]] * _length
+    else:
+        _a = float(pos_b[1] - pos_a[1]) / (pos_b[0] - pos_a[0])
+        _b = pos_a[1] - _a * pos_a[0]
+        
+        if abs(pos_b[0] - pos_a[0]) > abs(pos_b[1] - pos_a[1]):
+            if pos_a[0] > pos_b[0]:
+                pos_a, pos_b = pos_b, pos_a
+            # x0 -> x1 is bigger to y0 -> y1
+            _x = range(pos_a[0], pos_b[0] + 1)
+            _y = [round(_a * item + _b) for item in _x]
+        else:
+            if pos_a[1] > pos_b[1]:
+                pos_a, pos_b = pos_b, pos_a
+            # y0 -> y1 is bigger than x0 -> x1
+            _y = range(pos_a[1], pos_b[1] + 1)
+            _x = [round((item - _b) / _a) for item in _y]
+    return numpy.asarray([_x, _y], dtype=float)
+
+def generate_slice(path, array):
+    """
+        Generate the slice of the array along the path.
+        
+        >>> array = [range(10)]*10
+        >>> path = generate_path([0, 0], [0, 4])
+        >>> generate_slice(path, array)
+        [0, 1, 2, 3, 4]
+        
+        >>> path = generate_path([0, 1], [4, 1])
+        >>> generate_slice(path, array)
+        [1, 1, 1, 1, 1]
+    """
+    return [array[int(_x)][int(_y)] for _x, _y in zip(path[0], path[1])]
+
+if __name__ == "__main__":
+    
+    try:
+        matplotlib.__version__
+    except NameError:
+        import matplotlib
+        matplotlib.use('Agg')
+        from matplotlib import pylab
+    import doctest
+    doctest.testmod()

Added: trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/glade/dialog_experiment_properties.glade
===================================================================
--- trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/glade/dialog_experiment_properties.glade	                        (rev 0)
+++ trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/glade/dialog_experiment_properties.glade	2012-08-20 10:43:48 UTC (rev 12094)
@@ -0,0 +1,771 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<interface>
+  <requires lib="gtk+" version="2.16"/>
+  <!-- interface-naming-policy project-wide -->
+  <object class="GtkWindow" id="ExpProp">
+    <property name="visible">True</property>
+    <property name="can_focus">False</property>
+    <property name="title" translatable="yes">Properties</property>
+    <property name="default_width">300</property>
+    <property name="default_height">400</property>
+    <property name="icon_name">preferences-desktop</property>
+    <signal name="destroy" handler="destroy" swapped="no"/>
+    <child>
+      <object class="GtkVBox" id="vbox1">
+        <property name="visible">True</property>
+        <property name="can_focus">False</property>
+        <child>
+          <object class="GtkNotebook" id="notebook1">
+            <property name="visible">True</property>
+            <property name="can_focus">True</property>
+            <child>
+              <object class="GtkVBox" id="vbox2">
+                <property name="visible">True</property>
+                <property name="can_focus">False</property>
+                <child>
+                  <object class="GtkHBox" id="hbox2">
+                    <property name="visible">True</property>
+                    <property name="can_focus">False</property>
+                    <child>
+                      <object class="GtkLabel" id="label1">
+                        <property name="visible">True</property>
+                        <property name="can_focus">False</property>
+                        <property name="label" translatable="yes">Author :</property>
+                      </object>
+                      <packing>
+                        <property name="expand">True</property>
+                        <property name="fill">True</property>
+                        <property name="position">0</property>
+                      </packing>
+                    </child>
+                    <child>
+                      <object class="GtkEntry" id="text_author">
+                        <property name="visible">True</property>
+                        <property name="can_focus">True</property>
+                        <property name="invisible_char">●</property>
+                        <property name="primary_icon_activatable">False</property>
+                        <property name="secondary_icon_activatable">False</property>
+                        <property name="primary_icon_sensitive">True</property>
+                        <property name="secondary_icon_sensitive">True</property>
+                      </object>
+                      <packing>
+                        <property name="expand">True</property>
+                        <property name="fill">True</property>
+                        <property name="position">1</property>
+                      </packing>
+                    </child>
+                  </object>
+                  <packing>
+                    <property name="expand">False</property>
+                    <property name="fill">False</property>
+                    <property name="position">0</property>
+                  </packing>
+                </child>
+                <child>
+                  <object class="GtkFrame" id="frame_description">
+                    <property name="visible">True</property>
+                    <property name="can_focus">False</property>
+                    <property name="label_xalign">0</property>
+                    <property name="shadow_type">none</property>
+                    <child>
+                      <object class="GtkAlignment" id="alignment1">
+                        <property name="visible">True</property>
+                        <property name="can_focus">False</property>
+                        <property name="left_padding">12</property>
+                        <child>
+                          <object class="GtkScrolledWindow" id="scrolledwindow1">
+                            <property name="visible">True</property>
+                            <property name="can_focus">True</property>
+                            <property name="hscrollbar_policy">automatic</property>
+                            <property name="vscrollbar_policy">automatic</property>
+                            <property name="shadow_type">in</property>
+                            <child>
+                              <object class="GtkTextView" id="text_description">
+                                <property name="visible">True</property>
+                                <property name="can_focus">True</property>
+                              </object>
+                            </child>
+                          </object>
+                        </child>
+                      </object>
+                    </child>
+                    <child type="label">
+                      <object class="GtkLabel" id="label2">
+                        <property name="visible">True</property>
+                        <property name="can_focus">False</property>
+                        <property name="label" translatable="yes"><b>Description</b></property>
+                        <property name="use_markup">True</property>
+                      </object>
+                    </child>
+                  </object>
+                  <packing>
+                    <property name="expand">True</property>
+                    <property name="fill">True</property>
+                    <property name="position">1</property>
+                  </packing>
+                </child>
+              </object>
+              <packing>
+                <property name="tab_fill">False</property>
+              </packing>
+            </child>
+            <child type="tab">
+              <object class="GtkLabel" id="General">
+                <property name="visible">True</property>
+                <property name="can_focus">False</property>
+                <property name="label" translatable="yes">General</property>
+              </object>
+              <packing>
+                <property name="tab_fill">False</property>
+              </packing>
+            </child>
+            <child>
+              <object class="GtkVBox" id="vbox3">
+                <property name="visible">True</property>
+                <property name="can_focus">False</property>
+                <child>
+                  <object class="GtkFrame" id="frame_time_lapse">
+                    <property name="can_focus">False</property>
+                    <property name="label_xalign">0</property>
+                    <property name="shadow_type">in</property>
+                    <child>
+                      <object class="GtkAlignment" id="alignment3">
+                        <property name="visible">True</property>
+                        <property name="can_focus">False</property>
+                        <property name="left_padding">12</property>
+                        <child>
+                          <object class="GtkVBox" id="vbox5">
+                            <property name="visible">True</property>
+                            <property name="can_focus">False</property>
+                            <child>
+                              <object class="GtkHBox" id="hbox4">
+                                <property name="visible">True</property>
+                                <property name="can_focus">False</property>
+                                <child>
+                                  <object class="GtkLabel" id="label_inject">
+                                    <property name="visible">True</property>
+                                    <property name="can_focus">False</property>
+                                    <property name="label" translatable="yes">Injection time</property>
+                                  </object>
+                                  <packing>
+                                    <property name="expand">False</property>
+                                    <property name="fill">False</property>
+                                    <property name="position">0</property>
+                                  </packing>
+                                </child>
+                                <child>
+                                  <object class="GtkSpinButton" id="entry_injection_index">
+                                    <property name="visible">True</property>
+                                    <property name="can_focus">True</property>
+                                    <property name="invisible_char">●</property>
+                                    <property name="primary_icon_activatable">False</property>
+                                    <property name="secondary_icon_activatable">False</property>
+                                    <property name="primary_icon_sensitive">True</property>
+                                    <property name="secondary_icon_sensitive">True</property>
+                                    <property name="adjustment">adjust_injection_index</property>
+                                  </object>
+                                  <packing>
+                                    <property name="expand">False</property>
+                                    <property name="fill">False</property>
+                                    <property name="pack_type">end</property>
+                                    <property name="position">1</property>
+                                  </packing>
+                                </child>
+                              </object>
+                              <packing>
+                                <property name="expand">True</property>
+                                <property name="fill">True</property>
+                                <property name="position">0</property>
+                              </packing>
+                            </child>
+                          </object>
+                        </child>
+                      </object>
+                    </child>
+                    <child type="label">
+                      <object class="GtkLabel" id="label4">
+                        <property name="visible">True</property>
+                        <property name="can_focus">False</property>
+                        <property name="label" translatable="yes"><b>Time Lapse</b></property>
+                        <property name="use_markup">True</property>
+                      </object>
+                    </child>
+                  </object>
+                  <packing>
+                    <property name="expand">False</property>
+                    <property name="fill">False</property>
+                    <property name="position">0</property>
+                  </packing>
+                </child>
+                <child>
+                  <object class="GtkFrame" id="frame_system">
+                    <property name="visible">True</property>
+                    <property name="can_focus">False</property>
+                    <property name="label_xalign">0</property>
+                    <property name="shadow_type">in</property>
+                    <child>
+                      <object class="GtkAlignment" id="alignment2">
+                        <property name="visible">True</property>
+                        <property name="can_focus">False</property>
+                        <property name="left_padding">12</property>
+                        <child>
+                          <object class="GtkVBox" id="vbox4">
+                            <property name="visible">True</property>
+                            <property name="can_focus">False</property>
+                            <child>
+                              <object class="GtkHBox" id="hbox3">
+                                <property name="visible">True</property>
+                                <property name="can_focus">False</property>
+                                <child>
+                                  <object class="GtkLabel" id="label_spring">
+                                    <property name="visible">True</property>
+                                    <property name="can_focus">False</property>
+                                    <property name="label" translatable="yes">Spring constant</property>
+                                  </object>
+                                  <packing>
+                                    <property name="expand">False</property>
+                                    <property name="fill">False</property>
+                                    <property name="position">0</property>
+                                  </packing>
+                                </child>
+                                <child>
+                                  <object class="GtkEntry" id="entry_spring_constant">
+                                    <property name="visible">True</property>
+                                    <property name="can_focus">True</property>
+                                    <property name="invisible_char">●</property>
+                                    <property name="primary_icon_activatable">False</property>
+                                    <property name="secondary_icon_activatable">False</property>
+                                    <property name="primary_icon_sensitive">True</property>
+                                    <property name="secondary_icon_sensitive">True</property>
+                                  </object>
+                                  <packing>
+                                    <property name="expand">False</property>
+                                    <property name="fill">False</property>
+                                    <property name="pack_type">end</property>
+                                    <property name="position">1</property>
+                                  </packing>
+                                </child>
+                              </object>
+                              <packing>
+                                <property name="expand">False</property>
+                                <property name="fill">False</property>
+                                <property name="position">0</property>
+                              </packing>
+                            </child>
+                            <child>
+                              <object class="GtkHBox" id="hbox5">
+                                <property name="visible">True</property>
+                                <property name="can_focus">False</property>
+                                <child>
+                                  <object class="GtkLabel" id="label5">
+                                    <property name="visible">True</property>
+                                    <property name="can_focus">False</property>
+                                    <property name="label" translatable="yes">Glass stiffness</property>
+                                  </object>
+                                  <packing>
+                                    <property name="expand">False</property>
+                                    <property name="fill">False</property>
+                                    <property name="position">0</property>
+                                  </packing>
+                                </child>
+                                <child>
+                                  <object class="GtkSpinButton" id="spin_stiff_glass">
+                                    <property name="visible">True</property>
+                                    <property name="can_focus">True</property>
+                                    <property name="invisible_char">●</property>
+                                    <property name="primary_icon_activatable">False</property>
+                                    <property name="secondary_icon_activatable">False</property>
+                                    <property name="primary_icon_sensitive">True</property>
+                                    <property name="secondary_icon_sensitive">True</property>
+                                    <property name="adjustment">adjust_deflection_sensitivity</property>
+                                    <property name="digits">3</property>
+                                  </object>
+                                  <packing>
+                                    <property name="expand">False</property>
+                                    <property name="fill">False</property>
+                                    <property name="pack_type">end</property>
+                                    <property name="position">1</property>
+                                  </packing>
+                                </child>
+                              </object>
+                              <packing>
+                                <property name="expand">False</property>
+                                <property name="fill">False</property>
+                                <property name="position">1</property>
+                              </packing>
+                            </child>
+                            <child>
+                              <object class="GtkVBox" id="vbox6">
+                                <property name="visible">True</property>
+                                <property name="can_focus">False</property>
+                                <child>
+                                  <object class="GtkHBox" id="plot_area">
+                                    <property name="visible">True</property>
+                                    <property name="can_focus">False</property>
+                                    <child>
+                                      <placeholder/>
+                                    </child>
+                                  </object>
+                                  <packing>
+                                    <property name="expand">True</property>
+                                    <property name="fill">True</property>
+                                    <property name="position">0</property>
+                                  </packing>
+                                </child>
+                                <child>
+                                  <object class="GtkVBox" id="box_nav_tool">
+                                    <property name="visible">True</property>
+                                    <property name="can_focus">False</property>
+                                    <child>
+                                      <placeholder/>
+                                    </child>
+                                  </object>
+                                  <packing>
+                                    <property name="expand">False</property>
+                                    <property name="fill">False</property>
+                                    <property name="position">1</property>
+                                  </packing>
+                                </child>
+                              </object>
+                              <packing>
+                                <property name="expand">True</property>
+                                <property name="fill">True</property>
+                                <property name="position">2</property>
+                              </packing>
+                            </child>
+                          </object>
+                        </child>
+                      </object>
+                    </child>
+                    <child type="label">
+                      <object class="GtkLabel" id="label3">
+                        <property name="visible">True</property>
+                        <property name="can_focus">False</property>
+                        <property name="label" translatable="yes"><b>System</b></property>
+                        <property name="use_markup">True</property>
+                      </object>
+                    </child>
+                  </object>
+                  <packing>
+                    <property name="expand">True</property>
+                    <property name="fill">True</property>
+                    <property name="position">1</property>
+                  </packing>
+                </child>
+              </object>
+              <packing>
+                <property name="position">1</property>
+              </packing>
+            </child>
+            <child type="tab">
+              <object class="GtkLabel" id="Config">
+                <property name="visible">True</property>
+                <property name="can_focus">False</property>
+                <property name="label" translatable="yes">Configuration</property>
+              </object>
+              <packing>
+                <property name="position">1</property>
+                <property name="tab_fill">False</property>
+              </packing>
+            </child>
+            <child>
+              <object class="GtkVBox" id="tab_plot">
+                <property name="visible">True</property>
+                <property name="can_focus">False</property>
+                <child>
+                  <object class="GtkFrame" id="frame1">
+                    <property name="visible">True</property>
+                    <property name="can_focus">False</property>
+                    <property name="label_xalign">0</property>
+                    <property name="shadow_type">in</property>
+                    <child>
+                      <object class="GtkAlignment" id="alignment4">
+                        <property name="visible">True</property>
+                        <property name="can_focus">False</property>
+                        <property name="left_padding">12</property>
+                        <child>
+                          <object class="GtkTable" id="table1">
+                            <property name="visible">True</property>
+                            <property name="can_focus">False</property>
+                            <property name="n_rows">2</property>
+                            <property name="n_columns">2</property>
+                            <child>
+                              <object class="GtkSpinButton" id="spin_save_plot_width">
+                                <property name="visible">True</property>
+                                <property name="can_focus">True</property>
+                                <property name="invisible_char">●</property>
+                                <property name="primary_icon_activatable">False</property>
+                                <property name="secondary_icon_activatable">False</property>
+                                <property name="primary_icon_sensitive">True</property>
+                                <property name="secondary_icon_sensitive">True</property>
+                                <signal name="value-changed" handler="on_spin_save_plot_width_value_changed" swapped="no"/>
+                              </object>
+                              <packing>
+                                <property name="x_options"></property>
+                                <property name="y_options"></property>
+                              </packing>
+                            </child>
+                            <child>
+                              <object class="GtkSpinButton" id="spin_save_plot_height">
+                                <property name="visible">True</property>
+                                <property name="can_focus">True</property>
+                                <property name="invisible_char">●</property>
+                                <property name="primary_icon_activatable">False</property>
+                                <property name="secondary_icon_activatable">False</property>
+                                <property name="primary_icon_sensitive">True</property>
+                                <property name="secondary_icon_sensitive">True</property>
+                                <signal name="value-changed" handler="on_spin_save_plot_height_value_changed" swapped="no"/>
+                              </object>
+                              <packing>
+                                <property name="top_attach">1</property>
+                                <property name="bottom_attach">2</property>
+                                <property name="x_options"></property>
+                                <property name="y_options"></property>
+                              </packing>
+                            </child>
+                            <child>
+                              <object class="GtkLabel" id="label8">
+                                <property name="visible">True</property>
+                                <property name="can_focus">False</property>
+                                <property name="label" translatable="yes">Width</property>
+                              </object>
+                              <packing>
+                                <property name="left_attach">1</property>
+                                <property name="right_attach">2</property>
+                                <property name="x_options"></property>
+                                <property name="y_options"></property>
+                              </packing>
+                            </child>
+                            <child>
+                              <object class="GtkLabel" id="label9">
+                                <property name="visible">True</property>
+                                <property name="can_focus">False</property>
+                                <property name="label" translatable="yes">Height</property>
+                              </object>
+                              <packing>
+                                <property name="left_attach">1</property>
+                                <property name="right_attach">2</property>
+                                <property name="top_attach">1</property>
+                                <property name="bottom_attach">2</property>
+                                <property name="x_options"></property>
+                                <property name="y_options"></property>
+                              </packing>
+                            </child>
+                          </object>
+                        </child>
+                      </object>
+                    </child>
+                    <child type="label">
+                      <object class="GtkLabel" id="label7">
+                        <property name="visible">True</property>
+                        <property name="can_focus">False</property>
+                        <property name="label" translatable="yes">Saved size</property>
+                        <property name="use_markup">True</property>
+                      </object>
+                    </child>
+                  </object>
+                  <packing>
+                    <property name="expand">False</property>
+                    <property name="fill">False</property>
+                    <property name="position">0</property>
+                  </packing>
+                </child>
+                <child>
+                  <object class="GtkFrame" id="Linewidth">
+                    <property name="visible">True</property>
+                    <property name="can_focus">False</property>
+                    <property name="label_xalign">0</property>
+                    <property name="shadow_type">in</property>
+                    <child>
+                      <object class="GtkAlignment" id="alignment5">
+                        <property name="visible">True</property>
+                        <property name="can_focus">False</property>
+                        <property name="left_padding">12</property>
+                        <child>
+                          <object class="GtkVBox" id="vbox7">
+                            <property name="visible">True</property>
+                            <property name="can_focus">False</property>
+                            <child>
+                              <object class="GtkHBox" id="hbox6">
+                                <property name="visible">True</property>
+                                <property name="can_focus">False</property>
+                                <child>
+                                  <object class="GtkSpinButton" id="spin_linewidth">
+                                    <property name="visible">True</property>
+                                    <property name="can_focus">True</property>
+                                    <property name="invisible_char">●</property>
+                                    <property name="primary_icon_activatable">False</property>
+                                    <property name="secondary_icon_activatable">False</property>
+                                    <property name="primary_icon_sensitive">True</property>
+                                    <property name="secondary_icon_sensitive">True</property>
+                                    <property name="digits">1</property>
+                                    <property name="numeric">True</property>
+                                    <signal name="value-changed" handler="on_spin_linewidth_value_changed" swapped="no"/>
+                                  </object>
+                                  <packing>
+                                    <property name="expand">False</property>
+                                    <property name="fill">False</property>
+                                    <property name="position">0</property>
+                                  </packing>
+                                </child>
+                                <child>
+                                  <object class="GtkLabel" id="label12">
+                                    <property name="visible">True</property>
+                                    <property name="can_focus">False</property>
+                                    <property name="label" translatable="yes">Linewidth</property>
+                                  </object>
+                                  <packing>
+                                    <property name="expand">False</property>
+                                    <property name="fill">False</property>
+                                    <property name="position">1</property>
+                                  </packing>
+                                </child>
+                              </object>
+                              <packing>
+                                <property name="expand">False</property>
+                                <property name="fill">False</property>
+                                <property name="position">0</property>
+                              </packing>
+                            </child>
+                            <child>
+                              <object class="GtkCheckButton" id="check_bw_plot">
+                                <property name="label" translatable="yes">Gray scale plot.</property>
+                                <property name="visible">True</property>
+                                <property name="can_focus">True</property>
+                                <property name="receives_default">False</property>
+                                <property name="use_action_appearance">False</property>
+                                <property name="draw_indicator">True</property>
+                              </object>
+                              <packing>
+                                <property name="expand">True</property>
+                                <property name="fill">True</property>
+                                <property name="position">1</property>
+                              </packing>
+                            </child>
+                            <child>
+                              <placeholder/>
+                            </child>
+                            <child>
+                              <placeholder/>
+                            </child>
+                          </object>
+                        </child>
+                      </object>
+                    </child>
+                    <child type="label">
+                      <object class="GtkLabel" id="label11">
+                        <property name="visible">True</property>
+                        <property name="can_focus">False</property>
+                        <property name="label" translatable="yes">Plot Options</property>
+                        <property name="use_markup">True</property>
+                      </object>
+                    </child>
+                  </object>
+                  <packing>
+                    <property name="expand">False</property>
+                    <property name="fill">False</property>
+                    <property name="position">1</property>
+                  </packing>
+                </child>
+                <child>
+                  <object class="GtkFrame" id="Linewidth1">
+                    <property name="visible">True</property>
+                    <property name="can_focus">False</property>
+                    <property name="label_xalign">0</property>
+                    <property name="shadow_type">in</property>
+                    <child>
+                      <object class="GtkAlignment" id="alignment6">
+                        <property name="visible">True</property>
+                        <property name="can_focus">False</property>
+                        <property name="left_padding">12</property>
+                        <child>
+                          <object class="GtkVBox" id="vbox9">
+                            <property name="visible">True</property>
+                            <property name="can_focus">False</property>
+                            <child>
+                              <object class="GtkCheckButton" id="check_plot_hist_gauss">
+                                <property name="label" translatable="yes">Display fit on histograms</property>
+                                <property name="visible">True</property>
+                                <property name="can_focus">True</property>
+                                <property name="receives_default">False</property>
+                                <property name="use_action_appearance">False</property>
+                                <property name="draw_indicator">True</property>
+                              </object>
+                              <packing>
+                                <property name="expand">False</property>
+                                <property name="fill">False</property>
+                                <property name="position">0</property>
+                              </packing>
+                            </child>
+                            <child>
+                              <object class="GtkCheckButton" id="histo_y_rel">
+                                <property name="label" translatable="yes">Relative y axis</property>
+                                <property name="visible">True</property>
+                                <property name="can_focus">True</property>
+                                <property name="receives_default">False</property>
+                                <property name="use_action_appearance">False</property>
+                                <property name="draw_indicator">True</property>
+                              </object>
+                              <packing>
+                                <property name="expand">True</property>
+                                <property name="fill">True</property>
+                                <property name="position">1</property>
+                              </packing>
+                            </child>
+                            <child>
+                              <placeholder/>
+                            </child>
+                          </object>
+                        </child>
+                      </object>
+                    </child>
+                    <child type="label">
+                      <object class="GtkLabel" id="label14">
+                        <property name="visible">True</property>
+                        <property name="can_focus">False</property>
+                        <property name="label" translatable="yes">Histogram Options</property>
+                        <property name="use_markup">True</property>
+                      </object>
+                    </child>
+                  </object>
+                  <packing>
+                    <property name="expand">False</property>
+                    <property name="fill">False</property>
+                    <property name="position">2</property>
+                  </packing>
+                </child>
+                <child>
+                  <object class="GtkFrame" id="frame2">
+                    <property name="visible">True</property>
+                    <property name="can_focus">False</property>
+                    <property name="label_xalign">0</property>
+                    <property name="shadow_type">in</property>
+                    <child>
+                      <object class="GtkAlignment" id="alignment_group">
+                        <property name="visible">True</property>
+                        <property name="can_focus">False</property>
+                        <property name="left_padding">12</property>
+                        <child>
+                          <object class="GtkTable" id="table_group">
+                            <property name="visible">True</property>
+                            <property name="can_focus">False</property>
+                            <property name="n_rows">2</property>
+                            <property name="n_columns">3</property>
+                            <child>
+                              <placeholder/>
+                            </child>
+                            <child>
+                              <placeholder/>
+                            </child>
+                            <child>
+                              <placeholder/>
+                            </child>
+                            <child>
+                              <placeholder/>
+                            </child>
+                            <child>
+                              <placeholder/>
+                            </child>
+                            <child>
+                              <placeholder/>
+                            </child>
+                          </object>
+                        </child>
+                      </object>
+                    </child>
+                    <child type="label">
+                      <object class="GtkLabel" id="label10">
+                        <property name="visible">True</property>
+                        <property name="can_focus">False</property>
+                        <property name="label" translatable="yes">Group</property>
+                        <property name="use_markup">True</property>
+                      </object>
+                    </child>
+                  </object>
+                  <packing>
+                    <property name="expand">False</property>
+                    <property name="fill">False</property>
+                    <property name="position">3</property>
+                  </packing>
+                </child>
+              </object>
+              <packing>
+                <property name="position">2</property>
+                <property name="tab_fill">False</property>
+              </packing>
+            </child>
+            <child type="tab">
+              <object class="GtkLabel" id="label6">
+                <property name="visible">True</property>
+                <property name="can_focus">False</property>
+                <property name="label" translatable="yes">Graph</property>
+              </object>
+              <packing>
+                <property name="position">2</property>
+                <property name="tab_fill">False</property>
+              </packing>
+            </child>
+          </object>
+          <packing>
+            <property name="expand">True</property>
+            <property name="fill">True</property>
+            <property name="position">0</property>
+          </packing>
+        </child>
+        <child>
+          <object class="GtkHBox" id="hbox1">
+            <property name="visible">True</property>
+            <property name="can_focus">False</property>
+            <child>
+              <object class="GtkButton" id="button_validate">
+                <property name="label">gtk-ok</property>
+                <property name="visible">True</property>
+                <property name="can_focus">True</property>
+                <property name="receives_default">True</property>
+                <property name="use_action_appearance">False</property>
+                <property name="use_stock">True</property>
+                <signal name="clicked" handler="on_button_validate_clicked" swapped="no"/>
+              </object>
+              <packing>
+                <property name="expand">True</property>
+                <property name="fill">True</property>
+                <property name="position">0</property>
+              </packing>
+            </child>
+            <child>
+              <object class="GtkButton" id="button_cancel">
+                <property name="label">gtk-cancel</property>
+                <property name="visible">True</property>
+                <property name="can_focus">True</property>
+                <property name="receives_default">True</property>
+                <property name="use_action_appearance">False</property>
+                <property name="use_stock">True</property>
+                <signal name="clicked" handler="on_button_cancel_clicked" swapped="no"/>
+              </object>
+              <packing>
+                <property name="expand">True</property>
+                <property name="fill">True</property>
+                <property name="position">1</property>
+              </packing>
+            </child>
+          </object>
+          <packing>
+            <property name="expand">False</property>
+            <property name="fill">False</property>
+            <property name="position">1</property>
+          </packing>
+        </child>
+      </object>
+    </child>
+  </object>
+  <object class="GtkAdjustment" id="adjust_deflection_sensitivity">
+    <property name="upper">100</property>
+    <property name="step_increment">1</property>
+    <property name="page_increment">10</property>
+  </object>
+  <object class="GtkAdjustment" id="adjust_injection_index">
+    <property name="upper">100</property>
+    <property name="step_increment">1</property>
+    <property name="page_increment">10</property>
+  </object>
+</interface>

Added: trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/glade/dialog_flatten.glade
===================================================================
--- trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/glade/dialog_flatten.glade	                        (rev 0)
+++ trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/glade/dialog_flatten.glade	2012-08-20 10:43:48 UTC (rev 12094)
@@ -0,0 +1,142 @@
+<?xml version="1.0"?>
+<interface>
+  <requires lib="gtk+" version="2.16"/>
+  <!-- interface-naming-policy project-wide -->
+  <object class="GtkDialog" id="FlattenDialog">
+    <property name="border_width">5</property>
+    <property name="title" translatable="yes">Flatten Image</property>
+    <property name="default_width">400</property>
+    <property name="default_height">300</property>
+    <property name="icon">../Icon/openfovea.png</property>
+    <property name="type_hint">normal</property>
+    <property name="has_separator">False</property>
+    <child internal-child="vbox">
+      <object class="GtkVBox" id="dialog-vbox4">
+        <property name="visible">True</property>
+        <property name="spacing">2</property>
+        <child>
+          <object class="GtkTable" id="table3">
+            <property name="visible">True</property>
+            <property name="n_rows">2</property>
+            <property name="n_columns">2</property>
+            <child>
+              <object class="GtkLabel" id="label14">
+                <property name="visible">True</property>
+                <property name="label" translatable="yes">Original</property>
+                <attributes>
+                  <attribute name="weight" value="bold"/>
+                </attributes>
+              </object>
+              <packing>
+                <property name="x_options"></property>
+                <property name="y_options"></property>
+              </packing>
+            </child>
+            <child>
+              <object class="GtkLabel" id="label15">
+                <property name="visible">True</property>
+                <property name="label" translatable="yes">Flatten</property>
+                <attributes>
+                  <attribute name="weight" value="bold"/>
+                </attributes>
+              </object>
+              <packing>
+                <property name="left_attach">1</property>
+                <property name="right_attach">2</property>
+                <property name="x_options"></property>
+                <property name="y_options"></property>
+              </packing>
+            </child>
+            <child>
+              <object class="GtkHBox" id="view_before_flatten">
+                <property name="visible">True</property>
+                <child>
+                  <placeholder/>
+                </child>
+              </object>
+              <packing>
+                <property name="top_attach">1</property>
+                <property name="bottom_attach">2</property>
+              </packing>
+            </child>
+            <child>
+              <object class="GtkHBox" id="view_after_flatten">
+                <property name="visible">True</property>
+                <child>
+                  <placeholder/>
+                </child>
+              </object>
+              <packing>
+                <property name="left_attach">1</property>
+                <property name="right_attach">2</property>
+                <property name="top_attach">1</property>
+                <property name="bottom_attach">2</property>
+              </packing>
+            </child>
+          </object>
+          <packing>
+            <property name="position">1</property>
+          </packing>
+        </child>
+        <child>
+          <object class="GtkLabel" id="label1">
+            <property name="visible">True</property>
+            <property name="xalign">0.029999999329447746</property>
+            <property name="label" translatable="yes">Do not forget to recompute the point of contact 
+to propagate the flattening to the other images 
+of the current file.</property>
+            <property name="wrap">True</property>
+          </object>
+          <packing>
+            <property name="expand">False</property>
+            <property name="fill">False</property>
+            <property name="position">2</property>
+          </packing>
+        </child>
+        <child internal-child="action_area">
+          <object class="GtkHButtonBox" id="dialog-action_area4">
+            <property name="visible">True</property>
+            <property name="layout_style">end</property>
+            <child>
+              <object class="GtkButton" id="button_apply">
+                <property name="label">gtk-apply</property>
+                <property name="visible">True</property>
+                <property name="can_focus">True</property>
+                <property name="receives_default">True</property>
+                <property name="use_stock">True</property>
+              </object>
+              <packing>
+                <property name="expand">False</property>
+                <property name="fill">False</property>
+                <property name="position">0</property>
+              </packing>
+            </child>
+            <child>
+              <object class="GtkButton" id="button_cancel">
+                <property name="label">gtk-cancel</property>
+                <property name="visible">True</property>
+                <property name="can_focus">True</property>
+                <property name="receives_default">True</property>
+                <property name="use_stock">True</property>
+              </object>
+              <packing>
+                <property name="expand">False</property>
+                <property name="fill">False</property>
+                <property name="position">1</property>
+              </packing>
+            </child>
+          </object>
+          <packing>
+            <property name="expand">False</property>
+            <property name="pack_type">end</property>
+            <property name="position">0</property>
+          </packing>
+        </child>
+      </object>
+    </child>
+    <action-widgets>
+      <action-widget response="1">button_apply</action-widget>
+      <action-widget response="0">button_cancel</action-widget>
+    </action-widgets>
+  </object>
+</interface>

Added: trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/glade/openfovea.glade
===================================================================
--- trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/glade/openfovea.glade	                        (rev 0)
+++ trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/glade/openfovea.glade	2012-08-20 10:43:48 UTC (rev 12094)
@@ -0,0 +1,4628 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<interface>
+  <requires lib="gtk+" version="2.16"/>
+  <object class="GtkWindow" id="MainWindow">
+    <property name="visible">True</property>
+    <property name="can_focus">False</property>
+    <property name="title" translatable="yes">Open Fovea</property>
+    <property name="default_width">255</property>
+    <property name="default_height">256</property>
+    <property name="icon">../Icon/openfovea.png</property>
+    <signal name="destroy" handler="on_MainWindow_destroy" swapped="no"/>
+    <child>
+      <object class="GtkVBox" id="vbox6">
+        <property name="visible">True</property>
+        <property name="can_focus">False</property>
+        <child>
+          <object class="GtkMenuBar" id="menubar1">
+            <property name="visible">True</property>
+            <property name="can_focus">False</property>
+            <child>
+              <object class="GtkMenuItem" id="menu_file">
+                <property name="visible">True</property>
+                <property name="can_focus">False</property>
+                <property name="use_action_appearance">False</property>
+                <property name="label" translatable="yes">_File</property>
+                <property name="use_underline">True</property>
+                <child type="submenu">
+                  <object class="GtkMenu" id="menu1">
+                    <property name="can_focus">False</property>
+                    <child>
+                      <object class="GtkImageMenuItem" id="new_experiment">
+                        <property name="label">gtk-new</property>
+                        <property name="visible">True</property>
+                        <property name="can_focus">False</property>
+                        <property name="use_action_appearance">False</property>
+                        <property name="use_underline">True</property>
+                        <property name="use_stock">True</property>
+                        <signal name="activate" handler="on_new_experiment_activate" swapped="no"/>
+                      </object>
+                    </child>
+                    <child>
+                      <object class="GtkImageMenuItem" id="open_experiment">
+                        <property name="label">gtk-open</property>
+                        <property name="visible">True</property>
+                        <property name="can_focus">False</property>
+                        <property name="use_action_appearance">False</property>
+                        <property name="use_underline">True</property>
+                        <property name="use_stock">True</property>
+                        <signal name="activate" handler="on_open_experiment_activate" swapped="no"/>
+                      </object>
+                    </child>
+                    <child>
+                      <object class="GtkImageMenuItem" id="save_experiment">
+                        <property name="label">gtk-save</property>
+                        <property name="visible">True</property>
+                        <property name="can_focus">False</property>
+                        <property name="use_action_appearance">False</property>
+                        <property name="use_underline">True</property>
+                        <property name="use_stock">True</property>
+                        <signal name="activate" handler="on_save_experiment_activate" swapped="no"/>
+                      </object>
+                    </child>
+                    <child>
+                      <object class="GtkImageMenuItem" id="save_experiment_as">
+                        <property name="label">gtk-save-as</property>
+                        <property name="visible">True</property>
+                        <property name="can_focus">False</property>
+                        <property name="use_action_appearance">False</property>
+                        <property name="use_underline">True</property>
+                        <property name="use_stock">True</property>
+                        <signal name="activate" handler="on_save_experiment_as_activate" swapped="no"/>
+                      </object>
+                    </child>
+                    <child>
+                      <object class="GtkSeparatorMenuItem" id="<séparateur>">
+                        <property name="visible">True</property>
+                        <property name="can_focus">False</property>
+                      </object>
+                    </child>
+                    <child>
+                      <object class="GtkMenuItem" id="export_item">
+                        <property name="visible">True</property>
+                        <property name="can_focus">False</property>
+                        <property name="use_action_appearance">False</property>
+                        <property name="label" translatable="yes">export</property>
+                        <property name="use_underline">True</property>
+                        <child type="submenu">
+                          <object class="GtkMenu" id="menu_export">
+                            <property name="visible">True</property>
+                            <property name="can_focus">False</property>
+                            <child>
+                              <object class="GtkMenuItem" id="menu_export_stiffness">
+                                <property name="visible">True</property>
+                                <property name="can_focus">False</property>
+                                <property name="tooltip_text" translatable="yes">Export the stiffness data
+in csv files.</property>
+                                <property name="use_action_appearance">False</property>
+                                <property name="label" translatable="yes">Stiffness</property>
+                                <property name="use_underline">True</property>
+                                <signal name="activate" handler="on_menu_export_stiffness_activate" swapped="no"/>
+                              </object>
+                            </child>
+                            <child>
+                              <object class="GtkMenuItem" id="menu_export_average_stiffness_tomography">
+                                <property name="visible">True</property>
+                                <property name="can_focus">False</property>
+                                <property name="tooltip_text" translatable="yes">Export the average
+stiffness tomography
+in csv file.</property>
+                                <property name="use_action_appearance">False</property>
+                                <property name="label" translatable="yes">Average stiffness
+tomography</property>
+                                <property name="use_underline">True</property>
+                                <signal name="activate" handler="on_menu_export_average_stiffness_tomography_activate" swapped="no"/>
+                              </object>
+                            </child>
+                            <child>
+                              <object class="GtkMenuItem" id="menu_export_map">
+                                <property name="visible">True</property>
+                                <property name="can_focus">False</property>
+                                <property name="tooltip_text" translatable="yes">Export the maps
+as an image.</property>
+                                <property name="use_action_appearance">False</property>
+                                <property name="label" translatable="yes">Maps</property>
+                                <property name="use_underline">True</property>
+                                <signal name="activate" handler="on_menu_export_map_activate" swapped="no"/>
+                              </object>
+                            </child>
+                            <child>
+                              <object class="GtkImageMenuItem" id="menu_export_curve">
+                                <property name="label" translatable="yes">Current curve</property>
+                                <property name="visible">True</property>
+                                <property name="can_focus">False</property>
+                                <property name="tooltip_text" translatable="yes">Export the current curve
+to a csv file.</property>
+                                <property name="use_action_appearance">False</property>
+                                <property name="image">image4</property>
+                                <property name="use_stock">False</property>
+                                <signal name="activate" handler="on_menu_export_curve_activate" swapped="no"/>
+                              </object>
+                            </child>
+                            <child>
+                              <object class="GtkImageMenuItem" id="menu_export_event_prop">
+                                <property name="label" translatable="yes">Event properties</property>
+                                <property name="visible">True</property>
+                                <property name="can_focus">False</property>
+                                <property name="tooltip_text" translatable="yes">Export the event properties
+position, force, loading-rate, ...
+in a csv file.</property>
+                                <property name="use_action_appearance">False</property>
+                                <property name="image">image3</property>
+                                <property name="use_stock">False</property>
+                                <signal name="activate" handler="on_menu_export_event_prop_activate" swapped="no"/>
+                              </object>
+                            </child>
+                            <child>
+                              <object class="GtkImageMenuItem" id="menu_export_evt_nbr">
+                                <property name="label" translatable="yes">nbr event per curves</property>
+                                <property name="visible">True</property>
+                                <property name="can_focus">False</property>
+                                <property name="tooltip_text" translatable="yes">Exports the number of event
+per curves in a csv file.</property>
+                                <property name="use_action_appearance">False</property>
+                                <property name="image">image5</property>
+                                <property name="use_stock">False</property>
+                                <signal name="activate" handler="on_menu_export_evt_nbr_activate" swapped="no"/>
+                              </object>
+                            </child>
+                          </object>
+                        </child>
+                      </object>
+                    </child>
+                    <child>
+                      <object class="GtkSeparatorMenuItem" id="separatormenuitem1">
+                        <property name="visible">True</property>
+                        <property name="can_focus">False</property>
+                      </object>
+                    </child>
+                    <child>
+                      <object class="GtkMenuItem" id="show_header">
+                        <property name="visible">True</property>
+                        <property name="can_focus">False</property>
+                        <property name="use_action_appearance">False</property>
+                        <property name="label" translatable="yes">show header</property>
+                        <property name="use_underline">True</property>
+                        <signal name="activate" handler="on_show_header_activate" swapped="no"/>
+                      </object>
+                    </child>
+                    <child>
+                      <object class="GtkImageMenuItem" id="quitter1">
+                        <property name="label">gtk-quit</property>
+                        <property name="visible">True</property>
+                        <property name="can_focus">False</property>
+                        <property name="use_action_appearance">False</property>
+                        <property name="use_underline">True</property>
+                        <property name="use_stock">True</property>
+                        <signal name="activate" handler="on_MainWindow_destroy" swapped="no"/>
+                      </object>
+                    </child>
+                  </object>
+                </child>
+              </object>
+            </child>
+            <child>
+              <object class="GtkMenuItem" id="menu_edit">
+                <property name="visible">True</property>
+                <property name="can_focus">False</property>
+                <property name="use_action_appearance">False</property>
+                <property name="label" translatable="yes">_Edition</property>
+                <property name="use_underline">True</property>
+                <child type="submenu">
+                  <object class="GtkMenu" id="menu2">
+                    <property name="can_focus">False</property>
+                    <child>
+                      <object class="GtkImageMenuItem" id="couper1">
+                        <property name="label">gtk-cut</property>
+                        <property name="can_focus">False</property>
+                        <property name="use_action_appearance">False</property>
+                        <property name="use_underline">True</property>
+                        <property name="use_stock">True</property>
+                      </object>
+                    </child>
+                    <child>
+                      <object class="GtkImageMenuItem" id="copier1">
+                        <property name="label">gtk-copy</property>
+                        <property name="can_focus">False</property>
+                        <property name="use_action_appearance">False</property>
+                        <property name="use_underline">True</property>
+                        <property name="use_stock">True</property>
+                      </object>
+                    </child>
+                    <child>
+                      <object class="GtkImageMenuItem" id="coller1">
+                        <property name="label">gtk-paste</property>
+                        <property name="can_focus">False</property>
+                        <property name="use_action_appearance">False</property>
+                        <property name="use_underline">True</property>
+                        <property name="use_stock">True</property>
+                      </object>
+                    </child>
+                    <child>
+                      <object class="GtkImageMenuItem" id="supprimer1">
+                        <property name="label">gtk-delete</property>
+                        <property name="can_focus">False</property>
+                        <property name="use_action_appearance">False</property>
+                        <property name="use_underline">True</property>
+                        <property name="use_stock">True</property>
+                      </object>
+                    </child>
+                    <child>
+                      <object class="GtkImageMenuItem" id="ReloadModules1">
+                        <property name="label">Reload modules</property>
+                        <property name="can_focus">False</property>
+                        <property name="use_action_appearance">False</property>
+                        <property name="use_underline">True</property>
+                        <property name="use_stock">True</property>
+                      </object>
+                    </child>
+                    <child>
+                      <object class="GtkImageMenuItem" id="exp_prop">
+                        <property name="label">gtk-preferences</property>
+                        <property name="visible">True</property>
+                        <property name="can_focus">False</property>
+                        <property name="tooltip_text" translatable="yes">Edit the experiment 
+properties</property>
+                        <property name="use_action_appearance">False</property>
+                        <property name="use_underline">True</property>
+                        <property name="use_stock">True</property>
+                        <signal name="activate" handler="on_exp_prop_activate" swapped="no"/>
+                      </object>
+                    </child>
+                    <child>
+                      <object class="GtkMenuItem" id="group">
+                        <property name="visible">True</property>
+                        <property name="can_focus">False</property>
+                        <property name="tooltip_text" translatable="yes">Manage the groups</property>
+                        <property name="use_action_appearance">False</property>
+                        <property name="label" translatable="yes">group</property>
+                        <property name="use_underline">True</property>
+                        <signal name="activate" handler="on_group_activate" swapped="no"/>
+                      </object>
+                    </child>
+                    <child>
+                      <object class="GtkMenuItem" id="menu_mask">
+                        <property name="visible">True</property>
+                        <property name="can_focus">False</property>
+                        <property name="tooltip_text" translatable="yes">Create or modify mask for
+the arrays.</property>
+                        <property name="use_action_appearance">False</property>
+                        <property name="label" translatable="yes">mask</property>
+                        <property name="use_underline">True</property>
+                        <signal name="activate" handler="on_menu_mask_activate" swapped="no"/>
+                      </object>
+                    </child>
+                  </object>
+                </child>
+              </object>
+            </child>
+            <child>
+              <object class="GtkMenuItem" id="menuitem3">
+                <property name="visible">True</property>
+                <property name="can_focus">False</property>
+                <property name="use_action_appearance">False</property>
+                <property name="label" translatable="yes">_Options</property>
+                <property name="use_underline">True</property>
+                <child type="submenu">
+                  <object class="GtkMenu" id="menu3">
+                    <property name="can_focus">False</property>
+                    <child>
+                      <object class="GtkCheckMenuItem" id="apply_on_all">
+                        <property name="visible">True</property>
+                        <property name="can_focus">False</property>
+                        <property name="use_action_appearance">False</property>
+                        <property name="label" translatable="yes">apply on all</property>
+                        <property name="use_underline">True</property>
+                        <signal name="toggled" handler="on_apply_on_all_toggled" swapped="no"/>
+                      </object>
+                    </child>
+                    <child>
+                      <object class="GtkImageMenuItem" id="compare_exp">
+                        <property name="label" translatable="yes">compare experiment</property>
+                        <property name="visible">True</property>
+                        <property name="can_focus">False</property>
+                        <property name="use_action_appearance">False</property>
+                        <property name="image">image2</property>
+                        <property name="use_stock">False</property>
+                        <signal name="activate" handler="on_compare_exp_activate" swapped="no"/>
+                      </object>
+                    </child>
+                    <child>
+                      <object class="GtkMenuItem" id="flatten_piezo">
+                        <property name="visible">True</property>
+                        <property name="can_focus">False</property>
+                        <property name="tooltip_text" translatable="yes">Open a dialog to flatten
+the piezo image.</property>
+                        <property name="use_action_appearance">False</property>
+                        <property name="label" translatable="yes">flatten image</property>
+                        <property name="use_underline">True</property>
+                        <signal name="activate" handler="on_flatten_activate" swapped="no"/>
+                      </object>
+                    </child>
+                  </object>
+                </child>
+              </object>
+            </child>
+            <child>
+              <object class="GtkMenuItem" id="menuitem4">
+                <property name="visible">True</property>
+                <property name="can_focus">False</property>
+                <property name="use_action_appearance">False</property>
+                <property name="label" translatable="yes">_Aide</property>
+                <property name="use_underline">True</property>
+                <child type="submenu">
+                  <object class="GtkMenu" id="menu4">
+                    <property name="can_focus">False</property>
+                    <child>
+                      <object class="GtkMenuItem" id="about">
+                        <property name="visible">True</property>
+                        <property name="can_focus">False</property>
+                        <property name="use_action_appearance">False</property>
+                        <property name="label" translatable="yes">À _propos</property>
+                        <property name="use_underline">True</property>
+                        <signal name="activate" handler="on_about_activate" swapped="no"/>
+                      </object>
+                    </child>
+                  </object>
+                </child>
+              </object>
+            </child>
+          </object>
+          <packing>
+            <property name="expand">False</property>
+            <property name="fill">False</property>
+            <property name="position">0</property>
+          </packing>
+        </child>
+        <child>
+          <object class="GtkNotebook" id="notebook1">
+            <property name="visible">True</property>
+            <property name="can_focus">True</property>
+            <property name="scrollable">True</property>
+            <property name="enable_popup">True</property>
+            <child>
+              <object class="GtkVBox" id="vbox_display">
+                <property name="visible">True</property>
+                <property name="can_focus">False</property>
+                <child>
+                  <object class="GtkHBox" id="navigation_box">
+                    <property name="visible">True</property>
+                    <property name="can_focus">False</property>
+                    <child>
+                      <object class="GtkTable" id="navigation_table">
+                        <property name="visible">True</property>
+                        <property name="can_focus">False</property>
+                        <property name="n_rows">3</property>
+                        <property name="n_columns">3</property>
+                        <child>
+                          <object class="GtkButton" id="button_next">
+                            <property name="label">gtk-go-forward</property>
+                            <property name="width_request">88</property>
+                            <property name="height_request">32</property>
+                            <property name="visible">True</property>
+                            <property name="can_focus">True</property>
+                            <property name="receives_default">False</property>
+                            <property name="tooltip_text">Go to the right position in the scan</property>
+                            <property name="use_action_appearance">False</property>
+                            <property name="use_stock">True</property>
+                            <signal name="clicked" handler="on_button_next_clicked" swapped="no"/>
+                          </object>
+                          <packing>
+                            <property name="left_attach">2</property>
+                            <property name="right_attach">3</property>
+                            <property name="top_attach">1</property>
+                            <property name="bottom_attach">2</property>
+                          </packing>
+                        </child>
+                        <child>
+                          <object class="GtkButton" id="button_up">
+                            <property name="label">gtk-go-up</property>
+                            <property name="width_request">112</property>
+                            <property name="height_request">32</property>
+                            <property name="visible">True</property>
+                            <property name="can_focus">True</property>
+                            <property name="receives_default">False</property>
+                            <property name="tooltip_text">Go to a upper position in the scan</property>
+                            <property name="use_action_appearance">False</property>
+                            <property name="use_stock">True</property>
+                            <signal name="clicked" handler="on_button_up_clicked" swapped="no"/>
+                          </object>
+                          <packing>
+                            <property name="left_attach">1</property>
+                            <property name="right_attach">2</property>
+                          </packing>
+                        </child>
+                        <child>
+                          <object class="GtkButton" id="button_prev">
+                            <property name="label">gtk-go-back</property>
+                            <property name="width_request">88</property>
+                            <property name="height_request">32</property>
+                            <property name="visible">True</property>
+                            <property name="can_focus">True</property>
+                            <property name="receives_default">False</property>
+                            <property name="has_tooltip">True</property>
+                            <property name="tooltip_text">Go to the left position in the scan</property>
+                            <property name="use_action_appearance">False</property>
+                            <property name="use_stock">True</property>
+                            <signal name="clicked" handler="on_button_prev_clicked" swapped="no"/>
+                          </object>
+                          <packing>
+                            <property name="top_attach">1</property>
+                            <property name="bottom_attach">2</property>
+                          </packing>
+                        </child>
+                        <child>
+                          <object class="GtkButton" id="button_down">
+                            <property name="label">gtk-go-down</property>
+                            <property name="width_request">112</property>
+                            <property name="height_request">32</property>
+                            <property name="visible">True</property>
+                            <property name="can_focus">True</property>
+                            <property name="receives_default">False</property>
+                            <property name="has_tooltip">True</property>
+                            <property name="tooltip_text">Go to a lower position in the scan</property>
+                            <property name="use_action_appearance">False</property>
+                            <property name="use_stock">True</property>
+                            <signal name="clicked" handler="on_button_down_clicked" swapped="no"/>
+                          </object>
+                          <packing>
+                            <property name="left_attach">1</property>
+                            <property name="right_attach">2</property>
+                            <property name="top_attach">2</property>
+                            <property name="bottom_attach">3</property>
+                          </packing>
+                        </child>
+                        <child>
+                          <object class="GtkHBox" id="position_box">
+                            <property name="visible">True</property>
+                            <property name="can_focus">False</property>
+                            <child>
+                              <object class="GtkLabel" id="label_pos_x">
+                                <property name="width_request">38</property>
+                                <property name="height_request">17</property>
+                                <property name="visible">True</property>
+                                <property name="can_focus">False</property>
+                                <property name="label" translatable="yes">0</property>
+                                <property name="justify">center</property>
+                              </object>
+                              <packing>
+                                <property name="expand">True</property>
+                                <property name="fill">True</property>
+                                <property name="position">0</property>
+                              </packing>
+                            </child>
+                            <child>
+                              <object class="GtkVSeparator" id="vseparator1">
+                                <property name="width_request">16</property>
+                                <property name="height_request">32</property>
+                                <property name="visible">True</property>
+                                <property name="can_focus">False</property>
+                              </object>
+                              <packing>
+                                <property name="expand">False</property>
+                                <property name="fill">True</property>
+                                <property name="position">1</property>
+                              </packing>
+                            </child>
+                            <child>
+                              <object class="GtkLabel" id="label_pos_y">
+                                <property name="width_request">38</property>
+                                <property name="height_request">17</property>
+                                <property name="visible">True</property>
+                                <property name="can_focus">False</property>
+                                <property name="label" translatable="yes">0</property>
+                                <property name="justify">center</property>
+                              </object>
+                              <packing>
+                                <property name="expand">True</property>
+                                <property name="fill">True</property>
+                                <property name="position">2</property>
+                              </packing>
+                            </child>
+                          </object>
+                          <packing>
+                            <property name="left_attach">1</property>
+                            <property name="right_attach">2</property>
+                            <property name="top_attach">1</property>
+                            <property name="bottom_attach">2</property>
+                          </packing>
+                        </child>
+                        <child>
+                          <placeholder/>
+                        </child>
+                        <child>
+                          <placeholder/>
+                        </child>
+                        <child>
+                          <placeholder/>
+                        </child>
+                        <child>
+                          <placeholder/>
+                        </child>
+                      </object>
+                      <packing>
+                        <property name="expand">False</property>
+                        <property name="fill">False</property>
+                        <property name="position">0</property>
+                      </packing>
+                    </child>
+                    <child>
+                      <object class="GtkVSeparator" id="vseparator2">
+                        <property name="visible">True</property>
+                        <property name="can_focus">False</property>
+                      </object>
+                      <packing>
+                        <property name="expand">False</property>
+                        <property name="fill">False</property>
+                        <property name="position">1</property>
+                      </packing>
+                    </child>
+                    <child>
+                      <object class="GtkVBox" id="list_file_box">
+                        <property name="visible">True</property>
+                        <property name="can_focus">False</property>
+                        <child>
+                          <object class="GtkLabel" id="label4">
+                            <property name="visible">True</property>
+                            <property name="can_focus">False</property>
+                            <property name="xalign">0</property>
+                            <property name="yalign">0</property>
+                            <property name="label" translatable="yes">List of files</property>
+                          </object>
+                          <packing>
+                            <property name="expand">False</property>
+                            <property name="fill">False</property>
+                            <property name="position">0</property>
+                          </packing>
+                        </child>
+                        <child>
+                          <object class="GtkComboBox" id="list_file_combo_box">
+                            <property name="visible">True</property>
+                            <property name="can_focus">False</property>
+                            <signal name="changed" handler="on_list_file_combo_box_changed" swapped="no"/>
+                          </object>
+                          <packing>
+                            <property name="expand">False</property>
+                            <property name="fill">False</property>
+                            <property name="position">1</property>
+                          </packing>
+                        </child>
+                        <child>
+                          <placeholder/>
+                        </child>
+                      </object>
+                      <packing>
+                        <property name="expand">False</property>
+                        <property name="fill">False</property>
+                        <property name="position">2</property>
+                      </packing>
+                    </child>
+                  </object>
+                  <packing>
+                    <property name="expand">False</property>
+                    <property name="fill">False</property>
+                    <property name="position">0</property>
+                  </packing>
+                </child>
+                <child>
+                  <object class="GtkHSeparator" id="hseparator1">
+                    <property name="visible">True</property>
+                    <property name="can_focus">False</property>
+                  </object>
+                  <packing>
+                    <property name="expand">False</property>
+                    <property name="fill">True</property>
+                    <property name="position">1</property>
+                  </packing>
+                </child>
+                <child>
+                  <object class="GtkHBox" id="hbox3">
+                    <property name="visible">True</property>
+                    <property name="can_focus">False</property>
+                    <child>
+                      <object class="GtkFrame" id="frame1">
+                        <property name="visible">True</property>
+                        <property name="can_focus">False</property>
+                        <property name="label_xalign">0</property>
+                        <property name="label_yalign">0</property>
+                        <property name="shadow_type">none</property>
+                        <child>
+                          <object class="GtkAlignment" id="curve_display_list">
+                            <property name="visible">True</property>
+                            <property name="can_focus">False</property>
+                            <property name="xalign">0</property>
+                            <property name="yalign">0</property>
+                            <property name="left_padding">12</property>
+                            <child>
+                              <object class="GtkVBox" id="vbox3">
+                                <property name="visible">True</property>
+                                <property name="can_focus">False</property>
+                                <child>
+                                  <object class="GtkCheckButton" id="check_display_fc_trace">
+                                    <property name="label" translatable="yes">Forward force curve</property>
+                                    <property name="visible">True</property>
+                                    <property name="can_focus">True</property>
+                                    <property name="receives_default">False</property>
+                                    <property name="use_action_appearance">False</property>
+                                    <property name="use_underline">True</property>
+                                    <property name="active">True</property>
+                                    <property name="draw_indicator">True</property>
+                                    <signal name="clicked" handler="on_check_display_fc_trace_clicked" swapped="no"/>
+                                  </object>
+                                  <packing>
+                                    <property name="expand">False</property>
+                                    <property name="fill">False</property>
+                                    <property name="position">0</property>
+                                  </packing>
+                                </child>
+                                <child>
+                                  <object class="GtkCheckButton" id="check_display_fc_retrace">
+                                    <property name="label" translatable="yes">Retraction force curve</property>
+                                    <property name="visible">True</property>
+                                    <property name="can_focus">True</property>
+                                    <property name="receives_default">False</property>
+                                    <property name="use_action_appearance">False</property>
+                                    <property name="use_underline">True</property>
+                                    <property name="draw_indicator">True</property>
+                                    <signal name="clicked" handler="on_check_display_fc_retrace_clicked" swapped="no"/>
+                                  </object>
+                                  <packing>
+                                    <property name="expand">False</property>
+                                    <property name="fill">False</property>
+                                    <property name="position">1</property>
+                                  </packing>
+                                </child>
+                                <child>
+                                  <object class="GtkCheckButton" id="check_display_poc">
+                                    <property name="label" translatable="yes">Point of contact</property>
+                                    <property name="visible">True</property>
+                                    <property name="can_focus">True</property>
+                                    <property name="receives_default">False</property>
+                                    <property name="use_action_appearance">False</property>
+                                    <property name="use_underline">True</property>
+                                    <property name="draw_indicator">True</property>
+                                    <signal name="clicked" handler="on_check_display_poc_clicked" swapped="no"/>
+                                  </object>
+                                  <packing>
+                                    <property name="expand">False</property>
+                                    <property name="fill">False</property>
+                                    <property name="position">2</property>
+                                  </packing>
+                                </child>
+                                <child>
+                                  <object class="GtkCheckButton" id="check_display_event">
+                                    <property name="label" translatable="yes">Event on curve</property>
+                                    <property name="visible">True</property>
+                                    <property name="can_focus">True</property>
+                                    <property name="receives_default">False</property>
+                                    <property name="use_action_appearance">False</property>
+                                    <property name="use_underline">True</property>
+                                    <property name="draw_indicator">True</property>
+                                    <signal name="clicked" handler="on_check_display_event_clicked" swapped="no"/>
+                                  </object>
+                                  <packing>
+                                    <property name="expand">False</property>
+                                    <property name="fill">False</property>
+                                    <property name="position">3</property>
+                                  </packing>
+                                </child>
+                                <child>
+                                  <object class="GtkCheckButton" id="check_display_indent">
+                                    <property name="label" translatable="yes">Indentation curve</property>
+                                    <property name="visible">True</property>
+                                    <property name="can_focus">True</property>
+                                    <property name="receives_default">False</property>
+                                    <property name="use_action_appearance">False</property>
+                                    <property name="use_underline">True</property>
+                                    <property name="draw_indicator">True</property>
+                                    <signal name="clicked" handler="on_check_display_indent_clicked" swapped="no"/>
+                                  </object>
+                                  <packing>
+                                    <property name="expand">False</property>
+                                    <property name="fill">False</property>
+                                    <property name="position">4</property>
+                                  </packing>
+                                </child>
+                              </object>
+                            </child>
+                          </object>
+                        </child>
+                        <child type="label">
+                          <object class="GtkLabel" id="label5">
+                            <property name="visible">True</property>
+                            <property name="can_focus">False</property>
+                            <property name="xalign">0</property>
+                            <property name="yalign">0</property>
+                            <property name="label" translatable="yes"><b>Window to display</b></property>
+                            <property name="use_markup">True</property>
+                          </object>
+                        </child>
+                      </object>
+                      <packing>
+                        <property name="expand">False</property>
+                        <property name="fill">True</property>
+                        <property name="position">0</property>
+                      </packing>
+                    </child>
+                    <child>
+                      <object class="GtkVBox" id="array_display_box">
+                        <property name="visible">True</property>
+                        <property name="can_focus">False</property>
+                        <child>
+                          <object class="GtkButton" id="button_piezzo_array">
+                            <property name="label" translatable="yes">Piezo Height</property>
+                            <property name="visible">True</property>
+                            <property name="can_focus">True</property>
+                            <property name="receives_default">True</property>
+                            <property name="use_action_appearance">False</property>
+                            <signal name="clicked" handler="on_button_piezzo_array_clicked" swapped="no"/>
+                          </object>
+                          <packing>
+                            <property name="expand">False</property>
+                            <property name="fill">False</property>
+                            <property name="position">0</property>
+                          </packing>
+                        </child>
+                        <child>
+                          <object class="GtkButton" id="button_topography_array">
+                            <property name="label" translatable="yes">Topography</property>
+                            <property name="visible">True</property>
+                            <property name="can_focus">True</property>
+                            <property name="receives_default">True</property>
+                            <property name="use_action_appearance">False</property>
+                            <signal name="clicked" handler="on_button_topography_array_clicked" swapped="no"/>
+                          </object>
+                          <packing>
+                            <property name="expand">False</property>
+                            <property name="fill">False</property>
+                            <property name="position">1</property>
+                          </packing>
+                        </child>
+                        <child>
+                          <object class="GtkButton" id="button_stiffness_array">
+                            <property name="label" translatable="yes">Stiffness</property>
+                            <property name="visible">True</property>
+                            <property name="can_focus">True</property>
+                            <property name="receives_default">True</property>
+                            <property name="use_action_appearance">False</property>
+                            <signal name="clicked" handler="on_button_stiffness_array_clicked" swapped="no"/>
+                          </object>
+                          <packing>
+                            <property name="expand">False</property>
+                            <property name="fill">False</property>
+                            <property name="position">2</property>
+                          </packing>
+                        </child>
+                        <child>
+                          <object class="GtkButton" id="button_event_array">
+                            <property name="label" translatable="yes">Event </property>
+                            <property name="visible">True</property>
+                            <property name="can_focus">True</property>
+                            <property name="receives_default">True</property>
+                            <property name="use_action_appearance">False</property>
+                            <signal name="clicked" handler="on_button_event_array_clicked" swapped="no"/>
+                          </object>
+                          <packing>
+                            <property name="expand">False</property>
+                            <property name="fill">False</property>
+                            <property name="position">3</property>
+                          </packing>
+                        </child>
+                        <child>
+                          <object class="GtkButton" id="button_event_force_array">
+                            <property name="label" translatable="yes">Event force</property>
+                            <property name="visible">True</property>
+                            <property name="can_focus">True</property>
+                            <property name="receives_default">True</property>
+                            <property name="use_action_appearance">False</property>
+                            <signal name="clicked" handler="on_button_event_force_array_clicked" swapped="no"/>
+                          </object>
+                          <packing>
+                            <property name="expand">True</property>
+                            <property name="fill">True</property>
+                            <property name="position">4</property>
+                          </packing>
+                        </child>
+                        <child>
+                          <object class="GtkButton" id="button_event_dist_array">
+                            <property name="label" translatable="yes">Event distance</property>
+                            <property name="visible">True</property>
+                            <property name="can_focus">True</property>
+                            <property name="receives_default">True</property>
+                            <property name="tooltip_text" translatable="yes">Unbinding event rupture distance.</property>
+                            <property name="use_action_appearance">False</property>
+                            <signal name="clicked" handler="on_button_event_dist_array_clicked" swapped="no"/>
+                          </object>
+                          <packing>
+                            <property name="expand">True</property>
+                            <property name="fill">True</property>
+                            <property name="position">5</property>
+                          </packing>
+                        </child>
+                        <child>
+                          <object class="GtkButton" id="button_event_length_array">
+                            <property name="label" translatable="yes">Event length</property>
+                            <property name="visible">True</property>
+                            <property name="can_focus">True</property>
+                            <property name="receives_default">True</property>
+                            <property name="tooltip_text" translatable="yes">Unbinding event length as computed 
+with the event fit model.
+
+If not computed, go to the "Parameters" tab,
+select an event fit model and recompute
+the event detection.</property>
+                            <property name="use_action_appearance">False</property>
+                            <signal name="clicked" handler="on_button_event_length_array_clicked" swapped="no"/>
+                          </object>
+                          <packing>
+                            <property name="expand">True</property>
+                            <property name="fill">True</property>
+                            <property name="position">6</property>
+                          </packing>
+                        </child>
+                        <child>
+                          <object class="GtkButton" id="button_stiffness_tomo">
+                            <property name="label" translatable="yes">   Stiffness
+tomography</property>
+                            <property name="visible">True</property>
+                            <property name="can_focus">True</property>
+                            <property name="receives_default">True</property>
+                            <property name="tooltip_text" translatable="yes">Display the detailed stiffness
+of the object with projection in
+x, y and z.</property>
+                            <property name="use_action_appearance">False</property>
+                            <signal name="clicked" handler="on_button_stiffness_tomo_clicked" swapped="no"/>
+                          </object>
+                          <packing>
+                            <property name="expand">True</property>
+                            <property name="fill">True</property>
+                            <property name="position">7</property>
+                          </packing>
+                        </child>
+                        <child>
+                          <object class="GtkButton" id="button_mean_stiffness_tomo">
+                            <property name="label" translatable="yes">Mean Stiffness
+  tomography</property>
+                            <property name="visible">True</property>
+                            <property name="can_focus">True</property>
+                            <property name="receives_default">True</property>
+                            <property name="tooltip_text" translatable="yes">Display the average stiffness
+in function of the depth.</property>
+                            <property name="use_action_appearance">False</property>
+                            <signal name="clicked" handler="on_button_mean_stiffness_tomo_clicked" swapped="no"/>
+                          </object>
+                          <packing>
+                            <property name="expand">True</property>
+                            <property name="fill">True</property>
+                            <property name="position">8</property>
+                          </packing>
+                        </child>
+                        <child>
+                          <object class="GtkButton" id="button_opengl">
+                            <property name="label" translatable="yes">OpenGL</property>
+                            <property name="visible">True</property>
+                            <property name="can_focus">True</property>
+                            <property name="receives_default">True</property>
+                            <property name="use_action_appearance">False</property>
+                            <signal name="clicked" handler="on_button_opengl_clicked" swapped="no"/>
+                          </object>
+                          <packing>
+                            <property name="expand">False</property>
+                            <property name="fill">False</property>
+                            <property name="position">9</property>
+                          </packing>
+                        </child>
+                      </object>
+                      <packing>
+                        <property name="expand">False</property>
+                        <property name="fill">False</property>
+                        <property name="position">1</property>
+                      </packing>
+                    </child>
+                    <child>
+                      <object class="GtkFrame" id="frame_mosaic">
+                        <property name="visible">True</property>
+                        <property name="can_focus">False</property>
+                        <property name="label_xalign">0</property>
+                        <property name="shadow_type">none</property>
+                        <child>
+                          <object class="GtkAlignment" id="alignment5">
+                            <property name="visible">True</property>
+                            <property name="can_focus">False</property>
+                            <property name="left_padding">12</property>
+                            <child>
+                              <object class="GtkVBox" id="vbox4">
+                                <property name="visible">True</property>
+                                <property name="can_focus">False</property>
+                                <child>
+                                  <object class="GtkButton" id="button_mosaic_piezo">
+                                    <property name="label" translatable="yes">Piezo Height</property>
+                                    <property name="visible">True</property>
+                                    <property name="can_focus">True</property>
+                                    <property name="receives_default">True</property>
+                                    <property name="use_action_appearance">False</property>
+                                    <signal name="clicked" handler="on_button_mosaic_piezo_clicked" swapped="no"/>
+                                  </object>
+                                  <packing>
+                                    <property name="expand">False</property>
+                                    <property name="fill">False</property>
+                                    <property name="position">0</property>
+                                  </packing>
+                                </child>
+                                <child>
+                                  <object class="GtkButton" id="button_mosaic_topography">
+                                    <property name="label" translatable="yes">Topography</property>
+                                    <property name="visible">True</property>
+                                    <property name="can_focus">True</property>
+                                    <property name="receives_default">True</property>
+                                    <property name="use_action_appearance">False</property>
+                                    <signal name="clicked" handler="on_button_mosaic_topography_clicked" swapped="no"/>
+                                  </object>
+                                  <packing>
+                                    <property name="expand">False</property>
+                                    <property name="fill">False</property>
+                                    <property name="position">1</property>
+                                  </packing>
+                                </child>
+                                <child>
+                                  <object class="GtkButton" id="button_mosaic_stiffness">
+                                    <property name="label" translatable="yes">Stiffness</property>
+                                    <property name="visible">True</property>
+                                    <property name="can_focus">True</property>
+                                    <property name="receives_default">True</property>
+                                    <property name="use_action_appearance">False</property>
+                                    <signal name="clicked" handler="on_button_mosaic_stiffness_clicked" swapped="no"/>
+                                  </object>
+                                  <packing>
+                                    <property name="expand">False</property>
+                                    <property name="fill">False</property>
+                                    <property name="position">2</property>
+                                  </packing>
+                                </child>
+                                <child>
+                                  <object class="GtkButton" id="button_mosaic_event">
+                                    <property name="label" translatable="yes">Event</property>
+                                    <property name="visible">True</property>
+                                    <property name="can_focus">True</property>
+                                    <property name="receives_default">True</property>
+                                    <property name="use_action_appearance">False</property>
+                                    <signal name="clicked" handler="on_button_mosaic_event_clicked" swapped="no"/>
+                                  </object>
+                                  <packing>
+                                    <property name="expand">False</property>
+                                    <property name="fill">False</property>
+                                    <property name="position">3</property>
+                                  </packing>
+                                </child>
+                                <child>
+                                  <object class="GtkButton" id="button_mosaic_event_force">
+                                    <property name="label" translatable="yes">Event force</property>
+                                    <property name="visible">True</property>
+                                    <property name="can_focus">True</property>
+                                    <property name="receives_default">True</property>
+                                    <property name="use_action_appearance">False</property>
+                                    <signal name="clicked" handler="on_button_mosaic_event_force_clicked" swapped="no"/>
+                                  </object>
+                                  <packing>
+                                    <property name="expand">True</property>
+                                    <property name="fill">True</property>
+                                    <property name="position">4</property>
+                                  </packing>
+                                </child>
+                              </object>
+                            </child>
+                          </object>
+                        </child>
+                        <child type="label">
+                          <object class="GtkLabel" id="label30">
+                            <property name="visible">True</property>
+                            <property name="can_focus">False</property>
+                            <property name="label" translatable="yes"><b>Mosaic</b></property>
+                            <property name="use_markup">True</property>
+                          </object>
+                        </child>
+                      </object>
+                      <packing>
+                        <property name="expand">False</property>
+                        <property name="fill">False</property>
+                        <property name="position">2</property>
+                      </packing>
+                    </child>
+                  </object>
+                  <packing>
+                    <property name="expand">False</property>
+                    <property name="fill">False</property>
+                    <property name="position">2</property>
+                  </packing>
+                </child>
+              </object>
+              <packing>
+                <property name="tab_fill">False</property>
+                <property name="reorderable">True</property>
+                <property name="detachable">True</property>
+              </packing>
+            </child>
+            <child type="tab">
+              <object class="GtkLabel" id="label2">
+                <property name="visible">True</property>
+                <property name="can_focus">False</property>
+                <property name="xalign">0</property>
+                <property name="yalign">0</property>
+                <property name="label" translatable="yes">Display</property>
+              </object>
+              <packing>
+                <property name="tab_fill">False</property>
+              </packing>
+            </child>
+            <child>
+              <object class="GtkVBox" id="compute_box">
+                <property name="visible">True</property>
+                <property name="can_focus">False</property>
+                <child>
+                  <object class="GtkHBox" id="Allboxes">
+                    <property name="visible">True</property>
+                    <property name="can_focus">False</property>
+                    <child>
+                      <object class="GtkFrame" id="frame_stiffness">
+                        <property name="visible">True</property>
+                        <property name="can_focus">False</property>
+                        <property name="label_xalign">0</property>
+                        <child>
+                          <object class="GtkAlignment" id="alignment2">
+                            <property name="visible">True</property>
+                            <property name="can_focus">False</property>
+                            <property name="left_padding">12</property>
+                            <child>
+                              <object class="GtkVBox" id="stiffness_box">
+                                <property name="visible">True</property>
+                                <property name="can_focus">False</property>
+                                <property name="spacing">2</property>
+                                <child>
+                                  <object class="GtkHBox" id="deep_box">
+                                    <property name="visible">True</property>
+                                    <property name="can_focus">False</property>
+                                    <child>
+                                      <object class="GtkEntry" id="entry_number_deep">
+                                        <property name="visible">True</property>
+                                        <property name="can_focus">True</property>
+                                        <property name="invisible_char">●</property>
+                                        <property name="width_chars">5</property>
+                                        <property name="text" translatable="yes">4</property>
+                                        <property name="xalign">0.5</property>
+                                      </object>
+                                      <packing>
+                                        <property name="expand">False</property>
+                                        <property name="fill">False</property>
+                                        <property name="position">0</property>
+                                      </packing>
+                                    </child>
+                                    <child>
+                                      <object class="GtkLabel" id="label7">
+                                        <property name="visible">True</property>
+                                        <property name="can_focus">False</property>
+                                        <property name="xalign">0</property>
+                                        <property name="label" translatable="yes"> segment(s) of </property>
+                                      </object>
+                                      <packing>
+                                        <property name="expand">False</property>
+                                        <property name="fill">False</property>
+                                        <property name="position">1</property>
+                                      </packing>
+                                    </child>
+                                    <child>
+                                      <object class="GtkEntry" id="entry_size_deep">
+                                        <property name="visible">True</property>
+                                        <property name="can_focus">True</property>
+                                        <property name="invisible_char">●</property>
+                                        <property name="width_chars">5</property>
+                                        <property name="text" translatable="yes">50</property>
+                                        <property name="xalign">0.5</property>
+                                      </object>
+                                      <packing>
+                                        <property name="expand">False</property>
+                                        <property name="fill">False</property>
+                                        <property name="position">2</property>
+                                      </packing>
+                                    </child>
+                                    <child>
+                                      <object class="GtkLabel" id="label9">
+                                        <property name="visible">True</property>
+                                        <property name="can_focus">False</property>
+                                        <property name="xalign">0</property>
+                                        <property name="label" translatable="yes">nm.</property>
+                                      </object>
+                                      <packing>
+                                        <property name="expand">False</property>
+                                        <property name="fill">False</property>
+                                        <property name="position">3</property>
+                                      </packing>
+                                    </child>
+                                  </object>
+                                  <packing>
+                                    <property name="expand">False</property>
+                                    <property name="fill">False</property>
+                                    <property name="position">0</property>
+                                  </packing>
+                                </child>
+                                <child>
+                                  <object class="GtkButton" id="button_compute_stiffness">
+                                    <property name="label" translatable="yes">Compute Stiffness</property>
+                                    <property name="visible">True</property>
+                                    <property name="can_focus">True</property>
+                                    <property name="receives_default">True</property>
+                                    <property name="use_action_appearance">False</property>
+                                    <property name="use_underline">True</property>
+                                    <signal name="clicked" handler="on_button_compute_stiffness_clicked" swapped="no"/>
+                                  </object>
+                                  <packing>
+                                    <property name="expand">False</property>
+                                    <property name="fill">False</property>
+                                    <property name="position">1</property>
+                                  </packing>
+                                </child>
+                                <child>
+                                  <object class="GtkCheckButton" id="check_compute_poc">
+                                    <property name="label" translatable="yes">re-compute point of contact</property>
+                                    <property name="visible">True</property>
+                                    <property name="can_focus">True</property>
+                                    <property name="receives_default">False</property>
+                                    <property name="use_action_appearance">False</property>
+                                    <property name="active">True</property>
+                                    <property name="draw_indicator">True</property>
+                                    <signal name="toggled" handler="on_check_compute_poc_toggled" swapped="no"/>
+                                  </object>
+                                  <packing>
+                                    <property name="expand">False</property>
+                                    <property name="fill">False</property>
+                                    <property name="position">2</property>
+                                  </packing>
+                                </child>
+                              </object>
+                            </child>
+                          </object>
+                        </child>
+                        <child type="label">
+                          <object class="GtkLabel" id="label13">
+                            <property name="visible">True</property>
+                            <property name="can_focus">False</property>
+                            <property name="label" translatable="yes"><b>Stiffness</b></property>
+                            <property name="use_markup">True</property>
+                          </object>
+                        </child>
+                      </object>
+                      <packing>
+                        <property name="expand">False</property>
+                        <property name="fill">False</property>
+                        <property name="position">0</property>
+                      </packing>
+                    </child>
+                    <child>
+                      <object class="GtkFrame" id="frame_event">
+                        <property name="visible">True</property>
+                        <property name="can_focus">False</property>
+                        <property name="label_xalign">0</property>
+                        <child>
+                          <object class="GtkAlignment" id="alignment3">
+                            <property name="visible">True</property>
+                            <property name="can_focus">False</property>
+                            <property name="left_padding">12</property>
+                            <child>
+                              <object class="GtkVBox" id="event_box">
+                                <property name="visible">True</property>
+                                <property name="can_focus">False</property>
+                                <property name="spacing">1</property>
+                                <child>
+                                  <object class="GtkHBox" id="hbox1">
+                                    <property name="can_focus">False</property>
+                                    <child>
+                                      <object class="GtkLabel" id="label26">
+                                        <property name="visible">True</property>
+                                        <property name="can_focus">False</property>
+                                        <property name="label" translatable="yes">Detection : </property>
+                                      </object>
+                                      <packing>
+                                        <property name="expand">False</property>
+                                        <property name="fill">False</property>
+                                        <property name="position">0</property>
+                                      </packing>
+                                    </child>
+                                    <child>
+                                      <object class="GtkComboBox" id="combo_event_detect">
+                                        <property name="visible">True</property>
+                                        <property name="can_focus">False</property>
+                                      </object>
+                                      <packing>
+                                        <property name="expand">True</property>
+                                        <property name="fill">True</property>
+                                        <property name="position">1</property>
+                                      </packing>
+                                    </child>
+                                  </object>
+                                  <packing>
+                                    <property name="expand">False</property>
+                                    <property name="fill">False</property>
+                                    <property name="position">0</property>
+                                  </packing>
+                                </child>
+                                <child>
+                                  <object class="GtkHBox" id="hbox5">
+                                    <property name="can_focus">False</property>
+                                    <child>
+                                      <object class="GtkLabel" id="label27">
+                                        <property name="visible">True</property>
+                                        <property name="can_focus">False</property>
+                                        <property name="label" translatable="yes">Threshold : </property>
+                                      </object>
+                                      <packing>
+                                        <property name="expand">False</property>
+                                        <property name="fill">False</property>
+                                        <property name="position">0</property>
+                                      </packing>
+                                    </child>
+                                    <child>
+                                      <object class="GtkComboBox" id="combo_event_thresh">
+                                        <property name="visible">True</property>
+                                        <property name="can_focus">False</property>
+                                      </object>
+                                      <packing>
+                                        <property name="expand">True</property>
+                                        <property name="fill">True</property>
+                                        <property name="position">1</property>
+                                      </packing>
+                                    </child>
+                                  </object>
+                                  <packing>
+                                    <property name="expand">False</property>
+                                    <property name="fill">False</property>
+                                    <property name="position">1</property>
+                                  </packing>
+                                </child>
+                                <child>
+                                  <object class="GtkButton" id="button_detect_events">
+                                    <property name="label" translatable="yes">Detect Events</property>
+                                    <property name="visible">True</property>
+                                    <property name="can_focus">True</property>
+                                    <property name="receives_default">True</property>
+                                    <property name="use_action_appearance">False</property>
+                                    <property name="use_underline">True</property>
+                                    <signal name="clicked" handler="on_button_detect_events_clicked" swapped="no"/>
+                                  </object>
+                                  <packing>
+                                    <property name="expand">False</property>
+                                    <property name="fill">False</property>
+                                    <property name="position">2</property>
+                                  </packing>
+                                </child>
+                                <child>
+                                  <object class="GtkHBox" id="hbox16">
+                                    <property name="visible">True</property>
+                                    <property name="can_focus">False</property>
+                                    <child>
+                                      <object class="GtkButton" id="button_regenerate_random">
+                                        <property name="label" translatable="yes">Regenerate random</property>
+                                        <property name="visible">True</property>
+                                        <property name="can_focus">True</property>
+                                        <property name="receives_default">True</property>
+                                        <property name="use_action_appearance">False</property>
+                                        <signal name="clicked" handler="on_button_regenerate_random_clicked" swapped="no"/>
+                                      </object>
+                                      <packing>
+                                        <property name="expand">False</property>
+                                        <property name="fill">False</property>
+                                        <property name="position">0</property>
+                                      </packing>
+                                    </child>
+                                    <child>
+                                      <object class="GtkSpinButton" id="spin_nbr_rand_event">
+                                        <property name="visible">True</property>
+                                        <property name="can_focus">True</property>
+                                        <property name="tooltip_text" translatable="yes">Number of random event</property>
+                                        <property name="invisible_char">●</property>
+                                        <property name="adjustment">adj_nbr_rand_event</property>
+                                      </object>
+                                      <packing>
+                                        <property name="expand">False</property>
+                                        <property name="fill">False</property>
+                                        <property name="position">1</property>
+                                      </packing>
+                                    </child>
+                                  </object>
+                                  <packing>
+                                    <property name="expand">False</property>
+                                    <property name="fill">False</property>
+                                    <property name="position">3</property>
+                                  </packing>
+                                </child>
+                              </object>
+                            </child>
+                          </object>
+                        </child>
+                        <child type="label">
+                          <object class="GtkLabel" id="label16">
+                            <property name="visible">True</property>
+                            <property name="can_focus">False</property>
+                            <property name="label" translatable="yes"><b>Events</b></property>
+                            <property name="use_markup">True</property>
+                          </object>
+                        </child>
+                      </object>
+                      <packing>
+                        <property name="expand">False</property>
+                        <property name="fill">False</property>
+                        <property name="position">1</property>
+                      </packing>
+                    </child>
+                  </object>
+                  <packing>
+                    <property name="expand">False</property>
+                    <property name="fill">False</property>
+                    <property name="position">0</property>
+                  </packing>
+                </child>
+                <child>
+                  <object class="GtkHBox" id="hbox4">
+                    <property name="visible">True</property>
+                    <property name="can_focus">False</property>
+                    <child>
+                      <object class="GtkFrame" id="frame_rel_stiffness">
+                        <property name="visible">True</property>
+                        <property name="can_focus">False</property>
+                        <property name="label_xalign">0</property>
+                        <child>
+                          <object class="GtkAlignment" id="alignment1">
+                            <property name="visible">True</property>
+                            <property name="can_focus">False</property>
+                            <property name="left_padding">12</property>
+                            <child>
+                              <object class="GtkVBox" id="vbox1">
+                                <property name="visible">True</property>
+                                <property name="can_focus">False</property>
+                                <child>
+                                  <object class="GtkHBox" id="hbox6">
+                                    <property name="visible">True</property>
+                                    <property name="can_focus">False</property>
+                                    <child>
+                                      <object class="GtkSpinButton" id="max_rel_stiffness">
+                                        <property name="visible">True</property>
+                                        <property name="can_focus">True</property>
+                                        <property name="invisible_char">●</property>
+                                        <property name="adjustment">adj_rel_stiff_max_dist</property>
+                                      </object>
+                                      <packing>
+                                        <property name="expand">False</property>
+                                        <property name="fill">False</property>
+                                        <property name="position">0</property>
+                                      </packing>
+                                    </child>
+                                    <child>
+                                      <object class="GtkLabel" id="label17">
+                                        <property name="visible">True</property>
+                                        <property name="can_focus">False</property>
+                                        <property name="label" translatable="yes">pixel distance</property>
+                                      </object>
+                                      <packing>
+                                        <property name="expand">False</property>
+                                        <property name="fill">False</property>
+                                        <property name="position">1</property>
+                                      </packing>
+                                    </child>
+                                  </object>
+                                  <packing>
+                                    <property name="expand">True</property>
+                                    <property name="fill">True</property>
+                                    <property name="position">0</property>
+                                  </packing>
+                                </child>
+                                <child>
+                                  <object class="GtkButton" id="button_compute_rel_stiffness">
+                                    <property name="label" translatable="yes">Compute relative stiffness</property>
+                                    <property name="visible">True</property>
+                                    <property name="can_focus">True</property>
+                                    <property name="receives_default">True</property>
+                                    <property name="use_action_appearance">False</property>
+                                    <signal name="clicked" handler="on_button_compute_rel_stiffness_clicked" swapped="no"/>
+                                  </object>
+                                  <packing>
+                                    <property name="expand">False</property>
+                                    <property name="fill">False</property>
+                                    <property name="position">1</property>
+                                  </packing>
+                                </child>
+                              </object>
+                            </child>
+                          </object>
+                        </child>
+                        <child type="label">
+                          <object class="GtkLabel" id="label11">
+                            <property name="visible">True</property>
+                            <property name="can_focus">False</property>
+                            <property name="label" translatable="yes"><b>Relative stiffness</b></property>
+                            <property name="use_markup">True</property>
+                          </object>
+                        </child>
+                      </object>
+                      <packing>
+                        <property name="expand">False</property>
+                        <property name="fill">False</property>
+                        <property name="position">0</property>
+                      </packing>
+                    </child>
+                  </object>
+                  <packing>
+                    <property name="expand">False</property>
+                    <property name="fill">False</property>
+                    <property name="position">1</property>
+                  </packing>
+                </child>
+              </object>
+              <packing>
+                <property name="position">1</property>
+                <property name="reorderable">True</property>
+              </packing>
+            </child>
+            <child type="tab">
+              <object class="GtkLabel" id="label14">
+                <property name="visible">True</property>
+                <property name="can_focus">False</property>
+                <property name="xalign">0</property>
+                <property name="yalign">0</property>
+                <property name="label" translatable="yes">Compute</property>
+              </object>
+              <packing>
+                <property name="position">1</property>
+                <property name="tab_fill">False</property>
+              </packing>
+            </child>
+            <child>
+              <object class="GtkHBox" id="parameter_box">
+                <property name="visible">True</property>
+                <property name="can_focus">False</property>
+                <child>
+                  <object class="GtkVBox" id="vbox13">
+                    <property name="visible">True</property>
+                    <property name="can_focus">False</property>
+                    <child>
+                      <object class="GtkFrame" id="frame5">
+                        <property name="visible">True</property>
+                        <property name="can_focus">False</property>
+                        <property name="label_xalign">0</property>
+                        <property name="shadow_type">none</property>
+                        <child>
+                          <object class="GtkAlignment" id="alignment11">
+                            <property name="visible">True</property>
+                            <property name="can_focus">False</property>
+                            <property name="left_padding">12</property>
+                            <child>
+                              <object class="GtkVBox" id="vbox15">
+                                <property name="visible">True</property>
+                                <property name="can_focus">False</property>
+                                <child>
+                                  <object class="GtkHBox" id="hbox2">
+                                    <property name="visible">True</property>
+                                    <property name="can_focus">False</property>
+                                    <child>
+                                      <object class="GtkLabel" id="label25">
+                                        <property name="visible">True</property>
+                                        <property name="can_focus">False</property>
+                                        <property name="xalign">0</property>
+                                        <property name="label" translatable="yes">Model : </property>
+                                      </object>
+                                      <packing>
+                                        <property name="expand">False</property>
+                                        <property name="fill">False</property>
+                                        <property name="position">0</property>
+                                      </packing>
+                                    </child>
+                                    <child>
+                                      <object class="GtkComboBox" id="combo_hertz_model">
+                                        <property name="visible">True</property>
+                                        <property name="can_focus">False</property>
+                                        <property name="tooltip_text" translatable="yes">Change the model of your cantilever tip.
+
+Please modify the tip size according to the model.
+
+* Sphere model : radius of the tip [nm] 
+                            typical value : 30
+* Cone model : semi-opening angle [rad]
+                            typical value : 0.35</property>
+                                      </object>
+                                      <packing>
+                                        <property name="expand">True</property>
+                                        <property name="fill">True</property>
+                                        <property name="position">1</property>
+                                      </packing>
+                                    </child>
+                                  </object>
+                                  <packing>
+                                    <property name="expand">False</property>
+                                    <property name="fill">False</property>
+                                    <property name="position">0</property>
+                                  </packing>
+                                </child>
+                                <child>
+                                  <object class="GtkHBox" id="hbox29">
+                                    <property name="visible">True</property>
+                                    <property name="can_focus">False</property>
+                                    <child>
+                                      <object class="GtkLabel" id="label_tip_size">
+                                        <property name="visible">True</property>
+                                        <property name="can_focus">False</property>
+                                        <property name="label" translatable="yes">Tip size : </property>
+                                      </object>
+                                      <packing>
+                                        <property name="expand">False</property>
+                                        <property name="fill">False</property>
+                                        <property name="position">0</property>
+                                      </packing>
+                                    </child>
+                                    <child>
+                                      <object class="GtkSpinButton" id="spin_carac">
+                                        <property name="visible">True</property>
+                                        <property name="can_focus">True</property>
+                                        <property name="tooltip_text" translatable="yes">Change the caracteristic of
+your cantilever tip.</property>
+                                        <property name="invisible_char">●</property>
+                                        <property name="adjustment">adj_tip_size</property>
+                                        <property name="digits">2</property>
+                                      </object>
+                                      <packing>
+                                        <property name="expand">True</property>
+                                        <property name="fill">True</property>
+                                        <property name="position">1</property>
+                                      </packing>
+                                    </child>
+                                  </object>
+                                  <packing>
+                                    <property name="expand">False</property>
+                                    <property name="fill">False</property>
+                                    <property name="position">1</property>
+                                  </packing>
+                                </child>
+                                <child>
+                                  <object class="GtkHBox" id="hbox25">
+                                    <property name="visible">True</property>
+                                    <property name="can_focus">False</property>
+                                    <child>
+                                      <object class="GtkLabel" id="label43">
+                                        <property name="visible">True</property>
+                                        <property name="can_focus">False</property>
+                                        <property name="label" translatable="yes">Poisson ratio : </property>
+                                      </object>
+                                      <packing>
+                                        <property name="expand">False</property>
+                                        <property name="fill">False</property>
+                                        <property name="position">0</property>
+                                      </packing>
+                                    </child>
+                                    <child>
+                                      <object class="GtkSpinButton" id="spin_poisson_ratio">
+                                        <property name="visible">True</property>
+                                        <property name="can_focus">True</property>
+                                        <property name="invisible_char">●</property>
+                                        <property name="adjustment">adj_poisson_ratio</property>
+                                        <property name="digits">2</property>
+                                        <property name="update_policy">if-valid</property>
+                                        <signal name="value-changed" handler="on_spin_poisson_ratio_value_changed" swapped="no"/>
+                                      </object>
+                                      <packing>
+                                        <property name="expand">True</property>
+                                        <property name="fill">True</property>
+                                        <property name="position">1</property>
+                                      </packing>
+                                    </child>
+                                  </object>
+                                  <packing>
+                                    <property name="expand">False</property>
+                                    <property name="fill">False</property>
+                                    <property name="position">2</property>
+                                  </packing>
+                                </child>
+                                <child>
+                                  <object class="GtkHBox" id="hbox32">
+                                    <property name="visible">True</property>
+                                    <property name="can_focus">False</property>
+                                    <child>
+                                      <object class="GtkLabel" id="label59">
+                                        <property name="visible">True</property>
+                                        <property name="can_focus">False</property>
+                                        <property name="xalign">0</property>
+                                        <property name="label" translatable="yes">Method : </property>
+                                      </object>
+                                      <packing>
+                                        <property name="expand">False</property>
+                                        <property name="fill">False</property>
+                                        <property name="position">0</property>
+                                      </packing>
+                                    </child>
+                                    <child>
+                                      <object class="GtkComboBox" id="combo_stiff_method">
+                                        <property name="visible">True</property>
+                                        <property name="can_focus">False</property>
+                                        <property name="has_tooltip">True</property>
+                                        <property name="tooltip_markup" translatable="yes">Change the method of computing the stiffness.
+
+* Raw : fits the raw data with the corresponding model.
+* Extrema : makes a linear fit between the two extrem
+                          points in the slice. The indentation axis is
+                          modified according to the used model.</property>
+                                        <property name="tooltip_text" translatable="yes">Change the method of computing the stiffness.
+
+* Raw : fits the raw data with the corresponding model.
+* Extrema : makes a linear fit between the two extrem
+                          points in the slice. The indentation axis is
+                          modified according to the used model.</property>
+                                      </object>
+                                      <packing>
+                                        <property name="expand">True</property>
+                                        <property name="fill">True</property>
+                                        <property name="position">1</property>
+                                      </packing>
+                                    </child>
+                                  </object>
+                                  <packing>
+                                    <property name="expand">False</property>
+                                    <property name="fill">False</property>
+                                    <property name="position">3</property>
+                                  </packing>
+                                </child>
+                              </object>
+                            </child>
+                          </object>
+                        </child>
+                        <child type="label">
+                          <object class="GtkLabel" id="label39">
+                            <property name="visible">True</property>
+                            <property name="can_focus">False</property>
+                            <property name="label" translatable="yes"><b>Stiffness</b></property>
+                            <property name="use_markup">True</property>
+                          </object>
+                        </child>
+                      </object>
+                      <packing>
+                        <property name="expand">False</property>
+                        <property name="fill">False</property>
+                        <property name="position">0</property>
+                      </packing>
+                    </child>
+                    <child>
+                      <placeholder/>
+                    </child>
+                  </object>
+                  <packing>
+                    <property name="expand">False</property>
+                    <property name="fill">False</property>
+                    <property name="position">0</property>
+                  </packing>
+                </child>
+                <child>
+                  <object class="GtkVBox" id="vbox7">
+                    <property name="visible">True</property>
+                    <property name="can_focus">False</property>
+                    <child>
+                      <object class="GtkFrame" id="frame4">
+                        <property name="visible">True</property>
+                        <property name="can_focus">False</property>
+                        <property name="label_xalign">0</property>
+                        <property name="shadow_type">none</property>
+                        <child>
+                          <object class="GtkAlignment" id="alignment10">
+                            <property name="visible">True</property>
+                            <property name="can_focus">False</property>
+                            <property name="left_padding">12</property>
+                            <child>
+                              <object class="GtkVBox" id="vbox12">
+                                <property name="visible">True</property>
+                                <property name="can_focus">False</property>
+                                <child>
+                                  <object class="GtkButton" id="button_event_calib">
+                                    <property name="label" translatable="yes">Adjust sensitivity</property>
+                                    <property name="visible">True</property>
+                                    <property name="can_focus">True</property>
+                                    <property name="receives_default">True</property>
+                                    <property name="use_action_appearance">False</property>
+                                    <signal name="clicked" handler="on_button_event_calib_clicked" swapped="no"/>
+                                  </object>
+                                  <packing>
+                                    <property name="expand">False</property>
+                                    <property name="fill">False</property>
+                                    <property name="position">0</property>
+                                  </packing>
+                                </child>
+                                <child>
+                                  <object class="GtkHBox" id="ev_fit_box">
+                                    <property name="visible">True</property>
+                                    <property name="can_focus">False</property>
+                                    <child>
+                                      <object class="GtkLabel" id="evt_fit_label">
+                                        <property name="visible">True</property>
+                                        <property name="can_focus">False</property>
+                                        <property name="xalign">0</property>
+                                        <property name="label" translatable="yes">Event fit model : </property>
+                                      </object>
+                                      <packing>
+                                        <property name="expand">False</property>
+                                        <property name="fill">False</property>
+                                        <property name="position">0</property>
+                                      </packing>
+                                    </child>
+                                    <child>
+                                      <object class="GtkComboBox" id="combo_ev_fit_model">
+                                        <property name="visible">True</property>
+                                        <property name="can_focus">False</property>
+                                        <signal name="changed" handler="on_combo_ev_fit_model_changed" swapped="no"/>
+                                      </object>
+                                      <packing>
+                                        <property name="expand">True</property>
+                                        <property name="fill">True</property>
+                                        <property name="position">1</property>
+                                      </packing>
+                                    </child>
+                                  </object>
+                                  <packing>
+                                    <property name="expand">False</property>
+                                    <property name="fill">False</property>
+                                    <property name="position">1</property>
+                                  </packing>
+                                </child>
+                                <child>
+                                  <object class="GtkHBox" id="hbox24">
+                                    <property name="visible">True</property>
+                                    <property name="can_focus">False</property>
+                                    <child>
+                                      <object class="GtkLabel" id="label38">
+                                        <property name="visible">True</property>
+                                        <property name="can_focus">False</property>
+                                        <property name="xpad">9</property>
+                                        <property name="label" translatable="yes">Event distance threshold</property>
+                                      </object>
+                                      <packing>
+                                        <property name="expand">False</property>
+                                        <property name="fill">False</property>
+                                        <property name="position">0</property>
+                                      </packing>
+                                    </child>
+                                    <child>
+                                      <object class="GtkSpinButton" id="spin_ev_threshold_dist">
+                                        <property name="visible">True</property>
+                                        <property name="can_focus">True</property>
+                                        <property name="invisible_char">●</property>
+                                        <property name="digits">2</property>
+                                        <signal name="value-changed" handler="on_spin_ev_threshold_dist_value_changed" swapped="no"/>
+                                      </object>
+                                      <packing>
+                                        <property name="expand">False</property>
+                                        <property name="fill">False</property>
+                                        <property name="position">1</property>
+                                      </packing>
+                                    </child>
+                                  </object>
+                                  <packing>
+                                    <property name="expand">False</property>
+                                    <property name="fill">False</property>
+                                    <property name="position">2</property>
+                                  </packing>
+                                </child>
+                                <child>
+                                  <object class="GtkHBox" id="hbox31">
+                                    <property name="visible">True</property>
+                                    <property name="can_focus">False</property>
+                                    <child>
+                                      <object class="GtkLabel" id="label57">
+                                        <property name="visible">True</property>
+                                        <property name="can_focus">False</property>
+                                        <property name="xpad">9</property>
+                                        <property name="label" translatable="yes">Event length threshold</property>
+                                      </object>
+                                      <packing>
+                                        <property name="expand">False</property>
+                                        <property name="fill">False</property>
+                                        <property name="position">0</property>
+                                      </packing>
+                                    </child>
+                                    <child>
+                                      <object class="GtkSpinButton" id="spin_ev_length_thresh_min">
+                                        <property name="visible">True</property>
+                                        <property name="can_focus">True</property>
+                                        <property name="invisible_char">●</property>
+                                        <property name="digits">2</property>
+                                        <signal name="value-changed" handler="on_spin_ev_length_thresh_min_value_changed" swapped="no"/>
+                                      </object>
+                                      <packing>
+                                        <property name="expand">False</property>
+                                        <property name="fill">False</property>
+                                        <property name="position">1</property>
+                                      </packing>
+                                    </child>
+                                    <child>
+                                      <object class="GtkSpinButton" id="spin_ev_length_thresh_max">
+                                        <property name="visible">True</property>
+                                        <property name="can_focus">True</property>
+                                        <property name="invisible_char">●</property>
+                                        <property name="digits">2</property>
+                                        <signal name="value-changed" handler="on_spin_ev_length_thresh_max_value_changed" swapped="no"/>
+                                      </object>
+                                      <packing>
+                                        <property name="expand">False</property>
+                                        <property name="fill">False</property>
+                                        <property name="position">2</property>
+                                      </packing>
+                                    </child>
+                                  </object>
+                                  <packing>
+                                    <property name="expand">False</property>
+                                    <property name="fill">False</property>
+                                    <property name="position">3</property>
+                                  </packing>
+                                </child>
+                              </object>
+                            </child>
+                          </object>
+                        </child>
+                        <child type="label">
+                          <object class="GtkLabel" id="label22">
+                            <property name="visible">True</property>
+                            <property name="can_focus">False</property>
+                            <property name="label" translatable="yes"><b>Events</b></property>
+                            <property name="use_markup">True</property>
+                          </object>
+                        </child>
+                      </object>
+                      <packing>
+                        <property name="expand">False</property>
+                        <property name="fill">False</property>
+                        <property name="position">0</property>
+                      </packing>
+                    </child>
+                    <child>
+                      <object class="GtkFrame" id="frame_PoC_param">
+                        <property name="visible">True</property>
+                        <property name="can_focus">False</property>
+                        <property name="label_xalign">0</property>
+                        <property name="shadow_type">none</property>
+                        <child>
+                          <object class="GtkAlignment" id="alignment6">
+                            <property name="visible">True</property>
+                            <property name="can_focus">False</property>
+                            <property name="left_padding">12</property>
+                            <child>
+                              <object class="GtkVBox" id="vbox5">
+                                <property name="visible">True</property>
+                                <property name="can_focus">False</property>
+                                <child>
+                                  <object class="GtkButton" id="button_poc_calib">
+                                    <property name="label" translatable="yes">Adjust sensitivity</property>
+                                    <property name="visible">True</property>
+                                    <property name="can_focus">True</property>
+                                    <property name="receives_default">True</property>
+                                    <property name="use_action_appearance">False</property>
+                                    <signal name="clicked" handler="on_button_poc_calib_clicked" swapped="no"/>
+                                  </object>
+                                  <packing>
+                                    <property name="expand">False</property>
+                                    <property name="fill">False</property>
+                                    <property name="position">0</property>
+                                  </packing>
+                                </child>
+                                <child>
+                                  <object class="GtkComboBox" id="combo_poc_method">
+                                    <property name="visible">True</property>
+                                    <property name="can_focus">False</property>
+                                    <signal name="changed" handler="on_combo_poc_method_changed" swapped="no"/>
+                                  </object>
+                                  <packing>
+                                    <property name="expand">False</property>
+                                    <property name="fill">False</property>
+                                    <property name="position">1</property>
+                                  </packing>
+                                </child>
+                                <child>
+                                  <object class="GtkCheckButton" id="check_limit_poc_slide">
+                                    <property name="label" translatable="yes">Limit sliding</property>
+                                    <property name="visible">True</property>
+                                    <property name="can_focus">True</property>
+                                    <property name="receives_default">False</property>
+                                    <property name="use_action_appearance">False</property>
+                                    <property name="draw_indicator">True</property>
+                                    <signal name="toggled" handler="on_check_limit_poc_slide_toggled" swapped="no"/>
+                                  </object>
+                                  <packing>
+                                    <property name="expand">False</property>
+                                    <property name="fill">False</property>
+                                    <property name="position">2</property>
+                                  </packing>
+                                </child>
+                                <child>
+                                  <object class="GtkHBox" id="hbox28">
+                                    <property name="visible">True</property>
+                                    <property name="can_focus">False</property>
+                                    <child>
+                                      <object class="GtkLabel" id="label44">
+                                        <property name="visible">True</property>
+                                        <property name="can_focus">False</property>
+                                        <property name="label" translatable="yes">Fit segment size</property>
+                                      </object>
+                                      <packing>
+                                        <property name="expand">True</property>
+                                        <property name="fill">True</property>
+                                        <property name="position">0</property>
+                                      </packing>
+                                    </child>
+                                    <child>
+                                      <object class="GtkSpinButton" id="spin_fit_seg_size">
+                                        <property name="visible">True</property>
+                                        <property name="can_focus">True</property>
+                                        <property name="invisible_char">●</property>
+                                        <property name="adjustment">adj_fit_seg_size</property>
+                                        <property name="digits">2</property>
+                                        <signal name="value-changed" handler="on_spin_fit_seg_size_value_changed" swapped="no"/>
+                                      </object>
+                                      <packing>
+                                        <property name="expand">True</property>
+                                        <property name="fill">True</property>
+                                        <property name="position">1</property>
+                                      </packing>
+                                    </child>
+                                  </object>
+                                  <packing>
+                                    <property name="expand">True</property>
+                                    <property name="fill">True</property>
+                                    <property name="position">3</property>
+                                  </packing>
+                                </child>
+                              </object>
+                            </child>
+                          </object>
+                        </child>
+                        <child type="label">
+                          <object class="GtkLabel" id="label18">
+                            <property name="visible">True</property>
+                            <property name="can_focus">False</property>
+                            <property name="label" translatable="yes"><b>Point of contact</b></property>
+                            <property name="use_markup">True</property>
+                          </object>
+                        </child>
+                      </object>
+                      <packing>
+                        <property name="expand">False</property>
+                        <property name="fill">False</property>
+                        <property name="position">1</property>
+                      </packing>
+                    </child>
+                    <child>
+                      <placeholder/>
+                    </child>
+                  </object>
+                  <packing>
+                    <property name="expand">False</property>
+                    <property name="fill">False</property>
+                    <property name="position">1</property>
+                  </packing>
+                </child>
+              </object>
+              <packing>
+                <property name="position">2</property>
+                <property name="tab_fill">False</property>
+              </packing>
+            </child>
+            <child type="tab">
+              <object class="GtkLabel" id="label15">
+                <property name="visible">True</property>
+                <property name="can_focus">False</property>
+                <property name="xalign">0</property>
+                <property name="yalign">0</property>
+                <property name="label" translatable="yes">Parameters</property>
+              </object>
+              <packing>
+                <property name="position">2</property>
+                <property name="tab_fill">False</property>
+              </packing>
+            </child>
+            <child>
+              <object class="GtkVBox" id="Result_box">
+                <property name="visible">True</property>
+                <property name="can_focus">False</property>
+                <child>
+                  <object class="GtkScrolledWindow" id="scrolledwindow1">
+                    <property name="visible">True</property>
+                    <property name="can_focus">True</property>
+                    <child>
+                      <object class="GtkViewport" id="viewport1">
+                        <property name="visible">True</property>
+                        <property name="can_focus">False</property>
+                        <property name="resize_mode">queue</property>
+                        <child>
+                          <object class="GtkHBox" id="hbox17">
+                            <property name="visible">True</property>
+                            <property name="can_focus">False</property>
+                            <child>
+                              <object class="GtkVBox" id="vbox_ev_force">
+                                <property name="visible">True</property>
+                                <property name="can_focus">False</property>
+                                <child>
+                                  <object class="GtkLabel" id="label_force">
+                                    <property name="visible">True</property>
+                                    <property name="can_focus">False</property>
+                                    <property name="label" translatable="yes">Force</property>
+                                  </object>
+                                  <packing>
+                                    <property name="expand">False</property>
+                                    <property name="fill">False</property>
+                                    <property name="position">0</property>
+                                  </packing>
+                                </child>
+                                <child>
+                                  <object class="GtkButton" id="button_ev_force_hist">
+                                    <property name="label" translatable="yes">Histogram</property>
+                                    <property name="visible">True</property>
+                                    <property name="can_focus">True</property>
+                                    <property name="receives_default">True</property>
+                                    <property name="use_action_appearance">False</property>
+                                    <signal name="clicked" handler="on_button_ev_force_hist_clicked" swapped="no"/>
+                                  </object>
+                                  <packing>
+                                    <property name="expand">False</property>
+                                    <property name="fill">False</property>
+                                    <property name="position">1</property>
+                                  </packing>
+                                </child>
+                                <child>
+                                  <object class="GtkHBox" id="hbox10">
+                                    <property name="visible">True</property>
+                                    <property name="can_focus">False</property>
+                                    <child>
+                                      <object class="GtkVBox" id="force_hist_min">
+                                        <property name="visible">True</property>
+                                        <property name="can_focus">False</property>
+                                        <child>
+                                          <object class="GtkLabel" id="label12">
+                                            <property name="visible">True</property>
+                                            <property name="can_focus">False</property>
+                                            <property name="label" translatable="yes">min</property>
+                                          </object>
+                                          <packing>
+                                            <property name="expand">False</property>
+                                            <property name="fill">False</property>
+                                            <property name="position">0</property>
+                                          </packing>
+                                        </child>
+                                        <child>
+                                          <object class="GtkSpinButton" id="ev_force_hist_min">
+                                            <property name="visible">True</property>
+                                            <property name="can_focus">True</property>
+                                            <property name="invisible_char">●</property>
+                                            <property name="digits">2</property>
+                                          </object>
+                                          <packing>
+                                            <property name="expand">False</property>
+                                            <property name="fill">False</property>
+                                            <property name="position">1</property>
+                                          </packing>
+                                        </child>
+                                      </object>
+                                      <packing>
+                                        <property name="expand">False</property>
+                                        <property name="fill">False</property>
+                                        <property name="position">0</property>
+                                      </packing>
+                                    </child>
+                                    <child>
+                                      <object class="GtkVBox" id="force_hist_max">
+                                        <property name="visible">True</property>
+                                        <property name="can_focus">False</property>
+                                        <child>
+                                          <object class="GtkLabel" id="label8">
+                                            <property name="visible">True</property>
+                                            <property name="can_focus">False</property>
+                                            <property name="label" translatable="yes">max</property>
+                                          </object>
+                                          <packing>
+                                            <property name="expand">False</property>
+                                            <property name="fill">False</property>
+                                            <property name="position">0</property>
+                                          </packing>
+                                        </child>
+                                        <child>
+                                          <object class="GtkSpinButton" id="ev_force_hist_max">
+                                            <property name="visible">True</property>
+                                            <property name="can_focus">True</property>
+                                            <property name="invisible_char">●</property>
+                                            <property name="digits">2</property>
+                                          </object>
+                                          <packing>
+                                            <property name="expand">False</property>
+                                            <property name="fill">False</property>
+                                            <property name="position">1</property>
+                                          </packing>
+                                        </child>
+                                      </object>
+                                      <packing>
+                                        <property name="expand">False</property>
+                                        <property name="fill">False</property>
+                                        <property name="position">1</property>
+                                      </packing>
+                                    </child>
+                                  </object>
+                                  <packing>
+                                    <property name="expand">False</property>
+                                    <property name="fill">False</property>
+                                    <property name="position">2</property>
+                                  </packing>
+                                </child>
+                                <child>
+                                  <object class="GtkVBox" id="force_hist_col_size">
+                                    <property name="visible">True</property>
+                                    <property name="can_focus">False</property>
+                                    <child>
+                                      <object class="GtkLabel" id="label6">
+                                        <property name="visible">True</property>
+                                        <property name="can_focus">False</property>
+                                        <property name="label" translatable="yes">col size</property>
+                                      </object>
+                                      <packing>
+                                        <property name="expand">False</property>
+                                        <property name="fill">False</property>
+                                        <property name="position">0</property>
+                                      </packing>
+                                    </child>
+                                    <child>
+                                      <object class="GtkSpinButton" id="ev_force_hist_size">
+                                        <property name="visible">True</property>
+                                        <property name="can_focus">True</property>
+                                        <property name="invisible_char">●</property>
+                                        <property name="digits">3</property>
+                                      </object>
+                                      <packing>
+                                        <property name="expand">False</property>
+                                        <property name="fill">False</property>
+                                        <property name="position">1</property>
+                                      </packing>
+                                    </child>
+                                  </object>
+                                  <packing>
+                                    <property name="expand">False</property>
+                                    <property name="fill">False</property>
+                                    <property name="position">3</property>
+                                  </packing>
+                                </child>
+                              </object>
+                              <packing>
+                                <property name="expand">False</property>
+                                <property name="fill">False</property>
+                                <property name="position">0</property>
+                              </packing>
+                            </child>
+                            <child>
+                              <object class="GtkVSeparator" id="vseparator3">
+                                <property name="visible">True</property>
+                                <property name="can_focus">False</property>
+                              </object>
+                              <packing>
+                                <property name="expand">False</property>
+                                <property name="fill">False</property>
+                                <property name="position">1</property>
+                              </packing>
+                            </child>
+                            <child>
+                              <object class="GtkVBox" id="vbox_ev_lr">
+                                <property name="visible">True</property>
+                                <property name="can_focus">False</property>
+                                <child>
+                                  <object class="GtkLabel" id="label_lr">
+                                    <property name="visible">True</property>
+                                    <property name="can_focus">False</property>
+                                    <property name="label" translatable="yes">Loading rate</property>
+                                  </object>
+                                  <packing>
+                                    <property name="expand">False</property>
+                                    <property name="fill">False</property>
+                                    <property name="position">0</property>
+                                  </packing>
+                                </child>
+                                <child>
+                                  <object class="GtkButton" id="button_ev_lr_hist">
+                                    <property name="label" translatable="yes">Histogram</property>
+                                    <property name="visible">True</property>
+                                    <property name="can_focus">True</property>
+                                    <property name="receives_default">True</property>
+                                    <property name="use_action_appearance">False</property>
+                                    <signal name="clicked" handler="on_button_ev_lr_hist_clicked" swapped="no"/>
+                                  </object>
+                                  <packing>
+                                    <property name="expand">False</property>
+                                    <property name="fill">False</property>
+                                    <property name="position">1</property>
+                                  </packing>
+                                </child>
+                                <child>
+                                  <object class="GtkHBox" id="hbox8">
+                                    <property name="visible">True</property>
+                                    <property name="can_focus">False</property>
+                                    <child>
+                                      <object class="GtkVBox" id="lr_hist_min">
+                                        <property name="visible">True</property>
+                                        <property name="can_focus">False</property>
+                                        <child>
+                                          <object class="GtkLabel" id="label20">
+                                            <property name="visible">True</property>
+                                            <property name="can_focus">False</property>
+                                            <property name="label" translatable="yes">min</property>
+                                          </object>
+                                          <packing>
+                                            <property name="expand">False</property>
+                                            <property name="fill">False</property>
+                                            <property name="position">0</property>
+                                          </packing>
+                                        </child>
+                                        <child>
+                                          <object class="GtkSpinButton" id="ev_lr_hist_min">
+                                            <property name="visible">True</property>
+                                            <property name="can_focus">True</property>
+                                            <property name="invisible_char">●</property>
+                                            <property name="digits">2</property>
+                                          </object>
+                                          <packing>
+                                            <property name="expand">False</property>
+                                            <property name="fill">False</property>
+                                            <property name="position">1</property>
+                                          </packing>
+                                        </child>
+                                      </object>
+                                      <packing>
+                                        <property name="expand">False</property>
+                                        <property name="fill">False</property>
+                                        <property name="position">0</property>
+                                      </packing>
+                                    </child>
+                                    <child>
+                                      <object class="GtkVBox" id="lr_hist_max">
+                                        <property name="visible">True</property>
+                                        <property name="can_focus">False</property>
+                                        <child>
+                                          <object class="GtkLabel" id="label21">
+                                            <property name="visible">True</property>
+                                            <property name="can_focus">False</property>
+                                            <property name="label" translatable="yes">max</property>
+                                          </object>
+                                          <packing>
+                                            <property name="expand">False</property>
+                                            <property name="fill">False</property>
+                                            <property name="position">0</property>
+                                          </packing>
+                                        </child>
+                                        <child>
+                                          <object class="GtkSpinButton" id="ev_lr_hist_max">
+                                            <property name="visible">True</property>
+                                            <property name="can_focus">True</property>
+                                            <property name="invisible_char">●</property>
+                                            <property name="digits">2</property>
+                                          </object>
+                                          <packing>
+                                            <property name="expand">False</property>
+                                            <property name="fill">False</property>
+                                            <property name="position">1</property>
+                                          </packing>
+                                        </child>
+                                      </object>
+                                      <packing>
+                                        <property name="expand">False</property>
+                                        <property name="fill">False</property>
+                                        <property name="position">1</property>
+                                      </packing>
+                                    </child>
+                                  </object>
+                                  <packing>
+                                    <property name="expand">False</property>
+                                    <property name="fill">False</property>
+                                    <property name="position">2</property>
+                                  </packing>
+                                </child>
+                                <child>
+                                  <object class="GtkVBox" id="lr_hist_col_size">
+                                    <property name="visible">True</property>
+                                    <property name="can_focus">False</property>
+                                    <child>
+                                      <object class="GtkLabel" id="label10">
+                                        <property name="visible">True</property>
+                                        <property name="can_focus">False</property>
+                                        <property name="label" translatable="yes">col size</property>
+                                      </object>
+                                      <packing>
+                                        <property name="expand">False</property>
+                                        <property name="fill">False</property>
+                                        <property name="position">0</property>
+                                      </packing>
+                                    </child>
+                                    <child>
+                                      <object class="GtkSpinButton" id="ev_lr_hist_size">
+                                        <property name="visible">True</property>
+                                        <property name="can_focus">True</property>
+                                        <property name="invisible_char">●</property>
+                                        <property name="digits">3</property>
+                                      </object>
+                                      <packing>
+                                        <property name="expand">False</property>
+                                        <property name="fill">False</property>
+                                        <property name="position">1</property>
+                                      </packing>
+                                    </child>
+                                  </object>
+                                  <packing>
+                                    <property name="expand">False</property>
+                                    <property name="fill">False</property>
+                                    <property name="position">3</property>
+                                  </packing>
+                                </child>
+                              </object>
+                              <packing>
+                                <property name="expand">False</property>
+                                <property name="fill">False</property>
+                                <property name="position">2</property>
+                              </packing>
+                            </child>
+                            <child>
+                              <object class="GtkVSeparator" id="vseparator4">
+                                <property name="visible">True</property>
+                                <property name="can_focus">False</property>
+                              </object>
+                              <packing>
+                                <property name="expand">False</property>
+                                <property name="fill">True</property>
+                                <property name="position">3</property>
+                              </packing>
+                            </child>
+                            <child>
+                              <object class="GtkVBox" id="vbox_ev_dist">
+                                <property name="visible">True</property>
+                                <property name="can_focus">False</property>
+                                <child>
+                                  <object class="GtkLabel" id="label_dist">
+                                    <property name="visible">True</property>
+                                    <property name="can_focus">False</property>
+                                    <property name="label" translatable="yes">Distance</property>
+                                  </object>
+                                  <packing>
+                                    <property name="expand">False</property>
+                                    <property name="fill">False</property>
+                                    <property name="position">0</property>
+                                  </packing>
+                                </child>
+                                <child>
+                                  <object class="GtkButton" id="button_ev_dist_hist">
+                                    <property name="label" translatable="yes">Histogram</property>
+                                    <property name="visible">True</property>
+                                    <property name="can_focus">True</property>
+                                    <property name="receives_default">True</property>
+                                    <property name="use_action_appearance">False</property>
+                                    <signal name="clicked" handler="on_button_ev_dist_hist_clicked" swapped="no"/>
+                                  </object>
+                                  <packing>
+                                    <property name="expand">False</property>
+                                    <property name="fill">False</property>
+                                    <property name="position">1</property>
+                                  </packing>
+                                </child>
+                                <child>
+                                  <object class="GtkHBox" id="hbox18">
+                                    <property name="visible">True</property>
+                                    <property name="can_focus">False</property>
+                                    <child>
+                                      <object class="GtkVBox" id="lr_hist_min1">
+                                        <property name="visible">True</property>
+                                        <property name="can_focus">False</property>
+                                        <child>
+                                          <object class="GtkLabel" id="label35">
+                                            <property name="visible">True</property>
+                                            <property name="can_focus">False</property>
+                                            <property name="label" translatable="yes">min</property>
+                                          </object>
+                                          <packing>
+                                            <property name="expand">False</property>
+                                            <property name="fill">False</property>
+                                            <property name="position">0</property>
+                                          </packing>
+                                        </child>
+                                        <child>
+                                          <object class="GtkSpinButton" id="ev_dist_hist_min">
+                                            <property name="visible">True</property>
+                                            <property name="can_focus">True</property>
+                                            <property name="invisible_char">●</property>
+                                            <property name="digits">2</property>
+                                          </object>
+                                          <packing>
+                                            <property name="expand">False</property>
+                                            <property name="fill">False</property>
+                                            <property name="position">1</property>
+                                          </packing>
+                                        </child>
+                                      </object>
+                                      <packing>
+                                        <property name="expand">False</property>
+                                        <property name="fill">False</property>
+                                        <property name="position">0</property>
+                                      </packing>
+                                    </child>
+                                    <child>
+                                      <object class="GtkVBox" id="lr_hist_max1">
+                                        <property name="visible">True</property>
+                                        <property name="can_focus">False</property>
+                                        <child>
+                                          <object class="GtkLabel" id="label36">
+                                            <property name="visible">True</property>
+                                            <property name="can_focus">False</property>
+                                            <property name="label" translatable="yes">max</property>
+                                          </object>
+                                          <packing>
+                                            <property name="expand">False</property>
+                                            <property name="fill">False</property>
+                                            <property name="position">0</property>
+                                          </packing>
+                                        </child>
+                                        <child>
+                                          <object class="GtkSpinButton" id="ev_dist_hist_max">
+                                            <property name="visible">True</property>
+                                            <property name="can_focus">True</property>
+                                            <property name="invisible_char">●</property>
+                                            <property name="digits">2</property>
+                                          </object>
+                                          <packing>
+                                            <property name="expand">False</property>
+                                            <property name="fill">False</property>
+                                            <property name="position">1</property>
+                                          </packing>
+                                        </child>
+                                      </object>
+                                      <packing>
+                                        <property name="expand">False</property>
+                                        <property name="fill">False</property>
+                                        <property name="position">1</property>
+                                      </packing>
+                                    </child>
+                                  </object>
+                                  <packing>
+                                    <property name="expand">False</property>
+                                    <property name="fill">False</property>
+                                    <property name="position">2</property>
+                                  </packing>
+                                </child>
+                                <child>
+                                  <object class="GtkVBox" id="lr_hist_col_size1">
+                                    <property name="visible">True</property>
+                                    <property name="can_focus">False</property>
+                                    <child>
+                                      <object class="GtkLabel" id="label37">
+                                        <property name="visible">True</property>
+                                        <property name="can_focus">False</property>
+                                        <property name="label" translatable="yes">col size</property>
+                                      </object>
+                                      <packing>
+                                        <property name="expand">False</property>
+                                        <property name="fill">False</property>
+                                        <property name="position">0</property>
+                                      </packing>
+                                    </child>
+                                    <child>
+                                      <object class="GtkSpinButton" id="ev_dist_hist_size">
+                                        <property name="visible">True</property>
+                                        <property name="can_focus">True</property>
+                                        <property name="invisible_char">●</property>
+                                        <property name="digits">3</property>
+                                      </object>
+                                      <packing>
+                                        <property name="expand">False</property>
+                                        <property name="fill">False</property>
+                                        <property name="position">1</property>
+                                      </packing>
+                                    </child>
+                                  </object>
+                                  <packing>
+                                    <property name="expand">False</property>
+                                    <property name="fill">False</property>
+                                    <property name="position">3</property>
+                                  </packing>
+                                </child>
+                              </object>
+                              <packing>
+                                <property name="expand">False</property>
+                                <property name="fill">False</property>
+                                <property name="position">4</property>
+                              </packing>
+                            </child>
+                            <child>
+                              <object class="GtkVSeparator" id="vseparator5">
+                                <property name="visible">True</property>
+                                <property name="can_focus">False</property>
+                              </object>
+                              <packing>
+                                <property name="expand">False</property>
+                                <property name="fill">True</property>
+                                <property name="position">5</property>
+                              </packing>
+                            </child>
+                            <child>
+                              <object class="GtkVBox" id="vbox_ev_dist1">
+                                <property name="visible">True</property>
+                                <property name="can_focus">False</property>
+                                <child>
+                                  <object class="GtkLabel" id="label_stiff">
+                                    <property name="visible">True</property>
+                                    <property name="can_focus">False</property>
+                                    <property name="label" translatable="yes">Stiffness</property>
+                                  </object>
+                                  <packing>
+                                    <property name="expand">False</property>
+                                    <property name="fill">False</property>
+                                    <property name="position">0</property>
+                                  </packing>
+                                </child>
+                                <child>
+                                  <object class="GtkButton" id="button_ev_stiff_hist">
+                                    <property name="label" translatable="yes">Histogram</property>
+                                    <property name="visible">True</property>
+                                    <property name="can_focus">True</property>
+                                    <property name="receives_default">True</property>
+                                    <property name="use_action_appearance">False</property>
+                                    <signal name="clicked" handler="on_button_ev_stiff_hist_clicked" swapped="no"/>
+                                  </object>
+                                  <packing>
+                                    <property name="expand">False</property>
+                                    <property name="fill">False</property>
+                                    <property name="position">1</property>
+                                  </packing>
+                                </child>
+                                <child>
+                                  <object class="GtkHBox" id="hbox20">
+                                    <property name="visible">True</property>
+                                    <property name="can_focus">False</property>
+                                    <child>
+                                      <object class="GtkVBox" id="lr_hist_min2">
+                                        <property name="visible">True</property>
+                                        <property name="can_focus">False</property>
+                                        <child>
+                                          <object class="GtkLabel" id="label40">
+                                            <property name="visible">True</property>
+                                            <property name="can_focus">False</property>
+                                            <property name="label" translatable="yes">min</property>
+                                          </object>
+                                          <packing>
+                                            <property name="expand">False</property>
+                                            <property name="fill">False</property>
+                                            <property name="position">0</property>
+                                          </packing>
+                                        </child>
+                                        <child>
+                                          <object class="GtkSpinButton" id="ev_stiff_hist_min">
+                                            <property name="visible">True</property>
+                                            <property name="can_focus">True</property>
+                                            <property name="invisible_char">●</property>
+                                          </object>
+                                          <packing>
+                                            <property name="expand">False</property>
+                                            <property name="fill">False</property>
+                                            <property name="position">1</property>
+                                          </packing>
+                                        </child>
+                                      </object>
+                                      <packing>
+                                        <property name="expand">False</property>
+                                        <property name="fill">False</property>
+                                        <property name="position">0</property>
+                                      </packing>
+                                    </child>
+                                    <child>
+                                      <object class="GtkVBox" id="lr_hist_max2">
+                                        <property name="visible">True</property>
+                                        <property name="can_focus">False</property>
+                                        <child>
+                                          <object class="GtkLabel" id="label41">
+                                            <property name="visible">True</property>
+                                            <property name="can_focus">False</property>
+                                            <property name="label" translatable="yes">max</property>
+                                          </object>
+                                          <packing>
+                                            <property name="expand">False</property>
+                                            <property name="fill">False</property>
+                                            <property name="position">0</property>
+                                          </packing>
+                                        </child>
+                                        <child>
+                                          <object class="GtkSpinButton" id="ev_stiff_hist_max">
+                                            <property name="visible">True</property>
+                                            <property name="can_focus">True</property>
+                                            <property name="invisible_char">●</property>
+                                          </object>
+                                          <packing>
+                                            <property name="expand">False</property>
+                                            <property name="fill">False</property>
+                                            <property name="position">1</property>
+                                          </packing>
+                                        </child>
+                                      </object>
+                                      <packing>
+                                        <property name="expand">False</property>
+                                        <property name="fill">False</property>
+                                        <property name="position">1</property>
+                                      </packing>
+                                    </child>
+                                  </object>
+                                  <packing>
+                                    <property name="expand">False</property>
+                                    <property name="fill">False</property>
+                                    <property name="position">2</property>
+                                  </packing>
+                                </child>
+                                <child>
+                                  <object class="GtkVBox" id="lr_hist_col_size2">
+                                    <property name="visible">True</property>
+                                    <property name="can_focus">False</property>
+                                    <child>
+                                      <object class="GtkLabel" id="label42">
+                                        <property name="visible">True</property>
+                                        <property name="can_focus">False</property>
+                                        <property name="label" translatable="yes">col size</property>
+                                      </object>
+                                      <packing>
+                                        <property name="expand">False</property>
+                                        <property name="fill">False</property>
+                                        <property name="position">0</property>
+                                      </packing>
+                                    </child>
+                                    <child>
+                                      <object class="GtkSpinButton" id="ev_stiff_hist_size">
+                                        <property name="visible">True</property>
+                                        <property name="can_focus">True</property>
+                                        <property name="invisible_char">●</property>
+                                      </object>
+                                      <packing>
+                                        <property name="expand">False</property>
+                                        <property name="fill">False</property>
+                                        <property name="position">1</property>
+                                      </packing>
+                                    </child>
+                                  </object>
+                                  <packing>
+                                    <property name="expand">False</property>
+                                    <property name="fill">False</property>
+                                    <property name="position">3</property>
+                                  </packing>
+                                </child>
+                                <child>
+                                  <object class="GtkCheckButton" id="check_stiff_ev_vs_notev">
+                                    <property name="label" translatable="yes">Event VS Not Event
+(No group for this)</property>
+                                    <property name="visible">True</property>
+                                    <property name="can_focus">True</property>
+                                    <property name="receives_default">False</property>
+                                    <property name="use_action_appearance">False</property>
+                                    <property name="draw_indicator">True</property>
+                                  </object>
+                                  <packing>
+                                    <property name="expand">False</property>
+                                    <property name="fill">False</property>
+                                    <property name="position">4</property>
+                                  </packing>
+                                </child>
+                              </object>
+                              <packing>
+                                <property name="expand">False</property>
+                                <property name="fill">False</property>
+                                <property name="position">6</property>
+                              </packing>
+                            </child>
+                            <child>
+                              <object class="GtkVSeparator" id="vseparator6">
+                                <property name="visible">True</property>
+                                <property name="can_focus">False</property>
+                              </object>
+                              <packing>
+                                <property name="expand">False</property>
+                                <property name="fill">True</property>
+                                <property name="position">7</property>
+                              </packing>
+                            </child>
+                            <child>
+                              <object class="GtkVBox" id="vbox_ev_dist2">
+                                <property name="visible">True</property>
+                                <property name="can_focus">False</property>
+                                <child>
+                                  <object class="GtkLabel" id="label_rel_stiff">
+                                    <property name="visible">True</property>
+                                    <property name="can_focus">False</property>
+                                    <property name="label" translatable="yes">Relative Stiffness</property>
+                                  </object>
+                                  <packing>
+                                    <property name="expand">False</property>
+                                    <property name="fill">False</property>
+                                    <property name="position">0</property>
+                                  </packing>
+                                </child>
+                                <child>
+                                  <object class="GtkButton" id="button_ev_relstiff_hist">
+                                    <property name="label" translatable="yes">Histogram</property>
+                                    <property name="visible">True</property>
+                                    <property name="can_focus">True</property>
+                                    <property name="receives_default">True</property>
+                                    <property name="use_action_appearance">False</property>
+                                    <signal name="clicked" handler="on_button_ev_relstiff_hist_clicked" swapped="no"/>
+                                  </object>
+                                  <packing>
+                                    <property name="expand">False</property>
+                                    <property name="fill">False</property>
+                                    <property name="position">1</property>
+                                  </packing>
+                                </child>
+                                <child>
+                                  <object class="GtkHBox" id="hbox21">
+                                    <property name="visible">True</property>
+                                    <property name="can_focus">False</property>
+                                    <child>
+                                      <object class="GtkVBox" id="rel_stiff_hist_min">
+                                        <property name="visible">True</property>
+                                        <property name="can_focus">False</property>
+                                        <child>
+                                          <object class="GtkLabel" id="label45">
+                                            <property name="visible">True</property>
+                                            <property name="can_focus">False</property>
+                                            <property name="label" translatable="yes">min</property>
+                                          </object>
+                                          <packing>
+                                            <property name="expand">False</property>
+                                            <property name="fill">False</property>
+                                            <property name="position">0</property>
+                                          </packing>
+                                        </child>
+                                        <child>
+                                          <object class="GtkSpinButton" id="ev_relstiff_hist_min">
+                                            <property name="visible">True</property>
+                                            <property name="can_focus">True</property>
+                                            <property name="invisible_char">●</property>
+                                            <property name="digits">2</property>
+                                          </object>
+                                          <packing>
+                                            <property name="expand">False</property>
+                                            <property name="fill">False</property>
+                                            <property name="position">1</property>
+                                          </packing>
+                                        </child>
+                                      </object>
+                                      <packing>
+                                        <property name="expand">False</property>
+                                        <property name="fill">False</property>
+                                        <property name="position">0</property>
+                                      </packing>
+                                    </child>
+                                    <child>
+                                      <object class="GtkVBox" id="rel_stiff_hist_max">
+                                        <property name="visible">True</property>
+                                        <property name="can_focus">False</property>
+                                        <child>
+                                          <object class="GtkLabel" id="label46">
+                                            <property name="visible">True</property>
+                                            <property name="can_focus">False</property>
+                                            <property name="label" translatable="yes">max</property>
+                                          </object>
+                                          <packing>
+                                            <property name="expand">False</property>
+                                            <property name="fill">False</property>
+                                            <property name="position">0</property>
+                                          </packing>
+                                        </child>
+                                        <child>
+                                          <object class="GtkSpinButton" id="ev_relstiff_hist_max">
+                                            <property name="visible">True</property>
+                                            <property name="can_focus">True</property>
+                                            <property name="invisible_char">●</property>
+                                            <property name="digits">2</property>
+                                          </object>
+                                          <packing>
+                                            <property name="expand">False</property>
+                                            <property name="fill">False</property>
+                                            <property name="position">1</property>
+                                          </packing>
+                                        </child>
+                                      </object>
+                                      <packing>
+                                        <property name="expand">False</property>
+                                        <property name="fill">False</property>
+                                        <property name="position">1</property>
+                                      </packing>
+                                    </child>
+                                  </object>
+                                  <packing>
+                                    <property name="expand">False</property>
+                                    <property name="fill">False</property>
+                                    <property name="position">2</property>
+                                  </packing>
+                                </child>
+                                <child>
+                                  <object class="GtkHBox" id="hbox22">
+                                    <property name="visible">True</property>
+                                    <property name="can_focus">False</property>
+                                    <child>
+                                      <object class="GtkVBox" id="relstiff_hist_col_size">
+                                        <property name="visible">True</property>
+                                        <property name="can_focus">False</property>
+                                        <child>
+                                          <object class="GtkLabel" id="label47">
+                                            <property name="visible">True</property>
+                                            <property name="can_focus">False</property>
+                                            <property name="label" translatable="yes">col size</property>
+                                          </object>
+                                          <packing>
+                                            <property name="expand">False</property>
+                                            <property name="fill">False</property>
+                                            <property name="position">0</property>
+                                          </packing>
+                                        </child>
+                                        <child>
+                                          <object class="GtkSpinButton" id="ev_relstiff_hist_size">
+                                            <property name="visible">True</property>
+                                            <property name="can_focus">True</property>
+                                            <property name="invisible_char">●</property>
+                                            <property name="digits">3</property>
+                                          </object>
+                                          <packing>
+                                            <property name="expand">False</property>
+                                            <property name="fill">False</property>
+                                            <property name="position">1</property>
+                                          </packing>
+                                        </child>
+                                      </object>
+                                      <packing>
+                                        <property name="expand">False</property>
+                                        <property name="fill">False</property>
+                                        <property name="position">0</property>
+                                      </packing>
+                                    </child>
+                                    <child>
+                                      <object class="GtkVBox" id="vbox11">
+                                        <property name="visible">True</property>
+                                        <property name="can_focus">False</property>
+                                        <child>
+                                          <object class="GtkLabel" id="label_dis">
+                                            <property name="visible">True</property>
+                                            <property name="can_focus">False</property>
+                                            <property name="label" translatable="yes">distance</property>
+                                          </object>
+                                          <packing>
+                                            <property name="expand">False</property>
+                                            <property name="fill">False</property>
+                                            <property name="position">0</property>
+                                          </packing>
+                                        </child>
+                                        <child>
+                                          <object class="GtkSpinButton" id="ev_relstiff_hist_dist">
+                                            <property name="visible">True</property>
+                                            <property name="can_focus">True</property>
+                                            <property name="invisible_char">●</property>
+                                            <property name="adjustment">spin_hist_rel_dist</property>
+                                          </object>
+                                          <packing>
+                                            <property name="expand">False</property>
+                                            <property name="fill">False</property>
+                                            <property name="position">1</property>
+                                          </packing>
+                                        </child>
+                                      </object>
+                                      <packing>
+                                        <property name="expand">False</property>
+                                        <property name="fill">False</property>
+                                        <property name="position">1</property>
+                                      </packing>
+                                    </child>
+                                  </object>
+                                  <packing>
+                                    <property name="expand">False</property>
+                                    <property name="fill">True</property>
+                                    <property name="position">3</property>
+                                  </packing>
+                                </child>
+                              </object>
+                              <packing>
+                                <property name="expand">False</property>
+                                <property name="fill">False</property>
+                                <property name="position">8</property>
+                              </packing>
+                            </child>
+                            <child>
+                              <object class="GtkVBox" id="vbox_ev_length">
+                                <property name="visible">True</property>
+                                <property name="can_focus">False</property>
+                                <child>
+                                  <object class="GtkLabel" id="label_ev_length">
+                                    <property name="visible">True</property>
+                                    <property name="can_focus">False</property>
+                                    <property name="label" translatable="yes">Length</property>
+                                  </object>
+                                  <packing>
+                                    <property name="expand">False</property>
+                                    <property name="fill">False</property>
+                                    <property name="position">0</property>
+                                  </packing>
+                                </child>
+                                <child>
+                                  <object class="GtkButton" id="button_ev_length_hist">
+                                    <property name="label" translatable="yes">Histogram</property>
+                                    <property name="visible">True</property>
+                                    <property name="can_focus">True</property>
+                                    <property name="receives_default">True</property>
+                                    <property name="use_action_appearance">False</property>
+                                    <signal name="clicked" handler="on_button_ev_length_hist_clicked" swapped="no"/>
+                                  </object>
+                                  <packing>
+                                    <property name="expand">False</property>
+                                    <property name="fill">False</property>
+                                    <property name="position">1</property>
+                                  </packing>
+                                </child>
+                                <child>
+                                  <object class="GtkHBox" id="hbox23">
+                                    <property name="visible">True</property>
+                                    <property name="can_focus">False</property>
+                                    <child>
+                                      <object class="GtkVBox" id="length_hist_min">
+                                        <property name="visible">True</property>
+                                        <property name="can_focus">False</property>
+                                        <child>
+                                          <object class="GtkLabel" id="label51">
+                                            <property name="visible">True</property>
+                                            <property name="can_focus">False</property>
+                                            <property name="label" translatable="yes">min</property>
+                                          </object>
+                                          <packing>
+                                            <property name="expand">False</property>
+                                            <property name="fill">False</property>
+                                            <property name="position">0</property>
+                                          </packing>
+                                        </child>
+                                        <child>
+                                          <object class="GtkSpinButton" id="ev_length_hist_min">
+                                            <property name="visible">True</property>
+                                            <property name="can_focus">True</property>
+                                            <property name="invisible_char">●</property>
+                                            <property name="digits">2</property>
+                                          </object>
+                                          <packing>
+                                            <property name="expand">False</property>
+                                            <property name="fill">False</property>
+                                            <property name="position">1</property>
+                                          </packing>
+                                        </child>
+                                      </object>
+                                      <packing>
+                                        <property name="expand">False</property>
+                                        <property name="fill">False</property>
+                                        <property name="position">0</property>
+                                      </packing>
+                                    </child>
+                                    <child>
+                                      <object class="GtkVBox" id="length_hist_max">
+                                        <property name="visible">True</property>
+                                        <property name="can_focus">False</property>
+                                        <child>
+                                          <object class="GtkLabel" id="label52">
+                                            <property name="visible">True</property>
+                                            <property name="can_focus">False</property>
+                                            <property name="label" translatable="yes">max</property>
+                                          </object>
+                                          <packing>
+                                            <property name="expand">False</property>
+                                            <property name="fill">False</property>
+                                            <property name="position">0</property>
+                                          </packing>
+                                        </child>
+                                        <child>
+                                          <object class="GtkSpinButton" id="ev_length_hist_max">
+                                            <property name="visible">True</property>
+                                            <property name="can_focus">True</property>
+                                            <property name="invisible_char">●</property>
+                                            <property name="digits">2</property>
+                                          </object>
+                                          <packing>
+                                            <property name="expand">False</property>
+                                            <property name="fill">False</property>
+                                            <property name="position">1</property>
+                                          </packing>
+                                        </child>
+                                      </object>
+                                      <packing>
+                                        <property name="expand">False</property>
+                                        <property name="fill">False</property>
+                                        <property name="position">1</property>
+                                      </packing>
+                                    </child>
+                                  </object>
+                                  <packing>
+                                    <property name="expand">False</property>
+                                    <property name="fill">False</property>
+                                    <property name="position">2</property>
+                                  </packing>
+                                </child>
+                                <child>
+                                  <object class="GtkVBox" id="length_hist_col_size">
+                                    <property name="visible">True</property>
+                                    <property name="can_focus">False</property>
+                                    <child>
+                                      <object class="GtkLabel" id="label53">
+                                        <property name="visible">True</property>
+                                        <property name="can_focus">False</property>
+                                        <property name="label" translatable="yes">col size</property>
+                                      </object>
+                                      <packing>
+                                        <property name="expand">False</property>
+                                        <property name="fill">False</property>
+                                        <property name="position">0</property>
+                                      </packing>
+                                    </child>
+                                    <child>
+                                      <object class="GtkSpinButton" id="ev_length_hist_size">
+                                        <property name="visible">True</property>
+                                        <property name="can_focus">True</property>
+                                        <property name="invisible_char">●</property>
+                                        <property name="digits">3</property>
+                                      </object>
+                                      <packing>
+                                        <property name="expand">False</property>
+                                        <property name="fill">False</property>
+                                        <property name="position">1</property>
+                                      </packing>
+                                    </child>
+                                  </object>
+                                  <packing>
+                                    <property name="expand">False</property>
+                                    <property name="fill">False</property>
+                                    <property name="position">3</property>
+                                  </packing>
+                                </child>
+                              </object>
+                              <packing>
+                                <property name="expand">False</property>
+                                <property name="fill">False</property>
+                                <property name="position">9</property>
+                              </packing>
+                            </child>
+                            <child>
+                              <object class="GtkVSeparator" id="vseparator7">
+                                <property name="visible">True</property>
+                                <property name="can_focus">False</property>
+                              </object>
+                              <packing>
+                                <property name="expand">False</property>
+                                <property name="fill">True</property>
+                                <property name="position">10</property>
+                              </packing>
+                            </child>
+                            <child>
+                              <object class="GtkVBox" id="vbox_ev_plength">
+                                <property name="visible">True</property>
+                                <property name="can_focus">False</property>
+                                <child>
+                                  <object class="GtkLabel" id="label_ev_plength">
+                                    <property name="visible">True</property>
+                                    <property name="can_focus">False</property>
+                                    <property name="label" translatable="yes">Persistent Length</property>
+                                  </object>
+                                  <packing>
+                                    <property name="expand">False</property>
+                                    <property name="fill">False</property>
+                                    <property name="position">0</property>
+                                  </packing>
+                                </child>
+                                <child>
+                                  <object class="GtkButton" id="button_ev_plength_hist">
+                                    <property name="label" translatable="yes">Histogram</property>
+                                    <property name="visible">True</property>
+                                    <property name="can_focus">True</property>
+                                    <property name="receives_default">True</property>
+                                    <property name="use_action_appearance">False</property>
+                                    <signal name="clicked" handler="on_button_ev_plength_hist_clicked" swapped="no"/>
+                                  </object>
+                                  <packing>
+                                    <property name="expand">False</property>
+                                    <property name="fill">False</property>
+                                    <property name="position">1</property>
+                                  </packing>
+                                </child>
+                                <child>
+                                  <object class="GtkHBox" id="hbox30">
+                                    <property name="visible">True</property>
+                                    <property name="can_focus">False</property>
+                                    <child>
+                                      <object class="GtkVBox" id="plength_hist_min">
+                                        <property name="visible">True</property>
+                                        <property name="can_focus">False</property>
+                                        <child>
+                                          <object class="GtkLabel" id="label54">
+                                            <property name="visible">True</property>
+                                            <property name="can_focus">False</property>
+                                            <property name="label" translatable="yes">min</property>
+                                          </object>
+                                          <packing>
+                                            <property name="expand">False</property>
+                                            <property name="fill">False</property>
+                                            <property name="position">0</property>
+                                          </packing>
+                                        </child>
+                                        <child>
+                                          <object class="GtkSpinButton" id="ev_plength_hist_min">
+                                            <property name="visible">True</property>
+                                            <property name="can_focus">True</property>
+                                            <property name="invisible_char">●</property>
+                                            <property name="digits">2</property>
+                                          </object>
+                                          <packing>
+                                            <property name="expand">False</property>
+                                            <property name="fill">False</property>
+                                            <property name="position">1</property>
+                                          </packing>
+                                        </child>
+                                      </object>
+                                      <packing>
+                                        <property name="expand">False</property>
+                                        <property name="fill">False</property>
+                                        <property name="position">0</property>
+                                      </packing>
+                                    </child>
+                                    <child>
+                                      <object class="GtkVBox" id="plength_hist_max">
+                                        <property name="visible">True</property>
+                                        <property name="can_focus">False</property>
+                                        <child>
+                                          <object class="GtkLabel" id="label55">
+                                            <property name="visible">True</property>
+                                            <property name="can_focus">False</property>
+                                            <property name="label" translatable="yes">max</property>
+                                          </object>
+                                          <packing>
+                                            <property name="expand">False</property>
+                                            <property name="fill">False</property>
+                                            <property name="position">0</property>
+                                          </packing>
+                                        </child>
+                                        <child>
+                                          <object class="GtkSpinButton" id="ev_plength_hist_max">
+                                            <property name="visible">True</property>
+                                            <property name="can_focus">True</property>
+                                            <property name="invisible_char">●</property>
+                                            <property name="digits">2</property>
+                                          </object>
+                                          <packing>
+                                            <property name="expand">False</property>
+                                            <property name="fill">False</property>
+                                            <property name="position">1</property>
+                                          </packing>
+                                        </child>
+                                      </object>
+                                      <packing>
+                                        <property name="expand">False</property>
+                                        <property name="fill">False</property>
+                                        <property name="position">1</property>
+                                      </packing>
+                                    </child>
+                                  </object>
+                                  <packing>
+                                    <property name="expand">False</property>
+                                    <property name="fill">False</property>
+                                    <property name="position">2</property>
+                                  </packing>
+                                </child>
+                                <child>
+                                  <object class="GtkVBox" id="plength_hist_col_size">
+                                    <property name="visible">True</property>
+                                    <property name="can_focus">False</property>
+                                    <child>
+                                      <object class="GtkLabel" id="label56">
+                                        <property name="visible">True</property>
+                                        <property name="can_focus">False</property>
+                                        <property name="label" translatable="yes">col size</property>
+                                      </object>
+                                      <packing>
+                                        <property name="expand">False</property>
+                                        <property name="fill">False</property>
+                                        <property name="position">0</property>
+                                      </packing>
+                                    </child>
+                                    <child>
+                                      <object class="GtkSpinButton" id="ev_plength_hist_size">
+                                        <property name="visible">True</property>
+                                        <property name="can_focus">True</property>
+                                        <property name="invisible_char">●</property>
+                                        <property name="digits">3</property>
+                                      </object>
+                                      <packing>
+                                        <property name="expand">False</property>
+                                        <property name="fill">False</property>
+                                        <property name="position">1</property>
+                                      </packing>
+                                    </child>
+                                  </object>
+                                  <packing>
+                                    <property name="expand">False</property>
+                                    <property name="fill">False</property>
+                                    <property name="position">3</property>
+                                  </packing>
+                                </child>
+                              </object>
+                              <packing>
+                                <property name="expand">False</property>
+                                <property name="fill">False</property>
+                                <property name="position">11</property>
+                              </packing>
+                            </child>
+                            <child>
+                              <object class="GtkVSeparator" id="vseparator8">
+                                <property name="visible">True</property>
+                                <property name="can_focus">False</property>
+                              </object>
+                              <packing>
+                                <property name="expand">False</property>
+                                <property name="fill">True</property>
+                                <property name="position">12</property>
+                              </packing>
+                            </child>
+                          </object>
+                        </child>
+                      </object>
+                    </child>
+                  </object>
+                  <packing>
+                    <property name="expand">True</property>
+                    <property name="fill">True</property>
+                    <property name="position">0</property>
+                  </packing>
+                </child>
+                <child>
+                  <object class="GtkHSeparator" id="hseparator2">
+                    <property name="visible">True</property>
+                    <property name="can_focus">False</property>
+                  </object>
+                  <packing>
+                    <property name="expand">False</property>
+                    <property name="fill">False</property>
+                    <property name="position">1</property>
+                  </packing>
+                </child>
+                <child>
+                  <object class="GtkFrame" id="frame2">
+                    <property name="visible">True</property>
+                    <property name="can_focus">False</property>
+                    <property name="label_xalign">0</property>
+                    <property name="shadow_type">none</property>
+                    <child>
+                      <object class="GtkAlignment" id="alignment8">
+                        <property name="visible">True</property>
+                        <property name="can_focus">False</property>
+                        <property name="left_padding">12</property>
+                        <child>
+                          <object class="GtkHBox" id="hbox19">
+                            <property name="visible">True</property>
+                            <property name="can_focus">False</property>
+                            <child>
+                              <object class="GtkVBox" id="vbox8">
+                                <property name="visible">True</property>
+                                <property name="can_focus">False</property>
+                                <child>
+                                  <object class="GtkButton" id="button_scatter_Force_LR">
+                                    <property name="label" translatable="yes">Force vs Loading rate</property>
+                                    <property name="visible">True</property>
+                                    <property name="can_focus">True</property>
+                                    <property name="receives_default">True</property>
+                                    <property name="use_action_appearance">False</property>
+                                    <signal name="clicked" handler="on_button_scatter_Force_LR_clicked" swapped="no"/>
+                                  </object>
+                                  <packing>
+                                    <property name="expand">False</property>
+                                    <property name="fill">False</property>
+                                    <property name="position">0</property>
+                                  </packing>
+                                </child>
+                                <child>
+                                  <object class="GtkButton" id="button_scatter_force_dist">
+                                    <property name="label" translatable="yes">Force vs Distance</property>
+                                    <property name="visible">True</property>
+                                    <property name="can_focus">True</property>
+                                    <property name="receives_default">True</property>
+                                    <property name="use_action_appearance">False</property>
+                                    <signal name="clicked" handler="on_button_scatter_force_dist_clicked" swapped="no"/>
+                                  </object>
+                                  <packing>
+                                    <property name="expand">True</property>
+                                    <property name="fill">True</property>
+                                    <property name="position">1</property>
+                                  </packing>
+                                </child>
+                                <child>
+                                  <object class="GtkButton" id="button_scatter_force_stiffness">
+                                    <property name="label" translatable="yes">Force vs Stiffness</property>
+                                    <property name="visible">True</property>
+                                    <property name="can_focus">True</property>
+                                    <property name="receives_default">True</property>
+                                    <property name="use_action_appearance">False</property>
+                                    <signal name="clicked" handler="on_button_scatter_force_stiffness_clicked" swapped="no"/>
+                                  </object>
+                                  <packing>
+                                    <property name="expand">True</property>
+                                    <property name="fill">True</property>
+                                    <property name="position">2</property>
+                                  </packing>
+                                </child>
+                              </object>
+                              <packing>
+                                <property name="expand">False</property>
+                                <property name="fill">False</property>
+                                <property name="position">0</property>
+                              </packing>
+                            </child>
+                            <child>
+                              <object class="GtkVBox" id="vbox9">
+                                <property name="visible">True</property>
+                                <property name="can_focus">False</property>
+                                <child>
+                                  <object class="GtkButton" id="button_scatter_LR_Dist">
+                                    <property name="label" translatable="yes">Loading rate vs Distance</property>
+                                    <property name="visible">True</property>
+                                    <property name="can_focus">True</property>
+                                    <property name="receives_default">True</property>
+                                    <property name="use_action_appearance">False</property>
+                                    <signal name="clicked" handler="on_button_scatter_LR_Dist_clicked" swapped="no"/>
+                                  </object>
+                                  <packing>
+                                    <property name="expand">True</property>
+                                    <property name="fill">True</property>
+                                    <property name="position">0</property>
+                                  </packing>
+                                </child>
+                                <child>
+                                  <object class="GtkButton" id="button_scatter_LR_Stiffness">
+                                    <property name="label" translatable="yes">Loading rate vs Stiffness</property>
+                                    <property name="visible">True</property>
+                                    <property name="can_focus">True</property>
+                                    <property name="receives_default">True</property>
+                                    <property name="use_action_appearance">False</property>
+                                    <signal name="clicked" handler="on_button_scatter_LR_Stiffness_clicked" swapped="no"/>
+                                  </object>
+                                  <packing>
+                                    <property name="expand">True</property>
+                                    <property name="fill">True</property>
+                                    <property name="position">1</property>
+                                  </packing>
+                                </child>
+                                <child>
+                                  <object class="GtkButton" id="button_scatter_Dist_Stiffness">
+                                    <property name="label" translatable="yes">Distance vs Stiffness</property>
+                                    <property name="visible">True</property>
+                                    <property name="can_focus">True</property>
+                                    <property name="receives_default">True</property>
+                                    <property name="use_action_appearance">False</property>
+                                    <signal name="clicked" handler="on_button_scatter_Dist_Stiffness_clicked" swapped="no"/>
+                                  </object>
+                                  <packing>
+                                    <property name="expand">True</property>
+                                    <property name="fill">True</property>
+                                    <property name="position">2</property>
+                                  </packing>
+                                </child>
+                              </object>
+                              <packing>
+                                <property name="expand">False</property>
+                                <property name="fill">False</property>
+                                <property name="position">1</property>
+                              </packing>
+                            </child>
+                            <child>
+                              <object class="GtkVBox" id="vbox10">
+                                <property name="visible">True</property>
+                                <property name="can_focus">False</property>
+                                <child>
+                                  <object class="GtkButton" id="button_scatter_Force_RelStiff">
+                                    <property name="label" translatable="yes">Force vs Rel stiff</property>
+                                    <property name="visible">True</property>
+                                    <property name="can_focus">True</property>
+                                    <property name="receives_default">True</property>
+                                    <property name="use_action_appearance">False</property>
+                                    <signal name="clicked" handler="on_button_scatter_Force_RelStiff_clicked" swapped="no"/>
+                                  </object>
+                                  <packing>
+                                    <property name="expand">False</property>
+                                    <property name="fill">False</property>
+                                    <property name="position">0</property>
+                                  </packing>
+                                </child>
+                                <child>
+                                  <object class="GtkButton" id="button_scatter_LR_RelStiff">
+                                    <property name="label" translatable="yes">Loading rate vs Rel stiff</property>
+                                    <property name="visible">True</property>
+                                    <property name="can_focus">True</property>
+                                    <property name="receives_default">True</property>
+                                    <property name="use_action_appearance">False</property>
+                                    <signal name="clicked" handler="on_button_scatter_LR_RelStiff_clicked" swapped="no"/>
+                                  </object>
+                                  <packing>
+                                    <property name="expand">True</property>
+                                    <property name="fill">True</property>
+                                    <property name="position">1</property>
+                                  </packing>
+                                </child>
+                                <child>
+                                  <object class="GtkButton" id="button_scatter_Dist_RelStiff">
+                                    <property name="label" translatable="yes">Distance vs Rel stiff</property>
+                                    <property name="visible">True</property>
+                                    <property name="can_focus">True</property>
+                                    <property name="receives_default">True</property>
+                                    <property name="use_action_appearance">False</property>
+                                    <signal name="clicked" handler="on_button_scatter_Dist_RelStiff_clicked" swapped="no"/>
+                                  </object>
+                                  <packing>
+                                    <property name="expand">True</property>
+                                    <property name="fill">True</property>
+                                    <property name="position">2</property>
+                                  </packing>
+                                </child>
+                              </object>
+                              <packing>
+                                <property name="expand">False</property>
+                                <property name="fill">False</property>
+                                <property name="position">2</property>
+                              </packing>
+                            </child>
+                          </object>
+                        </child>
+                      </object>
+                    </child>
+                    <child type="label">
+                      <object class="GtkLabel" id="label34">
+                        <property name="visible">True</property>
+                        <property name="can_focus">False</property>
+                        <property name="label" translatable="yes"><b>Scatter plots</b></property>
+                        <property name="use_markup">True</property>
+                      </object>
+                    </child>
+                  </object>
+                  <packing>
+                    <property name="expand">False</property>
+                    <property name="fill">False</property>
+                    <property name="position">2</property>
+                  </packing>
+                </child>
+                <child>
+                  <object class="GtkButton" id="button_regenerate_event_properties">
+                    <property name="label">gtk-refresh</property>
+                    <property name="visible">True</property>
+                    <property name="can_focus">True</property>
+                    <property name="receives_default">True</property>
+                    <property name="use_action_appearance">False</property>
+                    <property name="use_stock">True</property>
+                    <signal name="clicked" handler="on_button_regenerate_event_properties_clicked" swapped="no"/>
+                  </object>
+                  <packing>
+                    <property name="expand">False</property>
+                    <property name="fill">False</property>
+                    <property name="position">3</property>
+                  </packing>
+                </child>
+              </object>
+              <packing>
+                <property name="position">3</property>
+              </packing>
+            </child>
+            <child type="tab">
+              <object class="GtkLabel" id="label1">
+                <property name="visible">True</property>
+                <property name="can_focus">False</property>
+                <property name="label" translatable="yes">Ev. Histo.</property>
+              </object>
+              <packing>
+                <property name="position">3</property>
+                <property name="tab_fill">False</property>
+              </packing>
+            </child>
+            <child>
+              <object class="GtkVBox" id="Tab_Plot">
+                <property name="visible">True</property>
+                <property name="can_focus">False</property>
+                <child>
+                  <object class="GtkFrame" id="frameRelativeStiffness">
+                    <property name="visible">True</property>
+                    <property name="can_focus">False</property>
+                    <property name="label_xalign">0</property>
+                    <child>
+                      <object class="GtkAlignment" id="alignment4">
+                        <property name="visible">True</property>
+                        <property name="can_focus">False</property>
+                        <property name="left_padding">12</property>
+                        <child>
+                          <object class="GtkVBox" id="vbox2">
+                            <property name="visible">True</property>
+                            <property name="can_focus">False</property>
+                            <child>
+                              <object class="GtkHBox" id="hbox11">
+                                <property name="visible">True</property>
+                                <property name="can_focus">False</property>
+                                <child>
+                                  <object class="GtkLabel" id="label24">
+                                    <property name="visible">True</property>
+                                    <property name="can_focus">False</property>
+                                    <property name="label" translatable="yes">pixel distance</property>
+                                  </object>
+                                  <packing>
+                                    <property name="expand">False</property>
+                                    <property name="fill">False</property>
+                                    <property name="position">0</property>
+                                  </packing>
+                                </child>
+                                <child>
+                                  <object class="GtkSpinButton" id="spin_rel_stiff_plot_dist">
+                                    <property name="visible">True</property>
+                                    <property name="can_focus">True</property>
+                                    <property name="tooltip_text" translatable="yes">Set the pixel distance of the 
+relative stiffness to plot</property>
+                                    <property name="invisible_char">●</property>
+                                    <property name="adjustment">adj_plot_rel_dist</property>
+                                  </object>
+                                  <packing>
+                                    <property name="expand">False</property>
+                                    <property name="fill">False</property>
+                                    <property name="position">1</property>
+                                  </packing>
+                                </child>
+                              </object>
+                              <packing>
+                                <property name="expand">False</property>
+                                <property name="fill">False</property>
+                                <property name="position">0</property>
+                              </packing>
+                            </child>
+                            <child>
+                              <object class="GtkHBox" id="hbox12">
+                                <property name="visible">True</property>
+                                <property name="can_focus">False</property>
+                                <child>
+                                  <object class="GtkLabel" id="label28">
+                                    <property name="visible">True</property>
+                                    <property name="can_focus">False</property>
+                                    <property name="label" translatable="yes">Exclude </property>
+                                  </object>
+                                  <packing>
+                                    <property name="expand">False</property>
+                                    <property name="fill">False</property>
+                                    <property name="position">0</property>
+                                  </packing>
+                                </child>
+                                <child>
+                                  <object class="GtkSpinButton" id="spin_range_rel_stiff">
+                                    <property name="visible">True</property>
+                                    <property name="can_focus">True</property>
+                                    <property name="invisible_char">●</property>
+                                    <property name="adjustment">adj_rel_stiff_limite</property>
+                                    <property name="digits">2</property>
+                                  </object>
+                                  <packing>
+                                    <property name="expand">False</property>
+                                    <property name="fill">False</property>
+                                    <property name="position">1</property>
+                                  </packing>
+                                </child>
+                                <child>
+                                  <object class="GtkLabel" id="label29">
+                                    <property name="visible">True</property>
+                                    <property name="can_focus">False</property>
+                                    <property name="label" translatable="yes"> times stiffer or softer.</property>
+                                  </object>
+                                  <packing>
+                                    <property name="expand">False</property>
+                                    <property name="fill">False</property>
+                                    <property name="position">2</property>
+                                  </packing>
+                                </child>
+                              </object>
+                              <packing>
+                                <property name="expand">False</property>
+                                <property name="fill">False</property>
+                                <property name="position">1</property>
+                              </packing>
+                            </child>
+                          </object>
+                        </child>
+                      </object>
+                    </child>
+                    <child type="label">
+                      <object class="GtkLabel" id="label_plot_rel_stiff">
+                        <property name="visible">True</property>
+                        <property name="can_focus">False</property>
+                        <property name="label" translatable="yes"><b>Relative stiffness</b></property>
+                        <property name="use_markup">True</property>
+                      </object>
+                    </child>
+                  </object>
+                  <packing>
+                    <property name="expand">False</property>
+                    <property name="fill">False</property>
+                    <property name="position">0</property>
+                  </packing>
+                </child>
+                <child>
+                  <object class="GtkFrame" id="frameNbrEvtTL">
+                    <property name="visible">True</property>
+                    <property name="can_focus">False</property>
+                    <property name="label_xalign">0</property>
+                    <child>
+                      <object class="GtkAlignment" id="alignment7">
+                        <property name="visible">True</property>
+                        <property name="can_focus">False</property>
+                        <property name="left_padding">12</property>
+                        <child>
+                          <object class="GtkHBox" id="hbox15">
+                            <property name="visible">True</property>
+                            <property name="can_focus">False</property>
+                            <child>
+                              <object class="GtkButton" id="button_plot_nbr_event_tl">
+                                <property name="label" translatable="yes">Show</property>
+                                <property name="visible">True</property>
+                                <property name="can_focus">True</property>
+                                <property name="receives_default">True</property>
+                                <property name="use_action_appearance">False</property>
+                                <signal name="clicked" handler="on_button_plot_nbr_event_tl_clicked" swapped="no"/>
+                              </object>
+                              <packing>
+                                <property name="expand">False</property>
+                                <property name="fill">False</property>
+                                <property name="position">0</property>
+                              </packing>
+                            </child>
+                          </object>
+                        </child>
+                      </object>
+                    </child>
+                    <child type="label">
+                      <object class="GtkLabel" id="labelNbr_evt">
+                        <property name="visible">True</property>
+                        <property name="can_focus">False</property>
+                        <property name="label" translatable="yes"><b>Number events</b></property>
+                        <property name="use_markup">True</property>
+                      </object>
+                    </child>
+                  </object>
+                  <packing>
+                    <property name="expand">False</property>
+                    <property name="fill">False</property>
+                    <property name="position">1</property>
+                  </packing>
+                </child>
+              </object>
+              <packing>
+                <property name="position">4</property>
+                <property name="tab_fill">False</property>
+                <property name="reorderable">True</property>
+              </packing>
+            </child>
+            <child type="tab">
+              <object class="GtkLabel" id="label_note_plot">
+                <property name="visible">True</property>
+                <property name="can_focus">False</property>
+                <property name="label" translatable="yes">Plot</property>
+              </object>
+              <packing>
+                <property name="position">4</property>
+                <property name="tab_fill">False</property>
+              </packing>
+            </child>
+            <child>
+              <object class="GtkTable" id="table1">
+                <property name="can_focus">False</property>
+                <property name="n_rows">2</property>
+                <property name="n_columns">2</property>
+                <child>
+                  <object class="GtkTable" id="table2">
+                    <property name="visible">True</property>
+                    <property name="can_focus">False</property>
+                    <property name="n_rows">2</property>
+                    <property name="n_columns">2</property>
+                    <child>
+                      <object class="GtkHBox" id="hbox7">
+                        <property name="visible">True</property>
+                        <property name="can_focus">False</property>
+                        <child>
+                          <object class="GtkLabel" id="label31">
+                            <property name="visible">True</property>
+                            <property name="can_focus">False</property>
+                            <property name="label" translatable="yes">z slice</property>
+                          </object>
+                          <packing>
+                            <property name="expand">False</property>
+                            <property name="fill">False</property>
+                            <property name="position">0</property>
+                          </packing>
+                        </child>
+                        <child>
+                          <object class="GtkSpinButton" id="spinbutton1">
+                            <property name="visible">True</property>
+                            <property name="can_focus">True</property>
+                            <property name="invisible_char">●</property>
+                          </object>
+                          <packing>
+                            <property name="expand">True</property>
+                            <property name="fill">True</property>
+                            <property name="position">1</property>
+                          </packing>
+                        </child>
+                      </object>
+                      <packing>
+                        <property name="x_options"></property>
+                        <property name="y_options"></property>
+                      </packing>
+                    </child>
+                    <child>
+                      <object class="GtkHBox" id="hbox13">
+                        <property name="visible">True</property>
+                        <property name="can_focus">False</property>
+                        <child>
+                          <object class="GtkLabel" id="label32">
+                            <property name="visible">True</property>
+                            <property name="can_focus">False</property>
+                            <property name="label" translatable="yes">x slice</property>
+                          </object>
+                          <packing>
+                            <property name="expand">False</property>
+                            <property name="fill">False</property>
+                            <property name="position">0</property>
+                          </packing>
+                        </child>
+                        <child>
+                          <object class="GtkSpinButton" id="spinbutton2">
+                            <property name="visible">True</property>
+                            <property name="can_focus">True</property>
+                            <property name="invisible_char">●</property>
+                          </object>
+                          <packing>
+                            <property name="expand">True</property>
+                            <property name="fill">True</property>
+                            <property name="position">1</property>
+                          </packing>
+                        </child>
+                      </object>
+                      <packing>
+                        <property name="top_attach">1</property>
+                        <property name="bottom_attach">2</property>
+                        <property name="x_options"></property>
+                        <property name="y_options"></property>
+                      </packing>
+                    </child>
+                    <child>
+                      <object class="GtkHBox" id="hbox14">
+                        <property name="visible">True</property>
+                        <property name="can_focus">False</property>
+                        <child>
+                          <object class="GtkLabel" id="label33">
+                            <property name="visible">True</property>
+                            <property name="can_focus">False</property>
+                            <property name="label" translatable="yes">y slice</property>
+                          </object>
+                          <packing>
+                            <property name="expand">False</property>
+                            <property name="fill">False</property>
+                            <property name="position">0</property>
+                          </packing>
+                        </child>
+                        <child>
+                          <object class="GtkSpinButton" id="spinbutton5">
+                            <property name="visible">True</property>
+                            <property name="can_focus">True</property>
+                            <property name="invisible_char">●</property>
+                          </object>
+                          <packing>
+                            <property name="expand">True</property>
+                            <property name="fill">True</property>
+                            <property name="position">1</property>
+                          </packing>
+                        </child>
+                      </object>
+                      <packing>
+                        <property name="left_attach">1</property>
+                        <property name="right_attach">2</property>
+                        <property name="top_attach">1</property>
+                        <property name="bottom_attach">2</property>
+                        <property name="x_options"></property>
+                        <property name="y_options"></property>
+                      </packing>
+                    </child>
+                    <child>
+                      <object class="GtkButton" id="button_compute_tomo">
+                        <property name="label" translatable="yes">reconstruct tomo</property>
+                        <property name="visible">True</property>
+                        <property name="can_focus">True</property>
+                        <property name="receives_default">True</property>
+                        <property name="tooltip_text" translatable="yes">Tomography volume has
+to be reconstructed each
+time the stiffness is 
+computed</property>
+                        <property name="use_action_appearance">False</property>
+                        <signal name="clicked" handler="on_button_compute_tomo_clicked" swapped="no"/>
+                      </object>
+                      <packing>
+                        <property name="left_attach">1</property>
+                        <property name="right_attach">2</property>
+                      </packing>
+                    </child>
+                  </object>
+                  <packing>
+                    <property name="left_attach">1</property>
+                    <property name="right_attach">2</property>
+                    <property name="x_options"></property>
+                    <property name="y_options"></property>
+                  </packing>
+                </child>
+                <child>
+                  <object class="GtkHBox" id="display_z_slice">
+                    <property name="visible">True</property>
+                    <property name="can_focus">False</property>
+                    <child>
+                      <placeholder/>
+                    </child>
+                  </object>
+                </child>
+                <child>
+                  <object class="GtkHBox" id="display_x_slice">
+                    <property name="visible">True</property>
+                    <property name="can_focus">False</property>
+                    <child>
+                      <placeholder/>
+                    </child>
+                  </object>
+                  <packing>
+                    <property name="top_attach">1</property>
+                    <property name="bottom_attach">2</property>
+                  </packing>
+                </child>
+                <child>
+                  <object class="GtkHBox" id="display_y_slice">
+                    <property name="visible">True</property>
+                    <property name="can_focus">False</property>
+                    <child>
+                      <placeholder/>
+                    </child>
+                  </object>
+                  <packing>
+                    <property name="left_attach">1</property>
+                    <property name="right_attach">2</property>
+                    <property name="top_attach">1</property>
+                    <property name="bottom_attach">2</property>
+                  </packing>
+                </child>
+              </object>
+              <packing>
+                <property name="position">5</property>
+                <property name="tab_fill">False</property>
+              </packing>
+            </child>
+            <child type="tab">
+              <object class="GtkLabel" id="label_tomo">
+                <property name="can_focus">False</property>
+                <property name="label" translatable="yes">Tomography</property>
+              </object>
+              <packing>
+                <property name="position">5</property>
+                <property name="tab_fill">False</property>
+              </packing>
+            </child>
+            <child>
+              <object class="GtkVBox" id="vbox14">
+                <property name="visible">True</property>
+                <property name="can_focus">False</property>
+                <child>
+                  <object class="GtkHBox" id="hbox26">
+                    <property name="visible">True</property>
+                    <property name="can_focus">False</property>
+                    <child>
+                      <object class="GtkVBox" id="vbox_ev_force1">
+                        <property name="visible">True</property>
+                        <property name="can_focus">False</property>
+                        <child>
+                          <object class="GtkLabel" id="label_ym">
+                            <property name="visible">True</property>
+                            <property name="can_focus">False</property>
+                            <property name="label" translatable="yes">Young modulus</property>
+                          </object>
+                          <packing>
+                            <property name="expand">False</property>
+                            <property name="fill">False</property>
+                            <property name="position">0</property>
+                          </packing>
+                        </child>
+                        <child>
+                          <object class="GtkButton" id="button_young_modulus_hist">
+                            <property name="label" translatable="yes">Histogram</property>
+                            <property name="visible">True</property>
+                            <property name="can_focus">True</property>
+                            <property name="receives_default">True</property>
+                            <property name="use_action_appearance">False</property>
+                            <signal name="clicked" handler="on_button_young_modulus_hist_clicked" swapped="no"/>
+                          </object>
+                          <packing>
+                            <property name="expand">False</property>
+                            <property name="fill">False</property>
+                            <property name="position">1</property>
+                          </packing>
+                        </child>
+                        <child>
+                          <object class="GtkHBox" id="hbox27">
+                            <property name="visible">True</property>
+                            <property name="can_focus">False</property>
+                            <child>
+                              <object class="GtkVBox" id="box_ym_hist_min">
+                                <property name="visible">True</property>
+                                <property name="can_focus">False</property>
+                                <child>
+                                  <object class="GtkLabel" id="label48">
+                                    <property name="visible">True</property>
+                                    <property name="can_focus">False</property>
+                                    <property name="label" translatable="yes">min</property>
+                                  </object>
+                                  <packing>
+                                    <property name="expand">False</property>
+                                    <property name="fill">False</property>
+                                    <property name="position">0</property>
+                                  </packing>
+                                </child>
+                                <child>
+                                  <object class="GtkSpinButton" id="spin_ym_hist_min">
+                                    <property name="visible">True</property>
+                                    <property name="can_focus">True</property>
+                                    <property name="invisible_char">●</property>
+                                    <property name="digits">2</property>
+                                  </object>
+                                  <packing>
+                                    <property name="expand">False</property>
+                                    <property name="fill">False</property>
+                                    <property name="position">1</property>
+                                  </packing>
+                                </child>
+                              </object>
+                              <packing>
+                                <property name="expand">False</property>
+                                <property name="fill">False</property>
+                                <property name="position">0</property>
+                              </packing>
+                            </child>
+                            <child>
+                              <object class="GtkVBox" id="box_ym_hist_max">
+                                <property name="visible">True</property>
+                                <property name="can_focus">False</property>
+                                <child>
+                                  <object class="GtkLabel" id="label49">
+                                    <property name="visible">True</property>
+                                    <property name="can_focus">False</property>
+                                    <property name="label" translatable="yes">max</property>
+                                  </object>
+                                  <packing>
+                                    <property name="expand">False</property>
+                                    <property name="fill">False</property>
+                                    <property name="position">0</property>
+                                  </packing>
+                                </child>
+                                <child>
+                                  <object class="GtkSpinButton" id="spin_ym_hist_max">
+                                    <property name="visible">True</property>
+                                    <property name="can_focus">True</property>
+                                    <property name="invisible_char">●</property>
+                                    <property name="digits">2</property>
+                                  </object>
+                                  <packing>
+                                    <property name="expand">False</property>
+                                    <property name="fill">False</property>
+                                    <property name="position">1</property>
+                                  </packing>
+                                </child>
+                              </object>
+                              <packing>
+                                <property name="expand">False</property>
+                                <property name="fill">False</property>
+                                <property name="position">1</property>
+                              </packing>
+                            </child>
+                          </object>
+                          <packing>
+                            <property name="expand">False</property>
+                            <property name="fill">False</property>
+                            <property name="position">2</property>
+                          </packing>
+                        </child>
+                        <child>
+                          <object class="GtkVBox" id="box_ym_hist_col_size">
+                            <property name="visible">True</property>
+                            <property name="can_focus">False</property>
+                            <child>
+                              <object class="GtkLabel" id="label50">
+                                <property name="visible">True</property>
+                                <property name="can_focus">False</property>
+                                <property name="label" translatable="yes">col size</property>
+                              </object>
+                              <packing>
+                                <property name="expand">False</property>
+                                <property name="fill">False</property>
+                                <property name="position">0</property>
+                              </packing>
+                            </child>
+                            <child>
+                              <object class="GtkSpinButton" id="spin_ym_hist_size">
+                                <property name="visible">True</property>
+                                <property name="can_focus">True</property>
+                                <property name="invisible_char">●</property>
+                                <property name="digits">3</property>
+                              </object>
+                              <packing>
+                                <property name="expand">False</property>
+                                <property name="fill">False</property>
+                                <property name="position">1</property>
+                              </packing>
+                            </child>
+                          </object>
+                          <packing>
+                            <property name="expand">False</property>
+                            <property name="fill">False</property>
+                            <property name="position">3</property>
+                          </packing>
+                        </child>
+                        <child>
+                          <object class="GtkVBox" id="vbox16">
+                            <property name="visible">True</property>
+                            <property name="can_focus">False</property>
+                            <child>
+                              <object class="GtkLabel" id="label58">
+                                <property name="visible">True</property>
+                                <property name="can_focus">False</property>
+                                <property name="label" translatable="yes">Depth Nb</property>
+                              </object>
+                              <packing>
+                                <property name="expand">True</property>
+                                <property name="fill">True</property>
+                                <property name="position">0</property>
+                              </packing>
+                            </child>
+                            <child>
+                              <object class="GtkSpinButton" id="spin_ym_hist_depth_nb">
+                                <property name="visible">True</property>
+                                <property name="can_focus">True</property>
+                                <property name="invisible_char">●</property>
+                              </object>
+                              <packing>
+                                <property name="expand">True</property>
+                                <property name="fill">True</property>
+                                <property name="position">1</property>
+                              </packing>
+                            </child>
+                          </object>
+                          <packing>
+                            <property name="expand">False</property>
+                            <property name="fill">False</property>
+                            <property name="position">4</property>
+                          </packing>
+                        </child>
+                      </object>
+                      <packing>
+                        <property name="expand">False</property>
+                        <property name="fill">False</property>
+                        <property name="position">0</property>
+                      </packing>
+                    </child>
+                    <child>
+                      <placeholder/>
+                    </child>
+                  </object>
+                  <packing>
+                    <property name="expand">True</property>
+                    <property name="fill">True</property>
+                    <property name="position">0</property>
+                  </packing>
+                </child>
+                <child>
+                  <placeholder/>
+                </child>
+              </object>
+              <packing>
+                <property name="position">6</property>
+              </packing>
+            </child>
+            <child type="tab">
+              <object class="GtkLabel" id="label_stiffnes">
+                <property name="visible">True</property>
+                <property name="can_focus">False</property>
+                <property name="label" translatable="yes">Mechanical prop.</property>
+              </object>
+              <packing>
+                <property name="position">6</property>
+                <property name="tab_fill">False</property>
+              </packing>
+            </child>
+          </object>
+          <packing>
+            <property name="expand">True</property>
+            <property name="fill">True</property>
+            <property name="position">1</property>
+          </packing>
+        </child>
+        <child>
+          <object class="GtkProgressBar" id="progressbar_general">
+            <property name="visible">True</property>
+            <property name="can_focus">False</property>
+          </object>
+          <packing>
+            <property name="expand">False</property>
+            <property name="fill">False</property>
+            <property name="position">2</property>
+          </packing>
+        </child>
+        <child>
+          <object class="GtkHBox" id="hbox9">
+            <property name="visible">True</property>
+            <property name="can_focus">False</property>
+            <child>
+              <placeholder/>
+            </child>
+            <child>
+              <object class="GtkLabel" id="label_switch_state">
+                <property name="visible">True</property>
+                <property name="can_focus">False</property>
+              </object>
+              <packing>
+                <property name="expand">False</property>
+                <property name="fill">False</property>
+                <property name="pack_type">end</property>
+                <property name="position">1</property>
+              </packing>
+            </child>
+          </object>
+          <packing>
+            <property name="expand">False</property>
+            <property name="fill">False</property>
+            <property name="position">3</property>
+          </packing>
+        </child>
+      </object>
+    </child>
+  </object>
+  <object class="GtkAboutDialog" id="aboutdialog">
+    <property name="can_focus">False</property>
+    <property name="border_width">5</property>
+    <property name="window_position">center</property>
+    <property name="icon">../Icon/openfovea.png</property>
+    <property name="type_hint">normal</property>
+    <property name="program_name">OpenFovea</property>
+    <property name="version">0.1a160</property>
+    <property name="comments" translatable="yes">OpenFovea is an open source software 
+written in the Laboratory of living matter (EPFL, CH)
+
+Please cite the original article that present
+OpenFovea if you use this software.</property>
+    <property name="website">http://www.freesbi.ch/en/openfovea</property>
+    <property name="website_label" translatable="yes">Home page</property>
+    <property name="license" translatable="yes">This package is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version.
+
+This package is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License along with this package; if not, write to the Free Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301 USA</property>
+    <property name="authors">Charles Roduit</property>
+    <property name="logo">../Icon/CellFovea.png</property>
+    <property name="wrap_license">True</property>
+    <child internal-child="vbox">
+      <object class="GtkBox" id="dialog-vbox1">
+        <property name="visible">True</property>
+        <property name="can_focus">False</property>
+        <property name="spacing">2</property>
+        <child internal-child="action_area">
+          <object class="GtkButtonBox" id="dialog-action_area1">
+            <property name="visible">True</property>
+            <property name="can_focus">False</property>
+            <property name="events">GDK_BUTTON_PRESS_MASK | GDK_STRUCTURE_MASK</property>
+            <property name="layout_style">end</property>
+          </object>
+          <packing>
+            <property name="expand">False</property>
+            <property name="fill">True</property>
+            <property name="pack_type">end</property>
+            <property name="position">0</property>
+          </packing>
+        </child>
+        <child>
+          <placeholder/>
+        </child>
+      </object>
+    </child>
+  </object>
+  <object class="GtkAdjustment" id="adj_fit_seg_size">
+    <property name="upper">1</property>
+    <property name="value">0.29999999999999999</property>
+    <property name="step_increment">0.01</property>
+    <property name="page_increment">0.10000000000000001</property>
+  </object>
+  <object class="GtkAdjustment" id="adj_injection_index">
+    <property name="upper">100</property>
+    <property name="step_increment">1</property>
+    <property name="page_increment">10</property>
+  </object>
+  <object class="GtkAdjustment" id="adj_nbr_rand_event">
+    <property name="upper">100</property>
+    <property name="step_increment">1</property>
+    <property name="page_increment">10</property>
+  </object>
+  <object class="GtkAdjustment" id="adj_plot_rel_dist">
+    <property name="upper">100</property>
+    <property name="step_increment">1</property>
+    <property name="page_increment">10</property>
+    <signal name="value-changed" handler="on_adj_plot_rel_dist_value_changed" swapped="no"/>
+  </object>
+  <object class="GtkAdjustment" id="adj_poisson_ratio">
+    <property name="upper">0.5</property>
+    <property name="value">0.29999999999999999</property>
+    <property name="step_increment">0.01</property>
+    <property name="page_increment">0.10000000000000001</property>
+  </object>
+  <object class="GtkAdjustment" id="adj_rel_stiff_limite">
+    <property name="upper">100</property>
+    <property name="step_increment">0.10000000000000001</property>
+    <property name="page_increment">0.5</property>
+    <signal name="value-changed" handler="on_adj_rel_stiff_limite_value_changed" swapped="no"/>
+  </object>
+  <object class="GtkAdjustment" id="adj_rel_stiff_max_dist">
+    <property name="upper">100</property>
+    <property name="value">3</property>
+    <property name="step_increment">1</property>
+    <property name="page_increment">10</property>
+  </object>
+  <object class="GtkAdjustment" id="adj_tip_size">
+    <property name="upper">100</property>
+    <property name="value">20</property>
+    <property name="step_increment">1</property>
+    <property name="page_increment">10</property>
+  </object>
+  <object class="GtkListStore" id="choose_event_detection">
+    <columns>
+      <!-- column-name gchararray1 -->
+      <column type="gchararray"/>
+    </columns>
+    <data>
+      <row>
+        <col id="0" translatable="yes">Noise (Default)</col>
+      </row>
+      <row>
+        <col id="0" translatable="yes">Fuzzy</col>
+      </row>
+    </data>
+  </object>
+  <object class="GtkListStore" id="choose_hertz_model">
+    <columns>
+      <!-- column-name gchararray1 -->
+      <column type="gchararray"/>
+    </columns>
+    <data>
+      <row>
+        <col id="0" translatable="yes">Cone</col>
+      </row>
+      <row>
+        <col id="0" translatable="yes">Sphere</col>
+      </row>
+    </data>
+  </object>
+  <object class="GtkListStore" id="choose_poc_model">
+    <columns>
+      <!-- column-name gchararray1 -->
+      <column type="gchararray"/>
+    </columns>
+  </object>
+  <object class="GtkListStore" id="choose_threshold_event">
+    <columns>
+      <!-- column-name gchararray1 -->
+      <column type="gchararray"/>
+    </columns>
+    <data>
+      <row>
+        <col id="0" translatable="yes">Fixed</col>
+      </row>
+      <row>
+        <col id="0" translatable="yes">Auto</col>
+      </row>
+    </data>
+  </object>
+  <object class="GtkDialog" id="dialog_compare_experiment">
+    <property name="can_focus">False</property>
+    <property name="border_width">5</property>
+    <property name="type_hint">normal</property>
+    <child internal-child="vbox">
+      <object class="GtkBox" id="dialog-vbox2">
+        <property name="visible">True</property>
+        <property name="can_focus">False</property>
+        <property name="spacing">2</property>
+        <child internal-child="action_area">
+          <object class="GtkButtonBox" id="dialog-action_area2">
+            <property name="visible">True</property>
+            <property name="can_focus">False</property>
+            <property name="layout_style">end</property>
+            <child>
+              <object class="GtkButton" id="button_compare_exp_validate">
+                <property name="label">gtk-ok</property>
+                <property name="visible">True</property>
+                <property name="can_focus">True</property>
+                <property name="receives_default">True</property>
+                <property name="use_action_appearance">False</property>
+                <property name="use_stock">True</property>
+                <property name="yalign">0.46000000834465027</property>
+                <signal name="clicked" handler="on_button_compare_exp_validate_clicked" swapped="no"/>
+              </object>
+              <packing>
+                <property name="expand">False</property>
+                <property name="fill">False</property>
+                <property name="position">0</property>
+              </packing>
+            </child>
+            <child>
+              <object class="GtkButton" id="button_compare_exp_cancel">
+                <property name="label">gtk-cancel</property>
+                <property name="visible">True</property>
+                <property name="can_focus">True</property>
+                <property name="receives_default">True</property>
+                <property name="use_action_appearance">False</property>
+                <property name="use_stock">True</property>
+                <signal name="clicked" handler="on_button_compare_exp_cancel_clicked" swapped="no"/>
+              </object>
+              <packing>
+                <property name="expand">False</property>
+                <property name="fill">False</property>
+                <property name="position">1</property>
+              </packing>
+            </child>
+          </object>
+          <packing>
+            <property name="expand">False</property>
+            <property name="fill">True</property>
+            <property name="pack_type">end</property>
+            <property name="position">0</property>
+          </packing>
+        </child>
+        <child>
+          <object class="GtkVBox" id="vbox1_compare_exp">
+            <property name="visible">True</property>
+            <property name="can_focus">False</property>
+            <child>
+              <object class="GtkHBox" id="hbox1_compare_exp">
+                <property name="visible">True</property>
+                <property name="can_focus">False</property>
+                <property name="spacing">15</property>
+                <child>
+                  <object class="GtkLabel" id="comp_exp_filename">
+                    <property name="visible">True</property>
+                    <property name="can_focus">False</property>
+                    <property name="label" translatable="yes">No file loaded</property>
+                  </object>
+                  <packing>
+                    <property name="expand">False</property>
+                    <property name="fill">False</property>
+                    <property name="position">0</property>
+                  </packing>
+                </child>
+                <child>
+                  <object class="GtkButton" id="open_exp_compare">
+                    <property name="label" translatable="yes">Choose file</property>
+                    <property name="visible">True</property>
+                    <property name="can_focus">True</property>
+                    <property name="receives_default">True</property>
+                    <property name="use_action_appearance">False</property>
+                    <signal name="clicked" handler="on_open_exp_compare_clicked" swapped="no"/>
+                  </object>
+                  <packing>
+                    <property name="expand">False</property>
+                    <property name="fill">False</property>
+                    <property name="position">1</property>
+                  </packing>
+                </child>
+              </object>
+              <packing>
+                <property name="expand">False</property>
+                <property name="fill">False</property>
+                <property name="position">0</property>
+              </packing>
+            </child>
+            <child>
+              <object class="GtkFrame" id="frame3">
+                <property name="visible">True</property>
+                <property name="can_focus">False</property>
+                <property name="label_xalign">0</property>
+                <property name="shadow_type">in</property>
+                <child>
+                  <object class="GtkAlignment" id="alignment9">
+                    <property name="visible">True</property>
+                    <property name="can_focus">False</property>
+                    <property name="left_padding">12</property>
+                    <child>
+                      <object class="GtkTable" id="table1_compare_exp">
+                        <property name="visible">True</property>
+                        <property name="can_focus">False</property>
+                        <property name="n_rows">3</property>
+                        <property name="n_columns">2</property>
+                        <child>
+                          <object class="GtkLabel" id="label_experiment">
+                            <property name="visible">True</property>
+                            <property name="can_focus">False</property>
+                            <property name="label" translatable="yes">Experiment</property>
+                          </object>
+                        </child>
+                        <child>
+                          <object class="GtkLabel" id="label19">
+                            <property name="visible">True</property>
+                            <property name="can_focus">False</property>
+                            <property name="label" translatable="yes">label</property>
+                          </object>
+                          <packing>
+                            <property name="left_attach">1</property>
+                            <property name="right_attach">2</property>
+                          </packing>
+                        </child>
+                        <child>
+                          <object class="GtkLabel" id="label_main_filename">
+                            <property name="visible">True</property>
+                            <property name="can_focus">False</property>
+                            <property name="label" translatable="yes">No file loaded</property>
+                          </object>
+                          <packing>
+                            <property name="top_attach">1</property>
+                            <property name="bottom_attach">2</property>
+                          </packing>
+                        </child>
+                        <child>
+                          <object class="GtkLabel" id="label_comp_filename">
+                            <property name="visible">True</property>
+                            <property name="can_focus">False</property>
+                            <property name="label" translatable="yes">No file loaded</property>
+                          </object>
+                          <packing>
+                            <property name="top_attach">2</property>
+                            <property name="bottom_attach">3</property>
+                          </packing>
+                        </child>
+                        <child>
+                          <object class="GtkEntry" id="entry_main_label">
+                            <property name="visible">True</property>
+                            <property name="can_focus">True</property>
+                            <property name="invisible_char">●</property>
+                          </object>
+                          <packing>
+                            <property name="left_attach">1</property>
+                            <property name="right_attach">2</property>
+                            <property name="top_attach">1</property>
+                            <property name="bottom_attach">2</property>
+                          </packing>
+                        </child>
+                        <child>
+                          <object class="GtkEntry" id="entry_comp_label">
+                            <property name="visible">True</property>
+                            <property name="can_focus">True</property>
+                            <property name="invisible_char">●</property>
+                          </object>
+                          <packing>
+                            <property name="left_attach">1</property>
+                            <property name="right_attach">2</property>
+                            <property name="top_attach">2</property>
+                            <property name="bottom_attach">3</property>
+                          </packing>
+                        </child>
+                      </object>
+                    </child>
+                  </object>
+                </child>
+                <child type="label">
+                  <object class="GtkLabel" id="label3">
+                    <property name="visible">True</property>
+                    <property name="can_focus">False</property>
+                    <property name="label" translatable="yes"><b>Legend label</b></property>
+                    <property name="use_markup">True</property>
+                  </object>
+                </child>
+              </object>
+              <packing>
+                <property name="expand">True</property>
+                <property name="fill">True</property>
+                <property name="padding">13</property>
+                <property name="position">1</property>
+              </packing>
+            </child>
+            <child>
+              <object class="GtkHBox" id="hbox2_compare_exp">
+                <property name="visible">True</property>
+                <property name="can_focus">False</property>
+                <property name="spacing">12</property>
+                <child>
+                  <object class="GtkLabel" id="label23">
+                    <property name="visible">True</property>
+                    <property name="can_focus">False</property>
+                    <property name="label" translatable="yes">Plot type :</property>
+                  </object>
+                  <packing>
+                    <property name="expand">False</property>
+                    <property name="fill">False</property>
+                    <property name="position">0</property>
+                  </packing>
+                </child>
+                <child>
+                  <object class="GtkComboBox" id="combo_plot_color_type">
+                    <property name="visible">True</property>
+                    <property name="can_focus">False</property>
+                    <property name="model">list_plot_color_type</property>
+                    <child>
+                      <object class="GtkCellRendererText" id="cellrenderertext1"/>
+                      <attributes>
+                        <attribute name="text">0</attribute>
+                      </attributes>
+                    </child>
+                  </object>
+                  <packing>
+                    <property name="expand">False</property>
+                    <property name="fill">False</property>
+                    <property name="position">1</property>
+                  </packing>
+                </child>
+              </object>
+              <packing>
+                <property name="expand">False</property>
+                <property name="fill">False</property>
+                <property name="position">2</property>
+              </packing>
+            </child>
+          </object>
+          <packing>
+            <property name="expand">False</property>
+            <property name="fill">False</property>
+            <property name="position">1</property>
+          </packing>
+        </child>
+      </object>
+    </child>
+    <action-widgets>
+      <action-widget response="0">button_compare_exp_validate</action-widget>
+      <action-widget response="0">button_compare_exp_cancel</action-widget>
+    </action-widgets>
+  </object>
+  <object class="GtkImage" id="image1">
+    <property name="visible">True</property>
+    <property name="can_focus">False</property>
+    <property name="stock">gtk-missing-image</property>
+  </object>
+  <object class="GtkImage" id="image2">
+    <property name="visible">True</property>
+    <property name="can_focus">False</property>
+    <property name="stock">gtk-zoom-fit</property>
+  </object>
+  <object class="GtkImage" id="image3">
+    <property name="visible">True</property>
+    <property name="can_focus">False</property>
+    <property name="xalign">0.50999999046325684</property>
+    <property name="yalign">0.51999998092651367</property>
+    <property name="pixbuf">../Icon/event.png</property>
+  </object>
+  <object class="GtkImage" id="image4">
+    <property name="visible">True</property>
+    <property name="can_focus">False</property>
+    <property name="xpad">3</property>
+    <property name="pixbuf">../Icon/export_curve.png</property>
+  </object>
+  <object class="GtkImage" id="image5">
+    <property name="visible">True</property>
+    <property name="can_focus">False</property>
+    <property name="pixbuf">../Icon/two_evt.png</property>
+  </object>
+  <object class="GtkListStore" id="list_plot_color_type">
+    <columns>
+      <!-- column-name gchararray1 -->
+      <column type="gchararray"/>
+    </columns>
+    <data>
+      <row>
+        <col id="0" translatable="yes">Color</col>
+      </row>
+      <row>
+        <col id="0" translatable="yes">Black and White</col>
+      </row>
+    </data>
+  </object>
+  <object class="GtkAdjustment" id="spin_hist_rel_dist">
+    <property name="upper">100</property>
+    <property name="step_increment">1</property>
+    <property name="page_increment">10</property>
+  </object>
+</interface>

Added: trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/glade/plot.glade
===================================================================
--- trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/glade/plot.glade	                        (rev 0)
+++ trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/glade/plot.glade	2012-08-20 10:43:48 UTC (rev 12094)
@@ -0,0 +1,104 @@
+<?xml version="1.0"?>
+<interface>
+  <requires lib="gtk+" version="2.16"/>
+  <!-- interface-naming-policy project-wide -->
+  <object class="GtkWindow" id="WindowPlot">
+    <property name="title" translatable="yes">Force Curve</property>
+    <property name="default_width">300</property>
+    <property name="default_height">300</property>
+    <property name="destroy_with_parent">True</property>
+    <property name="icon">../Icon/openfovea.png</property>
+    <child>
+      <object class="GtkVBox" id="vboxPlot">
+        <property name="visible">True</property>
+        <property name="orientation">vertical</property>
+        <child>
+          <object class="GtkHBox" id="hbox9">
+            <property name="visible">True</property>
+            <child>
+              <object class="GtkVBox" id="boxPlot">
+                <property name="visible">True</property>
+                <property name="orientation">vertical</property>
+                <child>
+                  <placeholder/>
+                </child>
+              </object>
+              <packing>
+                <property name="position">0</property>
+              </packing>
+            </child>
+            <child>
+              <object class="GtkVScrollbar" id="scrollbar_depth">
+                <property name="orientation">vertical</property>
+              </object>
+              <packing>
+                <property name="expand">False</property>
+                <property name="fill">False</property>
+                <property name="position">1</property>
+              </packing>
+            </child>
+          </object>
+          <packing>
+            <property name="position">0</property>
+          </packing>
+        </child>
+        <child>
+          <object class="GtkHBox" id="customizeBar">
+            <property name="visible">True</property>
+            <child>
+              <object class="GtkVBox" id="vbox12">
+                <property name="visible">True</property>
+                <property name="orientation">vertical</property>
+                <child>
+                  <object class="GtkHScrollbar" id="scrollbar_max"/>
+                  <packing>
+                    <property name="position">0</property>
+                  </packing>
+                </child>
+                <child>
+                  <object class="GtkHScrollbar" id="scrollbar_min"/>
+                  <packing>
+                    <property name="position">1</property>
+                  </packing>
+                </child>
+              </object>
+              <packing>
+                <property name="position">0</property>
+              </packing>
+            </child>
+            <child>
+              <object class="GtkButton" id="button_modify_plot">
+                <property name="label" translatable="yes">color scale</property>
+                <property name="can_focus">True</property>
+                <property name="receives_default">True</property>
+              </object>
+              <packing>
+                <property name="expand">False</property>
+                <property name="fill">False</property>
+                <property name="position">1</property>
+              </packing>
+            </child>
+          </object>
+          <packing>
+            <property name="expand">False</property>
+            <property name="fill">False</property>
+            <property name="position">1</property>
+          </packing>
+        </child>
+        <child>
+          <object class="GtkHBox" id="box_nav_tool">
+            <property name="visible">True</property>
+            <child>
+              <placeholder/>
+            </child>
+          </object>
+          <packing>
+            <property name="expand">False</property>
+            <property name="fill">False</property>
+            <property name="position">2</property>
+          </packing>
+        </child>
+      </object>
+    </child>
+  </object>
+</interface>

Added: trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/glade/stiffness_plot.glade
===================================================================
--- trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/glade/stiffness_plot.glade	                        (rev 0)
+++ trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/glade/stiffness_plot.glade	2012-08-20 10:43:48 UTC (rev 12094)
@@ -0,0 +1,163 @@
+<?xml version="1.0"?>
+<interface>
+  <requires lib="gtk+" version="2.16"/>
+  <!-- interface-naming-policy project-wide -->
+  <object class="GtkWindow" id="WindowPlot">
+    <property name="default_width">400</property>
+    <property name="default_height">500</property>
+    <child>
+      <object class="GtkVBox" id="vbox1">
+        <property name="visible">True</property>
+        <property name="orientation">vertical</property>
+        <child>
+          <object class="GtkHBox" id="hbox1">
+            <property name="visible">True</property>
+            <child>
+              <object class="GtkHBox" id="hbox13">
+                <property name="visible">True</property>
+                <child>
+                  <object class="GtkLabel" id="label32">
+                    <property name="visible">True</property>
+                    <property name="label" translatable="yes">x slice</property>
+                  </object>
+                  <packing>
+                    <property name="expand">False</property>
+                    <property name="fill">False</property>
+                    <property name="position">0</property>
+                  </packing>
+                </child>
+                <child>
+                  <object class="GtkSpinButton" id="spin_x">
+                    <property name="visible">True</property>
+                    <property name="can_focus">True</property>
+                    <property name="invisible_char">&#x25CF;</property>
+                    <property name="adjustment">adjust_x</property>
+                  </object>
+                  <packing>
+                    <property name="expand">False</property>
+                    <property name="fill">False</property>
+                    <property name="position">1</property>
+                  </packing>
+                </child>
+              </object>
+              <packing>
+                <property name="position">0</property>
+              </packing>
+            </child>
+            <child>
+              <object class="GtkHBox" id="hbox14">
+                <property name="visible">True</property>
+                <child>
+                  <object class="GtkLabel" id="label33">
+                    <property name="visible">True</property>
+                    <property name="label" translatable="yes">y slice</property>
+                  </object>
+                  <packing>
+                    <property name="expand">False</property>
+                    <property name="fill">False</property>
+                    <property name="position">0</property>
+                  </packing>
+                </child>
+                <child>
+                  <object class="GtkSpinButton" id="spin_y">
+                    <property name="visible">True</property>
+                    <property name="can_focus">True</property>
+                    <property name="invisible_char">&#x25CF;</property>
+                    <property name="adjustment">adjust_y</property>
+                  </object>
+                  <packing>
+                    <property name="expand">False</property>
+                    <property name="fill">False</property>
+                    <property name="position">1</property>
+                  </packing>
+                </child>
+              </object>
+              <packing>
+                <property name="position">1</property>
+              </packing>
+            </child>
+            <child>
+              <object class="GtkHBox" id="hbox7">
+                <property name="visible">True</property>
+                <child>
+                  <object class="GtkLabel" id="label31">
+                    <property name="visible">True</property>
+                    <property name="label" translatable="yes">z slice</property>
+                  </object>
+                  <packing>
+                    <property name="expand">False</property>
+                    <property name="fill">False</property>
+                    <property name="position">0</property>
+                  </packing>
+                </child>
+                <child>
+                  <object class="GtkSpinButton" id="spin_z">
+                    <property name="visible">True</property>
+                    <property name="can_focus">True</property>
+                    <property name="invisible_char">&#x25CF;</property>
+                    <property name="adjustment">adjust_z</property>
+                  </object>
+                  <packing>
+                    <property name="expand">False</property>
+                    <property name="fill">False</property>
+                    <property name="position">1</property>
+                  </packing>
+                </child>
+              </object>
+              <packing>
+                <property name="position">2</property>
+              </packing>
+            </child>
+          </object>
+          <packing>
+            <property name="expand">False</property>
+            <property name="fill">False</property>
+            <property name="position">0</property>
+          </packing>
+        </child>
+        <child>
+          <object class="GtkHBox" id="boxPlot">
+            <property name="visible">True</property>
+            <child>
+              <placeholder/>
+            </child>
+          </object>
+          <packing>
+            <property name="position">1</property>
+          </packing>
+        </child>
+        <child>
+          <object class="GtkHScrollbar" id="scrollbar_max"/>
+          <packing>
+            <property name="expand">False</property>
+            <property name="fill">False</property>
+            <property name="position">2</property>
+          </packing>
+        </child>
+        <child>
+          <object class="GtkHScrollbar" id="scrollbar_min"/>
+          <packing>
+            <property name="expand">False</property>
+            <property name="fill">False</property>
+            <property name="position">3</property>
+          </packing>
+        </child>
+      </object>
+    </child>
+  </object>
+  <object class="GtkAdjustment" id="adjust_z">
+    <property name="upper">100</property>
+    <property name="step_increment">1</property>
+    <property name="page_increment">10</property>
+  </object>
+  <object class="GtkAdjustment" id="adjust_x">
+    <property name="upper">100</property>
+    <property name="step_increment">1</property>
+    <property name="page_increment">10</property>
+  </object>
+  <object class="GtkAdjustment" id="adjust_y">
+    <property name="upper">100</property>
+    <property name="step_increment">1</property>
+    <property name="page_increment">10</property>
+  </object>
+</interface>

Added: trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/openfovea_gui.py
===================================================================
--- trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/openfovea_gui.py	                        (rev 0)
+++ trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/openfovea_gui.py	2012-08-20 10:43:48 UTC (rev 12094)
@@ -0,0 +1,2990 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+"""
+    Module for the GTK gui of OpenFovea.
+"""
+
+import gtk
+import os.path
+import sys
+import locale
+import threading
+import time
+import datetime
+from glib import GError
+
+import numpy
+#####################
+## Graphic library ##
+#####################
+import plot_gtk
+# for script installation
+from pkg_resources import resource_filename
+######################
+## Internal library ##
+######################
+from common import APP_NAME, APP_VERSION
+import classes
+from classes import NotReadyError
+from plot_generic import PlotProperties, PlotData
+
+try:
+    from fovea_toolbox.opengl_gtk import TopoWindow as TopoGL
+except ImportError:
+    # OpenGL is not installed.
+    OPENGL_INSTALLED = False
+except RuntimeError:
+    # OpenGL cannot be loaded...
+    OPENGL_INSTALLED = False
+else:
+    OPENGL_INSTALLED = True
+
+import dialog_experiment_properties
+from dialog_export_map import MapDisplay
+from dialog_mask_properties import MaskProperties
+from dialog_flatten import FlattenDialog
+from simple_window_gtk import FileGroup
+from fovea_toolbox import misc
+
+DEBUG = 0
+
+
+def combo_box_set_list(combox, item_list, default=0):
+    """
+    Sets the combobox list
+    """
+    preexist = 0
+    # Reinitialize or create the model
+    model = combox.get_model()
+    if model:
+        model.clear()
+        preexist = 1
+    else:
+        model = gtk.ListStore(str)
+
+    for item in item_list:
+        model.append([item])
+    # Pack it if it doesn't preexist
+    if not preexist:
+        combox.set_model(model)
+        cell = gtk.CellRendererText()
+        combox.pack_start(cell, True)
+        combox.add_attribute(cell, 'text', 0)
+    # And set the first item active
+    combox.set_active(default)
+
+
+class OpenFoveaMainGui(object):
+    """
+        OpenFovea GTK Gui.
+
+        Contains all the buttons and dialog to handle experiment post
+        processing.
+    """
+
+    def __init__(self, arg=None):
+        # Defaults parameters
+        if os.name == 'posix':
+            _home = os.environ['HOME']
+        elif os.name == 'nt':
+            _home = os.environ['HOMEPATH']
+        self.config = {'current': os.getcwd(),
+                          'home': _home,
+                          'config': os.path.join(
+                                            _home,
+                                            '.config',
+                                            'OpenFovea.conf'),
+                          'folder-fv': os.getcwd(),
+                          'folder-aex': os.getcwd(),
+                          'folder-export': os.getcwd(),
+                          'msgid': datetime.datetime(1900, 1, 1),
+                          'linewidth': 1.5,  # The width of the line in the
+                                              # curve plots.
+                          'connect-server': None}
+        self.apply_on_all = 0
+        # try to recover preferences...
+        if os.path.isfile(self.config['config']):
+            config_fid = open(self.config['config'])
+            for line in config_fid.readlines():
+                splitted_line = line.strip('\n').split(' = ')
+                if splitted_line[0] == 'msgid':
+                    self.config[splitted_line[0]] = \
+                        datetime.datetime.strptime(splitted_line[1],
+                                                   '%Y, %m, %d')
+                elif splitted_line[0] == 'linewidth':
+                    self.config[splitted_line[0]] = float(splitted_line[1])
+                elif splitted_line[0] == 'connect-server':
+                    self.config[splitted_line[0]] = eval(splitted_line[1])
+                elif splitted_line[0] in self.config.keys():
+                    self.config[splitted_line[0]] = \
+                                            splitted_line[1]
+            if 'folder-export' not in self.config:
+                self.config['folder-export'] = os.getcwd()
+        # Get authorization for connection
+        if self.config['connect-server'] is None:
+            answer = ask_message(['Allow internet connection ?',
+                    '<b>Do you allow OpenFovea to connect server ?</b>\n\n' +
+                    'The connection is usefull to display message\n' +
+                    'about new release, or important bugs.'])
+            if answer == gtk.RESPONSE_YES:
+                self.config['connect-server'] = True
+            elif answer == gtk.RESPONSE_NO:
+                self.config['connect-server'] = False
+        ###
+        # Get message from the OpenFovea website in order to display news.
+        # This will be used for update announce or important news.
+        if self.config['connect-server']:
+            message, new_id = misc.get_message(self.config['msgid'],
+                                               APP_NAME, APP_VERSION)
+            if message is not None:
+                display_message(message[1:])
+                self.config['msgid'] = new_id
+        ###
+        # Initialize the gui
+        ###
+        builder = gtk.Builder()
+        try:
+            glade_filename = resource_filename('openfovea',
+                                               'glade/openfovea.glade')
+        except NotImplementedError:
+            # We are in a windows executable...
+            glade_filename = os.path.join(os.path.dirname(sys.executable),
+                                          ('openfovea/glade/openfovea.glade'))
+        builder.add_from_file(glade_filename)
+        self.exp_filename = None
+        self.window = builder.get_object("MainWindow")
+        self.about_dialog_win = builder.get_object('aboutdialog')
+        self.about_dialog = builder.get_object("aboutdialog")
+        self.properties_dialog = None
+        self.compare_exp_dialog = \
+                            builder.get_object('dialog_compare_experiment')
+        # connect signals
+        builder.connect_signals(self)
+        ## The variables
+        self.plot_properties = PlotProperties()
+        self.plot_properties.color_type = 'color'
+        self.data_hist = PlotData()
+        self.experiment = None
+        self.temp_exp_compare = None
+        self.experiment_compare = None
+        self.force_volume = None
+        self.widget = {
+            'progressbar': builder.get_object("progressbar_general"),
+            'check_display_fc_trace': builder.get_object(
+                                                'check_display_fc_trace'),
+            'check_display_fc_retrace': builder.get_object(
+                                                'check_display_fc_retrace'),
+            'check_display_poc': builder.get_object(
+                                                'check_display_poc'),
+            'check_display_indent': builder.get_object(
+                                                'check_display_indent'),
+            'check_display_event': builder.get_object(
+                                                'check_display_event'),
+            'check_limit_poc_slide': builder.get_object(
+                                                'check_limit_poc_slide'),
+            'check_compute_poc': builder.get_object('check_compute_poc'),
+            'check_stiff_ev_vs_notev': builder.get_object(
+                                                'check_stiff_ev_vs_notev'),
+            'combo_list_files': builder.get_object('list_file_combo_box'),
+            'combo_hertz_model': builder.get_object('combo_hertz_model'),
+            'combo_stiff_method': builder.get_object('combo_stiff_method'),
+            'combo_event_detect': builder.get_object('combo_event_detect'),
+            'combo_event_thresh': builder.get_object('combo_event_thresh'),
+            'combo_poc_method': builder.get_object('combo_poc_method'),
+            'combo_ev_fit_model': builder.get_object(
+                                                    'combo_ev_fit_model'),
+            'entry_number_deep': builder.get_object("entry_number_deep"),
+            'entry_size_deep': builder.get_object('entry_size_deep'),
+            'entry_glass_slope': builder.get_object('entry_glass_slope'),
+            'label_pos_x': builder.get_object('label_pos_x'),
+            'label_pos_y': builder.get_object('label_pos_y'),
+            'label_switch_state': builder.get_object('label_switch_state'),
+            'spin_ev_force_hist_min': builder.get_object('ev_force_hist_min'),
+            'spin_ev_force_hist_max': builder.get_object('ev_force_hist_max'),
+            'spin_ev_force_hist_size': builder.get_object(
+                                                    'ev_force_hist_size'),
+            'spin_max_rel_stiffness': builder.get_object('max_rel_stiffness'),
+            'spin_ev_lr_hist_min': builder.get_object('ev_lr_hist_min'),
+            'spin_ev_lr_hist_max': builder.get_object('ev_lr_hist_max'),
+            'spin_ev_lr_hist_size': builder.get_object('ev_lr_hist_size'),
+            'spin_ev_dist_hist_min': builder.get_object('ev_dist_hist_min'),
+            'spin_ev_dist_hist_max': builder.get_object('ev_dist_hist_max'),
+            'spin_ev_dist_hist_size': builder.get_object('ev_dist_hist_size'),
+            'spin_ev_length_hist_min': builder.get_object(
+                                                'ev_length_hist_min'),
+            'spin_ev_length_hist_max': builder.get_object(
+                                                'ev_length_hist_max'),
+            'spin_ev_length_hist_size': builder.get_object(
+                                                'ev_length_hist_size'),
+            'spin_ev_plength_hist_min': builder.get_object(
+                                                'ev_plength_hist_min'),
+            'spin_ev_plength_hist_max': builder.get_object(
+                                                'ev_plength_hist_max'),
+            'spin_ev_plength_hist_size': builder.get_object(
+                                                'ev_plength_hist_size'),
+            'spin_ev_stiff_hist_min': builder.get_object('ev_stiff_hist_min'),
+            'spin_ev_stiff_hist_max': builder.get_object('ev_stiff_hist_max'),
+            'spin_ev_stiff_hist_size': builder.get_object(
+                                                'ev_stiff_hist_size'),
+            'spin_ev_relstiff_hist_min': builder.get_object(
+                                                'ev_relstiff_hist_min'),
+            'spin_ev_relstiff_hist_max': builder.get_object(
+                                                'ev_relstiff_hist_max'),
+            'spin_ev_relstiff_hist_size': builder.get_object(
+                                                'ev_relstiff_hist_size'),
+            'spin_ev_relstiff_hist_dist': builder.get_object(
+                                                'ev_relstiff_hist_dist'),
+            'spin_rel_stiff_plot_dist': builder.get_object(
+                                                'spin_rel_stiff_plot_dist'),
+            'spin_nbr_rand_event': builder.get_object('spin_nbr_rand_event'),
+            'spin_ev_threshold_dist': builder.get_object(
+                                                'spin_ev_threshold_dist'),
+            'spin_poisson_ratio': builder.get_object('spin_poisson_ratio'),
+            # Option menu
+            'apply_on_all': builder.get_object('apply_on_all'),
+            # Parameters tab
+            'spin_fit_seg_size': builder.get_object('spin_fit_seg_size'),
+            'spin_ev_length_thresh_min': builder.get_object(
+                                                'spin_ev_length_thresh_min'),
+            'spin_ev_length_thresh_max': builder.get_object(
+                                                'spin_ev_length_thresh_max'),
+            # Mechanical prop.
+            'spin_young_modulus_hist_min': builder.get_object(
+                                                'spin_ym_hist_min'),
+            'spin_young_modulus_hist_max': builder.get_object(
+                                                'spin_ym_hist_max'),
+            'spin_young_modulus_hist_size': builder.get_object(
+                                                'spin_ym_hist_size'),
+            'spin_tip_carac': builder.get_object('spin_carac'),
+            'spin_ym_hist_depth_nb': builder.get_object(
+                                                'spin_ym_hist_depth_nb'),
+            }
+        self.signal = {
+            ### Dictionnary that contains the signal from the object.
+            ### This is auto - generated with :
+            ### widgetname_fctname
+        }
+        self.widget_exp_compare = {
+            'comp_exp_filename': builder.get_object('comp_exp_filename'),
+            'label_main_filename': builder.get_object('label_main_filename'),
+            'label_comp_filename': builder.get_object('label_comp_filename'),
+            'entry_main_label': builder.get_object('entry_main_label'),
+            'entry_comp_label': builder.get_object('entry_comp_label'),
+            'combo_plot_color_type': builder.get_object(
+                                                'combo_plot_color_type'),
+        }
+        if not OPENGL_INSTALLED:
+            builder.get_object('button_opengl').hide()
+        #####
+        ## Compute tab
+        #####
+        combo_box_set_list(self.widget['combo_event_detect'],
+                            ['Noise', 'Fuzzy'])
+        combo_box_set_list(self.widget['combo_event_thresh'],
+                            ['Fixed', 'Auto (Noise)'])
+        #####
+        ## Parameter tab
+        #####
+        combo_box_set_list(self.widget['combo_poc_method'],
+                           ['deriv', 'curve_fit'])
+        self.widget['combo_poc_method'].set_active(1)
+
+        adjustment = gtk.Adjustment(value=0, lower=0, upper=1000,
+                                    step_incr=1, page_incr=10, page_size=0)
+        self.widget['spin_ev_threshold_dist'].set_adjustment(adjustment)
+
+        adjustment = gtk.Adjustment(value=0, lower=0, upper=2000,
+                                    step_incr=1, page_incr=10, page_size=0)
+        self.widget['spin_ev_length_thresh_min'].set_adjustment(adjustment)
+
+        adjustment = gtk.Adjustment(value=0, lower=0, upper=1000,
+                                    step_incr=1, page_incr=10, page_size=0)
+        self.widget['spin_ev_length_thresh_max'].set_adjustment(adjustment)
+
+        combo_box_set_list(self.widget['combo_hertz_model'],
+                           ['Cone', 'Sphere'])
+        combo_box_set_list(self.widget['combo_stiff_method'],
+                           ['Raw', 'Linear', 'Extrema', 'Median'])
+        self.widget['combo_hertz_model'].set_active(1)
+        self.widget['combo_stiff_method'].set_active(0)
+        self.widget['spin_tip_carac'].set_value(40)
+        self.widget['spin_poisson_ratio'].set_value(0.3)
+        combo_box_set_list(self.widget['combo_ev_fit_model'],
+                                                    ['None', 'wlc', 'fjc'])
+        #####
+        ## Event tab
+        #####
+
+        # The windows used for the plots
+        self.win_plot = {'Curve Plot': 0,
+                    'Indent Plot': 0,
+                    'Topography Map': 0,
+                    'Piezo Height': 0,
+                    'Stiffness Map': 0,
+                    'Event Map': 0,
+                    'Event Force Map': 0,
+                    'Event Distance Map': 0,
+                    'Event Length Map': 0,
+                    'Stiffness Tomo': 0,
+                    'Average Stiffness Tomo': 0,
+                    'Mosaic Piezo': 0,
+                    'Mosaic Topo': 0,
+                    'Mosaic Stiffness': 0,
+                    'Mosaic Event': 0,
+                    'Mosaic Event Force': 0,
+                    'Hist Event Force': 0,
+                    'Hist Event LR': 0,
+                    'Hist Event Dist': 0,
+                    'Hist Event Stiff': 0,
+                    'Hist Event Rel Stiff': 0,
+                    'Hist Event Length': 0,
+                    'Hist Event Persistent Length': 0,
+                    'TL Rel Stiffness': 0,
+                    'TL Nbr Event': 0,
+                    'Scatter_FvsLR': 0,
+                    'Scatter_FvsDist': 0,
+                    'Scatter_FvsStiff': 0,
+                    'Scatter_LRvsDist': 0,
+                    'Scatter_LRvsStiff': 0,
+                    'Scatter_DistvsStiff': 0,
+                    'Scatter_FvsRelStiff': 0,
+                    'Scatter_LRvsRelStiff': 0,
+                    'Scatter_DistvsRelStiff': 0,
+                    'Slice_on_map': 0,
+                    'Hist Young Modulus': 0,
+                    }
+        if arg is not None:
+            self.on_open_experiment_activate(arg)
+    ##########################################################################
+    # Misc part of the window
+
+    # bottom
+    def display_progressbar(self, fraction, text=''):
+        """
+            Display the progress bar.
+        """
+        if fraction == None:
+            self.widget['progressbar'].set_property('visible', True)
+            self.widget['progressbar'].set_fraction(0)
+            self.widget['progressbar'].set_text('')
+        elif type(fraction) != str:
+            while gtk.events_pending():
+                gtk.main_iteration()
+            if not self.widget['progressbar'].get_property('visible'):
+                self.widget['progressbar'].set_property('visible', True)
+            self.widget['progressbar'].set_fraction(fraction)
+            self.widget['progressbar'].set_text(text)
+            self.widget['progressbar'].show()
+        elif fraction == 'pulse':
+            while gtk.events_pending():
+                gtk.main_iteration()
+            self.widget['progressbar'].pulse()
+            self.widget['progressbar'].set_text(text)
+            self.widget['progressbar'].show()
+
+    def update_switch(self):
+        """
+            Update switches in the lower part of the GUI.
+        """
+        # generate the text
+        text = ''
+        _fvid = self.experiment.file['current']
+        for key in self.experiment.switch_dict:
+            text += key + ' : ' + str(self.experiment.get_switch(key)) + ' | '
+        self.widget['label_switch_state'].set_text(text)
+        _thresh = self.experiment.file['list'][_fvid].get_switch('ev_thresh')
+        self.widget['spin_ev_threshold_dist'].set_value(_thresh)
+        self.widget['spin_poisson_ratio'].set_value(
+           self.experiment.file['list'][_fvid].get_parameter('poisson_ratio'))
+        _thresh = self.experiment.file['list'][_fvid].get_switch(
+                                                            'ev_fit_length')
+        if _thresh[0] is not None:
+            self.widget['spin_ev_length_thresh_max'].set_value(_thresh[0])
+        else:
+            self.widget['spin_ev_length_thresh_max'].set_value(0)
+        if _thresh[1] is not None:
+            self.widget['spin_ev_length_thresh_max'].set_value(_thresh[1])
+        else:
+            self.widget['spin_ev_length_thresh_max'].set_value(0)
+
+    def update_hist(self, label, max_val, min_val=0):
+        """
+            Update the histogram properties.
+        """
+        meth_name = 'on_button_%s_clicked' % label
+        # First disconnect the signal from the widget. Otherwise, it will plot
+        # automatically. This is not wanted in case of loading new files, ...
+        for item in ['min', 'max', 'size']:
+            widget_name = 'spin_%s_%s' % (label, item)
+            signal_name = '%s_min_%s' % (widget_name, meth_name)
+            if signal_name in self.signal:
+                self.widget[widget_name].disconnect(self.signal[signal_name])
+        widget_name = 'spin_%s_max' % label
+        self.widget[widget_name].set_adjustment(
+                        gtk.Adjustment(value=max_val,
+                                       lower=min_val,
+                                       upper=max_val * 10,
+                                       step_incr=max_val / 100,
+                                       page_incr=max_val / 25,
+                                       page_size=0))
+        self.widget[widget_name].set_text(str(max_val))
+
+        widget_name = 'spin_%s_min' % label
+        self.widget[widget_name].set_adjustment(
+                        gtk.Adjustment(value=min_val,
+                                       lower=min_val,
+                                       upper=max_val,
+                                       step_incr=max_val / 100,
+                                       page_incr=max_val / 25,
+                                       page_size=0))
+        self.widget[widget_name].set_text(str(min_val))
+
+        widget_name = 'spin_%s_size' % label
+        self.widget[widget_name].set_adjustment(
+                        gtk.Adjustment(value=max_val / 10,
+                                       lower=0,
+                                       upper=max_val,
+                                       step_incr=max_val / 1000,
+                                       page_incr=max_val / 250,
+                                       page_size=0))
+        self.widget[widget_name].set_text(str(max_val / 10))
+        meth = getattr(self, meth_name)
+        # Last : connect signal from the spins
+        for item in ['min', 'max', 'size']:
+            widget_name = 'spin_%s_%s' % (label, item)
+            signal_name = '%s_min_%s' % (widget_name, meth_name)
+            self.signal[signal_name] = \
+                    self.widget[widget_name].connect('value_changed', meth)
+
+    def update(self, what):
+        """
+            Update the GUI.
+        """
+        if what == 'show gride position':
+            self.widget['label_pos_x'].set_text(str(self.force_volume.pos_x))
+            self.widget['label_pos_y'].set_text(str(self.force_volume.pos_y))
+            try:
+                self.win_plot['Piezo Height'].mark_pos(
+                                                self.force_volume.pos_x,
+                                                self.force_volume.pos_y)
+            except (KeyError, StandardError):
+                pass
+            try:
+                self.win_plot['Stiffness Map'].mark_pos(
+                                                self.force_volume.pos_x,
+                                                self.force_volume.pos_y)
+            except (KeyError, StandardError):
+                pass
+            try:
+                self.win_plot['Event Map'].mark_pos(
+                                                self.force_volume.pos_x,
+                                                self.force_volume.pos_y)
+            except (KeyError, StandardError):
+                pass
+            try:
+                self.win_plot['Topography Map'].mark_pos(
+                                                self.force_volume.pos_x,
+                                                self.force_volume.pos_y)
+            except (KeyError, StandardError):
+                pass
+        elif what == 'show glass slope':
+            self.widget['entry_glass_slope'].set_text(
+                                    str(self.force_volume.stiffness['glass']))
+        elif what == 'gui':
+            if self.force_volume is None:
+                return
+            self.widget['spin_max_rel_stiffness'].set_value(
+                                self.experiment.parameters['rel_stiff_dist'])
+            self.widget['entry_number_deep'].set_text(
+                                str(self.force_volume.stiffness['nb_parts']))
+            self.widget['entry_size_deep'].set_text(
+                                str(self.force_volume.stiffness['size_parts']))
+            self.widget['spin_nbr_rand_event'].set_value(
+                                self.force_volume.event['nbr_random'])
+            self.widget['spin_fit_seg_size'].set_value(
+                                self.force_volume.stiffness['poc_len_slice'])
+            if self.force_volume.stiffness['hertz_model'] == 'Cone':
+                self.widget['combo_hertz_model'].set_active(0)
+            elif self.force_volume.stiffness['hertz_model'] == 'Sphere':
+                self.widget['combo_hertz_model'].set_active(1)
+            if self.force_volume.stiffness['fit_method'] == 'Raw':
+                self.widget['combo_stiff_method'].set_active(0)
+            elif self.force_volume.stiffness['fit_method'] == 'Linear':
+                self.widget['combo_stiff_method'].set_active(1)
+            elif self.force_volume.stiffness['fit_method'] == 'Extrema':
+                self.widget['combo_stiff_method'].set_active(2)
+            elif self.force_volume.stiffness['fit_method'] == 'Median':
+                self.widget['combo_stiff_method'].set_active(3)
+            self.widget['spin_tip_carac'].set_value(
+                                self.force_volume.stiffness['point_carac'])
+            if self.force_volume.header['event_fit_model'] == None:
+                self.widget['combo_ev_fit_model'].set_active(0)
+            elif self.force_volume.header['event_fit_model'] == 'wlc':
+                self.widget['combo_ev_fit_model'].set_active(1)
+            elif self.force_volume.header['event_fit_model'] == 'fjc':
+                self.widget['combo_ev_fit_model'].set_active(2)
+
+            # Update switch apply_on_all.
+            if self.experiment.get_switch('all') == 'Yes':
+                self.widget['apply_on_all'].set_active(True)
+            elif self.experiment.get_switch('all') == 'No':
+                self.widget['apply_on_all'].set_active(False)
+            self.update('hist entry')
+        elif what == 'hist entry':
+            ##
+            ## Histograms
+            ##
+            try:
+                max_dist_hist = self.force_volume.trace_x[-1]
+            except TypeError:
+                max_dist_hist = 10000
+            self.update_hist('ev_force_hist', max_val=1.)
+            self.update_hist('ev_lr_hist', max_val=1.)
+
+            self.update_hist('ev_dist_hist',
+                             max_val=max_dist_hist)
+            self.update_hist('ev_relstiff_hist', max_val=10., min_val=-10.)
+            # Take the maximum stiffness
+            stiff_max = 1.e8
+            exp = 7
+            for fvo in self.experiment.file['list']:
+                if fvo.get_array('Stiffness') is not None:
+                    try:
+                        stiff_max = fvo.get_array('Stiffness').max()
+                    except ValueError:
+                        pass
+            if stiff_max:
+                try:
+                    exp = int(numpy.log10(stiff_max)) + 1
+                except ValueError:
+                    exp = 7
+            else:
+                exp = 7
+            self.update_hist('ev_stiff_hist', max_val=10. ** exp)
+            self.update_hist('young_modulus_hist', max_val=10. ** exp)
+            self.update_hist('ev_length_hist',
+                             max_val=max_dist_hist * 2)
+            self.update_hist('ev_plength_hist',
+                             max_val=max_dist_hist * 2)
+            #fvo.get_array('Stiffness').shape[2]
+            # update max depth in for the plot.
+            spin_depth = ['spin_ym_hist_depth_nb']
+            meth_name = 'on_button_young_modulus_hist_clicked'
+            if fvo.get_array('Stiffness') is not None:
+                for item in spin_depth:
+                    # disconnect the widget from the signal
+                    signal_name = '%s_min_%s' % (meth_name, item)
+                    if signal_name in self.signal:
+                        self.widget[item].disconnect(self.signal[signal_name])
+                    self.widget[item].set_adjustment(
+                        gtk.Adjustment(
+                                value=0,
+                                lower=0,
+                                upper=fvo.get_array('Stiffness').shape[2],
+                                step_incr=1,
+                                page_incr=1,
+                                page_size=0))
+                    # and reconnect it
+                    meth = getattr(self, meth_name)
+                    # Last : connect signal from the spins
+                    self.signal[signal_name] = \
+                            self.widget[item].connect('value_changed', meth)
+
+        elif what == 'fv display prop':
+            self.force_volume.plot_who['Av'] = \
+                           self.widget['check_display_fc_trace'].get_active()
+            self.force_volume.plot_who['Re'] = \
+                           self.widget['check_display_fc_retrace'].get_active()
+            self.force_volume.plot_who['PoC'] = \
+                           self.widget['check_display_poc'].get_active()
+            self.force_volume.plot_who['Event'] = \
+                           self.widget['check_display_event'].get_active()
+            self.force_volume.plot_who['Indent'] = \
+                           self.widget['check_display_indent'].get_active()
+        elif what == 'plots':
+            for item in self.win_plot:
+                if self.win_plot[item]:
+                    self.win_plot[item].set_size(
+                                    self.experiment.parameters['plot_size'][0],
+                                    self.experiment.parameters['plot_size'][1])
+                    if self.win_plot[item].get_type() == 'histogram':
+                        self.win_plot[item].set_y_rel(
+                                    self.experiment.parameters['histo_y_rel'])
+
+        self.update_switch()
+
+    def regenerate_plot(self, ptype='normal'):
+        """
+            Regenerate a window plot and returns the window and widgets.
+        """
+        builder = gtk.Builder()
+        if ptype == 'normal':
+            try:
+                _glade_filename = resource_filename('openfovea',
+                                                    'glade/plot.glade')
+            except NotImplementedError:
+                _glade_filename = 'openfovea/glade/plot.glade'
+        elif ptype == 'tomography':
+            try:
+                _glade_filename = resource_filename('openfovea',
+                                                'glade/stiffness_plot.glade')
+            except NotImplementedError:
+                _glade_filename = 'openfovea/glade/stiffness_plot.glade'
+        try:
+            builder.add_from_file(_glade_filename)
+        except:  # In windows environment...
+            print ptype
+            if ptype == 'tomography':
+                glade_filename = os.path.join(os.path.dirname(sys.executable),
+                                        'openfovea/glade/stiffness_plot.glade')
+            elif ptype == 'normal':
+                glade_filename = os.path.join(os.path.dirname(sys.executable),
+                                        'openfovea/glade/plot.glade')
+            else:
+                glade_filename = os.path.join(os.path.dirname(sys.executable),
+                                        'openfovea/glade/plot.glade')
+            builder.add_from_file(glade_filename)
+        window = builder.get_object("WindowPlot")
+        builder.connect_signals(self)
+        if ptype == 'normal':
+            widget = {
+            'plot_area': builder.get_object('boxPlot'),
+            'scrollbar_min': builder.get_object('scrollbar_min'),
+            'scrollbar_max': builder.get_object('scrollbar_max'),
+            'scrollbar_depth': builder.get_object('scrollbar_depth'),
+            'box_nav_tool': builder.get_object('box_nav_tool'),
+            'button_modify_plot': builder.get_object('button_modify_plot')}
+        elif ptype == 'tomography':
+            widget = {
+            'plot_area': builder.get_object('boxPlot'),
+            'display_x': builder.get_object('display_x'),
+            'display_y': builder.get_object('display_y'),
+            'display_z': builder.get_object('display_z'),
+            'adjust_x': builder.get_object('adjust_x'),
+            'adjust_y': builder.get_object('adjust_y'),
+            'adjust_z': builder.get_object('adjust_z'),
+            'scrollbar_min': builder.get_object('scrollbar_min'),
+            'scrollbar_max': builder.get_object('scrollbar_max')}
+        return [window, widget]
+
+    def modify_window(self, window, how):
+        """
+            Modify the specified window.
+
+            window = 'Curve Plot' : add the scale bars to modify the events /
+                                    PoC detection threshold.
+        """
+
+        # Curve Plot window modification to tune the event detection
+        if window == 'Curve Plot':
+            if how == 'Event detection':
+                self.win_plot['Curve Plot'].widget['scrollbar_max'].\
+                            set_property('visible', True)
+                self.win_plot['Curve Plot'].widget['scrollbar_max'].\
+                            set_adjustment(gtk.Adjustment(
+                               self.force_volume.header['event_detect_weight'],
+                               0.0, 5, 0.1, 0.5, 0))
+                self.win_plot['Curve Plot'].widget['scrollbar_max'].\
+                            connect_object("change-value",
+                                            self.change_event_weight, None)
+            if how == 'PoC detection':
+                self.win_plot['Curve Plot'].widget['scrollbar_depth'].\
+                            set_property('visible', True)
+                self.win_plot['Curve Plot'].widget['scrollbar_depth'].\
+                            set_adjustment(gtk.Adjustment(
+                                self.force_volume.stiffness['poc_threshold'],
+                                0.0, 10, 0.1, 0.5, 0))
+                self.win_plot['Curve Plot'].widget['scrollbar_depth'].\
+                            connect_object("change-value",
+                                            self.change_poc_threshold, None)
+
+    def close_all_windows(self):
+        """
+            Close all the plot windows.
+            Usefull when loading new experiment.
+        """
+        for window in self.win_plot:
+            if exist(self.win_plot[window]):
+                self.win_plot[window].on_win_plot_destroy('from_gui')
+
+    def on_gride_click(self, event):
+        """
+            Event when user click on the array.
+        """
+        if event.inaxes is not None:
+            # Create the factor (1 if [0;1000[, 1000 if [1000:1e6[, ...)
+            scan_size = self.force_volume.header['scan_size']
+            pix_size = self.force_volume.header['pixel_size']
+            factor = [1000 ** (int(numpy.log10(i) / 3)) for i in scan_size]
+            x_pos = event.xdata * factor[0] / pix_size[0]
+            y_pos = event.ydata * factor[1] / pix_size[1]
+            if event.button == 1:
+                # Left mouse button ==> goto
+                self.force_volume.go_to(int(x_pos), int(y_pos))
+                self.plot_curve()
+                self.update('show gride position')
+            elif event.button == 3:
+                # Right mouse button ==> slice
+                self.path_gride(event.inaxes)
+
+    def on_gride_motion(self, event):
+        """
+            Event when mouse is moving on the array.
+        """
+        if event.inaxes is not None:
+            self.path_gride(event.inaxes)
+
+    def path_gride(self, axe_id):
+        """
+            Slice the array.
+        """
+        path = None
+        for item in self.win_plot:
+            # Find the window where user click
+            if self.win_plot[item]:
+                _axis = self.win_plot[item].axis
+                if type(_axis) == dict and 'array' in _axis:
+                    if _axis['array'] == axe_id:
+                        path = self.win_plot[item].get_path()
+
+        if path is not None:
+            # Points list is defined.
+            this_slice = self.force_volume.get_path('all', path)
+
+            if not exist(self.win_plot['Slice_on_map']):
+                window, widget = self.regenerate_plot()
+                self.win_plot['Slice_on_map'] = plot_gtk.plotInteractiveCurve(
+                                            window, widget, win_title='Slices')
+                                        #xlabel = '[nm]',
+                                        #ylabel = '???',
+                                        #title = 'Slice of...',
+                                        #win_title = 'Slice of...')
+                self.win_plot['Slice_on_map'].plot(this_slice[0],
+                                                     this_slice[1],
+                                                     this_slice[2])
+            else:
+                self.win_plot['Slice_on_map'].modify_plot(this_slice[0],
+                                                            this_slice[1])
+
+    def on_mosaic_click(self, event):
+        """
+            Change the current FV scan by clicking on the corresponding scan in
+            the mosaic view.
+        """
+        for item in self.win_plot:
+            if isinstance(self.win_plot[item], plot_gtk.plotMosaic):
+                if self.win_plot[item].axis.count(event.inaxes):
+                    _index = self.win_plot[item].axis.index(event.inaxes)
+                    self.force_volume = self.experiment.get_file(_index)
+                    self.update('fv display prop')
+                    self.update('gui')
+                    self.widget['combo_list_files'].set_active(_index)
+
+    def on_mosaic_pick(self, event):
+        """
+            Change the corresponding scan state according to the picked object.
+            For example, by clicking on the "M" box, it changes the mask state.
+        """
+        for item in self.win_plot:
+            if isinstance(self.win_plot[item], plot_gtk.plotMosaic):
+                if self.win_plot[item].axis.count(event.mouseevent.inaxes):
+                    [axis, otype] = self.win_plot[item].index(event)
+                    if otype == 'mask':
+                        current = \
+                          self.experiment.file['list'][axis].get_switch('mask')
+                        self.experiment.file['list'][axis].set_switch('mask',
+                                                                not(current))
+
+    def change_event_weight(self, widget, jump, value):
+        """
+            Change the event detection dependency to noise. Done with the scale
+            bar.
+        """
+
+        if DEBUG:
+            print "Changing event weight..."
+            print widget, jump
+        self.experiment.parameters['event_detect_weight'] = value
+        self.plot_curve()
+
+    def change_poc_threshold(self, widget, jump, value):
+        """
+            Change the point of contact detection threshold. Done with the
+            scale bar.
+        """
+
+        if DEBUG:
+            print "Changing poc threshold..."
+            print widget, jump
+        self.experiment.PoC_threshold = value
+        self.plot_curve()
+
+    #############################################################
+    ## File Menu
+    def on_new_experiment_activate(self, widget):
+        '''
+            Creates a new experiment by asking the user to point where the AFM
+            files are.
+        '''
+        if DEBUG:
+            print "Make new experiment. Call from :"
+            print widget
+        # Call the file chooser dialog.
+        # In order to open directory, change action in
+        # gtk.FILE_CHOOSER_ACTION_SELECT_FOLDER
+        chooser = gtk.FileChooserDialog(
+                                title='Choose folder',
+                                action=gtk.FILE_CHOOSER_ACTION_SELECT_FOLDER,
+                                buttons=(gtk.STOCK_CANCEL,
+                                         gtk.RESPONSE_CANCEL,
+                                         gtk.STOCK_OPEN,
+                                         gtk.RESPONSE_OK))
+        chooser.set_select_multiple(False)
+        chooser.set_default_response(gtk.RESPONSE_OK)
+        chooser.set_local_only(False)
+        chooser.set_filename(self.config['folder-fv'])
+        response = chooser.run()
+        # Analyse the answer
+        if response == gtk.RESPONSE_OK:
+            folder = u'' + chooser.get_filenames()[0]
+        elif response == gtk.RESPONSE_CANCEL:
+            chooser.destroy()
+            return
+        else:
+            return
+
+        chooser.destroy()
+        self.experiment = classes.FVFolder()
+        _thread = threading.Thread(
+                            target=self.experiment.load_folder, args=(folder,))
+        _thread.start()
+        while _thread.isAlive():
+            self.display_progressbar(self.experiment.counter['num'],
+                                     self.experiment.counter['text'])
+            time.sleep(0.1)
+        self.force_volume = self.experiment.get_file(0)
+        # File was correctly loaded, saving the folder in preferences...
+        self.config['folder-fv'] = folder
+        self.exp_filename = None
+        # update file list comboBox...
+        combo_box_set_list(self.widget['combo_list_files'],
+                           self.experiment.file['name'])
+        #self.update('gui')
+        self.display_progressbar(None)
+        self.close_all_windows()
+
+    def load_exp(self):
+        '''
+            Loads an aex file. This is the generic function.
+        '''
+        # Call FileChooser dialog...
+        chooser = gtk.FileChooserDialog(title='Choose file to open',
+                                        action=gtk.FILE_CHOOSER_ACTION_OPEN,
+                                        buttons=(gtk.STOCK_CANCEL,
+                                                  gtk.RESPONSE_CANCEL,
+                                                  gtk.STOCK_OPEN,
+                                                  gtk.RESPONSE_OK))
+        chooser.set_select_multiple(False)
+        chooser.set_default_response(gtk.RESPONSE_OK)
+        chooser.set_local_only(False)
+        chooser.set_current_folder(self.config['folder-aex'])
+        ext_filter = gtk.FileFilter()
+        ext_filter.add_pattern('*.aex')
+        ext_filter.set_name('aex - Afm Experiment XML')
+        chooser.add_filter(ext_filter)
+        response = chooser.run()
+        # Analyse output:
+        if response == gtk.RESPONSE_OK:
+            file_item = u'' + chooser.get_filenames()[0]
+        elif response == gtk.RESPONSE_CANCEL:
+            chooser.destroy()
+            return
+        else:
+            chooser.destroy()
+            return
+        chooser.destroy()
+        experiment = self.__load_exp(file_item)
+        return experiment
+
+    def __load_exp(self, file_item):
+        experiment = classes.FVFolder()
+        _thread = threading.Thread(target=experiment.load_aex,
+                                   args=(file_item, ))
+        _thread.start()
+        self.display_progressbar('pulse')
+        while _thread.isAlive():
+            self.display_progressbar('pulse', experiment.counter['text'])
+            time.sleep(0.1)
+        # File was correctly loaded, saving the folder in preferences...
+        self.config['folder-aex'] = os.path.split(file_item)[0]
+        experiment.counter['num'] = 0  # reset the counter
+        self.display_progressbar(None)
+        return experiment
+
+    def on_open_experiment_activate(self, arg):
+        """
+             Load experiment.
+        """
+
+        if DEBUG:
+            print "Open experiment. Call from :"
+            print arg
+        if type(arg) in [str, unicode]:
+            _experiment = self.__load_exp(arg)
+        else:
+            _experiment = self.load_exp()
+        if _experiment is not None:
+            # If smth is loaded, get it into memory. Else, keep the same.
+            self.experiment = _experiment
+            self.window.set_title(("%s : %s") % (WIN_TITLE,
+                                               self.experiment.short_name))
+            self.force_volume = self.experiment.get_file(0)
+            self.exp_filename = self.experiment.filename
+            # update file list comboBox...
+            combo_box_set_list(self.widget['combo_list_files'],
+                               self.experiment.file['name'])
+            self.update('gui')
+            self.update('hist entry')
+            self.update_switch()
+            self.close_all_windows()
+
+    def on_open_exp_compare_activated(self, widget):
+        """
+            Load experiment for comparison.
+        """
+
+        if DEBUG:
+            print "Make experiment to compare. Call from :"
+            print widget
+        self.experiment_compare = self.load_exp()
+
+    def on_save_experiment_as_activate(self, widget):
+        '''
+        Saves data and results in an aex file.
+        '''
+        if DEBUG:
+            print "Save experiment. Call from :"
+            print widget
+        chooser = gtk.FileChooserDialog(title='Save file to ...',
+                                        action=gtk.FILE_CHOOSER_ACTION_SAVE,
+                                        buttons=(gtk.STOCK_CANCEL,
+                                                  gtk.RESPONSE_CANCEL,
+                                                  gtk.STOCK_SAVE,
+                                                  gtk.RESPONSE_OK))
+        chooser.set_default_response(gtk.RESPONSE_OK)
+        chooser.set_local_only(False)
+        chooser.set_current_folder(self.config['folder-aex'])
+        response = chooser.run()
+        # Analyse output:
+        if response == gtk.RESPONSE_OK:
+            self.exp_filename = u'' + chooser.get_filenames()[0]
+        else:
+            chooser.destroy()
+            return
+        chooser.destroy()
+        self.save_exp()
+
+        self.window.set_title(("%s : %s") % (WIN_TITLE,
+                                             self.experiment.short_name))
+
+    def on_save_experiment_activate(self, widget):
+        """
+            Save the experiment.
+        """
+
+        if self.exp_filename is not None and os.path.isfile(self.exp_filename):
+            self.save_exp()
+        else:
+            self.on_save_experiment_as_activate(widget)
+
+    def save_exp(self):
+        """
+            Save the experiment.
+        """
+        #self.experiment.save(file_item)
+        _thread = threading.Thread(target=self.experiment.save,
+                                   args=(self.exp_filename, ))
+        _thread.start()
+        self.display_progressbar('pulse')
+        while _thread.isAlive():
+            self.display_progressbar('pulse', self.experiment.counter['text'])
+            time.sleep(0.1)
+        # File was correctly saved. Saving the folder in preferences...
+        self.config['folder-aex'] = os.path.split(self.exp_filename)[0]
+        self.experiment.counter['num'] = 0
+        self.display_progressbar(None)
+
+    def on_menu_export_stiffness_activate(self, widget):
+        """
+            Export the computed stiffness on a csv file
+        """
+        if DEBUG:
+            print "Export stiffness. Called from :"
+            print widget
+
+        chooser = gtk.FileChooserDialog(title='Export stiffness',
+                                        action=gtk.FILE_CHOOSER_ACTION_SAVE,
+                                        buttons=(gtk.STOCK_CANCEL,
+                                                  gtk.RESPONSE_CANCEL,
+                                                  gtk.STOCK_SAVE,
+                                                  gtk.RESPONSE_OK))
+        chooser.set_default_response(gtk.RESPONSE_OK)
+        chooser.set_local_only(False)
+        chooser.set_current_folder(self.config['folder-export'])
+        response = chooser.run()
+        if response == gtk.RESPONSE_OK:
+            filename = chooser.get_filenames()[0]
+            self.experiment.export_stiffness(filename)
+            self.config['folder-export'] = os.path.split(filename)[0]
+        elif response == gtk.RESPONSE_CANCEL:
+            chooser.destroy()
+            return
+        else:
+            chooser.destroy()
+            return
+        chooser.destroy()
+
+    def on_menu_export_average_stiffness_tomography_activate(self, widget):
+        """
+            Export the average stiffness on a csv file
+        """
+        if DEBUG:
+            print "Export average stiffness. Called from :"
+            print widget
+        chooser = gtk.FileChooserDialog(title='Export average stiffness',
+                                        action=gtk.FILE_CHOOSER_ACTION_SAVE,
+                                        buttons=(gtk.STOCK_CANCEL,
+                                                  gtk.RESPONSE_CANCEL,
+                                                  gtk.STOCK_SAVE,
+                                                  gtk.RESPONSE_OK))
+        chooser.set_default_response(gtk.RESPONSE_OK)
+        chooser.set_local_only(False)
+        chooser.set_current_folder(self.config['folder-export'])
+        response = chooser.run()
+        if response == gtk.RESPONSE_OK:
+            filename = chooser.get_filenames()[0]
+            self.experiment.export_average_stiffness_tomo(filename)
+            self.config['folder-export'] = os.path.split(filename)[0]
+        elif response == gtk.RESPONSE_CANCEL:
+            chooser.destroy()
+            return
+        else:
+            chooser.destroy()
+            return
+        chooser.destroy()
+
+    def on_menu_export_map_activate(self, widget):
+        """
+            Export the stiffness map of the file as a png file.
+        """
+        if DEBUG:
+            print "Export map. Called from :"
+            print widget
+        array_dict = {}
+        for item in self.force_volume.get_array('keys'):
+            array_dict[item] = self.force_volume.get_array(item)
+        export = MapDisplay(array_dict,
+                            folder=self.config['folder-export'],
+                            depth=self.force_volume.stiffness['size_parts'],
+                            fvname=self.force_volume.name,
+                            scan_size=self.force_volume.header['scan_size'])
+        export.run()
+
+    def on_menu_export_curve_activate(self, widget):
+        """
+            Export the force indentation curve as csv file.
+        """
+        if DEBUG:
+            print "Export curve. Called from :"
+            print widget
+        chooser = gtk.FileChooserDialog(title='Export FD curve',
+                                        action=gtk.FILE_CHOOSER_ACTION_SAVE,
+                                        buttons=(gtk.STOCK_CANCEL,
+                                                  gtk.RESPONSE_CANCEL,
+                                                  gtk.STOCK_SAVE,
+                                                  gtk.RESPONSE_OK))
+        chooser.set_default_response(gtk.RESPONSE_OK)
+        chooser.set_local_only(False)
+        chooser.set_current_folder(self.config['folder-export'])
+        response = chooser.run()
+        if response == gtk.RESPONSE_OK:
+            filename = chooser.get_filenames()[0]
+            self.force_volume.export_curve(filename, 'both')
+            self.config['folder-export'] = os.path.split(filename)[0]
+        elif response == gtk.RESPONSE_CANCEL:
+            chooser.destroy()
+            return
+        else:
+            chooser.destroy()
+            return
+        chooser.destroy()
+
+    def on_menu_export_event_prop_activate(self, widget):
+        """
+            Export the event properties as csv files.
+        """
+
+        if DEBUG:
+            print "Export evnt. Called from :"
+            print widget
+        chooser = gtk.FileChooserDialog(title='Export event properties',
+                                        action=gtk.FILE_CHOOSER_ACTION_SAVE,
+                                        buttons=(gtk.STOCK_CANCEL,
+                                                  gtk.RESPONSE_CANCEL,
+                                                  gtk.STOCK_SAVE,
+                                                  gtk.RESPONSE_OK))
+        chooser.set_default_response(gtk.RESPONSE_OK)
+        chooser.set_local_only(False)
+        chooser.set_current_folder(self.config['folder-export'])
+        response = chooser.run()
+        if response == gtk.RESPONSE_OK:
+            filename = chooser.get_filenames()[0]
+            self.experiment.export_events(filename)
+            self.config['folder-export'] = os.path.split(filename)[0]
+        elif response == gtk.RESPONSE_CANCEL:
+            chooser.destroy()
+            return
+        else:
+            chooser.destroy()
+            return
+        chooser.destroy()
+
+    def on_menu_export_evt_nbr_activate(self, widget):
+        """
+            Export the number of evt per curves in csv file.
+        """
+
+        if DEBUG:
+            print "Export evnt. Called from :"
+            print widget
+        chooser = gtk.FileChooserDialog(title='Export event number per curves',
+                                        action=gtk.FILE_CHOOSER_ACTION_SAVE,
+                                        buttons=(gtk.STOCK_CANCEL,
+                                                  gtk.RESPONSE_CANCEL,
+                                                  gtk.STOCK_SAVE,
+                                                  gtk.RESPONSE_OK))
+        chooser.set_default_response(gtk.RESPONSE_OK)
+        chooser.set_local_only(False)
+        chooser.set_current_folder(self.config['folder-export'])
+        response = chooser.run()
+        if response == gtk.RESPONSE_OK:
+            filename = chooser.get_filenames()[0]
+            self.experiment.export_nbr_events(filename)
+            self.config['folder-export'] = os.path.split(filename)[0]
+        elif response == gtk.RESPONSE_CANCEL:
+            chooser.destroy()
+            return
+        else:
+            chooser.destroy()
+            return
+        chooser.destroy()
+
+    def on_menu_mask_activate(self, widget):
+        """
+            Generate masks.
+        """
+
+        if DEBUG:
+            print "Activate mask. Called from :"
+            print widget
+        mask_edit = MaskProperties(self.force_volume)
+        answer = mask_edit.run()
+        del answer
+        mask_edit.destroy()
+        self.experiment.update_switch()
+        self.update('gui')
+    ##
+    ## Edition Menu
+
+    ########
+    ## dialog experiment properties
+    def on_exp_prop_activate(self, widget):
+        '''
+        Create the properties dialog.
+        '''
+        if DEBUG:
+            print "Property dialog. Called from :"
+            print widget
+
+        self.properties_dialog = dialog_experiment_properties.main_win(
+            author=self.experiment.author,
+            comment=self.experiment.comment,
+            spring_constant=self.experiment.parameters['spring_constant'],
+            inject_index=[self.experiment.parameters['injection_index'],
+                          len(self.experiment.file['list'])],
+            stiff_glass=self.experiment.parameters['glass'],
+            trace_curve=[self.force_volume.trace_x, self.force_volume.trace_y],
+            plot_size=self.experiment.parameters['plot_size'],
+            group=self.experiment.group,
+            linewidth=self.config['linewidth'],
+            histo_y_rel=self.experiment.parameters['histo_y_rel'],
+            plot_hist_gauss=self.experiment.parameters['plot_hist_gauss'],
+            plot_color=self.plot_properties.color_type
+            )
+        self.properties_dialog.validate = self.properties_dialog_validate
+
+    def properties_dialog_validate(self):
+        '''
+        The ending function of the experiment properties dialog.
+        The changed data are stored in the experiment
+        '''
+        # We redefine this function to catch the final signal from the window
+        self.experiment.author = self.properties_dialog.author
+        self.experiment.comment = self.properties_dialog.comment
+        self.experiment.parameters['injection_index'] = \
+                                    int(self.properties_dialog.inject_index[0])
+        self.experiment.set_parameters('spring_constant',
+                                        self.properties_dialog.spring_cst)
+        self.experiment.set_parameters('glass',
+                                        self.properties_dialog.stiff_glass)
+        self.experiment.set_parameters('plot_size',
+                                        self.properties_dialog.save_size)
+        gprop = self.properties_dialog.group
+        for key in ['label', 'display']:
+            self.experiment.set_group_prop(key, -1, gprop[key])
+        self.config['linewidth'] = self.properties_dialog.linewidth
+        self.experiment.parameters['histo_y_rel'] = \
+                                       self.properties_dialog.histo_y_rel
+        self.experiment.set_parameters('plot_hist_gauss',
+                                       self.properties_dialog.plot_hist_gauss)
+        self.plot_properties.color_type = self.properties_dialog.plot_color
+        self.properties_dialog.destroy()
+        self.update('plots')
+    ##
+
+    ####
+    ## Group
+    def on_group_activate(self, widget):
+        """
+            Manage the groups.
+        """
+
+        if DEBUG:
+            print "Activate group. Called from :"
+            print widget
+        win = FileGroup(self.experiment.file['name'],
+                        self.experiment.file['group'])
+        result = win.run()
+        if result is not None:
+            self.experiment.set_group(result)
+        win.destroy()
+    ##
+
+    ###############
+    ## Option Menu
+    def on_apply_on_all_toggled(self, widget):
+        """
+            Switch the "apply_on_all" state.
+        """
+
+        self.apply_on_all = widget.get_active()
+        self.experiment.set_switch('all', widget.get_active())
+        self.update('gui')
+
+    def on_show_header_activate(self, widget):
+        """
+            Show the current FV header in a window.
+        """
+
+        if DEBUG:
+            print "Show header. Called from :"
+            print widget
+        if self.force_volume is None:
+            # Stop execution here if no files loaded
+            display_error('no_fv')
+            return
+        treestore = create_header_tree(self.force_volume.header)
+        treeview = gtk.TreeView(treestore)
+        tvcolumn = gtk.TreeViewColumn('File Header')
+        treeview.append_column(tvcolumn)
+        cell = gtk.CellRendererText()
+        tvcolumn.pack_start(cell, True)
+        tvcolumn.add_attribute(cell, 'text', 0)
+        treeview.set_search_column(0)
+        tvcolumn.set_sort_column_id(0)
+        treeview.set_reorderable(True)
+
+        # Create a new window
+        window = gtk.Window(gtk.WINDOW_TOPLEVEL)
+        window.set_title('File Header')
+
+        window.set_size_request(200, 200)
+
+        #window.connect("delete_event", self.delete_event)
+        window.add(treeview)
+        window.show_all()
+
+    def on_flatten_activate(self, widget):
+        """
+            Open the flatten dialog
+        """
+        self.flatten_dialog = FlattenDialog(
+                                self.force_volume.get_array('Piezo', raw=True))
+        new_array = self.flatten_dialog.run()
+        self.force_volume.set_array('Piezo', new_array)
+        self.flatten_dialog.destroy()
+
+    ###########################################################################
+    ## Display tab
+    def on_button_up_clicked(self, widget):
+        """
+            Navigate in the array to the upper FC.
+        """
+        if self.force_volume is None:
+            # Stop execution here if no files loaded
+            display_error('no_fv')
+            return
+        self.update_stiffness_param(self.force_volume, widget)
+        self.force_volume.go_up()
+        self.plot_curve()
+        self.update('show gride position')
+
+    def on_button_down_clicked(self, widget):
+        """
+            Navigat in the array to the down FC.
+        """
+
+        if self.force_volume is None:
+            # Stop execution here if no files loaded
+            display_error('no_fv')
+            return
+        self.update_stiffness_param(self.force_volume, widget)
+        self.force_volume.go_down()
+        self.plot_curve()
+        self.update('show gride position')
+
+    def on_button_next_clicked(self, widget):
+        """
+            Navigate in the array to the next FC.
+        """
+        if self.force_volume is None:
+            # Stop execution here if no files loaded
+            display_error('no_fv')
+            return
+        self.update_stiffness_param(self.force_volume, widget)
+        try:
+            self.force_volume.go_next()
+        except StopIteration:
+            pass
+        self.plot_curve()
+        self.update('show gride position')
+
+    def on_button_prev_clicked(self, widget):
+        """
+            Navigate in the array to the previous FC.
+        """
+        if self.force_volume is None:
+            # Stop execution here if no files loaded
+            display_error('no_fv')
+            return
+        self.update_stiffness_param(self.force_volume, widget)
+        self.force_volume.go_prev()
+        self.plot_curve()
+        self.update('show gride position')
+
+    def on_list_file_combo_box_changed(self, signal):
+        """
+            Change the current FV scan according to the list change.
+        """
+
+        self.force_volume = self.experiment.get_file(signal.get_active())
+        self.update('fv display prop')
+        self.update('gui')
+
+    def on_check_display_fc_trace_clicked(self, widget):
+        """
+            Switch the display of approach curve.
+        """
+        if self.force_volume is None:
+            # Stop execution here if no files loaded
+            display_error('no_fv')
+            return
+        if widget.get_active():
+            self.force_volume.set_to_plot('Av', 1)
+        else:
+            self.force_volume.set_to_plot('Av', 0)
+            if not self.force_volume.to_plot('Re'):
+                self.win_plot['Curve Plot'].on_win_plot_destroy()
+        self.plot_curve()
+
+    def on_check_display_fc_retrace_clicked(self, widget):
+        """
+            Switch the display of retraction curve.
+        """
+        if self.force_volume is None:
+            # Stop execution here if no files loaded
+            display_error('no_fv')
+            return
+        if widget.get_active():
+            self.force_volume.set_to_plot('Re', 1)
+        else:
+            self.force_volume.set_to_plot('Re', 0)
+            if not self.force_volume.to_plot('Av'):
+                self.win_plot['Curve Plot'].on_win_plot_destroy()
+        self.plot_curve()
+
+    def on_check_display_poc_clicked(self, widget):
+        """
+            Switch the display of point of contact on approach curve.
+        """
+        if self.force_volume is None:
+            # Stop execution here if no files loaded
+            display_error('no_fv')
+            return
+        if widget.get_active():
+            self.force_volume.set_to_plot('PoC', 1)
+        else:
+            self.force_volume.set_to_plot('PoC', 0)
+        self.plot_curve()
+
+    def on_check_display_event_clicked(self, widget):
+        """
+            Switch the display of event on retraction curve.
+        """
+        if self.force_volume is None:
+            # Stop execution here if no files loaded
+            display_error('no_fv')
+            return
+        if widget.get_active():
+            self.force_volume.set_to_plot('Event', 1)
+        else:
+            self.force_volume.set_to_plot('Event', 0)
+        self.plot_curve()
+
+    def on_check_display_indent_clicked(self, widget):
+        """
+            Switch the display of indentation curve.
+        """
+        if self.force_volume is None:
+            # Stop execution here if no files loaded
+            display_error('no_fv')
+            return
+        if widget.get_active():
+            self.force_volume.set_to_plot('Indent', 1)
+        else:
+            self.force_volume.set_to_plot('Indent', 0)
+            self.win_plot['Indent Plot'].on_win_plot_destroy()
+        self.plot_curve()
+
+    def on_button_piezzo_array_clicked(self, widget):
+        """
+            Display the piezo array.
+        """
+        if self.force_volume is None:
+            display_error('no_fv')
+            return
+        try:
+            array = self.force_volume.get_array('Piezo')
+        except NotReadyError:
+            answer = ask_message(['Piezo array not loaded',
+                                  'Piezo array is not loaded.\n' +
+                                  'Do you want to load it ?\n\n' +
+                                  'This can take minutes...\n\n' +
+                                  'Note that if you compute the stiffness\n' +
+                                  'Piezo array is automagically loaded.'])
+            if answer == gtk.RESPONSE_YES:
+                self.force_volume.force_piezo_loading()
+                array = self.force_volume.get_array('Piezo')
+            elif answer == gtk.RESPONSE_NO:
+                return
+        if not exist(self.win_plot['Piezo Height']):
+            [window, widget] = self.regenerate_plot()
+            self.win_plot['Piezo Height'] = plot_gtk.plotGride(
+                                    window, widget,
+                                    title=PLOT_WINDOW['piezo array'][2],
+                                    win_title=PLOT_WINDOW['piezo array'][1])
+            self.win_plot['Piezo Height'].figure.canvas.mpl_connect(
+                                                        'button_press_event',
+                                                        self.on_gride_click)
+            self.win_plot['Piezo Height'].figure.canvas.mpl_connect(
+                                                        'motion_notify_event',
+                                                        self.on_gride_motion)
+        self.win_plot['Piezo Height'].set_size(
+                                    self.experiment.parameters['plot_size'])
+        self.win_plot['Piezo Height'].plot(
+                                    array,
+                                    self.force_volume.header['scan_size'],
+                                    cmap=self.plot_properties.get_cmap('Piezo'))
+
+    def on_button_topography_array_clicked(self, widget):
+        """
+            Display the topography (zero-force) array.
+        """
+        if self.force_volume is None:
+            display_error('no_fv')
+            return
+        if self.force_volume.get_array('Topography') is None:
+            display_error('no_compute', 'topography')
+            return
+        if not exist(self.win_plot['Topography Map']):
+            [window, widget] = self.regenerate_plot()
+            self.win_plot['Topography Map'] = plot_gtk.plotGride(
+                                window, widget,
+                                title=PLOT_WINDOW['topography array'][2],
+                                win_title=PLOT_WINDOW['topography array'][1])
+            self.win_plot['Topography Map'].figure.canvas.mpl_connect(
+                                                        'button_press_event',
+                                                        self.on_gride_click)
+            self.win_plot['Topography Map'].figure.canvas.mpl_connect(
+                                                        'motion_notify_event',
+                                                        self.on_gride_motion)
+        self.win_plot['Topography Map'].set_size(
+                                    self.experiment.parameters['plot_size'])
+        self.win_plot['Topography Map'].plot(
+                                self.force_volume.get_array('Topography'),
+                                self.force_volume.header['scan_size'],
+                                cmap=self.plot_properties.get_cmap('Topography'))
+
+    def on_button_stiffness_array_clicked(self, widget):
+        """
+            Display the stiffness array.
+        """
+        if self.force_volume is None:
+            display_error('no_fv')
+            return
+        if not self.force_volume.has_stiffness:
+            display_error('no_compute', 'stiffness')
+            return
+        if not exist(self.win_plot['Stiffness Map']):
+            [window, widget] = self.regenerate_plot()
+            self.win_plot['Stiffness Map'] = plot_gtk.plotGride(
+                                window, widget,
+                                title=PLOT_WINDOW['stiffness array'][2],
+                                win_title=PLOT_WINDOW['stiffness array'][1])
+            self.win_plot['Stiffness Map'].figure.canvas.mpl_connect(
+                                                        'button_press_event',
+                                                        self.on_gride_click)
+            self.win_plot['Stiffness Map'].figure.canvas.mpl_connect(
+                                                        'motion_notify_event',
+                                                        self.on_gride_motion)
+        self.win_plot['Stiffness Map'].set_size(
+                                    self.experiment.parameters['plot_size'])
+        self.win_plot['Stiffness Map'].plot(
+                                self.force_volume.get_array('Stiffness'),
+                                self.force_volume.header['scan_size'],
+                                cmap=self.plot_properties.get_cmap('Stiffness'))
+
+    def on_button_event_array_clicked(self, widget):
+        """
+            Display the event number array.
+        """
+        if self.force_volume is None:
+            display_error('no_fv')
+            return
+        if self.force_volume.get_array('Event') is None:
+            display_error('no_compute', 'event')
+            return
+        if not exist(self.win_plot['Event Map']):
+            [window, widget] = self.regenerate_plot()
+            self.win_plot['Event Map'] = plot_gtk.plotGride(
+                                    window, widget,
+                                    title=PLOT_WINDOW['ev_pos array'][2],
+                                    win_title=PLOT_WINDOW['ev_pos array'][1])
+            self.win_plot['Event Map'].figure.canvas.mpl_connect(
+                                                        'button_press_event',
+                                                        self.on_gride_click)
+        self.win_plot['Event Map'].set_size(
+                                    self.experiment.parameters['plot_size'])
+        self.win_plot['Event Map'].plot(
+                                        self.force_volume.get_array('Event'),
+                                        self.force_volume.header['scan_size'],
+                                    cmap=self.plot_properties.get_cmap('Event'))
+
+    def on_button_event_force_array_clicked(self, widget):
+        """
+            Display the event force array.
+        """
+        if self.force_volume is None:
+            display_error('no_fv')
+            return
+        if self.force_volume.get_array('Event force') is None:
+            display_error('no_compute', 'event')
+            return
+        if not exist(self.win_plot['Event Force Map']):
+            [window, widget] = self.regenerate_plot()
+            self.win_plot['Event Force Map'] = plot_gtk.plotGride(
+                                    window, widget,
+                                    title=PLOT_WINDOW['ev_force array'][2],
+                                    win_title=PLOT_WINDOW['ev_force array'][1])
+            self.win_plot['Event Force Map'].figure.canvas.mpl_connect(
+                                                        'button_press_event',
+                                                        self.on_gride_click)
+        self.win_plot['Event Force Map'].set_size(
+                                    self.experiment.parameters['plot_size'])
+        self.win_plot['Event Force Map'].plot(
+                            self.force_volume.get_array('Event force'),
+                            self.force_volume.header['scan_size'],
+                            cmap=self.plot_properties.get_cmap('Event force'))
+
+    def on_button_event_dist_array_clicked(self, widget):
+        """
+            Display the event force array.
+        """
+        if self.force_volume is None:
+            display_error('no_fv')
+            return
+        if self.force_volume.get_array('Event distance') is None:
+            display_error('no_compute', 'event distance')
+            return
+        if not exist(self.win_plot['Event Distance Map']):
+            [window, widget] = self.regenerate_plot()
+            self.win_plot['Event Distance Map'] = plot_gtk.plotGride(
+                                    window, widget,
+                                    title=PLOT_WINDOW['ev_dist array'][2],
+                                    win_title=PLOT_WINDOW['ev_dist array'][1])
+            self.win_plot['Event Distance Map'].figure.canvas.mpl_connect(
+                                                        'button_press_event',
+                                                        self.on_gride_click)
+        self.win_plot['Event Distance Map'].set_size(
+                                    self.experiment.parameters['plot_size'])
+        self.win_plot['Event Distance Map'].plot(
+                            self.force_volume.get_array('Event distance'),
+                            self.force_volume.header['scan_size'],
+                        cmap=self.plot_properties.get_cmap('Event distance'))
+
+    def on_button_event_length_array_clicked(self, widget):
+        """
+            Display the event number array.
+        """
+        if self.force_volume is None:
+            display_error('no_fv')
+            return
+        if self.force_volume.get_array('Event length') is None:
+            display_error('no_compute', 'event length')
+            return
+        if not exist(self.win_plot['Event Length Map']):
+            [window, widget] = self.regenerate_plot()
+            self.win_plot['Event Length Map'] = plot_gtk.plotGride(
+                                    window, widget,
+                                    title=PLOT_WINDOW['ev_len array'][2],
+                                    win_title=PLOT_WINDOW['ev_len array'][1])
+            self.win_plot['Event Length Map'].figure.canvas.mpl_connect(
+                                                        'button_press_event',
+                                                        self.on_gride_click)
+        self.win_plot['Event Length Map'].set_size(
+                                    self.experiment.parameters['plot_size'])
+        self.win_plot['Event Length Map'].plot(
+                            self.force_volume.get_array('Event length'),
+                            self.force_volume.header['scan_size'],
+                            cmap=self.plot_properties.get_cmap('Event length'))
+
+    def on_button_stiffness_tomo_clicked(self, widget):
+        """
+            Dispaly the stiffness tomography slices in x-y-z.
+        """
+        if self.force_volume is None:
+            display_error('no_fv')
+            return
+        if not self.force_volume.has_stiffness:
+            display_error('no_compute', 'stiffness')
+            return
+        self.force_volume.stiffness_tomography_array()
+        if not exist(self.win_plot['Stiffness Tomo']):
+            [window, widget] = self.regenerate_plot('tomography')
+            self.win_plot['Stiffness Tomo'] = plot_gtk.plotTomo(
+                            window, widget,
+                            self.force_volume.get_array('Stiffness tomo'),
+                            scan_size=self.force_volume.header['scan_size'],
+                            title='Stiffness Tomo')
+        self.win_plot['Stiffness Tomo'].set_size(
+                                    self.experiment.parameters['plot_size'])
+        self.win_plot['Stiffness Tomo'].get_pos = \
+                                    self.on_stiffness_tomo_window_clicked
+
+    def on_stiffness_tomo_window_clicked(self):
+        """
+            When clicking on the stiffness tomography window, it goes to the
+            corresponding force-distance curve.
+        """
+        if self.force_volume is None:
+            display_error('no_fv')
+            return
+        self.force_volume.go_to(self.win_plot['Stiffness Tomo'].slice[0],
+                                self.win_plot['Stiffness Tomo'].slice[1])
+        self.update('show gride position')
+        self.plot_curve()
+
+    def on_button_mean_stiffness_tomo_clicked(self, widget):
+        """
+            Distplay the mean stiffness tomography.
+        """
+        if self.force_volume is None:
+            display_error('no_fv')
+            return
+        if not self.force_volume.has_stiffness:
+            display_error('no_compute', 'stiffness')
+            return
+        if not exist(self.win_plot['Average Stiffness Tomo']):
+            [window, widget] = self.regenerate_plot()
+            self.win_plot['Average Stiffness Tomo'] = plot_gtk.errorBar(
+                                                window, widget)
+
+        if self.apply_on_all:
+            mean_tomo = self.experiment.average_stiffness
+            self.win_plot['Average Stiffness Tomo'].average_stiffness(
+                                        mean_tomo,
+                                        group=self.experiment.file['group'],
+                                        group_info=self.experiment.group)
+        else:
+            mean_tomo = self.force_volume.compute_average_stiffness()
+            self.win_plot['Average Stiffness Tomo'].average_stiffness(
+                                            mean_tomo)
+        self.win_plot['Average Stiffness Tomo'].set_size(
+                                    self.experiment.parameters['plot_size'])
+
+    ## Mosaics
+    def mosaic_clicked(self, atype, widget=None):
+        """
+            Generic function to display mosaic view.
+        """
+        if self.force_volume is None:
+            display_error('no_fv')
+            return
+        if DEBUG:
+            print "Mosaic plot. Called from :"
+            print widget
+        array_list = self.experiment.get_arrays(atype)
+        mask_list = self.experiment.get_masked_list()
+        # MOSAIC_PLOT is a dict which contains the values for mosaic name :
+        # mosaic_name[0] = name of the window plot
+        # mosaic_name[1] = title of the window
+        # mosaic_name[2] = title of the plot
+        # mosaic_name[3] = cmap
+        mosaic_name = MOSAIC_PLOT[atype]
+        if not exist(self.win_plot[mosaic_name[0]]):
+            [window, widget] = self.regenerate_plot()
+            self.win_plot[mosaic_name[0]] = plot_gtk.plotMosaic(
+                                                        window, widget,
+                                                        title=mosaic_name[1])
+            self.win_plot[mosaic_name[0]].figure.canvas.mpl_connect(
+                                                        'button_press_event',
+                                                        self.on_mosaic_click)
+            self.win_plot[mosaic_name[0]].figure.canvas.mpl_connect(
+                                                        'pick_event',
+                                                        self.on_mosaic_pick)
+        self.win_plot[mosaic_name[0]].set_size(
+                                    self.experiment.parameters['plot_size'])
+        self.win_plot[mosaic_name[0]].plot(array_list,
+                                        title=mosaic_name[2],
+                                        list_name=self.experiment.file['name'],
+                                        cmap=mosaic_name[3],
+                                        list_mask=mask_list)
+
+    def on_button_mosaic_piezo_clicked(self, widget):
+        """
+            Display the mosaic view of piezo image.
+        """
+        self.mosaic_clicked('Piezo', widget)
+
+    def on_button_mosaic_topography_clicked(self, widget):
+        """
+            Display the mosaic view of topography.
+        """
+        self.mosaic_clicked('Topography', widget)
+
+    def on_button_mosaic_stiffness_clicked(self, widget):
+        """
+            Display the mosaic view of stiffness.
+        """
+        self.mosaic_clicked('Stiffness', widget)
+
+    def on_button_mosaic_event_clicked(self, widget):
+        """
+            Display the mosaic view of event nbr.
+        """
+        self.mosaic_clicked('Event', widget)
+
+    def on_button_mosaic_event_force_clicked(self, widget):
+        """
+            Display the mosaic view of event force.
+        """
+        self.mosaic_clicked('Event force', widget)
+
+    def on_button_opengl_clicked(self, widget):
+        """
+            Display the stiffness tomography using OpenGL.
+        """
+        if DEBUG:
+            print "OpenGL. Called from :"
+            print widget
+        self.force_volume.stiffness_tomography_array()
+        # get the min and max values from the tomography display :
+        if exist(self.win_plot['Stiffness Tomo']):
+            clut = (self.win_plot['Stiffness Tomo'].colorScaleMin,
+                    self.win_plot['Stiffness Tomo'].colorScaleMax)
+        else:
+            clut = None
+        topogl = TopoGL(self.force_volume.get_array('Stiffness tomo'),
+                        clut=clut)
+        topogl.run()
+
+    ###########################################################################
+    ## Compute tab
+    def update_stiffness_param(self, force_volume, widget=None):
+        """
+            Update the stiffness parameters.
+        """
+        if DEBUG:
+            print "Updating stiffness parameters. Called by :"
+            print widget
+        # Update the Hertz model and the tip caracteristics.
+        _hertz_model = self.widget['combo_hertz_model'].get_active_text()
+        _stiff_method = self.widget['combo_stiff_method'].get_active_text()
+        _tip_carac = self.widget['spin_tip_carac'].get_value()
+        force_volume.change_model(model=_hertz_model, carac=_tip_carac)
+        force_volume.set_parameters('stiffness_fit_method', _stiff_method)
+        # Update the segmentations parameters.
+        force_volume.change_segment_number(
+                            self.widget['entry_number_deep'].get_text())
+        force_volume.change_segment_depth(
+                            self.widget['entry_size_deep'].get_text())
+        # Update the point of contact detection algorythm.
+        _poc_model = self.widget['combo_poc_method'].get_active_text()
+        force_volume.stiffness['poc_method'] = _poc_model
+        _limit_poc_slide = self.widget['check_limit_poc_slide'].get_active()
+        force_volume.stiffness['limit_slide'] = _limit_poc_slide
+        _fit_seg_size = self.widget['spin_fit_seg_size'].get_value()
+        force_volume.change_poc_seg_size(_fit_seg_size)
+        # Update whether to recompute or not.
+        _recompute_poc = self.widget['check_compute_poc'].get_active()
+        force_volume.stiffness['recompute_poc'] = _recompute_poc
+
+    def on_button_compute_stiffness_clicked(self, widget):
+        """
+            Launch the stiffness computation.
+        """
+        if DEBUG:
+            print "Compute stiffness. Called from :"
+            print widget
+        if self.apply_on_all:
+            number_of_files = len(self.experiment.file['list'])
+            this_file_nb = 0
+            for force_volume, file_name in zip(self.experiment.file['list'],
+                                              self.experiment.file['name']):
+                counter_begin = float(this_file_nb) / number_of_files
+                counter_end = float(this_file_nb + 1) / number_of_files
+                counter_text = " of file " + file_name
+                self._compute_stiffness(force_volume,
+                                        counter_begin,
+                                        counter_end,
+                                        counter_text)
+                this_file_nb += 1
+        else:
+            self._compute_stiffness(self.force_volume)
+        # updates the histogram tabs according to the latest computations.
+        self.update('hist entry')
+        self.display_progressbar(None)
+
+    def on_check_compute_poc_toggled(self, widget):
+        """
+            Change the state of forcing the detection of point of contact.
+        """
+        if self.force_volume is not None:
+            self.update_stiffness_param(self.force_volume, widget)
+
+    def _compute_stiffness(self, force_volume, counter_begin=0,
+                           counter_end=1, counter_text=''):
+        """
+            Compute the stiffness. This is for one file.
+        """
+        # Update the computation properties
+        self.update_stiffness_param(force_volume)
+        # Start the computation
+        _thread = threading.Thread(target=force_volume.compute_stiffness)
+        _thread.start()
+        while _thread.isAlive():
+            self.display_progressbar(counter_begin +
+                                float(force_volume.counter['num']) *
+                                (counter_end - counter_begin),
+                                force_volume.counter['text'] + counter_text)
+            time.sleep(0.1)
+        force_volume.counter['num'] = 0
+
+    def update_evt_parameters(self, force_volume):
+        evt_fit_model = self.widget['combo_ev_fit_model'].get_active_text()
+        if evt_fit_model == 'None':
+            evt_fit_model = None
+        force_volume.set_parameters('evt_fit', evt_fit_model)
+        force_volume.header['event_detect_weight'] = \
+                        self.experiment.parameters['event_detect_weight']
+
+    def on_button_detect_events_clicked(self, widget):
+        """
+            Launch the event detection.
+        """
+        if DEBUG:
+            print "Detect events. Called from :"
+            print widget
+        if self.apply_on_all:
+            number_of_files = len(self.experiment.file['list'])
+            this_file_nb = 0
+            for force_volume, file_name in zip(self.experiment.file['list'],
+                                              self.experiment.file['name']):
+                counter_begin = float(this_file_nb) / number_of_files
+                counter_end = float(this_file_nb + 1) / number_of_files
+                counter_text = " of file " + file_name
+                self._compute_evt(force_volume,
+                                        counter_begin,
+                                        counter_end,
+                                        counter_text)
+                this_file_nb += 1
+        else:
+            self._compute_evt(self.force_volume)
+        self.update('hist entry')
+        self.display_progressbar(None)
+
+    def _compute_evt(self, force_volume, counter_begin=0,
+                           counter_end=1, counter_text=''):
+        """
+            Compute the stiffness. This is for one file.
+        """
+        # Update the computation properties
+        self.update_evt_parameters(force_volume)
+        # Start the computation
+        _thread = threading.Thread(target=force_volume.compute_events)
+        _thread.start()
+        while _thread.isAlive():
+            self.display_progressbar(counter_begin +
+                                float(force_volume.counter['num']) *
+                                (counter_end - counter_begin),
+                                force_volume.counter['text'] + counter_text)
+            time.sleep(0.1)
+        force_volume.counter['num'] = 0
+
+    def on_combo_ev_fit_model_changed(self, widget):
+        if self.force_volume is not None:
+            self.experiment.parameters['event_fit_model'] = \
+                            self.widget['combo_ev_fit_model'].get_active_text()
+            self.plot_curve()
+
+    def on_button_regenerate_random_clicked(self, widget):
+        """
+            Regenerate the random event array.
+        """
+        if DEBUG:
+            print "Regenerate random. Called from :"
+            print widget
+        nbr_rand_event = self.widget['spin_nbr_rand_event'].get_value()
+        if self.apply_on_all:
+            for force_volume in self.experiment.file['list']:
+                force_volume.generate_random_event(nbr_rand_event)
+            else:
+                self.force_volume.generate_random_event(nbr_rand_event)
+
+    def on_button_compute_rel_stiffness_clicked(self, widget):
+        """
+            Compute the relative stiffness
+        """
+        if DEBUG:
+            print "Compute rel stiff. Called from :"
+            print widget
+        self.experiment.parameters['rel_stiff_dist'] = \
+                        int(self.widget['spin_max_rel_stiffness'].get_value())
+        if self.apply_on_all:
+            self.experiment.compute_relative_stiffness()
+        else:
+            self.force_volume.change_relative_distance(
+                            int(self.experiment.parameters['rel_stiff_dist']))
+            self.force_volume.compute_relative_stiffness()
+
+    ###########################################################################
+    ## Parameter tab
+    def on_spin_poisson_ratio_value_changed(self, widget):
+        """
+            Change the poisson ratio of the material.
+        """
+        if self.experiment is not None:
+            self.experiment.set_parameters('poisson_ratio', widget.get_value())
+
+    def on_button_event_calib_clicked(self, widget):
+        """
+            Modify the calibration of the event detection.
+        """
+
+        if DEBUG:
+            print "Calib event. Called from :"
+            print widget
+        # Turn on the "Retraction force curve" and "Event on curve display"
+        self.widget['check_display_fc_retrace'].set_active(True)
+        self.force_volume.set_to_plot('Re', 1)
+        self.widget['check_display_event'].set_active(True)
+        self.force_volume.set_to_plot('Event', 1)
+        self.modify_window('Curve Plot', 'Event detection')
+        self.plot_curve()
+
+    def on_spin_ev_threshold_dist_value_changed(self, widget):
+        """
+            Change the event filter based on its distance on the curve.
+        """
+        self.experiment.set_switch('ev_dist', widget.get_value())
+        adjustment = widget.get_adjustment()
+        adjustment.set_upper(widget.get_value() + 1000)
+        self.update_switch()
+
+    def on_spin_ev_length_thresh_min_value_changed(self, widget):
+        """
+            Change the event filter based on its minimum length computed from
+            the fit.
+        """
+        self.update_ev_length_thresh()
+        adjustment = widget.get_adjustment()
+        adjustment.set_upper(widget.get_value() + 1000)
+
+    def on_spin_ev_length_thresh_max_value_changed(self, widget):
+        """
+            Change the event filter based on its maximum length computed from
+            the fit.
+        """
+        self.update_ev_length_thresh()
+        adjustment = widget.get_adjustment()
+        adjustment.set_upper(widget.get_value() + 1000)
+
+    def update_ev_length_thresh(self):
+        """
+            Update the threshold fit based on the length computed from the fit.
+        """
+        min_length = self.widget['spin_ev_length_thresh_min'].get_value()
+        max_length = self.widget['spin_ev_length_thresh_max'].get_value()
+        self.experiment.set_switch('ev_fit_length', [min_length, max_length])
+
+    def on_button_poc_calib_clicked(self, widget):
+        """
+            Change the calibration of the point of contact detection
+        """
+        if DEBUG:
+            print "Calib poc. Called from :"
+            print widget
+        # Turn on the "Approach force curve" and "PoC on curve display"
+        self.widget['check_display_fc_trace'].set_active(True)
+        self.force_volume.set_to_plot('Av', 1)
+        self.widget['check_display_poc'].set_active(True)
+        self.force_volume.set_to_plot('PoC', 1)
+        self.modify_window('Curve Plot', 'PoC detection')
+        self.plot_curve()
+
+    def on_combo_poc_method_changed(self, widget):
+        """
+            Change the method of the point of contact detection
+        """
+
+        if DEBUG:
+            print "Change poc method. Called from :"
+            print widget
+        if self.force_volume is not None:
+            self.update_stiffness_param(self.force_volume, widget)
+
+    def on_check_limit_poc_slide_toggled(self, widget):
+        """
+            Limits the sliding of point of contact detection.
+        """
+
+        if DEBUG:
+            print "Check limit poc. Called from :"
+            print widget
+        if self.force_volume is not None:
+            self.update_stiffness_param(self.force_volume, widget)
+
+    def on_spin_fit_seg_size_value_changed(self, widget):
+        """
+            Change the segment size of indentation curve
+        """
+        if DEBUG:
+            print "Spin fit seg. Called from :"
+            print widget
+        if self.force_volume is not None:
+            self.update_stiffness_param(self.force_volume)
+        self.plot_curve()
+    ##
+
+    #############################################################
+    ## Histograms tab
+    def disp_hist(self, data_type, widget=None):
+        """
+            This is the generic function called to plot the histogram.
+
+            data_type is a string that describes the data you want to plot.
+
+            Can be :
+
+              * 'force' to plot the force.
+              * 'lr' to plot the loading rate
+              * 'dist' to plot the distance of the unbinding
+              * 'stiff' to plot the stiffness on pixel where event occured
+              * 'relstiff' to plot the relative stiffness of pixels where event
+                occured
+        """
+        if DEBUG:
+            print "Disp histogram. Called by :"
+            print widget
+        if self.force_volume is None:
+            return
+        if data_type not in PLOT_LABEL.keys():
+            raise TypeError
+        if widget in [self.widget['spin_ev_force_hist_max'],
+                      self.widget['spin_ev_lr_hist_max'],
+                      self.widget['spin_ev_length_hist_max'],
+                      self.widget['spin_ev_plength_hist_max'],
+                      self.widget['spin_ev_stiff_hist_max'],
+                      self.widget['spin_ev_relstiff_hist_max']]:
+            curr_val = widget.get_value()
+            widget.set_range(0, curr_val * 10)
+        # Set the label of the plot
+        [title, xlabel, window_name] = PLOT_LABEL[data_type]
+        # Set the range and type of the plot
+        # data_hist is a PlotData object that stores the plot properties
+        self.experiment.data_hist.set_range(data_type,
+                                            self.get_histo_range(data_type))
+        self.experiment.data_hist.set_type(data_type)
+        # We have a special case for the stiffness where we can compare event
+        # versus non event. We check thank's to a checkbox :
+        stiff_case = self.widget['check_stiff_ev_vs_notev'].get_active() and \
+                     (data_type == 'stiff')
+        if self.apply_on_all or self.plot_properties.plot_compare:
+            # When we compare different experiments, we take the whole files
+            if stiff_case:
+                [event_att, event_group, fid, coord] = \
+                                self.experiment.get_event_att('stiff_ev')
+                [noevent_att, noevent_group, noevent_fid, noevent_coord] = \
+                                self.experiment.get_event_att('stiff_notev')
+            else:
+                [event_att, event_group, fid, coord] = \
+                                    self.experiment.get_event_att(data_type)
+                self.experiment.data_hist.set_data(data_type, event_att)
+                self.experiment.data_hist.set_group(data_type, event_group)
+                self.experiment.data_hist.nbr_curves = \
+                                    self.experiment.parameters['number_curves']
+                if self.plot_properties.plot_compare:
+                    self.experiment_compare.data_hist.set_range(data_type,
+                                            self.get_histo_range(data_type))
+                    self.experiment_compare.data_hist.nbr_curves = \
+                            self.experiment_compare.parameters['number_curves']
+                    self.experiment_compare.data_hist.set_type(data_type)
+                    self.experiment_compare.data_hist.set_data(data_type,
+                            self.experiment_compare.get_event_att(data_type))
+                    self.experiment_compare.event_gauss_fit(data_type)
+        else:
+            if stiff_case:
+                event_att = self.force_volume.get_event_prop('stiff_ev')
+                noevent_att = self.force_volume.get_event_prop('stiff_notev')
+            else:
+                # Reinitialize the group, because the number of event can
+                # change.
+                self.experiment.data_hist.set_group(data_type, None)
+                try:
+                    data = self.force_volume.get_event_prop(data_type)
+                except TypeError:
+                    display_error('no_compute', data_type)
+                    return
+                self.experiment.data_hist.set_data(data_type, data)
+                self.experiment.data_hist.nbr_curves = \
+                                    self.force_volume.header['number_curves']
+                #self.experiment.event_gauss_fit(data_type)
+                #ev_prop = self.experiment.event_stat[data_type]
+        ### Set the groups.
+        if self.apply_on_all and not self.plot_properties.plot_compare:
+            # We put the group properties to the histogram.
+            self.experiment.data_hist.set_group_prop('all',
+                                                     self.experiment.group)
+        if not exist(self.win_plot[window_name]):
+            [window, widget] = self.regenerate_plot()
+            self.win_plot[window_name] = plot_gtk.plotHist(
+                            window, widget,
+                            title=title,
+                            xlabel=xlabel,
+                            y_rel=self.experiment.parameters['histo_y_rel'])
+        if not self.plot_properties.plot_compare:
+            if stiff_case:
+                self.win_plot[window_name].hist(event_att, noevent_att,
+                                label='event', label2='not event',
+                                hist_range=self.get_histo_range(data_type),
+                                y2=True)
+            else:
+                try:
+                    self.win_plot[window_name].hist(self.experiment.data_hist)
+                except IndexError:
+                    pass
+                else:
+                    if self.experiment.parameters['plot_hist_gauss']:
+                        self.experiment.event_gauss_fit(data_type)
+                        self.win_plot[window_name].gauss(
+                                        self.experiment.event_stat[data_type])
+        else:
+            # we compare two experiments :
+            self.win_plot[window_name].hist(
+                                self.experiment.data_hist,
+                                self.experiment_compare.data_hist,
+                                label=self.plot_properties.main_exp_label,
+                                label2=self.plot_properties.comp_exp_label,
+                                color_type=self.plot_properties.color_type)
+        # Set the size of the window...
+        self.win_plot[window_name].set_size(
+                                self.experiment.parameters['plot_size'])
+
+    def on_button_ev_force_hist_clicked(self, widget):
+        """
+            Display the histogram of force.
+        """
+        self.disp_hist('force', widget)
+
+    def on_button_ev_lr_hist_clicked(self, widget):
+        """
+            Display the histogram of loading rate.
+        """
+        self.disp_hist('lr', widget)
+
+    def on_button_ev_dist_hist_clicked(self, widget=None):
+        """
+            Display the histogram of distance.
+        """
+        self.disp_hist('dist', widget)
+
+    def on_button_ev_stiff_hist_clicked(self, widget):
+        """
+            Display the histogram of stiffness.
+        """
+        self.disp_hist('stiff', widget)
+
+    def on_button_ev_relstiff_hist_clicked(self, widget):
+        """
+            Display the histogram of relative stiffness.
+        """
+        self.disp_hist('relstiff', widget)
+
+    def on_button_ev_length_hist_clicked(self, widget):
+        """
+            Display the histogram of relative stiffness.
+        """
+        self.disp_hist('length', widget)
+
+    def on_button_ev_plength_hist_clicked(self, widget):
+        """
+            Display the histogram of relative stiffness.
+        """
+        self.disp_hist('plength', widget)
+
+    def disp_scatter(self, data_type, widget=None):
+        """
+            The generic function to display the scatter plot.
+        """
+        if DEBUG:
+            print "Disp scatter. Called by :"
+            print widget
+        self.experiment.data_hist.set_range(data_type[0],
+                                            self.get_histo_range(data_type[0]))
+        self.experiment.data_hist.set_range(data_type[1],
+                                            self.get_histo_range(data_type[1]))
+        if self.apply_on_all:
+            [data, group, fid, coord] = \
+                                    self.experiment.get_event_att(data_type[0])
+            del fid, coord
+            self.experiment.data_hist.set_data(data_type[0], data)
+            self.experiment.data_hist.set_group(data_type[0], group)
+            [data, group, fid, coord] = \
+                                    self.experiment.get_event_att(data_type[1])
+            self.experiment.data_hist.set_data(data_type[1], data)
+            self.experiment.data_hist.set_group(data_type[1], group)
+            self.experiment.data_hist.nbr_curves = \
+                                    self.experiment.parameters['number_curves']
+            # We put the group properties to the histogram.
+            self.experiment.data_hist.set_group_prop('all',
+                                                    self.experiment.group)
+        else:
+            self.experiment.data_hist.set_group(data_type[0], None)
+            self.experiment.data_hist.set_group(data_type[1], None)
+            self.experiment.data_hist.set_data(data_type[0],
+                                self.force_volume.get_event_prop(data_type[0]))
+            self.experiment.data_hist.set_data(data_type[1],
+                                self.force_volume.get_event_prop(data_type[1]))
+            self.experiment.data_hist.nbr_curves = \
+                                self.force_volume.header['number_curves']
+        # The labels
+        label_x = PLOT_LABEL[data_type[0]]
+        label_y = PLOT_LABEL[data_type[1]]
+        [plot_name, plot_title] = PLOT_WINDOW[data_type[0] + data_type[1]]
+        if not exist(self.win_plot[plot_name]):
+            [window, widget] = self.regenerate_plot()
+            self.win_plot[plot_name] = plot_gtk.plotScatter(
+                                                window, widget,
+                                                title=plot_title,
+                                                xlabel=label_x[1],
+                                                ylabel=label_y[1])
+            #if data_type[0] == 'lr':
+            #    self.win_plot[plot_name].set_xscale('log')
+        self.win_plot[plot_name].display(self.experiment.data_hist, data_type)
+        self.win_plot[plot_name].set_size(
+                                    self.experiment.parameters['plot_size'])
+
+    def on_button_scatter_Force_LR_clicked(self, widget):
+        """
+            Display the scatter plot of force vs loading rate.
+        """
+        self.disp_scatter(['force', 'lr'], widget)
+
+    def on_button_scatter_force_dist_clicked(self, widget):
+        """
+            Display the scatter plot of force vs distance.
+        """
+        self.disp_scatter(['dist', 'force'], widget)
+
+    def on_button_scatter_force_stiffness_clicked(self, widget):
+        """
+            Display the scatter plot of force vs stiffness.
+        """
+        self.disp_scatter(['force', 'stiff'], widget)
+
+    def on_button_scatter_LR_Dist_clicked(self, widget):
+        """
+            Display the scatter plot of loading rate vs distance.
+        """
+        self.disp_scatter(['dist', 'lr'], widget)
+
+    def on_button_scatter_LR_Stiffness_clicked(self, widget):
+        """
+            Display the scatter plot of loading rate vs stiffness.
+        """
+        self.disp_scatter(['lr', 'stiff'], widget)
+
+    def on_button_scatter_Dist_Stiffness_clicked(self, widget):
+        """
+            Display the scatter plot of distance vs stiffness.
+        """
+        self.disp_scatter(['dist', 'stiff'], widget)
+
+    def on_button_scatter_Force_RelStiff_clicked(self, widget):
+        """
+            Display the scatter plot of force vs relative stiffness.
+        """
+        self.disp_scatter(['relstiff', 'force'], widget)
+
+    def on_button_scatter_LR_RelStiff_clicked(self, widget):
+        """
+            Display the scatter plot of loading rate vs relative stiffness.
+        """
+        self.disp_scatter(['relstiff', 'lr'], widget)
+
+    def on_button_scatter_Dist_RelStiff_clicked(self, widget):
+        """
+            Display the scatter plot of distance vs rel.stiffness.
+        """
+        self.disp_scatter(['relstiff', 'dist'], widget)
+
+    def get_histo_range(self, d_type):
+        """
+            Get the histogram range of the specified type.
+        """
+        if d_type in ['force', 'lr', 'dist', 'stiff', 'relstiff',
+                      'length', 'plength']:
+            base_name = d_type
+        elif d_type in ['force_base']:
+            base_name = d_type[:-5]
+        min_val = self.widget[
+                            'spin_ev_' + base_name + '_hist_min'].get_value()
+        max_val = self.widget[
+                            'spin_ev_' + base_name + '_hist_max'].get_value()
+        col_size = self.widget[
+                            'spin_ev_' + base_name + '_hist_size'].get_value()
+        if d_type is 'relstiff':
+            dist = int(self.widget['spin_ev_relstiff_hist_dist'].get_value())
+            return [min_val, max_val, col_size, dist]
+        return [min_val, max_val, col_size]
+
+    def on_button_regenerate_event_properties_clicked(self, widget):
+        """
+            Regenerate the event properties.
+        """
+        if DEBUG:
+            print "Regenerate event. Call by :"
+            print widget
+        self.experiment.clear_event_prop_list()
+
+    ###########################################################################
+    ## Plot tab
+    def on_adj_plot_rel_dist_value_changed(self, widget):
+        """
+            Changing the relative distance value for the plot.
+        """
+        self.plot_rel_dist(widget.get_value())
+
+    def plot_rel_dist(self, dist):
+        """
+            Plot the relative stiffness at a specified distance.
+        """
+        dist = int(dist)
+        [data, group, fid, coord] = self.experiment.get_event_att('relstiff')
+        del coord
+        self.experiment.data_hist.set_type('relstiff')
+        self.experiment.data_hist.set_data('relstiff', data)
+        self.experiment.data_hist.set_range('relstiff',
+                                            [None, None, None, dist])
+        self.experiment.data_hist.set_group('relstiff', group)
+        self.experiment.data_hist.set_fid('relstiff', fid)
+        [data, group, fid, coord] = self.experiment.get_event_att(
+                                                                'relstiffctl')
+        self.experiment.data_hist.set_type('relstiffctl')
+        self.experiment.data_hist.set_data('relstiffctl', data)
+        self.experiment.data_hist.set_range('relstiffctl',
+                                            [None, None, None, dist])
+        self.experiment.data_hist.set_group('relstiffctl', group)
+        self.experiment.data_hist.set_fid('relstiffctl', fid)
+        if not exist(self.win_plot['TL Rel Stiffness']):
+            [window, widget] = self.regenerate_plot()
+            self.win_plot['TL Rel Stiffness'] = plot_gtk.TimeLapse(
+                                            window, widget,
+                                            title='Event relative stiffness',
+                                            win_title='Relative Stiffness')
+        self.win_plot['TL Rel Stiffness'].displayPlot(
+                                            self.experiment.data_hist)
+
+    def on_adj_rel_stiff_limite_value_changed(self, widget):
+        """
+            Modification of limit values of relative stiffness.
+        """
+        range_val = widget.get_value()
+        self.experiment.compute_relative_stiffness(exclude=range_val)
+        self.plot_rel_dist(self.widget['spin_rel_stiff_plot_dist'].get_value())
+
+    def on_button_plot_nbr_event_tl_clicked(self, widget):
+        """
+            Plots the number of event per scans.
+        """
+        event_nbr_list = self.experiment.event_nbr_list()
+        _px = range(len(event_nbr_list))
+        if not exist(self.win_plot['TL Nbr Event']):
+            [window, widget] = self.regenerate_plot()
+            self.win_plot['TL Nbr Event'] = plot_gtk.plotCurves(
+                                                window, widget,
+                                                xlabel='Time',
+                                                ylabel='Number of events',
+                                                title='Number of events',
+                                                win_title='Number of events')
+            self.win_plot['TL Nbr Event'].ylim = 0
+
+        self.win_plot['TL Nbr Event'].displayPlot(_px, event_nbr_list,
+                                                  linestyle='bo-')
+
+    ###########################################################################
+    ## Tomography tab
+    def on_button_compute_tomo_clicked(self, widget=None):
+        """
+            Computes the stiffness tomography.
+        """
+        if DEBUG:
+            print "Compute tomo. Call from :"
+            print widget
+        self.force_volume.stiffness_tomography_array()
+
+    def on_MainWindow_destroy(self, widget, data=None):
+        '''
+        Destroys the window
+        '''
+        if DEBUG:
+            print "Destroy main window :"
+            print widget, data
+        # saves the preferences...
+        if not(os.path.isdir(os.path.split(self.config['config'])[0])):
+            os.makedirs(os.path.split(self.config['config'])[0])
+        conf_id = open(self.config['config'], 'wb')
+        for keys in self.config.keys():
+            if keys == 'msgid':
+                conf_id.write(keys + ' = ' +
+                            self.config[keys].strftime('%Y, %m, %d') + '\n')
+            elif keys in ['linewidth', 'connect-server']:
+                conf_id.write(keys + ' = ' +
+                            str(self.config[keys]) + '\n')
+            else:
+                conf_id.write(keys + ' = ' + self.config[keys] + '\n')
+        conf_id.write('')
+        conf_id.close()
+        gtk.main_quit()
+
+    ###########################################################################
+    ## Mechanical prop. tab
+    def hist_mech_prop(self, dtype, depth=0):
+        """
+            Display histogram of mechanical properties.
+        """
+        [title, xlabel, window_name] = PLOT_LABEL[dtype]
+        self.experiment.set_data_hist(dtype, self.get_mech_histo_range(dtype),
+                                      depth=depth)
+        if not exist(self.win_plot[window_name]):
+            [window, widget] = self.regenerate_plot()
+            self.win_plot[window_name] = plot_gtk.plotHist(
+                            window, widget,
+                            title=title,
+                            xlabel=xlabel,
+                            y_rel=self.experiment.parameters['histo_y_rel'])
+        self.win_plot[window_name].hist(self.experiment.data_hist)
+        if self.experiment.parameters['plot_hist_gauss']:
+            self.win_plot[window_name].gauss(
+                            self.experiment.event_stat['stiff'])
+        self.win_plot[window_name].set_size(
+                            self.experiment.parameters['plot_size'])
+
+    def on_button_young_modulus_hist_clicked(self, widget):
+        """
+            Display histogram of young modulus.
+        """
+        if DEBUG:
+            print "Young modulus :"
+            print widget
+        # Get the depth value :
+        depth = self.widget['spin_ym_hist_depth_nb'].get_value()
+        self.hist_mech_prop('young_modulus', depth=depth)
+
+    def get_mech_histo_range(self, dtype):
+        """
+            Get the range of histogram of mechanical properties.
+        """
+        if dtype in ['young_modulus']:
+            base_name = dtype
+        min_val = self.widget['spin_' + base_name + '_hist_min'].get_value()
+        max_val = self.widget['spin_' + base_name + '_hist_max'].get_value()
+        col_size = self.widget['spin_' + base_name + '_hist_size'].get_value()
+        return [min_val, max_val, col_size]
+
+    ###########################################################################
+    #                               About dialog
+    def on_about_activate(self, widget):
+        '''
+        Display the about dialog.
+        '''
+        if DEBUG:
+            print "About dialog called from :"
+            print widget
+        self.about_dialog.run()
+        self.about_dialog.hide()
+
+    ###########################################################################
+    #                       Compare Experiment Dialog
+    def on_compare_exp_activate(self, widget):
+        """
+            Displays the compare experiment dialog
+        """
+        if DEBUG:
+            print "Compare experiment. Call from :"
+            print widget
+        if self.experiment is not None:
+            self.widget_exp_compare['label_main_filename'].set_label(
+                                            self.experiment.short_name)
+        self.compare_exp_dialog.run()
+        self.compare_exp_dialog.hide()
+
+    def on_open_exp_compare_clicked(self, widget):
+        """
+            Opens the compare experiment
+        """
+        if DEBUG:
+            print "Compare experiment. Call from :"
+            print widget
+        self.temp_exp_compare = self.load_exp()
+        self.widget_exp_compare['comp_exp_filename'].set_label(
+                                            self.temp_exp_compare.short_name)
+        self.widget_exp_compare['label_comp_filename'].set_label(
+                                            self.temp_exp_compare.short_name)
+
+    def on_button_compare_exp_validate_clicked(self, widget):
+        """
+            Compare experiments.
+        """
+        if DEBUG:
+            print "validation of compare expexperiment :"
+            print widget
+        self.experiment_compare = self.temp_exp_compare
+        del self.temp_exp_compare
+        self.plot_properties.main_exp_label = \
+                        self.widget_exp_compare['entry_main_label'].get_text()
+        self.plot_properties.comp_exp_label = \
+                        self.widget_exp_compare['entry_comp_label'].get_text()
+        col_type = self.widget_exp_compare[
+                                         'combo_plot_color_type'].get_active()
+        if col_type == 0:
+            self.plot_properties.color_type = 'color'
+        elif col_type == 1:
+            self.plot_properties.color_type = 'bw'
+        self.plot_properties.plot_compare = True
+
+    def on_button_compare_exp_cancel_clicked(self, widget):
+        """
+            Cancel the modification of the comparison
+        """
+        if DEBUG:
+            print "compare experiment called by : "
+            print widget
+        if hasattr(self, 'temp_exp_compare'):
+            del self.temp_exp_compare
+        if hasattr(self, 'experiment_compare'):
+            del self.experiment_compare
+        self.plot_properties.comp_exp_label = None
+        self.plot_properties.plot_compare = False
+
+    def plot_curve(self):
+        """
+            Plot the curve according to the user choice.
+        """
+        [_px, _py] = [self.force_volume.trace_x, self.force_volume.trace_y]
+        if self.force_volume.to_plot('Av'):
+            if not exist(self.win_plot['Curve Plot']):
+                [window, widget] = self.regenerate_plot()
+                self.win_plot['Curve Plot'] = plot_gtk.plotCurves(
+                                          window, widget,
+                                          title='Deflection-Distance Curve',
+                                          linewidth=self.config['linewidth'])
+            self.win_plot['Curve Plot'].displayPlot(_px, _py)
+            if self.force_volume.to_plot('PoC'):
+                [poc, _cx, _cy, error, seg_slice, deriv] = \
+                                    self.force_volume.get_poc_display()
+                self.win_plot['Curve Plot'].hold('On')
+                if deriv is not None:
+                    self.win_plot['Curve Plot'].displayPlot(deriv[0],
+                                                              deriv[1])
+                self.win_plot['Curve Plot'].displayPlot(_cx, _cy,
+                                                          'g-', alpha=0.3)
+                self.win_plot['Curve Plot'].displayPlot(_px[poc: poc + 1],
+                                                          _py[poc: poc + 1],
+                                                          'go')
+                self.win_plot['Curve Plot'].displayPlot(_cx, _cy + error,
+                                                          'r-', alpha=0.5)
+                self.win_plot['Curve Plot'].displayPlot(_cx, _cy - error,
+                                                          'r-', alpha=0.5)
+                self.win_plot['Curve Plot'].displayPlot(_px[seg_slice],
+                                                          _py[seg_slice],
+                                                          'r-', alpha=1)
+                self.win_plot['Curve Plot'].hold('Off')
+        if self.force_volume.to_plot('Re'):
+            [_rx, _ry] = [self.force_volume.retrace_x,
+                          self.force_volume.retrace_y]
+            if not exist(self.win_plot['Curve Plot']):
+                [window, widget] = self.regenerate_plot()
+                self.win_plot['Curve Plot'] = plot_gtk.plotCurves(
+                                          window, widget,
+                                          title='Deflection-Distance Curve',
+                                          linewidth=self.config['linewidth'])
+            if self.force_volume.to_plot('Av'):
+                self.win_plot['Curve Plot'].hold('On')
+            self.win_plot['Curve Plot'].displayPlot(_rx, _ry, 'r-')
+            self.win_plot['Curve Plot'].hold('Off')
+            if self.force_volume.to_plot('Event'):
+                det_event = self.force_volume.current_curve(
+                        'Event',
+                        [self.experiment.parameters['event_detect_weight'],
+                        self.experiment.parameters['event_fit_model']])
+                self.win_plot['Curve Plot'].hold('On')
+                if det_event:
+                    for event in det_event:
+                        self.win_plot['Curve Plot'].displayPlot(
+                                                    _rx[event['Slice']],
+                                                    _ry[event['Slice']], 'g')
+                        self.win_plot['Curve Plot'].displayPlot(
+                                                    [_rx[event['min']]],
+                                                    [_ry[event['min']]], 'go')
+                        self.win_plot['Curve Plot'].displayPlot(
+                                                    [_rx[event['max']]],
+                                                    [_ry[event['max']]], 'wo')
+                        self.win_plot['Curve Plot'].displayPlot(
+                                                    event['fit_x'],
+                                                    event['fit_y'],
+                                                    'c')
+                self.win_plot['Curve Plot'].hold('Off')
+        if exist(self.win_plot['Curve Plot']):
+            self.win_plot['Curve Plot'].set_size(
+                                    self.experiment.parameters['plot_size'])
+        if self.force_volume.to_plot('Indent'):
+            all_plot = False
+            [poc, _cx, _cy, error, seg_slice, deriv] = \
+                                        self.force_volume.get_poc_display()
+            [_px, _py] = self.force_volume.get_current_indent_curve('trace')
+            [part_x, part_y] = self.force_volume.get_segments_indent()
+            # Prepare dots coordinates to plot
+            dot_x = [item[-1] for item in part_x]
+            dot_y = [item[-1] for item in part_y]
+            if not exist(self.win_plot['Indent Plot']):
+                [window, widget] = self.regenerate_plot()
+                self.win_plot['Indent Plot'] = plot_gtk.plotCurves(
+                                          window, widget,
+                                          title='Indention Curve',
+                                          xlabel='Indentation [nm]',
+                                          ylabel='Force [nN]',
+                                          linewidth=self.config['linewidth'])
+            self.win_plot['Indent Plot'].set_size(
+                                    self.experiment.parameters['plot_size'])
+            if all_plot:
+                self.win_plot['Indent Plot'].displayPlot(_px, _py)
+            else:
+                self.win_plot['Indent Plot'].displayPlot(
+                                                    _px[:poc] - _px[poc - 1],
+                                                    _py[:poc] - _py[poc - 1])
+            self.win_plot['Indent Plot'].hold('On')
+            if all_plot:
+
+                self.win_plot['Indent Plot'].displayPlot(dot_x, dot_y,
+                                                         'ko', alpha=0.4)
+            else:
+                self.win_plot['Indent Plot'].displayPlot(dot_x - _px[poc - 1],
+                                                         dot_y - _py[poc - 1],
+                                                         'ko', alpha=0.4)
+            if DEBUG and self.force_volume.to_plot('Re'):
+                [_rx, _ry] = self.force_volume.get_current_indent_curve(
+                                                                    'retrace')
+                self.win_plot['Indent Plot'].displayPlot(_rx, _ry, 'r-')
+                if self.force_volume.to_plot('Event'):
+                    det_event = self.force_volume.current_curve(
+                            'Event',
+                            self.experiment.parameters['event_detect_weight'])
+                    self.win_plot['Indent Plot'].hold('On')
+                    if det_event:
+                        for event in det_event:
+                            self.win_plot['Indent Plot'].displayPlot(
+                                                    _rx[event['Slice']],
+                                                    _ry[event['Slice']], 'g')
+                            self.win_plot['Indent Plot'].displayPlot(
+                                                    [_rx[event['min']]],
+                                                    [_ry[event['min']]], 'go')
+                            self.win_plot['Indent Plot'].displayPlot(
+                                                    [_rx[event['max']]],
+                                                    [_ry[event['max']]], 'wo')
+            self.win_plot['Indent Plot'].hold('Off')
+
+
+def exist(win_plot):
+    """
+        Test the existance of a window plot.
+    """
+    if win_plot == 0:
+        return 0
+    return not win_plot.destroyed
+
+
+def create_header_tree(header):
+    """
+        >>> test = create_header_tree(None)
+    """
+    treestore = gtk.TreeStore(str)
+    for parent in HEADER.keys():
+        piter = treestore.append(None, ['%s' % parent])
+        for child in HEADER[parent]:
+            treestore.append(piter, ['%s : %s' % (child, str(header[child]))])
+    return treestore
+
+
+def display_error(message, mtype=''):
+    """
+        Display an error message.
+    """
+    if message == 'no_fv':
+        msg = ('%s\n%s\n%s') % (
+              "No force volume file loaded.\n",
+              "Please load fv file using file>new to create new experiment",
+              "or file>load to load a saved experiment.")
+    if message == 'no_compute':
+        msg = "The %s is not compute. Please compute it first." % mtype
+    dialog = gtk.MessageDialog(type=gtk.MESSAGE_ERROR,
+                               buttons=gtk.BUTTONS_OK,
+                               message_format=msg)
+    dialog.set_title('Error')
+
+    try:
+        _icon = resource_filename('openfovea', 'Icon/openfovea.png')
+    except NotImplementedError:
+        _icon = 'openfovea/Icon/openfovea.png'
+    try:
+        dialog.set_icon_from_file(_icon)
+    except GError:
+        pass
+    if dialog.run():
+        dialog.destroy()
+
+
+def display_message(message):
+    """
+        Display a message box with the given message.
+    """
+    _msg = ''
+
+    for _line in message[1:]:
+        _msg += _line
+        _msg += '\n'
+    _msg = _msg[:-2]
+    dialog = gtk.MessageDialog(type=gtk.MESSAGE_INFO, buttons=gtk.BUTTONS_OK)
+    dialog.set_properties('secondary-use-markup', True)
+    dialog.set_title(message[0])
+    dialog.set_markup(_msg)
+    try:
+        _icon = resource_filename('openfovea', 'Icon/openfovea.png')
+    except NotImplementedError:
+        _icon = 'openfovea/Icon/openfovea.png'
+    dialog.set_icon_from_file(_icon)
+    if dialog.run():
+        dialog.destroy()
+
+
+def ask_message(message):
+    """
+        Display a
+    """
+    dialog = gtk.MessageDialog(type=gtk.MESSAGE_QUESTION,
+                               buttons=gtk.BUTTONS_YES_NO)
+    dialog.set_default_response(gtk.RESPONSE_YES)
+    dialog.set_properties('secondary-use-markup', True)
+    dialog.set_title(message[0])
+    dialog.set_markup(message[1])
+    try:
+        _icon = resource_filename('openfovea', 'Icon/openfovea.png')
+    except NotImplementedError:
+        _icon = 'openfovea/Icon/openfovea.png'
+    dialog.set_icon_from_file(_icon)
+    response = dialog.run()
+    dialog.destroy()
+    return response
+WIN_TITLE = "Open Fovea"
+HEADER = {
+'Equipment': ['Microscope',
+               'spring_constant'],
+'Parameters': [  # 'force_bytes_per_pixel',
+                 # 'hard_z_scale',
+                 # 'image_scale',
+                'sensit_deflection',
+                 # 'sens_z_scan'
+               ],
+'Scan': [  # 'image_mode',
+          'scan_size',
+           # 'force_samples_per_curve',
+           # 'image_number_lines',
+          'number_curves',
+           # 'ramp_size',
+           # 'size_x',
+           # 'size_y'
+          'size'],
+'Misc': ['date', 'note'],
+#'Data': [  # 'force_data_length',
+#           # 'force_data_offset',
+#           # 'image_length',
+#           # 'image_offset',
+#          'image_samps_per_line',
+#          'matrix_length',
+#          'x_factor']
+}
+# Label = label : [title, x_label, window_name]
+PLOT_LABEL = {
+'force': ['Event force', 'Force [nN]', 'Hist Event Force'],
+'force_base': ['Event force relative to baseline', 'Force [nN]',
+                'Hist Event Force'],
+'lr': ['Loading rate', 'Loading rate [nN/s]', 'Hist Event LR'],
+'dist': ['Event distance', 'distance [nm]', 'Hist Event Dist'],
+'stiff': ['Event stiffness', 'Stiffness [Pa]', 'Hist Event Stiff'],
+'relstiff': ['Event relative stiffness', 'Stiffness [Pa]',
+              'Hist Event Rel Stiff'],
+'young_modulus': ['Young modulus', 'Stiffness [Pa]', 'Hist Young Modulus'],
+'length': ['Event length', 'Length [nm]', 'Hist Event Length'],
+'plength': ['Event persistent length', 'Persistent length [nm]',
+                'Hist Event Persistent Length']}
+# Window = window : [window name, window title, graph title]
+PLOT_WINDOW = {
+'forcelr': ['Scatter_FvsLR', 'Scatter Force VS Loading rate'],
+'lrforce': ['Scatter_FvsLR', 'Scatter Force VS Loading rate'],
+'forcedist': ['Scatter_FvsDist', 'Scatter Force VS Distance'],
+'distforce': ['Scatter_FvsDist', 'Scatter Force VS Distance'],
+'forcestiff': ['Scatter_FvsStiff', 'Scatter Force VS Stiffness'],
+'stiffforce': ['Scatter_FvsStiff', 'Scatter Force VS Stiffness'],
+
+'force_baselr': ['Scatter_FvsLR', 'Scatter Force VS Loading rate'],
+'lrforce_base': ['Scatter_FvsLR', 'Scatter Force VS Loading rate'],
+'force_basedist': ['Scatter_FvsDist', 'Scatter Loading rate VS Stiffness'],
+'distforce_base': ['Scatter_FvsDist', 'Scatter Loading rate VS Stiffness'],
+'force_basestiff': ['Scatter_FvsStiff', 'Scatter Force VS Stiffness'],
+'stiffforce_base': ['Scatter_FvsStiff', 'Scatter Force VS Stiffness'],
+
+'lrdist': ['Scatter_LRvsDist', 'Scatter Loading rate VS Distance'],
+'distlr': ['Scatter_LRvsDist', 'Scatter Loading rate VS Distance'],
+'lrstiff': ['Scatter_LRvsStiff', 'Scatter Loading rate VS Stiffness'],
+'stifflr': ['Scatter_LRvsStiff', 'Scatter Loading rate VS Stiffness'],
+'diststiff': ['Scatter_DistvsStiff', 'Scatter Distance VS Stiffness'],
+'stiffdist': ['Scatter_DistvsStiff', 'Scatter Distance VS Stiffness'],
+'forcerelstiff': ['Scatter_FvsRelStiff',
+                   'Scatter Force VS Relative Stiffness'],
+'relstiffforce': ['Scatter_FvsRelStiff',
+                   'Scatter Force VS Relative Stiffness'],
+'lrrelstiff': ['Scatter_LRvsRelStiff',
+                'Scatter Loading Rate VS Realtive Stiffness'],
+'relstifflr': ['Scatter_LRvsRelStiff',
+                'Scatter Loading Rate VS Realtive Stiffness'],
+'distrelstiff': ['Scatter_DistvsRelStiff',
+                  'Scatter Distance VS Relative Stiffness'],
+'relstiffdist': ['Scatter_DistvsRelStiff',
+                  'Scatter Distance VS Relative Stiffness'],
+'poc array': [None, 'poc_map', 'Point of contact'],
+'piezo array': ['Piezo Height', 'Piezo_Map', 'Piezo Height'],
+'topography array': ['Topography Map', 'Topo_map',
+                      'Topography (zero force image)'],
+'stiffness array': ['Stiffness Map', 'Stiff_map', 'Stiffness'],
+'ev_pos array': ['Event Map', 'Ev_pos_map', 'Event position'],
+'ev_force array': ['Event Force Map', 'Ev_force_map', 'Event force'],
+'ev_dist array': ['Event Distance Map', 'Ev_dist_map', 'Event distance'],
+'ev_len array': ['Event Length Map', 'Ev_len_map', 'Event length']}
+
+WINDOW2ARRAY = {
+    'Topography Map': 'Topography',
+    'Piezo Height': 'Piezo',
+    'Stiffness Map': 'Stiffness',
+    'Event Map': 'Event',
+    'Event Force Map': 'Event force',
+    'Event Distance Map': 'Event dist'}
+
+# MOSAIC_PLOT is a dict which contains the values for mosaic name :
+# mosaic_name[0] = name of the window plot
+# mosaic_name[1] = title of the window
+# mosaic_name[2] = title of the plot
+# mosaic_name[3] = cmap
+MOSAIC_PLOT = {
+    'Piezo': ['Mosaic Piezo', 'Mosaic of piezo', 'Piezo images', 'afm image'],
+    'Topography': ['Mosaic Topo', 'Mosaic of topos', 'Topographies',
+                    'afm image'],
+    'Stiffness': ['Mosaic Stiffness', 'Mosaic of stiffness', 'Stiffness',
+                   'jet'],
+    'Event': ['Mosaic Event', 'Mosaic of events', 'Events', 'gray'],
+    'Event force': ['Mosaic Event Force', 'Mosaic of event force',
+                     'Event forces', 'gray']}
+
+
+def main(arg=None):
+    '''
+        OpenFovea main function
+    '''
+    if os.name == 'posix':
+        try:
+            if os.uname()[0] == 'Linux':
+                try:
+                    locale.setlocale(locale.LC_ALL, 'en_GB.UTF8')
+                except locale.Error:
+                    locale.setlocale(locale.LC_ALL, 'en_US.UTF8')
+            elif os.uname()[0] == 'Darwin':
+                locale.setlocale(locale.LC_ALL, 'en_GB')
+        except locale.Error:
+            gtk.MessageDialog(type=gtk.MESSAGE_ERROR)
+            message = \
+                "Locale en_GB does not seem to be installed on your system." +\
+                "\nPlease install it."
+            message_sec = "On Linux system : change the file" +\
+                  "\n/etc/locale.gen" +\
+                  "\nto uncomment the corresponding line and run, as root :" +\
+                  "\nlocale-gen"
+            error = gtk.MessageDialog(buttons=gtk.BUTTONS_CLOSE,
+                                  type=gtk.MESSAGE_ERROR,
+                                  message_format=message)
+            error.format_secondary_text(message_sec)
+            error.set_title('Installation Error')
+            error.run()
+    elif os.name == 'nt':
+        locale.setlocale(locale.LC_ALL, 'english')
+    app = OpenFoveaMainGui(arg)
+    app.window.show()
+    gtk.main()
+
+if __name__ == '__main__':
+    locale.setlocale(locale.LC_ALL, 'en_GB.UTF8')
+    APP = OpenFoveaMainGui()
+    APP.window.show()
+    gtk.main()
+
+    #toto = open('../welcome')
+    #message = toto.readlines()
+    #display_message(message)

Added: trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/plot_generic.py
===================================================================
--- trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/plot_generic.py	                        (rev 0)
+++ trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/plot_generic.py	2012-08-20 10:43:48 UTC (rev 12094)
@@ -0,0 +1,2224 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+'''
+This module contains the necessary tools to plot graphics independently from the
+gui.
+
+The examples saves the result in a folder named FIGURE_FOLDER. This is a string
+that contain the folder where the figure are plotted.
+'''
+
+# for script installation
+from pkg_resources import resource_filename # pylint: disable-msg=E0611
+import os, sys
+
+import pdb        # pdb.set_trace()
+import numpy
+from scipy import stats
+
+try:
+    matplotlib.__version__
+except NameError:
+    import matplotlib
+    matplotlib.use('Agg', warn=False)
+    import matplotlib.pyplot as plt
+
+from matplotlib.patches import Circle, Rectangle, FancyArrow
+from matplotlib.widgets import Cursor
+from matplotlib.ticker import NullFormatter
+from mpl_toolkits.axes_grid.anchored_artists import AnchoredText
+NULLFMT = NullFormatter()
+
+from fovea_toolbox import post_proc
+
+try:
+    NO_DATA_FILENAME = resource_filename('openfovea','Icon/NoData.png')
+except NotImplementedError:
+    NO_DATA_FILENAME = 'openfovea/Icon/NoData.png'
+try:
+    NO_DATA_IMAGE = matplotlib.image.imread(NO_DATA_FILENAME)
+except IOError:
+    NO_DATA_FILENAME = os.path.join(os.path.dirname(sys.executable), 'openfovea/Icon/NoData.png')
+    NO_DATA_IMAGE = matplotlib.image.imread(NO_DATA_FILENAME)
+class Plot(object):
+    """
+        This is the generic plot class that will be inherited from the other.
+        It has no plot capabilities, but have the standard attribute.
+    """
+    def __init__(self):
+        self.figure = plt.figure()
+        self.axis = self.figure.add_subplot(111)
+        self.colors = ['blue', 'green', 'red', 'cyan', 'magenta', 'yellow',
+                       'black', 'white']
+        self.win_size = [8, 6]
+        self.scale = ['linear', 'linear']
+        self.type = None
+    def save(self, filename):
+        """
+            Save your plot in a file.
+        """
+        
+        self.figure.savefig(filename)
+        
+    def hold(self, value):
+        """
+            Change the hold state of the axis.
+            Accepted values are :
+            
+                * 'On' or True to make two plots.
+                * 'Off' or False to override the last plot.
+        """
+        
+        if value in ('On', True):
+            self.axis.hold(True)
+        elif value in ('Off', False):
+            self.axis.hold(False)
+        
+    def set_size(self, width, height, deep=False):
+        """
+            Change the size of the figure.
+        """
+        # Figure size is inch * dpi
+        #dpi = self.figure.get_dpi()
+        #inch = self.figure.get_size_inches()
+        #
+        ##
+        # Normally, the figure size in pixel is the inch * dpi.
+        # But I see that it's inch * 100... I force it to 100 and wait for explanations later.
+        new_inch = [float(width) / 100, float(height) / 100]
+        self.win_size = new_inch
+        if deep:
+            self.figure.set_size_inches(new_inch)
+    def set_xscale(self, scale=None):
+        if scale is not None:
+            self.scale[0] = scale
+        self.axis.set_xscale(self.scale[0])
+    def get_type(self):
+        return self.type
+class Curve(Plot):
+    """
+        Plot a curve on a window. Stores the standard values required for the
+        plot in OpenFovea so that I don't have to think about it later.
+        
+        >>> import numpy
+        
+        >>> x_data = numpy.arange(0, 10, 0.1)
+        >>> y_data = numpy.sin(x_data)
+        >>> y_data_2 = numpy.sin(x_data + 1)
+        
+        >>> test = Curve(xlabel = 'x axis', ylabel = 'y axis', title = 'plot title')
+        >>> test.plot(x_data, y_data)
+        >>> test.hold(True)
+        >>> test.plot(x_data, y_data_2, linestyle='go')
+        >>> test.save(FIGURE_FOLDER + 'plot.svg')
+    """
+    
+    def __init__(self, xlabel='Scanner Extention [nm]',
+                       ylabel='Cantilever Deflection [nm]',
+                       title='Force-Distance curve',
+                       linewidth=1.5):
+        Plot.__init__(self)
+        
+        self.xlabel = xlabel
+        self.ylabel = ylabel
+        self.title = title
+        self.axis.hold(False)
+        self.axis.set_xlabel(self.xlabel)
+        self.axis.set_ylabel(self.ylabel)
+        self.axis.set_title(self.title)
+        self.axis.grid(True)
+        self.lim = None
+        self.linewidth = linewidth
+        self.type = 'curve'
+    def plot(self, x_data, y_data, linestyle='b-', alpha=1):
+        """
+            Plot your data with the specified style.
+        """
+        if self.lim is not None:
+            # The plot has already been initialized. Then, we get the current
+            # limit in order to restore it after the plot.
+            self.lim['x'] = self.axis.get_xlim()
+            self.lim['y'] = self.axis.get_ylim()
+        self.axis.plot(x_data, y_data, linestyle, linewidth=self.linewidth, alpha=alpha)
+        self.__reinitialize()
+        
+    def __reinitialize(self):
+        """
+            This is to reinitialize your plot. You don't need to manually call
+            it, as it is automatically called when you do a plot.
+        """
+        
+        self.axis.set_xlabel(self.xlabel)
+        self.axis.set_ylabel(self.ylabel)
+        self.axis.set_title(self.title)
+#        if self.ylim is not None:
+#            self.axis.set_ylim(self.ylim)
+        if self.lim is not None:
+            self.axis.set_xlim(self.lim['x'])
+            self.axis.set_ylim(self.lim['y'])
+        else:
+            self.lim = {'x' : self.axis.get_xlim(),
+                        'y' : self.axis.get_ylim()}
+            
+        self.axis.grid(True)
+class ErrorBar(Curve):
+    def __init__(self, xlabel='Depth [nm]',
+                       ylabel='Young Modulus [Pa]',
+                       title='Mean Stiffness',):
+        Curve.__init__(self, xlabel, ylabel, title)
+        self.axis2 = self.axis.twinx()
+        self.pretty_axis()
+    def average_stiffness(self, data, group=None, group_info=None, linestyle='b-', style='isol', show_count=True):
+        """
+            Plot the errorbar with the specified style
+            
+            * Parameters :
+                data : list
+                group : list
+                group_info : list
+                linestyle : str
+                style : str
+                    Defines the style of the average. This is pertinent only
+                    with grouped data.
+                    'isol' : each item of a group is isolated. The average and
+                             standard deviation reflects the population
+                             homogeneity. If one file is 245 ± 10 and the other
+                             is 255 ± 15, the result will be 250 ± 5.
+                    'merge' : Each item of a group is merged. The average and
+                              standard deviation reflects the pixels
+                              homogeneity. If one file is 245 ± 10 with 10
+                              values, the other is 255 ± 15 with 20 values, the
+                              result will be 251 ± 13
+        """
+        self.axis.cla()
+        self.axis2.cla()
+        if group is not None:
+            # data is a set of several measurements each of them belonging to a
+            # group
+            if group_info is None:
+                # no information about the groups...
+                group_info = {'id' : numpy.unique(group),
+                      'label' : ['group %i'%gid for gid in numpy.unique(group)],
+                      'display' : [True for gid in numpy.unique(group)], 
+                      }
+            group = numpy.array(group)
+            list_group = [group_info['id'][i] for i in numpy.nonzero(group_info['display'])[0]]
+            for item in list_group:
+                #pdb.set_trace()
+                gindex = group_info['id'].index(item)
+                index_list = numpy.nonzero(group == group_info['id'][gindex])[0]
+                # We recover the data that has to be plotted
+                _data = [data[i]['mean'] for i in index_list]
+                _std = [data[i]['std'] for i in index_list]
+                _count = [data[i]['count'] for i in index_list]
+                # Here, we have the maximum depth in the files of the current group.
+                _deep = [data[i]['deep'] for i in index_list]
+                _tot_size = [len(item) for item in _deep]
+                #_max_size = max([len(item) for item in _deep])
+                deep = _deep[_tot_size.index(max(_tot_size))]
+                if style == 'merge':
+                    # We have to fill with 0 the arrays that are smaller.
+                    _data = numpy.array([list(item) + [0] * (max(_tot_size) - len(item))
+                                                            for item in _data])
+                    _std = numpy.array([list(item) + [0] * (max(_tot_size) - len(item))
+                                                            for item in _std])
+                    _count = numpy.array([list(item) + [0] * (max(_tot_size) - len(item))
+                                                            for item in _count])
+                    new_mean = (_data * _count).sum(0) / _count.sum(0)
+                    new_std = (_std ** 2 * (_count - 1)).sum(0) / _count.sum(0) - 1
+                    new_std = new_std ** 0.5
+                elif style == 'isol':
+                    # We have to fill with nan the arrays that are smaller.
+                    new_data = numpy.ma.array(numpy.zeros((len(_data), max(_tot_size))),
+                                          mask=numpy.ones((len(_data),
+                                                           max(_tot_size))))
+                    new_count = numpy.zeros((len(_data), max(_tot_size)))
+                    for i in range(len(_data)):
+                        new_count[i,:len(_count[i])] = _count[i]
+                    new_count = new_count.sum(0)
+                    for i in range(len(_data)):
+                        new_data[i][:len(_data[i])] = _data[i]
+                        new_data[i].mask[0:len(_data[i])] = 0
+                    new_mean = new_data.mean(0)
+                    new_std = new_data.std(0)
+#                    _data = numpy.array([list(item) + [nan] * (max(_tot_size) - len(item))
+#                                                            for item in _data])
+#                    _std = numpy.array([list(item) + [nan] * (max(_tot_size) - len(item))
+#                                                            for item in _std])
+#                    _count = numpy.array([list(item) + [nan] * (max(_tot_size) - len(item))
+#                                                            for item in _count])
+#                    new_mean = _data.mean(0)
+#                    new_std = _data.std(0)
+                self.plot(deep, new_mean, new_std, label=group_info['label'][gindex])
+                if show_count:
+                    self.plot_y2(deep, new_count)
+        else:
+            self.plot(data['deep'], data['mean'], data['std'])
+            if show_count:
+                self.plot_y2(data['deep'], data['count'])
+        self.pretty_axis(show_y2=show_count)
+    def pretty_axis(self, show_y2=False):
+        yaxis = self.axis.get_yaxis()
+        yaxis.set_label_position('left')
+        yaxis.set_ticks_position('left')
+        yaxis = self.axis2.get_yaxis()
+        yaxis.set_label_position('right')
+        yaxis.set_ticks_position('right')
+        yaxis.set_visible(show_y2)
+        
+    def plot(self, data_x, data_y, y_err, label=None, linestyle='b-'):
+        self.axis.hold(True)
+        self.axis.errorbar(data_x, data_y, y_err, label=label)
+        self.axis.hold(False)
+        if label is not None:
+            self.axis.legend(loc='best')
+    def plot_y2(self, data_x, data_y, linestyle='--'):
+        self.axis2.plot(data_x, data_y, linestyle)
+        self.axis2.set_ylabel('Number of data')
+        
+class Array(Plot):
+    """
+        Plot an array. It can behaves differently corresponding to the array
+        type you give.
+            
+        >>> import numpy
+        
+        >>> data = numpy.random.randn(10,10)
+        >>> test = Array('Random array')
+        >>> test.plot(data)
+        >>> test.save(FIGURE_FOLDER + 'array_pixel.svg')
+        
+        If the scan size is specified, the array is recognized as nanometric
+        scale image.
+        
+        >>> test.title = 'Random array in nanometer'
+        >>> test.plot(data, scan_size=[1000, 1000])
+        >>> test.save(FIGURE_FOLDER + 'array_nm.svg')
+        
+        A scale bar can be added to show the correlation between color and
+        values.
+        
+        >>> test.colorbar = True
+        >>> test.plot(data, scan_size=[1000, 1000])
+        >>> test.save(FIGURE_FOLDER + 'array_cb.svg')
+        
+        If the data is changed, the colormap is updated :
+        
+        >>> data = data*100
+        >>> test.plot(data, scan_size=[1000, 1000])
+        >>> test.vmax = 140
+        >>> test.save(FIGURE_FOLDER + 'array_cb100.svg')
+        
+        And you can plot a marker at a position given in pixel :
+        
+        >>> test.colorbar = False
+        >>> test.plot(data, scan_size=[1000, 1000])
+        >>> test.marker = (5, 4)
+        >>> test.save(FIGURE_FOLDER + 'array_marker.png')
+    """
+    
+    def __init__(self, title='Data array',):
+        Plot.__init__(self)
+        self.type = 'pcolor'
+        # definitions for the axes
+        left = 0.15
+        bottom = 0.15
+        ar_width = 0.7
+        cb_width = 0.03
+        height = 0.75
+        plot_dist = 0.03
+        
+        left_bar = left + ar_width + plot_dist
+        rect_arr = [left, bottom, ar_width, height]
+        rect_cb = [left_bar, bottom, cb_width, height]
+        
+        self.figure.clf()
+        self.axis = {'array' : self.figure.add_axes(rect_arr),
+                     'colorbar' : self.figure.add_axes(rect_cb)
+                     }
+        ## Default values:
+        self.array = None # stores the array
+        self.scale = {'size' : None, # Is the size of the scan
+                      'unit' : '[pixel]', # is the unit of the size
+                      'array' : None, # Is the array to display the label
+                      'voxel_size' : [1, 1], # The size of a pixel
+                      'initialized' : False,
+                      'show' : True
+                      }
+        self.color_scale = {'min' : None,
+                            'max' : None,
+                            'colorbar' : False, # Do we plot or not the
+                                                # scalebar.
+                            'cmap' : 'gray'}
+                            
+        self.p_marker = {'display' : False,
+                         'indice_x' : None,
+                         'indice_y' : None,
+                        'patch' : None} # matplotlib patch object to mark the
+                                         # position
+        self.path = { 'start' : None, # The start point
+                      'stop' : None, # The end point
+                      'list' : None, # The list of points that define the path
+                      'plot' : None, # Contain the curve traced on the plot array.
+                      'grab' : None, # Which point to grab = 'start' or 'stop'
+                      'refresh' : None, # Contains the list of points that define the path. Is erased when used.
+                      }
+        #TODO Remove self.trace and self.show_trace
+        self.trace = None # Contain the curve traced on the plot array.
+        self.title = title
+        
+    def __setattr__(self, att, value):
+        if att is 'colorbar':
+            self.__dict__['color_scale']['colorbar'] = value
+        elif att is 'cmap':
+            self.__dict__['color_scale']['cmap'] = value
+        elif att is 'vmin':
+            self.__dict__['color_scale']['min'] = value
+            if self.array is not None:
+                self.plot()
+        elif att is 'vmax' :
+            self.__dict__['color_scale']['max'] = value
+            if self.array is not None:
+                self.plot()
+        elif att is 'marker':
+            self.__dict__['p_marker']['display'] = True
+            self.__dict__['p_marker']['indice_x'] = value[0]
+            self.__dict__['p_marker']['indice_y'] = value[1]
+            #self.mark_pos(value)
+            self.mark_pos()#plot()
+        else:
+            self.__dict__[att] = value
+    def __getattr__(self, att):
+        if att is 'colorbar':
+            return self.__dict__['color_scale']['colorbar']
+        else:
+            return self.__dict__[att]
+    def plot(self, array=None, scan_size=None):
+        """
+            Displays the array.
+            The scan size has to be in nanometer.
+        """
+        ## Initialize the variables
+        self.axis['array'].cla()
+        if array is not None:
+            self.array = array
+        if type(self.array) == numpy.ma.core.MaskedArray and \
+                                        numpy.all(self.array.mask.all(True)):
+            self.axis['array'].imshow(NO_DATA_IMAGE)
+            self.axis['array'].set_axis_off()
+            self.axis['colorbar'].set_visible(False)
+            return
+            #raise ValueError, 'Array with only masked values.'
+        if not self.scale['initialized']:
+            if scan_size in [0, None]:
+                scan_size = None
+            elif 0 in scan_size:
+                scan_size = None
+            shape = self.array.shape
+            self.scale['array'] = [numpy.arange(0, shape[0]+1) for i in range(2)]
+            self.scale['size'] = [1 for i in range(2)]
+            self.scale['unit'] =  ['[pixel]' for i in range(2)]
+            self.scale['voxel_size'] = [1 for i in range(2)]
+        if scan_size is not None:
+            shape = self.array.shape
+            if isinstance(scan_size, (int, float)):
+                scan_size = [float(scan_size), float(scan_size)]
+            else:
+                scan_size = [float(dim) for dim in scan_size]
+            for dim in range(2):
+                if scan_size[dim] < 1000:
+                    self.scale['unit'][dim] = '[nm]'
+                    self.scale['size'][dim] = scan_size[dim]
+                elif scan_size[dim] >= 1000:
+                    self.scale['unit'][dim] = r'[$\mathregular{\mu}$m]'
+                    self.scale['size'][dim] = scan_size[dim] / 1000.
+                self.scale['array'][dim] = numpy.arange(
+                                0,
+                                self.scale['size'][dim] + self.scale['size'][dim] / shape[0],
+                                self.scale['size'][dim] / shape[0])
+                self.scale['voxel_size'][dim] = self.scale['size'][dim]/shape[dim]
+            self.scale['initialized'] = True
+#        if not self.scale['initialized']:
+#            self.scale['array'] = [numpy.arange(0, shape[0]+1) for i in range(2)]
+#            self.scale['unit'] =  ['[pixel]' for i in range(2)]
+        # Plot
+        self.axis['array'].set_title(self.title)
+        image = self.axis['array'].pcolormesh(self.scale['array'][0],
+                         self.scale['array'][1],
+                         self.array.transpose(),
+                         vmin=self.color_scale['min'],
+                         vmax=self.color_scale['max'],
+                         cmap=self.color_scale['cmap'])
+        self.axis['array'].axis([0, self.scale['array'][0][-1],
+                                 0, self.scale['array'][1][-1]])
+        if self.scale['show']:
+            self.axis['array'].set_xlabel('Size ' + self.scale['unit'][0])
+            self.axis['array'].set_ylabel('Size ' + self.scale['unit'][1])
+        else:
+            self.axis['array'].set_xticks([])
+            self.axis['array'].set_yticks([])
+        if self.color_scale['colorbar']:
+            self.axis['colorbar'].set_visible(True)
+            self.axis['colorbar'].cla()
+            self.figure.colorbar(image, self.axis['colorbar'])
+        else:
+            self.axis['colorbar'].set_visible(False)
+        if self.p_marker['display']:
+            self.mark_pos()
+            
+    def mark_pos(self):
+        """
+            Mark the position of the cursor.
+        """
+        pos_x = self.p_marker['indice_x'] * self.scale['voxel_size'][0]
+        pos_y = self.p_marker['indice_y'] * self.scale['voxel_size'][1]
+        if self.p_marker['patch'] is not None:
+            self.p_marker['patch'].set_xy((pos_x, pos_y))
+        else:
+            self.p_marker['patch'] = Rectangle((pos_x, pos_y),
+                                                self.scale['voxel_size'][0],
+                                                self.scale['voxel_size'][1],
+                                                zorder=10)
+            self.p_marker['patch'].set_antialiased(True)
+            self.p_marker['patch'].set_linewidth(1)
+            self.p_marker['patch'].set_facecolor((1.0, 1.0, 1.0, 1.0))
+            self.p_marker['patch'].set_alpha(0.7)
+            self.axis['array'].hold(True)
+            self.axis['array'].add_patch(self.p_marker['patch'])
+    def on_gride_click(self, event):
+        if event.button == 1:
+            # Left mouse button ==> goto
+            return [event.xdata, event.ydata]
+        elif event.button == 3:
+            # Right mouse button ==> slice
+            posx = int(event.xdata / self.scale['voxel_size'][0])
+            posy = int(event.ydata / self.scale['voxel_size'][1])
+            self.set_path(posx, posy)
+    def show_trace(self, trace):
+        """
+            Show the trace.
+        """
+        if self.trace is None:
+            self.trace = self.axis['array'].plot(trace[0], trace[1], picker=5,
+                                                 linewidth = 4, alpha=0.5)
+        else:
+            self.trace[0].set_data(trace)
+    def set_path(self, posx, posy):
+        """
+            Create a path on the gride.
+        """
+        if self.path['start'] is None:
+            self.path['start'] = [posx, posy]
+        elif self.path['stop'] is None:
+            self.path['stop'] = [posx, posy]
+            # Create the path and show it
+            self.path['list'] = post_proc.generate_path(self.path['start'],
+                                                        self.path['stop'])
+            self.path['refresh'] = self.path['list']
+            plot_list = self.path['list']
+            if self.path['plot'] is None:
+                self.path['plot'] = self.axis['array'].plot(
+                                    plot_list[0] * self.scale['voxel_size'][0],
+                                    plot_list[1] * self.scale['voxel_size'][1],
+                                    color = 'white', linewidth = 5, alpha = 0.6)
+            else: 
+                self.path['plot'][0].set_data(plot_list *
+                                              self.scale['voxel_size'][0])
+        else:
+            picker = 3
+            if ((posx - picker < self.path['start'][0] < posx + picker) and
+                 (posy - picker < self.path['start'][1] < posy + picker)):
+            #if [posx, posy] == self.path['start']:
+                self.path['grab'] = 'start'
+            if ((posx - picker < self.path['stop'][0] < posx + picker) and
+                 (posy - picker < self.path['stop'][1] < posy + picker)):
+                self.path['grab'] = 'stop'
+    def get_path(self):
+        """
+            Get the path and erase it.
+        """
+        path, self.path['refresh'] = self.path['refresh'], None
+        return path
+    def on_button_release(self, event):
+        self.path['grab'] = None
+    def move_mouse(self, event):
+        """
+            What to do when the mouse is moved...
+        """
+        if not event.inaxes:
+            return
+        if self.path['grab'] == 'start':
+            self.path['start'] = [int(event.xdata / self.scale['voxel_size'][0]),
+                                  int(event.ydata / self.scale['voxel_size'][1])]
+            plot_list = self.path['list']
+            self.path['list'] = post_proc.generate_path(self.path['start'], self.path['stop'])
+            self.path['plot'][0].set_data(plot_list * self.scale['voxel_size'][0])
+            self.path['refresh'] = self.path['list']
+        elif self.path['grab'] == 'stop':
+            self.path['stop'] = [int(event.xdata / self.scale['voxel_size'][0]),
+                                  int(event.ydata / self.scale['voxel_size'][1])]
+            plot_list = self.path['list']
+            self.path['list'] = post_proc.generate_path(self.path['start'], self.path['stop'])
+            self.path['plot'][0].set_data(plot_list * self.scale['voxel_size'][0])
+            self.path['refresh'] = self.path['list']
+        #print event.xdata
+
+class TimeLapse(Plot):
+    """
+        Plots the time laps with a barplot displaying the average before and
+        after a treatment.
+
+        For example :
+        
+        >>> import numpy
+        
+        Let's make some difference between data before 100 and after 100
+        
+        Data between 0-9 belong to group "0" and between 10-14 to group "1"
+
+        >>> test = TimeLapse()
+        
+        
+        Let's do with DataPlot object.
+        
+        Our data is made of 15 data points with 10 measurments each. Relative
+        stiffness is computed on 3 distances. So let's generate the final list
+        like this :
+        
+        >>> tl_array = numpy.random.randn(15 * 10)
+        >>> data = [tl_array for i in range(3)]
+        
+        >>> ctl_array = numpy.random.randn(15 * 10)
+        >>> data_ctl = [ctl_array/(i+1) for i in range(3)]
+        
+        We generate the file index :
+        
+        >>> index = numpy.mgrid[0:15, 0:10][0]
+        >>> index.shape = 15 * 10
+        
+        >>> group = [0 for i in range(10*10)] + [1 for i in range(5*10)]
+        >>> group = [group for i in range(3)]
+        >>> plot_data = PlotData()
+        
+        >>> plot_data.set_type('relstiff')
+        >>> plot_data.set_data('relstiff', data)
+        >>> plot_data.set_range('relstiff', [-5, 5, 0.1, 0])
+        >>> plot_data.set_group('relstiff', group)
+        >>> plot_data.set_fid('relstiff', index)
+        
+        And the same with the control (and let's add a group to look):
+        
+        >>> plot_data.set_data('relstiffctl', data_ctl)
+        >>> plot_data.set_range('relstiffctl', [-5, 5, 0.1, 0])
+        >>> plot_data.set_group('relstiffctl', group)
+        >>> plot_data.set_fid('relstiffctl', index)
+        
+        >>> test.plot(plot_data)
+        >>> test.save(FIGURE_FOLDER + 'PlotData_tl_group_ctl')
+    """
+    #TODO Clean old compatibility for vectors, all should go through DataPlot
+    #objects
+    def __init__(self, xlabel='Time',
+                       ylabel='Stiffness',
+                       title='Relative Stiffness'):
+        
+        Plot.__init__(self)
+        self.type = 'plot-bar'
+        # definitions for the axes
+        #
+        #       <----tl_width----> <bar_width>
+        #       +----------------+ +---------+ ^
+        #       |                | |         | |
+        #       |   Time-Lapse   | |   Bar   | height
+        #       |                | |         | |
+        # left  +----------------+ +---------+ v
+        #    bottom              <->
+        #                     plot_dist
+        
+        # definitions for the axes
+        left = 0.05
+        bottom = 0.1
+        tl_width = 0.7
+        bar_width = 0.22
+        height = 0.8
+        plot_dist = 0
+        
+        left_bar = left + tl_width + plot_dist
+        rect_tl = [left, bottom, tl_width, height]
+        rect_hist = [left_bar, bottom, bar_width, height]
+        
+        self.figure = plt.figure(figsize=(10, 2))
+        self.axis = {'tl' : self.figure.add_axes(rect_tl),
+                     'bar' : self.figure.add_axes(rect_hist)
+                     }
+        self.sem = 1
+    def plot(self, data, data_ctl=None, baseline=0):
+        """
+            Plots the data
+        """
+        # pylint: disable-msg=R0913
+        # disable the "too many argument" warning from pylint
+        
+        # Defines the properties of the box plot
+        box = {'size' : 0.45, # the size of the box
+               'slide' : 0.4}# how far the box slides
+                             # (between data and data_ctl)
+                             
+        ## Get the values to plot :
+        if not isinstance(data, PlotData):
+            raise AttributeError, "Data has to be a PlotData object."
+        indice = data.get_group('relstiff')
+        fileid = data.get_fid('relstiff')
+        if data_ctl is None:
+            fileid_ctl = data.get_fid('relstiffctl')
+            data_ctl = data.get_data('relstiffctl')
+            group_ctl = data.get_group('relstiffctl')
+        data = data.get_data('relstiff')
+        
+        time = numpy.unique(fileid)
+        
+        if indice is None:
+            indice = numpy.zeros(data.shape[0])
+        res_tl = compute_indice_stat(data, fileid)
+        res_bar = compute_indice_stat(data, indice)
+        
+        # Prepare the axes :
+        self.axis['tl'].cla()
+        self.axis['bar'].cla()
+        # And plot.
+        self.axis['tl'].errorbar(time, res_tl['mean'], res_tl['sem'],
+                                 fmt='-', color='black')
+        
+        self.axis['bar'].bar(res_bar['indice'], res_bar['mean'],
+                             width=box['size'], color='black', alpha=0.5)
+        self.axis['bar'].errorbar(res_bar['indice'] + box['size']/2.,
+                                  res_bar['mean'], res_bar['sem'],
+                                  fmt=None, ecolor='k')
+                                  
+        if data_ctl is not None:
+            # We have control to plot in dashed line :
+            if isinstance(data_ctl, PlotData):
+                # Another data set is given for the control.
+                indice_ctl = data_ctl.get_group('relstiff')
+                fileid_ctl = data_ctl.get_fid('relstiff')
+                group_ctl = data_ctl.get_group('relstiff')
+                data_ctl = data_ctl.get_data('relstiff')
+                
+            res_tl_ctl = compute_indice_stat(data_ctl, fileid_ctl)
+            res_bar_ctl = compute_indice_stat(data_ctl, group_ctl)
+            self.axis['tl'].hold(True)
+            time = numpy.unique(fileid_ctl)
+            self.axis['tl'].errorbar(time,
+                                     res_tl_ctl['mean'], res_tl_ctl['sem'],
+                                     fmt='--', color='gray')
+            
+            self.axis['bar'].bar(
+                    res_bar_ctl['indice'] + box['slide'], res_bar_ctl['mean'],
+                    width=box['size'], color='white', alpha=0.5)
+                    
+            self.axis['bar'].errorbar(
+                    res_bar_ctl['indice'] + box['slide'] + box['size'] / 2,
+                    res_bar_ctl['mean'], res_bar_ctl['sem'],
+                    fmt=None, ecolor='k')
+            self.axis['tl'].hold(False)
+                    
+        # Display the baseline in the time-lapse
+        self.axis['tl'].hold(True)
+        
+        baseline = [[time[0]-0.5, time[-1]+0.5],
+                    [baseline, baseline]]
+        
+        self.axis['tl'].plot(baseline[0], baseline[1], 'k-')
+        self.axis['tl'].set_xlim(baseline[0][0], baseline[0][1])
+        
+        # Control the plot axis
+        # 1) make y axis the same for both and do not display bar one
+        # 2) change the x axis of bar to display 'Before' and 'After'
+        tl_y_lim = self.axis['tl'].get_ylim()
+        bar_y_lim = self.axis['bar'].get_ylim()
+        
+        min_y = min(tl_y_lim[0], bar_y_lim[0])
+        max_y = max(tl_y_lim[1], bar_y_lim[1])
+        # 1)
+        self.axis['tl'].set_ylim(min_y, max_y)
+        self.axis['bar'].set_ylim(min_y, max_y)
+        self.axis['bar'].set_yticks([])
+        # 2)
+        self.axis['bar'].set_xticks(res_bar['indice'] + box['slide'] +
+                                    (box['size'] - box['slide']) / 2)
+        self.axis['bar'].set_xticklabels(res_bar['indice'])
+
+class Mosaic(Plot):
+    """
+        Plots the mosaic of several arrays.
+        
+        >>> from numpy.random import randn
+        >>> import pylab
+        
+        >>> array_list = [randn(10,10), randn(10,10), randn(15,15)]
+        >>> list_name = ['first and a very long text to test it...', 'second', 'third']
+        >>> test = Mosaic()
+        >>> test.plot(array_list, list_name = list_name)
+        >>> test.save(FIGURE_FOLDER + 'mosaic_test.png')
+        
+        Note that mask annotation is pickable.
+    """
+
+    def __init__(self):
+        Plot.__init__(self)
+        self.type = 'mosaic'
+        self.figure.clf()
+        self.axis = list()
+        self.text_annotation = list()
+        self.mask_annotation = list()
+        
+    
+    def plot(self, list_array, title = 'Mosaic plot',
+                   list_name = None, cmap = 'gray', list_mask = None):
+        """
+            Plot the Mosaic of arrays.
+        """
+        
+        #self.__init__()
+        size_list = len(list_array)
+        nbr_line = numpy.round(numpy.sqrt(size_list))
+        nbr_col = numpy.ceil(numpy.sqrt(size_list))
+        # Create the list of name
+        if list_name is None:
+            list_name = ['Image ' + '{0:0>2}'.format(v)
+                         for v in xrange(size_list)]
+        # Create the list of mask
+        if list_mask is None:
+            list_mask = [False for i in range(size_list)]
+        # Create the list of subplots
+        for item in xrange(len(list_array)):
+            new_array = None
+            self.axis.append(self.figure.add_subplot(nbr_line, nbr_col, item+1))
+            # determine what to plot
+            if list_array[item] is not None:
+                if list_array[item].ndim > 2:
+                    # This is a 3d array, then take the first one.
+                    if isinstance(list_array[item], numpy.ma.core.MaskedArray):
+                        if 0 in list_array[item][:, :, 0].mask:
+                            new_array = list_array[item][:, :, 0]
+                        else:
+                            new_array = None
+                else :
+                    # This is a 2d array, then take it like this.
+                    new_array = list_array[item]
+            # Plot it in the subplot.
+            if new_array is not None:
+                self.axis[item].pcolorfast(new_array.transpose(),
+                                           cmap=cmap)
+            else:
+                self.axis[item].imshow(NO_DATA_IMAGE)
+            self.axis[item].set_axis_off()
+        for item in xrange(len(list_array)):
+            # Annotate with the name given in the list.
+            ax_box = self.axis[item].get_position().get_points()
+            middle = (ax_box[0][0] + (ax_box[1][0] - ax_box[0][0]) / 2,
+                      ax_box[0][1] + (ax_box[1][1] - ax_box[0][1]) / 2)
+            self.text_annotation.append(
+                    self.axis[-1].annotate(list_name[item],
+                           xy=middle, xycoords = 'figure pixels',
+                           horizontalalignment = 'center',
+                           verticalalignment = 'center',
+                           fontsize = 12,
+                           fontweight = 'bold',
+                           bbox=dict(boxstyle="round", fc="0.8", alpha=0.8),
+                           visible = False
+                           )
+                    )
+            # Annotate with 'M' if masked, or nothing if not.
+            if list_mask[item]:
+                mask_color = 'red'
+                alpha = 0.7
+            else:
+                mask_color = 'green'
+                alpha = 0.3
+            bottom_right = (0,0)#ax_box[0][0], ax_box[0][1])
+            self.mask_annotation.append(
+                self.axis[item].annotate('M',
+                            xy=bottom_right, xycoords = 'axes fraction',
+                            horizontalalignment = 'left',
+                            verticalalignment = 'bottom',
+                            fontsize = 12,
+                            fontweight = 'bold',
+                            bbox=dict(boxstyle='round', fc=mask_color, alpha=alpha),
+                            visible = True, 
+                            picker=20,
+                            alpha=alpha)
+                )
+        self.figure.suptitle(title)
+        self.figure.canvas.mpl_connect('axes_enter_event', self.enter_array)
+        self.figure.canvas.mpl_connect('axes_leave_event', self.leave_array)
+        self.figure.canvas.mpl_connect('motion_notify_event', self.enter_array)
+        #self.figure.canvas.mpl_connect('pick_event', self.on_pick)
+    def index(self, event):
+        """
+            Get the index number of the axes and the object type where a mouse event occured.
+            
+            You can directly access the axis number of a mouse event :
+            
+            [index, otype] = mosaic.index(event)
+        """
+        axe = self.axis.index(event.mouseevent.inaxes)
+        if self.mask_annotation.count(event.artist):
+            # This is the mask artist that was clicked.
+            obj = 'mask'
+        return [axe, obj]
+    def enter_array(self, event):
+        """
+            Responsible for the mouse motion event, when the cursor enter an
+            axis.
+        """
+        
+        try:
+            self.text_annotation[self.axis.index(event.inaxes)].set_visible(
+                                                            True)
+            self.text_annotation[self.axis.index(event.inaxes)].xytext = \
+                                                            (event.x, event.y)
+        except ValueError:
+            pass
+    def leave_array(self, event):
+        """
+            Responsible for the mouse motion event, when the cursor leave an
+            axis.
+        """
+        try:
+            self.text_annotation[self.axis.index(event.inaxes)].set_visible(False)
+        except ValueError:
+            pass
+        
+class Histogram(Plot):
+    """
+        Plot the histogram of a data set.
+        This is an enhanced version of the hist function of matplotlib.
+        
+        >>> from numpy.random import randn
+        >>> data = randn(1000)
+        >>> test = Histogram(xlabel='Random [AU]')
+        
+        There is a simple way to plot your data just by giving your data array :
+
+        >>> test.plot(data)
+        >>> test.save(FIGURE_FOLDER + 'simple_hist.png')
+        
+        But there is a more advanced way, which is to make an instance of the
+        PlotData class, set it's properties and send it to plot :
+        
+        >>> plot_data = PlotData()
+        >>> plot_data.set_data('force', data)
+        >>> plot_data.set_range('force', [-5, 5, 0.1])
+        >>> test.plot(plot_data)
+        >>> test.save(FIGURE_FOLDER + 'PlotData_class_hist.png')
+        
+        Comparing several datasets is possible. Note that the second set of data
+        does not need to set the range. The range of the first one will be used.
+        
+        >>> plot_data2 = PlotData()
+        >>> plot_data2.set_data('force', data + 1.2)
+        >>> test.plot(plot_data, plot_data2, color_type='color')
+        >>> test.save(FIGURE_FOLDER + 'PlotData_cmpare_hist.png')
+        
+        We can also plot the kernel density estimation over the plot :
+        
+        >>> from fovea_toolbox.post_proc import find_gauss_fit
+        >>> result = find_gauss_fit(data, 1024)
+        >>> test.plot(plot_data)
+        >>> test.show_fit(result)
+        >>> test.save(FIGURE_FOLDER + 'PlotData_fit.png')
+        
+        You can also define some groups and plot the data according to the group
+        they belong to.
+        
+        >>> from numpy.random import rand
+        >>> data = randn(100)
+        >>> data2 = rand(100)
+        >>> data3 = randn(100) * rand(100)
+        >>> merged = list(data)+list(data2)+list(data3)
+        >>> group = [0 for i in range(100)] + \
+                    [1 for i in range(100)] + \
+                    [2 for i in range(100)]
+        
+        >>> plot_data = PlotData()
+        >>> plot_data.set_data('force', merged)
+        >>> plot_data.set_group('force', group)
+        >>> plot_data.set_range('force', [-5, 5, 0.1])
+        >>> test.plot(plot_data)
+        >>> test.save(FIGURE_FOLDER + 'PlotData_with_group.png')
+    """
+    
+    def __init__(self, xlabel = '...', title='Histogram', data_type='', y_rel=False):
+        Plot.__init__(self)
+        self.type = 'histogram'
+        self.xlabel = xlabel
+        self.axis2 = None
+        self.title = title
+        self.data = None
+        self.data2 = None
+        self.label, self.label2 = None, None
+        self.index = None
+        self.data_type = data_type
+        self.max_hist = None # Stores the maximum of histogram to scale the fit.
+        self.range = None # Stores the x_range of the histogram.
+        self.relative = y_rel # The y axis in relative or absolute mode.
+        self.text_annotation = {'list' : list(),
+                                'grabbed' : None,
+                                'clicked' : [0,0]}
+    def plot(self, data, data2 = None, label = None, label2 = None,
+                    hist_range = None, color_type = 'color', y2=False):
+        """
+            Plots the histogram.
+        """
+        frequency_factor = 1
+        if isinstance(data, PlotData):
+            self.range = data.range
+            if self.relative and  (data.nbr_curves is not None):
+                frequency_factor = 1 / float(data.nbr_curves)
+            else:
+                frequency_factor = 1
+            group = data.group
+            group_label = data.get_group_prop('label')
+            group_visible = data.get_group_prop('display')
+            group_id = data.get_group_prop('id')
+            data = data.data
+        else:
+            group = [0 for i in range(len(data))]
+            group_label = None
+            group_visible = [True]
+            group_id = [0]
+            self.range = hist_range
+        if isinstance(data2, PlotData):
+            if self.relative and (data2.nbr_curves is not None):
+                frequency_factor2 = 1 / float(data2.nbr_curves)
+            else:
+                frequency_factor2 = 1
+            group2 = data2.group
+            data2 = data2.data
+        elif data2 is not None:
+            group2 = [0 for i in range(len(data2))]
+            frequency_factor2 = 1
+        group = numpy.asanyarray(group)
+        data = numpy.asanyarray(data)
+        index = numpy.isfinite(data)
+        self.label = label
+        self.label2 = label2
+        if self.label is None:
+            self.label = '...'
+        if self.label2 is None:
+            self.label = '...'
+        if color_type == 'color':
+            color = ['blue', 'red']
+            edgecolor = ['black', 'black']
+        elif color_type == 'bw':
+            color = ['black', 'white']
+            edgecolor = ['black', 'black']
+        group = group[index]
+        list_group = [group_id[i] for i in numpy.nonzero(group_visible)[0]]
+        #list_group = numpy.unique(group)
+        self.data = data[index]
+        if data2 is not None:
+            group2 = numpy.asanyarray(group2)
+            data2 = numpy.asanyarray(data2)
+            index = numpy.isfinite(data2)
+            self.data2 = data2[index]
+        self.axis.cla()
+        if self.axis2 is not None:
+            self.axis2.cla()
+            self.axis.cla()
+            if data2 is None:
+                self.axis2.yaxis.set_visible(False)
+            else:
+                self.axis2.yaxis.set_visible(True)
+        if self.range == None:
+            if data2 is None:
+                for indice in range(group.min(), group.max()+1):
+                    pl_x = self.axis.hist(self.data[group==indice], alpha=0.5)
+            else:
+                pl_x = self.axis.hist(self.data)
+            if data2 is not None:
+                pl_x2 = self.axis.hist(self.data2, alpha=0.5)
+        else:
+            index = (self.range[0] < self.data) * (self.data < self.range[1])
+            if data2 is None:
+                _i = 0
+                for item in list_group:
+                    indice = index * (group == item)
+                    pl_x = numpy.histogram(self.data[indice],
+                                      numpy.arange(self.range[0],
+                                                   self.range[1],
+                                                   self.range[2]))
+                    pl_x = (pl_x[0] * frequency_factor, pl_x[1])
+                    self.axis.bar(pl_x[1][:-1],
+                                  pl_x[0],
+                                  color=self.colors[_i],
+                                  width=self.range[2],
+                                  label=group_label[item],#'Group ' + str(item),
+                                  alpha=0.5)
+                    _i += 1
+            else:
+                pl_x = numpy.histogram(self.data[index],
+                                      numpy.arange(self.range[0],
+                                                   self.range[1],
+                                                   self.range[2]))
+                pl_x = (pl_x[0] * frequency_factor, pl_x[1])
+                
+                if y2:
+                    if self.axis2 is None:
+                        self.axis2 = self.axis.twinx()
+                    axis = self.axis2
+                    self.axis.yaxis.tick_left()
+                    axis.yaxis.tick_right()
+                else:
+                    axis = self.axis
+                bar1 = self.axis.bar(pl_x[1][:-1],
+                                  pl_x[0],
+                                  width=self.range[2],
+                                  label=self.label,
+                                  alpha=0.5,
+                                  color=color[0],
+                                  edgecolor=edgecolor[0])
+                
+                index = ((self.range[0] < self.data2) *
+                        (self.data2 < self.range[1]))
+                self.data2 = self.data2[index]
+                
+                
+                pl_x2 = numpy.histogram(self.data2,
+                                       numpy.arange(self.range[0],
+                                                   self.range[1],
+                                                   self.range[2]))
+                pl_x2 = (pl_x2[0] * frequency_factor2, pl_x2[1])
+                bar2 = axis.bar(pl_x2[1][:-1],
+                                  pl_x2[0],
+                                  width=self.range[2],
+                                  label=self.label2,
+                                  alpha=0.5,
+                                  color=color[1],
+                                  edgecolor=edgecolor[1])
+                __max = max(max(pl_x[0]), max(pl_x2[0]))
+                __max = __max + __max*5/100.
+                if not y2:
+                    self.axis.set_ylim(0, __max)
+                #if label2 is not None:
+        if len(list_group) > 1 or data2 is not None:
+            if y2:
+                leg = plt.legend((bar1[0], bar2[0]),
+                                 (self.label, self.label2),
+                                 'best')
+                self.axis2.set_ylabel(self.label2)
+                self.axis.set_ylabel(self.label)
+            else:
+                leg = self.axis.legend(loc='best')
+            if leg is not None:
+                # If there is a legend... otherwise, make nothing.
+                frame  = leg.get_frame()
+                frame.set_alpha(0.4)
+        if len(pl_x[0]):
+            self.max_hist = max(pl_x[0])
+        else :
+            self.max_hist = self.range[1]
+        self.axis.set_xlabel(self.xlabel)
+        if self.range is not None:
+            self.axis.set_xlim(self.range[0], self.range[1])
+
+    def show_fit(self, prop):
+        self.text_annotation['list'] = list()
+        prop['kde'][1] = (prop['kde'][1] * self.max_hist /
+                          max(prop['kde'][1]) * 0.9)
+        prop['maxima'][1] = (prop['maxima'][1] * self.max_hist /
+                             max(prop['maxima'][1]) * 0.9)
+        self.axis.plot(prop['kde'][0], prop['kde'][1], linewidth = 1.5)
+        for [p_x, p_y, mean, std, count] in zip(prop['maxima'][0],
+                                            prop['maxima'][1],
+                                            prop['mean'],
+                                            prop['std'],
+                                            prop['count']):
+                                            
+            text = "Mean : " + str(round(mean, 4)) + "\n" +\
+                   "Std : " + str(round(std, 4)) + "\n" +\
+                   "Count : " + str(count)
+            self.text_annotation['list'].append(
+                self.axis.annotate("Peak : " + str(round(p_x, 4)) + "\n" + text,
+                                xy=(p_x, p_y), xytext=(p_x, p_y + p_y/20),
+                                textcoords='data',
+                                arrowprops=dict(arrowstyle="->",
+                                                connectionstyle="arc3"),
+                                                bbox=dict(boxstyle="round",
+                                                          fc="0.8",
+                                                          alpha=0.5)
+                                )
+                                )
+        if self.range is not None:
+            self.axis.set_xlim(self.range[0], self.range[1])
+        self.figure.canvas.mpl_connect('button_press_event',
+                                        self.grab_annotation)
+        self.figure.canvas.mpl_connect('button_release_event',
+                                        self.release_annotation)
+        self.figure.canvas.mpl_connect('motion_notify_event',
+                                        self.move_annotation)
+    def grab_annotation(self, event):
+        for item in self.text_annotation['list']:
+            text_pos = item.get_position()
+            bbox = item.get_bbox_patch()
+            if text_pos[0] < event.x < text_pos[0] + bbox.get_width():
+                if text_pos[1] < event.y < text_pos[1] + bbox.get_height():
+                    self.text_annotation['grabbed'] = item
+                    if event.inaxes:
+                        self.text_annotation['clicked'] = [
+                                                   event.xdata - item.xytext[0],
+                                                   event.ydata - item.xytext[1]]
+                    else:
+                        self.text_annotation['clicked'] = [0,0]
+    def release_annotation(self, event):
+        self.text_annotation['grabbed'] = None
+    def move_annotation(self, event):
+        #print "...", self.text_annotation['grabbed']
+        if self.text_annotation['grabbed'] is not None:
+            try:
+                if event.inaxes:
+                    pos_x = event.xdata - self.text_annotation['clicked'][0]
+                    pos_y = event.ydata - self.text_annotation['clicked'][1]
+                    self.text_annotation['grabbed'].xytext = (pos_x , pos_y)
+            except TypeError:
+                pass
+class Scatter(Plot):
+    """
+        Displays a scatter plot of the data provided.
+        The data are PlotData objects.
+        
+        >>> from numpy.random import randn
+        >>> data = randn(1000)
+        >>> data2 = randn(1000)*2 + 1.5
+        
+        >>> plot_data = PlotData()
+        >>> plot_data.set_data('force', data)
+        >>> plot_data.set_data('lr', data2)
+        >>> plot_data.set_range('force', [-5, 5, 0.1])
+        >>> plot_data.set_range('lr', [-5, 10, 0.2])
+        
+        >>> test = Scatter(xlabel='data1', ylabel='data2', title='test of scatter')
+        >>> #print plot_data.get_data('force')
+        >>> test.plot(plot_data, ['force', 'lr'])
+        >>> test.save(FIGURE_FOLDER + 'PlotData_Scatter.png')
+        >>> test.type = "Density"
+        >>> test.refresh()
+        >>> test.save(FIGURE_FOLDER + 'PlotData_Density.png')
+        
+        You can also define some groups and plot the data according to the group
+        they belong to.
+        
+        >>> from numpy.random import rand
+        >>> data = randn(100)
+        >>> data2 = rand(100)
+        >>> data3 = randn(100) * rand(100)
+        >>> merged = list(data)+list(data2)+list(data3)
+        >>> group = [0 for i in range(100)] + \
+                    [1 for i in range(100)] + \
+                    [2 for i in range(100)]
+        
+        >>> data4 = randn(100)
+        >>> data5 = rand(100)
+        >>> data6 = randn(100) * rand(100)
+        >>> merged2 = list(data4)+list(data5)+list(data6)
+        >>> group2 = [0 for i in range(100)] + \
+                    [1 for i in range(100)] + \
+                    [2 for i in range(100)]
+        
+        >>> plot_data = PlotData()
+        
+        >>> plot_data.set_data('force', merged)
+        >>> plot_data.set_group('force', group)
+        >>> plot_data.set_range('force', [-5, 5, 0.1])
+        
+        >>> plot_data.set_data('lr', merged2)
+        >>> plot_data.set_group('lr', group2)
+        >>> plot_data.set_range('lr', [-5, 5, 0.1])
+        
+        >>> test = Scatter(xlabel='data1', ylabel='data2', title='test of scatter')
+        >>> test.plot(plot_data, ['force', 'lr'])
+        >>> test.save(FIGURE_FOLDER + 'PlotData_Scatter_with_group.png')
+    """
+    
+    def __init__(self, xlabel='...', ylabel='...', title=''):
+        Plot.__init__(self)
+        self.xlabel = xlabel
+        self.ylabel = ylabel
+        self.type = 'scatter'
+        self.markers = ['o', # circle
+                        's', # square
+                        '^', # triangle up
+                        '>', # triangle right
+                        'v', # triangle down
+                        '<', # triangle left
+                        'd', # diamond
+                        'p', # pentagram
+                        'h', # hexagon
+                        '8', # octagon
+                        '+', # plus
+                        'x', # cross
+                        ]
+        self.data_x, self.data_y = None, None # Store the variables
+        self.range_x, self.range_y = None, None # Store the ranges
+        self.group_x, self.group_y = None, None # Store the groups
+        
+        # definitions for the axes
+        
+        #                          h-size
+        #       <-----width------> <---->
+        #       +----------------+          ^
+        #       |  hist_x        |          |
+        #       |                |          | h-size
+        #       +----------------+          v
+        #       +----------------+ +----+   ^
+        #       |                | | h  |   |
+        #       |                | | i  |   |
+        #       |   Scatter      | | s  |   |
+        #       |                | | t  |   |
+        #       |                | | -  |   |
+        #       |                | | y  |   |
+        # left  +----------------+ +----+   v
+        #    bottom              <->
+        #                     plot_dist
+        left, width = 0.1, 0.65
+        bottom, height = 0.1, 0.65
+        h_size = 0.2
+        bottom_h = left_h = left + width + 0.02
+
+        rect_scatter = [left, bottom, width, height]
+        rect_histx = [left, bottom_h, width, h_size]
+        rect_histy = [left_h, bottom, h_size, height]
+        
+        self.figure.clf()
+        
+        self.axis_scatter = self.figure.add_axes(rect_scatter)
+        self.axis_histx = self.figure.add_axes(rect_histx)
+        self.axis_histy = self.figure.add_axes(rect_histy)
+        self.clear()
+    def clear(self):
+        """
+            Reinitialize the plots.
+        """
+        
+        self.axis_histx.cla()
+        self.axis_histy.cla()
+        # no labels
+        self.axis_histx.xaxis.set_major_formatter(NULLFMT)
+        self.axis_histy.yaxis.set_major_formatter(NULLFMT)
+    def plot(self, data, data_type):
+        """
+            Plot the data.
+            The data has to be a PlotData object.
+            data_type is a list of two string representing the data to plot.
+        """
+        self.clear()
+        self.data_x = numpy.asarray(data.get_data(data_type[0]))
+        self.data_y = numpy.asarray(data.get_data(data_type[1]))
+        self.range_x = data.get_range(data_type[0])
+        self.range_y = data.get_range(data_type[1])
+        self.group_x = data.get_group(data_type[0])
+        self.group_y = data.get_group(data_type[1])
+        self.group_prop = { 'id' : data.get_group_prop('id'),
+                            'label' : data.get_group_prop('label'),
+                            'display' : data.get_group_prop('display')}
+        if self.type == 'scatter':
+            self.__scatter()
+        elif self.type == 'density':
+            self.__density()
+        else:
+            return
+            
+        x_index = ((self.range_x.min < self.data_x) *
+                   (self.data_x < self.range_x.max))
+        y_index = ((self.range_y.min < self.data_y) *
+                   (self.data_y < self.range_y.max))
+        self.axis_histx.hist(self.data_x[x_index],
+                                 numpy.arange(self.range_x.min,
+                                              self.range_x.max,
+                                              self.range_x.bin_size)
+                                 )
+        self.set_xscale(plot='hist')
+        self.axis_histy.hist(self.data_y[y_index],
+                                 numpy.arange(self.range_y.min,
+                                              self.range_y.max,
+                                              self.range_y.bin_size),
+                                 orientation='horizontal'
+                                 )
+    def refresh(self):
+        """
+            Refresh the graph without changing the data. Used to toogle between
+            scatter and density plot.
+        """
+        
+        if self.type == 'scatter':
+            self.__scatter()
+        elif self.type == 'density':
+            self.__density()
+        else:
+            return
+        
+    def __scatter(self):
+        """
+            Specific code to display the scatter plot.
+        """
+        
+        #list_group = numpy.unique(self.group_x)
+        list_group = [i for i in numpy.nonzero(self.group_prop['display'])[0]]
+        list_group = numpy.asarray(list_group)
+        if len(list_group) > 1:
+            use_group = 1
+            x_g_index = [self.group_x == i for i in list_group]
+            y_g_index = [self.group_y == i for i in list_group]
+        else:
+            use_group = 0
+        self.axis_scatter.cla()
+        if use_group:
+            for i in list_group:
+                try:
+                    index = list(list_group).index(i)
+                    self.axis_scatter.scatter(self.data_x[x_g_index[index]],
+                                          self.data_y[y_g_index[index]],
+                                          label=self.group_prop['label'][i],
+                                          #label='Group ' + str(i),
+                                          c=self.colors[index],
+                                          marker=self.markers[index],
+                                          alpha=0.5)
+                except ValueError, msg:
+                    if msg.args[0] == \
+                             'zero-size array to ufunc.reduce without identity':
+                        pass
+                    else:
+                        raise ValueError, msg
+                else:
+                    leg = self.axis_scatter.legend(loc='best')
+                    frame  = leg.get_frame()
+                    frame.set_alpha(0.4)
+        else:
+            self.axis_scatter.scatter(self.data_x, self.data_y, alpha=0.5)
+        self.axis_scatter.set_xlabel(self.xlabel)
+        self.axis_scatter.set_ylabel(self.ylabel)
+        self.set_xscale(plot='scatter')
+        self.axis_scatter.axis([self.range_x.min, self.range_x.max,
+                                self.range_y.min, self.range_y.max])
+        
+    def __density(self):
+        """
+            Specific code to display the density plot.
+        """
+        
+        self.axis_scatter.cla()
+        ## make the density plot
+        # Beginn...
+        finite = numpy.isfinite(self.data_x) * numpy.isfinite(self.data_y)
+        in_range = ((self.data_x < self.range_x.max) *
+                    (self.data_x > self.range_x.min) *
+                    (self.data_y < self.range_y.max) *
+                    (self.data_y > self.range_y.min))
+        index = finite * in_range
+        
+        vect_x = ((self.data_x - self.range_x.min) /
+             (self.range_x.max - self.range_x.min)) * 128
+            
+        vect_y = ((self.data_y - self.range_y.min) /
+             (self.range_y.max - self.range_y.min)) * 128
+             
+        lin_vect = numpy.asanyarray([vect_x[index], vect_y[index]])
+        kde = stats.kde.gaussian_kde(lin_vect)
+        # Regular grid to evaluate kde upon
+        mesh = numpy.mgrid[0:128, 0: 128]
+        grid_coords = numpy.append(mesh[0].reshape(-1, 1),
+                                    mesh[1].reshape(-1, 1),
+                                    axis=1)
+        arr_z = kde(grid_coords.T)
+        arr_z = arr_z.reshape(128, 128)
+        self.axis_scatter.imshow(arr_z.transpose(1, 0),
+                             origin='lower',
+                             extent=(self.range_x.min,
+                                     self.range_x.max,
+                                     self.range_y.min,
+                                     self.range_y.max),
+                             aspect='auto')
+        self.axis_scatter.set_xlabel(self.xlabel)
+        self.axis_scatter.set_ylabel(self.ylabel)
+        #self.set_xscale()
+    def set_xscale(self, scale=None, plot=None):
+        if scale is not None:
+            self.scale[0] = scale
+        if plot == 'scatter':
+            self.axis_scatter.set_xscale(self.scale[0])
+            self.axis_scatter.axis([self.range_x.min, self.range_x.max,
+                                    self.range_y.min, self.range_y.max])
+        elif plot == 'hist':
+            self.axis_histx.set_xscale(self.scale[0])
+            self.axis_histx.set_xlim(self.range_x.min, self.range_x.max)
+class Tomo(Plot):
+    """
+        Plot the interior of a 3D array.
+        
+        >>> from numpy.random import randn
+        >>> data = randn(64, 64, 100)
+        
+        Consider that the data are recorded on a square of 2µm per 2µm
+        
+        >>> test = Tomo(data, [2000, 2000])
+        >>> test.plot([20, 10, 50]) # Let's plot the position x=20, y=10, z=50
+        >>> test.save(FIGURE_FOLDER + 'Tomography.png')
+    """
+    
+    def __init__(self, tomo_array, scan_size=None):
+        Plot.__init__(self)
+        self.type='tomography'
+        # Defines the axes :
+        #                         plot_dist
+        #                            <->
+        #           <-----width------> <-----width------>
+        #           +----------------+                      ^
+        #           |                |                      |
+        #           |                |                      |
+        #           |   display Y    |                      | Height
+        #           |                |                      |
+        #           |                |                      |
+        #           |                |                      | ^
+        # bottom_2  +----------------+                      v plot_dist
+        #           +----------------+ +----------------+   ^ v
+        #           |                | |                |   |
+        #           |                | |                |   |
+        #           |   display X    | | display Z      |   | Height
+        #           |                | |                |   |
+        #           |                | |                |   |
+        #           |                | |                |   |
+        # bottom    +----------------+ +----------------+   v
+        #                              ^
+        #          left                L left_2
+        
+        width, height = 0.35, 0.35
+        left, bottom = 0.1, 0.1
+        plot_dist = 0.1
+        bottom_2 = bottom + width + plot_dist
+        left_2 = left + height + plot_dist
+
+        rect = {'display_x' : [left, bottom, width, height],
+                'display_y' : [left, bottom_2, width, height],
+                'display_z' : [left_2, bottom, width, height]}
+        self.figure.clf()
+        self.axis = dict()
+        self.cursor = dict()
+        for key, rectangle in zip(rect.keys(), rect.values()):
+            self.axis[key] = self.figure.add_axes(rectangle)
+            self.cursor[key] = Cursor(self.axis[key], useblit=True,
+                                     color='green', alpha=0.3, linewidth=2)
+        
+        ## Define the labels
+        self.unit = ['', '', '']
+        self.scale = {'x' : None,
+                      'y' : None,
+                      'z' : None,
+                      'scan_size' : None}
+        self.pixel_size = [None, None]
+        self.__set_label(tomo_array.shape, scan_size)
+        
+        ##
+        self.tomo_array = tomo_array
+        self.slice = [0, 0, 0] # the current slice [x, y, z]
+        self.colorScaleMax = self.tomo_array.max()
+        self.colorScaleMin = 0
+        
+    def plot(self, position, color_scale_min=None, color_scale_max=None):
+        if color_scale_min is not None:
+            self.colorScaleMin = color_scale_min
+        if color_scale_max is not None:
+            self.colorScaleMax = color_scale_max
+        self.slice = position
+        self.plot_x()
+        self.plot_y()
+        self.plot_z()
+    def plot_x(self):
+        '''
+        Refresh the x slice plot
+        '''
+        self.axis['display_x'].cla()
+        self.axis['display_x'].pcolor(
+                                self.scale['y'], self.scale['z'],
+                                self.tomo_array[self.slice[0],
+                                                :,
+                                                :].transpose(),
+                                vmin = self.colorScaleMin,
+                                vmax = self.colorScaleMax)
+        self.axis['display_x'].set_xlabel('Size' + self.unit[0])
+    def plot_y(self):
+        '''
+        Refresh the y slice plot
+        '''
+        self.axis['display_y'].cla()
+        self.axis['display_y'].pcolor(
+                                self.scale['x'], self.scale['z'],
+                                self.tomo_array[:,
+                                                self.slice[1],
+                                                :].transpose(),
+                                vmin = self.colorScaleMin,
+                                vmax = self.colorScaleMax)
+        self.axis['display_y'].set_xlabel('Size' + self.unit[1])
+    def plot_z(self):
+        '''
+        Refresh the z slice plot
+        '''
+        self.axis['display_z'].cla()
+        self.axis['display_z'].pcolor(
+                                self.scale['x'], self.scale['y'],
+                                self.tomo_array[:,
+                                                :,
+                                                self.slice[2]].transpose(),
+                                vmin = self.colorScaleMin,
+                                vmax = self.colorScaleMax)
+        self.axis['display_z'].set_xlabel('Size ' + self.unit[2])
+        self.axis['display_z'].set_ylabel('Size ' + self.unit[2])
+    def __set_label(self, shape, scan_size=None):
+        _scan_size = list(scan_size)
+        if scan_size is not None:
+            for dim in range(2):
+                if scan_size[dim] < 1000:
+                    self.unit[dim] = '[nm]'
+                elif scan_size[dim] >= 1000:
+                    self.unit[dim] = r'[$\mathregular{\mu}$m]'
+                    _scan_size[dim] = _scan_size[dim] / 1000.
+            self.scale['x'] = numpy.arange(0,
+                                           _scan_size[0] + _scan_size[0] / shape[0],
+                                           _scan_size[0] / shape[0])
+            self.scale['y'] = numpy.arange(0,
+                                           _scan_size[1] + _scan_size[1] / shape[1],
+                                           _scan_size[1] / shape[1])
+            self.scale['z'] = numpy.arange(0, shape[2])
+            self.pixel_size = [_scan_size[0] / shape[0], _scan_size[1] / shape[1]]
+        else:
+            self.scale['x'] = numpy.arange(0, shape[0])
+            self.scale['y'] = numpy.arange(0, shape[1])
+            self.scale['z'] = numpy.arange(0, shape[2])
+            self.pixel_size = [1,1]
+
+class InteractiveLinePlot(Plot):
+    """
+        Plots several lines in as many plots as the number of lines.
+        
+        * Parameters :
+            array_x : array_like
+                The x array that is common for all plots.
+            arrays : list of array_like
+                The y arrays that defines the plots.
+            label : list of str
+                The label that will be display to identify the plots.
+        
+        * Output :
+        
+        >>> import numpy
+        >>> array_x = numpy.arange(0, 6, 0.1)
+        >>> array_1 = array_x * 2
+        >>> array_2 = numpy.sin(array_x)
+        >>> array_3 = numpy.cos(array_x)
+        >>> test = InteractiveLinePlot()
+        >>> test.plot(array_x, [array_1, array_2, array_3],\
+                               ['linear', 'cos', 'sin'])
+    """
+    
+    def __init__(self):
+        Plot.__init__(self)
+        self.figure.clf()
+        
+        self.figure.canvas.mpl_connect('button_press_event',
+                                       self.button_press_event)
+        self.figure.canvas.mpl_connect('motion_notify_event',
+                                       self.mouse_move)
+        self.figure.canvas.mpl_connect('button_release_event',
+                                                    self.button_release_event)
+        self.figure.canvas.mpl_connect('pick_event', self.on_pick)
+        self.array_x = None
+        self.arrays_y = None
+        self.picked = None
+        self.info = None
+        self.plot_list = None
+    def button_press_event(self, event):
+        """
+            Function called when user click on the figure.
+            It hides visible graph we click on or display hidden graph we click
+            on.
+        """
+        
+        if event.inaxes in self.axis:
+            if event.button == 3:
+                
+                # right click
+                modify = self.axis.index(event.inaxes)
+                self.toggle_display(modify)
+            elif event.button == 1:
+                self.info_display(event)
+    def button_release_event(self, event):
+        self.picked = None
+    def toggle_display(self, axis_nbr):
+        """
+            Display or hide the axis.
+        """
+        
+        if self.axis[axis_nbr].get_visible():
+            # We hide this subplot and push all ones below to replace it.
+            # The hidden plot goes to the end of the display.
+            self.axis[axis_nbr].set_visible(False)
+            cur = self.axis[axis_nbr].get_geometry()
+            for item in self.axis:
+                tgeo = item.get_geometry()
+                if tgeo[2] > cur[2]:
+                    item.change_geometry(tgeo[0], tgeo[1], tgeo[2]-1)
+            
+            self.axis[axis_nbr].change_geometry(cur[0], cur[1], 
+                                              len(self.axis))
+        else:
+            self.axis[axis_nbr].set_visible(True)
+    def plot(self, array_x, arrays, label):
+        """
+            Fuction called to display the graph.
+        """
+        self.figure.clf()
+        self.axis = []
+        self.array_x = array_x
+        self.arrays_y = arrays
+        self.arrows = {'begin' : [None for i in range(len(arrays))],
+                       'end' : [None for i in range(len(arrays))]}
+        tot_nbr = len(arrays)
+        self.info = []
+        for nbr in range(1, len(arrays)+1):
+            self.axis.append(self.figure.add_subplot(
+                                int(str(tot_nbr) + str(1) + str(nbr))
+                                ))
+            self.info.append(
+                        self.axis[nbr-1].annotate('Right click on axes to get info',
+                               xy=[1.05, 0.7], xycoords = 'axes fraction',
+                               horizontalalignment = 'left',
+                               verticalalignment = 'center',
+                               fontsize = 10,
+                               #fontweight = 'bold',
+                               bbox=dict(boxstyle="round", fc="0.8", alpha=0.8),
+                               visible = True
+                               )
+                        )
+        self.plot_list = list()
+        for array, axis, label in zip(arrays, self.axis, label):
+            self.plot_list.append(axis.plot(array_x, array))
+            at = AnchoredText(label, loc=9, prop=None, pad=0., borderpad=0.5,
+                              frameon=False)
+            axis.add_artist(at)
+        self.figure.subplots_adjust(left=0.05, right=0.6)
+    def modify_plot(self, array_x, arrays):
+        self.array_x = array_x
+        self.arrays_y = arrays
+        for plots, array_y, axis in zip(self.plot_list, arrays, self.axis):
+            plots[0].set_data(array_x, array_y)
+            axis.set_xlim(min(array_x), max(array_x))
+            axis.set_ylim(min(array_y), max(array_y))
+    def info_display(self, event):
+        axis_nbr = self.axis.index(event.inaxes)
+        index = numpy.nonzero(self.array_x >= event.xdata)[0][0]
+        pos = [self.array_x[index], self.arrays_y[axis_nbr][index]]
+        if self.arrows['begin'][axis_nbr] == None:
+            self.create_arrow(index, 'begin')
+        if self.arrows['end'][axis_nbr] == None:
+            self.create_arrow(index, 'end')
+        else:
+            self.move_arrow(index)
+            self.get_info()
+    def create_arrow(self, index, side):
+        for axis_nbr in range(len(self.axis)):
+            lim = self.axis[axis_nbr].get_ylim()
+            length = (lim[1]-lim[0]) / 10.
+            lim = self.axis[axis_nbr].get_xlim()
+            width =  (lim[1]-lim[0]) / 50.
+            if type(self.arrays_y[axis_nbr][0]) == numpy.ma.core.MaskedArray:
+                pos = [self.array_x[index], self.arrays_y[axis_nbr][0][index]]
+            else:
+                pos = [self.array_x[index], self.arrays_y[axis_nbr][index]]
+            arrows = [FancyArrow(pos[0], pos[1] + length,
+                                    0, -length,
+                                    length_includes_head=True,
+                                    head_length=length, head_width=None,
+                                    width=width, picker=5),
+                        FancyArrow(pos[0], pos[1] - length,
+                                     0, length,
+                                     length_includes_head=True,
+                                     head_length=length, head_width=None,
+                                     width=width, picker=5)]
+            self.arrows[side][axis_nbr] = arrows
+            self.axis[axis_nbr].add_patch(self.arrows[side][axis_nbr][0])
+            self.axis[axis_nbr].add_patch(self.arrows[side][axis_nbr][1])
+    def move_arrow(self, index):
+        if self.picked == None:
+            return
+        for axis_nbr in range(len(self.axis)):
+            if type(self.arrays_y[axis_nbr][0]) == numpy.ma.core.MaskedArray:
+                pos = [self.array_x[index], self.arrays_y[axis_nbr][0][index]]
+            else:
+                pos = [self.array_x[index], self.arrays_y[axis_nbr][index]]
+            init_pos = self.arrows[self.picked][axis_nbr][0].get_xy()
+            diff = [pos[0] - init_pos[0][0], pos[1] - init_pos[0][1]]
+            init_pos += diff
+            init_pos = self.arrows[self.picked][axis_nbr][1].get_xy()
+            init_pos += diff
+    def mouse_move(self, event):
+        if not event.inaxes:
+            return
+        if event.button == 1:
+            self.info_display(event)
+    def on_pick(self, event):
+        nbr_graph = len(self.axis)
+        for gnb in range(nbr_graph):
+            res = (self.arrows['begin'][gnb][0] == event.artist) + (self.arrows['begin'][gnb][1] == event.artist)
+            if res:
+                self.picked = 'begin'
+            res = False
+            try:
+                res = (self.arrows['end'][gnb][0] == event.artist) + (self.arrows['end'][gnb][1] == event.artist)
+            except:
+                pass
+            if res:
+                self.picked = 'end'
+    def get_info(self):
+        xdata = [self.arrows['begin'][0][0].get_xy()[0][0],
+                 self.arrows['end'][0][0].get_xy()[0][0]]
+        indexes = [numpy.nonzero(self.array_x >= xdata[0])[0][0],
+                   numpy.nonzero(self.array_x >= xdata[1])[0][0]]
+        for axis in range(len(self.axis)):
+            text = self.create_info_text(axis, indexes)
+            self.info[axis].set_text(text)
+    def create_info_text(self, axis_nbr, indexes):
+        if type(self.arrays_y[axis_nbr][0]) == numpy.ma.core.MaskedArray:
+            pos = [[self.array_x[indexes[0]], self.arrays_y[axis_nbr][0][indexes[0]]],
+                   [self.array_x[indexes[1]], self.arrays_y[axis_nbr][0][indexes[1]]]]
+        else:
+            pos = [[self.array_x[indexes[0]], self.arrays_y[axis_nbr][indexes[0]]],
+                   [self.array_x[indexes[1]], self.arrays_y[axis_nbr][indexes[1]]]]
+
+        text = "Start Point : %.2f, %.2f\n"%(pos[0][0], pos[0][1]) +\
+               "End Point : %.2f, %.2f\n"%(pos[1][0], pos[1][1]) +\
+               "Horizontal distance : %.2f\n"%(pos[1][0]-pos[0][0]) +\
+               "Vertical distance : %.2f"%(pos[1][1]-pos[0][1])
+        return text
+
+class PlotData(object):
+    """
+        Stores the data and the propeties specific to this data set.
+    """
+    def __init__(self):
+        self.group_prop = {'id' : [],
+                           'label' : [],
+                           'display' : [],
+                           'set' : False}
+        self.group_dict = dict()
+        self.data_dict = dict()
+        self.range_dict = dict()
+        self.fileid_dict = dict()
+        self.coord_dict = dict()
+        for item in PLOT_DATA:
+            prop = PLOT_DATA[item]
+            self.group_dict[item] = prop[0]
+            self.data_dict[item] = prop[1]
+            self.range_dict[item] = prop[2]
+            self.fileid_dict[item] = prop[3]
+            self.coord_dict[item] = prop[4]
+        self.label = None
+        self.nbr_curves = None
+        self.type = 'force'
+
+    def __getattr__(self, att):# pylint disable-msg=R0911
+        if att is 'data':
+            if self.type in PLOT_DATA_TYPE['simple']:
+                return self.data_dict[self.type]
+            elif self.type in PLOT_DATA_TYPE['dist']:
+                return self.data_dict[self.type][
+                                                self.range_dict[self.type].dist]
+        elif att is 'range':
+            return self.range_dict[self.type].range
+        elif att is 'group':
+            if self.type in PLOT_DATA_TYPE['simple']:
+#                print "In PlotData.group..."
+#                print self.group_dict[self.type]
+                return self.group_dict[self.type]
+            elif self.type in PLOT_DATA_TYPE['dist']:
+                return self.group_dict[self.type][
+                                                self.range_dict[self.type].dist]
+    def get_group_prop(self, gtype):
+        """
+            Get the group property.
+                Parameters:
+                    gtype : str
+                        'id'
+                        'label'
+                        'display'
+        """
+        if self.group_prop['set']:
+            return self.group_prop[gtype]
+        else:
+            if gtype == 'id':
+                return numpy.unique(self.group)
+            elif gtype == 'label':
+                return ["Groupe %i"%numpy.unique(self.group)[0]]
+            elif gtype == 'display':
+                return [True]
+            else:
+                raise TypeError, "%s is not recognized attribute."
+    def set_group_prop(self, gtype, data):
+        """
+            Set the group property.
+                Parameter:
+                    gtype : str
+                    data : list
+        """
+        if gtype == 'all':
+            if data is not None:
+                self.group_prop = data
+                self.group_prop['set'] = True
+            else:
+                self.group_prop = {'id' : [],
+                                   'label' : [],
+                                   'display' : [],
+                                   'set' : False}
+        else:
+            self.group_prop[gtype] = data
+    def set_range(self, data_type, d_range):
+        """
+            Set the range of the data to plot.
+        """
+        if data_type in PLOT_DATA.keys():
+            self.range_dict[data_type].set_range(d_range)
+        else:
+            raise TypeError, "Data type %s not known." % data_type
+    def set_dist(self, dist):
+        """
+            Set the distance at which we want to get the relative values.
+        """
+        for data_type in PLOT_DATA_TYPE['dist']:
+            self.range_dict[data_type].dist = dist
+    def set_data(self, data_type, data):
+        """
+            Store the data to plot.
+        """
+        if type(data) is list:
+            if data_type in PLOT_DATA_TYPE['dist']:
+                data = [numpy.array(i) for i in data]
+            else:
+                data = numpy.asanyarray(data)
+        if data_type in PLOT_DATA.keys():
+            self.data_dict[data_type] = data
+            if self.group_dict[data_type] is None:
+                # Group is not related to current data, then reinitialize it.
+                if data_type in PLOT_DATA_TYPE['dist']:
+                    this_shape = [len(i) for i in data]
+                    group = []
+                    for item in this_shape:
+                        group.append([0 for this in range(item)])
+                    self.set_group(data_type, group)
+                else:
+                    self.set_group(data_type, [0 for i in range(len(data))])
+        else:
+            raise TypeError, "Data type %s not known." % data_type
+    def set_group(self, data_type, group):
+        """
+            Store the group of the data to plot.
+        """
+        if data_type in PLOT_DATA.keys():
+            self.group_dict[data_type] = group
+        else:
+            raise TypeError, "Data type %s not known." % data_type
+    def set_fid(self, data_type, fid):
+        """
+            Store the file index of the data to plot.
+        """
+        if data_type in PLOT_DATA.keys():
+            self.fileid_dict[data_type] = fid
+        else:
+            raise TypeError, "Data type %s not known." % data_type
+    def set_coord(self, data_type, coord):
+        """
+            Store the coordinate of the data to plot.
+        """
+        if data_type in PLOT_DATA.keys():
+            self.coord_dict[data_type] = coord
+        else:
+            raise TypeError, "Data type %s not known." % data_type
+        
+    def set_type(self, data_type):
+        """
+            Set the data type you want to plot
+        """
+        
+        if data_type in PLOT_DATA.keys():
+            self.type = data_type
+        else:
+            raise TypeError
+    def get_data(self, data_type, group=None):
+        """
+            Get the data that is stored.
+        """
+        if group == None:
+            group = self.group_prop['id']
+        totake = numpy.asarray([sum([i==j for j in group]) for i in self.group_dict[data_type]], dtype=bool)
+        
+        if data_type in PLOT_DATA_TYPE['simple']:
+            return self.data_dict[data_type][totake]
+        elif data_type in PLOT_DATA_TYPE['dist']:
+            try:
+                return self.data_dict[data_type][
+                                                self.range_dict[data_type].dist][totake]
+            except TypeError, message:
+                if str(message) == "'NoneType' object is unsubscriptable":
+                    return None
+    def get_range(self, data_type):
+        """
+            Get the range of the data.
+        """
+        return self.range_dict[data_type]
+    def get_group(self, data_type):
+        """
+            Get the group of the data.
+        """
+        # change the type and store the old one
+        old_data_type, self.type = self.type, data_type
+        
+        group = self.group
+        
+        self.type = old_data_type
+        
+        return group
+    def get_fid(self, data_type):
+        """
+            Get the file index of the data.
+        """
+        return self.fileid_dict[data_type]
+    def get_coord(self, data_type):
+        """
+            Get the file index of the data.
+        """
+        return self.coord_dict[data_type]
+        
+class PlotRange(object): # pylint: disable-msg=R0903
+    """
+        Stores the range of the display
+    """
+    def __init__(self):
+        self.min = None
+        self.max = None
+        self.bin_size = None
+        self.dist = None
+    def __setattr__(self, att, value):
+        if att is 'min':
+            if self.max is not None:
+                self.__dict__[att] = min(value, self.max)
+            else:
+                self.__dict__[att] = value
+        elif att is 'max':
+            if self.min is not None:
+                self.__dict__[att] = max(value, self.min)
+            else:
+                self.__dict__[att] = value
+        else:
+            self.__dict__[att] = value
+    def __getattr__(self, att):
+        if att is 'range':
+            return [self.min, self.max, self.bin_size]
+    def set_range(self, d_range):
+        """
+            set the range of the data.
+        """
+        if d_range[0] is not None:
+            self.min = d_range[0]
+        if d_range[1] is not None:
+            self.max = d_range[1]
+        if d_range[2] is not None:
+            self.bin_size = d_range[2]
+        try:
+            if d_range[3] is not None:
+                self.dist = d_range[3]
+        except IndexError:
+            pass
+        
+class PlotProperties(object): # pylint: disable-msg=R0903
+    """
+        Stores the plot properties
+    """
+    def __init__(self):
+        self.main_exp_label = None
+        self.comp_exp_label = None
+        self.color_type = 'bw'
+        self.plot_compare = False
+        self.min = None
+        self.max = None
+        self.bin_size = None
+        self.absolute = True
+        self.__type = {'Stiffness': 'jet',
+                       'Piezo': 'copper',
+                       'Topography': 'copper',
+                       'Event': 'gray',
+                       'Event force': 'gray',
+                       'Event distance': 'gray',
+                       'Event length': 'gray'}
+
+    def __setattr__(self, att, value):
+        if att is 'color_type':
+            if value in ['bw', 'black and white', 'BW']:
+                self.__dict__[att] = 'bw'
+            elif value in ['color', 'Color']:
+                self.__dict__[att] = 'color'
+        else:
+            self.__dict__[att] = value
+
+    def get_cmap(self, ptype):
+        if self.color_type == 'bw':
+            return 'gray'
+        else:
+            return self.__type[ptype]
+
+
+### Some useful functions
+def compute_array_stat(data):
+    """
+        Compute the statistic of the data for each time point.
+        For example :
+        
+        >>> import numpy
+        
+        # Let's generate an array of data filled with 1 and 2
+        
+        >>> data = numpy.ones((15,10))
+        >>> data[10:] = 2
+        
+        >>> indice = numpy.zeros(15)
+        >>> indice[10:] = 1
+        >>> result = compute_array_stat(data)
+        
+        # here is the result
+        
+        >>> result['mean']
+        array([ 1.,  1.,  1.,  1.,  1.,  1.,  1.,  1.,  1.,  1.,  2.,  2.,  2.,
+                2.,  2.])
+        >>> result['std']
+        array([ 0.,  0.,  0.,  0.,  0.,  0.,  0.,  0.,  0.,  0.,  0.,  0.,  0.,
+                0.,  0.])
+        >>> result['count']
+        array([ 10.,  10.,  10.,  10.,  10.,  10.,  10.,  10.,  10.,  10.,  10.,
+                10.,  10.,  10.,  10.])
+    """
+    mean = data.mean(1)
+    std = data.std(1)
+    if type(data) == numpy.ma.core.MaskedArray:
+        count = data.count(1)
+    else:
+        count = numpy.ones(data.shape[0]) * data.shape[1]
+    sem = std / numpy.sqrt(count)
+    
+    result = {'mean' : mean,
+              'std' : std,
+              'count' : count,
+              'sem' : sem}
+    return result
+    
+def compute_indice_stat(data, indice):
+    """
+        Compute the statistic of the data, according to the indice.
+        For example :
+        
+        >>> import numpy
+        
+        # Let's generate an array of data filled with 1 and 2
+        
+        >>> data = numpy.ones((150))
+        >>> data[100:] = 2
+        
+        >>> indice = numpy.zeros(150)
+        >>> indice[100:] = 1
+        >>> result = compute_indice_stat(data, indice)
+        
+        # here is the result
+        
+        >>> result['indice']
+        array([ 0.,  1.])
+        >>> result['mean']
+        array([ 1.,  2.])
+        >>> result['std']
+        array([ 0.,  0.])
+        >>> result['count']
+        array([ 100.,   50.])
+        
+        Let's make the same, but with on dimension vector.
+        
+        >>> data.shape = 15 * 10
+        >>> indice = [0 for i in range(10 * 10)] + [1 for i in range(5 * 10)]
+        
+        >>> result = compute_indice_stat(data, indice)
+        
+        # here is the result
+        
+        >>> result['indice']
+        array([0, 1])
+        >>> result['mean']
+        array([ 1.,  2.])
+        >>> result['std']
+        array([ 0.,  0.])
+        >>> result['count']
+        array([ 100.,   50.])
+        
+    """
+    indice_list = numpy.unique(indice)
+    mean = list()
+    std = list()
+    count = list()
+    sem = list()
+    indice_finite = numpy.isfinite(data)
+    for index in indice_list:
+        # doi_indice points to data with the good indice and which are finite
+        doi_indice = indice_finite * (indice == index)
+        doi = data[doi_indice] # doi means data of interrest
+        if len(doi):
+            mean.append(doi.mean())
+            std.append(doi.std())
+        else:
+            mean.append(numpy.nan)
+            std.append(numpy.nan)
+        if type(doi) == numpy.ma.core.MaskedArray:
+            count.append(doi.count())
+        elif len(doi.shape) == 2:
+            count.append(doi.shape[0] * doi.shape[1])
+        elif len(doi.shape) == 1:
+            count.append(doi.shape[0])
+    # change list to array_
+    mean, std, count = numpy.array(mean), numpy.array(std), numpy.array(count, dtype=float)
+    # Exclude values that have no count.
+    indice = count == 0.
+    mean[indice], std[indice], count[indice] = numpy.nan, numpy.nan, numpy.nan
+    sem = std / numpy.sqrt(count)
+    result = {'mean' : mean,
+              'std' : std,
+              'count' : count,
+              'sem' : sem,
+              'indice' : indice_list}
+    return result
+
+
+# PLOT_DATA stores the properties of standard properties.
+# [group_dict, data_dict, range_dict, fileid_dict, coord_dict]
+PLOT_DATA = {'force' : [None, None, PlotRange(), None, None],
+             'force_base' : [None, None, PlotRange(), None, None],
+             'lr' : [None, None, PlotRange(), None, None],
+             'dist' : [None, None, PlotRange(),None, None],
+             'stiff': [None, None, PlotRange(), None, None],
+             'stiff_ev': [None, None, PlotRange(), None, None],
+             'stiff_notev': [None, None, PlotRange(), None, None],
+             'relstiff' : [None, None, PlotRange(), None, None],
+             'relstiffctl' : [None, None, PlotRange(), None, None],
+             'young_modulus': [None, None, PlotRange(), None, None],
+             'length' : [None, None, PlotRange(), None, None],
+             'plength' : [None, None, PlotRange(), None, None]}
+PLOT_DATA_TYPE = {'simple' : ['force', 'force_base', 'lr',  'dist', 'stiff',
+                              'stiff_ev', 'stiff_notev', 'length', 'plength'],
+                  'dist' : ['relstiff', 'relstiffctl']}
+
+if __name__ == '__main__':
+    import doctest
+    FIGURE_FOLDER = 'Tests/Graphs/'
+    
+    doctest.testmod()

Added: trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/plot_gtk.py
===================================================================
--- trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/plot_gtk.py	                        (rev 0)
+++ trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/plot_gtk.py	2012-08-20 10:43:48 UTC (rev 12094)
@@ -0,0 +1,702 @@
+#!/usr/bin/env python
+# -*- coding: UTF-8 -*-
+'''
+This module contains the necessary tools to plot graphics in gtk
+'''
+# TODO: Separate the generic plot from the GTK-only
+
+import pygtk
+#import gnome.ui
+import gtk
+# for script installation
+from pkg_resources import resource_filename
+#import pdb
+
+import numpy
+from scipy import stats
+##############
+## Graphic library ##
+##############
+try:
+    matplotlib.__version__
+except NameError:
+    import matplotlib
+    matplotlib.use('Agg')
+    
+from matplotlib.figure import Figure
+from matplotlib.backends.backend_gtkagg import \
+                                FigureCanvasGTKAgg as FigureCanvas
+from matplotlib.backends.backend_gtkagg import \
+                                NavigationToolbar2GTKAgg as NavigationToolbar
+from matplotlib import cm # colormap
+from matplotlib.patches import Circle, Rectangle
+from matplotlib.image import imread
+from matplotlib.widgets import Cursor
+from matplotlib.ticker import NullFormatter
+nullfmt = NullFormatter() 
+
+# Internal classes
+import classes
+import plot_generic
+#from fovea_toolbox.post_proc import gauss_fit, compute_gauss
+
+try:
+    no_data_filename = resource_filename('openfovea','Icon/NoData.png')
+except NotImplementedError:
+    no_data_filename = 'openfovea/Icon/NoData.png'
+
+class plot(object):
+    """
+        This is the generic plot class that will be inherited from the other.
+        It has no plot capabilities, but have the standard attribute.
+    """
+    def __init__(self, window, widget, plot_generic):
+        self.window = window
+        self.widget = widget
+        self.window.set_property('visible', True)
+        self.window.connect('destroy', self.on_win_plot_destroy)
+        self.plot_generic = plot_generic
+        self.axis = plot_generic.axis
+        self.figure = plot_generic.figure
+        self.canvas = FigureCanvas(self.figure) # a gtk.DrawingArea 
+        self.canvas.show() 
+        self.graphview = self.widget['plot_area']
+        self.graphview.pack_start(self.canvas, True, True)
+        # below is optional if you want the navigation toolbar
+        if 'box_nav_tool' in self.widget.keys():
+            self.navToolbar =  FoveaNavToolbar(self.canvas, self.window)
+            self.navToolbar.plot_gen = self.plot_generic
+            self.navToolbar.lastDir = '/var/tmp/'
+            self.widget['box_nav_tool'].pack_start(self.navToolbar)
+            self.navToolbar.show()
+            #self.navToolbar.connect('button_press_event', self.press)
+        self.destroyed = 0
+    def show(self):
+        if not self.window.get_property('visible'):
+            raise StandardError
+        self.figure.subplots_adjust(left=0.2, bottom=0.12)
+        self.canvas.draw_idle()
+    def on_win_plot_destroy(self, *signal):
+        self.destroyed = 1
+        self.window.destroy()
+    def hold(self, value):
+        """
+            Change the hold of the figure.
+        """
+        self.plot_generic.hold(value)
+    def set_size(self, size, size2=None):
+        """
+            Change the size of the figure.
+        """
+        if size2 == None:
+            self.plot_generic.set_size(size[0], size[1])
+        else:
+            self.plot_generic.set_size(size, size2)
+    def set_xscale(self, scale):
+        self.plot_generic.set_xscale(scale)
+        self.show()
+    def get_type(self):
+        return self.plot_generic.get_type()
+class plotCurves(plot):
+    def __init__(self, window, widget, xlabel='Scanner Extention [nm]',
+                       ylabel='Cantilever Deflection [nm]',
+                       title='Force-Distance curve',
+                       win_title='Force Curve',
+                       linewidth=1.5):
+        _plot_generic = plot_generic.Curve(xlabel, ylabel, title, linewidth)
+        plot.__init__(self, window, widget, _plot_generic)
+        self.window.set_title(win_title)
+        
+    def displayPlot(self, X, Y, linestyle='b-', alpha=1):
+        """
+            Display the plot.
+        """
+        if self.navToolbar.auto:
+            self.plot_generic.lim = None
+        self.plot_generic.plot(X, Y, linestyle=linestyle, alpha=alpha)
+        self.show()
+        
+class plotGride(plot):
+    '''
+    Plots the given matrix corresponding to the type.
+    
+    Type can be :
+        basic = 2D matrix
+        
+        In the following cases, plot is a forceVolume object
+        stiffness = plot the stiffness of the object
+        piezzoHeight = plot the piezzo height of the object
+        zeroForceImage = plot the zero force Image of the object
+    '''
+    def __init__(self, window, widget, title = 'Stiffness',
+                                                      win_title = 'Gride Plot'):
+    
+        _plot_generic = plot_generic.Array(title)
+        
+        self.scaleMax = None
+        self.array = {'scan_size' : None,
+                      'data' : None}
+        
+        plot.__init__(self, window, widget, _plot_generic)
+        # Set the properties of the GUI
+        window.set_title(win_title)
+        self.widget['scrollbar_min'].set_property('visible', True)
+        self.widget['scrollbar_max'].set_property('visible', True)
+        self.widget['scrollbar_min'].connect_object("change-value",
+                                                    self.change_scale_min,
+                                                    None)
+        self.widget['scrollbar_max'].connect_object("change-value",
+                                                    self.change_scale_max,
+                                                    None)
+        
+        self.widget['scrollbar_depth'].connect_object("change-value",
+                                                    self.change_depth,
+                                                    None)
+                                                    
+        self.widget['button_modify_plot'].set_label('Color scale')
+        self.widget['button_modify_plot'].connect_object(
+                                            'clicked',
+                                            self.color_scale,
+                                            self.widget['button_modify_plot'])
+        self.widget['button_modify_plot'].set_property('visible', True)
+        self.figure.canvas.mpl_connect('button_press_event',
+                                         self.on_gride_click)
+        self.figure.canvas.mpl_connect('button_release_event', self.on_button_release)
+        self.figure.canvas.mpl_connect('motion_notify_event', self.move_mouse)
+    def __getattr__(self, att):
+        if att == 'path_refresh':
+            return self.plot_generic.path_refresh
+        elif att == 'path':
+            return self.plot_generic.path
+    def plot(self, dispArray, scanSize = None, nanVal= 80e9, cmap = 'gray'):
+        self.cmap = cmap
+        if self.scaleMax == None:
+            # The scale hasn't yet been initialized. Then do it.
+            try:
+                self.scaleMax = numpy.nanmax(dispArray)
+            except TypeError:
+                # In windows, numpy.nanmax seems to not work in this case...
+                self.scaleMax = numpy.max(
+                            dispArray[numpy.array((numpy.isnan(dispArray)-1),
+                            dtype=bool)])
+            if type(self.scaleMax) == numpy.ma.core.MaskedArray:
+                self.scaleMax = 0
+            self.widget['scrollbar_min'].set_adjustment(
+                                gtk.Adjustment(0.0,  0.00,
+                                               self.scaleMax,
+                                               self.scaleMax / 100,
+                                               self.scaleMax / 25,
+                                               0))
+            self.widget['scrollbar_max'].set_adjustment(
+                                gtk.Adjustment(self.scaleMax, 0.00,
+                                               self.scaleMax,
+                                               self.scaleMax / 100,
+                                               self.scaleMax / 25,
+                                               0))
+        self.array['data'] = dispArray
+        if scanSize is not None:
+            self.array['scan_size'] = scanSize
+        if self.array['data'].ndim == 3:
+            self.widget['scrollbar_depth'].set_property('visible', True)
+            self.widget['scrollbar_depth'].set_adjustment(
+                                gtk.Adjustment(0.0, 0.00,
+                                               self.array['data'].shape[2],
+                                               1, 5, 1.0))
+            self.depth = 0
+        self.__plot()
+    def __plot(self):
+        if self.array['data'].ndim == 3:
+            if self.depth >= self.array['data'].shape[2]:
+                self.depth = self.array['data'].shape[2] - 1
+            elif self.depth < 0:
+                self.depth = 0
+            disp_array = self.array['data'][:,:,self.depth]
+        else:
+            disp_array = self.array['data']
+        self.plot_generic.cmap = self.cmap
+        self.plot_generic.plot(disp_array, scan_size=self.array['scan_size'])
+        self.show()
+    def get_path(self):
+        return self.plot_generic.get_path()
+    def change_depth(self, widget, jump, value):
+        self.depth = value
+        self.__plot()
+    def change_scale_min(self, widget, jump, value):
+        self.plot_generic.vmin = value
+        self.show()
+    def change_scale_max(self, widget, jump, value):
+        self.plot_generic.vmax = value
+        self.show()
+    def color_scale(self, widget):
+        self.plot_generic.colorbar = not(self.plot_generic.colorbar)
+        self.__plot()
+        self.show()
+    def mark_pos(self, pos_x, pos_y):
+        self.plot_generic.marker = (pos_x, pos_y)
+        self.show()
+    def show_trace(self, trace):
+        self.plot_generic.show_trace(trace)
+        self.show()
+    def on_gride_click(self, event):
+        self.plot_generic.on_gride_click(event)
+        self.show()
+    def on_button_release(self, event):
+        self.plot_generic.on_button_release(event)
+        self.show()
+    def move_mouse(self, event):
+        self.plot_generic.move_mouse(event)
+        self.show()
+class errorBar(plot):
+    def __init__(self, window, widget, xlabel='Depth',
+                        ylabel='Stiffness',
+                        title='mean stiffness',
+                        win_title='Mean Stiffness'):
+        _plot_generic = plot_generic.ErrorBar(xlabel, ylabel, title)
+        plot.__init__(self, window, widget, _plot_generic)
+        # Add button to toggle the display of the number of data.
+        self.widget['button_modify_plot'].set_label('Hide nbr data')
+        self.widget['button_modify_plot'].connect_object(
+                                            'clicked',
+                                            self.toogle_plot,
+                                            self.widget['button_modify_plot'])
+        self.widget['button_modify_plot'].set_property('visible', True)
+        self.init_data = {'data' : None, 
+                          'group' : None, 
+                          'group_info' : None,
+                          'linestyle' : 'b-'}
+       # self.plot_gen = plot_generic.ErrorBar(xlabel, ylabel, title)
+    def average_stiffness(self, data, group=None, group_info=None, linestyle='b-'):
+        self.init_data['data'] = data
+        self.init_data['group'] = group
+        self.init_data['group_info'] = group_info
+        self.init_data['linestyle'] = linestyle
+        self.__refresh_average_stiffness()
+    def __refresh_average_stiffness(self):
+        # If the button label is set to hide, we have to show it, and inversly.
+        if self.widget['button_modify_plot'].get_label() == 'Hide nbr data':
+            show_count = True
+        elif self.widget['button_modify_plot'].get_label() == 'Show nbr data':
+            show_count = False
+        self.plot_generic.average_stiffness(self.init_data['data'],
+                                           self.init_data['group'],
+                                           self.init_data['group_info'],
+                                           self.init_data['linestyle'],
+                                           show_count=show_count)
+        self.show()
+    def plot(self, data_x, data_y, y_err, linestyle='b-'):
+        """
+            Data is organized like this :
+        """
+        
+        self.plot_generic.plot(data_x, data_y, y_err, linestyle)
+        self.show()
+    def toogle_plot(self, widget):
+        """
+            Toogle between density and scatter plot
+        """
+        if widget.get_label() == 'Hide nbr data':
+            widget.set_label('Show nbr data')
+        elif widget.get_label() == 'Show nbr data':
+            widget.set_label('Hide nbr data')
+        self.__refresh_average_stiffness()
+class TimeLapse(plotCurves):
+    def __init__(self, window, widget, xlabel='Time',
+                        ylabel='Stiffness',
+                        title='Relative Stiffness',
+                        win_title='Relative Stiffness'):
+        _plot_generic = plot_generic.TimeLapse(xlabel, ylabel, title)
+        plot.__init__(self, window, widget, _plot_generic)
+        self.window.set_title(win_title)
+    def displayPlot(self, data, data_ctl=None, baseline=0):
+        """
+            Displays the plot.
+            
+            See plot_generic.TimeLapse documentation for details
+        """
+        
+        self.plot_generic.plot(data, data_ctl, baseline)
+        self.show()
+
+class plotMosaic(plotGride):
+    '''
+    Plots a mosaic of arrays. The input has to be a list of arrays.
+    When you create an instance of plotMosaic, you can plot a list of arrays
+    in a single window with subplots.
+    
+    For example, if you have several arrays like array_1, array_2, array_3 put
+    them in a single list :
+    
+    >>> list_of_array = (array_1, array_2, array_3)
+    >>> new_mosaic = plotMosaic()
+    >>> new_mosaic.plot(list_of_array)
+    
+    This will open a new window with your array plotted.
+    '''
+    def __init__(self, window, widget, title = 'Mosaic plot'):
+        '''
+        Create a new instance of the class plotMosaic.
+        window = builder object of the window where you want to plot your data
+        widget = builder object of widget that are used for connection.
+        title = string that will be used as the name of the window
+        '''
+        _plot_generic = plot_generic.Mosaic()
+        plot.__init__(self, window, widget, _plot_generic)
+        self.window.set_title(title)
+    def plot(self, list_array, title = 'Mosaic plot', list_name=None,
+                                                    cmap = 'gray',
+                                                    list_mask=None):
+        '''
+        Plot your arrays.
+        
+        list_array = list of the array to be plotted. They do not need to have
+                     the same shape or size.
+                     
+        title = string that will be displayed as the general title of the grid.
+        
+        list_title = list of string. Each string will be used as a title for
+                     each grides. This can take some place and can be places
+                     over the above gride. So be carefull for the esthetic of
+                     your plot.
+        '''
+        if cmap in ('gray', 'grey', 'height'):
+            cmap = cm.gray
+        elif cmap in ('copper', 'afm image'):
+            cmap = cm.copper
+        elif cmap in ('jet', 'stiffness'):
+            cmap = cm.jet
+        self.plot_generic.plot(list_array, title, list_name, cmap, list_mask)
+        self.plot_generic.figure.canvas.mpl_connect('axes_enter_event',
+                                                    self.enter_array)
+        self.plot_generic.figure.canvas.mpl_connect('axes_leave_event',
+                                                    self.leave_array)
+        self.plot_generic.figure.canvas.mpl_connect('motion_notify_event',
+                                                    self.enter_array)
+#        self.plot_generic.figure.canvas.mpl_connect('pick_event', self.on_pick)
+    def enter_array(self, event):
+        self.plot_generic.enter_array(event)
+        self.show()
+    def leave_array(self, event):
+        self.plot_generic.leave_array(event)
+        self.show()
+    def index(self, event):
+        return self.plot_generic.index(event)
+#    def on_pick(self, event):
+#        self.plot_generic.on_pick(event)
+#        self.show()
+#        print "On plot_gtk"
+        
+class plotHist(plot):
+    '''
+    Plot the histogram of the list of values.
+    '''
+    def __init__(self, window, widget, xlabel = '', title='Histogram', y_rel=False):
+        _plot_generic = plot_generic.Histogram(xlabel, title, y_rel=y_rel)
+        plot.__init__(self, window, widget, _plot_generic)
+        self.window.set_title(title)
+    def hist(self, data, data2 = None, label = None, label2 = None,
+                            hist_range = None, color_type = 'color', y2=False, ):
+        self.plot_generic.plot(data, data2, label, label2,
+                                                    hist_range, color_type, y2)
+        self.show()
+    def gauss(self, prop):
+        self.plot_generic.show_fit(prop)
+        self.show()
+        self.plot_generic.figure.canvas.mpl_connect('motion_notify_event',
+                                                    self.move_annotation)
+    def move_annotation(self, event):
+        self.plot_generic.move_annotation(event)
+        self.show()
+    def set_y_rel(self, value):
+        if type(value) == bool:
+            self.plot_generic.relative = value
+        
+class plotScatter(plot):
+    """
+        Display the scatter plot of the choosen data.
+    """
+    
+    def __init__(self, window, widget, title='Scatter Plot',
+                                                        xlabel='', ylabel=''):
+        _plot_generic = plot_generic.Scatter(xlabel, ylabel, title)
+        plot.__init__(self, window, widget, _plot_generic)
+        self.window.set_title(title)
+        
+        self.widget['button_modify_plot'].set_label('Density plot')
+        self.widget['button_modify_plot'].connect_object(
+                                            'clicked',
+                                            self.toogle_plot,
+                                            self.widget['button_modify_plot'])
+        self.widget['button_modify_plot'].set_property('visible', True)
+    def display(self, data, data_type):
+        """
+            Display it.
+            Data has to be a PlotData object.
+        """
+        self.plot_generic.plot(data, data_type)
+        self.show()
+    def toogle_plot(self, widget):
+        """
+            Toogle between density and scatter plot
+        """
+        if widget.get_label() == 'Density plot':
+            widget.set_label('Scatter plot')
+            self.plot_generic.type = 'density'
+            self.plot_generic.refresh()
+            self.show()
+        elif widget.get_label() == 'Scatter plot':
+            widget.set_label('Density plot')
+            self.plot_generic.type = 'scatter'
+            self.plot_generic.refresh()
+            self.show()
+        self.show()
+class plotTomo(plot):
+    '''
+    Plot the stiffness tomography slices.
+    '''
+    def __init__(self, window, widget, tomo_array, scan_size=None,
+                                                            title='Tomography'):
+        _plot_generic = plot_generic.Tomo(tomo_array, scan_size)
+        plot.__init__(self, window, widget, _plot_generic)
+        self.window = window
+        self.widget = widget
+        self.slice = [0, 0, 0]
+        self.window.set_property('visible', True)
+        self.window.connect('destroy', self.on_win_plot_destroy)
+        self.move_cursor = 0
+        self.cur_size = 4
+        self.destroyed = 0
+        self.canvas.mpl_connect('motion_notify_event', self.onmouse_motion)
+        self.canvas.mpl_connect('button_press_event', self.on_gride_click)
+        
+        self.widget['adjust_x'].connect_object("value-changed",
+                                                self.on_adjust_x_value_changed,
+                                                self.widget['adjust_x'])
+        self.widget['adjust_y'].connect_object("value-changed",
+                                                self.on_adjust_y_value_changed,
+                                                self.widget['adjust_y'])
+        self.widget['adjust_z'].connect_object("value-changed",
+                                                self.on_spin_z_change_value,
+                                                self.widget['adjust_z'])
+        self.widget['adjust_x'].upper = tomo_array.shape[0]-1
+        self.widget['adjust_y'].upper = tomo_array.shape[1]-1
+        self.widget['adjust_z'].upper = tomo_array.shape[2]-1
+        
+        self.widget['scrollbar_min'].set_property('visible', True)
+        self.widget['scrollbar_max'].set_property('visible', True)
+        self.colorScaleMax = tomo_array.max()
+        self.colorScaleMin = 0
+        self.widget['scrollbar_min'].set_adjustment(
+                                gtk.Adjustment(0.0,  0.00,
+                                               self.colorScaleMax,
+                                               self.colorScaleMax / 100,
+                                               self.colorScaleMax / 25,
+                                               0))
+        self.widget['scrollbar_max'].set_adjustment(
+                                gtk.Adjustment(self.colorScaleMax,  0.00,
+                                               self.colorScaleMax,
+                                               self.colorScaleMax / 100,
+                                               self.colorScaleMax / 25,
+                                               0))
+        self.widget['scrollbar_min'].connect_object("change-value",
+                                                    self.change_scale_min,
+                                                    None)
+        self.widget['scrollbar_max'].connect_object("change-value",
+                                                    self.change_scale_max,
+                                                    None)
+        self.plot()
+    def on_win_plot_destroy(self, signal):
+        self.destroyed = 1
+        self.window.destroy()
+    def onmouse_motion(self, event):
+        '''
+        Catch the mouse motion in the axes. self.move_cursor has to be set to
+        True to have an action.
+        The other axis are refresh according to the movement of the mouse.
+        '''
+        if not self.move_cursor:
+            return
+        if event.inaxes == self.plot_generic.axis['display_x']:
+            y = self.plot_generic.scale['y'] > event.xdata
+            y = y.nonzero()[0][0]
+            z = self.plot_generic.scale['z'] > event.ydata
+            z = z.nonzero()[0][0]
+            self.widget['adjust_y'].set_value(y)
+            self.widget['adjust_z'].set_value(z)
+        elif event.inaxes == self.plot_generic.axis['display_y']:
+            x = self.plot_generic.scale['x'] > event.xdata
+            x = x.nonzero()[0][0]
+            z = self.plot_generic.scale['z'] > event.ydata
+            z = z.nonzero()[0][0]
+            x = numpy.floor(event.xdata)
+            z = numpy.floor(event.ydata)
+            self.widget['adjust_x'].set_value(x)
+            self.widget['adjust_z'].set_value(z)
+        elif event.inaxes == self.plot_generic.axis['display_z']:
+            x = self.plot_generic.scale['x'] > event.xdata
+            x = x.nonzero()[0][0]
+            y = self.plot_generic.scale['y'] > event.ydata
+            y = y.nonzero()[0][0]
+            self.widget['adjust_x'].set_value(x)
+            self.widget['adjust_y'].set_value(y)
+    def on_gride_click(self, event):
+        '''
+        Catch click in an axis and change the self.move_cursor value.
+        '''
+        if self.move_cursor:
+            self.get_pos()
+            self.move_cursor = False
+        else:
+            self.move_cursor = True
+    def plot(self):
+        self.plot_generic.plot(self.slice,
+                               self.colorScaleMin, self.colorScaleMax)
+        self.show()
+    def on_spin_z_change_value(self, widget):
+        self.slice[2] = widget.get_value()
+        self.plot()
+    def on_adjust_x_value_changed(self, widget):
+        self.slice[0] = widget.get_value()
+        self.plot()
+    def on_adjust_y_value_changed(self,widget):
+        self.slice[1] = widget.get_value()
+        self.plot()
+    def change_scale_min(self, widget, jump, value):
+        self.colorScaleMin = value
+        self.plot()
+    def change_scale_max(self, widget, jump, value):
+        self.colorScaleMax = value
+        self.plot()
+    def get_pos(self):
+        '''
+        Function to be overwritten by the writer in order to get the internal
+        values.
+        '''
+        pass
+
+class plotInteractiveCurve(plot):
+    """
+        Plots several curves in as many subplot as the number of curves.
+    """
+    def __init__(self, window, widget, win_title='Slices'):
+        _plot_generic = plot_generic.InteractiveLinePlot()
+        plot.__init__(self, window, widget, _plot_generic)
+        self.window.set_title(win_title)
+        self.window.resize(500, 500)
+    def show(self):
+        if not self.window.get_property('visible'):
+            raise StandardError
+        self.canvas.draw_idle()
+    def plot(self, array_x, arrays, labels):
+        self.plot_generic.plot(array_x, arrays, labels)
+        
+        self.plot_generic.figure.canvas.mpl_connect('button_press_event',
+                                                    self.button_press_event)
+        self.plot_generic.figure.canvas.mpl_connect('button_release_event',
+                                                    self.button_release_event)
+        self.plot_generic.figure.canvas.mpl_connect('motion_notify_event',
+                                                    self.mouse_move)
+        self.plot_generic.figure.canvas.mpl_connect('pick_event', self.on_pick)
+        self.show()
+    def modify_plot(self, array_x, arrays):
+        self.plot_generic.modify_plot(array_x, arrays)
+        self.show()
+    def button_press_event(self, event):
+        self.plot_generic.button_press_event(event)
+        self.show()
+    def mouse_move(self, event):
+        self.plot_generic.mouse_move(event)
+        self.show()
+    def on_pick(self, event):
+        self.plot_generic.on_pick(event)
+        self.show()
+    def button_release_event(self, event):
+        self.plot_generic.button_release_event(event)
+
+class FoveaNavToolbar(NavigationToolbar):
+
+    def __init__(self, plotCanvas, plotWindow):
+        NavigationToolbar.__init__(self, plotCanvas, plotWindow)
+        self.plot_gen = None
+        self.fig_size = [800, 800]
+        self.auto = 1
+    def home(self, event):
+        self.auto = 1
+        NavigationToolbar.home(self, event)
+    def press_zoom(self, event):
+        self.auto = 0
+        NavigationToolbar.press_zoom(self, event)
+    def save_figure(self, event):
+        # get the old size...
+        old_size = self.plot_gen.figure.get_size_inches().copy()
+        self.plot_gen.figure.set_size_inches(self.plot_gen.win_size)
+        #self.plot_gen.set_size()
+        NavigationToolbar.save_figure(self, event)
+        # return to the old size...
+        self.plot_gen.figure.set_size_inches(old_size)
+
+def regenerate_plot(self, type='normal'):
+    """
+        Create the gtk window where to plot the curves.
+    """
+    
+    builder = gtk.Builder()
+    if type == 'normal':
+        _glade_filename = resource_filename('openfovea', 'glade/plot.glade')
+    elif type == 'tomography':
+        _glade_filename = resource_filename('openfovea',
+                                            'glade/stiffness_plot.glade')
+    builder.add_from_file(_glade_filename)
+    window = builder.get_object("WindowPlot")
+    builder.connect_signals(self)
+    if type == 'normal':
+        widget = {
+        'plot_area' : builder.get_object('boxPlot'),
+        'scrollbar_min' : builder.get_object('scrollbar_min'),
+        'scrollbar_max' : builder.get_object('scrollbar_max'),
+        'scrollbar_depth' : builder.get_object('scrollbar_depth'),
+        'box_nav_tool' : builder.get_object('box_nav_tool'),
+        'button_modify_plot' : builder.get_object('button_modify_plot')
+        }
+    elif type == 'tomography':
+        widget = {
+        'plot_area' : builder.get_object('boxPlot'),
+        'display_x': builder.get_object('display_x'),
+        'display_y': builder.get_object('display_y'),
+        'display_z': builder.get_object('display_z'),
+        'adjust_x': builder.get_object('adjust_x'),
+        'adjust_y': builder.get_object('adjust_y'),
+        'adjust_z': builder.get_object('adjust_z'),
+        'scrollbar_min' : builder.get_object('scrollbar_min'),
+        'scrollbar_max' : builder.get_object('scrollbar_max')
+    }
+    
+    return [window, widget]
+    
+def main():
+    gtk.main()
+    return 0
+if __name__=='__main__':
+    import sys
+    import numpy
+    [window, widget] = regenerate_plot('normal')
+    window.connect('destroy', gtk.main_quit)
+    if sys.argv[1] == 'curve':
+        print('Creating vectors...')
+        X=numpy.asanyarray([1,2,3,4,5,6,7,8,9,10])
+        Y=numpy.asanyarray([1,3,4,3,2,4,5,6,7,8])
+        print('Plotting vectors...')
+        newPlot=plotCurves(window, widget)
+        newPlot.displayPlot(X,Y)
+        newPlot.set_size(800, 800)
+        main()
+    elif sys.argv[1] == 'gride':
+        gride = numpy.random.randn(64, 64)+2
+        newPlot = plotGride(window, widget)
+        newPlot.plot(gride, 2000)
+        main()
+    elif sys.argv[1] == 'mosaic':
+        mosaic = [numpy.random.randn(32, 32)+2 for i in range(10)]
+        list_mask = [1,0,0,0,1,1,0,0,1,0]
+        newPlot = plotMosaic(window, widget)
+        newPlot.plot(mosaic, list_mask=list_mask)
+        main()

Added: trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/simple_window_gtk.py
===================================================================
--- trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/simple_window_gtk.py	                        (rev 0)
+++ trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea/simple_window_gtk.py	2012-08-20 10:43:48 UTC (rev 12094)
@@ -0,0 +1,80 @@
+import pygtk
+pygtk.require('2.0')
+import gtk
+#from gtk.gtkgl.apputils import *
+
+class FileGroup(object):
+    def __init__(self, file_list, group_list=None):
+    
+        if group_list == None:
+            group_list = [0 for i in file_list]
+        self.lock = True # defines if we modify all the following value in the list
+        self.dialog = gtk.Dialog(title='File Group', buttons=(gtk.STOCK_OK, gtk.RESPONSE_OK,
+                gtk.STOCK_CANCEL, gtk.RESPONSE_CANCEL))
+        self.dialog.set_size_request(300, 300)
+        # Create scrolling window
+        self.scroll = gtk.ScrolledWindow()
+        self.scroll.set_policy(gtk.POLICY_AUTOMATIC, gtk.POLICY_AUTOMATIC)
+
+        self.scroll.show()
+        # Create the table.
+        self.table = gtk.Table(3, 2)
+        self.table.set_border_width(5)
+        self.table.set_col_spacings(5)
+        self.table.set_row_spacings(5)
+        self.table.show()
+        check = gtk.CheckButton(label='Lock')
+        check.set_active(True)
+        check.connect('toggled', self.on_check_toggled)
+        check.show()
+        self.table.attach(check, 0, 1, 0, 1)
+        # Fill the table with label and spin button
+        self.spin_button = []
+        index_list = range(1, len(file_list)+1)
+        for (item, index, group) in zip(file_list, index_list, group_list):
+            text = gtk.Label(str=item)
+            text.show()
+            self.table.attach(text, 0, 1, index, index + 1)
+            spin_button = gtk.SpinButton(gtk.Adjustment(value = group,
+                                               lower = 0, 
+                                               upper = 10, 
+                                               step_incr = 1, 
+                                               page_incr = 1, 
+                                               page_size = 0))
+            spin_button.connect('value_changed', self.on_spin_value_changed)
+            spin_button.show()
+            self.table.attach(spin_button, 1, 2, index, index + 1)
+            self.spin_button.append(spin_button)
+        self.scroll.add_with_viewport(self.table)
+        self.dialog.vbox.pack_start(self.scroll, True, True, 0)
+        #self.dialog.vbox.pack_start(self.table, True, True, 0)
+    def on_spin_value_changed(self, widget):
+        """
+            Change the value of the following items in the list
+        """
+        if not self.lock:
+            return
+        start = self.spin_button.index(widget)
+        if start+1 < len(self.spin_button):
+            self.spin_button[start+1].set_value(widget.get_value())
+    def on_check_toggled(self, widget):
+        self.lock = widget.get_active()
+    def run(self):
+        """
+            Runs the dialog
+        """
+        response = self.dialog.run()
+        if response == gtk.RESPONSE_OK:
+            group_list = []
+            for item in self.spin_button:
+                group_list.append(int(item.get_value()))
+            return group_list
+    def destroy(self):
+        self.dialog.destroy()
+        
+if __name__ == '__main__':
+    file_list = ['File number ' + str(i) for i in range(20)]
+    group_list = None
+    window = FileGroup(file_list, group_list)
+    response = window.run()
+    print response

Added: trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea-0.1a160.egg-info
===================================================================
--- trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea-0.1a160.egg-info	                        (rev 0)
+++ trunk/packages/openfovea/trunk/debian/openfovea/usr/share/pyshared/openfovea-0.1a160.egg-info	2012-08-20 10:43:48 UTC (rev 12094)
@@ -0,0 +1,10 @@
+Metadata-Version: 1.0
+Name: openfovea
+Version: 0.1a160
+Summary: Postprocessing of force volume data acquired with AFM./nOpenFovea is a software to postprocess AFM force volume/nexperiment. It is able to compute the stiffness of the/nscanned area, detect unbinding event and the zero force/ntopography. It comes with a user friendly graphical interface/nthat allow the user to select and display the data.
+Home-page: http://www.freesbi.ch/openfovea
+Author: Charles Roduit
+Author-email: charles.roduit at gmail.com
+License: GNU Public License v3
+Description: UNKNOWN
+Platform: UNKNOWN

Added: trunk/packages/openfovea/trunk/debian/openfovea.debhelper.log
===================================================================
--- trunk/packages/openfovea/trunk/debian/openfovea.debhelper.log	                        (rev 0)
+++ trunk/packages/openfovea/trunk/debian/openfovea.debhelper.log	2012-08-20 10:43:48 UTC (rev 12094)
@@ -0,0 +1,44 @@
+dh_auto_configure
+dh_auto_build
+dh_auto_test
+dh_prep
+dh_installdirs
+dh_auto_install
+dh_install
+dh_installdocs
+dh_installchangelogs
+dh_installexamples
+dh_installman
+dh_installcatalogs
+dh_installcron
+dh_installdebconf
+dh_installemacsen
+dh_installifupdown
+dh_installinfo
+dh_installinit
+dh_installmenu
+dh_installmime
+dh_installmodules
+dh_installlogcheck
+dh_installlogrotate
+dh_installpam
+dh_installppp
+dh_installudev
+dh_installwm
+dh_installxfonts
+dh_installgsettings
+dh_bugfiles
+dh_ucf
+dh_lintian
+dh_gconf
+dh_icons
+dh_perl
+dh_usrlocal
+dh_link
+dh_compress
+dh_fixperms
+dh_installdeb
+dh_gencontrol
+dh_md5sums
+dh_builddeb
+dh_builddeb

Added: trunk/packages/openfovea/trunk/debian/openfovea.postinst.debhelper
===================================================================
--- trunk/packages/openfovea/trunk/debian/openfovea.postinst.debhelper	                        (rev 0)
+++ trunk/packages/openfovea/trunk/debian/openfovea.postinst.debhelper	2012-08-20 10:43:48 UTC (rev 12094)
@@ -0,0 +1,7 @@
+
+# Automatically added by dh_python2:
+if which pycompile >/dev/null 2>&1; then
+	pycompile -p openfovea 
+fi
+
+# End automatically added section

Added: trunk/packages/openfovea/trunk/debian/openfovea.prerm.debhelper
===================================================================
--- trunk/packages/openfovea/trunk/debian/openfovea.prerm.debhelper	                        (rev 0)
+++ trunk/packages/openfovea/trunk/debian/openfovea.prerm.debhelper	2012-08-20 10:43:48 UTC (rev 12094)
@@ -0,0 +1,12 @@
+
+# Automatically added by dh_python2:
+if which pyclean >/dev/null 2>&1; then
+	pyclean -p openfovea 
+else
+	dpkg -L openfovea | grep \.py$ | while read file
+	do
+		rm -f "${file}"[co] >/dev/null
+  	done
+fi
+
+# End automatically added section

Added: trunk/packages/openfovea/trunk/debian/openfovea.substvars
===================================================================
--- trunk/packages/openfovea/trunk/debian/openfovea.substvars	                        (rev 0)
+++ trunk/packages/openfovea/trunk/debian/openfovea.substvars	2012-08-20 10:43:48 UTC (rev 12094)
@@ -0,0 +1,3 @@
+python:Versions=2.7
+python:Depends=python2.7, python (>= 2.7), python (<< 2.8), python (>= 2.7.1-0ubuntu2), python
+misc:Depends=


