[med-svn] [fw4spl] 01/03: Imported Upstream version 0.9.2
Corentin Desfarges
corentin-guest at moszumanska.debian.org
Fri Jan 23 15:48:05 UTC 2015
This is an automated email from the git hooks/post-receive script.
corentin-guest pushed a commit to branch master
in repository fw4spl.
commit b30a4b09687334bace3b82bf622a7461b22ce218
Author: Corentin Desfarges <corentin.desfarges at gmail.com>
Date: Fri Jan 23 16:22:08 2015 +0100
Imported Upstream version 0.9.2
---
Apps/VRRender/doc/Makefile | 88 ----
Apps/VRRender/doc/htmlhelpTowxHtmlHelp | 22 -
Apps/VRRender/doc/make.bat | 112 -----
Apps/VRRender/doc/makeall.sh | 43 --
Apps/VRRender/doc/source/2D_Landmarks.rst | 23 -
Apps/VRRender/doc/source/2D_MPR.rst | 42 --
Apps/VRRender/doc/source/3D_Distances.rst | 23 -
Apps/VRRender/doc/source/3D_Medical_Image_Visu.rst | 32 --
.../VRRender/doc/source/3D_Models_Manipulation.rst | 42 --
Apps/VRRender/doc/source/3D_Models_Properties.rst | 20 -
Apps/VRRender/doc/source/3D_Resection.rst | 53 ---
Apps/VRRender/doc/source/3D_Volume_Rendering.rst | 37 --
Apps/VRRender/doc/source/Acknowledgment.rst | 136 ------
Apps/VRRender/doc/source/Basic_Image_Filtering.rst | 12 -
Apps/VRRender/doc/source/Export_Data.rst | 8 -
Apps/VRRender/doc/source/Help_menu.rst | 12 -
Apps/VRRender/doc/source/Introduction.rst | 9 -
Apps/VRRender/doc/source/Licence.rst | 23 -
Apps/VRRender/doc/source/Minimal_config.rst | 31 --
Apps/VRRender/doc/source/Read_and_Select_Data.rst | 26 --
Apps/VRRender/doc/source/Shortcuts.rst | 138 ------
Apps/VRRender/doc/source/Start_VR_Planning.rst | 17 -
Apps/VRRender/doc/source/Tool_bar.rst | 11 -
Apps/VRRender/doc/source/Transfert_function.rst | 31 --
.../doc/source/What_is_Volume_Rendering.rst | 15 -
Apps/VRRender/doc/source/Windows_Installation.rst | 16 -
.../doc/source/_static/3D-New-Resection.png | Bin 219192 -> 0 bytes
.../doc/source/_static/3D-Planning-View-00.png | Bin 207145 -> 0 bytes
.../doc/source/_static/3D-Resect-First.png | Bin 252338 -> 0 bytes
.../source/_static/3D-Resect-cutting-planes.png | Bin 284064 -> 0 bytes
.../doc/source/_static/3D-Resect-manage.png | Bin 171825 -> 0 bytes
.../doc/source/_static/3D-Resect-plane-side.png | Bin 263504 -> 0 bytes
.../doc/source/_static/3D-Resect-start.png | Bin 189534 -> 0 bytes
.../doc/source/_static/3D-Resect-volume.png | Bin 242396 -> 0 bytes
Apps/VRRender/doc/source/_static/3D-distance.png | Bin 142029 -> 0 bytes
Apps/VRRender/doc/source/_static/3D-landmark.png | Bin 163292 -> 0 bytes
Apps/VRRender/doc/source/_static/3D-rotate.png | Bin 191571 -> 0 bytes
Apps/VRRender/doc/source/_static/3D-scan-1-3.png | Bin 222456 -> 0 bytes
.../doc/source/_static/3D-scan-GL-value.png | Bin 157133 -> 0 bytes
.../doc/source/_static/3D-scan-ax-front-sag.png | Bin 190004 -> 0 bytes
.../doc/source/_static/3D-scan-contrast.png | Bin 160927 -> 0 bytes
.../doc/source/_static/3D-show-hide-organs.png | Bin 208376 -> 0 bytes
.../doc/source/_static/3D-show-hide-scan.png | Bin 230334 -> 0 bytes
.../VRRender/doc/source/_static/3D-translation.png | Bin 79500 -> 0 bytes
.../doc/source/_static/3D-transparency.png | Bin 188677 -> 0 bytes
Apps/VRRender/doc/source/_static/3D-turn.png | Bin 152259 -> 0 bytes
Apps/VRRender/doc/source/_static/3D-zoom.png | Bin 93864 -> 0 bytes
.../doc/source/_static/Add-Find-View-landmark.png | Bin 5482 -> 0 bytes
Apps/VRRender/doc/source/_static/Add-landmark.png | Bin 1577 -> 0 bytes
Apps/VRRender/doc/source/_static/Add-plan1.png | Bin 2312 -> 0 bytes
Apps/VRRender/doc/source/_static/Add-plan2.png | Bin 2846 -> 0 bytes
Apps/VRRender/doc/source/_static/AddTool.png | Bin 1052 -> 0 bytes
Apps/VRRender/doc/source/_static/Find-landmark.png | Bin 2122 -> 0 bytes
Apps/VRRender/doc/source/_static/Mode-VR.png | Bin 1981 -> 0 bytes
Apps/VRRender/doc/source/_static/Negato-01.png | Bin 291839 -> 0 bytes
.../doc/source/_static/Negato-Distance.png | Bin 223655 -> 0 bytes
Apps/VRRender/doc/source/_static/Negato-Zoom.png | Bin 209461 -> 0 bytes
Apps/VRRender/doc/source/_static/Negato-axes.png | Bin 298175 -> 0 bytes
.../doc/source/_static/Negato-contrast.png | Bin 152816 -> 0 bytes
Apps/VRRender/doc/source/_static/Negato-filter.png | Bin 164233 -> 0 bytes
Apps/VRRender/doc/source/_static/Negato-info.png | Bin 276129 -> 0 bytes
.../doc/source/_static/Negato-landmarks.png | Bin 325920 -> 0 bytes
.../doc/source/_static/Negato-translate.png | Bin 240307 -> 0 bytes
Apps/VRRender/doc/source/_static/Resection.png | Bin 1439 -> 0 bytes
Apps/VRRender/doc/source/_static/Resection2.png | Bin 2287 -> 0 bytes
.../doc/source/_static/Tool-bar-planning.png | Bin 24281 -> 0 bytes
Apps/VRRender/doc/source/_static/VR-01.jpg | Bin 79308 -> 0 bytes
Apps/VRRender/doc/source/_static/VR-DEF.jpg | Bin 24294 -> 0 bytes
Apps/VRRender/doc/source/_static/VR-TF-01.jpg | Bin 34932 -> 0 bytes
Apps/VRRender/doc/source/_static/VR-TF-02.jpg | Bin 28750 -> 0 bytes
Apps/VRRender/doc/source/_static/VR-TF-AUTO-01.png | Bin 239456 -> 0 bytes
Apps/VRRender/doc/source/_static/VR-TF-AUTO-02.jpg | Bin 34801 -> 0 bytes
Apps/VRRender/doc/source/_static/VR-TF-AUTO-02.png | Bin 370325 -> 0 bytes
Apps/VRRender/doc/source/_static/VR-TF-DEF.jpg | Bin 56208 -> 0 bytes
Apps/VRRender/doc/source/_static/VR-TF-MPR-01.jpg | Bin 99344 -> 0 bytes
Apps/VRRender/doc/source/_static/VR-TF-MPR-02.jpg | Bin 101031 -> 0 bytes
Apps/VRRender/doc/source/_static/VR-cutting.jpg | Bin 33487 -> 0 bytes
Apps/VRRender/doc/source/_static/VR-manip.jpg | Bin 23377 -> 0 bytes
Apps/VRRender/doc/source/_static/VR.png | Bin 49100 -> 0 bytes
Apps/VRRender/doc/source/_static/VRPlanning.png | Bin 40972 -> 0 bytes
Apps/VRRender/doc/source/_static/VR_WLE_html.png | Bin 20559 -> 0 bytes
Apps/VRRender/doc/source/_static/VR_html.png | Bin 35500 -> 0 bytes
Apps/VRRender/doc/source/_static/View-INFO.png | Bin 260 -> 0 bytes
Apps/VRRender/doc/source/_static/View-landmark.png | Bin 2538 -> 0 bytes
.../doc/source/_static/acknowledgment/apple.png | Bin 65027 -> 0 bytes
.../doc/source/_static/acknowledgment/boost.png | Bin 7192 -> 0 bytes
.../doc/source/_static/acknowledgment/bzip2.png | Bin 6589 -> 0 bytes
.../doc/source/_static/acknowledgment/cfitsio.png | Bin 7683 -> 0 bytes
.../doc/source/_static/acknowledgment/dcmtk.png | Bin 6761 -> 0 bytes
.../doc/source/_static/acknowledgment/doxygen.png | Bin 11988 -> 0 bytes
.../doc/source/_static/acknowledgment/eclipse.png | Bin 13860 -> 0 bytes
.../doc/source/_static/acknowledgment/ehealth.png | Bin 411007 -> 0 bytes
.../doc/source/_static/acknowledgment/fits2itk.png | Bin 7367 -> 0 bytes
.../doc/source/_static/acknowledgment/fsf.png | Bin 6409 -> 0 bytes
.../doc/source/_static/acknowledgment/gcc.png | Bin 28137 -> 0 bytes
.../doc/source/_static/acknowledgment/gdcm.png | Bin 9736 -> 0 bytes
.../doc/source/_static/acknowledgment/itk.png | Bin 9372 -> 0 bytes
.../doc/source/_static/acknowledgment/libjpeg.png | Bin 2829 -> 0 bytes
.../doc/source/_static/acknowledgment/libpng.png | Bin 2655 -> 0 bytes
.../doc/source/_static/acknowledgment/libtiff.png | Bin 2118 -> 0 bytes
.../doc/source/_static/acknowledgment/libxml2.png | Bin 7940 -> 0 bytes
.../doc/source/_static/acknowledgment/linux-64.png | Bin 29352 -> 0 bytes
.../doc/source/_static/acknowledgment/linux.png | Bin 31211 -> 0 bytes
.../doc/source/_static/acknowledgment/log4cxx.png | Bin 6161 -> 0 bytes
.../doc/source/_static/acknowledgment/ms.png | Bin 13902 -> 0 bytes
.../doc/source/_static/acknowledgment/opengl.png | Bin 7428 -> 0 bytes
.../doc/source/_static/acknowledgment/python.png | Bin 2641 -> 0 bytes
.../doc/source/_static/acknowledgment/scons.png | Bin 5926 -> 0 bytes
.../doc/source/_static/acknowledgment/sphinx.png | Bin 4624 -> 0 bytes
.../doc/source/_static/acknowledgment/vim.png | Bin 15549 -> 0 bytes
.../doc/source/_static/acknowledgment/visualc.png | Bin 7902 -> 0 bytes
.../doc/source/_static/acknowledgment/vtk.png | Bin 8157 -> 0 bytes
.../source/_static/acknowledgment/vtkinria3d.png | Bin 10656 -> 0 bytes
.../doc/source/_static/acknowledgment/wix.png | Bin 17600 -> 0 bytes
.../doc/source/_static/acknowledgment/wx.png | Bin 9304 -> 0 bytes
.../doc/source/_static/acknowledgment/zlib.png | Bin 9172 -> 0 bytes
Apps/VRRender/doc/source/_static/axial-view.jpg | Bin 16033 -> 0 bytes
Apps/VRRender/doc/source/_static/basic.css | 414 ------------------
Apps/VRRender/doc/source/_static/camera-photo.png | Bin 864 -> 0 bytes
Apps/VRRender/doc/source/_static/danger.png | Bin 18201 -> 0 bytes
Apps/VRRender/doc/source/_static/default.css | 201 ---------
Apps/VRRender/doc/source/_static/distance.png | Bin 763 -> 0 bytes
Apps/VRRender/doc/source/_static/doctools.js | 232 ----------
Apps/VRRender/doc/source/_static/ehealth.png | Bin 411007 -> 0 bytes
Apps/VRRender/doc/source/_static/file.png | Bin 392 -> 0 bytes
Apps/VRRender/doc/source/_static/frontal-view.jpg | Bin 11859 -> 0 bytes
Apps/VRRender/doc/source/_static/icon-2D.png | Bin 1383 -> 0 bytes
Apps/VRRender/doc/source/_static/icon-3D.png | Bin 1796 -> 0 bytes
Apps/VRRender/doc/source/_static/icon-VR.png | Bin 1487 -> 0 bytes
Apps/VRRender/doc/source/_static/icon-axial.png | Bin 1556 -> 0 bytes
Apps/VRRender/doc/source/_static/icon-frontal.png | Bin 1883 -> 0 bytes
Apps/VRRender/doc/source/_static/icon-sagittal.png | Bin 2000 -> 0 bytes
Apps/VRRender/doc/source/_static/icon-windows.jpg | Bin 768 -> 0 bytes
Apps/VRRender/doc/source/_static/icone-F9.png | Bin 1906 -> 0 bytes
Apps/VRRender/doc/source/_static/icone-VR-01.jpg | Bin 947 -> 0 bytes
Apps/VRRender/doc/source/_static/icone-VR-02.jpg | Bin 820 -> 0 bytes
Apps/VRRender/doc/source/_static/icone-VR-03.jpg | Bin 904 -> 0 bytes
Apps/VRRender/doc/source/_static/icone-VR-04.jpg | Bin 849 -> 0 bytes
Apps/VRRender/doc/source/_static/icone-VR-05.jpg | Bin 898 -> 0 bytes
Apps/VRRender/doc/source/_static/icone-VR-06.jpg | Bin 984 -> 0 bytes
Apps/VRRender/doc/source/_static/info-patient.png | Bin 188609 -> 0 bytes
Apps/VRRender/doc/source/_static/jquery.js | 32 --
Apps/VRRender/doc/source/_static/minus.png | Bin 199 -> 0 bytes
Apps/VRRender/doc/source/_static/openDicom.png | Bin 1786 -> 0 bytes
.../doc/source/_static/openDicom_openFxz.png | Bin 2880 -> 0 bytes
Apps/VRRender/doc/source/_static/openFxz.png | Bin 1632 -> 0 bytes
Apps/VRRender/doc/source/_static/operation.png | Bin 3316 -> 0 bytes
Apps/VRRender/doc/source/_static/plus.png | Bin 199 -> 0 bytes
Apps/VRRender/doc/source/_static/pygments.css | 61 ---
Apps/VRRender/doc/source/_static/sagittal-view.jpg | Bin 10483 -> 0 bytes
Apps/VRRender/doc/source/_static/searchtools.js | 467 ---------------------
Apps/VRRender/doc/source/_static/sliceHide.png | Bin 947 -> 0 bytes
Apps/VRRender/doc/source/_static/sliceShow.png | Bin 545 -> 0 bytes
Apps/VRRender/doc/source/_static/video.png | Bin 3717 -> 0 bytes
Apps/VRRender/doc/source/_static/view_frontal.png | Bin 2048 -> 0 bytes
Apps/VRRender/doc/source/_static/view_profil.png | Bin 2215 -> 0 bytes
Apps/VRRender/doc/source/conf.py | 208 ---------
Apps/VRRender/doc/source/index.rst | 37 --
158 files changed, 2674 deletions(-)
diff --git a/Apps/VRRender/doc/Makefile b/Apps/VRRender/doc/Makefile
deleted file mode 100644
index d746c38..0000000
--- a/Apps/VRRender/doc/Makefile
+++ /dev/null
@@ -1,88 +0,0 @@
-# Makefile for Sphinx documentation
-#
-
-# You can set these variables from the command line.
-SPHINXOPTS =
-SPHINXBUILD = sphinx-build
-PAPER =
-
-# Internal variables.
-PAPEROPT_a4 = -D latex_paper_size=a4
-PAPEROPT_letter = -D latex_paper_size=letter
-ALLSPHINXOPTS = -d build/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) source
-
-.PHONY: help clean html dirhtml pickle json htmlhelp qthelp latex changes linkcheck doctest
-
-help:
- @echo "Please use \`make <target>' where <target> is one of"
- @echo " html to make standalone HTML files"
- @echo " dirhtml to make HTML files named index.html in directories"
- @echo " pickle to make pickle files"
- @echo " json to make JSON files"
- @echo " htmlhelp to make HTML files and a HTML help project"
- @echo " qthelp to make HTML files and a qthelp project"
- @echo " latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter"
- @echo " changes to make an overview of all changed/added/deprecated items"
- @echo " linkcheck to check all external links for integrity"
- @echo " doctest to run all doctests embedded in the documentation (if enabled)"
-
-clean:
- -rm -rf build/*
-
-html:
- $(SPHINXBUILD) -b html $(ALLSPHINXOPTS) build/html
- @echo
- @echo "Build finished. The HTML pages are in build/html."
-
-dirhtml:
- $(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) build/dirhtml
- @echo
- @echo "Build finished. The HTML pages are in build/dirhtml."
-
-pickle:
- $(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) build/pickle
- @echo
- @echo "Build finished; now you can process the pickle files."
-
-json:
- $(SPHINXBUILD) -b json $(ALLSPHINXOPTS) build/json
- @echo
- @echo "Build finished; now you can process the JSON files."
-
-htmlhelp:
- $(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) build/htmlhelp
- @echo
- @echo "Build finished; now you can run HTML Help Workshop with the" \
- ".hhp project file in build/htmlhelp."
-
-qthelp:
- $(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) build/qthelp
- @echo
- @echo "Build finished; now you can run "qcollectiongenerator" with the" \
- ".qhcp project file in build/qthelp, like this:"
- @echo "# qcollectiongenerator build/qthelp/VRRenderDoc.qhcp"
- @echo "To view the help file:"
- @echo "# assistant -collectionFile build/qthelp/VRRenderDoc.qhc"
-
-latex:
- $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) build/latex
- @echo
- @echo "Build finished; the LaTeX files are in build/latex."
- @echo "Run \`make all-pdf' or \`make all-ps' in that directory to" \
- "run these through (pdf)latex."
-
-changes:
- $(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) build/changes
- @echo
- @echo "The overview file is in build/changes."
-
-linkcheck:
- $(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) build/linkcheck
- @echo
- @echo "Link check complete; look for any errors in the above output " \
- "or in build/linkcheck/output.txt."
-
-doctest:
- $(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) build/doctest
- @echo "Testing of doctests in the sources finished, look at the " \
- "results in build/doctest/output.txt."
diff --git a/Apps/VRRender/doc/htmlhelpTowxHtmlHelp b/Apps/VRRender/doc/htmlhelpTowxHtmlHelp
deleted file mode 100755
index 9d02306..0000000
--- a/Apps/VRRender/doc/htmlhelpTowxHtmlHelp
+++ /dev/null
@@ -1,22 +0,0 @@
-#!/bin/bash
-
-test ! -d $1 && echo "$1 is not a dir" && exit 1
-
-for i in $1/*html
-do
- echo -n $i '... '
- sed -i 's,<div \+class="[^"]\+" \+id=\("[^"]\+"\) *>,<a name=\1 />&,' $i
- sed -i 's,<[a-z]\+ \+id=\("[^"]\+"\) *>,<a name=\1 />&,' $i
- echo ok
-done
-
-sed -i "s/Keyword/Name/g" $1/*hhk
-
-
-# images html theme defautl
-# mogrify -resize "850>" *.jpg
-
-# ipmages htmlhelp
-# mogrify -resize "1024>" *.jpg
-
-echo Done.
diff --git a/Apps/VRRender/doc/make.bat b/Apps/VRRender/doc/make.bat
deleted file mode 100644
index 0eb72e0..0000000
--- a/Apps/VRRender/doc/make.bat
+++ /dev/null
@@ -1,112 +0,0 @@
- at ECHO OFF
-
-REM Command file for Sphinx documentation
-
-set SPHINXBUILD=sphinx-build
-set ALLSPHINXOPTS=-d build/doctrees %SPHINXOPTS% source
-if NOT "%PAPER%" == "" (
- set ALLSPHINXOPTS=-D latex_paper_size=%PAPER% %ALLSPHINXOPTS%
-)
-
-if "%1" == "" goto help
-
-if "%1" == "help" (
- :help
- echo.Please use `make ^<target^>` where ^<target^> is one of
- echo. html to make standalone HTML files
- echo. dirhtml to make HTML files named index.html in directories
- echo. pickle to make pickle files
- echo. json to make JSON files
- echo. htmlhelp to make HTML files and a HTML help project
- echo. qthelp to make HTML files and a qthelp project
- echo. latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter
- echo. changes to make an overview over all changed/added/deprecated items
- echo. linkcheck to check all external links for integrity
- echo. doctest to run all doctests embedded in the documentation if enabled
- goto end
-)
-
-if "%1" == "clean" (
- for /d %%i in (build\*) do rmdir /q /s %%i
- del /q /s build\*
- goto end
-)
-
-if "%1" == "html" (
- %SPHINXBUILD% -b html %ALLSPHINXOPTS% build/html
- echo.
- echo.Build finished. The HTML pages are in build/html.
- goto end
-)
-
-if "%1" == "dirhtml" (
- %SPHINXBUILD% -b dirhtml %ALLSPHINXOPTS% build/dirhtml
- echo.
- echo.Build finished. The HTML pages are in build/dirhtml.
- goto end
-)
-
-if "%1" == "pickle" (
- %SPHINXBUILD% -b pickle %ALLSPHINXOPTS% build/pickle
- echo.
- echo.Build finished; now you can process the pickle files.
- goto end
-)
-
-if "%1" == "json" (
- %SPHINXBUILD% -b json %ALLSPHINXOPTS% build/json
- echo.
- echo.Build finished; now you can process the JSON files.
- goto end
-)
-
-if "%1" == "htmlhelp" (
- %SPHINXBUILD% -b htmlhelp %ALLSPHINXOPTS% build/htmlhelp
- echo.
- echo.Build finished; now you can run HTML Help Workshop with the ^
-.hhp project file in build/htmlhelp.
- goto end
-)
-
-if "%1" == "qthelp" (
- %SPHINXBUILD% -b qthelp %ALLSPHINXOPTS% build/qthelp
- echo.
- echo.Build finished; now you can run "qcollectiongenerator" with the ^
-.qhcp project file in build/qthelp, like this:
- echo.^> qcollectiongenerator build\qthelp\VRRenderDoc.qhcp
- echo.To view the help file:
- echo.^> assistant -collectionFile build\qthelp\VRRenderDoc.ghc
- goto end
-)
-
-if "%1" == "latex" (
- %SPHINXBUILD% -b latex %ALLSPHINXOPTS% build/latex
- echo.
- echo.Build finished; the LaTeX files are in build/latex.
- goto end
-)
-
-if "%1" == "changes" (
- %SPHINXBUILD% -b changes %ALLSPHINXOPTS% build/changes
- echo.
- echo.The overview file is in build/changes.
- goto end
-)
-
-if "%1" == "linkcheck" (
- %SPHINXBUILD% -b linkcheck %ALLSPHINXOPTS% build/linkcheck
- echo.
- echo.Link check complete; look for any errors in the above output ^
-or in build/linkcheck/output.txt.
- goto end
-)
-
-if "%1" == "doctest" (
- %SPHINXBUILD% -b doctest %ALLSPHINXOPTS% build/doctest
- echo.
- echo.Testing of doctests in the sources finished, look at the ^
-results in build/doctest/output.txt.
- goto end
-)
-
-:end
diff --git a/Apps/VRRender/doc/makeall.sh b/Apps/VRRender/doc/makeall.sh
deleted file mode 100755
index fe934ce..0000000
--- a/Apps/VRRender/doc/makeall.sh
+++ /dev/null
@@ -1,43 +0,0 @@
-#!/bin/bash
-# -*- coding: UTF8 -*-
-PROJ=VRRender
-
-test $(basename $(dirname $PWD)) = "$PROJ" && (
-
-
-make html htmlhelp latex && (
-
-(
-cd build
-#patch -p1 < ../patch.cedil
-)
-
-(
-cd build/latex
-make all-pdf
-)
-
-find build/ -type d -name .svn|xargs rm -rf
-
-./htmlhelpTowxHtmlHelp build/htmlhelp
-
-(
-cd build/htmlhelp/_images
-mogrify -resize "1024>" *.jpg *.png
-)
-
-
-(
-cd build/html/_images
-mogrify -resize "850>" *.jpg
-)
-
-(
-rm ../rc/doc.zip
-cd build/htmlhelp/
-zip -r ../../../rc/doc.zip ./
-)
-
-) || echo Error
-
-) || echo "Erreur: A executer dans $PROJ/doc"
diff --git a/Apps/VRRender/doc/source/2D_Landmarks.rst b/Apps/VRRender/doc/source/2D_Landmarks.rst
deleted file mode 100755
index 54ca553..0000000
--- a/Apps/VRRender/doc/source/2D_Landmarks.rst
+++ /dev/null
@@ -1,23 +0,0 @@
-2D MPR Landmarks and Distance Measurement
-=========================================
-
-.. index:: 2D landmark, 2D distance
-
-VR-Planning integrates a 3D landmarks positioning system in order to label a wanted 3D position of a voxel in the medical image. As described in the 3D medical image visualization, the management of these landmarks will be performed thanks to the following three buttons of the tool bar :
-
-.. image:: _static/Add-Find-View-landmark.png
- :align: center
-
-Thus, a 3D landmark can be positioned at the last selected voxel position by clicking on the ''Add landmark'' button of the tools bar. This action also open a small window allowing to name the landmark. The landmark then appears and can be moved in (an only in) the selected Negato view by simply selecting it through a mouse left button press, and by moving it in the view by keeping the left button pressed and releasing it in the wanted location.
-
-.. image:: _static/Negato-landmarks.png
- :align: center
-
-All 3D landmark position being recorded, it is possible to automatically reach a landmark position by clicking on the ''Find landmark'' button of the tools bar. The selection of the wanted landmark will then allow to automatically position the three Negatos (axial, frontal and sagittal views) on the 3D position of the landmark. Landmarks taking an important place on the selected view, it is also possible to hide or show all landmarks by using the ''Hide/Show landmarks'' button of the too [...]
-
-Distance computation is activated by using the button located in the bottom right part of each Negato. A single click adds a colorized distance segment in the Negato view. Each new click adds such a distance segment with each time a new color. Distances are computed between two 3D spheres that can be moved in the Negato by simply selecting it by pressing on the mouse left button, and by moving it in the view by keeping the left button pressed and releasing it in the wanted location. Dist [...]
-
-.. image:: _static/Negato-Distance.png
- :align: center
-
-
diff --git a/Apps/VRRender/doc/source/2D_MPR.rst b/Apps/VRRender/doc/source/2D_MPR.rst
deleted file mode 100755
index 3569345..0000000
--- a/Apps/VRRender/doc/source/2D_MPR.rst
+++ /dev/null
@@ -1,42 +0,0 @@
-2D Medical Image Multi-Planar Rendering (MPR)
-=============================================
-
-.. index:: 2D MPR, Multi Planar Rendering
-
-The 2D medical image visualization is selected by using the F2 shortcut or the forth icon of the tool bar :
-
-.. image:: _static/icon-2D.png
- :align: center
-
-The Multi-Planar Rendering (MPR) corresponds to the most standard visualization techniques developed and used on professional medical imaging workstations : three different views of the medical image in Axial, Frontal and Sagittal views. Each window is called Negato. VR-Planning provides such a 2D medical image view in one big left window (Negato1) and two smaller right windows (Negato2 and Negato 3).
-
-.. image:: _static/Negato-01.png
- :align: center
-
-It is easy to change the visualized axis of the Negato by using the axis selection menu at the left bottom part of each Negato. The visualized axes are automatically synchronized in order to keep the three Axial, Frontal and Sagittal views in three different windows.
-
-.. image:: _static/Negato-axes.png
- :align: center
-
-Each Negato indicates the minimum and maximum screened density [min,max], the standard density windowing size W and the middle density of the windowing L. As in the 3D medical image visualization, it is possible to improve the visualized grey-level by modifying the screened windowing. The parameterization of the visualized grey level window is done via the same technique as developed in all existing radiological software tools. When pressing the right mouse button in the image, it is pos [...]
-
-.. image:: _static/Negato-contrast.png
- :align: center
-
-Each Negato indicates the last selected voxel (voxel = volumic pixel), the coordinates (x,y,z) and the density of this voxel being indicated on the last line. Such a selection is performed by a simple left click in the image. Pressing (or clicking) the middle button provides the same information but adds an automatic synchronization of all views. When pressing the button, a full red cross centered on the selected voxel appears on all views while pressing the button.
-
-.. image:: _static/Negato-info.png
- :align: center
-
-It is also possible to zoom and to translate the image on each Negato in order to focus the attention on a part of the image. After a left click in the selected Negato, you can zoom with the mouse wheel or by using the combination of the ``Shift`` key and pressing the right button of the mouse. A movement from bottom to top increases the zoom, and a movement from top to bottom decreases the zoom.
-
-.. image:: _static/Negato-Zoom.png
- :align: center
-
-The translation is performed by using the combination of the ``shift`` key and pressing the left button of the mouse. In this case, a movement in any direction creates a translation in the same direction. The reset of translations and zooms is performed with the ``R`` key.
-
-.. image:: _static/Negato-translate.png
- :align: center
-
-The snapshot tool located at the left bottom part of each Negato allows to save the 2D-Slicer view in jpeg format. The snapshot is activated by a simple left button click on the picture icon localized at the bottom part of the window.
-
diff --git a/Apps/VRRender/doc/source/3D_Distances.rst b/Apps/VRRender/doc/source/3D_Distances.rst
deleted file mode 100755
index ed00eb7..0000000
--- a/Apps/VRRender/doc/source/3D_Distances.rst
+++ /dev/null
@@ -1,23 +0,0 @@
-3D Landmarks and Distance Measurement
-=====================================
-
-.. index:: 3D landmarks, 3D distance
-
-In order to label a wanted 3D position of a voxel in the medical image, VR-Planning integrates a 3D landmarks positioning system. The management of these landmarks will be performed thanks to the following three buttons of the tool bar corresponding respectively to ``Add landmark``, ``Find landmark`` and ``Hide/Show landmarks`` :
-
-.. image:: _static/Add-Find-View-landmark.png
- :align: center
-
-A 3D landmark can be positioned at the last selected voxel position by clicking on the ``Add landmark`` button of the tools bar. This action also open a small window allowing to name the landmark. The landmark then appears and can be moved in the Negato view by simply selecting it through a mouse left button press, and by moving it in the view by keeping the left button pressed and releasing it in the wanted location.
-
-.. image:: _static/3D-landmark.png
- :align: center
-
-All 3D landmark position being recorded, it is possible to automatically reach a landmark position by clicking on the ``Find landmark`` button of the tools bar. The selection of the wanted landmark will then allow to automatically position the three axial, frontal and sagittal planes on the 3D position of the landmark. 3D landmark taking an important place on the view, it is also possible to hide or show all landmarks by using the ``Hide/Show landmarks`` button of the tools bar. Finally, [...]
-
-VR-Planning also offers the possibility to compute distances in 3D view. Distance computation is activated by using the distance button located in the bottom right part of the view. A single click adds a colorized distance segment in the medical image view. Each new click adds such a distance segment with each time a new color. Distances are computed between two 3D spheres that can be moved in the medical image view by simply selecting it through a mouse left button press, and by moving [...]
-
-.. image:: _static/3D-distance.png
- :align: center
-
-
diff --git a/Apps/VRRender/doc/source/3D_Medical_Image_Visu.rst b/Apps/VRRender/doc/source/3D_Medical_Image_Visu.rst
deleted file mode 100755
index 1c20592..0000000
--- a/Apps/VRRender/doc/source/3D_Medical_Image_Visu.rst
+++ /dev/null
@@ -1,32 +0,0 @@
-3D Medical Image Visualization (including oblique plane)
-========================================================
-
-.. index:: 3D medical image, oblique plane
-
-VR-Planning allows to visualize the medical image in a 3D rendering of slices. This rendering is automatically activated when the patient is loaded. However, it is possible to hide this medical image visualization by a simple click on the ``Scan`` button located on the left bottom of the 3D window. A new click on the ``No scan`` button allows to show again the medical image.
-
-.. image:: _static/3D-show-hide-scan.png
- :align: center
-
-When the medical image is visible, two different modes of visualization are available. The default one slice view can thus be replaced by using the ``>`` button located in the bottom left part of the 3D window. The user can select and display three planes corresponding to the axial, frontal and sagittal view.
-
-.. image:: _static/3D-scan-1-3.png
- :align: center
-
-The default one slice view is an axial view. The bottom view selector allows to replace this axial view by a frontal or a sagittal view. The slice selection is then performed thanks to the slider located to the bottom part of the visualization window.
-
-.. image:: _static/3D-scan-ax-front-sag.png
- :align: center
-
-Finally in all mode, the medical image visualization can be modified by using the same interaction than in the 2D visualization. First of all, it is possible to select a voxel of the image and to obtain its coordinates (x,y,z) and its density through a simple left click (or press) in the medical image. These information are printed in the top left part of the window. The same information are obtained with a middle click that automatically synchronizes axial, frontal and sagittal view on [...]
-
-.. image:: _static/3D-scan-GL-value.png
- :align: center
-
-The parameterization of the visualized grey level window is done via the same technique as developed in all existing radiological software tools. When pressing the right mouse button in the image, it is possible to decrease or increase the middle value of the grey level window with up (increase) or down (decrease) movements of the mouse and the grey level window size with left (decrease) or right (increase) movements of the mouse.
-
-.. image:: _static/3D-scan-contrast.png
- :align: center
-
-
-
diff --git a/Apps/VRRender/doc/source/3D_Models_Manipulation.rst b/Apps/VRRender/doc/source/3D_Models_Manipulation.rst
deleted file mode 100755
index b596570..0000000
--- a/Apps/VRRender/doc/source/3D_Models_Manipulation.rst
+++ /dev/null
@@ -1,42 +0,0 @@
-3D Models Manipulation
-======================
-
-.. index:: 3D Models, 3D Visualisation
-
-The 3D model manipulations mode is automatically selected when you start VR-Planning. It is also possible to select this mode by using the F1 shortcut or the third icon of the tool bar :
-
-.. image:: _static/icon-3D.png
- :align: center
-
-The tool bar contains three recorded 3D views : axial, frontal and sagittal. These three views are activated by selecting the ``Axial view``, ``Frontal view`` and ``Sagittal view`` options in the ``3D Model`` menu, or by a simple click on the three last buttons of the tool bar :
-
-================================= =================================== ====================================
-.. image:: _static/icon-axial.png .. image:: _static/icon-frontal.png .. image:: _static/icon-sagittal.png
-================================= =================================== ====================================
-.. image:: _static/axial-view.jpg .. image:: _static/frontal-view.jpg .. image:: _static/sagittal-view.jpg
-================================= =================================== ====================================
-
-The 3D modeled patient can be moved through different interactions on the 3D image. Here is the list of these interactions :
-
-- Rotation around the center of the 3D view by a left mouse button press and a mouse dragging in direction of the rotation.
-
-.. image:: _static/3D-rotate.png
- :align: center
-
-- Translation by a shift + left mouse button press and a mouse dragging in direction of the translation. The translation can be reset by pressing the ``R`` key on the computer keyboard (reinitialisation of the point of view)
-
-.. image:: _static/3D-translation.png
- :align: center
-
-- Zoom by a Shift + right mouse button press and a mouse dragging up (zoom in) or down (zoom out). The same result is obtained only with the right button press (out of the 3D Scan), or by using Ctrl + right mouse button. The Zoom can be reset by pressing the ``R`` key on the computer keyboard (reinitialisation of the point of view).
-
-.. image:: _static/3D-zoom.png
- :align: center
-
-- Rotation around the central axe of the 3D view by a Ctrl + left mouse button press and a mouse dragging in direction of the rotation.
-
-.. image:: _static/3D-turn.png
- :align: center
-
-At any time, the user can take a jpeg picture of the 3D view by clicking on the picture icons at the bottom part of the windows.
-
diff --git a/Apps/VRRender/doc/source/3D_Models_Properties.rst b/Apps/VRRender/doc/source/3D_Models_Properties.rst
deleted file mode 100755
index 8d167b7..0000000
--- a/Apps/VRRender/doc/source/3D_Models_Properties.rst
+++ /dev/null
@@ -1,20 +0,0 @@
-3D Models Properties (show/hide organs)
-=======================================
-
-.. index:: Models Properties, Show organs, Hide organs
-
-The list of 3D modeled organs is available in the ``Organ Manager`` window that appears by selecting the ``Manage organs colors`` option in the ``3D Model`` menu, or by pressing F9 on the keyboard, or by clicking on the following button of the tool bar :
-
-.. image:: _static/icone-F9.png
- :align: center
-
-The ``Organ Manager`` window allows to display or hide any organ by using the check box. The ``Hide all organs`` check box allows to hide all organs.
-
-.. image:: _static/3D-show-hide-organs.png
- :align: center
-
-It also allows to modify its opacity thanks to a slider located at the bottom part of the property window.
-
-.. image:: _static/3D-transparency.png
- :align: center
-
diff --git a/Apps/VRRender/doc/source/3D_Resection.rst b/Apps/VRRender/doc/source/3D_Resection.rst
deleted file mode 100755
index e58e68a..0000000
--- a/Apps/VRRender/doc/source/3D_Resection.rst
+++ /dev/null
@@ -1,53 +0,0 @@
-VR-Planning Resection
-=====================
-
-.. index:: Resection, cutting plane
-
-VR-Planning allows to virtually resect any anatomical or pathological 3D modelled structure and to obtain the resulting volume and linked percentage of resection. VR-Planning not only gives the opportunity to perform several resections but also to plan several surgeries. The first step will thus consist in defining the operation by clicking on the ``New Resection`` button of the tool bar.
-
-.. image:: _static/operation.png
- :align: center
-
-Clicking on the ``New Resection`` button opens a window that proposes to create a new operation if no operation has been planned before. By clicking on OK, you can give an operation name (Operation_n by default). The validation with a click on the OK button then opens a new window containing the list of organs that will be possible to cut. By default, all visible organs are selected. After the selection of organs, a click on the OK button validates the operation definition and only organ [...]
-
-.. image:: _static/3D-Resect-start.png
- :align: center
-
-At this stage of the operation definition it is possible to add a cutting plane by using the ``Take plane points`` button.
-
-.. image:: _static/Add-plan2.png
- :align: center
-
-At any time, it is also possible to see the operation parameterisation by opening the ``Organ Manager`` window by a click on the organ manager button of the tool bar and by selecting the ``Operations`` tab in the window. The Organ Manager window offers the opportunity to modify selected organ properties. As we will see, it will also allow to modify cutting plane parameterization.
-
-.. image:: _static/3D-Resect-manage.png
- :align: center
-
-The resection requires the definition of one or several cutting planes. A cutting plane can be added by using the ``Take plane points`` button on the tool bar. After a click on this button, a cutting planes appears in the 3D view. The blue part will be the resecting part and the normal coloured part will be the safe part. Any cutting plane can be moved by selecting the three red control points (red square box). All control points can be selected and moved by a left button hold and mouse [...]
-
-.. image:: _static/3D-Resect-cutting-planes.png
- :align: center
-
-Any cutting plane separates the space into two areas: the resecting area and the safe area. It is possible to switch both areas by using the Organ Manager window. You must first select the wanted plane and then click on the ``change side`` tab to switch the resected area with the safe area as shown on the following image.
-
-.. image:: _static/3D-Resect-plane-side.png
- :align: center
-
-VR-Planning allows to add several cutting planes for each operation. At any time a simple click on the ``Take plane points`` button of the tool bar is sufficient to add and then displace the new cutting plane that will appear in the Organ Manager window in the ``Plane`` area of the ``Operation`` tab. A resection is then finalized by a simple click on the ``Resection`` button of the tool bar.
-
-.. image:: _static/3D-Resect-First.png
- :align: center
-
-After each resection, the ``Operation`` tab of the Organ Manager window indicates the resected part and the safe part list of organs. It is possible to change the rendering properties (colour and transparency) of each resected or safe part of organs. It is also possible to obtain the volume and percentage of both the safe and the resected part by selecting the wanted organs. Information appears then in the dedicated volume and ratio area of this window after a click on the ``Compute`` button.
-
-.. image:: _static/3D-Resect-volume.png
- :align: center
-
-One of the great improvements of VR-Planning in comparison with 3D VSP, which had been developed by IRCAD in 2001, is the opportunity to realize several resections on a same organ. It allows for instance to realize several segmentectomies on a same liver. To add a new resection, the user has to click on the ``New Resection`` button. It will then propose to choose between adding a new operation or adding a new resection. By selecting and validating a ``new resection``, a new window will a [...]
-
-.. image:: _static/3D-New-Resection.png
- :align: center
-
-The user can also choose to do a new operation, replacing the previously performed operation. To add a new resection, the user has to click on the ``New Resection`` button. It will then propose to choose between adding a new operation or adding a new resection. By selecting and validating a ``new operation``, a new window will appear allowing to change the name of the operation (by default operation_N). All interactions are then the same as for the first operation.
-
-Finally, you can change a resection or an operation by using the ``Operation`` tab of the ``Organ Manager`` window. The user has first to select the requested operation in the operation list. He/She will then be able to change a resection by adding or removing cutting planes. He/She must thus select the wanted resection in the same list and click on the ``Modify resection`` button. He/She will then be able to modify the cutting plane position, to add a cutting plane with the ``Take plane [...]
diff --git a/Apps/VRRender/doc/source/3D_Volume_Rendering.rst b/Apps/VRRender/doc/source/3D_Volume_Rendering.rst
deleted file mode 100755
index f8a3c93..0000000
--- a/Apps/VRRender/doc/source/3D_Volume_Rendering.rst
+++ /dev/null
@@ -1,37 +0,0 @@
-3D Volume Rendering
-===================
-
-.. index:: 3D Volume Rendering
-
-The VR-Planning visualization mode is started by pressing the F3 shortcut. It is also possible to select this mode by clicking on the VR icon of the tool bar :
-
-.. image:: _static/VR-01.jpg
- :align: center
-
-VR-Planning has been developed in order to be used in a fast way. Automated transfer functions (TF) have therefore been included in the software allowing users to save time by only selecting these transfer functions. This selection is performed in the TF selector box of the ``Transfer function editor``.
-
-.. image:: _static/VR-TF-AUTO-01.png
- :align: center
-
-As shown for medical use, the current software includes several pre-computed CT-scan transfer functions allowing to visualize bones, kidneys, liver, lungs, muscles, skin and vessels. More automated transfer functions provide standard transfer functions currently used in other applications. It is important to notice that in VR-Planning the color table of the transfer functions is applied on the Negato1 view. It can be highly useful to have a better medical image reading.
-
-.. image:: _static/VR-TF-AUTO-02.jpg
- :align: center
-
-It is possible to manipulate the Volume Rendering view with the same command than with the 2D MPR view, which means by using the mouse wheel or by using the combination of the ``Shift`` key and pressing the Right button for the zoom, by pressing the Left button and moving the mouse for the rotation, and by combining the ``Shift`` key and pressing the Left button for translation. In this case, a movement in any direction creates a translation in the same direction. The reset of translatio [...]
-
-.. image:: _static/VR-manip.jpg
- :align: center
-
-It is also possible to go directly to axial, frontal, and sagittal views by using the shortcut ``1``, ``2`` and ``3`` on the keyboard or the ``Volume Rendering`` menu by selecting ``Axial view``, ``Frontal view`` and ``Sagittal view`` options. In this same menu, the ``Snapshot rendering view`` option allows to take a picture of the Volume rendering view.
-
-Another important interest of VR-Planning is the ability to visualize only a part of the image by applying a cutting plane on the global image. Two major kinds of cutting planes are proposed. The first one is the standard axial, sagittal and frontal cutting plane. The second one is a mobile 3D cutting plane that can be placed anywhere in the volume. The selection of cutting planes (and unselection) is done with the ``Volume Rendering`` menu or via shortcuts : ``O`` for the ``View clippin [...]
-
-The clipping box provides 6 cutting planes: two axial, two frontal and two sagittal ones. The displacement of a cutting plane is then performed by pressing the left mouse button on the corresponding center sphere of this plane. When selected, the plane changes color and the sphere turns red. Displacement is then realized by moving the mouse. It is possible to remove the clipping box planes by selecting the ``Reset clipping box`` option in the ``Volume Rendering`` menu or by using the sho [...]
-
-.. image:: _static/VR-cutting.jpg
- :align: center
-
-This cutting box can also be reduced through a kind of in and out zoom by selecting the central volume sphere by a right button pressing, and then by adding a ``Shift`` pressing and an up (zoom out) and down (zoom in) movement of the mouse. In the same way, the cutting box can be translated by selecting the central volume sphere by pressing the left button, and then by adding a ``Shift`` pressing and a movement of the mouse.
-
-Furthermore, the clipping plane provides one cutting plane that can be moved thanks to the displacement and orientation of a vector that is normal in this cutting plane. The displacement is then performed by pressing the left mouse button on one of the two extremities of the vector. When selected, the vector turns red. Displacement is then realized by moving the mouse. When the cutting plane cuts the box, a red intersection appears. It is then possible to directly move the plane into the [...]
diff --git a/Apps/VRRender/doc/source/Acknowledgment.rst b/Apps/VRRender/doc/source/Acknowledgment.rst
deleted file mode 100755
index 89a1ae1..0000000
--- a/Apps/VRRender/doc/source/Acknowledgment.rst
+++ /dev/null
@@ -1,136 +0,0 @@
-
-.. _acknowledgment:
-
-Acknowledgment
-==============
-
-.. index:: Acknowledgment, open source, European, ICT, ehealth
-
-.. |EQC| replace:: European Commission
-.. _EQC: http://ec.europa.eu/information_society/activities/health
-
-.. _PASSPORT: http://www.passport-liver.eu/
-
-
-
-
-.. |boost| image:: _static/acknowledgment/boost.png
- :align: middle
-.. |cfitsio| image:: _static/acknowledgment/cfitsio.png
- :align: middle
-.. |dcmtk| image:: _static/acknowledgment/dcmtk.png
- :align: middle
-.. |fits2itk| image:: _static/acknowledgment/fits2itk.png
- :align: middle
-.. |itk| image:: _static/acknowledgment/itk.png
- :align: middle
-.. |vtk| image:: _static/acknowledgment/vtk.png
- :align: middle
-.. |libjpeg| image:: _static/acknowledgment/libjpeg.png
- :align: middle
-.. |libpng| image:: _static/acknowledgment/libpng.png
- :align: middle
-.. |libtiff| image:: _static/acknowledgment/libtiff.png
- :align: middle
-.. |libxml2| image:: _static/acknowledgment/libxml2.png
- :align: middle
-.. |log4cxx| image:: _static/acknowledgment/log4cxx.png
- :align: middle
-.. |opengl| image:: _static/acknowledgment/opengl.png
- :align: middle
-.. |vtkinria3d| image:: _static/acknowledgment/vtkinria3d.png
- :align: middle
-.. |python| image:: _static/acknowledgment/python.png
- :align: middle
-.. |sphinx| image:: _static/acknowledgment/sphinx.png
- :align: middle
-.. |wx| image:: _static/acknowledgment/wx.png
- :align: middle
-.. |zlib| image:: _static/acknowledgment/zlib.png
- :align: middle
-.. |bzip2| image:: _static/acknowledgment/bzip2.png
- :align: middle
-.. |gdcm| image:: _static/acknowledgment/gdcm.png
- :align: middle
-
-
-.. |doxygen| image:: _static/acknowledgment/doxygen.png
- :align: middle
-.. |eclipse| image:: _static/acknowledgment/eclipse.png
- :align: middle
-.. |vim| image:: _static/acknowledgment/vim.png
- :align: middle
-.. |fsf| image:: _static/acknowledgment/fsf.png
- :align: middle
-.. |gcc| image:: _static/acknowledgment/gcc.png
- :align: middle
-.. |scons| image:: _static/acknowledgment/scons.png
- :align: middle
-.. |visualc| image:: _static/acknowledgment/visualc.png
- :align: middle
-.. |wix| image:: _static/acknowledgment/wix.png
- :align: middle
-
-
-
-
-
-
-First of all, VR-Planning has partly been funded by the |EQC|_ within the ICT-2007.5.3 research project PASSPORT_.
-
-
-
-
-.. image:: _static/ehealth.png
- :align: center
-
-VR-Planning has been developed by Vincent Agnus, Arnaud Charnoz, Emilie Harquel, Alexandre Hostettler, Pascal Monnier, Johan Moreau, Nicolas Philipps and Julien Waechter, the project being managed by Prof. Luc Soler. Illustrations and logos have been realized by Juan Hernandez. Documentation and translation has been realized by Pamela Lhote and Luc Soler.
-
-The test and validation session has been performed by Mourad Bouhadjar, Anne-Blandine Osswald, and Prof. Luc Soler. 3D gallery and patient modeling have been realized by Mourad Bouhadjar, Anne-Blandine Osswald and Prof. Luc Soler.
-
-The website development has been supervised by the Websurg team under the management of Thomas Parent.
-
-This sofware has been tested at the University Hospital of Strasbourg. We would like to thank for their help the medical staff:
-- Endocrine and Digestive Surgical team : Prof. Jacques Marescaux, Prof. Didier Mutter, Prof. Bernard Dallemagne, Prof. Luc Soler, Dr. Michel Vix,
-
-VR-Planning has been built on the following projects :
-
-.. list-table::
-
- * - |boost|
- - |cfitsio|
- - |dcmtk|
- - |fits2itk|
- - |itk|
- - |vtk|
- - |vtkinria3d|
- * - |libjpeg|
- - |libpng|
- - |libtiff|
- - |libxml2|
- - |log4cxx|
- - |opengl|
- - |wx|
- * -
- - |python|
- - |sphinx|
- - |zlib|
- - |bzip2|
- - |gdcm|
- -
-
-
-VR-Planning has been developed with the following software :
-
-.. list-table::
-
- * - |doxygen|
- - |eclipse|
- - |vim|
- - |fsf|
- * - |gcc|
- - |scons|
- - |wix|
- - |visualc|
-
-
diff --git a/Apps/VRRender/doc/source/Basic_Image_Filtering.rst b/Apps/VRRender/doc/source/Basic_Image_Filtering.rst
deleted file mode 100755
index 0e98072..0000000
--- a/Apps/VRRender/doc/source/Basic_Image_Filtering.rst
+++ /dev/null
@@ -1,12 +0,0 @@
-VR-Planning basic image filtering
-===================================
-
-.. index:: filtering
-
-Several filters have been added in VR-Planning allowing to basically modify a selected image. When a filter is applied, a copy of the selected image is created and added in the ``series selector``. To distinguish the resulting image from the native image, the selector indicates a set of information allowing to precisely know the origin of the image and the parameter of the filter that has been used. This information is located in the comment area and is presented as follows: In : Operato [...]
-
-.. image:: _static/Negato-filter.png
- :align: center
-
-In VR-Planning, we have decided to limit the set of filters to three basic operators: Image Rotation (that allows a +/- 90 degrees rotation in axial, saggital or frontal axe), Improve image 2D (a 1 pixel radius 2D median filter), and Improve image 3D (a 1 voxel radius 3D median filter).
-
diff --git a/Apps/VRRender/doc/source/Export_Data.rst b/Apps/VRRender/doc/source/Export_Data.rst
deleted file mode 100755
index 084020d..0000000
--- a/Apps/VRRender/doc/source/Export_Data.rst
+++ /dev/null
@@ -1,8 +0,0 @@
-Export and Close data
-=====================
-
-.. index:: Export Data
-
-The file menu contains two useful export options. The first ``export selected patient`` option allows to record a selected patient in a VR-Planning format. It will include the distance measurement, the landmark positioning, the transfer function of the direct volume rendering, and the planned operation integratin the cutting planes position. The second ``export slices (jpg)`` option allows to record, in a selected folder, all DICOM slices of the selected image in a jpeg format.
-
-The file menu also contains two options allowing to close opened patient data. The ``Close all patients`` option will close all patients data and the ``Close selected image`` will only close the image seleted in the ``series selector`` window.
diff --git a/Apps/VRRender/doc/source/Help_menu.rst b/Apps/VRRender/doc/source/Help_menu.rst
deleted file mode 100755
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-Help Menu
-=========
-
-.. index:: Help
-
-VR-Planning include a ``Help`` menu including the VR-Planning documentation in an interactive window. All information contained in this document is thus available in this interactive help menu. Among this information, the list of shortcuts is an important help.
-
-Moreover, the ``Help`` menu contain several other useful options. The ``Edit Auto Update`` option, opens a window allowing to select (unselect) an automatic check of the VR-Planning software update. It also allows to select (unselect) the software statistic computation that will allow us to improve VR-Planning. In opposite, the ``Check update`` option allows to manually check the VR-Planning software update.
-
-*For any support request do not hesitate to contact : rd-support-vrplanning at ircad.fr*
-
-However, do not forget that VR-Planning can be used under a specific user license agreement. By using the VR-Planning, you accept the terms and conditions described in the :ref:`licence` chapter. VR-Planning *NOT* being FDA approved and having *NO* CE Mark, it comes with absolutely *NO Warranty*.
diff --git a/Apps/VRRender/doc/source/Introduction.rst b/Apps/VRRender/doc/source/Introduction.rst
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-Introduction
-============
-
-.. index:: IRCAD, Image Viewer, VR-Render
-
-
-VR-Planning is an IRCAD Surgical Planning Software working on Windows, Linux and MacOS. It allows to visualize 3D models of patients reconstucted from their DICOM Image by IRCAD R&D team, and also to virtually cut these models by providing an automatic volume and pourcentage computation. Three kinds of visualization are possible : 3D model visualization, 2D Dicom visualization and 3D Dicom direct volume rendering. You can also use VR-Planning to visualize your own DICOM medical images of [...]
-
-
diff --git a/Apps/VRRender/doc/source/Licence.rst b/Apps/VRRender/doc/source/Licence.rst
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index aa08f46..0000000
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-
-.. _licence:
-
-Licence
-=======
-
-.. index:: Licence
-
-By using the VR-Planning software, you accept the terms and conditions described hereinafter. If you do not accept them, you can not use this software. IRCAD grants you a non-exclusive license to use this software.
-
-EXCLUSION OF GUARANTEES : YOU ACKNOWLEDGE THAT IRCAD HAS NOT GIVEN YOU ANY EXPLICIT OR IMPLICIT GUARANTEE REGARDING THE VR-Planning SOFTWARE, ITS DATA MEDIUM AND ALL THE INCLUDED DOCUMENTS AND INFORMATION. YOU FURTHER ACKNOWLEDGE THAT THE SOFTWARE HAS BEEN PROVIDED **IN ITS PRESENT STATE** WITHOUT ANY GUARANTEE OF WHATEVER KIND. IRCAD GIVES NO GUARANTEE, EXPLICIT OR TACIT, SPECIFICALLY REGARDING THE COMPLIANCE WITH A NEED OF A PARTICULAR USE, MERCHANTABLE STATE OR QUALITY OR NON-VIOLATI [...]
-
-LIABILITY LIMITATION : UNDER NO CIRCUMSTANCES IRCAD WILL BE HELD LIABLE FOR THE DAMAGES THAT MIGHT BE CAUSED THROUGH THE USE OF THE VR-Planning SOFTWARE, LOSS OF USAGE OR INTERRUPTION OF ACTIVITY OR FOR ANY DIRECT, INDIRECT, SPECIAL OR CONSECUTIVE DAMAGE OF ANY KIND, SPECIFICALLY ANY LOSS OF BENEFIT OR LOSS OF PROFIT, NO MATTER WHAT KIND OF ACTION UNDERTAKEN, I.E. CONTRACTUAL, WRONGFUL (INCULDING IN CASE OF NEGLIGENCE), UNDER THE STRICT LIABILITY OF THE PRODUCT OR OTHER, REGARDLESS IF IR [...]
-
-VR-Planning uses a set of Open-Source libraries delivered with it :ref:`acknowledgment`.
-
-.. |danger| image:: _static/danger.png
- :align: middle
-
-.. warning::
-
- |danger| This software is *NOT FDA* approved and has *NO CE mark*
-
diff --git a/Apps/VRRender/doc/source/Minimal_config.rst b/Apps/VRRender/doc/source/Minimal_config.rst
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-Minimal Configuration
-=====================
-
-.. index:: Minimal Configuration, OS
-
-VR-Planning supports the following operating systems :
-
-
-
-.. |ms| image:: _static/acknowledgment/ms.png
- :align: middle
-.. |apple| image:: _static/acknowledgment/apple.png
- :align: middle
-.. |linux| image:: _static/acknowledgment/linux.png
- :align: middle
-.. |linux-64| image:: _static/acknowledgment/linux-64.png
- :align: middle
-
-
-.. list-table::
-
- * - |ms|
-.. - |apple|
-.. - |linux|
-.. - |linux-64|
-
-
-.. To works, VR-Planning requires a minimum of 2 Go (Mac OS, Linux, windows NT) or 3 Go (Vista/7) of RAM. The 3D rendering requires a 3D graphics card working under OpenGL.
-
-To works, VR-Planning requires a minimum of 2 Go (windows XP) or 3 Go (Vista/7) of RAM. The 3D rendering requires a 3D graphics card supporting OpenGL.
-
diff --git a/Apps/VRRender/doc/source/Read_and_Select_Data.rst b/Apps/VRRender/doc/source/Read_and_Select_Data.rst
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-Read and select data
-====================
-
-.. index:: Read Data, Select Data
-
-
-
-It is possible to load recorded patient by using the ``Import`` functions in the ``File`` menu. Three formats are available for reading : DICOM, MFO (VR-Anat IRCAD Format) and FXZ (VR-Planning IRCAD Format). The Dicom format is available through the first button of the tool bar, the two IRCAD formats being available from the second button :
-
-.. image:: _static/openDicom_openFxz.png
- :align: center
-
-
-A left click on the first icon, or a selection of the ``import DICOM`` option of the ``File`` menu allows to start the selection of a folder containing all DICOM slices of one or several medical images of the patient. The DICOM reader is the latest ITK version developed by Kitware and used by a large set of medical software applications.
-
-A left click on this icon, or a selection of the ``import data`` option of the ``File`` menu allows to load 3D modeled patient or exported DICOM images in two IRCAD format. The MFO format, as DICOM format, is a folder containing the 3D modelled patient data resulting of the VR-Anat software use. The Fxz is the specific VR-Planning format allowing to include in only one file one or several medical images and linked 3D models of one or several patients (see export data). This format will b [...]
-
-When a patient is loaded, it is possible to visualize (or hide) the ``series selector`` windows containing the parameters of the medical image or the patient information by clicking on the ``info`` button on the tool bar :
-
-.. image:: _static/View-INFO.png
- :align: center
-
-The ``series selector`` window contains the name of the patient, the kind of modality (Ct-scan, MRI, etc…), the acquisition date, the image size, the voxel size and the comments. By clicking on the up left window icon, the ``property`` window is opened (or closed). It contains the patient’s birthdate, his gender and the hospital name. When data are anonymous, real patient information are erased and replaced by generic data.
-
-.. image:: _static/info-patient.png
- :align: center
diff --git a/Apps/VRRender/doc/source/Shortcuts.rst b/Apps/VRRender/doc/source/Shortcuts.rst
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-Shortcuts
-=========
-
-.. index:: Shortcut, Shortcuts
-
-
-Global shortcuts
-----------------
-
-========== ================================
- Shortcut Action
-========== ================================
- Suppr Erase selected image
- F1 3D Model view
- F2 2D Medical Image view
- F3 3D Volume rendering view
- F9 Manage organs colors
- F12 HShow/Hide patient information
-========== ================================
-
-
-Global 3D manipulation (in 3D and Volume Rendering view only)
--------------------------------------------------------------
-
-=== ===============
- 1 axial view
- 2 frontal view
- 3 sagittal view
-=== ===============
-
-
-
-
-Global 3D-2D manipulation
--------------------------
-
-MD = Mouse drag which mean move the mouse by letting the selected button pressed.
-
-.. list-table::
-
- * - shift + left mouse button + MD
-
- shift + middle mouse button + MD
-
- ctrl + middle mouse button + MD
- - Translation
- * - mouse wheel (up or down)
-
- shift + Right mouse button + MD
-
- ctrl + Right mouse button + MD
- - Zoom
- * - R
- - Reset camera
-
-
-
-
-
-Specific manipulation for medical image (2D or 3D)
---------------------------------------------------
-
-.. list-table::
-
- * - left/right key
-
- shift + mouse wheel
- - modify current slice (after any click in selected slice)
- * - T/Y
- - modify axial slice
- * - G/H
- - modify frontal slice
- * - B/N
- - modify sagittal slice
- * - shift + R
- - reset window/level
- * - left mouse button
- - show pixel values
- * - middle mouse button
- - synchronize all views
- * - right mouse button
- - modify level and window
- * - ctrl + L
- - add a landmark on the last selected voxel
- * - ctrl + F
- - synchronize all views on selected landmark
- * - ctrl + V
- - hide/show landmarks
- * - right mouse click
- - remove distance/landmark
-
-
-
-Specific manipulation of the oblique plane
-------------------------------------------
-
-======================================================= ========================================================
- middle mouse button in center of plane : plane translation from his normal
-
- in corner : rotation in the plane
-
- in border : rotation of the plane around his normal
-
- ctrl + middle mouse button in center of plane : plane translation from his normal
-
- in corner : translation of the edge around the corner
-
- in border : translation of the edge
-
- shift + middle mouse button reslice plane (increase/decrease plane size)
-======================================================= ========================================================
-
-
-Specific manipulation of Volume rendering clipping box
-------------------------------------------------------
-
-
-========== ===================================
- O show/hide clipping box
- Ctrl + O reset clipping box
- T/Y clipping box axial translation
- G/H clipping box frontal translation
- B/N clipping box sagittal translation
- P show/hide clipping plane
- Ctrl + P reset clipping plane
-========== ===================================
-
-
-Specific manipulation of Transfer function editor
--------------------------------------------------
-
-========================= ==================
- left mouse button select points
- Ctrl + left mouse click new point
- double left mouse click edit point color
- right mouse click remove point
-========================= ==================
-
diff --git a/Apps/VRRender/doc/source/Start_VR_Planning.rst b/Apps/VRRender/doc/source/Start_VR_Planning.rst
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-Start VR-Planning
-===================
-
-.. index:: Start
-
-
-
-VR-Planning has been optimized for surgeon use. After installation, it will thus automatically recognize the IRCAD file format. By selecting the 3D clinical case (some 3D cases are freely available on www.websurg.com), VR-Planning will automatically start. However, you can also start VR-Planning for your own DICOM data or to select several IRCAD 3D modeled patients. IRCAD 3D modeled data are recognized and appear with the following VR-Planning icon :
-
-.. image:: _static/VRPlanning.png
- :align: center
-
-When VR-Planning is started by selecting a patient, the 3D model visualization window appears as shown on the following example.
-
-.. image:: _static/3D-Planning-View-00.png
- :align: center
-
diff --git a/Apps/VRRender/doc/source/Tool_bar.rst b/Apps/VRRender/doc/source/Tool_bar.rst
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-Tool Bar
-========
-
-.. index:: Tool Bar
-
-
-
-The easiest way to start VR-Planning is to use its tool bar. It contains respectively the following most used functions : Read Dicom image, read 3D modeled patient, 3D view, 2D scanner view, Direct volume rendering view, show/hide data information, add a 3D landmark, find a 3D landmark, hide/show 3D landmarks, show 3D organs list and properties, Axial view, Frontal view and Sagittal view, New operation, Add cutting plane, Compute Resection. All these functions will be explained in the fo [...]
-
-.. image:: _static/Tool-bar-planning.png
- :align: center
diff --git a/Apps/VRRender/doc/source/Transfert_function.rst b/Apps/VRRender/doc/source/Transfert_function.rst
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-Transfer Function Editor
-========================
-
-.. index:: Transfer Function, TF Editor
-
-VR-Planning has been developed in order to edit transfer functions. Seven buttons are thus available :
-- The ``Delete`` button (red cross) removes a selected transfer function in the list,
-- The ``New`` button (white paper) defines a new transfer function in the list,
-- The ``Reinitialize`` button (green arrow) reinitializes the native transfer functions,
-- The ``Rename`` button (A) allows to change the name of a selected transfer function.
-- The ``load`` (folder) and ``save`` (bleu arrow) buttons allow to load or save a transfer function in a selected location on the hard drive or on the network.
-
-When a new function is created, this function is set by default with the same parameter as the last selected one. It is possible and easy to change any transfer function (new or old) by using the transfer function editor. All TF are set by control points that can be removed by a simple right button click on the selected control point in the transfer function.
-
-.. image:: _static/VR-TF-01.jpg
- :align: center
-
-Addition of a new control point is done by pressing the control keyboard button and by clicking on the left mouse button on the transfer function. It is also possible to change the color of any control point by a double left button click on it. It then opens a color tab allowing to select the new requested color. The transparency and grey level of each control point can be modified by moving it by pressing the left mouse button and displacing it. These values can also be modified more pr [...]
-
-.. image:: _static/VR-TF-02.jpg
- :align: center
-
-It is finally possible to easily modify the transfert function by using the windowing parameterization techniques. This method allow to fastly adapt the pre-computed CT-scan transfer functions to the specificity of the selected image. It is thus possible to make a translation of the Transfert function in order to reduce the grey level value (Mouse Right button Pression and displacement from up to down), or in opposite in order to increase the grey level value (Mouse Right button Pression [...]
-
-.. image:: _static/VR-TF-MPR-01.jpg
- :align: center
-
-It is also possible to make a resizing of the Transfert function in order to reduce the grey level window (Mouse Right button Pression and displacement from right to left), or in opposite in order to increase the grey level window (Mouse Right button Pression and displacement from left to right) (see next image).
-
-.. image:: _static/VR-TF-MPR-02.jpg
- :align: center
diff --git a/Apps/VRRender/doc/source/What_is_Volume_Rendering.rst b/Apps/VRRender/doc/source/What_is_Volume_Rendering.rst
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-What is direct Volume Rendering ?
-=================================
-
-.. index:: Volume Rendering
-
-Volume Rendering (VR) is a well known visualization method for the 3D visualization of medical images. It is based on transparency and coloration of voxels. Indeed, a medical image is composed of a set of voxels, each voxel having a grey level that represents a physical property of the tissue (absorption of X ray in case of CT for instance). A voxel being a pixel in 3D, it is a square if slice thickness = pixel size or a rectangular box if slice thickness is different from the pixel size [...]
-
-.. image:: _static/VR-DEF.jpg
- :align: center
-
-The remaining problem is thus to select voxels that we want to see, and voxels that have to be put in transparency. Such a selection, called ``segmentation`` in computer sciences and consisting in delineating anatomical or pathological structures, is complex and time consuming. Another solution is to automatically replace all grey levels by colors, and add for each grey level an associated transparency level. This transformation is summarized in a transfer function that gives for each gr [...]
-
-.. image:: _static/VR-TF-DEF.jpg
- :align: center
-
diff --git a/Apps/VRRender/doc/source/Windows_Installation.rst b/Apps/VRRender/doc/source/Windows_Installation.rst
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-Windows Installation
-====================
-
-.. index:: Installation
-
-
-Installing VR-Planning is easy. Under Windows, the automatic install file
-``VR-Planning_n.msi`` starts with a double click on its icon. It starts a 5 step
-process where you will have to ``accept the terms in the license agreement``.
-It will further be possible to select the folder where the software will be
-installed. Indeed, the default folder can be avoid if you do not have the
-access right. In such a case, select a personal folder to install VR-Planning.
-After the final validation window, the setup software then installs VR-Planning
-on your computer and its icons on your desktop and it asks you for a last click
-on the finish button. The installation is completed.
-
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deleted file mode 100755
index c13ed68..0000000
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diff --git a/Apps/VRRender/doc/source/_static/doctools.js b/Apps/VRRender/doc/source/_static/doctools.js
deleted file mode 100755
index 9447678..0000000
--- a/Apps/VRRender/doc/source/_static/doctools.js
+++ /dev/null
@@ -1,232 +0,0 @@
-/// XXX: make it cross browser
-
-/**
- * make the code below compatible with browsers without
- * an installed firebug like debugger
- */
-if (!window.console || !console.firebug) {
- var names = ["log", "debug", "info", "warn", "error", "assert", "dir", "dirxml",
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- return true;
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-
- /**
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- TRANSLATIONS : {},
- PLURAL_EXPR : function(n) { return n == 1 ? 0 : 1; },
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- gettext : function(string) {
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- addTranslations : function(catalog) {
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- this.PLURAL_EXPR = new Function('n', 'return +(' + catalog.plural_expr + ')');
- this.LOCALE = catalog.locale;
- },
-
- /**
- * add context elements like header anchor links
- */
- addContextElements : function() {
- $('div[id] > :header:first').each(function() {
- $('<a class="headerlink">\u00B6</a>').
- attr('href', '#' + this.id).
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- });
- $('dt[id]').each(function() {
- $('<a class="headerlink">\u00B6</a>').
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- });
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-
- /**
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- }, 10);
- },
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- /**
- * highlight the search words provided in the url in the text
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- makeURL : function(relativeURL) {
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- },
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- getCurrentURL : function() {
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- var parts = path.split(/\//);
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diff --git a/Apps/VRRender/doc/source/_static/ehealth.png b/Apps/VRRender/doc/source/_static/ehealth.png
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diff --git a/Apps/VRRender/doc/source/_static/icon-2D.png b/Apps/VRRender/doc/source/_static/icon-2D.png
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diff --git a/Apps/VRRender/doc/source/_static/icon-axial.png b/Apps/VRRender/doc/source/_static/icon-axial.png
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diff --git a/Apps/VRRender/doc/source/_static/icon-frontal.png b/Apps/VRRender/doc/source/_static/icon-frontal.png
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diff --git a/Apps/VRRender/doc/source/_static/icon-sagittal.png b/Apps/VRRender/doc/source/_static/icon-sagittal.png
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diff --git a/Apps/VRRender/doc/source/_static/icon-windows.jpg b/Apps/VRRender/doc/source/_static/icon-windows.jpg
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diff --git a/Apps/VRRender/doc/source/_static/icone-F9.png b/Apps/VRRender/doc/source/_static/icone-F9.png
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diff --git a/Apps/VRRender/doc/source/_static/icone-VR-01.jpg b/Apps/VRRender/doc/source/_static/icone-VR-01.jpg
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diff --git a/Apps/VRRender/doc/source/_static/info-patient.png b/Apps/VRRender/doc/source/_static/info-patient.png
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diff --git a/Apps/VRRender/doc/source/_static/jquery.js b/Apps/VRRender/doc/source/_static/jquery.js
deleted file mode 100755
index 82b98e1..0000000
--- a/Apps/VRRender/doc/source/_static/jquery.js
+++ /dev/null
@@ -1,32 +0,0 @@
-/*
- * jQuery 1.2.6 - New Wave Javascript
- *
- * Copyright (c) 2008 John Resig (jquery.com)
- * Dual licensed under the MIT (MIT-LICENSE.txt)
- * and GPL (GPL-LICENSE.txt) licenses.
- *
- * $Date: 2008-05-24 14:22:17 -0400 (Sat, 24 May 2008) $
- * $Rev: 5685 $
- */
-(function(){var _jQuery=window.jQuery,_$=window.$;var jQuery=window.jQuery=window.$=function(selector,context){return new jQuery.fn.init(selector,context);};var quickExpr=/^[^<]*(<(.|\s)+>)[^>]*$|^#(\w+)$/,isSimple=/^.[^:#\[\.]*$/,undefined;jQuery.fn=jQuery.prototype={init:function(selector,context){selector=selector||document;if(selector.nodeType){this[0]=selector;this.length=1;return this;}if(typeof selector=="string"){var match=quickExpr.exec(selector);if(match&&(match[1]||!context)){ [...]
-return jQuery(context).find(selector);}else if(jQuery.isFunction(selector))return jQuery(document)[jQuery.fn.ready?"ready":"load"](selector);return this.setArray(jQuery.makeArray(selector));},jquery:"1.2.6",size:function(){return this.length;},length:0,get:function(num){return num==undefined?jQuery.makeArray(this):this[num];},pushStack:function(elems){var ret=jQuery(elems);ret.prevObject=this;return ret;},setArray:function(elems){this.length=0;Array.prototype.push.apply(this,elems);retur [...]
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diff --git a/Apps/VRRender/doc/source/_static/searchtools.js b/Apps/VRRender/doc/source/_static/searchtools.js
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index a243b15..0000000
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-/**
- * helper function to return a node containing the
- * search summary for a given text. keywords is a list
- * of stemmed words, hlwords is the list of normal, unstemmed
- * words. the first one is used to find the occurance, the
- * latter for highlighting it.
- */
-
-jQuery.makeSearchSummary = function(text, keywords, hlwords) {
- var textLower = text.toLowerCase();
- var start = 0;
- $.each(keywords, function() {
- var i = textLower.indexOf(this.toLowerCase());
- if (i > -1)
- start = i;
- });
- start = Math.max(start - 120, 0);
- var excerpt = ((start > 0) ? '...' : '') +
- $.trim(text.substr(start, 240)) +
- ((start + 240 - text.length) ? '...' : '');
- var rv = $('<div class="context"></div>').text(excerpt);
- $.each(hlwords, function() {
- rv = rv.highlightText(this, 'highlight');
- });
- return rv;
-}
-
-/**
- * Porter Stemmer
- */
-var PorterStemmer = function() {
-
- var step2list = {
- ational: 'ate',
- tional: 'tion',
- enci: 'ence',
- anci: 'ance',
- izer: 'ize',
- bli: 'ble',
- alli: 'al',
- entli: 'ent',
- eli: 'e',
- ousli: 'ous',
- ization: 'ize',
- ation: 'ate',
- ator: 'ate',
- alism: 'al',
- iveness: 'ive',
- fulness: 'ful',
- ousness: 'ous',
- aliti: 'al',
- iviti: 'ive',
- biliti: 'ble',
- logi: 'log'
- };
-
- var step3list = {
- icate: 'ic',
- ative: '',
- alize: 'al',
- iciti: 'ic',
- ical: 'ic',
- ful: '',
- ness: ''
- };
-
- var c = "[^aeiou]"; // consonant
- var v = "[aeiouy]"; // vowel
- var C = c + "[^aeiouy]*"; // consonant sequence
- var V = v + "[aeiou]*"; // vowel sequence
-
- var mgr0 = "^(" + C + ")?" + V + C; // [C]VC... is m>0
- var meq1 = "^(" + C + ")?" + V + C + "(" + V + ")?$"; // [C]VC[V] is m=1
- var mgr1 = "^(" + C + ")?" + V + C + V + C; // [C]VCVC... is m>1
- var s_v = "^(" + C + ")?" + v; // vowel in stem
-
- this.stemWord = function (w) {
- var stem;
- var suffix;
- var firstch;
- var origword = w;
-
- if (w.length < 3)
- return w;
-
- var re;
- var re2;
- var re3;
- var re4;
-
- firstch = w.substr(0,1);
- if (firstch == "y")
- w = firstch.toUpperCase() + w.substr(1);
-
- // Step 1a
- re = /^(.+?)(ss|i)es$/;
- re2 = /^(.+?)([^s])s$/;
-
- if (re.test(w))
- w = w.replace(re,"$1$2");
- else if (re2.test(w))
- w = w.replace(re2,"$1$2");
-
- // Step 1b
- re = /^(.+?)eed$/;
- re2 = /^(.+?)(ed|ing)$/;
- if (re.test(w)) {
- var fp = re.exec(w);
- re = new RegExp(mgr0);
- if (re.test(fp[1])) {
- re = /.$/;
- w = w.replace(re,"");
- }
- }
- else if (re2.test(w)) {
- var fp = re2.exec(w);
- stem = fp[1];
- re2 = new RegExp(s_v);
- if (re2.test(stem)) {
- w = stem;
- re2 = /(at|bl|iz)$/;
- re3 = new RegExp("([^aeiouylsz])\\1$");
- re4 = new RegExp("^" + C + v + "[^aeiouwxy]$");
- if (re2.test(w))
- w = w + "e";
- else if (re3.test(w)) {
- re = /.$/;
- w = w.replace(re,"");
- }
- else if (re4.test(w))
- w = w + "e";
- }
- }
-
- // Step 1c
- re = /^(.+?)y$/;
- if (re.test(w)) {
- var fp = re.exec(w);
- stem = fp[1];
- re = new RegExp(s_v);
- if (re.test(stem))
- w = stem + "i";
- }
-
- // Step 2
- re = /^(.+?)(ational|tional|enci|anci|izer|bli|alli|entli|eli|ousli|ization|ation|ator|alism|iveness|fulness|ousness|aliti|iviti|biliti|logi)$/;
- if (re.test(w)) {
- var fp = re.exec(w);
- stem = fp[1];
- suffix = fp[2];
- re = new RegExp(mgr0);
- if (re.test(stem))
- w = stem + step2list[suffix];
- }
-
- // Step 3
- re = /^(.+?)(icate|ative|alize|iciti|ical|ful|ness)$/;
- if (re.test(w)) {
- var fp = re.exec(w);
- stem = fp[1];
- suffix = fp[2];
- re = new RegExp(mgr0);
- if (re.test(stem))
- w = stem + step3list[suffix];
- }
-
- // Step 4
- re = /^(.+?)(al|ance|ence|er|ic|able|ible|ant|ement|ment|ent|ou|ism|ate|iti|ous|ive|ize)$/;
- re2 = /^(.+?)(s|t)(ion)$/;
- if (re.test(w)) {
- var fp = re.exec(w);
- stem = fp[1];
- re = new RegExp(mgr1);
- if (re.test(stem))
- w = stem;
- }
- else if (re2.test(w)) {
- var fp = re2.exec(w);
- stem = fp[1] + fp[2];
- re2 = new RegExp(mgr1);
- if (re2.test(stem))
- w = stem;
- }
-
- // Step 5
- re = /^(.+?)e$/;
- if (re.test(w)) {
- var fp = re.exec(w);
- stem = fp[1];
- re = new RegExp(mgr1);
- re2 = new RegExp(meq1);
- re3 = new RegExp("^" + C + v + "[^aeiouwxy]$");
- if (re.test(stem) || (re2.test(stem) && !(re3.test(stem))))
- w = stem;
- }
- re = /ll$/;
- re2 = new RegExp(mgr1);
- if (re.test(w) && re2.test(w)) {
- re = /.$/;
- w = w.replace(re,"");
- }
-
- // and turn initial Y back to y
- if (firstch == "y")
- w = firstch.toLowerCase() + w.substr(1);
- return w;
- }
-}
-
-
-/**
- * Search Module
- */
-var Search = {
-
- _index : null,
- _queued_query : null,
- _pulse_status : -1,
-
- init : function() {
- var params = $.getQueryParameters();
- if (params.q) {
- var query = params.q[0];
- $('input[name="q"]')[0].value = query;
- this.performSearch(query);
- }
- },
-
- /**
- * Sets the index
- */
- setIndex : function(index) {
- var q;
- this._index = index;
- if ((q = this._queued_query) !== null) {
- this._queued_query = null;
- Search.query(q);
- }
- },
-
- hasIndex : function() {
- return this._index !== null;
- },
-
- deferQuery : function(query) {
- this._queued_query = query;
- },
-
- stopPulse : function() {
- this._pulse_status = 0;
- },
-
- startPulse : function() {
- if (this._pulse_status >= 0)
- return;
- function pulse() {
- Search._pulse_status = (Search._pulse_status + 1) % 4;
- var dotString = '';
- for (var i = 0; i < Search._pulse_status; i++)
- dotString += '.';
- Search.dots.text(dotString);
- if (Search._pulse_status > -1)
- window.setTimeout(pulse, 500);
- };
- pulse();
- },
-
- /**
- * perform a search for something
- */
- performSearch : function(query) {
- // create the required interface elements
- this.out = $('#search-results');
- this.title = $('<h2>' + _('Searching') + '</h2>').appendTo(this.out);
- this.dots = $('<span></span>').appendTo(this.title);
- this.status = $('<p style="display: none"></p>').appendTo(this.out);
- this.output = $('<ul class="search"/>').appendTo(this.out);
-
- $('#search-progress').text(_('Preparing search...'));
- this.startPulse();
-
- // index already loaded, the browser was quick!
- if (this.hasIndex())
- this.query(query);
- else
- this.deferQuery(query);
- },
-
- query : function(query) {
- // stem the searchterms and add them to the
- // correct list
- var stemmer = new PorterStemmer();
- var searchterms = [];
- var excluded = [];
- var hlterms = [];
- var tmp = query.split(/\s+/);
- var object = (tmp.length == 1) ? tmp[0].toLowerCase() : null;
- for (var i = 0; i < tmp.length; i++) {
- // stem the word
- var word = stemmer.stemWord(tmp[i]).toLowerCase();
- // select the correct list
- if (word[0] == '-') {
- var toAppend = excluded;
- word = word.substr(1);
- }
- else {
- var toAppend = searchterms;
- hlterms.push(tmp[i].toLowerCase());
- }
- // only add if not already in the list
- if (!$.contains(toAppend, word))
- toAppend.push(word);
- };
- var highlightstring = '?highlight=' + $.urlencode(hlterms.join(" "));
-
- console.debug('SEARCH: searching for:');
- console.info('required: ', searchterms);
- console.info('excluded: ', excluded);
-
- // prepare search
- var filenames = this._index.filenames;
- var titles = this._index.titles;
- var terms = this._index.terms;
- var descrefs = this._index.descrefs;
- var modules = this._index.modules;
- var desctypes = this._index.desctypes;
- var fileMap = {};
- var files = null;
- var objectResults = [];
- var regularResults = [];
- $('#search-progress').empty();
-
- // lookup as object
- if (object != null) {
- for (var module in modules) {
- if (module.indexOf(object) > -1) {
- fn = modules[module];
- descr = _('module, in ') + titles[fn];
- objectResults.push([filenames[fn], module, '#module-'+module, descr]);
- }
- }
- for (var prefix in descrefs) {
- for (var name in descrefs[prefix]) {
- if (name.toLowerCase().indexOf(object) > -1) {
- match = descrefs[prefix][name];
- fullname = (prefix ? prefix + '.' : '') + name;
- descr = desctypes[match[1]] + _(', in ') + titles[match[0]];
- objectResults.push([filenames[match[0]], fullname, '#'+fullname, descr]);
- }
- }
- }
- }
-
- // sort results descending
- objectResults.sort(function(a, b) {
- return (a[1] > b[1]) ? -1 : ((a[1] < b[1]) ? 1 : 0);
- });
-
-
- // perform the search on the required terms
- for (var i = 0; i < searchterms.length; i++) {
- var word = searchterms[i];
- // no match but word was a required one
- if ((files = terms[word]) == null)
- break;
- if (files.length == undefined) {
- files = [files];
- }
- // create the mapping
- for (var j = 0; j < files.length; j++) {
- var file = files[j];
- if (file in fileMap)
- fileMap[file].push(word);
- else
- fileMap[file] = [word];
- }
- }
-
- // now check if the files don't contain excluded terms
- for (var file in fileMap) {
- var valid = true;
-
- // check if all requirements are matched
- if (fileMap[file].length != searchterms.length)
- continue;
-
- // ensure that none of the excluded terms is in the
- // search result.
- for (var i = 0; i < excluded.length; i++) {
- if (terms[excluded[i]] == file ||
- $.contains(terms[excluded[i]] || [], file)) {
- valid = false;
- break;
- }
- }
-
- // if we have still a valid result we can add it
- // to the result list
- if (valid)
- regularResults.push([filenames[file], titles[file], '', null]);
- }
-
- // delete unused variables in order to not waste
- // memory until list is retrieved completely
- delete filenames, titles, terms;
-
- // now sort the regular results descending by title
- regularResults.sort(function(a, b) {
- var left = a[1].toLowerCase();
- var right = b[1].toLowerCase();
- return (left > right) ? -1 : ((left < right) ? 1 : 0);
- });
-
- // combine both
- var results = regularResults.concat(objectResults);
-
- // print the results
- var resultCount = results.length;
- function displayNextItem() {
- // results left, load the summary and display it
- if (results.length) {
- var item = results.pop();
- var listItem = $('<li style="display:none"></li>');
- listItem.append($('<a/>').attr(
- 'href',
- item[0] + DOCUMENTATION_OPTIONS.FILE_SUFFIX +
- highlightstring + item[2]).html(item[1]));
- if (item[3]) {
- listItem.append($('<span> (' + item[3] + ')</span>'));
- Search.output.append(listItem);
- listItem.slideDown(5, function() {
- displayNextItem();
- });
- } else if (DOCUMENTATION_OPTIONS.HAS_SOURCE) {
- $.get('_sources/' + item[0] + '.txt', function(data) {
- listItem.append($.makeSearchSummary(data, searchterms, hlterms));
- Search.output.append(listItem);
- listItem.slideDown(5, function() {
- displayNextItem();
- });
- });
- } else {
- // no source available, just display title
- Search.output.append(listItem);
- listItem.slideDown(5, function() {
- displayNextItem();
- });
- }
- }
- // search finished, update title and status message
- else {
- Search.stopPulse();
- Search.title.text(_('Search Results'));
- if (!resultCount)
- Search.status.text(_('Your search did not match any documents. Please make sure that all words are spelled correctly and that you\'ve selected enough categories.'));
- else
- Search.status.text(_('Search finished, found %s page(s) matching the search query.').replace('%s', resultCount));
- Search.status.fadeIn(500);
- }
- }
- displayNextItem();
- }
-}
-
-$(document).ready(function() {
- Search.init();
-});
diff --git a/Apps/VRRender/doc/source/_static/sliceHide.png b/Apps/VRRender/doc/source/_static/sliceHide.png
deleted file mode 100755
index 14a1f34..0000000
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diff --git a/Apps/VRRender/doc/source/_static/sliceShow.png b/Apps/VRRender/doc/source/_static/sliceShow.png
deleted file mode 100755
index 84c4fe9..0000000
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diff --git a/Apps/VRRender/doc/source/_static/video.png b/Apps/VRRender/doc/source/_static/video.png
deleted file mode 100755
index ff4bca2..0000000
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diff --git a/Apps/VRRender/doc/source/_static/view_frontal.png b/Apps/VRRender/doc/source/_static/view_frontal.png
deleted file mode 100755
index f1bc533..0000000
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diff --git a/Apps/VRRender/doc/source/_static/view_profil.png b/Apps/VRRender/doc/source/_static/view_profil.png
deleted file mode 100755
index 40fd8a4..0000000
Binary files a/Apps/VRRender/doc/source/_static/view_profil.png and /dev/null differ
diff --git a/Apps/VRRender/doc/source/conf.py b/Apps/VRRender/doc/source/conf.py
deleted file mode 100644
index f160cc5..0000000
--- a/Apps/VRRender/doc/source/conf.py
+++ /dev/null
@@ -1,208 +0,0 @@
-# ***** BEGIN LICENSE BLOCK *****
-# FW4SPL - Copyright (C) IRCAD, 2009-2012.
-# Distributed under the terms of the GNU Lesser General Public License (LGPL) as
-# published by the Free Software Foundation.
-# ****** END LICENSE BLOCK ******
-
-# -*- coding: utf-8 -*-
-#
-# This file is execfile()d with the current directory set to its containing dir.
-#
-# Note that not all possible configuration values are present in this
-# autogenerated file.
-#
-# All configuration values have a default; values that are commented out
-# serve to show the default.
-
-import sys, os
-
-# If extensions (or modules to document with autodoc) are in another directory,
-# add these directories to sys.path here. If the directory is relative to the
-# documentation root, use os.path.abspath to make it absolute, like shown here.
-#sys.path.append(os.path.abspath('.'))
-
-# -- General configuration -----------------------------------------------------
-
-# Add any Sphinx extension module names here, as strings. They can be extensions
-# coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
-extensions = []
-
-# Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
-
-# The suffix of source filenames.
-source_suffix = '.rst'
-
-# The encoding of source files.
-source_encoding = 'utf-8'
-
-# The master toctree document.
-master_doc = 'index'
-
-# General information about the project.
-projectname = u'VR-Planning'
-project = projectname.replace('-','').replace(' ','')
-copyright = u'2010, IRCAD'
-
-# The version info for the project you're documenting, acts as replacement for
-# |version| and |release|, also used in various other places throughout the
-# built documents.
-#
-# The short X.Y version.
-version = '0.8'
-# The full version, including alpha/beta/rc tags.
-release = '0.8'
-
-# The language for content autogenerated by Sphinx. Refer to documentation
-# for a list of supported languages.
-#language = None
-language = 'en'
-
-# There are two options for replacing |today|: either, you set today to some
-# non-false value, then it is used:
-#today = ''
-# Else, today_fmt is used as the format for a strftime call.
-#today_fmt = '%B %d, %Y'
-today_fmt = '%Y'
-
-# List of documents that shouldn't be included in the build.
-#unused_docs = []
-
-# List of directories, relative to source directory, that shouldn't be searched
-# for source files.
-exclude_trees = []
-
-# The reST default role (used for this markup: `text`) to use for all documents.
-#default_role = None
-
-# If true, '()' will be appended to :func: etc. cross-reference text.
-#add_function_parentheses = True
-
-# If true, the current module name will be prepended to all description
-# unit titles (such as .. function::).
-#add_module_names = True
-
-# If true, sectionauthor and moduleauthor directives will be shown in the
-# output. They are ignored by default.
-show_authors = False
-
-# The name of the Pygments (syntax highlighting) style to use.
-pygments_style = 'sphinx'
-
-# A list of ignored prefixes for module index sorting.
-#modindex_common_prefix = []
-
-
-# -- Options for HTML output ---------------------------------------------------
-
-# The theme to use for HTML and HTML Help pages. Major themes that come with
-# Sphinx are currently 'default' and 'sphinxdoc'.
-html_theme = 'default'
-#html_theme = 'sphinxdoc'
-
-# Theme options are theme-specific and customize the look and feel of a theme
-# further. For a list of options available for each theme, see the
-# documentation.
-#html_theme_options = {}
-
-# Add any paths that contain custom themes here, relative to this directory.
-#html_theme_path = []
-
-# The name for this set of Sphinx documents. If None, it defaults to
-# "<project> v<release> documentation".
-#html_title = None
-
-# A shorter title for the navigation bar. Default is the same as html_title.
-#html_short_title = None
-
-# The name of an image file (relative to this directory) to place at the top
-# of the sidebar.
-html_logo = "_static/VR_html.png"
-
-# The name of an image file (within the static path) to use as favicon of the
-# docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32
-# pixels large.
-#html_favicon = None
-
-# Add any paths that contain custom static files (such as style sheets) here,
-# relative to this directory. They are copied after the builtin static files,
-# so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
-
-# If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
-# using the given strftime format.
-#html_last_updated_fmt = '%b %d, %Y'
-#html_last_updated_fmt = '%Y'
-
-# If true, SmartyPants will be used to convert quotes and dashes to
-# typographically correct entities.
-#html_use_smartypants = True
-
-# Custom sidebar templates, maps document names to template names.
-#html_sidebars = {}
-
-# Additional templates that should be rendered to pages, maps page names to
-# template names.
-#html_additional_pages = {}
-
-# If false, no module index is generated.
-html_use_modindex = False
-
-# If false, no index is generated.
-html_use_index = True
-
-# If true, the index is split into individual pages for each letter.
-#html_split_index = False
-
-# If true, links to the reST sources are added to the pages.
-#html_show_sourcelink = True
-
-html_show_sphinx = False
-html_show_sourcelink = False
-
-# If true, an OpenSearch description file will be output, and all pages will
-# contain a <link> tag referring to it. The value of this option must be the
-# base URL from which the finished HTML is served.
-#html_use_opensearch = ''
-
-# If nonempty, this is the file name suffix for HTML files (e.g. ".xhtml").
-#html_file_suffix = ''
-
-# Output file base name for HTML help builder.
-htmlhelp_basename = 'VR-Render Websurg Limited Edition'
-
-
-# -- Options for LaTeX output --------------------------------------------------
-
-
-latex_elements = {
- 'papersize' : 'a4',
- 'pointsize' : '12pt',
- }
-
-# Grouping the document tree into LaTeX files. List of tuples
-# (source start file, target name, title, author, documentclass [howto/manual]).
-latex_documents = [
- ('index', project+'.tex', projectname+u' Documentation',
- u'IRCAD', 'manual'),
-]
-
-# The name of an image file (relative to this directory) to place at the top of
-# the title page.
-latex_logo = "_static/"+project+".png"
-
-# For "manual" documents, if this is true, then toplevel headings are parts,
-# not chapters.
-latex_use_parts = False
-#latex_use_parts = True
-
-# Additional stuff for the LaTeX preamble.
-#latex_preamble = ''
-
-# Documents to append as an appendix to all manuals.
-#latex_appendices = []
-
-# If false, no module index is generated.
-#latex_use_modindex = True
-latex_use_modindex = False
-
diff --git a/Apps/VRRender/doc/source/index.rst b/Apps/VRRender/doc/source/index.rst
deleted file mode 100755
index 95bcc24..0000000
--- a/Apps/VRRender/doc/source/index.rst
+++ /dev/null
@@ -1,37 +0,0 @@
-.. VRPlanningDoc documentation master file, created by
- Luc SOLER on Fri Mar 12 12:00:00 2010.
- You can adapt this file completely to your liking, but it should at least
- contain the root `toctree` directive.
-
-Welcome to VR-Planning 0.2
-==========================
-
-Contents:
-
-
-.. toctree::
- :maxdepth: 2
-
- Introduction
- Windows_Installation
- Start_VR_Planning
- Tool_bar
- Read_and_Select_Data
- Export_Data
- 3D_Models_Manipulation
- 3D_Models_Properties
- 3D_Medical_Image_Visu
- 3D_Distances
- 3D_Resection
- 2D_MPR
- 2D_Landmarks
- Basic_Image_Filtering
- What_is_Volume_Rendering
- 3D_Volume_Rendering
- Transfert_function
- Help_menu
- Shortcuts
- Acknowledgment
- Minimal_config
- Licence
-
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