[med-svn] [mia] 02/11: Merge tag 'upstream/2.2.3'
Gert Wollny
gert-guest at moszumanska.debian.org
Wed Jan 14 11:08:14 UTC 2015
This is an automated email from the git hooks/post-receive script.
gert-guest pushed a commit to branch master
in repository mia.
commit 9f671b70116701e36ec7804c2c3ac8b3581e806e
Merge: d69f6c9 365a539
Author: Gert Wollny <gw.fossdev at gmail.com>
Date: Wed Jan 7 12:23:41 2015 +0100
Merge tag 'upstream/2.2.3'
Upstream version 2.2.3
CMakeLists.txt | 14 +-
ChangeLog | 9 +
.../test_combiner.cc => addons/jpg/jpeg-common.hh | 53 ++-
addons/jpg/jpg-gray.cc | 90 ++---
addons/jpg/jpg-rgb.cc | 74 ++---
addons/nifti/niftiimage.cc | 54 +--
addons/nifti/test_niftiimage.cc | 1 +
cmake/macros.cmake | 98 ++++--
doc/CMakeLists.txt | 42 ++-
doc/MiaDoctools.cmake | 187 +++++++++++
doc/__init__.py | 1 +
doc/extract_docu.py | 159 ---------
doc/mia-xmldoc2man.cmake | 5 +
doc/mia-xmldoc2nipype.cmake | 5 +
doc/miareadxml.py | 168 +++++++++-
doc/miaxml2html.py | 112 -------
doc/miaxml2man.py | 7 +-
doc/miaxml2nipype.py | 366 +++++++++++++++++++++
doc/miaxml2sgml.py | 2 +-
mia/2d/creator/circle.cc | 1 -
mia/2d/filter.cc | 1 -
mia/2d/filter/CMakeLists.txt | 3 +-
mia/2d/filter/labelscale.cc | 166 ++++++++++
mia/2d/{test_combiner.cc => filter/labelscale.hh} | 43 ++-
mia/2d/filter/test_labelscale.cc | 128 +++++++
mia/2d/filtertest.cc | 1 -
mia/2d/fullcost/CMakeLists.txt | 2 +-
mia/2d/fullcost/label.cc | 340 +++++++++++++++++++
mia/2d/fullcost/label.hh | 97 ++++++
mia/2d/fullcost/test_label.cc | 127 +++++++
mia/2d/imageiotest.cc | 1 -
mia/2d/imagetest.cc | 1 -
mia/2d/interpolator.cc | 2 -
mia/2d/register.cc | 3 +-
mia/2d/test_combiner.cc | 1 -
mia/2d/test_distance.cc | 1 -
mia/2d/test_filter.cc | 2 +-
mia/2d/test_filter_cast.cc | 1 -
mia/2d/test_fullcost.cc | 4 +-
mia/2d/test_ica.cc | 1 -
mia/2d/test_image.cc | 2 -
mia/2d/test_imageio.cc | 1 -
mia/2d/test_interpol.cc | 1 -
mia/2d/test_modelsolverreg.cc | 1 -
mia/2d/test_nfg.cc | 1 -
mia/2d/test_oldnewintegrate.cc | 1 -
mia/2d/test_ppmatrix.cc | 17 +-
mia/2d/test_regplugins.cc | 1 -
mia/2d/test_segframe.cc | 1 -
mia/2d/test_segmentation.cc | 1 -
mia/2d/test_shape.cc | 1 -
mia/2d/test_transformfactory.cc | 1 -
mia/2d/test_vectorfield_interpolator.cc | 1 -
mia/2d/test_vfio.cc | 1 -
mia/2d/vfiotest.cc | 1 -
mia/3d/datafield.cxx | 36 ++
mia/3d/datafield.hh | 14 +
mia/3d/fifof/morphological.cc | 1 -
mia/3d/fifof/regiongrow.cc | 2 +-
mia/3d/filter.cc | 2 -
mia/3d/filter/CMakeLists.txt | 1 +
mia/3d/filter/labelscale.cc | 177 ++++++++++
.../test_combiner.cc => 3d/filter/labelscale.hh} | 43 ++-
mia/3d/filter/test_bandpass.cc | 1 -
mia/3d/filter/test_binarize.cc | 1 -
mia/3d/filter/test_convert.cc | 1 -
mia/3d/filter/test_crop.cc | 1 -
mia/3d/filter/test_downscale.cc | 1 -
mia/3d/filter/test_gradnorm.cc | 1 -
mia/3d/filter/test_growmask.cc | 1 -
mia/3d/filter/test_invert.cc | 1 -
mia/3d/filter/test_kmeans.cc | 1 -
mia/3d/filter/test_label.cc | 1 -
mia/3d/filter/test_labelscale.cc | 169 ++++++++++
mia/3d/filter/test_load.cc | 1 -
mia/3d/filter/test_mask.cc | 1 -
mia/3d/filter/test_median.cc | 1 -
mia/3d/filter/test_mlv.cc | 1 -
mia/3d/filter/test_morphological.cc | 1 -
mia/3d/filter/test_reorient.cc | 1 -
mia/3d/filter/test_scale.cc | 1 -
mia/3d/filter/test_selectbig.cc | 1 -
mia/3d/filter/test_sepconv.cc | 1 -
mia/3d/filter/test_tee.cc | 1 -
mia/3d/fullcost/CMakeLists.txt | 2 +-
mia/3d/fullcost/label.cc | 321 ++++++++++++++++++
mia/3d/fullcost/label.hh | 100 ++++++
mia/3d/fullcost/test_label.cc | 203 ++++++++++++
mia/3d/image.hh | 21 ++
mia/3d/imageiotest.cc | 2 -
mia/3d/imagetest.cc | 1 -
mia/3d/interpolator.cc | 1 -
mia/3d/multireg.cc | 1 -
mia/3d/test_combiner.cc | 1 -
mia/3d/test_cost.cc | 3 -
mia/3d/test_deform.cc | 2 -
mia/3d/test_ica.cc | 1 -
mia/3d/test_image.cc | 1 -
mia/3d/test_interpol.cc | 1 -
mia/3d/test_nfg.cc | 1 -
mia/3d/test_orientation.cc | 3 -
mia/3d/test_regplugins.cc | 1 -
mia/3d/test_shape.cc | 1 -
mia/3d/test_transformfactory.cc | 2 -
mia/3d/test_vfio.cc | 2 -
mia/3d/transform/rotbend.cc | 72 ++--
mia/3d/transform/rotbend.hh | 6 +-
mia/3d/transform/test_rotbend.cc | 12 +-
mia/3d/vfiotest.cc | 3 +-
mia/core/CMakeLists.txt | 2 +
mia/core/attributes.hh | 6 +-
mia/core/cmdbooloption.cc | 8 +-
mia/core/cmdbooloption.hh | 3 +-
mia/core/cmdlineparser.cc | 182 +++++-----
mia/core/cmdlineparser.hh | 100 ++----
mia/core/cmdoption.cc | 19 +-
mia/core/cmdoption.hh | 5 +-
mia/core/cmdoptionflags.hh | 9 +-
mia/core/handler.hh | 12 +-
mia/core/minimizer/gdas.cc | 9 +-
mia/core/parameter.cc | 6 +-
.../test_combiner.cc => core/selftestcmdoption.cc} | 33 +-
mia/core/selftestcmdoption.hh | 89 +++++
mia/core/statistics.hh | 2 +-
mia/core/test_attributes.cc | 4 +-
miacore.pc.cmake | 3 +
src/2davgmasked.cc | 2 +-
src/2dcost.cc | 4 +-
src/2ddistance.cc | 37 ++-
src/2dgrayimage-combine-to-rgb.cc | 2 +-
src/2dimagecombine-dice.cc | 2 +-
src/2dimagefilter.cc | 4 -
src/2dimagefilterstack.cc | 6 -
src/2dimagefullstats.cc | 1 +
src/2dimageregistration.cc | 8 +-
src/2dimagestats.cc | 1 +
src/2dlerp.cc | 35 +-
src/2dmany2one-nonrigid.cc | 2 +-
src/2dmulti-force.cc | 51 ++-
src/2dmultiimageregistration.cc | 92 ++++++
src/2dmyocard-ica.cc | 3 +-
src/2dmyocard-icaseries.cc | 6 +-
src/2dmyoseries-compdice.cc | 1 +
src/2dmyoseries-dice.cc | 2 +-
src/2dsegcompare.cc | 2 +
src/2dseghausdorff.cc | 1 +
src/2dsegseriesstats.cc | 6 +-
src/2dseries-mincorr.cc | 4 +-
src/2dseries-segdistance.cc | 3 +
src/2dseries2sets.cc | 2 +-
src/2dserieshausdorff.cc | 1 +
src/2dstackfilter.cc | 5 +-
src/3dcost.cc | 2 +-
src/3ddistance-stats.cc | 5 +-
src/3dfield2norm.cc | 6 +-
src/3dgetsize.cc | 2 +-
src/3dgetslice.cc | 21 +-
src/3dimagecombine.cc | 2 +-
src/3dimagefilter.cc | 2 -
src/3dimagefilterstack.cc | 6 +-
src/3dimagestats.cc | 3 +-
src/3dlandmarks-distances.cc | 2 +-
src/3dlerp.cc | 33 +-
src/3dnonrigidreg.cc | 8 +-
src/3drigidreg.cc | 8 +-
src/3dseries-track-intensity.cc | 2 +-
src/3dvfcompare.cc | 6 +-
src/CMakeLists.txt | 20 +-
src/__init__.py | 1 +
src/filenumberpattern.cc | 1 +
src/fluid2d/CMakeLists.txt | 3 +-
src/fluid2d/main.cc | 6 +-
src/fluid3d/CMakeLists.txt | 3 +-
src/fluid3d/main.cc | 8 +-
src/isosurface/CMakeLists.txt | 4 +-
src/meshfilter.cc | 4 -
src/multihist.cc | 2 +-
src/myowavelettest.cc | 3 +-
src/plugin-help.cc | 2 +
src/test_plugins_as_installed.cc | 8 +-
180 files changed, 3563 insertions(+), 1019 deletions(-)
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