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commit 9f671b70116701e36ec7804c2c3ac8b3581e806e Merge: d69f6c9 365a539 Author: Gert Wollny <gw.foss...@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(-) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/mia.git _______________________________________________ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit