[med-svn] [mia] branch upstream updated (d1353bb -> 365a539)
Gert Wollny
gert-guest at moszumanska.debian.org
Wed Jan 14 11:08:17 UTC 2015
This is an automated email from the git hooks/post-receive script.
gert-guest pushed a change to branch upstream
in repository mia.
from d1353bb Imported Upstream version 2.2.2
new 365a539 Imported Upstream version 2.2.3
The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.
Summary of changes:
CMakeLists.txt | 14 +-
ChangeLog | 9 +
.../filter/vtxsort.hh => addons/jpg/jpeg-common.hh | 58 ++--
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/filter/{shaped_mean.hh => labelscale.hh} | 24 +-
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/{image.hh => label.hh} | 53 ++-
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 ++++++++++
mia/3d/filter/{tee.hh => labelscale.hh} | 23 +-
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/{image.hh => label.hh} | 59 +++-
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 +-
.../selftestcmdoption.cc} | 21 +-
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 ++-
...rigidreg-alt.cc => 2dmultiimageregistration.cc} | 36 +-
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, 3354 insertions(+), 1041 deletions(-)
copy mia/mesh/filter/vtxsort.hh => addons/jpg/jpeg-common.hh (53%)
create mode 100644 doc/MiaDoctools.cmake
create mode 100644 doc/__init__.py
delete mode 100644 doc/extract_docu.py
create mode 100644 doc/mia-xmldoc2man.cmake
create mode 100644 doc/mia-xmldoc2nipype.cmake
delete mode 100644 doc/miaxml2html.py
create mode 100644 doc/miaxml2nipype.py
create mode 100644 mia/2d/filter/labelscale.cc
copy mia/2d/filter/{shaped_mean.hh => labelscale.hh} (72%)
create mode 100644 mia/2d/filter/test_labelscale.cc
create mode 100644 mia/2d/fullcost/label.cc
copy mia/2d/fullcost/{image.hh => label.hh} (52%)
create mode 100644 mia/2d/fullcost/test_label.cc
create mode 100644 mia/3d/filter/labelscale.cc
copy mia/3d/filter/{tee.hh => labelscale.hh} (72%)
create mode 100644 mia/3d/filter/test_labelscale.cc
create mode 100644 mia/3d/fullcost/label.cc
copy mia/3d/fullcost/{image.hh => label.hh} (50%)
create mode 100644 mia/3d/fullcost/test_label.cc
copy mia/{3d/similarity_profile.cc => core/selftestcmdoption.cc} (72%)
create mode 100644 mia/core/selftestcmdoption.hh
copy src/{3dnonrigidreg-alt.cc => 2dmultiimageregistration.cc} (71%)
create mode 100644 src/__init__.py
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