[med-svn] [mia] branch upstream updated (1bb7eb8 -> 277c0d9)
Gert Wollny
gewo at moszumanska.debian.org
Wed Mar 22 02:40:19 UTC 2017
This is an automated email from the git hooks/post-receive script.
gewo pushed a change to branch upstream
in repository mia.
from 1bb7eb8 Imported Upstream version 2.4.3
new 277c0d9 New upstream version 2.4.4
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:
.travis.yml | 9 +-
CMakeLists.txt | 124 ++-
ChangeLog | 24 +
addons/CMakeLists.txt | 1 +
addons/dicom/CMakeLists.txt | 1 -
addons/dicom/dcm2d.cc | 2 +-
addons/dicom/dcm2d.hh | 2 +-
addons/dicom/dcm3d.cc | 2 +-
addons/dicom/dcm3d.hh | 2 +-
addons/dicom/dicom4mia.cc | 2 +-
addons/dicom/dicom4mia.hh | 2 +-
addons/dicom/getset.hh | 2 +-
addons/dicom/test_dcm2d.cc | 2 +-
addons/dicom/test_dcm3d.cc | 2 +-
addons/dicom/test_dicom4mia.cc | 2 +-
addons/hdf5/hdf5_3dimage.cc | 6 +-
addons/hdf5/hdf5_3dimage.hh | 2 +-
addons/hdf5/hdf5a_mia.cc | 22 +-
addons/hdf5/hdf5a_mia.hh | 2 +-
addons/hdf5/hdf5mia.cc | 12 +-
addons/hdf5/hdf5mia.hh | 26 +-
addons/hdf5/test_hdf5_3dimage.cc | 36 +-
addons/hdf5/test_hdf5mia.cc | 66 +-
addons/itpp/CMakeLists.txt | 52 +
{mia/core => addons/itpp}/ica.cc | 117 +--
{mia/core => addons/itpp}/ica.hh | 69 +-
{mia/core => addons/itpp}/test_ica.cc | 77 +-
addons/jpg/jpeg-common.hh | 2 +-
addons/jpg/jpg-gray.cc | 3 +-
addons/jpg/jpg-rgb.cc | 3 +-
addons/jpg/test_jpg.cc | 2 +-
addons/maxflow/2dmaxflow.cc | 2 +-
addons/maxflow/2dmaxflow.hh | 2 +-
addons/maxflow/test_2dmaxflow.cc | 2 +-
addons/nifti/CMakeLists.txt | 14 +-
addons/nifti/niftiimage.cc | 19 +-
addons/nifti/niftiimage.hh | 2 +-
addons/nifti/test_niftiimage.cc | 106 +-
addons/nlopt/nlopt.cc | 2 +-
addons/nlopt/nlopt.hh | 2 +-
addons/nlopt/test_nlopt.cc | 2 +-
addons/openexr/2dimgexr.cc | 2 +-
addons/openexr/2dvfexr.cc | 2 +-
addons/openexr/CMakeLists.txt | 8 +-
addons/openexr/test_openexr.cc | 34 +-
addons/png/png-gray.cc | 2 +-
addons/png/png-rgb.cc | 2 +-
addons/png/test_png.cc | 2 +-
addons/tiff/test_tiff.cc | 2 +-
addons/tiff/tiff.cc | 2 +-
addons/vistaio/2dtrans.cc | 2 +-
addons/vistaio/2dtrans.hh | 2 +-
addons/vistaio/2dvfvistaio.cc | 2 +-
addons/vistaio/2dvistaio.cc | 2 +-
addons/vistaio/2dvistaio.hh | 2 +-
addons/vistaio/3dtrans.cc | 2 +-
addons/vistaio/3dtrans.hh | 2 +-
addons/vistaio/3dvfvistaio.cc | 2 +-
addons/vistaio/3dvistaio.cc | 2 +-
addons/vistaio/3dvistaio.hh | 2 +-
addons/vistaio/test_2dtrans.cc | 2 +-
addons/vistaio/test_2dvistaio.cc | 2 +-
addons/vistaio/test_3dtrans.cc | 2 +-
addons/vistaio/test_3dvistaio.cc | 2 +-
addons/vistaio/test_vista4mia.cc | 2 +-
addons/vistaio/test_vistaio.cc | 2 +-
addons/vistaio/vista4mia.cc | 2 +-
addons/vistaio/vista4mia.hh | 16 +-
addons/vistaio/vistamesh.cc | 4 +-
addons/vtk/test_vtkimage.cc | 9 +-
addons/vtk/test_vtkmesh.cc | 2 +-
addons/vtk/test_vtkvf.cc | 2 +-
addons/vtk/vtkimage.cc | 56 +-
addons/vtk/vtkimage.hh | 2 +-
addons/vtk/vtkmesh.cc | 2 +-
addons/vtk/vtkmesh.hh | 2 +-
addons/vtk/vtkvf.cc | 2 +-
addons/vtk/vtkvf.hh | 2 +-
cmake/FindDCMTKnew.cmake | 2 +-
cmake/checkITPPBoolseparate.cmake | 17 +-
cmake/macros.cmake | 68 +-
cmake/pluginmacro.cmake | 56 +-
config.h.cmake | 2 +-
coverage.sh | 6 +-
doc/CMakeLists.txt | 2 +-
doc/MiaDoctools.cmake | 88 +-
doc/miareadxml.py | 135 +--
doc/miawritprogram.py | 10 +-
doc/miaxml2man.py | 105 +-
doc/miaxml2nipype.py | 21 +-
doc/miaxml2sgml.py | 47 +-
doc/reference.dox.cmake | 3 +-
mia/2d.hh | 2 +-
mia/2d/CMakeLists.txt | 51 +-
mia/2d/angle.cc | 2 +-
mia/2d/angle.hh | 2 +-
mia/2d/boundingbox.cc | 2 +-
mia/2d/boundingbox.hh | 2 +-
mia/2d/combiner/ops.cc | 2 +-
mia/2d/combiner/ops.hh | 2 +-
mia/2d/combiner/plugin.hh | 2 +-
mia/2d/combiner/test_ops.cc | 2 +-
mia/2d/correlation_weight.cc | 2 +-
mia/2d/correlation_weight.hh | 2 +-
mia/2d/cost.cc | 2 +-
mia/2d/cost.hh | 2 +-
mia/2d/cost/gncc.cc | 2 +-
mia/2d/cost/gncc.hh | 2 +-
mia/2d/cost/lncc.cc | 26 +-
mia/2d/cost/lncc.hh | 6 +-
mia/2d/cost/lsd.cc | 2 +-
mia/2d/cost/lsd.hh | 2 +-
mia/2d/cost/mi.cc | 2 +-
mia/2d/cost/mi.hh | 2 +-
mia/2d/cost/ncc.cc | 127 +--
mia/2d/cost/ncc.hh | 6 +-
mia/2d/cost/ngf.cc | 2 +-
mia/2d/cost/ngf.hh | 2 +-
mia/2d/cost/ssd-automask.cc | 2 +-
mia/2d/cost/ssd-automask.hh | 2 +-
mia/2d/cost/ssd.cc | 2 +-
mia/2d/cost/ssd.hh | 2 +-
mia/2d/cost/ssd2.cc | 2 +-
mia/2d/cost/ssd2.hh | 2 +-
mia/2d/cost/ssddf.cc | 2 +-
mia/2d/cost/test_divcurl.cc | 2 +-
mia/2d/cost/test_gncc.cc | 2 +-
mia/2d/cost/test_lncc.cc | 2 +-
mia/2d/cost/test_lsd.cc | 2 +-
mia/2d/cost/test_mi.cc | 2 +-
mia/2d/cost/test_ncc.cc | 2 +-
mia/2d/cost/test_ngf.cc | 2 +-
mia/2d/cost/test_ssd-automask.cc | 2 +-
mia/2d/cost/test_ssd.cc | 2 +-
mia/2d/cost/test_ssd2.cc | 2 +-
mia/2d/creator.cc | 2 +-
mia/2d/creator.hh | 2 +-
mia/2d/creator/circle.cc | 2 +-
mia/2d/creator/circle.hh | 2 +-
mia/2d/creator/test_circle.cc | 2 +-
mia/2d/cstkernel.cc | 2 +-
mia/2d/cstkernel.hh | 2 +-
mia/2d/datafield.cc | 48 +-
mia/2d/datafield.cxx | 184 ++--
mia/2d/datafield.hh | 199 +++-
mia/2d/defines2d.hh | 2 +-
mia/2d/deformer.hh | 2 +-
mia/2d/distance.cc | 2 +-
mia/2d/distance.hh | 2 +-
mia/2d/distances.cc | 2 +-
mia/2d/fftkernel.cc | 2 +-
mia/2d/fftkernel.hh | 2 +-
mia/2d/filter.cc | 2 +-
mia/2d/filter.hh | 3 +-
mia/2d/filter/adaptmed.cc | 2 +-
mia/2d/filter/adaptmed.hh | 2 +-
mia/2d/filter/admean.cc | 2 +-
mia/2d/filter/admean.hh | 2 +-
mia/2d/filter/aniso.cc | 2 +-
mia/2d/filter/aniso.hh | 2 +-
mia/2d/filter/bandpass.cc | 2 +-
mia/2d/filter/bandpass.hh | 2 +-
mia/2d/filter/binarize.cc | 2 +-
mia/2d/filter/binarize.hh | 2 +-
mia/2d/filter/classmap.cc | 2 +-
mia/2d/filter/combiner.cc | 2 +-
mia/2d/filter/combiner.hh | 2 +-
mia/2d/filter/convert.cc | 2 +-
mia/2d/filter/convert.hh | 2 +-
mia/2d/filter/crop.cc | 2 +-
mia/2d/filter/crop.hh | 2 +-
mia/2d/filter/cst.cc | 2 +-
mia/2d/filter/cst.hh | 2 +-
mia/2d/filter/distance.cc | 2 +-
mia/2d/filter/distance.hh | 2 +-
mia/2d/filter/downscale.cc | 2 +-
mia/2d/filter/downscale.hh | 2 +-
mia/2d/filter/fft.cc | 2 +-
mia/2d/filter/fft.hh | 2 +-
mia/2d/filter/frequency.cc | 2 +-
mia/2d/filter/gradnorm.cc | 2 +-
mia/2d/filter/gradnorm.hh | 2 +-
mia/2d/filter/harmmean.cc | 2 +-
mia/2d/filter/ianiso.cc | 2 +-
mia/2d/filter/invert.cc | 2 +-
mia/2d/filter/invert.hh | 2 +-
mia/2d/filter/kmeans.cc | 2 +-
mia/2d/filter/kmeans.hh | 2 +-
mia/2d/filter/kuwahara.cc | 2 +-
mia/2d/filter/label.cc | 2 +-
mia/2d/filter/label.hh | 2 +-
mia/2d/filter/labelmap.cc | 2 +-
mia/2d/filter/labelmap.hh | 2 +-
mia/2d/filter/labelscale.cc | 2 +-
mia/2d/filter/labelscale.hh | 2 +-
mia/2d/filter/lnfft.cc | 2 +-
mia/2d/filter/load.cc | 2 +-
mia/2d/filter/load.hh | 2 +-
mia/2d/filter/mask.cc | 2 +-
mia/2d/filter/mask.hh | 2 +-
mia/2d/filter/mean.cc | 2 +-
mia/2d/filter/mean.hh | 2 +-
mia/2d/filter/meanvar.cc | 2 +-
mia/2d/filter/meanvar.hh | 2 +-
mia/2d/filter/median.cc | 2 +-
mia/2d/filter/median.hh | 2 +-
mia/2d/filter/medianmad.cc | 2 +-
mia/2d/filter/medianmad.hh | 2 +-
mia/2d/filter/midpoint.cc | 2 +-
mia/2d/filter/mlv.cc | 2 +-
mia/2d/filter/mlv.hh | 2 +-
mia/2d/filter/morphological.cc | 2 +-
mia/2d/filter/morphological.hh | 2 +-
mia/2d/filter/ngfnorm.cc | 2 +-
mia/2d/filter/ngfnorm.hh | 2 +-
mia/2d/filter/noise.cc | 2 +-
mia/2d/filter/noise.hh | 2 +-
mia/2d/filter/regiongrow.cc | 2 +-
mia/2d/filter/regiongrow.hh | 2 +-
mia/2d/filter/rgg.cc | 2 +-
mia/2d/filter/scale.cc | 2 +-
mia/2d/filter/scale.hh | 2 +-
mia/2d/filter/seededwatershed.cc | 2 +-
mia/2d/filter/seededwatershed.hh | 2 +-
mia/2d/filter/selectbig.cc | 2 +-
mia/2d/filter/selectbig.hh | 2 +-
mia/2d/filter/sepconv.cc | 2 +-
mia/2d/filter/sepconv.hh | 2 +-
mia/2d/filter/shaped_mean.cc | 2 +-
mia/2d/filter/shaped_mean.hh | 2 +-
mia/2d/filter/sortlabel.cc | 2 +-
mia/2d/filter/sortlabel.hh | 2 +-
mia/2d/filter/tee.cc | 2 +-
mia/2d/filter/tee.hh | 2 +-
mia/2d/filter/test_adaptmed.cc | 2 +-
mia/2d/filter/test_admean.cc | 2 +-
mia/2d/filter/test_aniso.cc | 2 +-
mia/2d/filter/test_bandpass.cc | 2 +-
mia/2d/filter/test_binarize.cc | 2 +-
mia/2d/filter/test_combiner.cc | 4 +-
mia/2d/filter/test_convert.cc | 2 +-
mia/2d/filter/test_crop.cc | 2 +-
mia/2d/filter/test_cst.cc | 2 +-
mia/2d/filter/test_distance.cc | 2 +-
mia/2d/filter/test_downscale.cc | 2 +-
mia/2d/filter/test_fft.cc | 2 +-
mia/2d/filter/test_gradnorm.cc | 2 +-
mia/2d/filter/test_invert.cc | 2 +-
mia/2d/filter/test_kmeans.cc | 2 +-
mia/2d/filter/test_label.cc | 2 +-
mia/2d/filter/test_labelmap.cc | 2 +-
mia/2d/filter/test_labelscale.cc | 2 +-
mia/2d/filter/test_load.cc | 4 +-
mia/2d/filter/test_mask.cc | 2 +-
mia/2d/filter/test_mean.cc | 2 +-
mia/2d/filter/test_meanvar.cc | 2 +-
mia/2d/filter/test_median.cc | 2 +-
mia/2d/filter/test_medianmad.cc | 2 +-
mia/2d/filter/test_mlv.cc | 2 +-
mia/2d/filter/test_morphological.cc | 2 +-
mia/2d/filter/test_ngfnorm.cc | 2 +-
mia/2d/filter/test_noise.cc | 2 +-
mia/2d/filter/test_regiongrow.cc | 2 +-
mia/2d/filter/test_scale.cc | 2 +-
mia/2d/filter/test_seededwatershed.cc | 2 +-
mia/2d/filter/test_selectbig.cc | 2 +-
mia/2d/filter/test_sepconv.cc | 2 +-
mia/2d/filter/test_shaped_mean.cc | 2 +-
mia/2d/filter/test_sortlabel.cc | 2 +-
mia/2d/filter/test_tee.cc | 4 +-
mia/2d/filter/test_thinning.cc | 2 +-
mia/2d/filter/test_thresh.cc | 2 +-
mia/2d/filter/test_tmean.cc | 2 +-
mia/2d/filter/test_transform.cc | 2 +-
mia/2d/filter/test_watershed.cc | 2 +-
mia/2d/filter/thinning.cc | 2 +-
mia/2d/filter/thinning.hh | 2 +-
mia/2d/filter/thresh.cc | 2 +-
mia/2d/filter/thresh.hh | 2 +-
mia/2d/filter/tmean.cc | 2 +-
mia/2d/filter/tmean.hh | 2 +-
mia/2d/filter/transform.cc | 2 +-
mia/2d/filter/transform.hh | 2 +-
mia/2d/filter/variation.cc | 2 +-
mia/2d/filter/watershed.cc | 2 +-
mia/2d/filter/watershed.hh | 2 +-
mia/2d/filter/wmean.cc | 2 +-
mia/2d/filter/ws.cc | 2 +-
mia/2d/filterchain.hh | 2 +-
mia/2d/filtertest.cc | 2 +-
mia/2d/filtertest.hh | 2 +-
mia/2d/fullcost.cc | 2 +-
mia/2d/fullcost.hh | 2 +-
mia/2d/fullcost/image.cc | 2 +-
mia/2d/fullcost/image.hh | 2 +-
mia/2d/fullcost/label.cc | 2 +-
mia/2d/fullcost/label.hh | 2 +-
mia/2d/fullcost/maskedimage.cc | 2 +-
mia/2d/fullcost/maskedimage.hh | 2 +-
mia/2d/fullcost/test_image.cc | 2 +-
mia/2d/fullcost/test_label.cc | 2 +-
mia/2d/fullcost/test_maskedimage.cc | 2 +-
mia/2d/fuzzyclustersolver_cg.cc | 2 +-
mia/2d/fuzzyclustersolver_cg.hh | 2 +-
mia/2d/fuzzyclustersolver_sor.cc | 2 +-
mia/2d/fuzzyclustersolver_sor.hh | 2 +-
mia/2d/fuzzyseg.cc | 2 +-
mia/2d/fuzzyseg.hh | 2 +-
mia/2d/ground_truth_evaluator.cc | 2 +-
mia/2d/ground_truth_evaluator.hh | 2 +-
mia/2d/groundtruthproblem.cc | 2 +-
mia/2d/groundtruthproblem.hh | 2 +-
mia/2d/ica.cc | 2 +-
mia/2d/ica.hh | 2 +-
mia/2d/image.cc | 70 +-
mia/2d/image.hh | 72 +-
mia/2d/imageio.cc | 2 +-
mia/2d/imageio.hh | 2 +-
mia/2d/imageiotest.cc | 20 +-
mia/2d/imageiotest.hh | 2 +-
mia/2d/imagetest.cc | 2 +-
mia/2d/imagetest.hh | 2 +-
mia/2d/interpolator.cc | 96 +-
mia/2d/interpolator.cxx | 184 ++--
mia/2d/interpolator.hh | 75 +-
mia/2d/io/bmp.cc | 2 +-
mia/2d/io/raw.cc | 2 +-
mia/2d/io/test_xml.cc | 36 +-
mia/2d/io/xml.cc | 43 +-
mia/2d/io/xml.hh | 2 +-
mia/2d/iterator.cxx | 2 +-
mia/2d/iterator.hh | 24 +-
mia/2d/kernel/curv.cc | 2 +-
mia/2d/maskedcost.cc | 2 +-
mia/2d/maskedcost.hh | 2 +-
mia/2d/maskedcost/lncc.cc | 2 +-
mia/2d/maskedcost/lncc.hh | 2 +-
mia/2d/maskedcost/mi.cc | 2 +-
mia/2d/maskedcost/mi.hh | 2 +-
mia/2d/maskedcost/ncc.cc | 2 +-
mia/2d/maskedcost/ncc.hh | 2 +-
mia/2d/maskedcost/ssd.cc | 2 +-
mia/2d/maskedcost/ssd.hh | 2 +-
mia/2d/maskedcost/test_lncc.cc | 2 +-
mia/2d/maskedcost/test_mi.cc | 2 +-
mia/2d/maskedcost/test_ncc.cc | 2 +-
mia/2d/maskedcost/test_ssd.cc | 2 +-
mia/2d/matrix.hh | 2 +-
mia/2d/model.cc | 2 +-
mia/2d/model.hh | 2 +-
mia/2d/model/identity.cc | 2 +-
mia/2d/model/identity.hh | 2 +-
mia/2d/model/navier.cc | 2 +-
mia/2d/model/navier.hh | 2 +-
mia/2d/model/naviera.cc | 2 +-
mia/2d/model/naviera.hh | 2 +-
mia/2d/model/test_identity.cc | 2 +-
mia/2d/model/test_navier.cc | 2 +-
mia/2d/model/test_naviera.cc | 2 +-
mia/2d/modelsolverreg.cc | 2 +-
mia/2d/modelsolverreg.hh | 2 +-
mia/2d/morphshape.cc | 2 +-
mia/2d/morphshape.hh | 2 +-
mia/2d/multicost.cc | 2 +-
mia/2d/multicost.hh | 2 +-
mia/2d/nfg.cc | 2 +-
mia/2d/nfg.hh | 2 +-
mia/2d/nonrigidregister.cc | 2 +-
mia/2d/nonrigidregister.hh | 2 +-
mia/2d/perfusion.cc | 37 +-
mia/2d/perfusion.hh | 8 +-
mia/2d/polygon.cc | 2 +-
mia/2d/polygon.hh | 2 +-
mia/2d/ppmatrix.cc | 2 +-
mia/2d/ppmatrix.hh | 2 +-
mia/2d/register.cc | 2 +-
mia/2d/register.hh | 2 +-
mia/2d/rgbimageio.cc | 2 +-
mia/2d/rgbimageio.hh | 2 +-
mia/2d/rgbio/bmp.cc | 2 +-
mia/2d/rigidregister.cc | 2 +-
mia/2d/rigidregister.hh | 2 +-
mia/2d/segframe.cc | 61 +-
mia/2d/segframe.hh | 6 +-
mia/2d/segpoint.cc | 41 +-
mia/2d/segpoint.hh | 21 +-
mia/2d/segsection.cc | 66 +-
mia/2d/segsection.hh | 6 +-
mia/2d/segset.cc | 121 ++-
mia/2d/segset.hh | 15 +-
mia/2d/segsetwithimages.cc | 4 +-
mia/2d/segsetwithimages.hh | 10 +-
mia/2d/segstar.cc | 44 +-
mia/2d/segstar.hh | 6 +-
mia/2d/shape.cc | 2 +-
mia/2d/shape.hh | 4 +-
mia/2d/shapes/basic_shapes.cc | 2 +-
mia/2d/shapes/basic_shapes.hh | 2 +-
mia/2d/shapes/rect.cc | 2 +-
mia/2d/shapes/rect.hh | 2 +-
mia/2d/shapes/sphere.cc | 2 +-
mia/2d/shapes/sphere.hh | 2 +-
mia/2d/shapes/test_basic_shapes.cc | 2 +-
mia/2d/shapes/test_rect.cc | 2 +-
mia/2d/shapes/test_sphere.cc | 2 +-
mia/2d/similarity_profile.cc | 2 +-
mia/2d/similarity_profile.hh | 2 +-
mia/2d/sparse_image_solver.cc | 2 +-
mia/2d/sparse_image_solver.hh | 2 +-
mia/2d/splinepenalty/divcurl.cc | 2 +-
mia/2d/splinepenalty/divcurl.hh | 2 +-
mia/2d/splinepenalty/test_divcurl.cc | 10 +-
mia/2d/splinetransformpenalty.cc | 2 +-
mia/2d/splinetransformpenalty.hh | 2 +-
mia/2d/test_2d.cc | 2 +-
mia/2d/test_angle.cc | 2 +-
mia/2d/test_boundingbox.cc | 2 +-
mia/2d/test_combiner.cc | 2 +-
mia/2d/test_correlation_weight.cc | 2 +-
mia/2d/test_cost.cc | 2 +-
mia/2d/test_datafield.cc | 5 +-
mia/2d/test_distance.cc | 2 +-
mia/2d/test_divcurlmatrix.cc | 2 +-
mia/2d/test_filter.cc | 2 +-
mia/2d/test_filter_cast.cc | 29 +-
mia/2d/test_fullcost.cc | 2 +-
mia/2d/test_fullcost_mi_spline.cc | 2 +-
mia/2d/test_groundtruthproblem.cc | 2 +-
mia/2d/test_ica.cc | 33 +-
mia/2d/test_image.cc | 67 +-
mia/2d/test_imagecostbase.cc | 2 +-
mia/2d/test_imageio.cc | 2 +-
mia/2d/test_interpol.cc | 22 +-
mia/2d/test_iterator.cc | 7 +-
mia/2d/test_matrix.cc | 2 +-
mia/2d/test_modelsolverreg.cc | 2 +-
mia/2d/test_morphshape.cc | 2 +-
mia/2d/test_nfg.cc | 2 +-
mia/2d/test_nonrigidregister.cc | 2 +-
mia/2d/test_oldnewintegrate.cc | 2 +-
mia/2d/test_param.cc | 2 +-
mia/2d/test_perfusion.cc | 57 +-
mia/2d/test_polygon.cc | 2 +-
mia/2d/test_ppmatrix.cc | 42 +-
mia/2d/test_register.cc | 2 +-
mia/2d/test_regplugins.cc | 2 +-
mia/2d/test_rigidregister.cc | 2 +-
mia/2d/test_segframe.cc | 154 ++-
mia/2d/test_segmentation.cc | 384 ++++----
mia/2d/test_segpoint.cc | 2 +-
mia/2d/test_shape.cc | 2 +-
mia/2d/test_similarity_profile.cc | 2 +-
mia/2d/test_sparse_image_solver.cc | 2 +-
mia/2d/test_splinetransformpenalty.cc | 2 +-
mia/2d/test_trackpoint.cc | 2 +-
mia/2d/test_transform.cc | 2 +-
mia/2d/test_transformfactory.cc | 2 +-
mia/2d/test_transio.cc | 2 +-
mia/2d/test_vector.cc | 2 +-
...orfield_interpolator.cc => test_vectorfield.cc} | 71 +-
mia/2d/test_vectorfield_interpolator.cc | 17 +-
mia/2d/test_vfio.cc | 2 +-
mia/2d/timestep.cc | 2 +-
mia/2d/timestep.hh | 2 +-
mia/2d/timestep/direct.cc | 2 +-
mia/2d/timestep/direct.hh | 2 +-
mia/2d/timestep/fluid.cc | 2 +-
mia/2d/timestep/fluid.hh | 2 +-
mia/2d/timestep/test_direct.cc | 2 +-
mia/2d/timestep/test_fluid.cc | 2 +-
mia/2d/trackpoint.cc | 2 +-
mia/2d/trackpoint.hh | 2 +-
mia/2d/trait.hh | 2 +-
mia/2d/transform.cc | 2 +-
mia/2d/transform.hh | 10 +-
mia/2d/transform/affine.cc | 24 +-
mia/2d/transform/affine.hh | 6 +-
mia/2d/transform/rigid.cc | 16 +-
mia/2d/transform/rigid.hh | 4 +-
mia/2d/transform/rotation.cc | 16 +-
mia/2d/transform/rotation.hh | 4 +-
mia/2d/transform/spline.cc | 8 +-
mia/2d/transform/spline.hh | 4 +-
mia/2d/transform/test_affine.cc | 2 +-
mia/2d/transform/test_nonlinear.cc | 2 +-
mia/2d/transform/test_rigid.cc | 2 +-
mia/2d/transform/test_rotation.cc | 2 +-
mia/2d/transform/test_spline.cc | 8 +-
mia/2d/transform/test_translate.cc | 2 +-
mia/2d/transform/test_vectorfield.cc | 10 +-
mia/2d/transform/translate.cc | 6 +-
mia/2d/transform/translate.hh | 4 +-
mia/2d/transform/vectorfield.cc | 6 +-
mia/2d/transform/vectorfield.hh | 6 +-
mia/2d/transformfactory.cc | 2 +-
mia/2d/transformfactory.hh | 2 +-
mia/2d/transformio.cc | 2 +-
mia/2d/transformio.hh | 2 +-
mia/2d/transformmock.cc | 6 +-
mia/2d/transformmock.hh | 4 +-
mia/2d/transio/bbs.cc | 2 +-
mia/2d/transio/pbs.cc | 2 +-
mia/2d/transio/serialization.hh | 2 +-
mia/2d/transio/xml.cc | 2 +-
mia/2d/vector.hh | 2 +-
mia/2d/vectorfield.cc | 102 +-
mia/2d/vectorfield.hh | 52 +-
mia/2d/vfio.cc | 2 +-
mia/2d/vfio.hh | 2 +-
mia/2d/vfiotest.cc | 2 +-
mia/2d/vfregularizer.cc | 72 ++
mia/2d/vfregularizer.hh | 107 ++
mia/2d/vfregularizer/CMakeLists.txt | 8 +
mia/2d/vfregularizer/fluid.cc | 196 ++++
.../vfregularizer/fluid.hh} | 34 +-
mia/2d/vfregularizer/sor.cc | 147 +++
mia/2d/vfregularizer/sor.hh | 67 ++
mia/2d/vfregularizer/test_sor.cc | 187 ++++
mia/2d/vfregularizerkernel.cc | 145 +++
mia/2d/vfregularizerkernel.hh | 176 ++++
mia/2d/vfregularizerkernel/CMakeLists.txt | 9 +
mia/2d/vfregularizerkernel/fluid-generic.cc | 244 +++++
mia/2d/vfregularizerkernel/fluid-generic.hh | 74 ++
mia/2d/vfregularizerkernel/test_fluid-generic.cc | 202 ++++
mia/3d.hh | 2 +-
mia/3d/.gitignore | 3 -
mia/3d/2dimagefifofilter.cc | 2 +-
mia/3d/2dimagefifofilter.hh | 2 +-
mia/3d/CMakeLists.txt | 34 +-
mia/3d/affine_matrix.cc | 2 +-
mia/3d/affine_matrix.hh | 2 +-
mia/3d/camera.cc | 2 +-
mia/3d/camera.hh | 2 +-
mia/3d/combiner/labelxmap.cc | 2 +-
mia/3d/combiner/labelxmap.hh | 2 +-
mia/3d/combiner/ops.cc | 2 +-
mia/3d/combiner/ops.hh | 2 +-
mia/3d/combiner/plugin.hh | 2 +-
mia/3d/combiner/test_labelxmap.cc | 2 +-
mia/3d/combiner/test_ops.cc | 2 +-
mia/3d/cost.cc | 11 +-
mia/3d/cost.hh | 5 +-
mia/3d/cost/lncc.cc | 26 +-
mia/3d/cost/lncc.hh | 6 +-
mia/3d/cost/mi.cc | 2 +-
mia/3d/cost/mi.hh | 2 +-
mia/3d/cost/ncc.cc | 60 +-
mia/3d/cost/ncc.hh | 6 +-
mia/3d/cost/ngf.cc | 2 +-
mia/3d/cost/ngf.hh | 2 +-
mia/3d/cost/ssd-automask.cc | 2 +-
mia/3d/cost/ssd-automask.hh | 2 +-
mia/3d/cost/ssd.cc | 2 +-
mia/3d/cost/ssd.hh | 2 +-
mia/3d/cost/test_lncc.cc | 2 +-
mia/3d/cost/test_mi.cc | 2 +-
mia/3d/cost/test_ncc.cc | 2 +-
mia/3d/cost/test_ngf.cc | 2 +-
mia/3d/cost/test_ssd-automask.cc | 2 +-
mia/3d/cost/test_ssd.cc | 2 +-
mia/3d/cost/test_ssdautomask.cc | 2 +-
mia/3d/creator.cc | 2 +-
mia/3d/creator.hh | 2 +-
mia/3d/creator/lattic.cc | 2 +-
mia/3d/creator/lattic.hh | 2 +-
mia/3d/creator/sphere.cc | 2 +-
mia/3d/creator/sphere.hh | 2 +-
mia/3d/creator/test_lattic.cc | 2 +-
mia/3d/creator/test_sphere.cc | 2 +-
mia/3d/critical_point.cc | 2 +-
mia/3d/critical_point.hh | 2 +-
mia/3d/datafield.cc | 48 +-
mia/3d/datafield.cxx | 137 +--
mia/3d/datafield.hh | 134 ++-
mia/3d/defines3d.hh | 2 +-
mia/3d/deformer.hh | 2 +-
mia/3d/distance.cc | 2 +-
mia/3d/distance.hh | 2 +-
mia/3d/fifof/byslice.cc | 2 +-
mia/3d/fifof/byslice.hh | 2 +-
mia/3d/fifof/gauss.cc | 2 +-
mia/3d/fifof/gauss.hh | 2 +-
mia/3d/fifof/label.cc | 2 +-
mia/3d/fifof/label.hh | 2 +-
mia/3d/fifof/median.cc | 2 +-
mia/3d/fifof/median.hh | 2 +-
mia/3d/fifof/mlv.cc | 2 +-
mia/3d/fifof/mlv.hh | 2 +-
mia/3d/fifof/morphological.cc | 2 +-
mia/3d/fifof/morphological.hh | 2 +-
mia/3d/fifof/regiongrow.cc | 2 +-
mia/3d/fifof/regiongrow.hh | 2 +-
mia/3d/fifof/rgg.cc | 2 +-
mia/3d/fifof/rgg2pass.cc | 2 +-
mia/3d/fifof/test_byslice.cc | 2 +-
mia/3d/fifof/test_gauss.cc | 2 +-
mia/3d/fifof/test_label.cc | 2 +-
mia/3d/fifof/test_median.cc | 2 +-
mia/3d/fifof/test_mlv.cc | 2 +-
mia/3d/fifof/test_morphological.cc | 2 +-
mia/3d/fifof/test_regiongrow.cc | 2 +-
mia/3d/fifotestfixture.cc | 2 +-
mia/3d/fifotestfixture.hh | 2 +-
mia/3d/filter.cc | 2 +-
mia/3d/filter.hh | 2 +-
mia/3d/filter/aniso.cc | 2 +-
mia/3d/filter/bandpass.cc | 2 +-
mia/3d/filter/bandpass.hh | 2 +-
mia/3d/filter/binarize.cc | 2 +-
mia/3d/filter/binarize.hh | 2 +-
mia/3d/filter/combiner.cc | 2 +-
mia/3d/filter/combiner.hh | 2 +-
mia/3d/filter/convert.cc | 2 +-
mia/3d/filter/convert.hh | 2 +-
mia/3d/filter/crop.cc | 2 +-
mia/3d/filter/crop.hh | 2 +-
mia/3d/filter/distance.cc | 2 +-
mia/3d/filter/distance.hh | 2 +-
mia/3d/filter/downscale.cc | 2 +-
mia/3d/filter/downscale.hh | 2 +-
mia/3d/filter/gradnorm.cc | 2 +-
mia/3d/filter/gradnorm.hh | 2 +-
mia/3d/filter/growmask.cc | 2 +-
mia/3d/filter/growmask.hh | 2 +-
mia/3d/filter/invert.cc | 2 +-
mia/3d/filter/invert.hh | 2 +-
mia/3d/filter/kmeans.cc | 2 +-
mia/3d/filter/kmeans.hh | 2 +-
mia/3d/filter/label.cc | 2 +-
mia/3d/filter/label.hh | 2 +-
mia/3d/filter/labelmap.cc | 2 +-
mia/3d/filter/labelmap.hh | 2 +-
mia/3d/filter/labelscale.cc | 2 +-
mia/3d/filter/labelscale.hh | 2 +-
mia/3d/filter/load.cc | 2 +-
mia/3d/filter/load.hh | 2 +-
mia/3d/filter/lvdownscale.cc | 2 +-
mia/3d/filter/lvdownscale.hh | 2 +-
mia/3d/filter/mask.cc | 2 +-
mia/3d/filter/mask.hh | 2 +-
mia/3d/filter/mean.cc | 2 +-
mia/3d/filter/mean.hh | 2 +-
mia/3d/filter/median.cc | 2 +-
mia/3d/filter/median.hh | 2 +-
mia/3d/filter/mlv.cc | 2 +-
mia/3d/filter/mlv.hh | 2 +-
mia/3d/filter/morphological.cc | 2 +-
mia/3d/filter/morphological.hh | 2 +-
mia/3d/filter/msnormalizer.cc | 2 +-
mia/3d/filter/msnormalizer.hh | 2 +-
mia/3d/filter/reorient.cc | 2 +-
mia/3d/filter/reorient.hh | 2 +-
mia/3d/filter/resize.cc | 2 +-
mia/3d/filter/resize.hh | 2 +-
mia/3d/filter/scale.cc | 2 +-
mia/3d/filter/scale.hh | 2 +-
mia/3d/filter/seededwatershed.cc | 2 +-
mia/3d/filter/seededwatershed.hh | 2 +-
mia/3d/filter/selectbig.cc | 2 +-
mia/3d/filter/selectbig.hh | 2 +-
mia/3d/filter/sepconv.cc | 74 +-
mia/3d/filter/sepconv.hh | 24 +-
mia/3d/filter/tee.cc | 2 +-
mia/3d/filter/tee.hh | 2 +-
mia/3d/filter/test_bandpass.cc | 2 +-
mia/3d/filter/test_binarize.cc | 2 +-
mia/3d/filter/test_combiner.cc | 4 +-
mia/3d/filter/test_convert.cc | 2 +-
mia/3d/filter/test_crop.cc | 2 +-
mia/3d/filter/test_distance.cc | 2 +-
mia/3d/filter/test_downscale.cc | 7 +-
mia/3d/filter/test_gradnorm.cc | 2 +-
mia/3d/filter/test_growmask.cc | 2 +-
mia/3d/filter/test_invert.cc | 2 +-
mia/3d/filter/test_kmeans.cc | 2 +-
mia/3d/filter/test_label.cc | 2 +-
mia/3d/filter/test_labelmap.cc | 2 +-
mia/3d/filter/test_labelscale.cc | 2 +-
mia/3d/filter/test_load.cc | 4 +-
mia/3d/filter/test_lvdownscale.cc | 2 +-
mia/3d/filter/test_mask.cc | 2 +-
mia/3d/filter/test_mean.cc | 2 +-
mia/3d/filter/test_median.cc | 2 +-
mia/3d/filter/test_mlv.cc | 2 +-
mia/3d/filter/test_morphological.cc | 2 +-
mia/3d/filter/test_msnormalizer.cc | 2 +-
mia/3d/filter/test_reorient.cc | 2 +-
mia/3d/filter/test_resize.cc | 2 +-
mia/3d/filter/test_scale.cc | 2 +-
mia/3d/filter/test_seededwatershed.cc | 2 +-
mia/3d/filter/test_selectbig.cc | 2 +-
mia/3d/filter/test_sepconv.cc | 155 ++-
mia/3d/filter/test_tee.cc | 4 +-
mia/3d/filter/test_thinning.cc | 2 +-
mia/3d/filter/test_transform.cc | 2 +-
mia/3d/filter/test_watershed.cc | 2 +-
mia/3d/filter/thinning.cc | 2 +-
mia/3d/filter/thinning.hh | 2 +-
mia/3d/filter/transform.cc | 2 +-
mia/3d/filter/transform.hh | 2 +-
mia/3d/filter/watershed.cc | 2 +-
mia/3d/filter/watershed.hh | 2 +-
mia/3d/fullcost.cc | 2 +-
mia/3d/fullcost.hh | 2 +-
mia/3d/fullcost/image.cc | 2 +-
mia/3d/fullcost/image.hh | 2 +-
mia/3d/fullcost/label.cc | 2 +-
mia/3d/fullcost/label.hh | 2 +-
mia/3d/fullcost/maskedimage.cc | 2 +-
mia/3d/fullcost/maskedimage.hh | 2 +-
mia/3d/fullcost/taggedssd.cc | 2 +-
mia/3d/fullcost/taggedssd.hh | 2 +-
mia/3d/fullcost/test_image.cc | 2 +-
mia/3d/fullcost/test_label.cc | 2 +-
mia/3d/fullcost/test_maskedimage.cc | 2 +-
mia/3d/fullcost/test_taggedssd.cc | 2 +-
mia/3d/fuzzyclustersolver_cg.cc | 2 +-
mia/3d/fuzzyclustersolver_cg.hh | 2 +-
mia/3d/fuzzyseg.cc | 2 +-
mia/3d/fuzzyseg.hh | 2 +-
mia/3d/ica.cc | 2 +-
mia/3d/ica.hh | 2 +-
mia/3d/image.cc | 62 +-
mia/3d/image.hh | 50 +-
mia/3d/imagecollect.cc | 2 +-
mia/3d/imagecollect.hh | 2 +-
mia/3d/imagedraw.cc | 2 +-
mia/3d/imagedraw.cxx | 2 +-
mia/3d/imagedraw.hh | 2 +-
mia/3d/imageio.cc | 2 +-
mia/3d/imageio.hh | 2 +-
mia/3d/imageiotest.cc | 2 +-
mia/3d/imageiotest.hh | 2 +-
mia/3d/imagetest.cc | 2 +-
mia/3d/imagetest.hh | 2 +-
mia/3d/interpolator.cc | 21 +-
mia/3d/interpolator.cxx | 2 +-
mia/3d/interpolator.hh | 2 +-
mia/3d/io/analyze.cc | 2 +-
mia/3d/io/analyze.hh | 2 +-
mia/3d/io/inria.cc | 2 +-
mia/3d/io/vff.cc | 2 +-
mia/3d/iterator.cxx | 2 +-
mia/3d/iterator.hh | 12 +-
mia/3d/landmark.cc | 2 +-
mia/3d/landmark.hh | 2 +-
mia/3d/landmarklist.cc | 2 +-
mia/3d/landmarklist.hh | 2 +-
mia/3d/landmarklistio.cc | 2 +-
mia/3d/landmarklistio.hh | 2 +-
mia/3d/linear_transform.cc | 2 +-
mia/3d/linear_transform.hh | 2 +-
mia/3d/lmio/lmx.cc | 251 ++---
mia/3d/maskedcost.cc | 2 +-
mia/3d/maskedcost.hh | 2 +-
mia/3d/maskedcost/lncc.cc | 2 +-
mia/3d/maskedcost/lncc.hh | 2 +-
mia/3d/maskedcost/mi.cc | 2 +-
mia/3d/maskedcost/mi.hh | 2 +-
mia/3d/maskedcost/ncc.cc | 2 +-
mia/3d/maskedcost/ncc.hh | 2 +-
mia/3d/maskedcost/ssd.cc | 2 +-
mia/3d/maskedcost/ssd.hh | 2 +-
mia/3d/maskedcost/test_lncc.cc | 2 +-
mia/3d/maskedcost/test_mi.cc | 2 +-
mia/3d/maskedcost/test_ncc.cc | 2 +-
mia/3d/maskedcost/test_ssd.cc | 2 +-
mia/3d/matrix.cc | 2 +-
mia/3d/matrix.hh | 2 +-
mia/3d/model.cc | 2 +-
mia/3d/model.hh | 2 +-
mia/3d/multicost.cc | 2 +-
mia/3d/multicost.hh | 2 +-
mia/3d/multireg.cc | 2 +-
mia/3d/multireg.hh | 2 +-
mia/3d/nfg.cc | 2 +-
mia/3d/nfg.hh | 2 +-
mia/3d/nonrigidregister.cc | 2 +-
mia/3d/nonrigidregister.hh | 2 +-
mia/3d/orientation.cc | 16 +-
mia/3d/orientation.hh | 2 +-
mia/3d/ppmatrix.cc | 12 +-
mia/3d/ppmatrix.hh | 2 +-
mia/3d/quaternion.cc | 2 +-
mia/3d/quaternion.hh | 2 +-
mia/3d/reg3d/direct.cc | 2 +-
mia/3d/reg3d/fluid.cc | 2 +-
mia/3d/reg3d/navier.cc | 2 +-
mia/3d/reg3d/naviera.cc | 2 +-
mia/3d/reg3d/navierasse.cc | 2 +-
mia/3d/reg3d/navierpsse.cc | 2 +-
mia/3d/register.cc | 2 +-
mia/3d/register.hh | 2 +-
mia/3d/rigidregister.cc | 2 +-
mia/3d/rigidregister.hh | 2 +-
mia/3d/rot.cc | 2 +-
mia/3d/rot.hh | 2 +-
mia/3d/shape.cc | 2 +-
mia/3d/shape.hh | 2 +-
mia/3d/shapes/CMakeLists.txt | 39 +-
mia/3d/shapes/basic_shapes.cc | 2 +-
mia/3d/shapes/basic_shapes.hh | 2 +-
mia/3d/shapes/sphere.cc | 2 +-
mia/3d/shapes/sphere.hh | 2 +-
mia/3d/shapes/test_shapes.cc | 2 +-
mia/3d/similarity_profile.cc | 2 +-
mia/3d/similarity_profile.hh | 2 +-
mia/3d/splinepenalty/divcurl.cc | 2 +-
mia/3d/splinepenalty/divcurl.hh | 2 +-
mia/3d/splinepenalty/test_divcurl.cc | 2 +-
mia/3d/splinetransformpenalty.cc | 2 +-
mia/3d/splinetransformpenalty.hh | 2 +-
mia/3d/stackdisttrans.cc | 2 +-
mia/3d/stackdisttrans.hh | 2 +-
mia/3d/test_2dimagefifofilter.cc | 2 +-
mia/3d/test_3d.cc | 2 +-
mia/3d/test_affine_matrix.cc | 2 +-
mia/3d/test_combiner.cc | 2 +-
mia/3d/test_cost.cc | 2 +-
mia/3d/test_critical_points.cc | 2 +-
mia/3d/test_datafield.cc | 9 +-
mia/3d/test_deform.cc | 2 +-
mia/3d/test_distance.cc | 2 +-
mia/3d/test_fullcost.cc | 2 +-
mia/3d/test_ica.cc | 35 +-
mia/3d/test_image.cc | 31 +-
mia/3d/test_imagecollect.cc | 2 +-
mia/3d/test_imagedraw.cc | 2 +-
mia/3d/test_imageio.cc | 2 +-
mia/3d/test_interpol.cc | 26 +-
mia/3d/test_iterator.cc | 2 +-
mia/3d/test_landmark.cc | 2 +-
mia/3d/test_landmarklistio.cc | 2 +-
mia/3d/test_matrix.cc | 2 +-
mia/3d/test_nfg.cc | 2 +-
mia/3d/test_nonrigidregister.cc | 2 +-
mia/3d/test_orientation.cc | 2 +-
mia/3d/test_ppmatrix.cc | 2 +-
mia/3d/test_quaternion.cc | 2 +-
mia/3d/test_regplugins.cc | 2 +-
mia/3d/test_rigidregister.cc | 2 +-
mia/3d/test_rot.cc | 2 +-
mia/3d/test_shape.cc | 2 +-
mia/3d/test_similarity_profile.cc | 2 +-
mia/3d/test_splinetransformpenalty.cc | 2 +-
mia/3d/test_stackdisttrans.cc | 2 +-
mia/3d/test_trackpoint.cc | 2 +-
mia/3d/test_transform.cc | 2 +-
mia/3d/test_transformfactory.cc | 2 +-
mia/3d/test_transio.cc | 2 +-
mia/3d/test_vector.cc | 2 +-
mia/3d/test_vectorfield.cc | 195 +++-
mia/3d/test_vfio.cc | 2 +-
mia/3d/timestep.cc | 2 +-
mia/3d/timestep.hh | 2 +-
mia/3d/trackpoint.cc | 2 +-
mia/3d/trackpoint.hh | 2 +-
mia/3d/trait.hh | 2 +-
mia/3d/transform.cc | 7 +-
mia/3d/transform.hh | 12 +-
mia/3d/transform/affine.cc | 26 +-
mia/3d/transform/affine.hh | 4 +-
mia/3d/transform/axisrot.cc | 26 +-
mia/3d/transform/axisrot.hh | 4 +-
mia/3d/transform/raffine.cc | 26 +-
mia/3d/transform/raffine.hh | 4 +-
mia/3d/transform/rigid.cc | 26 +-
mia/3d/transform/rigid.hh | 4 +-
mia/3d/transform/rotation.cc | 14 +-
mia/3d/transform/rotation.hh | 4 +-
mia/3d/transform/rotbend.cc | 28 +-
mia/3d/transform/rotbend.hh | 4 +-
mia/3d/transform/spline.cc | 6 +-
mia/3d/transform/spline.hh | 4 +-
mia/3d/transform/test_affine.cc | 2 +-
mia/3d/transform/test_axisrot.cc | 2 +-
mia/3d/transform/test_nonlinear.cc | 2 +-
mia/3d/transform/test_raffine.cc | 2 +-
mia/3d/transform/test_rigid.cc | 2 +-
mia/3d/transform/test_rotation.cc | 2 +-
mia/3d/transform/test_rotbend.cc | 2 +-
mia/3d/transform/test_spline.cc | 6 +-
mia/3d/transform/test_translate.cc | 2 +-
mia/3d/transform/test_vectorfield.cc | 29 +-
mia/3d/transform/translate.cc | 4 +-
mia/3d/transform/translate.hh | 4 +-
mia/3d/transform/vectorfield.cc | 11 +-
mia/3d/transform/vectorfield.hh | 8 +-
mia/3d/transformfactory.cc | 2 +-
mia/3d/transformfactory.hh | 2 +-
mia/3d/transformio.cc | 2 +-
mia/3d/transformio.hh | 2 +-
mia/3d/transformmock.cc | 6 +-
mia/3d/transformmock.hh | 4 +-
mia/3d/transio/bbs.cc | 2 +-
mia/3d/transio/serialization.hh | 2 +-
mia/3d/transio/xml.cc | 2 +-
mia/3d/valueattributetranslator.hh | 2 +-
mia/3d/vector.hh | 2 +-
mia/3d/vectorfield.cc | 348 ++++++-
mia/3d/vectorfield.hh | 62 +-
mia/3d/vfio.cc | 8 +-
mia/3d/vfio.hh | 19 +-
mia/3d/vfiotest.cc | 2 +-
mia/3d/vfiotest.hh | 2 +-
mia/3d/vfregularizer.cc | 72 ++
mia/3d/vfregularizer.hh | 107 ++
mia/3d/vfregularizer/CMakeLists.txt | 8 +
mia/3d/vfregularizer/fluid.cc | 196 ++++
.../vfregularizer/fluid.hh} | 34 +-
mia/3d/vfregularizer/sor.cc | 152 +++
mia/3d/vfregularizer/sor.hh | 67 ++
mia/3d/vfregularizer/test_sor.cc | 127 ++-
mia/3d/vfregularizerkernel.cc | 146 +++
mia/3d/vfregularizerkernel.hh | 176 ++++
mia/3d/vfregularizerkernel/CMakeLists.txt | 9 +
mia/3d/vfregularizerkernel/fluid-generic.cc | 302 ++++++
mia/3d/vfregularizerkernel/fluid-generic.hh | 74 ++
mia/3d/vfregularizerkernel/test_fluid-generic.cc | 262 +++++
mia/core.hh | 2 +-
mia/core/CMakeLists.txt | 32 +-
mia/core/attribute_names.cc | 2 +-
mia/core/attribute_names.hh | 2 +-
mia/core/attributes.cc | 52 +-
mia/core/attributes.cxx | 2 +-
mia/core/attributes.hh | 42 +-
mia/core/attributetype.hh | 20 +-
mia/core/boundary_conditions.cc | 2 +-
mia/core/boundary_conditions.hh | 5 +-
mia/core/callback.cc | 2 +-
mia/core/callback.hh | 2 +-
mia/core/cmdbooloption.cc | 3 +-
mia/core/cmdbooloption.hh | 2 +-
mia/core/cmdlineparser.cc | 20 +-
mia/core/cmdlineparser.hh | 2 +-
mia/core/cmdoption.cc | 14 +-
mia/core/cmdoption.hh | 8 +-
mia/core/cmdoptionflags.hh | 2 +-
mia/core/cmdparamoption.hh | 8 +-
mia/core/cmdstringoption.cc | 3 +-
mia/core/cmdstringoption.hh | 2 +-
mia/core/cmdtranslateroption.cc | 2 +-
mia/core/cmdtranslateroption.hh | 2 +-
mia/core/cmeans.cc | 16 +-
mia/core/cmeans.hh | 2 +-
mia/core/cmeansinit/kmeans.cc | 2 +-
mia/core/cmeansinit/kmeans.hh | 2 +-
mia/core/cmeansinit/static.cc | 2 +-
mia/core/cmeansinit/static.hh | 2 +-
mia/core/cmeansinit/test_kmeans.cc | 2 +-
mia/core/cmeansinit/test_static.cc | 2 +-
mia/core/combiner.cc | 2 +-
mia/core/combiner.hh | 2 +-
mia/core/convergence_measure.cc | 85 ++
mia/core/convergence_measure.hh | 85 ++
mia/core/cost.cc | 2 +-
mia/core/cost.cxx | 2 +-
mia/core/cost.hh | 2 +-
mia/core/creator.cc | 2 +-
mia/core/creator.hh | 2 +-
mia/core/cstplan.hh | 2 +-
mia/core/datapool.cc | 15 +-
mia/core/datapool.hh | 9 +-
mia/core/defines.hh | 2 +-
mia/core/delayedparameter.hh | 2 +-
mia/core/dictmap.hh | 2 +-
mia/core/distance.cc | 2 +-
mia/core/distance.hh | 2 +-
mia/core/dlloader.cc | 2 +-
mia/core/dlloader.hh | 2 +-
mia/core/dummyhandler.cc | 2 +-
mia/core/dummyhandler.hh | 5 +-
mia/core/errormacro.cc | 94 ++
mia/core/errormacro.hh | 11 +-
mia/core/export_handler.hh | 2 +-
mia/core/factory.hh | 11 +-
mia/core/factory_trait.hh | 2 +-
mia/core/fastica.cc | 567 -----------
mia/core/fastica/CMakeLists.txt | 10 +-
mia/core/fastica/deflationnonlinearity.cc | 2 +-
mia/core/fastica/deflationnonlinearity.hh | 2 +-
mia/core/fastica/fastica.cc | 1037 ++++++++++++++++++++
mia/core/{ => fastica}/fastica.hh | 161 ++-
mia/core/fastica/test_deflationnonlinearity.cc | 2 +-
mia/core/{test_ica.cc => fastica/test_fastica.cc} | 340 ++++---
mia/core/fastica_nonlinearity.cc | 2 +-
mia/core/fastica_nonlinearity.hh | 2 +-
mia/core/fft1d_r2c.cc | 2 +-
mia/core/fft1d_r2c.hh | 2 +-
mia/core/fftslopeclassifier.cc | 2 +-
mia/core/fftslopeclassifier.hh | 2 +-
mia/core/fifofilter.cxx | 2 +-
mia/core/fifofilter.hh | 2 +-
mia/core/file.cc | 2 +-
mia/core/file.hh | 2 +-
mia/core/filetools.cc | 2 +-
mia/core/filetools.hh | 2 +-
mia/core/filter.cc | 2 +-
mia/core/filter.hh | 48 +-
mia/core/fixedwidthoutput.cc | 2 +-
mia/core/fixedwidthoutput.hh | 2 +-
mia/core/flags.hh | 2 +-
mia/core/flagstring.cc | 2 +-
mia/core/flagstring.hh | 2 +-
mia/core/fullstats.cc | 2 +-
mia/core/fullstats.hh | 2 +-
mia/core/gsl_defines.hh | 2 +-
mia/core/gsl_iterator.hh | 2 +-
mia/core/gsl_matrix.cc | 46 +-
mia/core/gsl_matrix.hh | 19 +-
mia/core/gsl_matrix_vector_ops.cc | 2 +-
mia/core/gsl_matrix_vector_ops.hh | 2 +-
mia/core/gsl_multimin.cc | 2 +-
mia/core/gsl_multimin.hh | 2 +-
mia/core/gsl_pca.cc | 2 +-
mia/core/gsl_pca.hh | 2 +-
mia/core/gsl_vector.cc | 50 +-
mia/core/gsl_vector.hh | 19 +-
mia/core/gsl_vector_dispatch.hh | 2 +-
mia/core/gsl_wavelet.cc | 2 +-
mia/core/gsl_wavelet.hh | 2 +-
mia/core/handler.cxx | 3 +-
mia/core/handler.hh | 2 +-
mia/core/handlerbase.cc | 3 +-
mia/core/handlerbase.hh | 5 +-
mia/core/histogram.hh | 2 +-
mia/core/history.cc | 2 +-
mia/core/history.hh | 2 +-
mia/core/hwcap.cc | 59 ++
mia/core/hwcap.hh | 49 +
mia/core/ica.cc | 485 +--------
mia/core/ica.hh | 202 ++--
mia/core/ica_template.cxx | 6 +-
mia/core/ica_template.hh | 12 +-
mia/core/icaanalysisbase.cc | 36 -
mia/core/icaanalysisbase.hh | 189 ----
mia/core/import_handler.hh | 2 +-
mia/core/index.cc | 2 +-
mia/core/index.hh | 2 +-
mia/core/info.cc | 4 +-
mia/core/interpolator1d.cc | 20 +-
mia/core/interpolator1d.cxx | 2 +-
mia/core/interpolator1d.hh | 2 +-
mia/core/iodata.cc | 2 +-
mia/core/iodata.hh | 2 +-
mia/core/iohandler.cxx | 2 +-
mia/core/iohandler.hh | 2 +-
mia/core/ioplugin.cc | 2 +-
mia/core/ioplugin.cxx | 3 +-
mia/core/ioplugin.hh | 2 +-
mia/core/kmeans.cc | 2 +-
mia/core/kmeans.hh | 2 +-
mia/core/labelmap.cc | 2 +-
mia/core/labelmap.hh | 2 +-
mia/core/meanvar.hh | 2 +-
mia/core/minimizer.cc | 2 +-
mia/core/minimizer.hh | 2 +-
mia/core/minimizer/gdas.cc | 2 +-
mia/core/minimizer/gdas.hh | 2 +-
mia/core/minimizer/gdsq.cc | 2 +-
mia/core/minimizer/gdsq.hh | 2 +-
mia/core/minimizer/gsl.cc | 2 +-
mia/core/minimizer/gsl.hh | 2 +-
mia/core/minimizer/test_gdas.cc | 2 +-
mia/core/minimizer/test_gdsq.cc | 2 +-
mia/core/minimizer/test_gsl.cc | 2 +-
mia/core/mitestimages.cc | 2 +-
mia/core/mitestimages.hh | 2 +-
mia/core/module.cc | 2 +-
mia/core/module.hh | 2 +-
mia/core/msgstream.cc | 2 +-
mia/core/msgstream.hh | 2 +-
mia/core/nccsum.cc | 2 +-
mia/core/nccsum.hh | 2 +-
mia/core/noise/gauss.cc | 2 +-
mia/core/noise/gauss.hh | 2 +-
mia/core/noise/test_gauss.cc | 2 +-
mia/core/noise/test_uniform.cc | 2 +-
mia/core/noise/uniform.cc | 2 +-
mia/core/noise/uniform.hh | 2 +-
mia/core/noisegen.cc | 2 +-
mia/core/noisegen.hh | 2 +-
mia/core/optionparser.cc | 2 +-
mia/core/optionparser.hh | 2 +-
mia/core/optparam.cc | 3 +-
mia/core/optparam.hh | 6 +-
mia/core/parallel.hh | 2 +-
mia/core/parallelcxx11.cc | 2 +-
mia/core/parallelcxx11.hh | 16 +-
mia/core/paramarray.hh | 90 ++
mia/core/parameter.cc | 147 ++-
mia/core/parameter.cxx | 9 +-
mia/core/parameter.hh | 106 +-
mia/core/paramoption.cc | 6 +-
mia/core/paramoption.hh | 2 +-
mia/core/paramtranslator.cc | 3 +-
mia/core/paramtranslator.hh | 2 +-
mia/core/pixeltype.cc | 4 +-
mia/core/pixeltype.hh | 22 +-
mia/core/plugin_base.cc | 4 +-
mia/core/plugin_base.cxx | 2 +-
mia/core/plugin_base.hh | 2 +-
mia/core/plugin_test.cc | 2 +-
mia/core/probmap.cc | 2 +-
mia/core/probmap.hh | 2 +-
mia/core/product_base.cc | 2 +-
mia/core/product_base.hh | 2 +-
mia/core/productcache.cc | 2 +-
mia/core/productcache.hh | 2 +-
mia/core/property_flags.cc | 2 +-
mia/core/property_flags.hh | 2 +-
mia/core/pwh.cc | 2 +-
mia/core/pwh.hh | 2 +-
mia/core/refholder.hh | 2 +-
mia/core/regmodel.cc | 2 +-
mia/core/regmodel.hh | 2 +-
mia/core/revision.cc | 2 +-
mia/core/scaler1d.cc | 2 +-
mia/core/scaler1d.hh | 2 +-
mia/core/searchpath.cc | 23 +-
mia/core/searchpath.hh | 2 +-
mia/core/selftestcmdoption.cc | 2 +-
mia/core/selftestcmdoption.hh | 2 +-
mia/core/seriesstats.cc | 2 +-
mia/core/seriesstats.hh | 2 +-
mia/core/shape.cc | 2 +-
mia/core/shape.cxx | 2 +-
mia/core/shape.hh | 2 +-
mia/core/simpson.hh | 2 +-
mia/core/singular_refobj.hh | 27 +-
mia/core/slopeclassifier.cc | 2 +-
mia/core/slopeclassifier.hh | 2 +-
mia/core/slopestatistics.cc | 2 +-
mia/core/slopestatistics.hh | 2 +-
mia/core/slopevector.hh | 2 +-
mia/core/spacial_kernel.cc | 2 +-
mia/core/spacial_kernel.hh | 5 +-
mia/core/spacialkernel/cdiff.cc | 2 +-
mia/core/spacialkernel/cdiff.hh | 2 +-
mia/core/spacialkernel/gauss.cc | 2 +-
mia/core/spacialkernel/gauss.hh | 2 +-
mia/core/spacialkernel/test_cdiff.cc | 2 +-
mia/core/spacialkernel/test_gauss.cc | 20 +-
mia/core/sparse_histogram.cc | 2 +-
mia/core/sparse_histogram.hh | 16 +-
mia/core/sparse_solver.hh | 2 +-
mia/core/splinebc/bc.cc | 2 +-
mia/core/splinebc/bc.hh | 2 +-
mia/core/splinebc/test_bc.cc | 2 +-
mia/core/splinekernel.cc | 2 +-
mia/core/splinekernel.hh | 5 +-
mia/core/splinekernel/bspline.cc | 2 +-
mia/core/splinekernel/bspline.hh | 2 +-
mia/core/splinekernel/test_bspline.cc | 2 +-
mia/core/splineparzenmi.cc | 2 +-
mia/core/splineparzenmi.hh | 8 +-
mia/core/sqmin.cc | 2 +-
mia/core/sqmin.hh | 2 +-
mia/core/statistics.hh | 2 +-
mia/core/streamredir.cc | 2 +-
mia/core/streamredir.hh | 2 +-
mia/core/svector.hh | 2 +-
mia/core/test_Vector.cc | 2 +-
mia/core/test_attributes.cc | 34 +-
mia/core/test_boundary_conditions.cc | 2 +-
mia/core/test_callback.cc | 2 +-
mia/core/test_cmdlineparser.cc | 28 +-
mia/core/test_cmdlineparseroutput.cc | 159 +--
mia/core/test_cmdoptionflags.cc | 2 +-
mia/core/test_cmdparamoption.cc | 2 +-
mia/core/test_cmdtranslatoroption.cc | 2 +-
mia/core/test_cmdxmlhelp.cc | 23 +-
mia/core/test_cmeans.cc | 2 +-
mia/core/test_convergence_measure.cc | 123 +++
mia/core/test_core.cc | 7 +-
mia/core/test_cost.cc | 2 +-
mia/core/test_cstplan.cc | 2 +-
mia/core/test_datapool.cc | 10 +-
mia/core/test_delayedparameter.cc | 2 +-
mia/core/test_dictmap.cc | 2 +-
mia/core/test_distance.cc | 2 +-
mia/core/test_factoryoption.cc | 5 +-
mia/core/test_fastica.cc | 184 ----
mia/core/test_fft1d.cc | 2 +-
mia/core/test_fftslopeclassifier.cc | 2 +-
mia/core/test_fifofilter.cc | 2 +-
mia/core/test_filetools.cc | 2 +-
mia/core/test_filter.cc | 68 +-
mia/core/test_fixedwidthoutput.cc | 2 +-
mia/core/test_flagstring.cc | 2 +-
mia/core/test_fullstats.cc | 2 +-
mia/core/test_gsl_matrix.cc | 38 +-
mia/core/test_gsl_matrix_vector_ops.cc | 2 +-
mia/core/test_gsl_multimin.cc | 2 +-
mia/core/test_gsl_pca.cc | 2 +-
mia/core/test_gsl_vector.cc | 40 +-
mia/core/test_handler.cc | 2 +-
mia/core/test_helpers.hh | 2 +-
mia/core/test_histogram.cc | 2 +-
mia/core/test_history.cc | 2 +-
mia/core/test_index.cc | 2 +-
mia/core/test_interpol.cc | 2 +-
mia/core/test_interpolator1d.cc | 6 +-
mia/core/test_iohandler.cc | 2 +-
mia/core/test_kernels.cc | 2 +-
mia/core/test_kmeans.cc | 6 +-
mia/core/test_labelmap.cc | 2 +-
mia/core/test_meanvar.cc | 2 +-
mia/core/test_minimizer.cc | 2 +-
mia/core/test_nccsum.cc | 2 +-
mia/core/test_noisegen.cc | 2 +-
mia/core/test_optionparser.cc | 2 +-
mia/core/test_optparam.cc | 2 +-
mia/core/test_parallelcxx11.cc | 2 +-
mia/core/test_parameter.cc | 75 +-
mia/core/test_parseroutput.cc | 2 +-
mia/core/test_pixeltype.cc | 9 +-
mia/core/test_probmap.cc | 2 +-
mia/core/test_productcache.cc | 2 +-
mia/core/test_property_flags.cc | 2 +-
mia/core/test_pwh.cc | 2 +-
mia/core/test_register.cc | 2 +-
mia/core/test_scaler1d.cc | 2 +-
mia/core/test_seriesstats.cc | 2 +-
mia/core/test_shape.cc | 2 +-
mia/core/test_simpson.cc | 2 +-
mia/core/test_singular_refobj.cc | 9 +-
mia/core/test_slopeclassifier.cc | 2 +-
mia/core/test_slopestatistics.cc | 2 +-
mia/core/test_sparse_histogram.cc | 2 +-
mia/core/test_sparse_solver.cc | 2 +-
mia/core/test_splinekernel.cc | 2 +-
mia/core/test_splineparzenmi.cc | 2 +-
mia/core/test_sqmin.cc | 2 +-
mia/core/test_statistics.cc | 2 +-
mia/core/test_streamredir.cc | 2 +-
mia/core/test_streamvector.cc | 2 +-
mia/core/test_threadedmsg.cc | 2 +-
mia/core/test_tools.cc | 2 +-
mia/core/test_utils.cc | 2 +-
mia/core/test_watch.cc | 4 +-
mia/core/test_waveletslopeclassifier.cc | 2 +-
mia/core/test_xmlinterface.cc | 182 +++-
mia/core/testplug/dummy1.cc | 2 +-
mia/core/testplug/dummy2.cc | 2 +-
mia/core/testplug/lala.cc | 2 +-
mia/core/testplug/lolo.cc | 2 +-
mia/core/testplugin.cc | 2 +-
mia/core/testplugin.hh | 2 +-
mia/core/threadedmsg.cc | 2 +-
mia/core/threadedmsg.hh | 2 +-
mia/core/tools.hh | 2 +-
mia/core/traits.hh | 2 +-
mia/core/transformation.hh | 2 +-
mia/core/type_traits.hh | 2 +-
mia/core/typedescr.cc | 30 +-
mia/core/typedescr.hh | 30 +-
mia/core/utils.cc | 2 +-
mia/core/utils.hh | 2 +-
mia/core/vector.hh | 2 +-
mia/core/watch.cc | 56 +-
mia/core/watch.hh | 24 +-
mia/core/waveletslopeclassifier.cc | 21 +-
mia/core/waveletslopeclassifier.hh | 9 +-
mia/core/xmlinterface.cc | 324 +++++-
mia/core/xmlinterface.hh | 111 ++-
mia/internal/autotest.hh | 2 +-
mia/internal/main.hh | 2 +-
mia/internal/pluginsettest.hh | 2 +-
mia/internal/plugintester.hh | 2 +-
mia/mesh.hh | 2 +-
mia/mesh/clist.hh | 2 +-
mia/mesh/filter.cc | 2 +-
mia/mesh/filter.hh | 2 +-
mia/mesh/filter/addscale.cc | 2 +-
mia/mesh/filter/addscale.hh | 2 +-
mia/mesh/filter/deltrianglesbynormal.cc | 2 +-
mia/mesh/filter/deltrianglesbynormal.hh | 2 +-
mia/mesh/filter/scale.cc | 2 +-
mia/mesh/filter/scale.hh | 2 +-
mia/mesh/filter/selectbig.cc | 2 +-
mia/mesh/filter/selectbig.hh | 2 +-
mia/mesh/filter/test_addscale.cc | 2 +-
mia/mesh/filter/test_deltrianglesbynormal.cc | 2 +-
mia/mesh/filter/test_scale.cc | 2 +-
mia/mesh/filter/test_selectbig.cc | 2 +-
mia/mesh/filter/test_vtxsort.cc | 2 +-
mia/mesh/filter/vtxsort.cc | 2 +-
mia/mesh/filter/vtxsort.hh | 2 +-
mia/mesh/io/gts.cc | 2 +-
mia/mesh/io/off.cc | 11 +-
mia/mesh/io/ply.cc | 64 +-
mia/mesh/io/stl.cc | 15 +-
mia/mesh/io/test_meshio.cc | 40 +-
mia/mesh/test_triangle_neighbourhood.cc | 2 +-
mia/mesh/test_triangulate.cc | 2 +-
mia/mesh/triangle_neighbourhood.cc | 2 +-
mia/mesh/triangle_neighbourhood.hh | 2 +-
mia/mesh/triangularMesh.cc | 2 +-
mia/mesh/triangularMesh.hh | 2 +-
mia/mesh/triangulate.hh | 2 +-
mia/template/bandpass.cxx | 2 +-
mia/template/bandpass.hh | 2 +-
mia/template/binarize.cxx | 2 +-
mia/template/binarize.hh | 2 +-
mia/template/combiner.cxx | 2 +-
mia/template/combiner.hh | 2 +-
mia/template/combiner_filter.hh | 2 +-
mia/template/convert.cxx | 50 +-
mia/template/convert.hh | 2 +-
mia/template/cvd_io_trait.hh | 2 +-
mia/template/dimtrait.hh | 2 +-
mia/template/divcurl.cxx | 2 +-
mia/template/divcurl.hh | 2 +-
mia/template/filter_chain.hh | 2 +-
mia/template/filtertest.hh | 2 +-
mia/template/fullcost.cxx | 2 +-
mia/template/fullcost.hh | 2 +-
mia/template/invert.cxx | 2 +-
mia/template/invert.hh | 2 +-
mia/template/labelmap.cxx | 2 +-
mia/template/labelmap.hh | 2 +-
mia/template/lsd.hh | 2 +-
mia/template/masked_cost.cxx | 2 +-
mia/template/masked_cost.hh | 2 +-
mia/template/mi.hh | 2 +-
mia/template/mi_masked.cxx | 2 +-
mia/template/mi_masked.hh | 2 +-
mia/template/multicost.cxx | 2 +-
mia/template/multicost.hh | 2 +-
mia/template/nonrigidregister.cxx | 2 +-
mia/template/nonrigidregister.hh | 2 +-
mia/template/normalize.hh | 2 +-
mia/template/seededwatershed.hh | 2 +-
mia/template/similarity_profile.cxx | 2 +-
mia/template/similarity_profile.hh | 2 +-
mia/template/ssd-automask.cxx | 2 +-
mia/template/ssd-automask.hh | 2 +-
mia/template/ssd.hh | 2 +-
mia/template/ssd_masked.cxx | 2 +-
mia/template/ssd_masked.hh | 2 +-
mia/template/trackpoint.cxx | 4 +-
mia/template/trackpoint.hh | 2 +-
mia/template/transformfactory.cxx | 2 +-
mia/template/transformfactory.hh | 2 +-
mia/template/watershed.hh | 2 +-
mia/test/testhelpers.hh | 2 +-
src/2davgmasked.cc | 2 +-
src/2dbinarycombine.cc | 2 +-
src/2dcost.cc | 2 +-
src/2ddeform.cc | 2 +-
src/2ddistance.cc | 2 +-
src/2deval-transformquantity.cc | 2 +-
src/2dfluid-syn-registration.cc | 464 +++++++++
src/2dforce.cc | 2 +-
src/2dfuzzysegment.cc | 2 +-
src/2dgrayimage-combine-to-rgb.cc | 2 +-
src/2dgroundtruthreg.cc | 6 +-
src/2dimagecombine-dice.cc | 2 +-
src/2dimagecombiner.cc | 2 +-
src/2dimagecreator.cc | 2 +-
src/2dimagefilter.cc | 2 +-
src/2dimagefilterstack.cc | 2 +-
src/2dimagefullstats.cc | 2 +-
src/2dimageregistration.cc | 2 +-
src/2dimageselect.cc | 2 +-
src/2dimageseries-maximum-intensity-projection.cc | 2 +-
src/2dimagestack-cmeans.cc | 2 +-
src/2dimagestats.cc | 2 +-
src/2dlerp.cc | 2 +-
src/2dmany2one-nonrigid.cc | 4 +-
src/2dmulti-force.cc | 2 +-
src/2dmulti-nrreg.cc | 2 +-
src/2dmultiimageregistration.cc | 2 +-
src/2dmultiimageto3d.cc | 2 +-
src/2dmultiimagevar.cc | 2 +-
src/2dmyocard-ica.cc | 25 +-
src/2dmyocard-icaseries.cc | 21 +-
src/2dmyocard-segment.cc | 15 +-
src/2dmyocard-upsloap.cc | 8 +-
src/2dmyoica-full.cc | 132 +--
src/2dmyoica-nonrigid-parallel.cc | 36 +-
src/2dmyoica-nonrigid.cc | 36 +-
src/2dmyoica-nonrigid2.cc | 30 +-
src/2dmyoicapgt.cc | 33 +-
src/2dmyomilles.cc | 30 +-
src/2dmyoperiodic-nonrigid.cc | 6 +-
src/2dmyopgt-nonrigid.cc | 6 +-
src/2dmyoserial-nonrigid.cc | 7 +-
src/2dmyoseries-compdice.cc | 5 +-
src/2dmyoseries-dice.cc | 5 +-
src/2dmyoset-all2one-nonrigid.cc | 6 +-
src/2dnrreg.cc | 2 +-
src/2dsegcompare.cc | 16 +-
src/2dseghausdorff.cc | 13 +-
src/2dsegment-ahmed.cc | 2 +-
src/2dsegment-fuzzyw.cc | 2 +-
src/2dsegment-local-cmeans.cc | 5 +-
src/2dsegment-local-kmeans.cc | 2 +-
src/2dsegment-per-pixel-kmeans.cc | 2 +-
src/2dsegmentcropbox.cc | 9 +-
src/2dsegseriesstats.cc | 8 +-
src/2dsegshift.cc | 18 +-
src/2dsegshiftperslice.cc | 18 +-
src/2dseries-mincorr.cc | 2 +-
src/2dseries-sectionmask.cc | 14 +-
src/2dseries-segdistance.cc | 4 +-
src/2dseries2dordermedian.cc | 2 +-
src/2dseries2sets.cc | 9 +-
src/2dseriescorr.cc | 2 +-
src/2dseriesgradMAD.cc | 2 +-
src/2dseriesgradvariation.cc | 2 +-
src/2dserieshausdorff.cc | 23 +-
src/2dseriessmoothgradMAD.cc | 2 +-
src/2dseriestovolume.cc | 4 +-
src/2dstack-cmeans-presegment.cc | 2 +-
src/2dstackfilter.cc | 2 +-
src/2dto3dimage.cc | 2 +-
src/2dto3dimageb.cc | 2 +-
src/2dtrackpixelmovement.cc | 2 +-
src/2dtransform.cc | 2 +-
src/2dtransformation-to-strain.cc | 2 +-
src/3dbinarycombine.cc | 2 +-
src/3dbrainextractT1.cc | 2 +-
src/3dcombine-imageseries.cc | 2 +-
src/3dcombine-mr-segmentations.cc | 2 +-
src/3dcost-translatedgrad.cc | 2 +-
src/3dcost.cc | 2 +-
src/3dcrispsegment.cc | 2 +-
src/3ddeform.cc | 2 +-
src/3ddistance-stats.cc | 2 +-
src/3ddistance.cc | 2 +-
src/3deval-transformquantity.cc | 2 +-
src/3dfield2norm.cc | 2 +-
src/3dfluid-syn-registration.cc | 464 +++++++++
src/3dforce.cc | 2 +-
src/3dfuzzysegment.cc | 2 +-
src/3dgetsize.cc | 2 +-
src/3dgetslice.cc | 2 +-
src/3dimageaddattributes.cc | 2 +-
src/3dimagecombine.cc | 2 +-
src/3dimagecreator.cc | 2 +-
src/3dimagefilter.cc | 2 +-
src/3dimagefilterstack.cc | 2 +-
src/3dimageselect.cc | 2 +-
src/3dimagestatistics-in-mask.cc | 2 +-
src/3dimagestats.cc | 2 +-
src/3dlandmarks-distances.cc | 2 +-
src/3dlandmarks-transform.cc | 2 +-
src/3dlerp.cc | 2 +-
src/3dmany2one-nonrigid.cc | 4 +-
src/3dmaskseeded.cc | 2 +-
src/3dmotioncompica-nonrigid.cc | 19 +-
src/3dmulti-nrreg.cc | 2 +-
src/3dnonrigidreg-alt.cc | 2 +-
src/3dnonrigidreg.cc | 2 +-
src/3dnrreg.cc | 2 +-
src/3dprealign-nonrigid.cc | 3 +-
src/3dpropose-boundingbox.cc | 2 +-
src/3drigidreg.cc | 2 +-
src/3dsegment-ahmed.cc | 2 +-
...t-local-cmeans.cc => 3dsegment-local-cmeans.cc} | 314 ++++--
src/3dserial-nonrigid.cc | 4 +-
src/3dseries-track-intensity.cc | 2 +-
src/3dtrackpixelmovement.cc | 2 +-
src/3dtransform.cc | 2 +-
src/3dtransform2vf.cc | 2 +-
src/3dvectorfieldcreate.cc | 2 +-
src/3dvf2transform.cc | 2 +-
src/3dvfcompare.cc | 2 +-
src/CMakeLists.txt | 28 +-
src/cmeans.cc | 2 +-
src/distance-mesh2mask.cc | 2 +-
src/filenumberpattern.cc | 2 +-
src/fluid2d/NR2DMatrix.hh | 2 +-
src/fluid2d/Pixel.hh | 2 +-
src/fluid2d/elast.cc | 4 +-
src/fluid2d/elast.hh | 2 +-
src/fluid2d/helpers.cc | 2 +-
src/fluid2d/helpers.hh | 2 +-
src/fluid2d/main.cc | 2 +-
src/fluid2d/types.hh | 2 +-
src/fluid2d/vfluid.cc | 2 +-
src/fluid2d/vfluid.hh | 2 +-
src/fluid3d/eqn_solver.cc | 3 +-
src/fluid3d/eqn_solver.hh | 2 +-
src/fluid3d/main.cc | 4 +-
src/fluid3d/sor_solver.cc | 2 +-
src/fluid3d/sor_solver.hh | 2 +-
src/fluid3d/typedefs.hh | 2 +-
src/fluid3d/vfluid.cc | 9 +-
src/fluid3d/vfluid.hh | 4 +-
src/isosurface/CMakeLists.txt | 4 +-
src/isosurface/iso.cc | 2 +-
src/isosurface/iso_backend.cc | 2 +-
src/isosurface/iso_from_slices.cc | 2 +-
src/isosurface/mesh_convert.cc | 2 +-
src/labelsort.cc | 2 +-
src/mesh-deformable-model.cc | 5 +-
src/mesh-to-maskimage.cc | 2 +-
src/meshdistance-to-stackmask.cc | 2 +-
src/meshfilter.cc | 2 +-
src/multihist.cc | 2 +-
src/multiimage-cmeans.cc | 2 +-
src/myowavelettest.cc | 2 +-
src/plugin-help.cc | 2 +-
src/raw2image.cc | 2 +-
src/raw2volume.cc | 2 +-
src/test_plugins_as_installed.cc | 2 +-
src/wavelettrans.cc | 2 +-
1510 files changed, 13800 insertions(+), 6674 deletions(-)
create mode 100644 addons/itpp/CMakeLists.txt
copy {mia/core => addons/itpp}/ica.cc (85%)
copy {mia/core => addons/itpp}/ica.hh (74%)
copy {mia/core => addons/itpp}/test_ica.cc (84%)
copy mia/2d/{test_vectorfield_interpolator.cc => test_vectorfield.cc} (51%)
create mode 100644 mia/2d/vfregularizer.cc
create mode 100644 mia/2d/vfregularizer.hh
create mode 100644 mia/2d/vfregularizer/CMakeLists.txt
create mode 100644 mia/2d/vfregularizer/fluid.cc
copy mia/{mesh/triangle_neighbourhood.hh => 2d/vfregularizer/fluid.hh} (55%)
create mode 100644 mia/2d/vfregularizer/sor.cc
create mode 100644 mia/2d/vfregularizer/sor.hh
create mode 100644 mia/2d/vfregularizer/test_sor.cc
create mode 100644 mia/2d/vfregularizerkernel.cc
create mode 100644 mia/2d/vfregularizerkernel.hh
create mode 100644 mia/2d/vfregularizerkernel/CMakeLists.txt
create mode 100644 mia/2d/vfregularizerkernel/fluid-generic.cc
create mode 100644 mia/2d/vfregularizerkernel/fluid-generic.hh
create mode 100644 mia/2d/vfregularizerkernel/test_fluid-generic.cc
delete mode 100644 mia/3d/.gitignore
create mode 100644 mia/3d/vfregularizer.cc
create mode 100644 mia/3d/vfregularizer.hh
create mode 100644 mia/3d/vfregularizer/CMakeLists.txt
create mode 100644 mia/3d/vfregularizer/fluid.cc
copy mia/{mesh/triangle_neighbourhood.hh => 3d/vfregularizer/fluid.hh} (55%)
create mode 100644 mia/3d/vfregularizer/sor.cc
create mode 100644 mia/3d/vfregularizer/sor.hh
create mode 100644 mia/3d/vfregularizerkernel.cc
create mode 100644 mia/3d/vfregularizerkernel.hh
create mode 100644 mia/3d/vfregularizerkernel/CMakeLists.txt
create mode 100644 mia/3d/vfregularizerkernel/fluid-generic.cc
create mode 100644 mia/3d/vfregularizerkernel/fluid-generic.hh
create mode 100644 mia/3d/vfregularizerkernel/test_fluid-generic.cc
create mode 100644 mia/core/convergence_measure.cc
create mode 100644 mia/core/convergence_measure.hh
create mode 100644 mia/core/errormacro.cc
delete mode 100644 mia/core/fastica.cc
create mode 100644 mia/core/fastica/fastica.cc
rename mia/core/{ => fastica}/fastica.hh (52%)
rename mia/core/{test_ica.cc => fastica/test_fastica.cc} (57%)
create mode 100644 mia/core/hwcap.cc
create mode 100644 mia/core/hwcap.hh
delete mode 100644 mia/core/icaanalysisbase.cc
delete mode 100644 mia/core/icaanalysisbase.hh
create mode 100644 mia/core/paramarray.hh
create mode 100644 mia/core/test_convergence_measure.cc
delete mode 100644 mia/core/test_fastica.cc
create mode 100644 src/2dfluid-syn-registration.cc
create mode 100644 src/3dfluid-syn-registration.cc
copy src/{2dsegment-local-cmeans.cc => 3dsegment-local-cmeans.cc} (53%)
--
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