[med-svn] [mia] branch upstream updated (653402b -> 397384e)

Gert Wollny gert-guest at moszumanska.debian.org
Sat Jul 23 14:52:58 UTC 2016


This is an automated email from the git hooks/post-receive script.

gert-guest pushed a change to branch upstream
in repository mia.

      from  653402b   Imported Upstream version 2.2.7
       new  397384e   Imported Upstream version 2.4.1

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                                        |  38 ++
 CMakeLists.txt                                     | 114 ++--
 ChangeLog                                          |  56 +-
 README.md                                          |   5 +
 addons/dicom/CMakeLists.txt                        |   2 +
 addons/dicom/dcm2d.cc                              |   8 +-
 addons/dicom/dcm2d.hh                              |   2 +-
 addons/dicom/dcm3d.cc                              |  12 +-
 addons/dicom/dcm3d.hh                              |   2 +-
 addons/dicom/dicom4mia.cc                          | 119 ++--
 addons/dicom/dicom4mia.hh                          |   2 +-
 addons/dicom/getset.hh                             |   2 +-
 addons/dicom/test_dcm2d.cc                         |   9 +-
 addons/dicom/test_dcm3d.cc                         |   6 +-
 addons/dicom/test_dicom4mia.cc                     |  20 +-
 addons/hdf5/CMakeLists.txt                         |  11 +-
 addons/hdf5/hdf5_3dimage.cc                        |   6 +-
 addons/hdf5/hdf5_3dimage.hh                        |   2 +-
 addons/hdf5/hdf5a_mia.cc                           |   2 +-
 addons/hdf5/hdf5a_mia.hh                           |   2 +-
 addons/hdf5/hdf5mia.cc                             |   2 +-
 addons/hdf5/hdf5mia.hh                             |  31 +-
 addons/hdf5/test_hdf5_3dimage.cc                   |   3 +-
 addons/hdf5/test_hdf5mia.cc                        |  40 +-
 addons/jpg/CMakeLists.txt                          |   4 +-
 addons/jpg/jpeg-common.hh                          |   2 +-
 addons/jpg/jpg-gray.cc                             |  12 +-
 addons/jpg/jpg-rgb.cc                              |  33 +-
 addons/jpg/test_jpg.cc                             | 159 +++++
 addons/maxflow/2dmaxflow.cc                        |   2 +-
 addons/maxflow/2dmaxflow.hh                        |   2 +-
 addons/maxflow/test_2dmaxflow.cc                   |   2 +-
 addons/nifti/CMakeLists.txt                        |  11 +-
 addons/nifti/niftiimage.cc                         | 283 +++++----
 addons/nifti/niftiimage.hh                         |   2 +-
 addons/nifti/test_niftiimage.cc                    |  11 +-
 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/test_openexr.cc                     |  91 ++-
 addons/png/CMakeLists.txt                          |   4 +-
 addons/png/png-gray.cc                             |   2 +-
 addons/png/png-rgb.cc                              |   6 +-
 addons/png/test_png.cc                             | 194 ++++++
 addons/tiff/CMakeLists.txt                         |   4 +-
 addons/tiff/test_tiff.cc                           | 243 +++++++
 addons/tiff/tiff.cc                                |   6 +-
 addons/vistaio/2dtrans.cc                          |   2 +-
 addons/vistaio/2dtrans.hh                          |   2 +-
 addons/vistaio/2dvfvistaio.cc                      |   2 +-
 addons/vistaio/2dvistaio.cc                        |   5 +-
 addons/vistaio/2dvistaio.hh                        |   2 +-
 addons/vistaio/3dtrans.cc                          |   2 +-
 addons/vistaio/3dtrans.hh                          |   2 +-
 addons/vistaio/3dvfvistaio.cc                      |   2 +-
 addons/vistaio/3dvistaio.cc                        |   8 +-
 addons/vistaio/3dvistaio.hh                        |   2 +-
 addons/vistaio/CMakeLists.txt                      |  11 +-
 addons/vistaio/test_2dtrans.cc                     |   2 +-
 addons/vistaio/test_2dvistaio.cc                   |  48 +-
 addons/vistaio/test_3dtrans.cc                     |   2 +-
 addons/vistaio/test_3dvistaio.cc                   |  52 +-
 addons/vistaio/test_vista4mia.cc                   |   6 +-
 addons/vistaio/test_vistaio.cc                     | 378 +++++++++++
 addons/vistaio/vista4mia.cc                        |  17 +-
 addons/vistaio/vista4mia.hh                        |  10 +-
 addons/vistaio/vistamesh.cc                        |  16 +-
 addons/vtk/test_vtkimage.cc                        |   2 +-
 addons/vtk/test_vtkmesh.cc                         |   2 +-
 addons/vtk/test_vtkvf.cc                           |   2 +-
 addons/vtk/vtkimage.cc                             |  12 +-
 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                           |  27 +-
 cmake/macros.cmake                                 |  27 +-
 cmake/pluginmacro.cmake                            |  58 +-
 config.h.cmake                                     |   2 +-
 coverage.sh                                        |  20 +
 doc/CMakeLists.txt                                 |  26 +-
 doc/reference.dox.cmake                            |   6 +-
 evaluate_coverage.sh                               |  28 +
 examples/2d/filter/simple.cc                       |   2 +-
 examples/2d/filter/simple.hh                       |   2 +-
 examples/2d/filter/test_simple.cc                  |   2 +-
 gsl++/CMakeLists.txt                               |  53 --
 gsl++/matrix.cc                                    | 102 ---
 gsl++/matrix.hh                                    |  76 ---
 gsl++/test_matrix.cc                               |  61 --
 gsl++/vector.cc                                    |  55 --
 gsl++/vector_template.cxx                          | 143 -----
 gsl++/vector_template.hh                           | 214 -------
 mia.hh                                             |   2 +-
 mia/2d.hh                                          |   2 +-
 mia/2d/CMakeLists.txt                              |   2 -
 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                                |  51 +-
 mia/2d/cost/gncc.hh                                |   2 +-
 mia/2d/cost/lncc.cc                                |  26 +-
 mia/2d/cost/lncc.hh                                |   2 +-
 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                                 |  19 +-
 mia/2d/cost/ncc.hh                                 |   2 +-
 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                            |   3 +-
 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/CMakeLists.txt                      |   4 +-
 mia/2d/creator/circle.cc                           |  24 +-
 mia/{3d/creator/sphere.hh => 2d/creator/circle.hh} |  31 +-
 mia/2d/creator/test_circle.cc                      | 120 ++++
 mia/2d/cstkernel.cc                                |   2 +-
 mia/2d/cstkernel.hh                                |   2 +-
 mia/2d/datafield.cc                                |  13 +-
 mia/2d/datafield.cxx                               |   8 +-
 mia/2d/datafield.hh                                |  37 +-
 mia/2d/defines2d.hh                                |  18 +-
 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                                   |   2 +-
 mia/2d/filter/CMakeLists.txt                       |   5 +-
 mia/2d/filter/adaptmed.cc                          |   5 +-
 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                              |  42 +-
 mia/2d/filter/mean.hh                              |   2 +-
 mia/2d/filter/meanvar.cc                           | 175 +++++
 mia/2d/filter/{thresh.hh => meanvar.hh}            |  28 +-
 mia/2d/filter/median.cc                            |   2 +-
 mia/2d/filter/median.hh                            |   2 +-
 mia/2d/filter/medianmad.cc                         | 183 ++++++
 mia/2d/filter/{thresh.hh => medianmad.hh}          |  28 +-
 mia/2d/filter/midpoint.cc                          |   2 +-
 mia/2d/filter/mlv.cc                               |  30 +-
 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                           |  45 +-
 mia/2d/filter/sepconv.hh                           |  14 +-
 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                     |   2 +-
 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                         |   2 +-
 mia/2d/filter/test_mask.cc                         |   2 +-
 mia/2d/filter/test_mean.cc                         |   2 +-
 mia/2d/filter/test_meanvar.cc                      | 134 ++++
 mia/2d/filter/test_median.cc                       |   2 +-
 mia/2d/filter/test_medianmad.cc                    | 130 ++++
 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                      |  74 ++-
 mia/2d/filter/test_shaped_mean.cc                  |   2 +-
 mia/2d/filter/test_sortlabel.cc                    |   2 +-
 mia/2d/filter/test_tee.cc                          |   2 +-
 mia/2d/filter/test_thinning.cc                     |   2 +-
 mia/2d/filter/test_thresh.cc                       |   2 +-
 mia/2d/filter/{test_mean.cc => test_tmean.cc}      |  97 +--
 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                            |   8 +-
 mia/2d/filter/thresh.hh                            |   2 +-
 mia/2d/filter/tmean.cc                             | 144 +++++
 mia/2d/filter/{mean.hh => tmean.hh}                |  19 +-
 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.cc                              |  76 ---
 mia/2d/filterchain.hh                              |   4 +-
 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                           |   4 +-
 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                      |  13 +-
 mia/2d/fullcost/test_maskedimage.cc                |  99 ++-
 mia/2d/fuzzyclustersolver_cg.cc                    |   2 +-
 mia/2d/fuzzyclustersolver_cg.hh                    |   2 +-
 mia/2d/fuzzyclustersolver_sor.cc                   |  34 +-
 mia/2d/fuzzyclustersolver_sor.hh                   |   2 +-
 mia/2d/fuzzyseg.cc                                 | 218 +------
 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                                    |  16 +-
 mia/2d/image.hh                                    |  13 +-
 mia/2d/imageio.cc                                  |   3 +-
 mia/2d/imageio.hh                                  |   5 +-
 mia/2d/imageiotest.cc                              |   2 +-
 mia/2d/imageiotest.hh                              |   2 +-
 mia/2d/imagetest.cc                                |   2 +-
 mia/2d/imagetest.hh                                |   2 +-
 mia/2d/interpolator.cc                             |  39 +-
 mia/2d/interpolator.cxx                            |   6 +-
 mia/2d/interpolator.hh                             |  12 +-
 mia/2d/io/bmp.cc                                   | 177 +++---
 mia/2d/io/raw.cc                                   |   2 +-
 mia/2d/io/test_xml.cc                              |   2 +-
 mia/2d/io/xml.cc                                   |   2 +-
 mia/2d/io/xml.hh                                   |   2 +-
 mia/2d/iterator.cxx                                |   2 +-
 mia/2d/iterator.hh                                 |   2 +-
 mia/2d/kernel/curv.cc                              |   2 +-
 mia/2d/maskedcost.cc                               |   2 +-
 mia/2d/maskedcost.hh                               |   2 +-
 mia/2d/maskedcost/lncc.cc                          |  23 +-
 mia/2d/maskedcost/lncc.hh                          |   2 +-
 mia/2d/maskedcost/mi.cc                            |   2 +-
 mia/2d/maskedcost/mi.hh                            |   2 +-
 mia/2d/maskedcost/ncc.cc                           |  30 +-
 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                                |  86 ++-
 mia/2d/perfusion.hh                                |  23 +-
 mia/2d/polygon.cc                                  |   2 +-
 mia/2d/polygon.hh                                  |   2 +-
 mia/2d/ppmatrix.cc                                 |  21 +-
 mia/2d/ppmatrix.hh                                 |  18 +-
 mia/2d/register.cc                                 |   2 +-
 mia/2d/register.hh                                 |  12 +-
 mia/2d/rgbimageio.cc                               |   6 +-
 mia/2d/rgbimageio.hh                               |   7 +-
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 mia/3d/quaternion.cc                               |   4 +-
 mia/3d/quaternion.hh                               |   9 +-
 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                       |  26 +-
 mia/3d/shapes/basic_shapes.cc                      | 115 +---
 .../dummy1.cc => 3d/shapes/basic_shapes.hh}        |  60 +-
 mia/3d/shapes/sphere.cc                            |   2 +-
 mia/3d/shapes/sphere.hh                            |   2 +-
 mia/3d/shapes/test_shapes.cc                       | 100 +++
 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                     | 177 ++++++
 mia/3d/test_datafield.cc                           |   2 +-
 mia/3d/test_deform.cc                              |  14 +-
 mia/3d/test_distance.cc                            |  14 +-
 mia/3d/test_fullcost.cc                            |   2 +-
 mia/3d/test_ica.cc                                 |  26 +-
 mia/3d/test_image.cc                               |   2 +-
 mia/3d/test_imagecollect.cc                        |   2 +-
 mia/3d/test_imagedraw.cc                           |   2 +-
 mia/3d/test_imageio.cc                             | 126 ++++
 mia/3d/test_interpol.cc                            |  48 +-
 mia/3d/test_iterator.cc                            |   2 +-
 mia/3d/test_landmark.cc                            |   2 +-
 mia/3d/test_landmarklistio.cc                      |   2 +-
 mia/3d/test_matrix.cc                              |   8 +-
 mia/3d/test_nfg.cc                                 |   2 +-
 mia/3d/test_nonrigidregister.cc                    |   4 +-
 mia/3d/test_orientation.cc                         |   4 +-
 mia/3d/test_ppmatrix.cc                            |  46 +-
 mia/3d/test_quaternion.cc                          |   3 +-
 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                              |  42 +-
 mia/3d/test_vectorfield.cc                         |   2 +-
 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                                |  11 +-
 mia/3d/transform.hh                                |   2 +-
 mia/3d/transform/affine.cc                         |   2 +-
 mia/3d/transform/affine.hh                         |   2 +-
 mia/3d/transform/axisrot.cc                        |   2 +-
 mia/3d/transform/axisrot.hh                        |   2 +-
 mia/3d/transform/raffine.cc                        |   2 +-
 mia/3d/transform/raffine.hh                        |   2 +-
 mia/3d/transform/rigid.cc                          |  15 +-
 mia/3d/transform/rigid.hh                          |   2 +-
 mia/3d/transform/rotation.cc                       |   2 +-
 mia/3d/transform/rotation.hh                       |   2 +-
 mia/3d/transform/rotbend.cc                        |   2 +-
 mia/3d/transform/rotbend.hh                        |   2 +-
 mia/3d/transform/spline.cc                         |  99 +--
 mia/3d/transform/spline.hh                         |   2 +-
 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                    |   4 +-
 mia/3d/transform/test_translate.cc                 |   2 +-
 mia/3d/transform/test_vectorfield.cc               |   2 +-
 mia/3d/transform/translate.cc                      |   2 +-
 mia/3d/transform/translate.hh                      |   2 +-
 mia/3d/transform/vectorfield.cc                    |   2 +-
 mia/3d/transform/vectorfield.hh                    |   2 +-
 mia/3d/transformfactory.cc                         |   2 +-
 mia/3d/transformfactory.hh                         |   2 +-
 mia/3d/transformio.cc                              |   3 +-
 mia/3d/transformio.hh                              |   5 +-
 mia/3d/transformmock.cc                            |   2 +-
 mia/3d/transformmock.hh                            |   2 +-
 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                              |  10 +-
 mia/3d/vectorfield.hh                              |   2 +-
 mia/3d/vfio.cc                                     |   2 +-
 mia/3d/vfio.hh                                     |   2 +-
 mia/3d/vfiotest.cc                                 |   2 +-
 mia/3d/vfiotest.hh                                 |   2 +-
 mia/3d/vfregularizer/test_sor.cc                   |   2 +-
 mia/core.hh                                        |   2 +-
 mia/core/CMakeLists.txt                            |  88 ++-
 mia/core/attribute_names.cc                        |   7 +-
 mia/core/attribute_names.hh                        |  13 +-
 mia/core/attributes.cc                             |   7 +-
 mia/core/attributes.cxx                            |   2 +-
 mia/core/attributes.hh                             |  45 +-
 mia/core/attributetype.hh                          |   2 +-
 mia/core/boundary_conditions.cc                    |   2 +-
 mia/core/boundary_conditions.hh                    |   8 +-
 mia/core/callback.cc                               |   2 +-
 mia/core/callback.hh                               |   2 +-
 mia/core/cmdbooloption.cc                          |   2 +-
 mia/core/cmdbooloption.hh                          |   2 +-
 mia/core/cmdlineparser.cc                          |  53 +-
 mia/core/cmdlineparser.hh                          | 308 +--------
 mia/core/cmdoption.cc                              |   2 +-
 mia/core/cmdoption.hh                              |   2 +-
 mia/core/cmdoptionflags.hh                         |   2 +-
 mia/core/cmdparamoption.hh                         | 463 ++++++++++++++
 mia/core/cmdstringoption.cc                        |   2 +-
 mia/core/cmdstringoption.hh                        |   2 +-
 mia/core/cmdtranslateroption.cc                    |   2 +-
 mia/core/cmdtranslateroption.hh                    |   2 +-
 mia/core/cmeans.cc                                 | 147 +++--
 mia/core/cmeans.hh                                 | 180 +++++-
 mia/core/cmeansinit/kmeans.cc                      |   8 +-
 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/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                               |   6 +-
 mia/core/datapool.hh                               |   8 +-
 mia/core/defines.hh                                |  23 +-
 mia/core/delayedparameter.hh                       |   2 +-
 mia/core/dictmap.hh                                |   2 +-
 mia/core/distance.cc                               |   2 +-
 mia/core/distance.hh                               |  32 +-
 mia/core/dlloader.cc                               |   2 +-
 mia/core/dlloader.hh                               |   2 +-
 mia/core/dummyhandler.cc                           |   9 +-
 mia/core/dummyhandler.hh                           |  11 +-
 mia/core/errormacro.hh                             |   2 +-
 mia/core/export_handler.hh                         |   2 +-
 mia/core/factory.hh                                |   2 +-
 mia/core/factory_trait.hh                          |   2 +-
 mia/core/fastica.cc                                | 567 +++++++++++++++++
 mia/core/fastica.hh                                | 231 +++++++
 mia/{mesh/io => core/fastica}/CMakeLists.txt       |  15 +-
 mia/core/fastica/deflationnonlinearity.cc          | 210 ++++++
 mia/core/fastica/deflationnonlinearity.hh          |  92 +++
 mia/core/fastica/test_deflationnonlinearity.cc     | 284 +++++++++
 mia/core/fastica_nonlinearity.cc                   | 150 +++++
 mia/core/fastica_nonlinearity.hh                   | 125 ++++
 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                              |  85 +--
 mia/core/filetools.hh                              |  28 +-
 mia/core/filter.cc                                 |   3 +-
 mia/core/filter.hh                                 |  38 +-
 mia/core/fixedwidthoutput.cc                       |   2 +-
 mia/core/fixedwidthoutput.hh                       |   2 +-
 mia/core/flags.hh                                  |   3 +-
 mia/core/flagstring.cc                             |   2 +-
 mia/core/flagstring.hh                             |   2 +-
 mia/core/fullstats.cc                              |   2 +-
 mia/core/fullstats.hh                              |   2 +-
 gsl++/gsldefines.hh => mia/core/gsl_defines.hh     |   2 +-
 mia/core/gsl_iterator.hh                           | 312 +++++++++
 mia/core/gsl_matrix.cc                             | 420 ++++++++++++
 mia/core/gsl_matrix.hh                             | 475 ++++++++++++++
 mia/core/gsl_matrix_vector_ops.cc                  | 187 ++++++
 .../vector.hh => mia/core/gsl_matrix_vector_ops.hh |  32 +-
 gsl++/multimin.cc => mia/core/gsl_multimin.cc      |  32 +-
 gsl++/multimin.hh => mia/core/gsl_multimin.hh      |  18 +-
 mia/core/gsl_pca.cc                                | 101 +++
 mia/core/gsl_pca.hh                                |  90 +++
 mia/core/gsl_vector.cc                             | 203 ++++++
 mia/core/gsl_vector.hh                             | 272 ++++++++
 .../core/gsl_vector_dispatch.hh                    |   2 +-
 gsl++/wavelet.cc => mia/core/gsl_wavelet.cc        |   7 +-
 gsl++/wavelet.hh => mia/core/gsl_wavelet.hh        |   4 +-
 mia/core/handler.cxx                               |  34 +-
 mia/core/handler.hh                                |   6 +-
 mia/core/handlerbase.cc                            |   2 +-
 mia/core/handlerbase.hh                            |   2 +-
 mia/core/histogram.hh                              |  52 +-
 mia/core/history.cc                                |   2 +-
 mia/core/history.hh                                |   2 +-
 mia/core/ica.cc                                    | 291 ++++-----
 mia/core/ica.hh                                    | 138 ++--
 mia/core/ica_template.cxx                          | 112 ++--
 mia/core/ica_template.hh                           |  33 +-
 mia/core/{shape.cc => icaanalysisbase.cc}          |  17 +-
 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                         |  40 +-
 mia/core/interpolator1d.cxx                        |  27 +-
 mia/core/interpolator1d.hh                         |   7 +-
 mia/core/iodata.cc                                 |   2 +-
 mia/core/iodata.hh                                 |   2 +-
 mia/core/iohandler.cxx                             |  26 +-
 mia/core/iohandler.hh                              |   4 +-
 mia/core/ioplugin.cc                               |   2 +-
 mia/core/ioplugin.cxx                              |   2 +-
 mia/core/ioplugin.hh                               |   2 +-
 mia/core/kmeans.cc                                 |  26 +-
 mia/core/kmeans.hh                                 | 101 ++-
 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                         |   8 +-
 mia/core/minimizer/gdas.hh                         |   2 +-
 mia/core/minimizer/gdsq.cc                         |   7 +-
 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                              |  17 +-
 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                               |   2 +-
 mia/core/optparam.hh                               |   2 +-
 mia/core/parallel.hh                               |  72 +++
 mia/core/{combiner.cc => parallelcxx11.cc}         |  21 +-
 mia/core/parallelcxx11.hh                          | 214 +++++++
 mia/core/parameter.cc                              |   2 +-
 mia/core/parameter.cxx                             |   2 +-
 mia/core/parameter.hh                              |   2 +-
 mia/core/paramoption.cc                            |   2 +-
 mia/core/paramoption.hh                            |   2 +-
 mia/core/paramtranslator.cc                        |   2 +-
 mia/core/paramtranslator.hh                        |   2 +-
 mia/core/pixeltype.cc                              |   2 +-
 mia/core/pixeltype.hh                              |   2 +-
 mia/core/plugin_base.cc                            |   2 +-
 mia/core/plugin_base.cxx                           |   2 +-
 mia/core/plugin_base.hh                            |   2 +-
 mia/core/plugin_test.cc                            |   2 +-
 mia/core/probmap.cc                                |  12 +-
 mia/core/probmap.hh                                |   2 +-
 mia/core/product_base.cc                           |   2 +-
 mia/core/product_base.hh                           |   2 +-
 mia/core/productcache.cc                           |   6 +-
 mia/core/productcache.hh                           |  12 +-
 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                               |   4 +-
 mia/core/scaler1d.cc                               |   2 +-
 mia/core/scaler1d.hh                               |   2 +-
 mia/core/searchpath.cc                             |   2 +-
 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 +-
 .../silence_cmake_missing_source_file_warning.c    |   2 -
 mia/core/simpson.hh                                |   2 +-
 mia/core/singular_refobj.hh                        |   2 +-
 mia/core/slopeclassifier.cc                        |   2 +-
 mia/core/slopeclassifier.hh                        |   2 +-
 mia/core/slopestatistics.cc                        |   4 +-
 mia/core/slopestatistics.hh                        |   2 +-
 mia/core/slopevector.hh                            |   2 +-
 mia/core/spacial_kernel.cc                         |   2 +-
 mia/core/spacial_kernel.hh                         |   2 +-
 mia/core/spacialkernel/cdiff.cc                    |  44 +-
 mia/core/spacialkernel/cdiff.hh                    |  20 +-
 mia/core/spacialkernel/gauss.cc                    |   2 +-
 mia/core/spacialkernel/gauss.hh                    |   2 +-
 mia/core/spacialkernel/test_cdiff.cc               |  51 +-
 mia/core/spacialkernel/test_gauss.cc               |   2 +-
 mia/core/sparse_histogram.cc                       |  59 ++
 mia/core/sparse_histogram.hh                       | 150 +++++
 mia/core/sparse_solver.hh                          |   2 +-
 mia/core/splinebc/bc.cc                            |   8 +-
 mia/core/splinebc/bc.hh                            |   2 +-
 mia/core/splinebc/test_bc.cc                       |  14 +-
 mia/core/splinekernel.cc                           |   2 +-
 mia/core/splinekernel.hh                           |   2 +-
 mia/core/splinekernel/bspline.cc                   |   6 +-
 mia/core/splinekernel/bspline.hh                   |   2 +-
 mia/core/splinekernel/test_bspline.cc              |   2 +-
 mia/core/splineparzenmi.cc                         |   2 +-
 mia/core/splineparzenmi.hh                         |   2 +-
 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                                |  20 +-
 mia/core/test_Vector.cc                            |   2 +-
 mia/core/test_attributes.cc                        |   4 +-
 mia/core/test_boundary_conditions.cc               |   2 +-
 mia/core/test_callback.cc                          |   2 +-
 mia/core/test_cmdlineparser.cc                     | 115 +++-
 mia/core/test_cmdlineparseroutput.cc               | 209 ++++++
 mia/core/test_cmdoptionflags.cc                    |   2 +-
 mia/core/test_cmdparamoption.cc                    |  72 +++
 mia/core/test_cmdtranslatoroption.cc               |   2 +-
 mia/core/test_cmdxmlhelp.cc                        | 213 +++++++
 mia/core/test_cmeans.cc                            |  89 ++-
 mia/core/test_core.cc                              |  27 +-
 mia/core/test_core_combined.cc                     |  16 +
 mia/core/test_cost.cc                              |   2 +-
 mia/core/test_cstplan.cc                           |   2 +-
 mia/core/test_datapool.cc                          |  39 +-
 mia/core/test_delayedparameter.cc                  |   2 +-
 mia/core/test_dictmap.cc                           |   2 +-
 mia/core/test_distance.cc                          |   6 +-
 mia/core/test_factoryoption.cc                     |   2 +-
 mia/core/test_fastica.cc                           | 184 ++++++
 mia/core/test_fft1d.cc                             |   2 +-
 mia/core/test_fftslopeclassifier.cc                |   2 +-
 mia/core/test_fifofilter.cc                        |   4 +-
 mia/core/test_filetools.cc                         |  43 +-
 mia/core/test_filter.cc                            |   2 +-
 mia/core/test_fixedwidthoutput.cc                  |   2 +-
 mia/core/test_flagstring.cc                        |   2 +-
 mia/core/test_fullstats.cc                         |   2 +-
 mia/core/test_gsl_matrix.cc                        | 707 +++++++++++++++++++++
 mia/core/test_gsl_matrix_vector_ops.cc             | 288 +++++++++
 .../core/test_gsl_multimin.cc                      |  24 +-
 mia/core/test_gsl_pca.cc                           |  83 +++
 .../test_vector.cc => mia/core/test_gsl_vector.cc  | 128 +++-
 mia/core/test_handler.cc                           |  10 +-
 mia/core/test_helpers.hh                           |   2 +-
 mia/core/test_histogram.cc                         |  18 +-
 mia/core/test_history.cc                           |   2 +-
 mia/core/test_ica.cc                               |  54 +-
 mia/core/test_index.cc                             |   2 +-
 mia/core/test_interpol.cc                          |   2 +-
 mia/core/test_interpolator1d.cc                    | 180 +++++-
 mia/core/test_iohandler.cc                         |  26 +-
 mia/core/test_kernels.cc                           |   2 +-
 mia/core/test_kmeans.cc                            |  14 +-
 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                          |  29 +-
 mia/core/test_parallelcxx11.cc                     | 103 +++
 mia/core/test_parameter.cc                         |  33 +-
 mia/core/test_parseroutput.cc                      |   2 +-
 mia/core/test_pixeltype.cc                         |   2 +-
 mia/core/test_probmap.cc                           |   2 +-
 mia/core/test_productcache.cc                      |  47 +-
 mia/core/test_property_flags.cc                    |   2 +-
 mia/core/test_pwh.cc                               |   2 +-
 mia/core/test_register.cc                          |   2 +-
 mia/core/test_scaler1d.cc                          |  28 +-
 mia/core/test_seriesstats.cc                       |   2 +-
 mia/core/test_shape.cc                             |   2 +-
 mia/core/test_simpson.cc                           |   2 +-
 mia/core/test_singular_refobj.cc                   |   2 +-
 mia/core/test_slopeclassifier.cc                   |   2 +-
 mia/core/test_slopestatistics.cc                   |   7 +-
 mia/core/test_sparse_histogram.cc                  | 133 ++++
 mia/core/test_sparse_solver.cc                     |   3 +-
 mia/core/test_splinekernel.cc                      |  11 +-
 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                      |  30 +-
 mia/core/test_threadedmsg.cc                       |  19 +-
 mia/core/test_tools.cc                             |   2 +-
 mia/core/test_utils.cc                             |   6 +-
 mia/core/test_watch.cc                             |   2 +-
 mia/core/test_waveletslopeclassifier.cc            |   2 +-
 mia/core/test_xmlinterface.cc                      |   2 +-
 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                             |   4 +-
 mia/core/threadedmsg.cc                            |  12 +-
 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                            |  24 +-
 mia/core/typedescr.cc                              |   2 +-
 mia/core/typedescr.hh                              |   2 +-
 mia/core/utils.cc                                  |   6 +-
 mia/core/utils.hh                                  |   6 +-
 mia/core/vector.hh                                 |  36 +-
 mia/core/watch.cc                                  |   2 +-
 mia/core/watch.hh                                  |   2 +-
 mia/core/waveletslopeclassifier.cc                 |   3 +-
 mia/core/waveletslopeclassifier.hh                 |   2 +-
 mia/core/xmlinterface.cc                           |  10 +-
 mia/core/xmlinterface.hh                           |   2 +-
 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 +-
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 mia/mesh/filter/deltrianglesbynormal.cc            |  12 +-
 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/CMakeLists.txt                         |   2 +
 mia/mesh/io/gts.cc                                 |   2 +-
 mia/mesh/io/off.cc                                 | 447 +++----------
 mia/mesh/io/ply.cc                                 | 332 ++++++++--
 mia/mesh/io/stl.cc                                 |  19 +-
 mia/mesh/io/test_meshio.cc                         | 593 +++++++++++++++++
 mia/mesh/test_triangle_neighbourhood.cc            | 273 +++++++-
 mia/mesh/test_triangulate.cc                       |   2 +-
 mia/mesh/triangle_neighbourhood.cc                 |   2 +-
 mia/mesh/triangle_neighbourhood.hh                 |   2 +-
 mia/mesh/triangularMesh.cc                         |  78 ++-
 mia/mesh/triangularMesh.hh                         |   9 +-
 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                           |   2 +-
 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                |  41 +-
 mia/template/similarity_profile.hh                 |   6 +-
 mia/template/ssd-automask.cxx                      |  51 +-
 mia/template/ssd-automask.hh                       |   5 +-
 mia/template/ssd.hh                                |   2 +-
 mia/template/ssd_masked.cxx                        |   2 +-
 mia/template/ssd_masked.hh                         |   2 +-
 mia/template/trackpoint.cxx                        |   2 +-
 mia/template/trackpoint.hh                         |   2 +-
 mia/template/transformfactory.cxx                  |   2 +-
 mia/template/transformfactory.hh                   |   2 +-
 mia/template/watershed.hh                          |   4 +-
 mia/test/testhelpers.hh                            |   2 +-
 miaconfig.h.cmake                                  |   3 +-
 octave/miaoct.cc                                   |   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                    |   4 +-
 src/2dforce.cc                                     |   2 +-
 src/2dfuzzysegment.cc                              |   2 +-
 src/2dgrayimage-combine-to-rgb.cc                  |   2 +-
 src/2dgroundtruthreg.cc                            |   5 +-
 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                         | 129 +---
 src/2dimagestats.cc                                |   2 +-
 src/2dlerp.cc                                      |   2 +-
 src/2dmany2one-nonrigid.cc                         |  13 +-
 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                               |  33 +-
 src/2dmyocard-icaseries.cc                         |   9 +-
 src/2dmyocard-segment.cc                           |  14 +-
 src/2dmyocard-upsloap.cc                           |   3 +-
 src/2dmyoica-full.cc                               | 191 +++---
 src/2dmyoica-nonrigid-parallel.cc                  |  35 +-
 src/2dmyoica-nonrigid.cc                           |  26 +-
 src/2dmyoica-nonrigid2.cc                          |  20 +-
 src/2dmyoicapgt.cc                                 |  79 ++-
 src/2dmyomilles.cc                                 |  19 +-
 src/2dmyoperiodic-nonrigid.cc                      |   4 +-
 src/2dmyopgt-nonrigid.cc                           |   5 +-
 src/2dmyoserial-nonrigid.cc                        |   4 +-
 src/2dmyoseries-compdice.cc                        |   4 +-
 src/2dmyoseries-dice.cc                            |   4 +-
 src/2dmyoset-all2one-nonrigid.cc                   |  12 +-
 src/2dnrreg.cc                                     |   2 +-
 src/2dsegcompare.cc                                |   2 +-
 src/2dseghausdorff.cc                              |   2 +-
 src/2dsegment-ahmed.cc                             |   6 +-
 src/2dsegment-fuzzyw.cc                            |   3 +-
 src/2dsegment-local-cmeans.cc                      | 438 +++++++++++++
 src/2dsegment-local-kmeans.cc                      | 366 +++++++++++
 src/2dsegment-per-pixel-kmeans.cc                  | 239 +++++++
 src/2dsegmentcropbox.cc                            |   2 +-
 src/2dsegseriesstats.cc                            |   4 +-
 src/2dsegshift.cc                                  |   2 +-
 src/2dsegshiftperslice.cc                          |   2 +-
 src/2dseries-mincorr.cc                            |   3 +-
 src/2dseries-sectionmask.cc                        |   2 +-
 src/2dseries-segdistance.cc                        |   6 +-
 src/2dseries2dordermedian.cc                       |   6 +-
 src/2dseries2sets.cc                               |   3 +-
 src/2dseriescorr.cc                                |   3 +-
 src/2dseriesgradMAD.cc                             |   6 +-
 src/2dseriesgradvariation.cc                       |   4 +-
 src/2dserieshausdorff.cc                           |   2 +-
 src/2dseriessmoothgradMAD.cc                       |   6 +-
 src/2dseriestovolume.cc                            |   2 +-
 src/2dstack-cmeans-presegment.cc                   | 144 +----
 src/2dstackfilter.cc                               |   4 +-
 src/2dto3dimage.cc                                 |   2 +-
 src/2dto3dimageb.cc                                |   2 +-
 src/2dtrackpixelmovement.cc                        |   4 +-
 src/2dtransform.cc                                 |   2 +-
 src/2dtransformation-to-strain.cc                  |   3 +-
 src/3dbinarycombine.cc                             |   2 +-
 src/3dbrainextractT1.cc                            |   2 +-
 src/3dcombine-imageseries.cc                       |   2 +-
 src/3dcombine-mr-segmentations.cc                  |   2 +-
 src/3dcost-translatedgrad.cc                       |   3 +-
 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                    |   4 +-
 src/3dfield2norm.cc                                |   2 +-
 src/3dforce.cc                                     |   6 +-
 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                       |   3 +-
 src/3dlandmarks-transform.cc                       |   3 +-
 src/3dlerp.cc                                      |   6 +-
 src/3dmany2one-nonrigid.cc                         |  13 +-
 src/3dmaskseeded.cc                                |   2 +-
 src/3dmotioncompica-nonrigid.cc                    |  23 +-
 src/3dmulti-nrreg.cc                               |   2 +-
 src/3dnonrigidreg-alt.cc                           |   2 +-
 src/3dnonrigidreg.cc                               |   2 +-
 src/3dnrreg.cc                                     |   2 +-
 src/3dprealign-nonrigid.cc                         |   4 +-
 src/3dpropose-boundingbox.cc                       |   2 +-
 src/3drigidreg.cc                                  |   2 +-
 src/3dsegment-ahmed.cc                             |   6 +-
 src/3dserial-nonrigid.cc                           |   4 +-
 src/3dseries-track-intensity.cc                    |   4 +-
 src/3dtrackpixelmovement.cc                        |   4 +-
 src/3dtransform.cc                                 |   3 +-
 src/3dtransform2vf.cc                              |   3 +-
 src/3dvectorfieldcreate.cc                         |   2 +-
 src/3dvf2transform.cc                              |   3 +-
 src/3dvfcompare.cc                                 |   3 +-
 src/CMakeLists.txt                                 |   9 +-
 src/cmeans.cc                                      |  30 +-
 src/distance-mesh2mask.cc                          |   4 +-
 src/filenumberpattern.cc                           |   5 +-
 src/fluid2d/NR2DMatrix.hh                          |   2 +-
 src/fluid2d/Pixel.hh                               |   2 +-
 src/fluid2d/elast.cc                               |   2 +-
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 src/fluid2d/helpers.cc                             |   2 +-
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 src/fluid2d/main.cc                                |   8 +-
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 src/fluid3d/eqn_solver.cc                          |   2 +-
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 src/fluid3d/main.cc                                |   2 +-
 src/fluid3d/sor_solver.cc                          |  31 +-
 src/fluid3d/sor_solver.hh                          |   2 +-
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 src/fluid3d/vfluid.cc                              |  51 +-
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 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                       |  21 +-
 src/mesh-to-maskimage.cc                           |   2 +-
 src/meshdistance-to-stackmask.cc                   |   6 +-
 src/meshfilter.cc                                  |   2 +-
 src/multihist.cc                                   |   2 +-
 src/multiimage-cmeans.cc                           |   2 +-
 src/myowavelettest.cc                              |   6 +-
 src/plugin-help.cc                                 |   2 +-
 src/raw2image.cc                                   |   2 +-
 src/raw2volume.cc                                  |   2 +-
 src/test_plugins_as_installed.cc                   |   9 +-
 src/wavelettrans.cc                                |   7 +-
 test/test_ioplugins.cc                             |   2 +-
 test/test_minimizer.cc                             |   4 +-
 testdata/4D.off                                    |   6 +
 testdata/EnIm1.dcm                                 | Bin 0 -> 266310 bytes
 testdata/ND.off                                    |   7 +
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 testdata/vertex_error.off                          |   7 +
 1517 files changed, 19113 insertions(+), 6892 deletions(-)
 create mode 100644 .travis.yml
 create mode 100644 addons/jpg/test_jpg.cc
 create mode 100644 addons/png/test_png.cc
 create mode 100644 addons/tiff/test_tiff.cc
 create mode 100644 addons/vistaio/test_vistaio.cc
 create mode 100755 coverage.sh
 create mode 100644 evaluate_coverage.sh
 delete mode 100644 gsl++/CMakeLists.txt
 delete mode 100644 gsl++/matrix.cc
 delete mode 100644 gsl++/matrix.hh
 delete mode 100644 gsl++/test_matrix.cc
 delete mode 100644 gsl++/vector.cc
 delete mode 100644 gsl++/vector_template.cxx
 delete mode 100644 gsl++/vector_template.hh
 copy mia/{3d/creator/sphere.hh => 2d/creator/circle.hh} (57%)
 create mode 100644 mia/2d/creator/test_circle.cc
 create mode 100644 mia/2d/filter/meanvar.cc
 copy mia/2d/filter/{thresh.hh => meanvar.hh} (66%)
 create mode 100644 mia/2d/filter/medianmad.cc
 copy mia/2d/filter/{thresh.hh => medianmad.hh} (65%)
 create mode 100644 mia/2d/filter/test_meanvar.cc
 create mode 100644 mia/2d/filter/test_medianmad.cc
 copy mia/2d/filter/{test_mean.cc => test_tmean.cc} (50%)
 create mode 100644 mia/2d/filter/tmean.cc
 copy mia/2d/filter/{mean.hh => tmean.hh} (69%)
 delete mode 100644 mia/2d/filterchain.cc
 copy mia/{core/testplug/dummy1.cc => 3d/shapes/basic_shapes.hh} (51%)
 create mode 100644 mia/3d/shapes/test_shapes.cc
 create mode 100644 mia/3d/test_critical_points.cc
 create mode 100644 mia/3d/test_imageio.cc
 create mode 100644 mia/core/cmdparamoption.hh
 create mode 100644 mia/core/fastica.cc
 create mode 100644 mia/core/fastica.hh
 copy mia/{mesh/io => core/fastica}/CMakeLists.txt (80%)
 create mode 100644 mia/core/fastica/deflationnonlinearity.cc
 create mode 100644 mia/core/fastica/deflationnonlinearity.hh
 create mode 100644 mia/core/fastica/test_deflationnonlinearity.cc
 create mode 100644 mia/core/fastica_nonlinearity.cc
 create mode 100644 mia/core/fastica_nonlinearity.hh
 rename gsl++/gsldefines.hh => mia/core/gsl_defines.hh (95%)
 create mode 100644 mia/core/gsl_iterator.hh
 create mode 100644 mia/core/gsl_matrix.cc
 create mode 100644 mia/core/gsl_matrix.hh
 create mode 100644 mia/core/gsl_matrix_vector_ops.cc
 rename gsl++/vector.hh => mia/core/gsl_matrix_vector_ops.hh (50%)
 rename gsl++/multimin.cc => mia/core/gsl_multimin.cc (89%)
 rename gsl++/multimin.hh => mia/core/gsl_multimin.hh (91%)
 create mode 100644 mia/core/gsl_pca.cc
 create mode 100644 mia/core/gsl_pca.hh
 create mode 100644 mia/core/gsl_vector.cc
 create mode 100644 mia/core/gsl_vector.hh
 rename gsl++/vector_dispatch.hh => mia/core/gsl_vector_dispatch.hh (96%)
 rename gsl++/wavelet.cc => mia/core/gsl_wavelet.cc (96%)
 rename gsl++/wavelet.hh => mia/core/gsl_wavelet.hh (93%)
 copy mia/core/{shape.cc => icaanalysisbase.cc} (78%)
 create mode 100644 mia/core/icaanalysisbase.hh
 create mode 100644 mia/core/parallel.hh
 copy mia/core/{combiner.cc => parallelcxx11.cc} (68%)
 create mode 100644 mia/core/parallelcxx11.hh
 delete mode 100644 mia/core/silence_cmake_missing_source_file_warning.c
 create mode 100644 mia/core/sparse_histogram.cc
 create mode 100644 mia/core/sparse_histogram.hh
 create mode 100644 mia/core/test_cmdlineparseroutput.cc
 create mode 100644 mia/core/test_cmdparamoption.cc
 create mode 100644 mia/core/test_cmdxmlhelp.cc
 create mode 100644 mia/core/test_core_combined.cc
 create mode 100644 mia/core/test_fastica.cc
 create mode 100644 mia/core/test_gsl_matrix.cc
 create mode 100644 mia/core/test_gsl_matrix_vector_ops.cc
 rename gsl++/test_multimin.cc => mia/core/test_gsl_multimin.cc (82%)
 create mode 100644 mia/core/test_gsl_pca.cc
 rename gsl++/test_vector.cc => mia/core/test_gsl_vector.cc (53%)
 create mode 100644 mia/core/test_parallelcxx11.cc
 create mode 100644 mia/core/test_sparse_histogram.cc
 create mode 100644 mia/mesh/io/test_meshio.cc
 create mode 100644 src/2dsegment-local-cmeans.cc
 create mode 100644 src/2dsegment-local-kmeans.cc
 create mode 100644 src/2dsegment-per-pixel-kmeans.cc
 create mode 100644 testdata/4D.off
 create mode 100644 testdata/EnIm1.dcm
 create mode 100644 testdata/ND.off
 create mode 100644 testdata/binary100x2uc.bmp
 create mode 100644 testdata/gray100x2c-4bit.bmp
 create mode 100644 testdata/gray100x2c.bmp
 create mode 100644 testdata/gray100x2uc-4bit.bmp
 create mode 100644 testdata/gray20x20c.bmp
 create mode 100644 testdata/gray20x20c.jpg
 create mode 100644 testdata/gray20x20c.tif
 create mode 100644 testdata/gray2x3-1.png
 create mode 100644 testdata/gray2x3-1.tif
 create mode 100644 testdata/gray2x3-16.png
 create mode 100644 testdata/gray2x3-16.tif
 create mode 100644 testdata/gray2x3-multiframe.tif
 create mode 100644 testdata/gray2x3.bmp
 create mode 100644 testdata/gray2x3.c
 create mode 100644 testdata/gray2x3.jpg
 create mode 100644 testdata/gray2x3.png
 create mode 100644 testdata/gray2x3.tif
 create mode 100644 testdata/octahedron-with-normals-and-color.off
 create mode 100644 testdata/octahedron-with-normals-and-color.ply
 create mode 100644 testdata/octahedron-with-normals-and-scale.ply
 create mode 100644 testdata/octahedron-with-normals.off
 create mode 100644 testdata/octahedron-with-normals.ply
 create mode 100644 testdata/octahedron.off
 create mode 100644 testdata/octahedron.ply
 create mode 100644 testdata/octahedron.stl
 create mode 100644 testdata/poly.off
 create mode 100644 testdata/rgb3x2-24bit.bmp
 create mode 100644 testdata/rgb3x2-24bit.jpg
 create mode 100644 testdata/rgb3x2-24bit.png
 create mode 100644 testdata/vertex_error.off

-- 
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