[Olena-patches] olena: branch fixes updated: olena-2.0-785-gffd0699

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in full, below. - Log ----------------------------------------------------------------- ffd0699 Remove an unnecessary #include from an example of the tutorial. ----------------------------------------------------------------------- Summary of changes: .dir-locals.el | 5 + ChangeLog | 63 +- configure.ac | 30 +- doc/Doxyfile.in | 4 +- doc/Makefile.am | 39 +- milena/ChangeLog | 1490 +- milena/Makefile.am | 1 + milena/apps/Makefile.am | 5 +- .../constrained-connectivity.cc | 10 +- milena/apps/generic-skel/Makefile.am | 115 + .../generic-skel/image2d-skel-unconstrained.cc | 92 + .../generic-skel/image2d-skel-with-end-points.cc | 94 + .../generic-skel/image3d-skel-unconstrained.cc | 109 + .../generic-skel/image3d-skel-with-1d-isthmuses.cc | 114 + .../generic-skel/image3d-skel-with-end-points.cc | 114 + milena/apps/generic-skel/image3d-skel.hh | 399 + .../test-image2d-skel-unconstrained.in} | 16 +- .../test-image2d-skel-with-end-points.in} | 16 +- .../generic-skel/test-mixed.in} | 17 +- milena/apps/graph-morpho/morpho.hh | 8 +- milena/apps/mesh-segm-skel/Makefile.am | 187 +- .../apps/mesh-segm-skel/mesh-complex-2-collapse.cc | 153 + .../mesh-complex-max-curv-1-collapse.cc | 386 + .../mesh-complex-max-curv-2-collapse.cc | 328 + ...ax-curv.cc => mesh-complex-max-curv-extrema.cc} | 109 +- .../mesh-segm-skel/mesh-complex-max-curv-segm.cc | 56 +- .../mesh-segm-skel/mesh-complex-max-curv-skel.cc | 328 + .../apps/mesh-segm-skel/mesh-complex-max-curv.cc | 17 +- ...curv-segm.cc => mesh-complex-pinv-curv-segm.cc} | 63 +- .../mesh-segm-skel/mesh-complex-pinv-curv-skel.cc | 344 + milena/apps/mesh-segm-skel/mesh-complex-segm.cc | 26 +- milena/apps/mesh-segm-skel/mesh-complex-skel.cc | 126 +- milena/apps/mesh-segm-skel/misc.hh | 15 +- .../apps/mesh-segm-skel/off-to-vtk-bin.cc | 48 +- milena/apps/mesh-segm-skel/save_bin_alt.hh | 310 +- .../test-mesh-complex-2-collapse.in} | 15 +- .../test-mesh-complex-max-curv-1-collapse.in} | 16 +- .../test-mesh-complex-max-curv-2-collapse.in} | 16 +- .../test-mesh-complex-max-curv-extrema.in} | 18 +- .../test-mesh-complex-max-curv-skel.in} | 18 +- .../test-mesh-complex-pinv-curv-segm.in} | 17 +- .../test-mesh-complex-pinv-curv-skel.in} | 18 +- .../mesh-segm-skel/test-mixed.in} | 17 +- milena/apps/morphers/recorder-bft.cc | 9 +- milena/doc/Doxyfile.in | 2 +- milena/doc/Makefile.am | 53 +- milena/doc/examples/devel/facade.cc.raw | 4 +- milena/doc/examples/devel/impl.cc.raw | 7 +- .../examples/split/tuto3_first_routine-1.cc.raw | 1 - milena/doc/examples/tuto3/first_routine.cc | 1 - milena/doc/figures/extend-1.ppm | Bin 12406 -> 12407 bytes milena/doc/figures/extend-2.ppm | Bin 16546 -> 16547 bytes milena/doc/figures/extend-3.ppm | Bin 16546 -> 16547 bytes milena/doc/figures/extend-4.ppm | 2 +- milena/doc/figures/extend-5.ppm | Bin 12406 -> 12407 bytes milena/doc/figures/fill-1.ppm | Bin 12406 -> 12407 bytes milena/doc/figures/fill-2.ppm | Bin 12406 -> 12407 bytes milena/doc/figures/fill-imageif-cfun-1.ppm | Bin 206 -> 207 bytes 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| 18 +- .../mln/core/image/dmorph/mutable_extension_ima.hh | 272 + milena/mln/core/image/image2d.hh | 5 - milena/mln/core/internal/classical_window_base.hh | 1 - milena/mln/core/internal/image_morpher.hh | 1 - .../{math/pi.hh => core/routine/mutable_extend.hh} | 47 +- milena/mln/core/site_set/p_set.hh | 14 +- milena/mln/fun/p2b/antilogy.hh | 1 - milena/mln/fun/p2b/tautology.hh | 1 - milena/mln/geom/complex_geometry.hh | 16 +- milena/mln/io/fld/write_header.hh | 9 +- milena/mln/io/off/load.hh | 27 +- milena/mln/io/off/save.hh | 6 +- milena/mln/io/pdf/load.hh | 8 +- milena/mln/io/pnm/save_header.hh | 10 +- milena/mln/io/raw/load.hh | 3 +- milena/mln/io/tiff/load.hh | 10 +- .../core/alias/dpoint2d.cc => mln/io/vtk/all.hh} | 32 +- milena/mln/io/vtk/load.hh | 615 + milena/mln/io/vtk/save.hh | 649 + milena/mln/make/attachment.hh | 53 +- milena/mln/make/cell.hh | 11 +- milena/mln/make/detachment.hh | 56 +- milena/mln/math/pi.hh | 10 +- milena/mln/morpho/tree/data.hh | 10 +- milena/mln/morpho/tree/impl/dual_hqueue.hh | 5 +- milena/mln/morpho/tree/impl/dual_union_find.hh | 13 +- milena/mln/morpho/watershed/topological.hh | 198 +- milena/mln/topo/connectivity_number_2d.hh | 130 + milena/mln/topo/connectivity_number_3d.hh | 309 + milena/mln/topo/detach.hh | 83 - milena/mln/topo/detach_cell.hh | 154 + milena/mln/topo/detach_pair.hh | 191 + milena/mln/topo/detach_point.hh | 114 + milena/mln/topo/is_facet.hh | 52 +- milena/mln/topo/is_n_face.hh | 16 +- milena/mln/topo/is_not_1d_isthmus.hh | 208 + milena/mln/topo/is_not_end_point.hh | 121 + milena/mln/topo/is_simple_2d.hh | 135 +- milena/mln/topo/is_simple_cell.hh | 114 +- milena/mln/topo/is_simple_pair.hh | 225 + milena/mln/topo/is_simple_point2d.hh | 142 + milena/mln/topo/is_simple_point3d.hh | 191 + milena/mln/topo/{is_n_face.hh => no_constraint.hh} | 46 +- milena/mln/topo/skeleton/breadth_first_thinning.hh | 171 +- .../mln/topo/skeleton/priority_driven_thinning.hh | 215 + milena/mln/transform/fft.hh | 705 + milena/mln/util/edge.hh | 3 +- milena/mln/util/timer.hh | 9 - milena/mln/version.hh.in | 19 +- milena/new-header | 4 +- milena/tests/core/alias/Makefile.am | 3 +- milena/tests/core/alias/dpoint2d.cc | 4 +- .../tests/core/alias/{dpoint2d.cc => neighb2d.cc} | 33 +- milena/tests/core/image/complex_image.hh | 20 +- milena/tests/io/Makefile.am | 5 +- milena/tests/io/dump/Makefile.am | 4 +- milena/tests/io/dump/dump.cc | 32 + milena/tests/io/{dump => vtk}/Makefile.am | 18 +- .../deskew.cc => milena/tests/io/vtk/load_bin.cc | 44 +- .../alias/dpoint2d.cc => io/vtk/load_save_bin.cc} | 33 +- milena/tests/io/vtk/save.cc | 106 + milena/tests/make/Makefile.am | 4 +- milena/tests/make/attachment.cc | 77 + milena/tests/make/detachment.cc | 98 + milena/tests/topo/Makefile.am | 13 +- milena/tests/topo/connectivity_numbers_2d.cc | 87 + milena/tests/topo/detach_pair.cc | 73 + milena/tests/topo/is_facet.cc | 80 + milena/tests/topo/is_simple_pair.cc | 73 + milena/tests/topo/skeleton/Makefile.am | 12 +- .../tests/topo/skeleton/breadth_first_thinning.cc | 52 +- .../skeleton/breadth_first_thinning_constrained.cc | 78 + .../topo/skeleton/priority_driven_thinning.cc | 92 + .../priority_driven_thinning_constrained.cc | 96 + milena/tests/transform/Makefile.am | 22 +- milena/tests/transform/fft.cc | 105 + milena/tests/unit_test/Makefile.am | 3 +- milena/tests/unit_test/cond_tests_fftw3 | 1 + milena/tests/unit_test/unit-tests.mk | 27 +- milena/tests/value/Makefile.am | 7 +- .../{core/alias/dpoint2d.cc => value/int_u32.cc} | 28 +- milena/tools/Makefile.am | 66 +- milena/tools/compute_local_configurations.cc | 109 + .../pi.hh => tools/connectivity_numbers_3d.cc} | 48 +- milena/tools/connectivity_numbers_3d.hh | 407 + .../tools/connectivity_numbers_3d_tbb.cc | 50 +- milena/tools/connectivity_numbers_3d_tbb.hh | 163 + milena/tools/gen_cxx_lut | 103 + .../tools/simple_point3d_lut.cc | 51 +- milena/tools/simple_point3d_lut.hh | 190 + .../simple_point3d_lut_26_6.cc} | 29 +- .../tools/simple_point3d_lut_tbb.cc | 41 +- milena/tools/simple_point3d_lut_tbb.hh | 185 + milena/tools/test_simple_point3d_lut_26_6.cc | 136 + milena/tools/tools.mk | 7 +- milena/trash/display_color_pretty.hh | 15 +- milena/trash/display_remove.hh | 13 +- milena/trash/display_save.hh | 14 +- milena/trash/display_save_and_show.hh | 10 +- milena/trash/display_show.hh | 10 +- milena/trash/neighb_get.hh | 6 +- scribo/ChangeLog | 90 +- scribo/demo/viewer/Makefile.am | 3 +- scribo/doc/Doxyfile.in | 2 +- scribo/doc/Makefile.am | 50 +- scribo/scribo/afp/components.hh | 12 - scribo/scribo/core/line_set.hh | 2 - scribo/scribo/core/object_groups.hh | 5 +- scribo/scribo/core/paragraph_set.hh | 3 +- scribo/scribo/estim/components_features.hh | 24 +- scribo/scribo/filter/objects_with_holes.hh | 33 +- scribo/scribo/filter/separators_in_borders.hh | 14 - scribo/scribo/io/xml/load.hh | 15 +- scribo/scribo/postprocessing/fill_object_holes.hh | 9 - scribo/scribo/preprocessing/deskew.hh | 7 +- scribo/scribo/preprocessing/deskew_crop.hh | 3 +- .../primitive/extract/lines_h_thick_and_thin.hh | 3 +- scribo/scribo/primitive/extract/non_text.hh | 4 - scribo/scribo/primitive/extract/non_text_kmean.hh | 5 +- .../primitive/extract/separators_nonvisible.hh | 65 +- scribo/scribo/text/clean_inplace.hh | 15 +- scribo/scribo/text/extract_paragraphs_hdoc.hh | 44 - scribo/scribo/text/merging.hh | 55 +- scribo/scribo/text/recognition.hh | 4 +- scribo/src/Makefile.am | 1 - scribo/src/binarization/Makefile.am | 5 - scribo/tests/preprocessing/crop.cc | 6 +- .../preprocessing/crop_without_localization.cc | 6 +- scribo/tests/preprocessing/deskew.cc | 6 +- scribo/tests/preprocessing/rotate_90.cc | 6 +- swilena/ChangeLog | 10 +- swilena/python/Makefile.am | 2 +- 228 files changed, 496835 insertions(+), 1716 deletions(-) create mode 100644 .dir-locals.el create mode 100644 milena/apps/generic-skel/Makefile.am create mode 100644 milena/apps/generic-skel/image2d-skel-unconstrained.cc create mode 100644 milena/apps/generic-skel/image2d-skel-with-end-points.cc create mode 100644 milena/apps/generic-skel/image3d-skel-unconstrained.cc create mode 100644 milena/apps/generic-skel/image3d-skel-with-1d-isthmuses.cc create mode 100644 milena/apps/generic-skel/image3d-skel-with-end-points.cc create mode 100644 milena/apps/generic-skel/image3d-skel.hh copy milena/{tests/topo/Makefile.am => apps/generic-skel/test-image2d-skel-unconstrained.in} (68%) copy milena/{tests/topo/Makefile.am => apps/generic-skel/test-image2d-skel-with-end-points.in} (67%) copy milena/{tests/topo/Makefile.am => apps/generic-skel/test-mixed.in} (63%) create mode 100644 milena/apps/mesh-segm-skel/mesh-complex-2-collapse.cc create mode 100644 milena/apps/mesh-segm-skel/mesh-complex-max-curv-1-collapse.cc create mode 100644 milena/apps/mesh-segm-skel/mesh-complex-max-curv-2-collapse.cc copy milena/apps/mesh-segm-skel/{mesh-complex-max-curv.cc => mesh-complex-max-curv-extrema.cc} (63%) create mode 100644 milena/apps/mesh-segm-skel/mesh-complex-max-curv-skel.cc copy milena/apps/mesh-segm-skel/{mesh-complex-max-curv-segm.cc => mesh-complex-pinv-curv-segm.cc} (72%) create mode 100644 milena/apps/mesh-segm-skel/mesh-complex-pinv-curv-skel.cc copy scribo/tests/preprocessing/deskew.cc => milena/apps/mesh-segm-skel/off-to-vtk-bin.cc (59%) copy milena/{tests/topo/Makefile.am => apps/mesh-segm-skel/test-mesh-complex-2-collapse.in} (73%) copy milena/{tests/topo/Makefile.am => apps/mesh-segm-skel/test-mesh-complex-max-curv-1-collapse.in} (64%) copy milena/{tests/topo/Makefile.am => apps/mesh-segm-skel/test-mesh-complex-max-curv-2-collapse.in} (64%) copy milena/{tests/topo/Makefile.am => apps/mesh-segm-skel/test-mesh-complex-max-curv-extrema.in} (54%) copy milena/{tests/topo/Makefile.am => apps/mesh-segm-skel/test-mesh-complex-max-curv-skel.in} (55%) copy milena/{tests/topo/Makefile.am => apps/mesh-segm-skel/test-mesh-complex-pinv-curv-segm.in} (60%) copy milena/{tests/topo/Makefile.am => apps/mesh-segm-skel/test-mesh-complex-pinv-curv-skel.in} (55%) copy milena/{tests/topo/Makefile.am => apps/mesh-segm-skel/test-mixed.in} (54%) delete mode 100755 milena/doc/generate_dist_files.sh delete mode 100755 milena/doc/tools/clearbanner.sh create mode 100755 milena/img/bunny.pgm create mode 100644 milena/mesh/bunny-holefilled.vtk create mode 100644 milena/mesh/pseudo-manifold.vtk create mode 100644 milena/mesh/teapot.vtk create mode 100644 milena/mesh/tetrahedron.vtk create mode 100644 milena/mln/core/image/dmorph/mutable_extension_ima.hh copy milena/mln/{math/pi.hh => core/routine/mutable_extend.hh} (59%) copy milena/{tests/core/alias/dpoint2d.cc => mln/io/vtk/all.hh} (73%) create mode 100644 milena/mln/io/vtk/load.hh create mode 100644 milena/mln/io/vtk/save.hh create mode 100644 milena/mln/topo/connectivity_number_2d.hh create mode 100644 milena/mln/topo/connectivity_number_3d.hh delete mode 100644 milena/mln/topo/detach.hh create mode 100644 milena/mln/topo/detach_cell.hh create mode 100644 milena/mln/topo/detach_pair.hh create mode 100644 milena/mln/topo/detach_point.hh create mode 100644 milena/mln/topo/is_not_1d_isthmus.hh create mode 100644 milena/mln/topo/is_not_end_point.hh create mode 100644 milena/mln/topo/is_simple_pair.hh create mode 100644 milena/mln/topo/is_simple_point2d.hh create mode 100644 milena/mln/topo/is_simple_point3d.hh copy milena/mln/topo/{is_n_face.hh => no_constraint.hh} (64%) create mode 100644 milena/mln/topo/skeleton/priority_driven_thinning.hh create mode 100644 milena/mln/transform/fft.hh copy milena/tests/core/alias/{dpoint2d.cc => neighb2d.cc} (68%) copy milena/tests/io/{dump => vtk}/Makefile.am (70%) copy scribo/tests/preprocessing/deskew.cc => milena/tests/io/vtk/load_bin.cc (62%) copy milena/tests/{core/alias/dpoint2d.cc => io/vtk/load_save_bin.cc} (72%) create mode 100644 milena/tests/io/vtk/save.cc create mode 100644 milena/tests/make/attachment.cc create mode 100644 milena/tests/make/detachment.cc create mode 100644 milena/tests/topo/connectivity_numbers_2d.cc create mode 100644 milena/tests/topo/detach_pair.cc create mode 100644 milena/tests/topo/is_facet.cc create mode 100644 milena/tests/topo/is_simple_pair.cc copy scribo/tests/preprocessing/deskew.cc => milena/tests/topo/skeleton/breadth_first_thinning.cc (50%) create mode 100644 milena/tests/topo/skeleton/breadth_first_thinning_constrained.cc create mode 100644 milena/tests/topo/skeleton/priority_driven_thinning.cc create mode 100644 milena/tests/topo/skeleton/priority_driven_thinning_constrained.cc create mode 100644 milena/tests/transform/fft.cc create mode 100644 milena/tests/unit_test/cond_tests_fftw3 copy milena/tests/{core/alias/dpoint2d.cc => value/int_u32.cc} (74%) create mode 100644 milena/tools/compute_local_configurations.cc copy milena/{mln/math/pi.hh => tools/connectivity_numbers_3d.cc} (64%) create mode 100644 milena/tools/connectivity_numbers_3d.hh copy scribo/tests/preprocessing/rotate_90.cc => milena/tools/connectivity_numbers_3d_tbb.cc (61%) create mode 100644 milena/tools/connectivity_numbers_3d_tbb.hh create mode 100755 milena/tools/gen_cxx_lut copy scribo/tests/preprocessing/rotate_90.cc => milena/tools/simple_point3d_lut.cc (60%) create mode 100644 milena/tools/simple_point3d_lut.hh copy milena/{tests/core/alias/dpoint2d.cc => tools/simple_point3d_lut_26_6.cc} (73%) copy scribo/tests/preprocessing/crop.cc => milena/tools/simple_point3d_lut_tbb.cc (58%) create mode 100644 milena/tools/simple_point3d_lut_tbb.hh create mode 100644 milena/tools/test_simple_point3d_lut_26_6.cc hooks/post-receive -- Olena, a generic and efficient image processing platform