July 2009 - Olena-patches

[PATCH 02/10] Build the reference documentation in the source dir.
by Roland Levillain 13 Jul '09

13 Jul '09

* doc/Makefile.am (USER_REFMAN_PDF): Set to user-refman.pdf. (USER_REFMAN_HTML): Set to user-refman-html. (DEVEL_REFMAN_PDF): Set to devel/latex/refman.pdf. (DEVEL_REFMAN_HTML): Set to devel/html. (ref-doc-pdf, $(srcdir)/$(USER_REFMAN_PDF)) (ref-doc-html, $(srcdir)/$(USER_REFMAN_HTML)) (ref-doc-devel-pdf, $(srcdir)/$(DEVEL_REFMAN_PDF)) (ref-doc-devel-html, $(srcdir)/$(DEVEL_REFMAN_HTML)) (fake-doc): Adjust. * doc/ref_guide/Makefile.am (REF_GUIDE_HH): Set to $(srcdir)/ref_guide.hh. (REF_GUIDE_PDF): Set to $(srcdir)/ref_guide.pdf ($(REF_GUIDE_HH), $(REF_GUIDE_PDF)): Adjust. * doc/tutorial/Makefile.am (TUTORIAL_HH): Set to $(srcdir)/tutorial.hh. (TUTORIAL_PDF): Set to $(srcdir)/tutorial.pdf. ($(TUTORIAL_HH), $(TUTORIAL_PDF)): Adjust. * doc/white_paper/Makefile.am (WHITE_PAPER_HTML): Set to $(srcdir)/white_paper_html/index.html. (WHITE_PAPER_PDF): Set to $(srcdir)/white_paper.pdf. ($(WHITE_PAPER_HTML), $(WHITE_PAPER_PDF), fake-doc): Adjust rules. --- milena/ChangeLog | 26 +++++++++++++++++++++ milena/doc/Makefile.am | 44 +++++++++++++++++++++-------------- milena/doc/ref_guide/Makefile.am | 33 +++++++++++++++++++++++--- milena/doc/tutorial/Makefile.am | 34 ++++++++++++++++++++++++--- milena/doc/white_paper/Makefile.am | 34 +++++++++++++++++++++++++-- 5 files changed, 142 insertions(+), 29 deletions(-) diff --git a/milena/ChangeLog b/milena/ChangeLog index faac29e..223d1d8 100644 --- a/milena/ChangeLog +++ b/milena/ChangeLog @@ -1,5 +1,31 @@ 2009-07-13 Roland Levillain <roland(a)lrde.epita.fr> + Build the reference documentation in the source dir. + + * doc/Makefile.am (USER_REFMAN_PDF): Set to user-refman.pdf. + (USER_REFMAN_HTML): Set to user-refman-html. + (DEVEL_REFMAN_PDF): Set to devel/latex/refman.pdf. + (DEVEL_REFMAN_HTML): Set to devel/html. + (ref-doc-pdf, $(srcdir)/$(USER_REFMAN_PDF)) + (ref-doc-html, $(srcdir)/$(USER_REFMAN_HTML)) + (ref-doc-devel-pdf, $(srcdir)/$(DEVEL_REFMAN_PDF)) + (ref-doc-devel-html, $(srcdir)/$(DEVEL_REFMAN_HTML)) + (fake-doc): Adjust. + * doc/ref_guide/Makefile.am (REF_GUIDE_HH): Set to + $(srcdir)/ref_guide.hh. + (REF_GUIDE_PDF): Set to $(srcdir)/ref_guide.pdf + ($(REF_GUIDE_HH), $(REF_GUIDE_PDF)): Adjust. + * doc/tutorial/Makefile.am (TUTORIAL_HH): Set to + $(srcdir)/tutorial.hh. + (TUTORIAL_PDF): Set to $(srcdir)/tutorial.pdf. + ($(TUTORIAL_HH), $(TUTORIAL_PDF)): Adjust. + * doc/white_paper/Makefile.am (WHITE_PAPER_HTML): Set to + $(srcdir)/white_paper_html/index.html. + (WHITE_PAPER_PDF): Set to $(srcdir)/white_paper.pdf. + ($(WHITE_PAPER_HTML), $(WHITE_PAPER_PDF), fake-doc): Adjust rules. + +2009-07-13 Roland Levillain <roland(a)lrde.epita.fr> + Polish clean rules. * apps/statues/Makefile.am (CLEANFILES): Add diff --git a/milena/doc/Makefile.am b/milena/doc/Makefile.am index 57c3810..a7d4647 100644 --- a/milena/doc/Makefile.am +++ b/milena/doc/Makefile.am @@ -79,35 +79,43 @@ $(srcdir)/ref_guide/ref_guide.hh: fig-convert ## Vaucanson's doc build system. (Do not forget to adjust Doxyfiles.) # Doxygen PDF documentation outputs. -USER_REFMAN_PDF = $(srcdir)/user/latex/refman.pdf -ref-doc-pdf: $(USER_REFMAN_PDF) +USER_REFMAN_PDF = user-refman.pdf +ref-doc-pdf: $(srcdir)/$(USER_REFMAN_PDF) # FIXME: Split in two rules: one generating the LaTeX file from the # Doxyfile, and another one generating the PDF from the LaTeX source. # Moreover, the LaTeX to PDF rule could be factored using a suffix # rule (as in LRDE's share/). -$(USER_REFMAN_PDF): $(srcdir)/Doxyfile_user_pdf $(srcdir)/figures.stamp $(EXTRA_DEPS) - $(DOXYGEN) $< - cd $(srcdir)/user/latex && $(MAKE) pdf - -USER_REFMAN_HTML = $(srcdir)/user/html -ref-doc-html: $(USER_REFMAN_HTML) -$(USER_REFMAN_HTML): $(srcdir)/Doxyfile_user $(srcdir)/figures.stamp $(EXTRA_DEPS) - $(DOXYGEN) $< +$(srcdir)/$(USER_REFMAN_PDF): $(srcdir)/Doxyfile_user_pdf $(srcdir)/figures.stamp $(EXTRA_DEPS) + $(DOXYGEN) $< \ + && cd $(srcdir)/user/latex \ + && $(MAKE) pdf \ + && cp -f refman.pdf ../../$(USER_REFMAN_PDF) + +# FIXME: Careful, `user-refman-pdf' is a directory, and this make rule +# depends on its timestamp, which is wrong. +USER_REFMAN_HTML = user-refman-html +ref-doc-html: $(srcdir)/$(USER_REFMAN_HTML) +$(srcdir)/$(USER_REFMAN_HTML): $(srcdir)/Doxyfile_user $(srcdir)/figures.stamp $(EXTRA_DEPS) + $(DOXYGEN) $< \ + && rm -fr $(srcdir)/$(USER_REFMAN_HTML) \ + && mv $(srcdir)/user/html $(srcdir)/$(USER_REFMAN_HTML) # Doxygen HTML documentation output directories. -DEVEL_REFMAN_PDF = $(srcdir)/devel/latex/refman.pdf -ref-doc-devel-pdf: $(DEVEL_REFMAN_PDF) +DEVEL_REFMAN_PDF = devel/latex/refman.pdf +ref-doc-devel-pdf: $(srcdir)/$(DEVEL_REFMAN_PDF) # FIXME: Split in two rules: one generating the LaTeX file from the # Doxyfile, and another one generating the PDF from the LaTeX source. # Moreover, the LaTeX to PDF rule could be factored using a suffix # rule (as in LRDE's share/). -$(DEVEL_REFMAN_PDF): $(srcdir)/Doxyfile_devel_pdf $(srcdir)/figures.stamp $(EXTRA_DEPS) +$(srcdir)/$(DEVEL_REFMAN_PDF): $(srcdir)/Doxyfile_devel_pdf $(srcdir)/figures.stamp $(EXTRA_DEPS) $(DOXYGEN) $< cd $(srcdir)/devel/latex && $(MAKE) $(AM_MAKEFLAGS) -DEVEL_REFMAN_HTML = $(srcdir)/devel/html -ref-doc-devel-html: $(DEVEL_REFMAN_HTML) -$(DEVEL_REFMAN_HTML): $(srcdir)/Doxyfile_devel $(srcdir)/figures.stamp $(EXTRA_DEPS) +# FIXME: Careful, `devel/html' is a directory, and this make rule +# depends on its timestamp, which is wrong. +DEVEL_REFMAN_HTML = devel/html +ref-doc-devel-html: $(srcdir)/$(DEVEL_REFMAN_HTML) +$(srcdir)/$(DEVEL_REFMAN_HTML): $(srcdir)/Doxyfile_devel $(srcdir)/figures.stamp $(EXTRA_DEPS) $(DOXYGEN) $< ## ---------- ## @@ -303,10 +311,10 @@ fake-doc: touch $(srcdir)/Doxyfile_user touch $(srcdir)/Doxyfile_user_pdf cd $(srcdir) && test -d user || mkdir user - for d in $(USER_REFMAN_HTML) $(srcdir)/user/latex; do \ + for d in $(srcdir)/$(USER_REFMAN_HTML) $(srcdir)/user/latex; do \ if test -d $$d; then touch $$d; else mkdir $$d; fi; \ done - touch $(USER_REFMAN_PDF) + touch $(srcdir)/$(USER_REFMAN_PDF) # The converse of the previous rule, voiding the timestamps. .PHONY: void-doc diff --git a/milena/doc/ref_guide/Makefile.am b/milena/doc/ref_guide/Makefile.am index d1af059..f13074f 100644 --- a/milena/doc/ref_guide/Makefile.am +++ b/milena/doc/ref_guide/Makefile.am @@ -25,6 +25,29 @@ $(SPLIT_OUTPUTS_SRCDIR):$(IMG_SRCDIR):$(SPLIT_EXAMPLES_SRCDIR):" ref-guide: ref-guide-html ref-guide-pdf +# FIXME: As in milena/doc/Makefile.am, we should probably strip +# $(srcdir) prefixes from target variables, e.g. instead of: +# +# FOO = $(srcdir)/foo.pdf +# $(FOO): foo.tex bar.tex +# dist_doc_DATA = $(FOO) +# +# we should use: +# +# FOO = foo.pdf +# $(srcdir)/$(FOO): foo.tex bar.tex +# dist_doc_DATA = $(FOO) +# +# since it minimizes installation issues (see milena/doc/Makefile.am +# and Vaucanson's doc/Makefile.am). + +# FIXME: Distributed products should be generated in the source dir. +# That's actually the case, *but* the current solution is not clean +# and might break sometimes. The clean approach is to create a +# temporary directory, try to generate the documentation there, and +# move its contents to the source dir in case of success. If the +# product is a directory, also refresh a timestamp (in the source +# dir). # Intermediate product for the various doc targets of the parent # directory. @@ -32,20 +55,22 @@ ref-guide: ref-guide-html ref-guide-pdf # This is not a bug: REF_GUIDE_HH is meant to have a `.hh' # extension, since it is later parsed by Doxygen, which complains # about `.html' files. -REF_GUIDE_HH = ref_guide.hh +REF_GUIDE_HH = $(srcdir)/ref_guide.hh ref-guide-html: $(REF_GUIDE_HH) $(REF_GUIDE_HH): ref_guide.tex $(srcdir)/../figures.stamp $(DOC_SRCDIR)/tools/todoxygen.sh \ - $< $(DOC_SRCDIR)/ref_guide $(DOC_SRCDIR) + $< $(DOC_SRCDIR)/ref_guide $(DOC_SRCDIR) \ + && mv -f ref_guide.hh $(srcdir) # Final product. -REF_GUIDE_PDF = ref_guide.pdf +REF_GUIDE_PDF = $(srcdir)/ref_guide.pdf ref-guide-pdf: $(REF_GUIDE_PDF) $(REF_GUIDE_PDF): ref_guide.tex $(srcdir)/../figures.stamp TEXINPUTS=$(TEXINPUTS) pdflatex $< TEXINPUTS=$(TEXINPUTS) pdflatex $< - TEXINPUTS=$(TEXINPUTS) pdflatex $< + TEXINPUTS=$(TEXINPUTS) pdflatex $< \ + && mv -f ref_guide.pdf $(srcdir) # FIXME: Regenerating figures.stamp requires make to go back to the # parent directory. We already do the opposite (descending from diff --git a/milena/doc/tutorial/Makefile.am b/milena/doc/tutorial/Makefile.am index ea4a84a..5cd7464 100644 --- a/milena/doc/tutorial/Makefile.am +++ b/milena/doc/tutorial/Makefile.am @@ -24,25 +24,51 @@ TEXINPUTS = $(DOC_SRCDIR):$(OUTPUTS_SRCDIR):$(IMG_SRCDIR): tutorial: tutorial-html tutorial-pdf +# FIXME: As in milena/doc/Makefile.am, we should probably strip +# $(srcdir) prefixes from target variables, e.g. instead of: +# +# FOO = $(srcdir)/foo.pdf +# $(FOO): foo.tex bar.tex +# dist_doc_DATA = $(FOO) +# +# we should use: +# +# FOO = foo.pdf +# $(srcdir)/$(FOO): foo.tex bar.tex +# dist_doc_DATA = $(FOO) +# +# since it minimizes installation issues (see milena/doc/Makefile.am +# and Vaucanson's doc/Makefile.am). + +# FIXME: Distributed products should be generated in the source dir. +# That's actually the case, *but* the current solution is not clean +# and might break sometimes. The clean approach is to create a +# temporary directory, try to generate the documentation there, and +# move its contents to the source dir in case of success. If the +# product is a directory, also refresh a timestamp (in the source +# dir). + # Intermediate product for the various doc targets of the parent # directory. # # This is not a bug: TUTORIAL_HH is meant to have a `.hh' extension, # since it is later parsed by Doxygen, which complains about `.html' # files. -TUTORIAL_HH = tutorial.hh +TUTORIAL_HH = $(srcdir)/tutorial.hh tutorial-html: $(TUTORIAL_HH) $(TUTORIAL_HH): tutorial.tex $(srcdir)/../figures.stamp $(DOC_SRCDIR)/tools/todoxygen.sh \ - $< $(DOC_SRCDIR)/tutorial $(DOC_SRCDIR) + $< $(DOC_SRCDIR)/tutorial $(DOC_SRCDIR) \ + && mv tutorial.hh $(srcdir) # Final product. -TUTORIAL_PDF = tutorial.pdf +TUTORIAL_PDF = $(srcdir)/tutorial.pdf tutorial-pdf: $(TUTORIAL_PDF) $(TUTORIAL_PDF): tutorial.tex $(srcdir)/../figures.stamp TEXINPUTS=$(TEXINPUTS) pdflatex $< TEXINPUTS=$(TEXINPUTS) pdflatex $< - TEXINPUTS=$(TEXINPUTS) pdflatex $< + TEXINPUTS=$(TEXINPUTS) pdflatex $< \ + && tutorial.pdf $(srcdir) # FIXME: Regenerating figures.stamp requires make to go back to the # parent directory. We already do the opposite (descending from diff --git a/milena/doc/white_paper/Makefile.am b/milena/doc/white_paper/Makefile.am index 6449bbb..df0a51b 100644 --- a/milena/doc/white_paper/Makefile.am +++ b/milena/doc/white_paper/Makefile.am @@ -38,20 +38,46 @@ EPSS = $(PNGS:png=eps) white-paper: white-paper-pdf white-paper-html -WHITE_PAPER_HTML = white_paper_html/index.html +# FIXME: As in milena/doc/Makefile.am, we should probably strip +# $(srcdir) prefixes from target variables, e.g. instead of: +# +# FOO = $(srcdir)/foo.pdf +# $(FOO): foo.tex bar.tex +# dist_doc_DATA = $(FOO) +# +# we should use: +# +# FOO = foo.pdf +# $(srcdir)/$(FOO): foo.tex bar.tex +# dist_doc_DATA = $(FOO) +# +# since it minimizes installation issues (see milena/doc/Makefile.am +# and Vaucanson's doc/Makefile.am). + +# FIXME: Distributed products should be generated in the source dir. +# That's actually the case, *but* the current solution is not clean +# and might break sometimes. The clean approach is to create a +# temporary directory, try to generate the documentation there, and +# move its contents to the source dir in case of success. If the +# product is a directory, also refresh a timestamp (in the source +# dir). + +WHITE_PAPER_HTML = $(srcdir)/white_paper_html/index.html white-paper-html: $(WHITE_PAPER_HTML) $(WHITE_PAPER_HTML): white_paper.tex $(EPSS) test -d white_paper_html || mkdir white_paper_html TEXINPUTS=$(TEXINPUTS) hevea -O -fix $< -o $@ $(top_srcdir)/milena/doc/tools/clearbanner.sh $@ + mv -f white_paper_html $(srcdir) -WHITE_PAPER_PDF = white_paper.pdf +WHITE_PAPER_PDF = $(srcdir)/white_paper.pdf white-paper-pdf: $(WHITE_PAPER_PDF) $(WHITE_PAPER_PDF): white_paper.tex $(PNGS) TEXINPUTS=$(TEXINPUTS) pdflatex $< TEXINPUTS=$(TEXINPUTS) pdflatex $< - TEXINPUTS=$(TEXINPUTS) pdflatex $< + TEXINPUTS=$(TEXINPUTS) pdflatex $< \ + && mv white_paper.pdf $(srcdir) dist_doc_DATA = \ @@ -76,7 +102,9 @@ clean-local: # Pretend the documentation is up-to-date. .PHONY: fake-doc fake-doc: + test -d figures || mkdir figures touch $(EPSS) + test -d $(srcdir)/white_paper_html || mkdir $(srcdir)/white_paper_html touch $(WHITE_PAPER_HTML) touch $(WHITE_PAPER_PDF) -- 1.6.1.2

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[PATCH 01/10] Polish clean rules.
by Roland Levillain 13 Jul '09

13 Jul '09

* apps/statues/Makefile.am (CLEANFILES): Add teapot-max-curv-skel.off, teapot-complex-max-curv.off, socket-max-curv-segm.off, teapot-max-curv-segm.off, socket-complex-max-curv-segm.off, teapot-complex-max-curv-segm.off, socket-max-curv-skel.off, teapot-max-curv.off and three-triangles-skel.off. --- milena/ChangeLog | 11 +++++++++++ milena/apps/statues/Makefile.am | 14 ++++++++++++++ 2 files changed, 25 insertions(+), 0 deletions(-) diff --git a/milena/ChangeLog b/milena/ChangeLog index 5a7dda9..faac29e 100644 --- a/milena/ChangeLog +++ b/milena/ChangeLog @@ -1,3 +1,14 @@ +2009-07-13 Roland Levillain <roland(a)lrde.epita.fr> + + Polish clean rules. + + * apps/statues/Makefile.am (CLEANFILES): Add + teapot-max-curv-skel.off, teapot-complex-max-curv.off, + socket-max-curv-segm.off, teapot-max-curv-segm.off, + socket-complex-max-curv-segm.off, + teapot-complex-max-curv-segm.off, socket-max-curv-skel.off, + teapot-max-curv.off and three-triangles-skel.off. + 2009-07-08 Guillaume Lazzara <guillaume.lazzara(a)lrde.epita.fr> Make sure the documentation license is GPL v2. diff --git a/milena/apps/statues/Makefile.am b/milena/apps/statues/Makefile.am index 0baf887..0185535 100644 --- a/milena/apps/statues/Makefile.am +++ b/milena/apps/statues/Makefile.am @@ -39,6 +39,7 @@ LDADD_trimesh = -L$(top_builddir)/external/trimesh/libsrc -ltrimesh $(GLLIBS) bin_PROGRAMS = TESTS = +CLEANFILES = # FIXME: Have program names embed the type of structure used (either # graph or complex). @@ -59,6 +60,7 @@ if ENABLE_TRIMESH # mesh_segm_LDADD = $(LDADD_trimesh) # # TESTS += test-mesh-segm +# CLEANFILES += socket-segm.off teapot-segm.off # FIXME: mesh_skel is unfinished. Anyway, it should be superseded by # another program, using no Trimesh code. @@ -86,6 +88,7 @@ if ENABLE_TRIMESH mesh_max_curv_LDFLAGS = $(LDFLAGS_trimesh) mesh_max_curv_LDADD = $(LDADD_trimesh) TESTS += test-mesh-max-curv + CLEANFILES += teapot-max-curv-skel.off endif ENABLE_TRIMESH ## ---------------------------------------------------- ## @@ -106,6 +109,7 @@ EXTRA_DIST = trimesh/README bin_PROGRAMS += mesh-complex-max-curv mesh_complex_max_curv_SOURCES = mesh-complex-max-curv.cc TESTS += test-mesh-complex-max-curv +CLEANFILES += teapot-complex-max-curv.off # FIXME: Write a program showing the local minima (and maxima) of # scalar-valued complex-based mesh (to see the curvature extrema). @@ -115,6 +119,9 @@ TESTS += test-mesh-complex-max-curv bin_PROGRAMS += mesh-complex-segm mesh_complex_segm_SOURCES = mesh-complex-segm.cc TESTS += test-mesh-complex-segm +CLEANFILES += \ + socket-max-curv-segm.off \ + teapot-max-curv-segm.off # Program computing the max curvature from a mesh, then segmenting it. # The advantage of this program over `mesh-complex-segm' is that the @@ -125,6 +132,9 @@ TESTS += test-mesh-complex-segm bin_PROGRAMS += mesh-complex-max-curv-segm mesh_complex_max_curv_segm_SOURCES = mesh-complex-max-curv-segm.cc TESTS += test-mesh-complex-max-curv-segm +CLEANFILES += \ + socket-complex-max-curv-segm.off \ + teapot-complex-max-curv-segm.off # FIXME: Implement `mesh-complex-pinv-curv-segm' (factor as much # code as possible with `mesh-complex-max-curv-segm'. @@ -137,3 +147,7 @@ TESTS += test-mesh-complex-max-curv-segm bin_PROGRAMS += mesh-complex-skel mesh_complex_skel_SOURCES = mesh-complex-skel.cc save_bin_alt.hh TESTS += test-mesh-complex-skel +CLEANFILES += \ + socket-max-curv-skel.off \ + teapot-max-curv.off \ + three-triangles-skel.off -- 1.6.1.2

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r4265: Add US segmentation method
by Fabien Freling 10 Jul '09

10 Jul '09

URL: https://svn.lrde.epita.fr/svn/oln/trunk/milena/sandbox ChangeLog: 2009-07-10 Fabien Freling <fabien.freling(a)lrde.epita.fr> Add US segmentation method. * fabien/igr/Makefile: Add target. * fabien/igr/filter_morpho_us.cc: Segment US morpho images. * fabien/igr/segment_us_morpho.sh: New script for converting outputs. --- Makefile | 5 ++ filter_morpho_us.cc | 95 +++++++++++++++++++++++++++++++++++++++++++++++++++ segment_us_morpho.sh | 44 +++++++++++++++++++++++ 3 files changed, 144 insertions(+) Index: trunk/milena/sandbox/fabien/igr/filter_morpho_us.cc =================================================================== --- trunk/milena/sandbox/fabien/igr/filter_morpho_us.cc (revision 0) +++ trunk/milena/sandbox/fabien/igr/filter_morpho_us.cc (revision 4265) @@ -0,0 +1,95 @@ +#include <mln/core/image/image2d.hh> +#include <mln/core/alias/neighb2d.hh> +#include <mln/core/image/image3d.hh> +#include <mln/core/alias/neighb3d.hh> +#include <mln/core/image/dmorph/image_if.hh> +#include <mln/core/image/dmorph/slice_image.hh> +#include <mln/core/var.hh> +#include <mln/pw/all.hh> + +#include <mln/io/dump/all.hh> + +#include <mln/value/int_u8.hh> +#include <mln/value/label_16.hh> +#include <mln/value/rgb8.hh> + +#include <mln/binarization/threshold.hh> +#include <mln/data/convert.hh> +#include <mln/data/fill.hh> +#include <mln/data/paste.hh> +#include <mln/geom/bbox.hh> +#include <mln/labeling/blobs.hh> +#include <mln/labeling/fill_holes.hh> +#include <mln/labeling/n_max.hh> +#include <mln/literal/colors.hh> +#include <mln/morpho/closing/volume.hh> +#include <mln/morpho/opening/volume.hh> +#include <mln/morpho/elementary/gradient_external.hh> +#include <mln/util/array.hh> + +#include <mln/accu/transform.hh> +#include <mln/accu/maj_h.hh> + +#include <mln/win/disk2d.hh> + + +using namespace mln; +using value::int_u8; +using value::label_16; +using value::rgb8; + + +int main (int argc, char* argv[]) +{ + if (argc != 6) + { + std::cout << "Usage: " << argv[0] << " input closing threshold opening size" << std::endl; + return 1; + } + + unsigned lambda = atoi(argv[2]); + unsigned threshold = atoi(argv[3]); + unsigned opening_lambda = atoi(argv[4]); + unsigned size = atoi(argv[5]); + + image3d<int_u8> input; + io::dump::load(input, argv[1]); + image3d<rgb8> output = data::convert(rgb8(), input); + + image3d<int_u8> closing = morpho::closing::volume(input, c6(), lambda); + io::dump::save(closing, "closing.dump"); + + image3d<bool> thres = binarization::threshold(closing, threshold); + io::dump::save(thres, "threshold.dump"); + + image3d<bool> opening = morpho::opening::volume(thres, c6(), opening_lambda); + io::dump::save(opening, "opening.dump"); + + box<point3d> b = geom::bbox(opening); + label_16 nlabels; + accu::maj_h<bool> maj; + for (int slice_index = b.pmin().sli(); slice_index <= b.pmax().sli(); ++slice_index) + { + mln_VAR(slice_image, slice(opening, slice_index)); + mln_VAR(slice_out, slice(output, slice_index)); + mln_VAR(slice_blobs, labeling::blobs(slice_image, c4(), nlabels)); + util::array<label_16> nmax = labeling::n_max(slice_blobs, nlabels, 2); + data::fill((slice_image | pw::value(slice_blobs) != pw::cst(nmax[1])).rw(), false); + + // Filtering. + image2d<bool> maj_slice = accu::transform(slice_image, maj, win::disk2d(size)); + + mln_VAR(slice_blobs2, labeling::blobs(maj_slice, c4(), nlabels)); + mln_VAR(slice_noholes, labeling::fill_holes(duplicate(maj_slice), c4(), nlabels)); + data::fill((slice_image | pw::value(slice_noholes) == true).rw(), true); + + mln_VAR(gradient, morpho::elementary::gradient_external(slice_image, c4())); + + data::fill((slice_out | pw::value(gradient) == true).rw(), literal::red); + } + + io::dump::save(opening, "maj.dump"); + io::dump::save(output, "output.dump"); + + return 0; +} Index: trunk/milena/sandbox/fabien/igr/Makefile =================================================================== --- trunk/milena/sandbox/fabien/igr/Makefile (revision 4264) +++ trunk/milena/sandbox/fabien/igr/Makefile (revision 4265) @@ -82,6 +82,11 @@ ##################### +filter_morpho_us: filter_morpho_us.cc + ${CXX} -I../../../ -I../ ${CXXFLAGS} $^ -o filter_morpho_us + +##################### + clean: rm -rf *.dump *.p?m *.plot *.log *.csv *.dSYM rm seg2d seg3d wsd2d wsd3d nbasins_finder grad clo_vol wst graph med thres matlab time_max first_slice_dicom Index: trunk/milena/sandbox/fabien/igr/segment_us_morpho.sh =================================================================== --- trunk/milena/sandbox/fabien/igr/segment_us_morpho.sh (revision 0) +++ trunk/milena/sandbox/fabien/igr/segment_us_morpho.sh (revision 4265) @@ -0,0 +1,44 @@ +#!/bin/sh + + +process () +{ + nlabels=`./filter_morpho_us $@` +#if [ $? -gt 0 ]; then +# echo "error: filter_morpho_us failed" +# exit +# fi + + ../bin/dump2pgm8b closing.dump closing.pgm + convert closing.pgm 01_closing.png + rm closing.dump closing.pgm + + ../bin/dump2pbm threshold.dump 3 threshold.pbm + convert threshold.pbm 02_threshold.png + rm threshold.dump threshold.pbm + + ../bin/dump2pbm opening.dump 3 opening.pbm + convert opening.pbm 03_opening.png + rm opening.dump opening.pbm + + ../bin/dump2pbm maj.dump 3 maj.pbm + convert maj.pbm 05_maj.png + rm maj.dump maj.pbm + +#../bin/dumpl16_to_colorize blobs.dump 3 $nlabels blobs.ppm +# convert blobs.ppm 04_blobs.png +# rm blobs.dump blobs.ppm + + ../bin/dump2ppm output.dump output.ppm + convert output.ppm 06_output.png + rm output.dump output.ppm + + # Cleanup. +#rm *.pgm *.ppm +} + + +# $1 = input.dump +# $2 = lambda +# $3 = threshold +process $@ Property changes on: trunk/milena/sandbox/fabien/igr/segment_us_morpho.sh ___________________________________________________________________ Name: svn:executable + *

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Re: [Olena-patches] [Olena] #32: Improve the integration of Doxygen into the (autoconfiscated) package
by Olena Trac 10 Jul '09

10 Jul '09

#32: Improve the integration of Doxygen into the (autoconfiscated) package --------------------------+------------------------------------------------- Reporter: levill_r | Owner: levill_r Type: enhancement | Status: new Priority: trivial | Milestone: Olena 1.1 Component: Olena | Version: 1.0 Resolution: | Keywords: --------------------------+------------------------------------------------- Changes (by levill_r): * milestone: Olena 1.0 => Olena 1.1 -- Ticket URL: <https://trac.lrde.org/olena/ticket/32#comment:4> Olena <http://olena.lrde.epita.fr> Olena, a generic and efficient C++ image processing library.

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Re: [Olena-patches] [Olena] #81: Olena 1.0 Reference Documentation
by Olena Trac 10 Jul '09

10 Jul '09

#81: Olena 1.0 Reference Documentation -----------------------+---------------------------------------------------- Reporter: levill_r | Owner: Olena Team Type: task | Status: closed Priority: minor | Milestone: Olena 1.0 Component: Milena | Version: 1.0 Resolution: fixed | Keywords: doc -----------------------+---------------------------------------------------- Changes (by levill_r): * status: new => closed * resolution: => fixed -- Ticket URL: <https://trac.lrde.org/olena/ticket/81#comment:3> Olena <http://olena.lrde.epita.fr> Olena, a generic and efficient C++ image processing library.

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Re: [Olena-patches] [Olena] #80: Olena 1.0 User Documentation
by Olena Trac 10 Jul '09

10 Jul '09

#80: Olena 1.0 User Documentation -----------------------+---------------------------------------------------- Reporter: levill_r | Owner: Olena Team Type: task | Status: closed Priority: major | Milestone: Olena 1.0 Component: Milena | Version: 1.0 Resolution: fixed | Keywords: vaucanson doc -----------------------+---------------------------------------------------- Changes (by levill_r): * status: new => closed * resolution: => fixed -- Ticket URL: <https://trac.lrde.org/olena/ticket/80#comment:7> Olena <http://olena.lrde.epita.fr> Olena, a generic and efficient C++ image processing library.

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Re: [Olena-patches] [Olena] #82: Olena 1.0 Tutorial
by Olena Trac 10 Jul '09

10 Jul '09

#82: Olena 1.0 Tutorial -----------------------+---------------------------------------------------- Reporter: levill_r | Owner: Olena Team Type: task | Status: closed Priority: major | Milestone: Olena 1.0 Component: Milena | Version: 1.0 Resolution: fixed | Keywords: -----------------------+---------------------------------------------------- Changes (by levill_r): * status: new => closed * resolution: => fixed Comment: Closing; written by Guillaume Lazzara. -- Ticket URL: <https://trac.lrde.org/olena/ticket/82#comment:2> Olena <http://olena.lrde.epita.fr> Olena, a generic and efficient C++ image processing library.

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Re: [Olena-patches] [Olena] #83: Olena 1.0 Whitepaper
by Olena Trac 10 Jul '09

10 Jul '09

#83: Olena 1.0 Whitepaper -----------------------+---------------------------------------------------- Reporter: levill_r | Owner: Olena Team Type: task | Status: closed Priority: major | Milestone: Olena 1.0 Component: Milena | Version: 1.0 Resolution: fixed | Keywords: -----------------------+---------------------------------------------------- Changes (by levill_r): * status: new => closed * resolution: => fixed Comment: Closing; written by Guillaume Lazzara. -- Ticket URL: <https://trac.lrde.org/olena/ticket/83#comment:4> Olena <http://olena.lrde.epita.fr> Olena, a generic and efficient C++ image processing library.

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[Olena] #191: Support g++ 3.4
by Olena Trac 10 Jul '09

10 Jul '09

#191: Support g++ 3.4 -------------------------+-------------------------------------------------- Reporter: theo | Owner: theo Type: enhancement | Status: new Priority: critical | Milestone: Olena 1.0 Component: Milena | Version: 1.0 Keywords: | -------------------------+-------------------------------------------------- g++ 3.4 is the default compiler on Cygwin. -- Ticket URL: <https://trac.lrde.org/olena/ticket/191> Olena <http://olena.lrde.epita.fr> Olena, a generic and efficient C++ image processing library.

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[Olena] #211: BSD Make compatibility
by Olena Trac 10 Jul '09

10 Jul '09

#211: BSD Make compatibility -------------------------+-------------------------------------------------- Reporter: levill_r | Owner: Olena Team Type: enhancement | Status: new Priority: minor | Milestone: Olena 1.1 Component: Olena | Version: 1.0 Keywords: | -------------------------+-------------------------------------------------- FreeBSD's `make` does not like some of our Makefiles (like source:trunk/milena/doc/Makefile.am), which prevents users to compile the project using just `make` (however `gmake` just runs fine). On Mac OS X, the command `bsdmake` is probably the same as FreeBSD's natural `make`. On Debian, the package `pmake` seems to be close to FreeBSD's `make`. -- Ticket URL: <https://trac.lrde.org/olena/ticket/211> Olena <http://olena.lrde.epita.fr> Olena, a generic and efficient C++ image processing library.

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