- Olena-patches

olena-2.0-17-gbc142a1 Render the recorder morpher more generic.
by Roland Levillain 21 Jun '12

21 Jun '12

* apps/morphers/recorder.hh (recorder<I>::sequence): Store a sequence of concrete images. Add missing inline keywords. Improve the documentation. --- milena/ChangeLog | 9 +++++++++ milena/apps/morphers/recorder.hh | 11 +++++++---- 2 files changed, 16 insertions(+), 4 deletions(-) diff --git a/milena/ChangeLog b/milena/ChangeLog index 5d791e6..6f9f9f0 100644 --- a/milena/ChangeLog +++ b/milena/ChangeLog @@ -1,3 +1,12 @@ +2012-06-21 Roland Levillain <roland(a)lrde.epita.fr> + + Render the recorder morpher more generic. + + * apps/morphers/recorder.hh (recorder<I>::sequence): Store a + sequence of concrete images. + Add missing inline keywords. + Improve the documentation. + 2011-11-28 Roland Levillain <roland(a)lrde.epita.fr> New morpher example: recording a breadth-first thinning. diff --git a/milena/apps/morphers/recorder.hh b/milena/apps/morphers/recorder.hh index f8fc4f4..a2222a3 100644 --- a/milena/apps/morphers/recorder.hh +++ b/milena/apps/morphers/recorder.hh @@ -1,4 +1,4 @@ -// Copyright (C) 2011 EPITA Research and Development Laboratory (LRDE) +// Copyright (C) 2011, 2012 EPITA Research and Development Laboratory (LRDE) // // This file is part of Olena. // @@ -27,7 +27,8 @@ # define APPS_MORPHERS_RECORDER_HH /// \file -/// \brief Morpher recording every change in the morphed image. +/// \brief Morpher recording every change in the morphed image, +/// storing snapshots of the morphed image at each write operation. /// /// \todo Split and move this into the library? @@ -55,7 +56,7 @@ template <typename I> struct recorder; /* FIXME: mln::decorated_image lacks a proper definition of properties! (see mln/core/image/imorph/decorated_image.hh). We use the following (minimal) set of properties as a workaround for the - recorder decoration. */ + recorder decoration. */ namespace mln { namespace trait @@ -93,7 +94,7 @@ struct recorder sequence.push_back(mln::duplicate(ima)); } - std::vector<I> sequence; + std::vector<mln_concrete(I)> sequence; }; /* Skeleton of an image decorated with a recorder. @@ -151,6 +152,7 @@ namespace mln // Helper. template <typename I> +inline mln::decorated_image< I, recorder<I> > record(mln::Image<I>& ima) { @@ -162,6 +164,7 @@ record(mln::Image<I>& ima) namespace ppm { template <typename I> + inline void save(const mln::decorated_image< I, recorder<I> >& rec, const std::string& prefix) -- 1.7.2.5

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olena-2.0-20-g72ee021 Add rules to build and run apps/morphers/iz.
by Roland Levillain 20 Jun '12

20 Jun '12

* apps/morphers/Makefile.am (noinst_PROGRAMS): Add iz. (iz_SOURCES): New. (EXTRA_DIST): Add iz_input.pbm. (iz_output.ppm): New target. (MOSTLYCLEANFILES): Add tmp_clo.pgm, tmp_dmap.pgm, tmp_ws_superpose.ppm, tmp_ws.ppm, tmp_lab.pgm, tmp_iz.pgm, tmp_iz.ppm and tmp_iz_input.ppm. --- milena/ChangeLog | 12 ++++++++++++ milena/apps/morphers/Makefile.am | 19 +++++++++++++++++-- 2 files changed, 29 insertions(+), 2 deletions(-) diff --git a/milena/ChangeLog b/milena/ChangeLog index b6a62e7..c5eb04c 100644 --- a/milena/ChangeLog +++ b/milena/ChangeLog @@ -1,3 +1,15 @@ +2012-06-20 Roland Levillain <roland(a)lrde.epita.fr> + + Add rules to build and run apps/morphers/iz. + + * apps/morphers/Makefile.am (noinst_PROGRAMS): Add iz. + (iz_SOURCES): New. + (EXTRA_DIST): Add iz_input.pbm. + (iz_output.ppm): New target. + (MOSTLYCLEANFILES): Add tmp_clo.pgm, tmp_dmap.pgm, + tmp_ws_superpose.ppm, tmp_ws.ppm, tmp_lab.pgm, tmp_iz.pgm, + tmp_iz.ppm and tmp_iz_input.ppm. + 2012-06-20 Thierry Geraud <thierry.geraud(a)lrde.epita.fr> New example demonstrating the use of influence zones. diff --git a/milena/apps/morphers/Makefile.am b/milena/apps/morphers/Makefile.am index 5dbcc7e..fd5edda 100644 --- a/milena/apps/morphers/Makefile.am +++ b/milena/apps/morphers/Makefile.am @@ -28,7 +28,8 @@ noinst_PROGRAMS = \ recorder-bft \ recorder-wst \ mask+recorder \ - lazy_recorder + lazy_recorder \ + iz noinst_HEADERS = recorder.hh lazy_recorder.hh @@ -38,6 +39,12 @@ recorder_bft_SOURCES = recorder-bft.cc image2d-skel.hh recorder_wst_SOURCES = recorder-wst.cc mask_recorder_SOURCES = mask+recorder.cc lazy_recorder_SOURCES = lazy_recorder.cc +iz_SOURCES = iz.cc + +EXTRA_DIST = iz_input.pbm +# This target is phony: `iz' never writes `iz_output.ppm' actually. +iz_output.ppm: iz$(EXEEXT) iz_input.pbm + ./$< $(srcdir)/iz_input.pbm $@ MOSTLYCLEANFILES = \ lena-mask-channel.ppm \ @@ -45,7 +52,15 @@ MOSTLYCLEANFILES = \ lena-fill-lazy??????.ppm \ lena-bft??????.pbm \ lena-wst??????.ppm \ - lena-roi-fill??????.ppm + lena-roi-fill??????.ppm \ + tmp_clo.pgm \ + tmp_dmap.pgm \ + tmp_ws_superpose.ppm \ + tmp_ws.ppm \ + tmp_lab.pgm \ + tmp_iz.pgm \ + tmp_iz.ppm \ + tmp_iz_input.ppm # FIXME: Also produce movies (see comments in recorder.cc and # mask+recorder.cc.) -- 1.7.2.5

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olena-2.0-19-g3864857 New example demonstrating the use of influence zones.
by Thierry Geraud 20 Jun '12

20 Jun '12

* apps/morphers/iz.cc: New. * apps/morphers/iz_input.pbm: New. Signed-off-by: Roland Levillain <roland(a)lrde.epita.fr> --- milena/ChangeLog | 7 ++ milena/apps/morphers/iz.cc | 129 +++++++++++++++++++++++++++++++++++++ milena/apps/morphers/iz_input.pbm | Bin 0 -> 21890 bytes 3 files changed, 136 insertions(+), 0 deletions(-) create mode 100644 milena/apps/morphers/iz.cc create mode 100644 milena/apps/morphers/iz_input.pbm diff --git a/milena/ChangeLog b/milena/ChangeLog index 920aac7..b6a62e7 100644 --- a/milena/ChangeLog +++ b/milena/ChangeLog @@ -1,3 +1,10 @@ +2012-06-20 Thierry Geraud <thierry.geraud(a)lrde.epita.fr> + + New example demonstrating the use of influence zones. + + * apps/morphers/iz.cc: New. + * apps/morphers/iz_input.pbm: New. + 2012-06-21 Roland Levillain <roland(a)lrde.epita.fr> New ``lazy'' recorder morpher in apps/morpher. diff --git a/milena/apps/morphers/iz.cc b/milena/apps/morphers/iz.cc new file mode 100644 index 0000000..d02fd40 --- /dev/null +++ b/milena/apps/morphers/iz.cc @@ -0,0 +1,129 @@ +#include <mln/core/image/image2d.hh> +#include <mln/core/alias/neighb2d.hh> + +#include <mln/data/fill.hh> +#include <mln/data/paste.hh> +#include <mln/data/convert.hh> +#include <mln/data/saturate.hh> + +#include <mln/labeling/value.hh> +#include <mln/labeling/colorize.hh> + +#include <mln/morpho/watershed/superpose.hh> +#include <mln/morpho/watershed/flooding.hh> +#include <mln/morpho/elementary/dilation.hh> +#include <mln/morpho/closing/area.hh> +#include <mln/morpho/closing/structural.hh> + +#include <mln/transform/distance_front.hh> +#include <mln/transform/influence_zone_front.hh> + +#include <mln/pw/all.hh> +#include <mln/core/image/dmorph/image_if.hh> +#include <mln/core/image/dmorph/sub_image.hh> + +#include <mln/make/w_window2d.hh> + +#include <mln/io/pbm/load.hh> +#include <mln/io/pbm/save.hh> +#include <mln/io/pgm/save.hh> +#include <mln/io/ppm/save.hh> + +#include <mln/literal/colors.hh> + + + + +void usage(char* argv[]) +{ + std::cerr << "usage: " << argv[0] << " input.pbm output.ppm" << std::endl; + std::abort(); +} + + +int main(int argc, char* argv[]) +{ + using namespace mln; + using value::int_u8; + + if (argc != 3) + usage(argv); + + image2d<bool> input, clo; + io::pbm::load(input, argv[1]); + + + /// Structural closing. + clo = morpho::closing::structural(input, + win::rectangle2d(5, 17)); + + io::pbm::save(clo, "tmp_clo.pgm"); + + + /// Distance map computation. + int ww[] = { 00, 11, 0, 11, 0, + 11, 7, 5, 7, 11, + 00, 5, 0, 5, 0, + 11, 7, 5, 7, 11, + 00, 11, 0, 11, 0 }; + + + image2d<int_u8> dmap; + dmap = transform::distance_front(clo, + c4(), make::w_window2d(ww), + mln_max(int_u8)); + dmap = morpho::closing::area(dmap, c4(), 500); + + io::pgm::save(dmap, "tmp_dmap.pgm"); + + + unsigned nbasins; + image2d<unsigned> ws = morpho::watershed::flooding(dmap, + c4(), + nbasins); + + io::ppm::save(labeling::colorize(value::rgb8(), ws), "tmp_ws.ppm"); + + { + image2d<value::rgb8> ws_ = data::convert(value::rgb8(), input); + data::fill((ws_ | (pw::value(ws) == pw::cst(0))).rw(), literal::red); + io::ppm::save(ws_, "tmp_ws_superpose.ppm"); + + // test% g++ -I. main.cc -DNDEBUG -O2 + // main.cc: In function ‘int main(int, char**)’: + // main.cc:85: error: no matching function for call to ‘convert(mln::image2d<bool>&, mln::value::rgb8)’ + + // /// Convert the image \p input by changing the value type. + // /// + // /// \param[in] v A value of the destination type. + // /// \param[in] input The input image. + // // + // template <typename V, typename I> + // mln_ch_value(I, V) + // convert(const V& v, const Image<I>& input); + } + + + image2d<unsigned> lab(input.domain()); + data::fill(lab, 0); + + unsigned nlabels; + data::paste(labeling::value(ws | make::box2d(0,0,input.nrows()-1,0), + 0, c4(), nlabels), + lab); + + io::pgm::save(data::saturate(value::int_u8(), lab), "tmp_lab.pgm"); + + + data::paste(transform::influence_zone_front(lab | (pw::value(ws) == pw::cst(0)), + c8(), + make::w_window2d(ww)), + lab); + io::pgm::save(data::saturate(value::int_u8(), lab), "tmp_iz.pgm"); + + image2d<value::rgb8> output = labeling::colorize(value::rgb8(), lab); + io::ppm::save(output, "tmp_iz.ppm"); + + data::fill((output | pw::value(input)).rw(), literal::white); + io::ppm::save(output, "tmp_iz_input.ppm"); +} diff --git a/milena/apps/morphers/iz_input.pbm b/milena/apps/morphers/iz_input.pbm new file mode 100644 index 0000000..8470277 Binary files /dev/null and b/milena/apps/morphers/iz_input.pbm differ -- 1.7.2.5

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olena-2.0-32-gcfc65f3 Ensure `bootstrap -r' regenerates all files.
by Roland Levillain 20 Jun '12

20 Jun '12

* bootstrap: Here. Aesthetic changes. --- ChangeLog | 7 +++++++ bootstrap | 23 +++++++++++++++++------ 2 files changed, 24 insertions(+), 6 deletions(-) diff --git a/ChangeLog b/ChangeLog index 9b0ab2e..6d7436a 100644 --- a/ChangeLog +++ b/ChangeLog @@ -1,3 +1,10 @@ +2012-06-20 Roland Levillain <roland(a)lrde.epita.fr> + + Ensure `bootstrap -r' regenerates all files. + + * bootstrap: Here. + Aesthetic changes. + 2012-06-11 Roland Levillain <roland(a)lrde.epita.fr> Remove non-distributed headers not required by Milena nor Scribo. diff --git a/bootstrap b/bootstrap index 481a93e..cd810a4 100755 --- a/bootstrap +++ b/bootstrap @@ -164,6 +164,11 @@ require hevea 1.10 -version # Regen files stored in the repository if asked so. if $regen_p; then + # Generate `milena/headers.mk'. + (cd milena && ../build-aux/generate_dist_headers.sh mln headers.mk) + # Generate `scribo/headers.mk'. + (cd scribo && ../build-aux/generate_dist_headers.sh scribo headers.mk) + # Generate files of Milena's documentation. # * Figures. ( @@ -175,7 +180,7 @@ if $regen_p; then ) # * Examples. rm -f milena/doc/examples.mk.tmp - milena/doc/gen-make-variable EXAMPLES \ + milena/doc/gen-make-variable EXAMPLES \ `find milena/doc/examples -name '*.cc' | sed 's,^milena/doc,\$(srcdir),'` \ >milena/doc/examples.mk.tmp mv -f milena/doc/examples.mk.tmp milena/doc/examples.mk @@ -194,7 +199,7 @@ if $regen_p; then `find milena/doc/examples \ -name \*.cc -a \! -path milena/doc/examples/trash/\* \ | sed -e 's,milena/doc/examples/,,' \ - -e 'y,/,_,' \ + -e 'y,/,_,' \ -e 's,$.*$\.cc$,$(srcdir)/outputs/\1.txt,'` \ >milena/doc/outputs.mk.tmp mv -f milena/doc/outputs.mk.tmp milena/doc/outputs.mk @@ -220,10 +225,16 @@ if $regen_p; then ) fi -# Generate unit test files. -run . ./build-aux/build_unit_test.sh `pwd`/milena/mln milena/tests/unit_test milena/tests/unit_test/disabled_tests mln - -# Generate unit test files for Scribo. +# Generate unit tests files. These actions are not part of the `-r' +# option, since unit tests files are not stored in the repository. +# +# * Milena unit tests files. +run . ./build-aux/build_unit_test.sh \ + milena/mln \ + milena/tests/unit_test \ + milena/tests/unit_test/disabled_tests \ + mln +# *Scribo unit tests files. run . ./build-aux/build_unit_test.sh \ scribo/scribo \ scribo/tests/unit_test \ -- 1.7.2.5

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olena-2.0-114-gd1d6d84 scribo/binarization/all.hh: Add more includes.
by Guillaume Lazzara 20 Jun '12

20 Jun '12

--- scribo/ChangeLog | 4 ++++ scribo/scribo/binarization/all.hh | 12 ++++++++++-- 2 files changed, 14 insertions(+), 2 deletions(-) diff --git a/scribo/ChangeLog b/scribo/ChangeLog index 2445c0b..2d8c5e8 100644 --- a/scribo/ChangeLog +++ b/scribo/ChangeLog @@ -1,5 +1,9 @@ 2012-06-20 Guillaume Lazzara <z(a)lrde.epita.fr> + * scribo/binarization/all.hh: Add more includes. + +2012-06-20 Guillaume Lazzara <z(a)lrde.epita.fr> + * scribo/binarization/otsu_threshold.hh: Fix namespace ambiguities. 2012-05-22 Guillaume Lazzara <z(a)lrde.epita.fr> diff --git a/scribo/scribo/binarization/all.hh b/scribo/scribo/binarization/all.hh index 5530861..d05f996 100644 --- a/scribo/scribo/binarization/all.hh +++ b/scribo/scribo/binarization/all.hh @@ -1,5 +1,5 @@ -// Copyright (C) 2010, 2011 EPITA Research and Development Laboratory -// (LRDE) +// Copyright (C) 2010, 2011, 2012 EPITA Research and Development +// Laboratory (LRDE) // // This file is part of Olena. // @@ -46,11 +46,19 @@ namespace scribo # include <scribo/binarization/global_threshold.hh> # include <scribo/binarization/global_threshold_auto.hh> +# include <scribo/binarization/kim.hh> + # include <scribo/binarization/local_threshold.hh> +# include <scribo/binarization/niblack.hh> + +# include <scribo/binarization/otsu.hh> + # include <scribo/binarization/sauvola.hh> # include <scribo/binarization/sauvola_ms.hh> # include <scribo/binarization/sauvola_ms_split.hh> # include <scribo/binarization/sauvola_threshold.hh> +# include <scribo/binarization/wolf.hh> + #endif // ! SCRIBO_BINARIZATION_ALL_HH -- 1.7.2.5

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olena-2.0-113-g22aace9 scribo/binarization/otsu.hh: Fix namespace ambiguities.
by Guillaume Lazzara 20 Jun '12

20 Jun '12

--- scribo/ChangeLog | 4 ++++ scribo/scribo/binarization/otsu_threshold.hh | 11 ++++++----- 2 files changed, 10 insertions(+), 5 deletions(-) diff --git a/scribo/ChangeLog b/scribo/ChangeLog index ef55400..2445c0b 100644 --- a/scribo/ChangeLog +++ b/scribo/ChangeLog @@ -1,3 +1,7 @@ +2012-06-20 Guillaume Lazzara <z(a)lrde.epita.fr> + + * scribo/binarization/otsu_threshold.hh: Fix namespace ambiguities. + 2012-05-22 Guillaume Lazzara <z(a)lrde.epita.fr> Small fixes in Scribo. diff --git a/scribo/scribo/binarization/otsu_threshold.hh b/scribo/scribo/binarization/otsu_threshold.hh index fa2d725..b2407a0 100644 --- a/scribo/scribo/binarization/otsu_threshold.hh +++ b/scribo/scribo/binarization/otsu_threshold.hh @@ -1,4 +1,5 @@ -// Copyright (C) 2011 EPITA Research and Development Laboratory (LRDE) +// Copyright (C) 2011, 2012 EPITA Research and Development Laboratory +// (LRDE) // // This file is part of Olena. // @@ -77,13 +78,13 @@ namespace scribo /* calculation of probability density */ - util::array<double> pdf(hist.nvalues()); //probability distribution + mln::util::array<double> pdf(hist.nvalues()); //probability distribution for(unsigned i = 0; i< maxval; ++i) pdf[i] = (double)hist[i] / nsites; - util::array<double> cdf(hist.nvalues()); //cumulative probability distribution - util::array<double> myu(hist.nvalues()); // mean value for separation + mln::util::array<double> cdf(hist.nvalues()); //cumulative probability distribution + mln::util::array<double> myu(hist.nvalues()); // mean value for separation /* cdf & myu generation */ cdf[0] = pdf[0]; @@ -100,7 +101,7 @@ namespace scribo and determines optimal threshold value */ mln_value(I) threshold = literal::zero; double max_sigma = 0.0; - util::array<double> sigma(hist.nvalues()); // inter-class variance + mln::util::array<double> sigma(hist.nvalues()); // inter-class variance for(int i = 0; i < (maxval - 1); ++i) { -- 1.7.2.5

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last-svn-commit-276-g19e5634 Use package metadata macros instead of hard-coded strings in I/Os.
by Roland Levillain 15 Jun '12

15 Jun '12

* mln/io/fld/write_header.hh (mln::io::fld::write_header) * mln/io/off/save.hh (mln::io::off::internal::off_saver<I, E>::operator()) * mln/io/pnm/save_header.hh (mln::io::pnm::save_header) * mln/io/vtk/save.hh (mln::io::vtk::internal::vtk_saver<I, E>::operator()): Here. * mln/version.hh.in (OLN_PACKAGE_URL, OLN_PACKAGE_AUTHORS): New macros. --- milena/ChangeLog | 14 ++++++++++++++ milena/mln/io/fld/write_header.hh | 9 ++++++--- milena/mln/io/off/save.hh | 9 ++++++--- milena/mln/io/pnm/save_header.hh | 10 +++++++--- milena/mln/io/vtk/save.hh | 3 ++- milena/mln/version.hh.in | 6 ++++++ 6 files changed, 41 insertions(+), 10 deletions(-) diff --git a/milena/ChangeLog b/milena/ChangeLog index 5b3737b..cebc7f6 100644 --- a/milena/ChangeLog +++ b/milena/ChangeLog @@ -1,5 +1,19 @@ 2011-07-11 Roland Levillain <roland(a)lrde.epita.fr> + Use package metadata macros instead of hard-coded strings in I/Os. + + * mln/io/fld/write_header.hh (mln::io::fld::write_header) + * mln/io/off/save.hh + (mln::io::off::internal::off_saver<I, E>::operator()) + * mln/io/pnm/save_header.hh (mln::io::pnm::save_header) + * mln/io/vtk/save.hh + (mln::io::vtk::internal::vtk_saver<I, E>::operator()): + Here. + * mln/version.hh.in (OLN_PACKAGE_URL, OLN_PACKAGE_AUTHORS): + New macros. + +2011-07-11 Roland Levillain <roland(a)lrde.epita.fr> + No longer consider mln/version.hh.in as handled by autoheader. * mln/version.hh.in (OLN_PACKAGE_BUGREPORT, OLN_PACKAGE_NAME) diff --git a/milena/mln/io/fld/write_header.hh b/milena/mln/io/fld/write_header.hh index c803528..d49ac13 100644 --- a/milena/mln/io/fld/write_header.hh +++ b/milena/mln/io/fld/write_header.hh @@ -1,4 +1,4 @@ -// Copyright (C) 2008, 2009, 2010 EPITA Research and Development +// Copyright (C) 2008, 2009, 2010, 2011 EPITA Research and Development // Laboratory (LRDE) // // This file is part of Olena. @@ -34,8 +34,10 @@ # include <iostream> +# include <mln/version.hh> # include <mln/io/fld/header.hh> + namespace mln { @@ -58,8 +60,9 @@ namespace mln write_header(std::ostream& file, const fld_header& h) { file << "# AVS field file" << std::endl; - file << "# Generated by Milena 1.0 http://olena.lrde.epita.fr" << std::endl; - file << "# EPITA Research and Development Laboratory (LRDE)" << std::endl; + file << "# Generated by " OLN_PACKAGE_STRING " (" OLN_PACKAGE_URL ")" + << std::endl + << "# " OLN_PACKAGE_AUTHORS << std::endl; file << "ndim=" << h.ndim << std::endl; for (int i = 0; i < h.ndim; i++) diff --git a/milena/mln/io/off/save.hh b/milena/mln/io/off/save.hh index 1ec747d..ba50d6b 100644 --- a/milena/mln/io/off/save.hh +++ b/milena/mln/io/off/save.hh @@ -1,4 +1,5 @@ -// Copyright (C) 2008, 2009 EPITA Research and Development Laboratory (LRDE) +// Copyright (C) 2008, 2009, 2011 EPITA Research and Development +// Laboratory (LRDE) // // This file is part of Olena. // @@ -40,6 +41,7 @@ # include <string> +# include <mln/version.hh> # include <mln/core/alias/complex_image.hh> # include <mln/core/image/complex_neighborhoods.hh> # include <mln/core/image/complex_neighborhood_piter.hh> @@ -247,8 +249,9 @@ namespace mln ostr << "OFF" << std::endl; // A comment. - ostr << "# Generated by Milena 1.0 http://olena.lrde.epita.fr\n" - << "# EPITA Research and Development Laboratory (LRDE)" + ostr << "# Generated by " OLN_PACKAGE_STRING " (" OLN_PACKAGE_URL ")" + << std::endl + << "# " OLN_PACKAGE_AUTHORS << std::endl; /* ``The next line states the number of vertices, the number diff --git a/milena/mln/io/pnm/save_header.hh b/milena/mln/io/pnm/save_header.hh index 17f3dfe..0f49596 100644 --- a/milena/mln/io/pnm/save_header.hh +++ b/milena/mln/io/pnm/save_header.hh @@ -1,4 +1,5 @@ -// Copyright (C) 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009 EPITA Research and Development Laboratory (LRDE) +// Copyright (C) 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009, +// 2011 EPITA Research and Development Laboratory (LRDE) // // This file is part of Olena. // @@ -33,6 +34,8 @@ # include <iostream> # include <fstream> +# include <mln/version.hh> + # include <mln/io/pnm/max_component.hh> # include <mln/value/rgb.hh> @@ -76,11 +79,12 @@ namespace mln abort(); } file << "P" << type << std::endl; - file << "# Generated by Milena 1.0 http://olena.lrde.epita.fr" << std::endl; - file << "# EPITA Research and Development Laboratory (LRDE)" << std::endl; // We have a two-line comment because xv is buggy for some // tiny binary images and their workaround is to have such a // two-line comment... + file << "# Generated by " OLN_PACKAGE_STRING " (" OLN_PACKAGE_URL ")" + << std::endl + << "# " OLN_PACKAGE_AUTHORS << std::endl; file << geom::ncols(ima) << ' ' << geom::nrows(ima) << std::endl; mln_value(I) i; diff --git a/milena/mln/io/vtk/save.hh b/milena/mln/io/vtk/save.hh index 142608a..e3b8893 100644 --- a/milena/mln/io/vtk/save.hh +++ b/milena/mln/io/vtk/save.hh @@ -41,6 +41,7 @@ # include <string> +# include <mln/version.hh> # include <mln/core/alias/complex_image.hh> # include <mln/core/image/complex_neighborhoods.hh> # include <mln/core/image/complex_neighborhood_piter.hh> @@ -283,7 +284,7 @@ namespace mln character `\n'. The header is 256 characters maximum. The header can be used to describe the data and include any other pertinent information.'' */ - ostr << "Generated by Milena 1.0 http://olena.lrde.epita.fr" + ostr << "Generated by " OLN_PACKAGE_STRING " (" OLN_PACKAGE_URL ")" << std::endl; /* ``3. The next part is the file format. The file format diff --git a/milena/mln/version.hh.in b/milena/mln/version.hh.in index 1dd45dd..6612aa2 100644 --- a/milena/mln/version.hh.in +++ b/milena/mln/version.hh.in @@ -32,4 +32,10 @@ /// The version of this package. #define OLN_PACKAGE_VERSION "@PACKAGE_VERSION@" +/// Home page for this package. +#define OLN_PACKAGE_URL "@PACKAGE_URL@" + +/// Authors of the package. +#define OLN_PACKAGE_AUTHORS "EPITA Research and Development Laboratory (LRDE)" + #endif // ! MLN_VERSION_HH -- 1.7.2.5

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last-svn-commit-277-gc7ca4da Add a VTK output routine in apps/generic-skel.
by Roland Levillain 15 Jun '12

15 Jun '12

* apps/generic-skel/image3d-skel.hh: Aesthetic changes. (save_vtk_polygons): New function. Use it... * apps/generic-skel/image3d-skel-unconstrained.cc, * apps/generic-skel/image3d-skel-with-end-points.cc: ...here, to save images in VTK format. * apps/generic-skel/Makefile.am (MOSTLYCLEANFILES): Add image3d-skel-unconstrained-input.vtk, image3d-skel-unconstrained-skel.vtk, image3d-skel-with-end-points-input.vtk and image3d-skel-with-end-points-skel.vtk, --- milena/ChangeLog | 16 +++ milena/apps/generic-skel/Makefile.am | 4 + .../generic-skel/image3d-skel-unconstrained.cc | 2 + .../generic-skel/image3d-skel-with-end-points.cc | 2 + milena/apps/generic-skel/image3d-skel.hh | 108 +++++++++++++++++++- 5 files changed, 129 insertions(+), 3 deletions(-) diff --git a/milena/ChangeLog b/milena/ChangeLog index cebc7f6..52e8f97 100644 --- a/milena/ChangeLog +++ b/milena/ChangeLog @@ -1,5 +1,21 @@ 2011-07-11 Roland Levillain <roland(a)lrde.epita.fr> + Add a VTK output routine in apps/generic-skel. + + * apps/generic-skel/image3d-skel.hh: Aesthetic changes. + (save_vtk_polygons): New function. + Use it... + * apps/generic-skel/image3d-skel-unconstrained.cc, + * apps/generic-skel/image3d-skel-with-end-points.cc: + ...here, to save images in VTK format. + * apps/generic-skel/Makefile.am (MOSTLYCLEANFILES): + Add image3d-skel-unconstrained-input.vtk, + image3d-skel-unconstrained-skel.vtk, + image3d-skel-with-end-points-input.vtk and + image3d-skel-with-end-points-skel.vtk, + +2011-07-11 Roland Levillain <roland(a)lrde.epita.fr> + Use package metadata macros instead of hard-coded strings in I/Os. * mln/io/fld/write_header.hh (mln::io::fld::write_header) diff --git a/milena/apps/generic-skel/Makefile.am b/milena/apps/generic-skel/Makefile.am index 425668c..ad89544 100644 --- a/milena/apps/generic-skel/Makefile.am +++ b/milena/apps/generic-skel/Makefile.am @@ -79,9 +79,13 @@ TESTS += \ # FIXME: Rename all outputs to have their names use their generator as prefix. MOSTLYCLEANFILES = \ image3d-skel-unconstrained-input.raw \ + image3d-skel-unconstrained-input.vtk \ image3d-skel-unconstrained-skel.raw \ + image3d-skel-unconstrained-skel.vtk \ image3d-skel-with-end-points-input.raw \ + image3d-skel-with-end-points-input.vtk \ image3d-skel-with-end-points-skel.raw \ + image3d-skel-with-end-points-skel.vtk \ picasso-skel-unconstrained.pbm \ picasso-skel-with-end-points.pbm \ tiny-skel-unconstrained.pbm \ diff --git a/milena/apps/generic-skel/image3d-skel-unconstrained.cc b/milena/apps/generic-skel/image3d-skel-unconstrained.cc index 954c00c..65ef1c1 100644 --- a/milena/apps/generic-skel/image3d-skel-unconstrained.cc +++ b/milena/apps/generic-skel/image3d-skel-unconstrained.cc @@ -76,6 +76,7 @@ int main() std::cerr << input.domain() << std::endl; save_raw_3d(input, "image3d-skel-unconstrained-input.raw"); + save_vtk_polygons(input, "image3d-skel-unconstrained-input.vtk"); // FIXME: Debug. unsigned n_fg_comps; @@ -101,4 +102,5 @@ int main() is_simple, detach); save_raw_3d(output, "image3d-skel-unconstrained-skel.raw"); + save_vtk_polygons(output, "image3d-skel-unconstrained-skel.vtk"); } diff --git a/milena/apps/generic-skel/image3d-skel-with-end-points.cc b/milena/apps/generic-skel/image3d-skel-with-end-points.cc index f692cde..e5c3774 100644 --- a/milena/apps/generic-skel/image3d-skel-with-end-points.cc +++ b/milena/apps/generic-skel/image3d-skel-with-end-points.cc @@ -77,6 +77,7 @@ int main() std::cerr << input.domain() << std::endl; save_raw_3d(input, "image3d-skel-with-end-points-input.raw"); + save_vtk_polygons(input, "image3d-skel-with-end-points-input.vtk"); // FIXME: Debug. unsigned n_fg_comps; @@ -109,4 +110,5 @@ int main() detach, constraint); save_raw_3d(output, "image3d-skel-with-end-points-skel.raw"); + save_vtk_polygons(output, "image3d-skel-with-end-points-skel.vtk"); } diff --git a/milena/apps/generic-skel/image3d-skel.hh b/milena/apps/generic-skel/image3d-skel.hh index ed8f7ae..7abf4fb 100644 --- a/milena/apps/generic-skel/image3d-skel.hh +++ b/milena/apps/generic-skel/image3d-skel.hh @@ -30,14 +30,24 @@ #ifndef APPS_GENERIC_SKEL_IMAGE3D_SKEL_HH # define APPS_GENERIC_SKEL_IMAGE3D_SKEL_HH +#include <mln/version.hh> + #include <mln/core/image/image3d.hh> #include <mln/math/sqr.hh> #include <mln/math/sqrt.hh> +/*------. +| I/O. | +`------*/ + // FIXME: Do not use a dedicated I/O routines. Either convert the data -// to another format, or move this routine into mln/io. +// to another format, or move thess routines into mln/io. + +// -------------------- // +// PGM (3D extension). // +// -------------------- // mln::image3d<bool> load_pgm_3d(const std::string& filename) @@ -81,6 +91,10 @@ load_pgm_3d(const std::string& filename) return ima; } +// ------------- // +// Raw 3D data. // +// ------------- // + void save_raw_3d(const mln::image3d<bool>& ima, const std::string& filename) { @@ -90,6 +104,94 @@ save_raw_3d(const mln::image3d<bool>& ima, const std::string& filename) file << static_cast<char>(ima(p) ? 0xff : 0x00); } +// ----- // +// VTK. // +// ----- // + +// Save a binary 3D image as a VTK file where each voxel is +// represented by a cube decomposed in 6 square faces. +void +save_vtk_polygons(const mln::image3d<bool>& ima, + const std::string& filename) +{ + std::ofstream file(filename.c_str()); + + // Header. + file + << "# vtk DataFile Version 2.0" << std::endl + << "Generated by " OLN_PACKAGE_STRING " (" OLN_PACKAGE_URL ")" << std::endl + << "ASCII" << std::endl + << std::endl; + + // Number of object (foreground) sites to represent as a cube. + unsigned ncubes = 0; + mln_piter_(mln::image3d<bool>) p(ima.domain()); + for_all(p) + if (ima(p)) + ++ncubes; + + /* FIXME: The current approach duplicates some of the vertices (when + they are shared by two cubes or more). */ + + // Points (locations). + file << "DATASET POLYDATA" << std::endl; + // Each site (voxel) is defined by the location of its 8 corners. + file << "POINTS " << ncubes * 8 << " float" << std::endl; + + // ``Radius'' (half-length) of a cube. + float r = 0.5; + + // Cubes (voxels). + for_all(p) + if (ima(p)) + file << p[0] - r << ' ' << p[1] - r << ' ' << p[2] - r << " " + << p[0] + r << ' ' << p[1] - r << ' ' << p[2] - r << " " + << p[0] + r << ' ' << p[1] + r << ' ' << p[2] - r << " " + << p[0] - r << ' ' << p[1] + r << ' ' << p[2] - r << " " + << p[0] - r << ' ' << p[1] - r << ' ' << p[2] + r << " " + << p[0] + r << ' ' << p[1] - r << ' ' << p[2] + r << " " + << p[0] + r << ' ' << p[1] + r << ' ' << p[2] + r << " " + << p[0] - r << ' ' << p[1] + r << ' ' << p[2] + r + << std::endl; + file << std::endl; + + /* FIXME: The current approach duplicates some of the faces (when + they are shared by two squares). */ + + // Decompose each cube as a set of squares (polygons). + file << "POLYGONS " + // Each square has 6 faces + << ncubes * 6 << ' ' + /* Each square face requires 5 parameters: 1 for the number of + vertices of the polygon (always `4'), and 4 for the indices of + the vertices of this polygon. */ + << ncubes * 6 * (1 + 4) << std::endl; + + // ``Draw'' the 6 faces of each cube. + for (unsigned i = 0; i < ncubes; ++i) + { + /* Vertices. The 8 vertices of associated with the `i'-th cube + have indices `8 * i' to `8 * i + 7'. */ + unsigned v[8] = + { 8 * i + 0, 8 * i + 1, 8 * i + 2, 8 * i + 3, + 8 * i + 4, 8 * i + 5, 8 * i + 6, 8 * i + 7 }; + // Square faces. + file + << "4 " << v[0] << ' ' << v[1] << ' ' << v[2] << ' ' << v[3] << '\n' + << "4 " << v[4] << ' ' << v[5] << ' ' << v[6] << ' ' << v[7] << '\n' + << "4 " << v[0] << ' ' << v[1] << ' ' << v[5] << ' ' << v[4] << '\n' + << "4 " << v[2] << ' ' << v[3] << ' ' << v[7] << ' ' << v[6] << '\n' + << "4 " << v[0] << ' ' << v[4] << ' ' << v[7] << ' ' << v[3] << '\n' + << "4 " << v[1] << ' ' << v[2] << ' ' << v[6] << ' ' << v[5] << '\n' + << std::flush; + } +} + + +/*--------------. +| Subsampling. | +`--------------*/ + // FIXME: Again, this is a dedicated routine. Use something from // subsample. mln::image3d<bool> @@ -97,11 +199,11 @@ subsampling_3d(const mln::image3d<bool>& input, unsigned factor) { using namespace mln; typedef image3d<bool> I; - /* This subsampling procedure may not tak into account pixels at the + /* This subsampling procedure may not take into account pixels at the end of each sloce/row/column if the corresponding dimension is not a multiple of FACTOR. */ I output(input.nslices() / factor, - input.nrows() / factor, + input.nrows() / factor, input.ncols() / factor); mln_piter_(I) po(output.domain()); for_all(po) -- 1.7.2.5

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last-svn-commit-278-g2278386 Introduce a better VTK output routine in apps/generic-skel.
by Roland Levillain 15 Jun '12

15 Jun '12

* apps/generic-skel/image3d-skel.hh (save_vtk_polyhedrons): New function. Use it... * apps/generic-skel/image3d-skel-unconstrained.cc, * apps/generic-skel/image3d-skel-with-end-points.cc: ...here, instead of save_vtk_polygons. --- milena/ChangeLog | 11 +++ .../generic-skel/image3d-skel-unconstrained.cc | 4 +- .../generic-skel/image3d-skel-with-end-points.cc | 4 +- milena/apps/generic-skel/image3d-skel.hh | 79 ++++++++++++++++++++ 4 files changed, 94 insertions(+), 4 deletions(-) diff --git a/milena/ChangeLog b/milena/ChangeLog index 52e8f97..b894eaa 100644 --- a/milena/ChangeLog +++ b/milena/ChangeLog @@ -1,5 +1,16 @@ 2011-07-11 Roland Levillain <roland(a)lrde.epita.fr> + Introduce a better VTK output routine in apps/generic-skel. + + * apps/generic-skel/image3d-skel.hh (save_vtk_polyhedrons): + New function. + Use it... + * apps/generic-skel/image3d-skel-unconstrained.cc, + * apps/generic-skel/image3d-skel-with-end-points.cc: + ...here, instead of save_vtk_polygons. + +2011-07-11 Roland Levillain <roland(a)lrde.epita.fr> + Add a VTK output routine in apps/generic-skel. * apps/generic-skel/image3d-skel.hh: Aesthetic changes. diff --git a/milena/apps/generic-skel/image3d-skel-unconstrained.cc b/milena/apps/generic-skel/image3d-skel-unconstrained.cc index 65ef1c1..236361d 100644 --- a/milena/apps/generic-skel/image3d-skel-unconstrained.cc +++ b/milena/apps/generic-skel/image3d-skel-unconstrained.cc @@ -76,7 +76,7 @@ int main() std::cerr << input.domain() << std::endl; save_raw_3d(input, "image3d-skel-unconstrained-input.raw"); - save_vtk_polygons(input, "image3d-skel-unconstrained-input.vtk"); + save_vtk_polyhedrons(input, "image3d-skel-unconstrained-input.vtk"); // FIXME: Debug. unsigned n_fg_comps; @@ -102,5 +102,5 @@ int main() is_simple, detach); save_raw_3d(output, "image3d-skel-unconstrained-skel.raw"); - save_vtk_polygons(output, "image3d-skel-unconstrained-skel.vtk"); + save_vtk_polyhedrons(output, "image3d-skel-unconstrained-skel.vtk"); } diff --git a/milena/apps/generic-skel/image3d-skel-with-end-points.cc b/milena/apps/generic-skel/image3d-skel-with-end-points.cc index e5c3774..32f3634 100644 --- a/milena/apps/generic-skel/image3d-skel-with-end-points.cc +++ b/milena/apps/generic-skel/image3d-skel-with-end-points.cc @@ -77,7 +77,7 @@ int main() std::cerr << input.domain() << std::endl; save_raw_3d(input, "image3d-skel-with-end-points-input.raw"); - save_vtk_polygons(input, "image3d-skel-with-end-points-input.vtk"); + save_vtk_polyhedrons(input, "image3d-skel-with-end-points-input.vtk"); // FIXME: Debug. unsigned n_fg_comps; @@ -110,5 +110,5 @@ int main() detach, constraint); save_raw_3d(output, "image3d-skel-with-end-points-skel.raw"); - save_vtk_polygons(output, "image3d-skel-with-end-points-skel.vtk"); + save_vtk_polyhedrons(output, "image3d-skel-with-end-points-skel.vtk"); } diff --git a/milena/apps/generic-skel/image3d-skel.hh b/milena/apps/generic-skel/image3d-skel.hh index 7abf4fb..051a50d 100644 --- a/milena/apps/generic-skel/image3d-skel.hh +++ b/milena/apps/generic-skel/image3d-skel.hh @@ -187,6 +187,85 @@ save_vtk_polygons(const mln::image3d<bool>& ima, } } +// Save a binary 3D image as a VTK file where each voxel is +// represented by a cube (voxel polyhedron). This routine generates +// smaller files than save_vtk_polygons. +void +save_vtk_polyhedrons(const mln::image3d<bool>& ima, + const std::string& filename) +{ + std::ofstream file(filename.c_str()); + + // Header. + file + << "# vtk DataFile Version 2.0" << std::endl + << "Generated by " OLN_PACKAGE_STRING " (" OLN_PACKAGE_URL ")" << std::endl + << "ASCII" << std::endl + << std::endl; + + // Number of object (foreground) sites to represent as a cube. + unsigned ncubes = 0; + mln_piter_(mln::image3d<bool>) p(ima.domain()); + for_all(p) + if (ima(p)) + ++ncubes; + + /* FIXME: The current approach duplicates some of the vertices (when + they are shared by two cubes or more). */ + + // Points (locations). + file << "DATASET UNSTRUCTURED_GRID" << std::endl; + // Each site (voxel) is defined by the location of its 8 corners. + file << "POINTS " << ncubes * 8 << " float" << std::endl; + + // ``Radius'' (half-length) of a cube. + float r = 0.5; + + // Cubes (voxels). + for_all(p) + if (ima(p)) + file << p[0] - r << ' ' << p[1] - r << ' ' << p[2] - r << " " + << p[0] + r << ' ' << p[1] - r << ' ' << p[2] - r << " " + << p[0] + r << ' ' << p[1] + r << ' ' << p[2] - r << " " + << p[0] - r << ' ' << p[1] + r << ' ' << p[2] - r << " " + << p[0] - r << ' ' << p[1] - r << ' ' << p[2] + r << " " + << p[0] + r << ' ' << p[1] - r << ' ' << p[2] + r << " " + << p[0] + r << ' ' << p[1] + r << ' ' << p[2] + r << " " + << p[0] - r << ' ' << p[1] + r << ' ' << p[2] + r + << std::endl; + file << std::endl; + + // Create a polyhedron for each voxel. + file << "CELLS " << ncubes << ' ' + /* Each cubes (VTK_VOXEL) requires 9 parameters: 1 for the number + of vertices of the cube (always `8'), and 8 for the indices of + the vertices of this polyhedron. */ + << ncubes * (1 + 8) << std::endl; + + // ``Draw'' the 6 faces of each cube. + for (unsigned i = 0; i < ncubes; ++i) + { + /* Vertices. The 8 vertices of associated with the `i'-th cube + have indices `8 * i' to `8 * i + 7'. */ + unsigned v[8] = + { 8 * i + 0, 8 * i + 1, 8 * i + 2, 8 * i + 3, + 8 * i + 4, 8 * i + 5, 8 * i + 6, 8 * i + 7 }; + // The order of the vertices follows the conventions of the VTK + // file format specification. + file << "8 " + << v[0] << ' ' << v[1] << ' ' << v[3] << ' ' << v[2] << ' ' + << v[4] << ' ' << v[5] << ' ' << v[7] << ' ' << v[6] + << std::endl; + } + file << std::endl; + + // Announce the type of cells used. + file << "CELL_TYPES " << ncubes << std::endl; + for (unsigned i = 0; i < ncubes; ++i) + // The VTK_VERTEX cell type has number `11'. + file << 11 << std::endl; +} + /*--------------. | Subsampling. | -- 1.7.2.5

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last-svn-commit-279-g7a9ba19 apps/generic-skel/image3d-skel.hh: Add `inline' qualifiers.
by Roland Levillain 15 Jun '12

15 Jun '12

--- milena/ChangeLog | 4 ++++ milena/apps/generic-skel/image3d-skel.hh | 7 +++++++ 2 files changed, 11 insertions(+), 0 deletions(-) diff --git a/milena/ChangeLog b/milena/ChangeLog index b894eaa..f329d34 100644 --- a/milena/ChangeLog +++ b/milena/ChangeLog @@ -1,3 +1,7 @@ +2011-07-12 Roland Levillain <roland(a)lrde.epita.fr> + + * apps/generic-skel/image3d-skel.hh: Add `inline' qualifiers. + 2011-07-11 Roland Levillain <roland(a)lrde.epita.fr> Introduce a better VTK output routine in apps/generic-skel. diff --git a/milena/apps/generic-skel/image3d-skel.hh b/milena/apps/generic-skel/image3d-skel.hh index 051a50d..2db9a5a 100644 --- a/milena/apps/generic-skel/image3d-skel.hh +++ b/milena/apps/generic-skel/image3d-skel.hh @@ -49,6 +49,7 @@ // PGM (3D extension). // // -------------------- // +inline mln::image3d<bool> load_pgm_3d(const std::string& filename) { @@ -95,6 +96,7 @@ load_pgm_3d(const std::string& filename) // Raw 3D data. // // ------------- // +inline void save_raw_3d(const mln::image3d<bool>& ima, const std::string& filename) { @@ -110,6 +112,7 @@ save_raw_3d(const mln::image3d<bool>& ima, const std::string& filename) // Save a binary 3D image as a VTK file where each voxel is // represented by a cube decomposed in 6 square faces. +inline void save_vtk_polygons(const mln::image3d<bool>& ima, const std::string& filename) @@ -190,6 +193,7 @@ save_vtk_polygons(const mln::image3d<bool>& ima, // Save a binary 3D image as a VTK file where each voxel is // represented by a cube (voxel polyhedron). This routine generates // smaller files than save_vtk_polygons. +inline void save_vtk_polyhedrons(const mln::image3d<bool>& ima, const std::string& filename) @@ -273,6 +277,7 @@ save_vtk_polyhedrons(const mln::image3d<bool>& ima, // FIXME: Again, this is a dedicated routine. Use something from // subsample. +inline mln::image3d<bool> subsampling_3d(const mln::image3d<bool>& input, unsigned factor) { @@ -326,6 +331,7 @@ subsampling_3d(const mln::image3d<bool>& input, unsigned factor) /// the torus. /// \param int_radius Internal radius of the torus. /// \param ext_radius External radius of the torus. +inline void draw_torus(mln::image3d<bool>& ima, unsigned axis_dim, unsigned int_radius, unsigned ext_radius) @@ -371,6 +377,7 @@ draw_torus(mln::image3d<bool>& ima, unsigned axis_dim, } /// Create a 3D image containing three intersecting tori. +inline mln::image3d<bool> make_triple_torus(mln::def::coord half_len = 100) { -- 1.7.2.5

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