[Olena-patches] r3526: Find threshold value thanks to watershed

URL: https://svn.lrde.epita.fr/svn/oln/trunk/milena/sandbox ChangeLog: 2009-03-13 Fabien Freling &lt;fabien.freling(a)lrde.epita.fr&gt; Find threshold value thanks to watershed. * fabien/bin/dumpi12_to_pgm.cc: New tool. * fabien/igr/Makefile: Update. * fabien/igr/check.sh: Update. * fabien/igr/graph.cc: Update. * fabien/igr/med.cc: Find median region value. * fabien/igr/thres.cc: Threshold image. --- TODO | 8 +++- bin/dumpi12_to_pgm.cc | 55 +++++++++++++++++++++++++++++++ igr/Makefile | 6 +++ igr/check.sh | 37 +++++++++++++-------- igr/graph.cc | 13 ++++++- igr/med.cc | 87 ++++++++++++++++++++++++++++++++++++++++++++++++++ igr/thres.cc | 67 ++++++++++++++++++++++++++++++++++++++ 7 files changed, 256 insertions(+), 17 deletions(-) Index: trunk/milena/sandbox/fabien/igr/graph.cc =================================================================== --- trunk/milena/sandbox/fabien/igr/graph.cc (revision 3525) +++ trunk/milena/sandbox/fabien/igr/graph.cc (revision 3526) @@ -11,11 +11,13 @@ #include <mln/io/dump/all.hh> #include <mln/io/dicom/load.hh> #include <mln/io/pgm/save.hh> +#include <mln/io/ppm/save.hh> #include <mln/value/int_u8.hh> #include <mln/value/int_u12.hh> #include <mln/value/label_16.hh> #include <mln/value/label_32.hh> +#include <mln/value/rgb8.hh> #include <mln/morpho/watershed/flooding.hh> @@ -53,6 +55,8 @@ #include <mln/extract/all.hh> #include <mln/make/region_adjacency_graph.hh> +#include <mln/debug/colorize.hh> + @@ -241,6 +245,7 @@ using value::int_u12; using value::label_16; using value::label_32; + using value::rgb8; typedef label_32 L; if (argc != 6) @@ -315,8 +320,12 @@ mln_VAR(wsd2_, morpho::elementary::dilation(extend(wsd2 | (pw::value(wsd2) == 0u), wsd2), c8())); data::fill((wsd2 | (pw::value(wsd2) == 0u)).rw(), wsd2_); - io::pgm::save(level::stretch(int_u8(), labeling::mean_values(dcm, wshed, nbasins)), "wsd_original.pgm"); - io::pgm::save(level::stretch(int_u8(), labeling::mean_values(dcm, wsd2, nbasins2)), "wsd_mean_colors.pgm"); + mln_VAR(original, level::stretch(int_u8(), labeling::mean_values(dcm, wshed, nbasins))); + mln_VAR(mean, level::stretch(int_u8(), labeling::mean_values(dcm, wsd2, nbasins2))); + io::pgm::save(original, "wsd_original.pgm"); + io::pgm::save(mean, "wsd_mean_colors.pgm"); + io::ppm::save(debug::colorize(rgb8(), wshed, nbasins), "wsd_colorize_01.ppm"); + io::ppm::save(debug::colorize(rgb8(), wsd2, nbasins2), "wsd_colorize_02.ppm"); } else { Index: trunk/milena/sandbox/fabien/igr/check.sh =================================================================== --- trunk/milena/sandbox/fabien/igr/check.sh (revision 3525) +++ trunk/milena/sandbox/fabien/igr/check.sh (revision 3526) @@ -4,22 +4,33 @@ { echo "Processing $3..." dist_max=10 + input=$1 + dim=$2 - ./grad $1 $2 - for lambda_closing in 10 50 100 500 1000 5000 10000 50000; do + ./grad $input $dim + for lambda_closing in 50 100 500 1000 5000 10000 50000; do echo " for lambda_closing = ${lambda_closing}"; - ./clo_vol grad.dump $2 ${lambda_closing} - nbasins=`./wst clo_vol.dump $2` - ../bin/dumpl32_to_colorize wst.dump $2 $nbasins results/colorize_${3}_${lambda_closing}.ppm + ./clo_vol grad.dump $dim ${lambda_closing} + nbasins=`./wst clo_vol.dump $dim` + ../bin/dumpl32_to_colorize wst.dump $dim $nbasins results/colorize_${3}_${lambda_closing}.ppm + median=`./med wst.dump $dim $input $nbasins` + ../bin/dumpi12_to_pgm med.dump $dim results/median_${3}_${lambda_closing}.pgm + ./thres med.dump $dim $median + mv bin_result.pbm results/result_${3}_${lambda_closing}.pbm - if [ ${lambda_closing} -eq 100 ]; then - for lambda_dist in 10 50 100; do - nbasins_after=`./graph wst.dump $2 $1 $lambda_dist $nbasins` - mv wsd_original.pgm results/graph_${3}_${lambda_closing}_${lambda_dist}_01.pgm - mv wsd_mean_colors.pgm results/graph_${3}_${lambda_closing}_${lambda_dist}_02.pgm - echo "nbasins was" $nbasins "and now is" $nbasins_after "( diff =" $(($nbasins - $nbasins_after)) ")" - done - fi +#if [ $2 -eq 2 ]; then +# if [ ${lambda_closing} -eq 100 ]; then +# for lambda_dist in 50 100 120 130 140 150; do +# nbasins_after=`./graph wst.dump $2 $1 $lambda_dist $nbasins` +# mv wsd_original.pgm results/graph_${3}_${lambda_closing}_${lambda_dist}_01.pgm +# mv wsd_mean_colors.pgm results/graph_${3}_${lambda_closing}_${lambda_dist}_02.pgm +# mv wsd_colorize_01.ppm results/graph_${3}_${lambda_closing}_${lambda_dist}_03.ppm +# mv wsd_colorize_02.ppm results/graph_${3}_${lambda_closing}_${lambda_dist}_04.ppm +# diff=$(($nbasins - $nbasins_after)) +# echo " dist = $lambda_dist | $nbasins -> $nbasins_after (diff = $diff ) $(($diff * 100 / $nbasins))%" +# done +# fi +# fi done # rm *.dump } Index: trunk/milena/sandbox/fabien/igr/med.cc =================================================================== --- trunk/milena/sandbox/fabien/igr/med.cc (revision 0) +++ trunk/milena/sandbox/fabien/igr/med.cc (revision 3526) @@ -0,0 +1,87 @@ +#include <iostream> +#include <mln/core/image/image2d.hh> +#include <mln/core/image/image3d.hh> +#include <mln/core/image/image_if.hh> + +#include <mln/core/alias/neighb2d.hh> +#include <mln/core/alias/window2d.hh> +#include <mln/core/alias/neighb3d.hh> +#include <mln/core/alias/window3d.hh> + +#include <mln/io/dump/all.hh> +#include <mln/io/dicom/load.hh> + +#include <mln/value/int_u8.hh> +#include <mln/value/int_u12.hh> +#include <mln/value/label_16.hh> +#include <mln/value/label_32.hh> + +#include <mln/core/var.hh> +#include <mln/core/routine/extend.hh> +#include <mln/accu/mean.hh> +#include <mln/accu/median_h.hh> +#include <mln/morpho/elementary/dilation.hh> +#include <mln/labeling/mean_values.hh> +#include <mln/level/compute.hh> +#include <mln/pw/all.hh> +#include <mln/util/array.hh> + + + +/////////////////// +// // +// Main Function // +// // +/////////////////// + + +int main(int argc, char *argv[]) +{ + using namespace mln; + using value::int_u8; + using value::int_u12; + using value::label_16; + using value::label_32; + typedef label_32 L; + + if (argc != 5) + { + std::cout << "Usage: " << argv[0] << " <ima.dump> <dimensions> <ima.dcm> <nbasins>" + << std::endl; + return 1; + } + + unsigned dim = atoi(argv[2]); + L nbasins = atoi(argv[4]); + if (dim != 2 && dim != 3) + { + std::cout << "<dimensions> invalid" << std::endl; + return 1; + } + + if (dim == 2) + { + image2d<L> labels; + io::dump::load(labels, argv[1]); + image2d<int_u12> dcm; + io::dicom::load(dcm, argv[3]); + + mln_VAR(wst_dilate, morpho::elementary::dilation(extend(labels | (pw::value(labels) == 0u), labels), c8())); + data::fill((labels | (pw::value(labels) == 0u)).rw(), wst_dilate); + mln_VAR(wst_mean, labeling::mean_values(dcm, labels, nbasins)); + + accu::mean<float> accu_mean; + util::array<float> means = level::compute(accu_mean, wst_mean); + + // FIXME: Take median value of means + + io::dump::save(wst_mean, "med.dump"); + std::cout << median << std::endl; + } + else + { + // FIXME + } + + return 0; +} Index: trunk/milena/sandbox/fabien/igr/thres.cc =================================================================== --- trunk/milena/sandbox/fabien/igr/thres.cc (revision 0) +++ trunk/milena/sandbox/fabien/igr/thres.cc (revision 3526) @@ -0,0 +1,67 @@ +#include <iostream> +#include <mln/core/image/image2d.hh> +#include <mln/core/image/image3d.hh> +#include <mln/core/image/image_if.hh> + +#include <mln/core/alias/neighb2d.hh> +#include <mln/core/alias/window2d.hh> +#include <mln/core/alias/neighb3d.hh> +#include <mln/core/alias/window3d.hh> + +#include <mln/io/dump/all.hh> +#include <mln/io/pbm/save.hh> + +#include <mln/value/int_u8.hh> +#include <mln/value/int_u12.hh> +#include <mln/value/label_16.hh> +#include <mln/value/label_32.hh> + +#include <mln/binarization/threshold.hh> + + + +/////////////////// +// // +// Main Function // +// // +/////////////////// + + +int main(int argc, char *argv[]) +{ + using namespace mln; + using value::int_u8; + using value::int_u12; + using value::label_16; + using value::label_32; + typedef label_32 L; + + if (argc != 4) + { + std::cout << "Usage: " << argv[0] << " <ima.dump> <dimensions> <threshold>" + << std::endl; + return 1; + } + + unsigned dim = atoi(argv[2]); + unsigned threshold = atoi(argv[3]); + if (dim != 2 && dim != 3) + { + std::cout << "<dimensions> invalid" << std::endl; + return 1; + } + + if (dim == 2) + { + image2d<int_u12> input; + io::dump::load(input, argv[1]); + image2d<bool> bin_result = binarization::threshold(input, threshold); + io::pbm::save(bin_result, "result.pbm"); + } + else + { + // FIXME + } + + return 0; +} Index: trunk/milena/sandbox/fabien/igr/Makefile =================================================================== --- trunk/milena/sandbox/fabien/igr/Makefile (revision 3525) +++ trunk/milena/sandbox/fabien/igr/Makefile (revision 3526) @@ -42,5 +42,11 @@ graph: graph.cc g++ -I../../../ ${DICOM_INC} ${DICOM_LIBS} ${CXXFLAGS} $^ -o graph +med: med.cc + g++ -I../../../ ${DICOM_INC} ${DICOM_LIBS} ${CXXFLAGS} $^ -o med + +thres: thres.cc + g++ -I../../../ ${CXXFLAGS} $^ -o thres + clean: rm -rf *.dump *.p?m *.plot *.log *.csv Index: trunk/milena/sandbox/fabien/TODO =================================================================== --- trunk/milena/sandbox/fabien/TODO (revision 3525) +++ trunk/milena/sandbox/fabien/TODO (revision 3526) @@ -28,5 +28,9 @@ [X] Batch process watershed with 2D, 3D and any combination of parameters [X] Cut into small tools [X] Test 3D workflow on 2D images -[ ] Create colorized colors for graph -[ ] Diff with % +[X] Create colorized colors for graph +[X] Diff with % +[ ] Find biggest dark regions (threshold value or median accu - median / 2 - ) + [ ] Learn regions value + [ ] Threshold +[ ] Profile for performance Index: trunk/milena/sandbox/fabien/bin/dumpi12_to_pgm.cc =================================================================== --- trunk/milena/sandbox/fabien/bin/dumpi12_to_pgm.cc (revision 0) +++ trunk/milena/sandbox/fabien/bin/dumpi12_to_pgm.cc (revision 3526) @@ -0,0 +1,55 @@ +#include <mln/core/image/image2d.hh> +#include <mln/make/image3d.hh> +#include <mln/debug/slices_2d.hh> + +#include <mln/value/int_u8.hh> +#include <mln/value/int_u12.hh> +#include <mln/value/label_32.hh> + +#include <mln/io/dump/load.hh> +#include <mln/io/pgm/save.hh> + +#include <mln/level/stretch.hh> + + +int usage(char* argv[]) +{ + std::cerr << "usage: " << argv[0] << " input.dump dim output.pgm" << std::endl; + return 1; +} + + + +int main(int argc, char* argv[]) +{ + using namespace mln; + using value::int_u8; + using value::int_u12; + using value::label_32; + using value::rgb8; + + if (argc != 4) + return usage(argv); + + unsigned dim = atoi(argv[2]); + unsigned nbasins = atoi(argv[3]); + if (dim != 2 && dim != 3) + { + std::cout << "<dimensions> invalid" << std::endl; + return 1; + } + + if (dim == 2) + { + image2d<int_u12> ima2d; + io::dump::load(ima2d, argv[1]); + image2d<int_u8> ima_pgm = level::stretch(int_u8(), ima2d); + io::pgm::save(ima_pgm, argv[3]); + } + else + { + // FIXME + } + + return 0; +}