[Olena-patches] r3603: Create plot files depending on labels

URL: https://svn.lrde.epita.fr/svn/oln/trunk/milena/sandbox ChangeLog: 2009-04-03 Fabien Freling &lt;fabien.freling(a)lrde.epita.fr&gt; Create plot files depending on labels. * fabien/igr/Makefile: Add new targets. * fabien/igr/check.sh: Update. * fabien/igr/clo_vol.cc: Minor update, helped for debug. * fabien/igr/fun_labels.cc: Create plot files with labels value. * fabien/igr/fun_labels.sh: New script file for testing fun_labels. * fabien/igr/time_smooth/linear.cc: Update tumeur point. --- TODO | 4 - igr/Makefile | 13 +-- igr/check.sh | 12 +-- igr/clo_vol.cc | 14 +++ igr/fun_labels.cc | 163 ++++++++++++++++++++++++++++++++++++++++++++++ igr/fun_labels.sh | 20 +++++ igr/time_smooth/linear.cc | 8 +- 7 files changed, 211 insertions(+), 23 deletions(-) Index: trunk/milena/sandbox/fabien/igr/clo_vol.cc =================================================================== --- trunk/milena/sandbox/fabien/igr/clo_vol.cc (revision 3602) +++ trunk/milena/sandbox/fabien/igr/clo_vol.cc (revision 3603) @@ -16,6 +16,13 @@ + + +#include <mln/canvas/morpho/attribute_filter.hh> +#include <mln/morpho/attribute/volume.hh> + + + /////////////////// // // // Main Function // @@ -53,9 +60,12 @@ } else { - image3d<int_u12> input; + typedef image3d<int_u12> I; + + I input; io::dump::load(input, argv[1]); - image3d<int_u12> clo = morpho::closing::volume(input, c6(), closure_lambda); + + I clo = morpho::closing::volume(input, c6(), closure_lambda); io::dump::save(clo, "clo_vol.dump"); } Index: trunk/milena/sandbox/fabien/igr/fun_labels.sh =================================================================== --- trunk/milena/sandbox/fabien/igr/fun_labels.sh (revision 0) +++ trunk/milena/sandbox/fabien/igr/fun_labels.sh (revision 3603) @@ -0,0 +1,20 @@ +#!/bin/zsh + +process_file () +{ + echo "Processing $3..." + input=$1 + dim=$2 + + ./grad $input $dim + for lambda_closing in 5000; do + echo " for lambda_closing = ${lambda_closing}"; + ./clo_vol grad.dump $dim ${lambda_closing} + nbasins=`./wst clo_vol.dump $dim` + echo " nbasins = $nbasins" +#../bin/dumpl32_to_colorize wst.dump $dim $nbasins colorize_${3}_${lambda_closing}.ppm + ./fun_labels wst.dump $dim $input $nbasins + done +} + +process_file "/Users/HiSoKa/Work/IGR/souris18/irm/IM_0052.dcm" 3 "52" Property changes on: trunk/milena/sandbox/fabien/igr/fun_labels.sh ___________________________________________________________________ Name: svn:executable + * Index: trunk/milena/sandbox/fabien/igr/check.sh =================================================================== --- trunk/milena/sandbox/fabien/igr/check.sh (revision 3602) +++ trunk/milena/sandbox/fabien/igr/check.sh (revision 3603) @@ -15,7 +15,7 @@ echo " nbasins = $nbasins" ../bin/dumpl32_to_colorize wst.dump $dim $nbasins results/colorize_${3}_${lambda_closing}.ppm median=`./med wst.dump $dim $input $nbasins` -#echo " median = $median" + echo " median = $median" threshold=$(($median / 2)) ../bin/dumpi12_to_pgm med.dump $dim results/median_${3}_${lambda_closing}.pgm ./thres med.dump $dim $threshold @@ -38,9 +38,9 @@ # rm *.dump } -process_file "/Users/HiSoKa/Work/IGR/souris18/irm/IM_0049.dcm" 2 "49" +#process_file "/Users/HiSoKa/Work/IGR/souris18/irm/IM_0049.dcm" 2 "49" process_file "/Users/HiSoKa/Work/IGR/souris18/irm/IM_0052.dcm" 3 "52" -process_file "/Users/HiSoKa/Work/IGR/souris18/irm/IM_0055.dcm" 2 "55" -process_file "/Users/HiSoKa/Work/IGR/souris18/irm/IM_0058.dcm" 2 "58" -process_file "/Users/HiSoKa/Work/IGR/souris18/irm/IM_0061.dcm" 3 "61" -process_file "/Users/HiSoKa/Work/IGR/souris18/irm/IM_0064.dcm" 3 "64" +#process_file "/Users/HiSoKa/Work/IGR/souris18/irm/IM_0055.dcm" 2 "55" +#process_file "/Users/HiSoKa/Work/IGR/souris18/irm/IM_0058.dcm" 2 "58" +#process_file "/Users/HiSoKa/Work/IGR/souris18/irm/IM_0061.dcm" 3 "61" +#process_file "/Users/HiSoKa/Work/IGR/souris18/irm/IM_0064.dcm" 3 "64" Index: trunk/milena/sandbox/fabien/igr/time_smooth/linear.cc =================================================================== --- trunk/milena/sandbox/fabien/igr/time_smooth/linear.cc (revision 3602) +++ trunk/milena/sandbox/fabien/igr/time_smooth/linear.cc (revision 3603) @@ -66,11 +66,11 @@ // Outputs // // // ///////////// - io::plot::save(ima_arr(point2d(160, 120)), "ref_tumeur.plot"); - io::plot::save(ima_linear(point2d(160, 120)), "linear_tumeur.plot"); - io::plot::save(ima_arr(point2d(34, 94)), "ref_air.plot"); + //io::plot::save(ima_arr(point2d(160, 120)), "ref_tumeur.plot"); + io::plot::save(ima_linear(point2d(156, 114)), "linear_tumeur.plot"); + //io::plot::save(ima_arr(point2d(34, 94)), "ref_air.plot"); io::plot::save(ima_linear(point2d(34, 94)), "linear_air.plot"); - io::plot::save(ima_arr(point2d(122, 115)), "ref_poumon.plot"); + //io::plot::save(ima_arr(point2d(122, 115)), "ref_poumon.plot"); io::plot::save(ima_linear(point2d(122, 115)), "linear_poumon.plot"); return 0; Index: trunk/milena/sandbox/fabien/igr/fun_labels.cc =================================================================== --- trunk/milena/sandbox/fabien/igr/fun_labels.cc (revision 0) +++ trunk/milena/sandbox/fabien/igr/fun_labels.cc (revision 3603) @@ -0,0 +1,163 @@ +#include <iostream> +#include <sstream> +#include <mln/core/image/image2d.hh> +#include <mln/core/image/image3d.hh> +#include <mln/core/image/image_if.hh> +#include <mln/core/image/slice_image.hh> +#include <mln/core/routine/duplicate.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/geom/nslis.hh> + +#include <mln/io/dump/all.hh> +#include <mln/io/dicom/load.hh> +#include <mln/io/plot/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/accu/mean.hh> +#include <mln/accu/median_h.hh> +#include <mln/level/compute.hh> +#include <mln/pw/all.hh> +#include <mln/util/array.hh> +#include <mln/util/set.hh> + + + +using namespace mln; +using value::int_u8; +using value::int_u12; +using value::label_16; +using value::label_32; + + +template <typename I, typename L, typename V> +inline +void plot_label(I ima, L ima_labels, V lbl) +{ + I ima_spe = duplicate(ima | pw::value(ima_labels) == pw::cst(lbl)); + util::array<float> arr; + for (int i = 0; i < ima_spe.domain().pmin().sli(); ++i) + arr.append(0.0); + for (int sli = ima_spe.domain().pmin().sli(); sli <= ima_spe.domain().pmax().sli(); ++sli) + { + image2d<int_u12> tmp_slice = duplicate(slice(ima_spe, sli)); + accu::mean<int_u12> accu_mean; + float mean = level::compute(accu_mean, tmp_slice); + arr.append(mean); + } + for (int i = ima_spe.domain().pmax().sli() + 1; i <= ima.domain().pmax().sli(); ++i) + arr.append(0.0); + std::ostringstream slabel; + slabel << "label_" << lbl << ".plot"; + io::plot::save(arr, slabel.str()); +} + + +template <typename I, typename L> +inline +void plot_point(I ima, L ima_labels, point2d point, const char* desc) +{ + util::array<float> arr; + label_32 prev_lbl; + int start = 0; + int count = 1; + for (unsigned sli = 0; sli < geom::nslis(ima); ++sli) + { + image2d<int_u12> ima_slice = duplicate(slice(ima, sli)); + image2d<label_32> lbl_slice = duplicate(slice(ima_labels, sli)); + if (sli == 0) + prev_lbl = lbl_slice(point); + if (lbl_slice(point) != prev_lbl) + { + std::ostringstream slabel; + slabel << desc << "_" << count << "_label_" << prev_lbl << ".plot"; + count++; + io::plot::save(arr, slabel.str(), start); + arr.clear(); + start = sli + 1; + } + // Taking the mean value of the region. + accu::mean<int_u12> accu_mean; + float mean = level::compute(accu_mean, ima_slice | pw::value(lbl_slice) == pw::cst(lbl_slice(point))); + arr.append(mean); + prev_lbl = lbl_slice(point); + } + if (!arr.is_empty()) + { + std::ostringstream slabel; + slabel << desc << "_" << count << "_label_" << prev_lbl << ".plot"; + io::plot::save(arr, slabel.str(), start); + } +} + + +/////////////////// +// // +// Main Function // +// // +/////////////////// + + +int main(int argc, char *argv[]) +{ + 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]); + if (dim != 2 && dim != 3) + { + std::cout << "<dimensions> invalid" << std::endl; + return 1; + } + + L nlabels = atoi(argv[4]); + + if (dim == 2) + { + // FIXME + } + else + { + point2d p_tumeur(156, 114); + point2d p_air(34, 94); + point2d p_poumon(122, 115); + image3d<L> ima_labels; + io::dump::load(ima_labels, argv[1]); + image3d<int_u12> ima; + io::dicom::load(ima, argv[3]); + + plot_point(ima, ima_labels, p_tumeur, "tumeur"); + plot_point(ima, ima_labels, p_air, "air"); + plot_point(ima, ima_labels, p_poumon, "poumon"); + /*util::set<L> lbl_set; + for (int sli = 0; sli < geom::nslis(ima_labels); ++sli) + { + image2d<L> tmp_slice = duplicate(slice(ima_labels, sli)); + lbl_set.insert(tmp_slice(p_tumeur)); + lbl_set.insert(tmp_slice(p_air)); + lbl_set.insert(tmp_slice(p_poumon)); + } + + util::set_fwd_iter<L> siter(lbl_set); + for_all(siter) + { + plot_label(ima, ima_labels, siter.element()); + }*/ + } + + return 0; +} Index: trunk/milena/sandbox/fabien/igr/Makefile =================================================================== --- trunk/milena/sandbox/fabien/igr/Makefile (revision 3602) +++ trunk/milena/sandbox/fabien/igr/Makefile (revision 3603) @@ -1,12 +1,4 @@ -CXX = llvm-g++ -CXXFLAGS = -DNDEBUG -O4 - -DICOM_INC = -I/usr/local/include/gdcm-2.0 -DICOM_LIBS = -lgdcmCommon -lgdcmDICT -lgdcmDSED -lgdcmIOD -lgdcmMSFF -lgdcmexpat -lgdcmjpeg12 -lgdcmjpeg16 -lgdcmjpeg8 -lgdcmopenjpeg -lgdcmuuid -lgdcmzlib \ - -framework CoreFoundation -DICOM = ${DICOM_INC} ${DICOM_LIBS} - -MAGICK = `Magick++-config --cppflags --ldflags --libs` +include Makefile.rules seg2d: seg_vol_irm.hh seg2d.cc ${CXX} -I../../../ ${DICOM} ${CXXFLAGS} seg2d.cc -o seg2d @@ -50,6 +42,9 @@ first_slice_dicom: first_slice_dicom.cc ${CXX} -I../../../ ${DICOM} ${MAGICK} ${CXXFLAGS} -lm $^ -o first_slice_dicom +fun_labels: fun_labels.cc + ${CXX} -I../../../ ${DICOM} ${CXXFLAGS} $^ -o fun_labels + 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/TODO =================================================================== --- trunk/milena/sandbox/fabien/TODO (revision 3602) +++ trunk/milena/sandbox/fabien/TODO (revision 3603) @@ -38,9 +38,9 @@ [ ] Profile for performance [X] ImageMagick support [ ] Integrate external libraries (GDCM, IM) -[ ] Send result images to lrde account +[X] Send result images to lrde account [X] Translate Matlab code [X] Subsample binary images [X] Fast projected histogram [ ] Triple histogram -[ ] Create plot for each kind of point with each method +[X] Create plot for each kind of point with each method