[Olena-patches] r4265: Add US segmentation method

URL: https://svn.lrde.epita.fr/svn/oln/trunk/milena/sandbox ChangeLog: 2009-07-10 Fabien Freling &lt;fabien.freling(a)lrde.epita.fr&gt; 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 + *