[Olena-patches] r3797: Create mean and deviation images

URL: https://svn.lrde.epita.fr/svn/oln/trunk/milena/sandbox ChangeLog: 2009-05-15 Fabien Freling &lt;fabien.freling(a)lrde.epita.fr&gt; Create mean and deviation images. * fabien/igr/fixed_seg/Makefile: New target for building fixed segmentation. * fabien/igr/fixed_seg/main.cc: Create mean image. * fabien/igr/smooth_fixed_seg/main.cc: Small update, on hold. --- fixed_seg/Makefile | 9 + fixed_seg/main.cc | 271 +++++++++++++++++++++++++++++++++++++++++++++++ smooth_fixed_seg/main.cc | 59 +++++++++- 3 files changed, 332 insertions(+), 7 deletions(-) Index: trunk/milena/sandbox/fabien/igr/smooth_fixed_seg/main.cc =================================================================== --- trunk/milena/sandbox/fabien/igr/smooth_fixed_seg/main.cc (revision 3796) +++ trunk/milena/sandbox/fabien/igr/smooth_fixed_seg/main.cc (revision 3797) @@ -34,8 +34,8 @@ #include <mln/morpho/dilation.hh> #include <mln/morpho/erosion.hh> #include <mln/morpho/closing/structural.hh> +#include <mln/morpho/closing/volume.hh> #include <mln/morpho/opening/structural.hh> -#include <mln/morpho/elementary/gradient.hh> #include <mln/morpho/watershed/flooding.hh> #include <mln/pw/all.hh> #include <mln/util/array.hh> @@ -46,9 +46,7 @@ #include <mln/world/inter_pixel/neighb2d.hh> #include <mln/world/inter_pixel/all.hh> -#include <mln/labeling/colorize.hh> -#include <mln/debug/println.hh> -#include <mln/trace/quiet.hh> +#include "../plot_label.hh" using namespace mln; @@ -133,13 +131,13 @@ int usage(const char* bin) { - std::cout << "Usage: " << bin << " input.dump" << std::endl; + std::cout << "Usage: " << bin << " input.dump closing_lambda" << std::endl; return 1; } int main(int argc, char* argv[]) { - if (argc != 2) + if (argc != 3) return usage(argv[0]); @@ -159,7 +157,6 @@ // Edges image creation. - //image2d<float> edges = dist_on_edges(ima_arr); typedef image_if<I, world::inter_pixel::is_pixel> Ix; Ix imax = world::inter_pixel::immerse(ima_arr); @@ -172,6 +169,54 @@ io::pgm::save(level::stretch(int_u8(), display_ima), "edges.pgm"); } + // Type change. + mln_VAR(e, level::stretch(int_u8(), edges)); + + + // Closing. + mln_VAR(clo, morpho::closing::volume(e, world::inter_pixel::e2e(), atoi(argv[2]))); + + { + // Display. + mln_VAR(display_clo, world::inter_pixel::display_edge(clo.unmorph_(), 0.0, 3)); + io::pgm::save(level::stretch(int_u8(), display_clo), "closing.pgm"); + } + + + // Watershed. + typedef label_16 L; + L nbasins; + mln_VAR(wst, morpho::watershed::flooding(clo, world::inter_pixel::e2e(), nbasins)); + + std::cout << "nbasins: " << nbasins << std::endl; + + mln_VAR(w_all, wst.unmorph_()); + //data::fill((w | (!world::inter_pixel::is_separator())).rw(), nbasins.next()); + mln_VAR(w_pixels, w_all | world::inter_pixel::is_pixel()); + data::paste(morpho::dilation(extend(w_pixels, pw::value(w_all)), c4().win()), w_all); + // edges -> dots + mln_VAR(w_dots, w_all | world::inter_pixel::dim2::is_dot()); + data::paste(morpho::erosion(extend(w_dots, pw::value(w_all)), c4().win()), w_all); + + //io::ppm::save(labeling::colorize(value::rgb8(), w, nbasins.next()), "result.ppm"); + io::pgm::save(labeling::wrap(int_u8(), w_all), "watershed.pgm"); + + + // Plots. + image2d<L> w_simple = world::inter_pixel::full2image(w_all); + plot_label(input, w_simple, 248u); + plot_label(input, w_simple, 241u); + plot_label(input, w_simple, 238u); + plot_label(input, w_simple, 251u); + plot_label(input, w_simple, 250u); + plot_label(input, w_simple, 249u); + plot_label(input, w_simple, 247u); + plot_label(input, w_simple, 232u); + plot_label(input, w_simple, 252u); + plot_label(input, w_simple, 246u); + plot_label(input, w_simple, 240u); + plot_label(input, w_simple, 237u); + return 0; } Index: trunk/milena/sandbox/fabien/igr/fixed_seg/main.cc =================================================================== --- trunk/milena/sandbox/fabien/igr/fixed_seg/main.cc (revision 0) +++ trunk/milena/sandbox/fabien/igr/fixed_seg/main.cc (revision 3797) @@ -0,0 +1,271 @@ +#include <algorithm> + +#include <mln/core/image/image1d.hh> +#include <mln/core/image/image2d.hh> +#include <mln/core/alias/neighb2d.hh> +#include <mln/core/image/image3d.hh> +#include <mln/core/image/slice_image.hh> +#include <mln/core/image/image_if.hh> +#include <mln/core/routine/duplicate.hh> +#include <mln/core/routine/extend.hh> +#include <mln/core/var.hh> + +#include <mln/io/dump/all.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/rgb8.hh> +#include <mln/value/float01_8.hh> + +#include <mln/accu/sum.hh> +#include <mln/accu/mean.hh> +#include <mln/accu/stat/deviation.hh> +#include <mln/data/fill.hh> +#include <mln/data/paste.hh> +#include <mln/debug/quiet.hh> +#include <mln/convert/from_to.hh> +#include <mln/fun/v2v/fit.hh> +#include <mln/labeling/compute.hh> +#include <mln/labeling/wrap.hh> +#include <mln/level/compute.hh> +#include <mln/level/convert.hh> +#include <mln/level/stretch.hh> +#include <mln/make/image2d.hh> +#include <mln/math/diff_abs.hh> +#include <mln/morpho/dilation.hh> +#include <mln/morpho/erosion.hh> +#include <mln/morpho/closing/area.hh> +#include <mln/morpho/elementary/gradient.hh> +#include <mln/morpho/watershed/flooding.hh> +#include <mln/pw/all.hh> +#include <mln/util/array.hh> + +#include <mln/world/inter_pixel/display_edge.hh> +#include <mln/world/inter_pixel/compute.hh> +#include <mln/world/inter_pixel/immerse.hh> +#include <mln/world/inter_pixel/neighb2d.hh> +#include <mln/world/inter_pixel/all.hh> + +#include <mln/labeling/colorize.hh> +#include <mln/debug/println.hh> +#include <mln/trace/quiet.hh> + +#include "../plot_label.hh" + +using namespace mln; +using value::int_u8; +using value::int_u12; +using value::label_16; +using value::float01_8; + +#define SATURATION 0.6 + + + + + +// Distance function. +//------------------- + +struct dist_t : Function_vv2v<dist_t> +{ + typedef float result; + + template <typename V> + float operator()(util::array<V> v1, util::array<V> v2) const + { + float res = 0.f; + + for (unsigned i = 0; i < v1.nelements(); ++i) + res += std::min(v1[i], v2[i]); + + image1d<V> tmp_ima; + image1d<V> tmp_ima2; + accu::sum<V> accu_sum; + + convert::from_to(v1, tmp_ima); + float sum_v1 = level::compute(accu_sum, tmp_ima); + + convert::from_to(v2, tmp_ima2); + float sum_v2 = level::compute(accu_sum, tmp_ima2); + + res /= std::max(sum_v1, sum_v2); + + return 1 - res; + } +} dist; + + + + + + + + +int usage(const char* bin) +{ + std::cout << "Usage: " << bin << " input.dump closing" << std::endl; + return 1; +} + +int main(int argc, char* argv[]) +{ + if (argc != 3) + return usage(argv[0]); + + + // Initialization. + image3d<int_u12> input; + io::dump::load(input, argv[1]); + typedef image2d<util::array<int_u12> > I; + I ima_arr; + initialize(ima_arr, slice(input, 0)); + for (unsigned int i = 0; i < input.nslices(); ++i) + { + image2d<int_u12> tmp_slice = duplicate(slice(input, i)); + mln_piter_(image2d<int_u12>) p(tmp_slice.domain()); + for_all(p) + ima_arr(p).append(tmp_slice(p)); + } + + + // Edges image creation. + typedef image_if<I, world::inter_pixel::is_pixel> Ix; + Ix imax = world::inter_pixel::immerse(ima_arr); + + // Edges distance computation. + mln_VAR(edges, world::inter_pixel::compute(imax, dist)); + mln_VAR(e, level::transform(edges, fun::v2v::fit<float>(SATURATION))); + typedef int_u12 E_TYPE; + + { + // Display. + mln_VAR(display_ima, world::inter_pixel::display_edge(e.unmorph_(), 0.0, 3)); + io::pgm::save(level::stretch(int_u8(), display_ima), "01_edges.pgm"); + } + + + + // Closing. + mln_VAR(clo, morpho::closing::area(e, world::inter_pixel::e2e(), atoi(argv[2]))); + + { + // Display. + mln_VAR(display_clo, world::inter_pixel::display_edge(clo.unmorph_(), 0.0, 3)); + io::pgm::save(level::stretch(int_u8(), display_clo), "03_closing.pgm"); + } + + + // Watershed. + typedef label_16 L; + L nbasins; + mln_VAR(wst, morpho::watershed::flooding(clo, world::inter_pixel::e2e(), nbasins)); + + std::cout << "nbasins: " << nbasins << std::endl; + + + mln_VAR(w_all, wst.unmorph_()); + //data::fill((w | (!world::inter_pixel::is_separator())).rw(), nbasins.next()); + mln_VAR(w_pixels, w_all | world::inter_pixel::is_pixel()); + data::paste(morpho::dilation(extend(w_pixels, pw::value(w_all)), c4().win()), w_all); + // edges -> dots + mln_VAR(w_dots, w_all | world::inter_pixel::dim2::is_dot()); + data::paste(morpho::erosion(extend(w_dots, pw::value(w_all)), c4().win()), w_all); + + //io::ppm::save(labeling::colorize(value::rgb8(), w, nbasins.next()), "result.ppm"); + io::pgm::save(labeling::wrap(int_u8(), w_all), "watershed.pgm"); + + + + // Mean distance. + accu::mean<E_TYPE> accu_mean; + util::array<float> means = labeling::compute(accu_mean, e, wst, nbasins); + + // Display. + { + typedef image_if<image2d<float>, world::inter_pixel::is_separator> Fsx; + Fsx ima_means; + initialize(ima_means, wst); + data::paste(wst, ima_means); + for (unsigned i = 1; i < means.nelements(); ++i) + data::fill((ima_means | pw::value(ima_means) == pw::cst(i)).rw(), means[i]); + mln_VAR(display_means, world::inter_pixel::display_edge(ima_means.unmorph_(), 0.0, 3)); + io::pgm::save(level::stretch(int_u8(), display_means), "04_means.pgm"); + } + + + + // Deviation. + util::array<accu::stat::deviation<float> > arr_dev; + for (unsigned i = 0; i < means.nelements(); ++i) + arr_dev.append(accu::stat::deviation<float> (means[i])); + util::array<float> deviations = labeling::compute(arr_dev, e, wst, nbasins); + + // Display. + { + typedef image_if<image2d<float>, world::inter_pixel::is_separator> Fsx; + Fsx ima_dev; + initialize(ima_dev, wst); + data::paste(wst, ima_dev); + for (unsigned i = 1; i < deviations.nelements(); ++i) + data::fill((ima_dev | pw::value(ima_dev) == pw::cst(i)).rw(), deviations[i]); + mln_VAR(display_dev, world::inter_pixel::display_edge(ima_dev.unmorph_(), 0.0, 3)); + io::pgm::save(level::stretch(int_u8(), display_dev), "05_dev.pgm"); + } + + + + // Plots labels. + image2d<L> w_simple = world::inter_pixel::full2image(w_all); + plot_label(input, w_simple, 191u); + plot_label(input, w_simple, 171u); + plot_label(input, w_simple, 188u); + + plot_label(input, w_simple, 16u); + + plot_label(input, w_simple, 187u); + + + + + + + + + + /*mln_VAR(clo, morpho::closing::volume(edges | world::inter_pixel::dim2::is_edge(), world::inter_pixel::e2e(), atoi(argv[2]))); + + // Debug. + //debug::println("clo", clo); + + // Display. + image2d<float> display_ima2 = world::inter_pixel::display_edge(clo.unmorph_(), 0.0, 3); + io::pgm::save(level::stretch(int_u8(), display_ima2), "edges2.pgm"); + + // Watershed. + typedef label_16 L; + L nbasins; + mln_VAR(wst, morpho::watershed::flooding(clo, world::inter_pixel::e2e(), nbasins)); + + // Debug. + //debug::println("wst", wst); + + // Extension. + image2d<L> w_all = wst.unmorph_(); + // edges -> pixel + mln_VAR(w_pixels, w_all | world::inter_pixel::dim2::is_pixel()); + data::paste(morpho::dilation(extend(w_pixels, pw::value(w_all)), c4().win()), w_all); + // edges -> dots + mln_VAR(w_dots, w_all | world::inter_pixel::dim2::is_dot()); + data::paste(morpho::erosion(extend(w_dots, pw::value(w_all)), c4().win()), w_all); + + + // Save labels map. + std::cout << "nbasins: " << nbasins << std::endl; + io::dump::save(wst.unmorph_(), "watershed_fixed.dump");*/ + + return 0; +} Index: trunk/milena/sandbox/fabien/igr/fixed_seg/Makefile =================================================================== --- trunk/milena/sandbox/fabien/igr/fixed_seg/Makefile (revision 0) +++ trunk/milena/sandbox/fabien/igr/fixed_seg/Makefile (revision 3797) @@ -0,0 +1,9 @@ +include ../Makefile.rules + +all: main.cc + ${CXX} -I../../../../ ${CXXFLAGS} $^ -o fixed_seg + + +clean: + rm -rf *.dump *.p?m *.plot *.log *.csv *.dSYM + rm seg_fixed