[Olena-patches] r3854: Add quantification after normalization

URL: https://svn.lrde.epita.fr/svn/oln/trunk/milena/sandbox ChangeLog: 2009-05-19 Fabien Freling &lt;fabien.freling(a)lrde.epita.fr&gt; Add quantification after normalization. * fabien/igr/fixed_seg/main.cc: Handle normalized data. * fabien/igr/norm.cc: Normalize. * fabien/igr/smooth_fixed_seg/main.cc: Test different filters. --- fixed_seg/main.cc | 204 ++++++++++++++++++++++++++++++++++++++--------- norm.cc | 14 ++- smooth_fixed_seg/main.cc | 63 +++++++++----- 3 files changed, 218 insertions(+), 63 deletions(-) Index: trunk/milena/sandbox/fabien/igr/smooth_fixed_seg/main.cc =================================================================== --- trunk/milena/sandbox/fabien/igr/smooth_fixed_seg/main.cc (revision 3853) +++ trunk/milena/sandbox/fabien/igr/smooth_fixed_seg/main.cc (revision 3854) @@ -25,16 +25,20 @@ #include <mln/data/fill.hh> #include <mln/data/paste.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/linear/convolve.hh> #include <mln/make/image2d.hh> +#include <mln/make/w_window1d.hh> #include <mln/math/diff_abs.hh> #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/closing/area.hh> #include <mln/morpho/opening/structural.hh> #include <mln/morpho/watershed/flooding.hh> #include <mln/pw/all.hh> @@ -54,6 +58,8 @@ using value::int_u12; using value::label_16; +#define SATURATION 0.5 + @@ -162,24 +168,25 @@ // Edges distance computation. mln_VAR(edges, world::inter_pixel::compute(imax, dist)); + mln_VAR(e, level::transform(edges, fun::v2v::fit<float>(SATURATION))); + io::dump::save(e.unmorph_(), "edges_int_u12.dump"); + typedef int_u12 E_TYPE; { // Display. - mln_VAR(display_ima, world::inter_pixel::display_edge(edges.unmorph_(), 0.0, 3)); - io::pgm::save(level::stretch(int_u8(), display_ima), "edges.pgm"); + 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"); } - // 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]))); + 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), "closing.pgm"); + io::pgm::save(level::stretch(int_u8(), display_clo), "03_closing.pgm"); } @@ -190,7 +197,9 @@ std::cout << "nbasins: " << nbasins << std::endl; + mln_VAR(w_all, wst.unmorph_()); + io::dump::save(w_all, "watershed_edges.dump"); //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); @@ -202,20 +211,32 @@ 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); + + // Mean distance. + + // Old code. + //accu::mean<E_TYPE> accu_mean; + //util::array<float> means = labeling::compute(accu_mean, e, wst, nbasins); + + // Theo version. + typedef accu::mean<int_u12,float,int_u12> A; + util::array<int_u12> means = labeling::compute(A(), 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"); + } + + return 0; Index: trunk/milena/sandbox/fabien/igr/norm.cc =================================================================== --- trunk/milena/sandbox/fabien/igr/norm.cc (revision 3853) +++ trunk/milena/sandbox/fabien/igr/norm.cc (revision 3854) @@ -20,6 +20,9 @@ // DEBUG #include <mln/core/var.hh> #include <mln/estim/min_max.hh> +#include <mln/io/pgm/save.hh> +#include <mln/level/stretch.hh> +#include <mln/value/int_u8.hh> /*#include <mln/accu/min.hh> #include <mln/accu/max.hh> #include <mln/level/compute.hh>*/ @@ -61,6 +64,9 @@ image2d<float> ima_ini = mean_slices(ima_f, first, last); + // Debug. + //io::pgm::save(level::stretch(value::int_u8(), ima_ini), "mean_slices.pgm"); + image3d<float> ima_result; initialize(ima_result, ima); @@ -80,17 +86,17 @@ int main(int argc, char *argv[]) { - if (argc != 3) + if (argc != 5) { - std::cout << "Usage: " << argv[0] << " ima.dump output.dump" + std::cout << "Usage: " << argv[0] << " ima.dump first_slice last_slice output.dump" << std::endl; return 1; } image3d<int_u12> ima; io::dump::load(ima, argv[1]); - image3d<float> norm = normalize(ima, 1, 8); - io::dump::save(norm, argv[2]); + image3d<float> norm = normalize(ima, atoi(argv[2]), atoi(argv[3])); + io::dump::save(norm, argv[4]); return 0; } Index: trunk/milena/sandbox/fabien/igr/fixed_seg/main.cc =================================================================== --- trunk/milena/sandbox/fabien/igr/fixed_seg/main.cc (revision 3853) +++ trunk/milena/sandbox/fabien/igr/fixed_seg/main.cc (revision 3854) @@ -1,6 +1,7 @@ #include <algorithm> #include <mln/core/image/image1d.hh> +#include <mln/core/alias/window1d.hh> #include <mln/core/image/image2d.hh> #include <mln/core/alias/neighb2d.hh> #include <mln/core/image/image3d.hh> @@ -22,7 +23,9 @@ #include <mln/accu/sum.hh> #include <mln/accu/mean.hh> +#include <mln/accu/image/all.hh> #include <mln/accu/stat/deviation.hh> +#include <mln/arith/div.hh> #include <mln/data/fill.hh> #include <mln/data/paste.hh> #include <mln/debug/quiet.hh> @@ -34,10 +37,13 @@ #include <mln/level/convert.hh> #include <mln/level/stretch.hh> #include <mln/make/image2d.hh> +#include <mln/make/w_window1d.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/closing/structural.hh> +#include <mln/morpho/opening/structural.hh> #include <mln/morpho/elementary/gradient.hh> #include <mln/morpho/watershed/flooding.hh> #include <mln/pw/all.hh> @@ -61,10 +67,73 @@ using value::label_16; using value::float01_8; -#define SATURATION 0.6 +const float saturation = 1.0; +namespace mln +{ + + struct int_u12_from_float : Function_v2v< int_u12_from_float > + { + typedef value::int_u12 result; + result operator()(float f) const + { + mln_precondition(f >= 0.f && f <= 1.f); + unsigned i = f / saturation * 4095; + return i > 4095 ? 4095 : i; + } + }; + + + template <typename I> + void io_save_edges_int_u12(const I& input, + value::int_u8 bg, + const std::string& filename) + { + mlc_equal(mln_value(I), value::int_u12)::check(); + mln_ch_value(I, value::int_u8) output; + initialize(output, input); + arith::div_cst(input, 16, output); + io::pgm::save(world::inter_pixel::display_edge(output.unmorph_(), + bg, + 3), + filename); + } + +} // end of namespace mln + + + +// Mean image. +//------------ +template <typename V> +inline +image1d<float> +mean_image(image1d<V>& input) +{ + window1d win_1; + win_1 + .insert(-2) + .insert(-1) + .insert(0) + .insert(1) + .insert(2); + + image1d<V> closing_ima = morpho::closing::structural(input, win_1); + image1d<V> opening_ima = morpho::opening::structural(input, win_1); + + image1d<accu::mean<float> > result; + + initialize(result, input); + + accu::image::init(result); + accu::image::take(result, closing_ima); + accu::image::take(result, opening_ima); + + return accu::image::to_result(result); +} + // Distance function. @@ -72,10 +141,10 @@ struct dist_t : Function_vv2v<dist_t> { - typedef float result; + typedef int_u12 result; template <typename V> - float operator()(util::array<V> v1, util::array<V> v2) const + int_u12 operator()(util::array<V> v1, util::array<V> v2) const { float res = 0.f; @@ -92,13 +161,51 @@ convert::from_to(v2, tmp_ima2); float sum_v2 = level::compute(accu_sum, tmp_ima2); + if (sum_v1 == 0 && sum_v2 == 0) + return 1; + res /= std::max(sum_v1, sum_v2); + res = 1 - res; + res = res * 4095; - return 1 - res; + return (int) res; } } dist; +/*struct dist_morpho_t : Function_vv2v<dist_morpho_t> +{ + typedef float result; + + template <typename V> + float operator()(util::array<V> v1, util::array<V> v2) const + { + float res = 0.f; + + accu::sum<V> accu_sum; + + image1d<V> tmp_ima; + convert::from_to(v1, tmp_ima); + image1d<float> morpho_ima = mean_image(tmp_ima); + float sum_v1 = level::compute(accu_sum, morpho_ima); + + image1d<V> tmp_ima2; + convert::from_to(v2, tmp_ima2); + image1d<float> morpho_ima2 = mean_image(tmp_ima2); + float sum_v2 = level::compute(accu_sum, morpho_ima2); + + mln_piter(image1d<float>) p(morpho_ima.domain()); + for_all(p) + res += std::min(morpho_ima(p), morpho_ima2(p)); + + if (sum_v1 == 0 && sum_v2 == 0) + return 1; + + res /= std::max(sum_v1, sum_v2); + + return 1 - res; + } +} dist_morpho;*/ @@ -107,28 +214,35 @@ int usage(const char* bin) { - std::cout << "Usage: " << bin << " input.dump closing" << std::endl; + std::cout << "Usage: " << bin << " input.dump min smooth lambda" << std::endl; return 1; } int main(int argc, char* argv[]) { - if (argc != 3) + if (argc != 5) return usage(argv[0]); + float min = atof(argv[2]); + unsigned is_smooth = atoi(argv[3]); + unsigned lambda = atoi(argv[4]); + // Initialization. - image3d<int_u12> input; + typedef float input_type; + image3d<input_type> input; io::dump::load(input, argv[1]); - typedef image2d<util::array<int_u12> > I; + int min_slice = input.bbox().pmin().sli(); + int max_slice = input.bbox().pmax().sli(); + typedef image2d<util::array<input_type> > I; I ima_arr; initialize(ima_arr, slice(input, 0)); - for (unsigned int i = 0; i < input.nslices(); ++i) + for (int i = min_slice; i <= max_slice; ++i) { - image2d<int_u12> tmp_slice = duplicate(slice(input, i)); - mln_piter_(image2d<int_u12>) p(tmp_slice.domain()); + image2d<input_type> tmp_slice = duplicate(slice(input, i)); + mln_piter_(image2d<input_type>) p(tmp_slice.domain()); for_all(p) - ima_arr(p).append(tmp_slice(p)); + ima_arr(p).append(tmp_slice(p) - min); // We set the minimum value to 0. } @@ -137,37 +251,31 @@ 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"); - } - + image_if<image2d<int_u12>, world::inter_pixel::is_separator> edges; + //if (!is_smooth) + edges = world::inter_pixel::compute(imax, dist); + //else + // edges = world::inter_pixel::compute(imax, dist_morpho); + //io::dump::save(edges.unmorph_(), "edges.dump"); + //mln_VAR(d, level::transform(edges, int_u12_from_float())); + io_save_edges_int_u12(edges, 0, "dist.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"); - } + /*mln_VAR(d_clo, morpho::closing::area(d, world::inter_pixel::e2e(), lambda)); + //io_save_edges_int_u12(d_clo, 0, "d_clo.pgm"); // Watershed. typedef label_16 L; L nbasins; - mln_VAR(wst, morpho::watershed::flooding(clo, world::inter_pixel::e2e(), nbasins)); + mln_VAR(wst, morpho::watershed::flooding(d_clo, world::inter_pixel::e2e(), nbasins)); - std::cout << "nbasins: " << nbasins << std::endl; + std::cout << "nbasins: " << nbasins << std::endl;*/ - mln_VAR(w_all, wst.unmorph_()); + /*mln_VAR(w_all, wst.unmorph_()); + io::dump::save(w_all, "watershed_edges.dump"); //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); @@ -176,12 +284,13 @@ 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"); + io::pgm::save(labeling::wrap(int_u8(), w_all), "watershed.pgm");*/ // Mean distance. - accu::mean<E_TYPE> accu_mean; + + /*accu::mean<E_TYPE> accu_mean; util::array<float> means = labeling::compute(accu_mean, e, wst, nbasins); // Display. @@ -194,12 +303,31 @@ 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"); + }*/ + + /*typedef accu::mean<int_u12,float,int_u12> A; + util::array<int_u12> m = labeling::compute(A(), d, wst, nbasins); + + { + util::array<int_u8> m_(nbasins.next()); + m_[0] = 1; // watershed line <=> 1 + for (unsigned l = 1; l <= nbasins; ++l) + { + m_[l] = m[l] / 16; + if (m_[l] < 2) m_[l] == 2; + // basin <=> 2..255 } + mln_VAR(d_m, level::transform(wst, m_)); + mln_VAR(out, world::inter_pixel::display_edge(d_m.unmorph_(), + 0, // background <=> 0 + 3)); + io::pgm::save(out, "dist_mean.pgm"); + }*/ // Deviation. - util::array<accu::stat::deviation<float> > arr_dev; + /*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); @@ -214,19 +342,19 @@ 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); + /*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); + plot_label(input, w_simple, 187u);*/