[Olena-patches] r3947: Add mean images output

URL: https://svn.lrde.epita.fr/svn/oln/trunk/milena/sandbox ChangeLog: 2009-06-02 Fabien Freling &lt;fabien.freling(a)lrde.epita.fr&gt; Add mean images output. * fabien/igr/check_dist.sh: New script for testing dist_edges. * fabien/igr/check_edges.sh: New script for testing distance and watershed computation. * fabien/igr/dist_edges.cc: Small update. * fabien/igr/mean_median_label.cc: Output images. * fabien/igr/tmax.sh: New script for testing. * fabien/igr/wst_edges.cc: Small update. --- check_dist.sh | 19 +++++++++++++++++ check_edges.sh | 43 ++++++++++++++++++++++++++++++++++++++ dist_edges.cc | 8 +++---- mean_median_label.cc | 57 +++++++++++++++++++++++++++++++-------------------- tmax.sh | 23 ++++++++++++++++++++ wst_edges.cc | 3 +- 6 files changed, 126 insertions(+), 27 deletions(-) Index: trunk/milena/sandbox/fabien/igr/mean_median_label.cc =================================================================== --- trunk/milena/sandbox/fabien/igr/mean_median_label.cc (revision 3946) +++ trunk/milena/sandbox/fabien/igr/mean_median_label.cc (revision 3947) @@ -86,6 +86,18 @@ filename); } + template <typename I> + void io_save_edges_float(const I& input, + value::int_u8 bg, + const std::string& filename) + { + mln_ch_value(I, value::int_u8) output = data::stretch(int_u8(), input); + io::pgm::save(world::inter_pixel::display_edge(output.unmorph_(), + bg, + 3), + filename); + } + } // end of namespace mln @@ -96,29 +108,34 @@ int usage(const char* bin) { - std::cout << "Usage: " << bin << " input.dump wst.dump" << std::endl; + std::cout << "Usage: " << bin << " dist.dump wst.dump nbasins" << std::endl; return 1; } int main(int argc, char* argv[]) { - if (argc != 3) + if (argc != 4) return usage(argv[0]); + label_16 nbasins = atoi(argv[3]); // Initialization. typedef float input_type; - image2d<input_type> input; - io::dump::load(input, argv[1]); - image2d<label_16> wst; - io::dump::load(input`, argv[1]); + image2d<int_u12> dist_input; + io::dump::load(dist_input, argv[1]); + mln_VAR(dist, dist_input | world::inter_pixel::is_separator()); + + image2d<label_16> wst_input; + io::dump::load(wst_input, argv[2]); + mln_VAR(wst, wst_input | world::inter_pixel::is_separator()); + // Mean distance. - accu::mean<E_TYPE> accu_mean; - util::array<float> means = labeling::compute(accu_mean, e, wst, nbasins); + accu::mean<input_type> accu_mean; + util::array<float> means = labeling::compute(accu_mean, dist, wst, nbasins); // Display. { @@ -127,13 +144,12 @@ 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), "means.pgm"); + data::fill((ima_means | pw::value(ima_means) == pw::cst(i)).rw(), (unsigned) means[i]); + io_save_edges_float(ima_means, 0u, "means.pgm"); } - typedef accu::mean<int_u12,float,int_u12> A; - util::array<int_u12> m = labeling::compute(A(), d, wst, nbasins); + typedef accu::mean<input_type> A; + util::array<input_type> m = labeling::compute(A(), dist, wst, nbasins); { util::array<int_u8> m_(nbasins.next()); @@ -141,14 +157,12 @@ for (unsigned l = 1; l <= nbasins; ++l) { m_[l] = m[l] / 16; - if (m_[l] < 2) m_[l] == 2; + if (m_[l] < 2u) + m_[l] = 2u; // 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"); + mln_VAR(d_m, data::transform(wst, m_)); + io_save_edges_float(d_m, 0u, "dist_mean.pgm"); } @@ -157,7 +171,7 @@ 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); + util::array<float> deviations = labeling::compute(arr_dev, dist, wst, nbasins); // Display. { @@ -167,8 +181,7 @@ 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), "dev.pgm"); + io_save_edges_float(ima_dev, 0u, "dev.pgm"); } Index: trunk/milena/sandbox/fabien/igr/tmax.sh =================================================================== --- trunk/milena/sandbox/fabien/igr/tmax.sh (revision 0) +++ trunk/milena/sandbox/fabien/igr/tmax.sh (revision 3947) @@ -0,0 +1,23 @@ +#!/bin/zsh + + +process_file () +{ + echo "Processing $1..." | cowsay + input=$1 + dim=$2 + + ./crop $input 0 50 90 149 230 170 crop.dump + ./norm crop.dump norm.dump + ./time_max_norm norm.dump + + convert tmax_max.pgm tmax_max.png + convert tmax_smooth_max.pgm tmax_smooth_max.png + convert tmax_time.pgm tmax_time.png + convert tmax_smooth_time.pgm tmax_smooth_time.png + rm tmax_*.pgm +} + +# 3D (2D + t) images only +make crop norm time_max_norm +process_file "/Users/HiSoKa/Work/IGR/souris18/irm/IM_0052.dcm" 3 52 Property changes on: trunk/milena/sandbox/fabien/igr/tmax.sh ___________________________________________________________________ Name: svn:executable + * Index: trunk/milena/sandbox/fabien/igr/check_edges.sh =================================================================== --- trunk/milena/sandbox/fabien/igr/check_edges.sh (revision 0) +++ trunk/milena/sandbox/fabien/igr/check_edges.sh (revision 3947) @@ -0,0 +1,43 @@ +#!/bin/sh + + +process () +{ + ./dist_edges $1 -1 $2 dist${2}.dump + if [ $? -gt 0 ]; then + echo "error: dist_edges failed" + exit + fi + nbasins=`./wst_edges dist${2}.dump $3` + if [ $? -gt 0 ]; then + echo "error: wst_edges failed" + exit + fi + ./mean_median_label dist${2}.dump watershed.dump $nbasins + if [ $? -gt 0 ]; then + echo "error: mean_median_label failed" + echo "nbasins: $nbasins" + exit + fi + + convert dist.pgm dist${2}.png + convert watershed.ppm watershed${2}.png + convert means.pgm means${2}.png + convert dist_mean.pgm dist_mean${2}.png + convert dev.pgm dev${2}.png + + cp watershed.dump watershed${2}.dump + + # Cleanup. + rm *.pgm *.ppm +} + +batch_process () +{ + process $1 1 $2 + process $1 2 $2 + process $1 3 $2 + process $1 4 $2 +} + +batch_process $1 $2 Property changes on: trunk/milena/sandbox/fabien/igr/check_edges.sh ___________________________________________________________________ Name: svn:executable + * Index: trunk/milena/sandbox/fabien/igr/wst_edges.cc =================================================================== --- trunk/milena/sandbox/fabien/igr/wst_edges.cc (revision 3946) +++ trunk/milena/sandbox/fabien/igr/wst_edges.cc (revision 3947) @@ -124,7 +124,8 @@ L nbasins; mln_VAR(wst, morpho::watershed::flooding(d_clo, world::inter_pixel::e2e(), nbasins)); - std::cout << "nbasins: " << nbasins << std::endl; + + std::cout << nbasins << std::endl; mln_VAR(w_all, wst.unmorph_()); Index: trunk/milena/sandbox/fabien/igr/check_dist.sh =================================================================== --- trunk/milena/sandbox/fabien/igr/check_dist.sh (revision 0) +++ trunk/milena/sandbox/fabien/igr/check_dist.sh (revision 3947) @@ -0,0 +1,19 @@ +#!/bin/sh + + +process () +{ + ./dist_edges $1 -1 $2 dist${2}.dump + convert dist.pgm dist${2}.png + rm dist*.pgm +} + +batch_process () +{ + process $1 1 + process $1 2 + process $1 3 + process $1 4 +} + +batch_process $1 $2 Property changes on: trunk/milena/sandbox/fabien/igr/check_dist.sh ___________________________________________________________________ Name: svn:executable + * Index: trunk/milena/sandbox/fabien/igr/dist_edges.cc =================================================================== --- trunk/milena/sandbox/fabien/igr/dist_edges.cc (revision 3946) +++ trunk/milena/sandbox/fabien/igr/dist_edges.cc (revision 3947) @@ -95,7 +95,7 @@ res /= std::max(sum_v1, sum_v2); res = 1 - res; - res = res * 4095; + res = (res * 4095) + 0.49; return (int) res; } @@ -123,7 +123,7 @@ res = res / v1.nelements(); res = 1 - res; - res = res * 4095; + res = (res * 4095) + 0.49; return (int) res; } @@ -152,7 +152,7 @@ res = min / max; res = 1 - res; - res = res * 4095; + res = (res * 4095) + 0.49; return (int) res; } @@ -181,7 +181,7 @@ res = res / v1.nelements(); //res = 1 - res; - res = res * 4095; + res = (res * 4095) + 0.49; return (int) res; }