[Olena-patches] r3500: Fix dicom_mask binary

URL: https://svn.lrde.epita.fr/svn/oln/trunk/milena/sandbox ChangeLog: 2009-03-09 Fabien Freling &lt;fabien.freling(a)lrde.epita.fr&gt; Fix dicom_mask binary. * fabien/bin/dicom_mask.cc: Fix bugs. * fabien/igr/watershed.cc: Update with watershed implementation. --- TODO | 2 ++ bin/dicom_mask.cc | 54 +++++++++++++++++++++++++++++++++++++++++++++++------- igr/watershed.cc | 37 ++++++++++++++++++++++++------------- 3 files changed, 73 insertions(+), 20 deletions(-) Index: trunk/milena/sandbox/fabien/igr/watershed.cc =================================================================== --- trunk/milena/sandbox/fabien/igr/watershed.cc (revision 3499) +++ trunk/milena/sandbox/fabien/igr/watershed.cc (revision 3500) @@ -52,6 +52,7 @@ #include <mln/draw/box.hh> #include <mln/level/stretch.hh> #include <mln/fun/v2v/id.hh> +#include <mln/fun/l2l/wrap.hh> #include <mln/core/image/line_graph_elt_neighborhood.hh> #include <mln/morpho/elementary/dilation.hh> #include <mln/labeling/mean_values.hh> @@ -121,7 +122,7 @@ { // Cf. sandbox/theo/color/segment_rgb_pixels.cc - util::array<vec3d_f> m_3f = labeling::compute(accu::mean<mln_value(I)>(), + util::array<float> m_3f = labeling::compute(accu::mean<mln_value(I)>(), input, // input color image w, // watershed labeling nbasins); @@ -129,11 +130,11 @@ util::array<mln_value(I)> m; convert::from_to(m_3f, m); - m[0] = literal::yellow; + m[0] = 150u; - io::ppm::save(level::transform(w, + /*io::ppm::save(level::transform(w, convert::to< fun::i2v::array<mln_value(I)> >(m)), - "wst_rag_wshd_color.ppm"); + "wst_rag_wshd_color.ppm");*/ return m; } @@ -159,7 +160,7 @@ typedef fun::i2v::array<mln_value(I)> vertex_values_t; vertex_values_t vertex_values; - // convert::from_to(mean_color_values(input, w, nbasins), vertex_values); + convert::from_to(mean_color_values(input, w, nbasins), vertex_values); mln_VAR(ima_v, (vertex_values | pv)); @@ -203,14 +204,14 @@ image2d<mln_value(I)> make_debug_graph_image(const I& input, const V& ima_v, const E& ima_e, - unsigned box_size, const value::rgb8& bg) + unsigned box_size, const value::int_u12& bg) { image2d<mln_value(I)> ima; initialize(ima, input); data::fill(ima, bg); debug::draw_graph(ima, ima_v.domain(), - pw::cst(mln_value(I)(literal::green)), + pw::cst(150u), edge_to_color<E, mln_value(I)>(ima_e)); dpoint2d tl(-box_size,-box_size); @@ -246,26 +247,35 @@ if (argc < 4) { - std::cout << "Usage: " << argv[0] << " <ima.dcm> <closure_lambda> <box_size>" + std::cout << "Usage: " << argv[0] << " <ima.dcm> <closure_lambda> <box_size> <dist_max>" << std::endl; return 1; } + unsigned closure_lambda = atoi(argv[2]); unsigned box_size = atoi(argv[3]); + unsigned dist_max = atoi(argv[4]); image2d<int_u12> dcm; io::dicom::load(dcm, argv[1]); + io::pgm::save(level::stretch(int_u8(), dcm), "wsd_01_src.pgm"); + image2d<int_u12> grad = morpho::gradient(dcm, win_c4p()); - image2d<int_u12> clo = morpho::closing::area(grad, c4(), atoi(argv[2])); + image2d<int_u12> clo = morpho::closing::area(grad, c4(), closure_lambda); label_16 nbasins; image2d<label_16> wshed = morpho::meyer_wst(clo, c4(), nbasins); + io::pgm::save(level::stretch(int_u8(), clo), "wsd_02.pgm"); + io::pgm::save(level::transform(wshed, fun::l2l::wrap<int_u8>()), "wsd_03.pgm"); + mln_VAR(vol2_, morpho::elementary::dilation(extend(wshed | (pw::value(wshed) == 0u), wshed), c8())); data::fill((wshed | (pw::value(wshed) == 0u)).rw(), vol2_); + io::pgm::save(level::transform(wshed, fun::l2l::wrap<int_u8>()), "wsd_04.pgm"); + /// Build graph util::graph g = make::graph(wshed, c4(), nbasins); // Build graph images and compute distance values with a RGB image. @@ -282,8 +292,7 @@ { unsigned v1 = e.element().v1(); unsigned v2 = e.element().v2(); - if (ima_e(e) <= (unsigned)(atoi(argv[5])) - && find_root(parent, v1) != find_root(parent, v2)) + if (ima_e(e) <= dist_max && find_root(parent, v1) != find_root(parent, v2)) parent[find_root(parent, v1)] = find_root(parent, v2); } @@ -302,6 +311,7 @@ --nbasins2; // nbasins2 does not count the basin with label 0. image2d<label_16> wsd2 = level::transform(wshed, f); + io::pgm::save(level::transform(wsd2, fun::l2l::wrap<int_u8>()), "wsd_05.pgm"); /// Reconstruct a graph from the simplified image. util::graph g2 = make::graph(wsd2, c4(), nbasins2); @@ -314,7 +324,8 @@ data::fill((wsd2 | (pw::value(wsd2) == 0u)).rw(), wsd2_); + io::pgm::save(level::transform(wsd2, fun::l2l::wrap<int_u8>()), "wsd_99_result.pgm"); //io::ppm::save(labeling::mean_values(dcm, wsd2, nbasins2), "wst_rag_mean_colors.ppm"); - //io::ppm::save(make_debug_graph_image(dcm, ima_v2, ima_e2, box_size, literal::white), "wst_rag_graph_image2_white.ppm"); - //io::ppm::save(make_debug_graph_image(dcm, ima_v2, ima_e2, box_size, literal::black), "wst_rag_graph_image2_black.ppm"); + io::pgm::save(make_debug_graph_image(dcm, ima_v2, ima_e2, box_size, 4095), "wsd_graph_image2_white.pgm"); + io::pgm::save(make_debug_graph_image(dcm, ima_v2, ima_e2, box_size, 0), "wsd_graph_image2_black.pgm"); } Index: trunk/milena/sandbox/fabien/TODO =================================================================== --- trunk/milena/sandbox/fabien/TODO (revision 3499) +++ trunk/milena/sandbox/fabien/TODO (revision 3500) @@ -21,3 +21,5 @@ [X] Create dicom2dump (2d, 3d, int_u8, int_u12) [ ] After threshold, take biggest object and then erode, dilate [ ] Fix n_max +[ ] Create routine for binary images (keep n big bg & m big objects) +[ ] US: projection of internal gradient Index: trunk/milena/sandbox/fabien/bin/dicom_mask.cc =================================================================== --- trunk/milena/sandbox/fabien/bin/dicom_mask.cc (revision 3499) +++ trunk/milena/sandbox/fabien/bin/dicom_mask.cc (revision 3500) @@ -1,5 +1,7 @@ #include <mln/core/concept/image.hh> #include <mln/core/image/image2d.hh> +#include <mln/core/alias/neighb2d.hh> +#include <mln/core/var.hh> #include <mln/geom/ncols.hh> #include <mln/geom/nrows.hh> @@ -9,6 +11,7 @@ #include <mln/io/pbm/save.hh> #include <mln/literal/colors.hh> +#include <mln/morpho/elementary/gradient_internal.hh> #include <mln/level/transform.hh> #include <mln/fun/v2b/threshold.hh> @@ -36,29 +39,66 @@ image2d<int_u8> input; io::dicom::load(input, argv[1]); - util::array<unsigned> xproj(geom::nrows(input), 0); - util::array<unsigned> yproj(geom::ncols(input), 0); + util::array<unsigned> xsrcproj(geom::nrows(input), 0); + util::array<unsigned> ysrcproj(geom::ncols(input), 0); - mln_piter_(image2d<int_u8>) p(input.domain()); + mln_piter_(image2d<int_u8>) psrc(input.domain()); + for_all(psrc) + { + xsrcproj[psrc.row()] += input(psrc); + ysrcproj[psrc.col()] += input(psrc); + } + std::ofstream fout_xsrc("xsrc.plot"); + for (unsigned int i = 0; i < xsrcproj.nelements(); ++i) + { + fout_xsrc << i << " " << xsrcproj[i] << std::endl; + } + std::ofstream fout_ysrc("ysrc.plot"); + for (unsigned int i = 0; i < ysrcproj.nelements(); ++i) + { + fout_ysrc << i << " " << ysrcproj[i] << std::endl; + } + + image2d<bool> ima = level::transform(input, fun::v2b::threshold<int_u8>(1)); + io::pbm::save(ima, argv[2]); + mln_VAR(grad_int, morpho::elementary::gradient_internal(ima, c4())); + + util::array<unsigned> xproj(geom::nrows(ima), 0); + util::array<unsigned> yproj(geom::ncols(ima), 0); + util::array<unsigned> xgradproj(geom::nrows(grad_int), 0); + util::array<unsigned> ygradproj(geom::ncols(grad_int), 0); + + mln_piter_(image2d<bool>) p(ima.domain()); for_all(p) { - xproj[p.row()] += input(p); - yproj[p.col()] += input(p); + if (ima(p)) + { + ++xproj[p.row()]; + ++yproj[p.col()]; + } + } + mln_piter_(image2d<int_u8>) pgrad(grad_int.domain()); + for_all(pgrad) + { + xgradproj[pgrad.row()] += grad_int(pgrad); + ygradproj[pgrad.col()] += grad_int(pgrad); } // Plot files std::ofstream fout_x("x.plot"); + std::ofstream fout_xgrad("xgrad.plot"); for (unsigned int i = 0; i < xproj.nelements(); ++i) { fout_x << i << " " << xproj[i] << std::endl; + fout_xgrad << i << " " << xgradproj[i] << std::endl; } std::ofstream fout_y("y.plot"); + std::ofstream fout_ygrad("ygrad.plot"); for (unsigned int i = 0; i < yproj.nelements(); ++i) { fout_y << i << " " << yproj[i] << std::endl; + fout_ygrad << i << " " << ygradproj[i] << std::endl; } - image2d<bool> ima = level::transform(input, fun::v2b::threshold<int_u8>(1)); - io::pbm::save(ima, argv[2]); }