April 2009 - Olena-patches

3711: Fix documentation distributed files.
by Guillaume Lazzara 27 Apr '09

27 Apr '09

* doc/examples/examples.mk, * doc/figures/figures.mk, * doc/outputs/outputs.mk, * doc/generate_dist_files.sh: do not add distributed files in EXTRA_DIST. * doc/examples/samples.mk: remove since useless now. --- milena/ChangeLog | 12 +++++ milena/doc/examples/examples.mk | 89 +------------------------------------ milena/doc/examples/samples.mk | 55 ----------------------- milena/doc/figures/figures.mk | 3 +- milena/doc/generate_dist_files.sh | 8 ++- milena/doc/outputs/outputs.mk | 4 +- 6 files changed, 23 insertions(+), 148 deletions(-) delete mode 100644 milena/doc/examples/samples.mk diff --git a/milena/ChangeLog b/milena/ChangeLog index 03a2bdb..10a5cc4 100644 --- a/milena/ChangeLog +++ b/milena/ChangeLog @@ -1,5 +1,17 @@ 2009-04-27 Guillaume Lazzara <lazzara(a)lrde.epita.fr> + Fix documentation distributed files. + + * doc/examples/examples.mk, + * doc/figures/figures.mk, + * doc/outputs/outputs.mk, + * doc/generate_dist_files.sh: do not add distributed files in + EXTRA_DIST. + + * doc/examples/samples.mk: remove since useless now. + +2009-04-27 Guillaume Lazzara <lazzara(a)lrde.epita.fr> + Fix seeds2tiling_roundness test. * mln/geom/chamfer.hh: Fix a too restrictive test (true == 1 but not > diff --git a/milena/doc/examples/examples.mk b/milena/doc/examples/examples.mk index 4449d52..3ae418c 100644 --- a/milena/doc/examples/examples.mk +++ b/milena/doc/examples/examples.mk @@ -1,96 +1,9 @@ ## Generated by ../generate_dist_files, do not modify. EXTRA_DIST += \ -examples/paste-call-1.cc \ -examples/dpoint-1.cc \ -examples/parray-append.cc \ -examples/trash \ -examples/trash/cpp_issue.cc \ -examples/trash/sub_image.cc \ -examples/trash/sub_image_if.cc \ -examples/trash/graph.cc \ -examples/trash/p_vaccess.cc \ -examples/trash/tuto_one.cc \ -examples/trash/win_multiple.cc \ -examples/trash/image2d.cc \ -examples/trash/image_plain.cc \ -examples/trash/p_run.cc \ -examples/trash/proxy.cc \ -examples/trash/p_array.2.cc \ -examples/trash/labeling_algo.cc \ -examples/trash/for_Z.cc \ -examples/trash/image_if.cc \ -examples/trash/p_key.cc \ -examples/trash/p_mutable_array_of.cc \ -examples/trash/p_queue.cc \ -examples/trash/image_flat.cc \ -examples/trash/p_image.cc \ -examples/trash/mk_graph.cc \ -examples/trash/box.cc \ -examples/trash/p_line2d.cc \ -examples/trash/p_array.cc \ -examples/trash/accu.cc \ -examples/trash/p_key.2.cc \ -examples/trash/window.cc \ -examples/trash/tuto_bis.cc \ -examples/trash/image_safe.cc \ -examples/trash/erosion.cc \ -examples/trash/vec.cc \ examples/fill-proto.cc.raw \ examples/ima2d-restricted-1.cc.raw \ -examples/graph-iter.cc \ -examples/labeling-compute.cc \ -examples/ima2d-7.cc \ examples/ima2d-restricted-2.cc.raw \ -examples/fill-subimage-cfun.cc \ -examples/ima-save.cc \ -examples/point-1.cc \ -examples/box2d-bbox.cc \ -examples/forall-piter.cc \ -examples/ima-size.cc \ -examples/tuto2 \ -examples/examples.mk \ -examples/tuto4 \ -examples/borderthickness.cc \ -examples/Makefile.in \ -examples/ima-load.cc \ -examples/ima-has.cc \ -examples/win-create-1.cc \ -examples/samples.mk \ -examples/tuto3 \ examples/tuto3/fill_non_generic.cc.raw \ -examples/tuto3/colorize.cc \ -examples/tuto3/println.cc \ -examples/tuto3/trace.cc \ -examples/tuto3/first_routine.cc \ examples/accu-wrong-instanciation.cc.raw \ -examples/accu-right-instanciation.cc \ -examples/ima2d-5.cc \ -examples/fill-subdomain.cc \ -examples/fill-subdomain-shorter.cc \ -examples/tuto3_rw_image.cc \ -examples/ima2d-2.cc \ -examples/extension-ignore.cc \ -examples/extend.cc \ -examples/Makefile.am \ -examples/parray-bbox.cc \ -examples/graph-data.cc \ -examples/mln_var.cc \ -examples/ima2d-4.cc \ -examples/predicate-1.cc \ -examples/ima2d-3.cc \ -examples/tuto2_first_image.cc \ -examples/ima2d-1.cc \ -examples/estim-sites.cc \ -examples/ima2d-6-clone.cc \ -examples/ima2d-restricted-3.cc.raw \ -examples/logical-not.cc \ -examples/fun-p2v-1.cc \ -examples/ima2d-rot.cc \ -examples/fill-part-image.cc \ -examples/domain-display.cc \ -examples/tuto4_genericity_and_algorithms.cc \ -examples/paste.cc \ -examples/fill.cc \ -examples/fill-call-1.cc \ -examples/win-create-2.cc +examples/ima2d-restricted-3.cc.raw diff --git a/milena/doc/examples/samples.mk b/milena/doc/examples/samples.mk deleted file mode 100644 index e0e3f5d..0000000 --- a/milena/doc/examples/samples.mk +++ /dev/null @@ -1,55 +0,0 @@ -## Generated by ../generate_dist_files, do not modify. - -EXTRA_DIST += \ -samples/paste-call-1.cc \ -samples/dpoint-1.cc \ -samples/parray-append.cc \ -samples/fill-proto.cc.raw \ -samples/ima2d-restricted-1.cc.raw \ -samples/graph-iter.cc \ -samples/labeling-compute.cc \ -samples/ima2d-7.cc \ -samples/ima2d-restricted-2.cc.raw \ -samples/fill-subimage-cfun.cc \ -samples/ima-save.cc \ -samples/point-1.cc \ -samples/box2d-bbox.cc \ -samples/forall-piter.cc \ -samples/ima-size.cc \ -samples/borderthickness.cc \ -samples/Makefile.in \ -samples/ima-load.cc \ -samples/ima-has.cc \ -samples/win-create-1.cc \ -samples/samples.mk \ -samples/accu-wrong-instanciation.cc.raw \ -samples/accu-right-instanciation.cc \ -samples/ima2d-5.cc \ -samples/fill-subdomain.cc \ -samples/fill-subdomain-shorter.cc \ -samples/tuto3_rw_image.cc \ -samples/ima2d-2.cc \ -samples/extension-ignore.cc \ -samples/extend.cc \ -samples/Makefile.am \ -samples/parray-bbox.cc \ -samples/graph-data.cc \ -samples/mln_var.cc \ -samples/ima2d-4.cc \ -samples/predicate-1.cc \ -samples/ima2d-3.cc \ -samples/tuto2_first_image.cc \ -samples/ima2d-1.cc \ -samples/estim-sites.cc \ -samples/ima2d-6-clone.cc \ -samples/ima2d-restricted-3.cc.raw \ -samples/logical-not.cc \ -samples/fun-p2v-1.cc \ -samples/ima2d-rot.cc \ -samples/fill-part-image.cc \ -samples/domain-display.cc \ -samples/tuto4_genericity_and_algorithms.cc \ -samples/paste.cc \ -samples/fill.cc \ -samples/fill-call-1.cc \ -samples/win-create-2.cc diff --git a/milena/doc/figures/figures.mk b/milena/doc/figures/figures.mk index 42d8724..2602b31 100644 --- a/milena/doc/figures/figures.mk +++ b/milena/doc/figures/figures.mk @@ -16,14 +16,15 @@ figures/tuto4_genericity_and_algorithms-9.ppm \ figures/logical-not-1.pbm \ figures/ima_save.pbm \ figures/tuto2_first_image-1.pbm \ -figures/figures.mk \ figures/fill-subimage-cfun-1.ppm \ figures/extend-3.ppm \ figures/fill-subdomain-4.ppm \ +figures/colorize-1.pgm \ figures/tuto4_genericity_and_algorithms-7.ppm \ figures/tuto4_genericity_and_algorithms-6.ppm \ figures/extend-5.ppm \ figures/logical-not-3.pbm \ +figures/colorize-2.ppm \ figures/tuto4_genericity_and_algorithms-3.pbm \ figures/tuto4_genericity_and_algorithms-1.ppm \ figures/extend-4.ppm \ diff --git a/milena/doc/generate_dist_files.sh b/milena/doc/generate_dist_files.sh index df2daad..e7c3b38 100755 --- a/milena/doc/generate_dist_files.sh +++ b/milena/doc/generate_dist_files.sh @@ -13,9 +13,11 @@ for dir in figures outputs examples; do echo "## Generated by ../generate_dist_files, do not modify." > $OUT echo >>$OUT $ECHO_N "EXTRA_DIST += " >> $OUT - for file in `find $dir -mindepth 1`; do - echo " \\" >> $OUT - $ECHO_N $file >> $OUT + for ftype in cc.raw p*m txt; do + for file in `find $dir -mindepth 1 -name *.$ftype`; do + echo " \\" >> $OUT + $ECHO_N $file >> $OUT + done done echo "" >> $OUT done diff --git a/milena/doc/outputs/outputs.mk b/milena/doc/outputs/outputs.mk index bb57832..ac10062 100644 --- a/milena/doc/outputs/outputs.mk +++ b/milena/doc/outputs/outputs.mk @@ -2,6 +2,7 @@ EXTRA_DIST += \ outputs/win-create-1-display.txt \ +outputs/trace.txt \ outputs/win-create-2.txt \ outputs/accu-right-instanciation.txt \ outputs/extend.txt \ @@ -29,12 +30,13 @@ outputs/fill-subdomain.txt \ outputs/ima-size.txt \ outputs/tuto2_first_image.txt \ outputs/logical-not.txt \ +outputs/colorize.txt \ outputs/ima2d-display-output-2.txt \ outputs/ima2d-decl-2.txt \ outputs/paste.txt \ -outputs/outputs.mk \ outputs/ima2d-6-clone.txt \ outputs/ima2d-7.txt \ +outputs/println.txt \ outputs/tuto3_rw_image.txt \ outputs/parray-bbox.txt \ outputs/domain-display.txt \ -- 1.5.6.5

1 0

3710: Fix seeds2tiling_roundness test.
by Guillaume Lazzara 27 Apr '09

27 Apr '09

* mln/geom/chamfer.hh: Fix a too restrictive test (true == 1 but not > 0). * mln/geom/seeds2tiling_roundness.hh: Fix wrong declaration/use of p_priority site_set. Priority was based on sites and not on priority values. --- milena/ChangeLog | 11 +++++++++++ milena/mln/geom/chamfer.hh | 8 ++++---- milena/mln/geom/seeds2tiling_roundness.hh | 13 +++++++------ 3 files changed, 22 insertions(+), 10 deletions(-) diff --git a/milena/ChangeLog b/milena/ChangeLog index 03d1aa9..03a2bdb 100644 --- a/milena/ChangeLog +++ b/milena/ChangeLog @@ -1,3 +1,14 @@ +2009-04-27 Guillaume Lazzara <lazzara(a)lrde.epita.fr> + + Fix seeds2tiling_roundness test. + + * mln/geom/chamfer.hh: Fix a too restrictive test (true == 1 but not > + 0). + + * mln/geom/seeds2tiling_roundness.hh: Fix wrong declaration/use of + p_priority site_set. Priority was based on sites and not on priority + values. + 2009-04-20 Thierry Geraud <thierry.geraud(a)lrde.epita.fr> Improve vector and matrix interoperability. diff --git a/milena/mln/geom/chamfer.hh b/milena/mln/geom/chamfer.hh index 4967a66..0358a83 100644 --- a/milena/mln/geom/chamfer.hh +++ b/milena/mln/geom/chamfer.hh @@ -1,5 +1,5 @@ -// Copyright (C) 2007, 2008 EPITA Research and Development Laboratory -// (LRDE) +// Copyright (C) 2007, 2008, 2009 EPITA Research and Development +// Laboratory (LRDE) // // This file is part of the Olena Library. This library is free // software; you can redistribute it and/or modify it under the terms @@ -78,8 +78,8 @@ namespace mln mln_piter(O) p(output.domain()); for_all(p) { - if (input(p) == true) - output(p) = 0; + if (input(p)) + output(p) = 0u; else output(p) = max; } diff --git a/milena/mln/geom/seeds2tiling_roundness.hh b/milena/mln/geom/seeds2tiling_roundness.hh index 865198b..4b37999 100644 --- a/milena/mln/geom/seeds2tiling_roundness.hh +++ b/milena/mln/geom/seeds2tiling_roundness.hh @@ -88,15 +88,16 @@ namespace mln I& ima = exact(ima_); const N& nbh = exact(nbh_); image2d<unsigned> dist = geom::chamfer(ima, w_win, max); + I out = duplicate(ima_); - p_priority<mln_psite(I), p_queue_fast<unsigned> > q; + p_priority<unsigned, p_queue_fast<mln_psite(I)> > q; // Init. { mln_piter(I) p(ima.domain()); for_all(p) - q.push(p, max - dist(p)); + q.push(max - dist(p), p); } @@ -104,14 +105,14 @@ namespace mln { while (! q.is_empty()) { - mln_psite(I) p = q.highest_priority(); - q.pop(); - if (out(p) != 0) // p has already been processed so ignore + mln_psite(I) p = q.pop_front(); + + if (out(p) != literal::zero) // p has already been processed so ignore continue; mln_niter(N) n(nbh, p); for_all(n) if (ima.has(n)) - if (out(n) != 0) + if (out(n) != literal::zero) out(p) = out(n); } } -- 1.5.6.5

1 0

r3705: Change data type, conversion to mln dump not yet effective
by Fabien Freling 24 Apr '09

24 Apr '09

URL: https://svn.lrde.epita.fr/svn/oln/trunk/milena/sandbox ChangeLog: 2009-04-24 Fabien Freling <fabien.freling(a)lrde.epita.fr> Change data type, conversion to mln dump not yet effective. * fabien/igr/mat2mln/raw2mlndata.cc: Change data type (double -> int). --- raw2mlndata.cc | 16 ++++++++++++++-- 1 file changed, 14 insertions(+), 2 deletions(-) Index: trunk/milena/sandbox/fabien/igr/mat2mln/raw2mlndata.cc =================================================================== --- trunk/milena/sandbox/fabien/igr/mat2mln/raw2mlndata.cc (revision 3704) +++ trunk/milena/sandbox/fabien/igr/mat2mln/raw2mlndata.cc (revision 3705) @@ -4,6 +4,13 @@ #include <mln/core/image/image3d.hh> #include <mln/io/dump/save.hh> +#include <mln/io/pgm/save.hh> +#include <mln/value/int_u8.hh> +#include <mln/level/stretch.hh> +#include <mln/core/image/slice_image.hh> +#include <mln/core/routine/duplicate.hh> +#include <mln/core/image/image2d.hh> + using namespace mln; @@ -11,7 +18,7 @@ { if (argc != 3) { - std::cout << "Usage: " << argv[0] << " input.raw output.raw" << std::endl; + std::cout << "Usage: " << argv[0] << " input.raw output.dump" << std::endl; return 1; } @@ -99,7 +106,7 @@ std::cout << "ncols: " << ncols << "; nrows: " << nrows << "; nslis: " << nslis << std::endl; // Data buffer. - typedef double V; + typedef int V; int data_size = ncols * nrows * nslis; V* data_buffer = new V[data_size]; input.seekg(offset); @@ -109,5 +116,10 @@ memcpy(ima.buffer(), data_buffer, data_size); io::dump::save(ima, argv[2]); + // Debug. + image2d<V> ima_debug; + ima_debug = duplicate(slice(ima, 50)); + io::pgm::save(level::stretch(value::int_u8(), ima_debug), "debug.pgm"); + return 0; }

1 0

r3704: Add binary tools for parsing of .mat files
by Fabien Freling 24 Apr '09

24 Apr '09

URL: https://svn.lrde.epita.fr/svn/oln/trunk/milena/sandbox ChangeLog: 2009-04-24 Fabien Freling <fabien.freling(a)lrde.epita.fr> Add binary tools for parsing of .mat files. * fabien/igr/mat2mln/mat2raw.cc: Uncompress .mat data. * fabien/igr/mat2mln/raw2mlndata.cc: Convert uncompressed .mat data to Milena dump format. * fabien/igr/seg_fixed.cc: Creation of edges between pixels. --- TODO | 4 + igr/mat2mln/mat2raw.cc | 52 ++++++++++++++++++++ igr/mat2mln/raw2mlndata.cc | 113 +++++++++++++++++++++++++++++++++++++++++++++ igr/seg_fixed.cc | 25 ++++++--- 4 files changed, 184 insertions(+), 10 deletions(-) Index: trunk/milena/sandbox/fabien/igr/seg_fixed.cc =================================================================== --- trunk/milena/sandbox/fabien/igr/seg_fixed.cc (revision 3703) +++ trunk/milena/sandbox/fabien/igr/seg_fixed.cc (revision 3704) @@ -59,6 +59,8 @@ res += std::min(ima_arr(p)[i], ima_arr(n)[i]); res /= std::max(ima_sum(p), ima_sum(n)); + std::cout << "dist = " << res << std::endl; + return res; } @@ -87,15 +89,21 @@ initialize(ima_sum, ima_arr); compute_sum_arrays(ima_sum, ima_arr); + std::cout << "can i has a loop?" << std::endl; mln_piter(image2d<util::array<I> >) p(ima_arr.domain()); - mln_niter(neighb2d) n(c4(), p); for_all(p) + { + std::cout << "for_all(p)" << std::endl; + mln_niter(neighb2d) n(c4(), p); for_all(n) { + std::cout << "for_all(n)" << std::endl; point2d location = get_edge_location(p, n); - if (edges(location) != -1) + std::cout << "location = " << p << " && edge = " << edges(location) << std::endl; + if (edges(location) == -1.f) edges(location) = compute_dist(ima_arr, ima_sum, p, n); } + } return edges; } @@ -112,23 +120,22 @@ int main(int argc, char* argv[]) { - typedef int_u12 I; - if (argc != 2) return usage(argv[0]); - image3d<I> input; - io::dump::save(input, argv[1]); - image2d<util::array<I> > ima_arr; + image3d<int_u12> input; + io::dump::load(input, argv[1]); + image2d<util::array<int_u12> > ima_arr; initialize(ima_arr, slice(input, 0)); for (unsigned int i = 0; i < input.nslices(); ++i) { - image2d<I> tmp_slice = duplicate(slice(input, i)); - mln_piter_(image2d<I>) p(tmp_slice.domain()); + 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)); } + std::cout << "ho hai _o/" << std::endl; image2d<float> edges = dist_on_edges(ima_arr); return 0; Index: trunk/milena/sandbox/fabien/igr/mat2mln/raw2mlndata.cc =================================================================== --- trunk/milena/sandbox/fabien/igr/mat2mln/raw2mlndata.cc (revision 0) +++ trunk/milena/sandbox/fabien/igr/mat2mln/raw2mlndata.cc (revision 3704) @@ -0,0 +1,113 @@ +#include <iostream> +#include <fstream> + +#include <mln/core/image/image3d.hh> +#include <mln/io/dump/save.hh> + +using namespace mln; + + +int main(int argc, char* argv[]) +{ + if (argc != 3) + { + std::cout << "Usage: " << argv[0] << " input.raw output.raw" << std::endl; + return 1; + } + + std::ifstream input(argv[1]); + + unsigned int size = 0; + unsigned int offset = 0; + + // Top level miMATRIX. + offset += 4; + input.seekg(offset); + input.read((char*) &size, sizeof (unsigned int)); + offset += sizeof (unsigned int); + std::cout << "Size: " << size << std::endl; + + // Array flags. + offset += 4; + input.seekg(offset); + input.read((char*) &size, sizeof (unsigned int)); + offset += sizeof (unsigned int); + std::cout << "Flags size: " << size << std::endl; + + // Dimensions array. + offset += size; + offset += 4; + input.seekg(offset); + input.read((char*) &size, sizeof (unsigned int)); + offset += sizeof (unsigned int); + std::cout << "Dimensions size: " << size << std::endl; + + // Array name. + offset += size; + offset += 4; + input.seekg(offset); + input.read((char*) &size, sizeof (unsigned int)); + offset += sizeof (unsigned int); + std::cout << "Name size: " << size << std::endl; + char* name = new char[size + 1]; + input.seekg(offset); + input.read((char*) name, size); + name[size + 1] = '\0'; + std::cout << "Array name: " << name << std::endl; + delete name; + offset += 8 - size % 8; + + std::cout << "----" << std::endl; + // FIXME: Decode data. + + offset = 128; + + // Data miMATRIX. + offset += 4; + input.seekg(offset); + input.read((char*) &size, sizeof (unsigned int)); + offset += sizeof (unsigned int); + std::cout << "Data size: " << size << std::endl; + + // Array flags. + offset += 4; + input.seekg(offset); + input.read((char*) &size, sizeof (unsigned int)); + offset += sizeof (unsigned int); + std::cout << "Flags size: " << size << std::endl; + + // Dimensions array. + offset += size; + offset += 4; + input.seekg(offset); + input.read((char*) &size, sizeof (unsigned int)); + offset += sizeof (unsigned int); + std::cout << "Dimensions size: " << size << std::endl; + std::cout << "Number of dimensions: " << size / 4 << std::endl; + int ncols = 0; + int nrows = 0; + int nslis = 0; + input.seekg(offset); + input.read((char*) &ncols, sizeof (unsigned int)); + offset += sizeof (unsigned int); + input.seekg(offset); + input.read((char*) &nrows, sizeof (unsigned int)); + offset += sizeof (unsigned int); + input.seekg(offset); + input.read((char*) &nslis, sizeof (unsigned int)); + offset += sizeof (unsigned int); + std::cout << "ncols: " << ncols << "; nrows: " << nrows << "; nslis: " << nslis << std::endl; + + // Data buffer. + typedef double V; + int data_size = ncols * nrows * nslis; + V* data_buffer = new V[data_size]; + input.seekg(offset); + input.read((char*) data_buffer, data_size); + + image3d<V> ima(nslis, nrows, ncols); + memcpy(ima.buffer(), data_buffer, data_size); + io::dump::save(ima, argv[2]); + + return 0; +} Index: trunk/milena/sandbox/fabien/igr/mat2mln/mat2raw.cc =================================================================== --- trunk/milena/sandbox/fabien/igr/mat2mln/mat2raw.cc (revision 0) +++ trunk/milena/sandbox/fabien/igr/mat2mln/mat2raw.cc (revision 3704) @@ -0,0 +1,52 @@ +#include <iostream> +#include <fstream> + +#include <zlib.h> + +int main(int argc, char* argv[]) +{ + if (argc != 3) + { + std::cout << "Usage: " << argv[0] << " input.mat output.raw" << std::endl; + return 1; + } + + std::ifstream input(argv[1]); + + // Fetch data. + unsigned int size; + input.seekg(132); + input.read((char*) &size, sizeof(unsigned int)); + std::cout << "Size: " << size << std::endl; + unsigned char* data_buffer = new unsigned char[size]; + input.read((char*) data_buffer, size); + input.close(); + + // Decompress. + unsigned long dest_size = 2 * size; + unsigned char* dest_buffer = new unsigned char[dest_size]; + int dezip_result = uncompress(dest_buffer, &dest_size, data_buffer, size); + + switch (dezip_result) + { + case Z_OK: + std::cout << "Z_OK" << std::endl; + std::cout << "Dest size: " << dest_size << std::endl; + break; + case Z_MEM_ERROR: + std::cout << "Z_MEM_ERROR" << std::endl; + break; + case Z_BUF_ERROR: + std::cout << "Z_BUF_ERROR" << std::endl; + break; + case Z_DATA_ERROR: + std::cout << "Z_DATA_ERROR" << std::endl; + break; + } + + // Write buffer to disk. + std::ofstream save_file(argv[2]); + save_file.write((char*) dest_buffer, dest_size); + + return 0; +} Index: trunk/milena/sandbox/fabien/TODO =================================================================== --- trunk/milena/sandbox/fabien/TODO (revision 3703) +++ trunk/milena/sandbox/fabien/TODO (revision 3704) @@ -49,7 +49,7 @@ [X] Fix spatial smooth [X] Crop volume 52 [X] Plot all labels (3, 4 labels for tumeur) -[ ] Prepare data for IGR +[X] Prepare data for IGR [X] crop->norm->tmax [X] crop->norm->space_smooth->tmax @@ -64,3 +64,5 @@ [X] fausses couleurs watershed [X] images moyennes +[ ] Watershed between pixels +[ ] Mat2Mln

1 0

r3699: Granulometry tests
by Edwin Carlinet 22 Apr '09

22 Apr '09

URL: https://svn.lrde.epita.fr/svn/oln/trunk/milena/sandbox ChangeLog: 2009-04-22 Edwin Carlinet <carlinet(a)lrde.epita.fr> Granulometry tests. * edwin/rush/exo2/test.cc: Experimentation related to sharpness. * edwin/rush/exo2/wst_from_tree.cc: Fix bugs linked to sharpness attribute. * edwin/rush/granulometry/granulometry.hh: Compute curve number of components / attribute value. * edwin/rush/granulometry/test.cc: Test file for granulometry. * edwin/rush/granulometry: New. * edwin/tree/components.hh: Minor fixes. * edwin/tree/propagate.hh: Minor fixes. --- rush/exo2/Makefile | 2 rush/exo2/test.cc | 131 +++++++++++++++++++++++++++++++++ rush/exo2/wst_from_tree.cc | 2 rush/granulometry/Makefile | 36 +++++++++ rush/granulometry/granulometry.hh | 149 ++++++++++++++++++++++++++++++++++++++ rush/granulometry/test.cc | 107 +++++++++++++++++++++++++++ tree/components.hh | 4 - tree/propagate.hh | 8 +- 8 files changed, 431 insertions(+), 8 deletions(-) Index: trunk/milena/sandbox/edwin/tree/propagate.hh =================================================================== --- trunk/milena/sandbox/edwin/tree/propagate.hh (revision 3698) +++ trunk/milena/sandbox/edwin/tree/propagate.hh (revision 3699) @@ -77,16 +77,16 @@ const p_array< mln_psite(A) >& component_list, const mln_value(A)& null) { - const A& attr_img = exact(attr_image); + const A& a = exact(attr_image); A out; - initialize(out, attr_img); + initialize(out, a); data::fill(out, null); mln_piter(p_array<mln_psite(A)>) p(component_list); for_all(p) { - out(p) = attr_img(p); - morpho::tree::propagate_node_to_descendants(p, tree, out); + out(p) = a(p); + morpho::tree::propagate_node_to_descendants(p, tree, out, a(p)); } morpho::tree::propagate_representant(tree, out); return out; Index: trunk/milena/sandbox/edwin/tree/components.hh =================================================================== --- trunk/milena/sandbox/edwin/tree/components.hh (revision 3698) +++ trunk/milena/sandbox/edwin/tree/components.hh (revision 3699) @@ -222,7 +222,7 @@ p_array< mln_psite(A) > components; mln_ch_value(A, bool) activity; p_array< mln_psite(A) > max_arr = tree.nodes(); - unsigned arr_pos; //position in max_array + unsigned arr_pos = 0; //position in max_array unsigned n = 0; unsigned* nb_leaves = uses_leaves ? new unsigned(0) : 0; @@ -237,7 +237,7 @@ p = max_arr[arr_pos]; if (a(p) == 0) break; - //std::cout << p << " " << a(p) << std::endl; + std::cout << p << " " << a(p) << std::endl; components.insert(p); morpho::tree::propagate_node_to_descendants(p, tree, activity, false, nb_leaves); morpho::tree::propagate_node_to_ancestors(p, tree, activity, false); Index: trunk/milena/sandbox/edwin/rush/granulometry/test.cc =================================================================== --- trunk/milena/sandbox/edwin/rush/granulometry/test.cc (revision 0) +++ trunk/milena/sandbox/edwin/rush/granulometry/test.cc (revision 3699) @@ -0,0 +1,107 @@ +// Copyright (C) 2007, 2008, 2009 EPITA Research and Development Laboratory +// (LRDE) +// +// This file is part of the Olena Library. This library is free +// software; you can redistribute it and/or modify it under the terms +// of the GNU General Public License version 2 as published by the +// Free Software Foundation. +// +// This library is distributed in the hope that it will be useful, +// but WITHOUT ANY WARRANTY; without even the implied warranty of +// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +// General Public License for more details. +// +// You should have received a copy of the GNU General Public License +// along with this library; see the file COPYING. If not, write to +// the Free Software Foundation, 51 Franklin Street, Fifth Floor, +// Boston, MA 02111-1307, USA. +// +// As a special exception, you may use this file as part of a free +// software library without restriction. Specifically, if other files +// instantiate templates or use macros or inline functions from this +// file, or you compile this file and link it with other files to +// produce an executable, this file does not by itself cause the +// resulting executable to be covered by the GNU General Public +// License. This exception does not however invalidate any other +// reasons why the executable file might be covered by the GNU General +// Public License. + +#include "granulometry.hh" + +#include <mln/core/image/image2d.hh> +#include <mln/core/alias/neighb2d.hh> +#include <mln/value/int_u8.hh> + +#include <mln/io/pgm/load.hh> + +#include <mln/level/sort_psites.hh> +#include <mln/morpho/tree/data.hh> +#include <mln/morpho/tree/compute_attribute_image.hh> +#include <mln/morpho/attribute/card.hh> + +#include <mln/data/fill.hh> +#include "../../tree/propagate_node.hh" + +#include <iostream> +#include <map> + +void usage(char** argv) +{ + std::cout << "Usage: " << argv[0] << " input.pgm" << std::endl; + abort(); +} + +int main(int argc, char** argv) +{ + using namespace mln; + using value::int_u8; + + if (argc != 2) + usage(argv); + + typedef image2d<int_u8> I; + I input; + io::pgm::load(input, argv[1]); + + typedef p_array<point2d> S; + typedef morpho::tree::data<I,S> tree_t; + + S s = level::sort_psites_decreasing(input); + tree_t tree(input, s, c4()); + + typedef mln_ch_value_(I, unsigned) A; + typedef morpho::attribute::card<I> card_t; + A a = morpho::tree::compute_attribute_image(card_t (), tree); + + + + { + typedef std::map<mln_value_(A), unsigned> F; + F f = morpho::tree::compute_attribute_curve_beta(tree, a); + + unsigned count; + mln_ch_value_(A, bool) activity; + initialize(activity, a); + F::iterator it; + for (it = f.begin(); it != f.end(); ++it) + { + mln_up_node_piter_(tree_t) n(tree); + data::fill(activity, true); + count = 0; + for_all(n) + if (a(n) >= it->first && activity(n)) + { + morpho::tree::propagate_node_to_ancestors(n, tree, activity, false); + count++; + } + + std::cout << it->first << " -> " << it->second << " = " << count + << std::endl; + mln_assertion(count == it->second); + } + } + + +} + + Index: trunk/milena/sandbox/edwin/rush/granulometry/granulometry.hh =================================================================== --- trunk/milena/sandbox/edwin/rush/granulometry/granulometry.hh (revision 0) +++ trunk/milena/sandbox/edwin/rush/granulometry/granulometry.hh (revision 3699) @@ -0,0 +1,149 @@ +// Copyright (C) 2007, 2008, 2009 EPITA Research and Development Laboratory +// (LRDE) +// +// This file is part of the Olena Library. This library is free +// software; you can redistribute it and/or modify it under the terms +// of the GNU General Public License version 2 as published by the +// Free Software Foundation. +// +// This library is distributed in the hope that it will be useful, +// but WITHOUT ANY WARRANTY; without even the implied warranty of +// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +// General Public License for more details. +// +// You should have received a copy of the GNU General Public License +// along with this library; see the file COPYING. If not, write to +// the Free Software Foundation, 51 Franklin Street, Fifth Floor, +// Boston, MA 02111-1307, USA. +// +// As a special exception, you may use this file as part of a free +// software library without restriction. Specifically, if other files +// instantiate templates or use macros or inline functions from this +// file, or you compile this file and link it with other files to +// produce an executable, this file does not by itself cause the +// resulting executable to be covered by the GNU General Public +// License. This exception does not however invalidate any other +// reasons why the executable file might be covered by the GNU General +// Public License. + +#ifndef GRANULOMETRY_HH_ +# define GRANULOMETRY_HH_ + +# include <mln/core/concept/image.hh> +# include <mln/core/site_set/p_array.hh> +# include <mln/morpho/tree/data.hh> + +# include <queue> +# include <map> + +namespace mln { + namespace morpho { + namespace tree { + + + template <typename T, typename A> + inline + std::map<mln_value(A), unsigned> + compute_attribute_curve_beta(const T& tree, const Image<A>& attr_img); + + + template <typename T, typename A> + inline + std::map<mln_value(A), unsigned> + compute_attribute_curve(const T& tree, const Image<A>& attr_img); + + +# ifndef MLN_INCLUDE_ONLY + + namespace internal { + + template <typename A> + struct attr_less + { + attr_less(const A& f) + : f_ (f) + { + } + + bool operator () (const mln_psite(A)& a, const mln_psite(A)& b) const + { + return (f_(a) < f_(b)); + } + + private: + const A& f_; + }; + + + } + + template <typename T, typename A> + inline + std::map<mln_value(A), unsigned> + compute_attribute_curve(const T& tree, const Image<A>& attr_img) + { + const A& a = exact(attr_img); + + std::map< mln_value(A), unsigned > f; + mln_node_piter(T) n(tree); + + for_all(n) + f[a(n)]++; + + + return f; + } + + + template <typename T, typename A> + inline + std::map<mln_value(A), unsigned> + compute_attribute_curve_beta(const T& tree, const Image<A>& attr_img) + { + const A& a = exact(attr_img); + + // TODO: precondition attribut croissant + + + typedef std::priority_queue< mln_psite(A), std::vector< mln_psite(A) >, internal::attr_less<A> > q_type; + std::map< mln_value(A), unsigned > f; + internal::attr_less<A> cmp(a); + q_type pqueue(cmp); + unsigned active_components = 1; + + pqueue.push(tree.nodes()[tree.nodes().nsites() - 1]); + + // TODO: push other roots + + while (!pqueue.empty()) + { + mln_value(A) node_v = a(pqueue.top()); + mln_psite(A) node; + std::cout << pqueue.top() << " : " << node_v << std::endl; + f[node_v] = pqueue.size(); + do { + ++active_components; + node = pqueue.top(); + pqueue.pop(); + + mln_piter(p_array< mln_psite(A) >) child(tree.children(node)); + for_all(child) + { + pqueue.push(child); + } + } while (!pqueue.empty() && a(pqueue.top()) == node_v); + } + // TODO: postcondition decroissant + return f; + } + + +# endif /* !MLN_INCLUDE_ONLY */ + + + } // end of namespace mln::morpho::tree + } // end of namespace mln::morpho +} // end of namespace mln + + +#endif /* !GRANULOMETRY_HH_ */ Index: trunk/milena/sandbox/edwin/rush/granulometry/Makefile =================================================================== --- trunk/milena/sandbox/edwin/rush/granulometry/Makefile (revision 0) +++ trunk/milena/sandbox/edwin/rush/granulometry/Makefile (revision 3699) @@ -0,0 +1,36 @@ +include makefile.rules +TARGET=test + +test_SRC=test.cc +test_OBJS=${test_SRC:.cc=.o} + +OLENADIR=$(MLN_DIR)/.. +MILENADIR=$(OLENADIR)/milena + +CXXFLAGS=-I$(MILENADIR) -I./ -W -Wall + + +CXXFLAGS += $(if $(DEBUG), -g -ggdb, -DNDEBUG\ + $(if $(RELEASE), -O3, -O1)) + +CXX=g++ +LD=g++ +LDFLAGS= + +all: $(TARGET) + + +$(TARGET): $($(TARGET)_OBJS) $($(TARGET)_SRC) + $(LD) $(LDFLAGS) -o $@ $($(TARGET)_OBJS) + +%.o: %.cc + $(CXX) $(CXXFLAGS) -c $< + +%.o: %.hh + $(CXX) $(CXXFLAGS) -c $< + +depend: + makedepend -- $(CXXFLAGS) -- -v $($(TARGET)_SRC) + +clean: + rm -f *.o $(TARGET) Index: trunk/milena/sandbox/edwin/rush/exo2/test.cc =================================================================== --- trunk/milena/sandbox/edwin/rush/exo2/test.cc (revision 0) +++ trunk/milena/sandbox/edwin/rush/exo2/test.cc (revision 3699) @@ -0,0 +1,131 @@ +#include <mln/morpho/attribute/volume.hh> +#include <mln/morpho/attribute/height.hh> +#include <mln/morpho/attribute/sharpness.hh> +#include <mln/morpho/tree/data.hh> +#include <mln/morpho/tree/compute_attribute_image.hh> +#include <mln/level/sort_psites.hh> +#include <mln/debug/println.hh> + +#include <mln/convert/all.hh> + +#include <mln/core/image/image1d.hh> +#include <mln/core/alias/neighb1d.hh> +#include <mln/value/int_u8.hh> + +#include "../../tree/components.hh" +#include "../../tree/propagate.hh" + +#include <mln/fun/p2v/ternary.hh> +#include <mln/pw/all.hh> + +namespace mln +{ + // Sharpness Attribute -> Height Attribute + template <typename P2V> + struct height_wrapper_ : Function_p2v< height_wrapper_<P2V> > + { + typedef unsigned result; + + height_wrapper_(const Function_p2v<P2V>& f) : + f_ (exact(f)) + { + mlc_is_a(mln_result(P2V), Accumulator)::check(); + } + + template <typename P> + unsigned operator() (const P& p) const + { + return f_(p).height(); + } + + private: + const P2V& f_; + }; + + // meta + template <typename P2V> + inline + height_wrapper_<P2V> + height_wrapper(const Function_p2v<P2V>& f) + { + return height_wrapper_<P2V>(f); + } +} + + + +int main() +{ + using namespace mln; + using value::int_u8; + + + const char arr[]= { 16, 0, 0, 0, 0, 15, 0, 14, 0, 0, 0, 16 }; + + + typedef image1d<int_u8> I; + I input; + convert::from_to(arr, input); + + + /***************************/ + /* Component tree creation */ + /***************************/ + typedef p_array<point1d> S; + typedef morpho::tree::data<I,S> tree_t; + + S s = level::sort_psites_decreasing(input); + tree_t t(input, s, c2()); + + + /******************************/ + /* Compute Attribute On Image */ + /******************************/ + { + typedef mln_ch_value_(I, unsigned) A; + typedef morpho::attribute::volume<I> attribute_t; + A a; + + // Attribute Pruning + a = morpho::tree::compute_attribute_image(attribute_t (), t); + debug::println("volume", a); + } + + mln_ch_value_(I, unsigned) height; + { + typedef mln_ch_value_(I, unsigned) A; + typedef morpho::attribute::height<I> attribute_t; + + // Attribute Pruning + height = morpho::tree::compute_attribute_image(attribute_t (), t); + debug::println("height", height); + } + + { + typedef mln_ch_value_(I, double) A; + typedef morpho::attribute::sharpness<I> attribute_t; + A a, component_img; + + // Attribute Pruning + a = morpho::tree::compute_attribute_image(attribute_t (), t); + debug::println("sharpness", a); + + // Component filtering + a = duplicate((fun::p2v::ternary(pw::value(height) > pw::cst(2), + pw::value(a), + pw::cst(0.0))) | a.domain()); + + debug::println("sharpness", a); + + + p_array< mln_psite_(A) > obj_array; + obj_array = morpho::tree::get_components(t, a); + std::cout << obj_array.nsites() << std::endl; + + component_img = morpho::tree::propagate_components(a, t, obj_array, 0); + + debug::println("sharpness", component_img); + } + + +} Property changes on: trunk/milena/sandbox/edwin/rush/exo2/test.cc ___________________________________________________________________ Name: svn:executable + * Index: trunk/milena/sandbox/edwin/rush/exo2/wst_from_tree.cc =================================================================== --- trunk/milena/sandbox/edwin/rush/exo2/wst_from_tree.cc (revision 3698) +++ trunk/milena/sandbox/edwin/rush/exo2/wst_from_tree.cc (revision 3699) @@ -200,7 +200,7 @@ obj_array = morpho::tree::get_components(t, a); std::cout << obj_array.nsites() << std::endl; - component_img = morpho::tree::propagate_components(a, t, obj_array, 1); + component_img = morpho::tree::propagate_components(a, t, obj_array, 1.1); // debug //I output = level::stretch(int_u8(), component_img); //adapt to 0-255 Index: trunk/milena/sandbox/edwin/rush/exo2/Makefile =================================================================== --- trunk/milena/sandbox/edwin/rush/exo2/Makefile (revision 3698) +++ trunk/milena/sandbox/edwin/rush/exo2/Makefile (revision 3699) @@ -13,7 +13,7 @@ SRC= OUT_IMG=superpose.pgm mean.pgm gradient.pgm closing.pgm -BIN=wst_from_closing wst_from_tree +BIN=wst_from_closing wst_from_tree test all: $(BIN)

1 0

r3697: inim: Implement line detection with boxes
by Warren Seine 21 Apr '09

21 Apr '09

URL: https://svn.lrde.epita.fr/svn/oln/trunk/milena/sandbox ChangeLog: 2009-04-21 Warren Seine <soow(a)lrde.epita.fr> inim: Implement line detection with boxes. Does not actually output the image. * boxes.cc: Add debug code and ugly implementation. --- boxes.cc | 106 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++--- 1 file changed, 102 insertions(+), 4 deletions(-) Index: trunk/milena/sandbox/inim/2010/boxes/boxes.cc =================================================================== --- trunk/milena/sandbox/inim/2010/boxes/boxes.cc (revision 3696) +++ trunk/milena/sandbox/inim/2010/boxes/boxes.cc (revision 3697) @@ -32,6 +32,7 @@ #include <mln/debug/println.hh> #include <scribo/text/extract_bboxes.hh> +#include <scribo/text/grouping/group_from_single_link.hh> #include <scribo/text/grouping/group_with_single_left_link.hh> #include <scribo/text/grouping/group_with_single_right_link.hh> #include <scribo/debug/save_linked_textbboxes_image.hh> @@ -47,6 +48,7 @@ #include <mln/io/pgm/save.hh> #include <mln/fun/l2l/wrap.hh> +#include <mln/math/abs.hh> int usage(const char *name) { @@ -54,28 +56,61 @@ return 1; } - -int main(int argc, char* argv[]) -{ using namespace scribo; using namespace mln; +typedef image2d<value::label_16> scribo_image; + +template< typename T > +double vec_y_norm(const T& t) +{ + return mln::math::abs(t[1] / t[0]); +} + +template< typename T > +double bboxes_y_mean(const T& bboxes) +{ + double mean = 0.; + + for (unsigned i = 1; i < bboxes.nelements(); i++) + { + mln_VAR(s, bboxes[i].pmax() - bboxes[i].pmin()); + mean += (s[1] / s[0]); + } + + mean /= static_cast<double>(bboxes.nelements()); + + return mean; +} + +int main(int argc, char* argv[]) +{ if (argc != 3) return usage(argv[0]); scribo::make::internal::debug_filename_prefix = "extract_text_double_link"; + std::cout << "Debug 1" << std::endl; + image2d<bool> input; io::pbm::load(input, argv[1]); + std::cout << "Debug 2" << std::endl; + logical::not_inplace(input); + std::cout << "Debug 3" << std::endl; + value::label_16 nbboxes; scribo::util::text<image2d<value::label_16> > text = text::extract_bboxes(input, c8(), nbboxes); + std::cout << "Debug 4" << std::endl; + text = filter::small_components(text,4); + std::cout << "Debug 5" << std::endl; + mln::util::array<unsigned> left_link = text::grouping::group_with_single_left_link(text, 30), right_link = text::grouping::group_with_single_right_link(text, 30); @@ -83,14 +118,19 @@ std::cout << "BEFORE - nbboxes = " << nbboxes << std::endl; + std::cout << "Debug 6" << std::endl; + scribo::debug::save_linked_textbboxes_image(input, text, left_link, right_link, literal::red, literal::cyan, literal::yellow, literal::green, scribo::make::debug_filename("links.ppm")); + std::cout << "Debug 7" << std::endl; + // Validation. - scribo::util::text<image2d<value::label_16> > grouped_text + + scribo::util::text< scribo_image > grouped_text = text::grouping::group_from_double_link(text, left_link, right_link); std::cout << "AFTER double grouping - nbboxes = " << grouped_text.bboxes().nelements() << std::endl; @@ -101,9 +141,67 @@ fun::l2l::wrap<value::int_u8>()), "tmp.pgm"); + std::cout << "Debug 8" << std::endl; + + + + + + + + mln_VAR(b, grouped_text.bboxes()); + std::cout << "Bounding boxes: " << std::endl << b << std::endl; + + mln_VAR(m, grouped_text.mass_centers()); + std::cout << "Mass centers: " << std::endl << m << std::endl; + + // Mean of the y components of the bounding boxes + double mean = bboxes_y_mean(b); + std::cout << "Mean: " << mean << std::endl; + + mln::util::array< unsigned > lines(m.size()); + + // Suppose that every component is on a different line + for (unsigned i = 1; i < m.size(); i++) + lines[i] = i; + + // Merge the lines if they are too close + for (unsigned i = 1; i < m.size(); i++) + for (unsigned j = i + 1; j < m.size(); j++) + { + if (i == j) + continue; + + double y_norm_diff = vec_y_norm(m[j] - m[i]); +// std::cout << "y_norm_diff: " << y_norm_diff << std::endl; + if (y_norm_diff > 1000) + { + std::cout << "(" << i << "," << j << ")" << std::endl; + continue; + } + if (y_norm_diff < mean * 2) + { + lines[j] = lines[i]; +// std::cout << "Associating " << i << " to " << j << std::endl; + } + } + + std::cout << "Lines: " << std::endl << lines << std::endl; + +// scribo::util::text< scribo_image > grouped_lines +// = text::grouping::group_from_single_link(text, lines); + + + + + + + + scribo::debug::save_textbboxes_image(input, grouped_text.bboxes(), literal::red, scribo::make::debug_filename("boxes.ppm")); + std::cout << "Debug 9" << std::endl; } -- :: Warren Seine // SooW :: :: warren.seine @ gmail.com :: :: EPITA CSI 2010 ::

1 0

r3695: Various update for IGR demo and new fixed segmentation
by Fabien Freling 21 Apr '09

21 Apr '09

URL: https://svn.lrde.epita.fr/svn/oln/trunk/milena/sandbox ChangeLog: 2009-04-21 Fabien Freling <fabien.freling(a)lrde.epita.fr> Various update for IGR demo and new fixed segmentation. * fabien/igr/Makefile: Add 'seg_fixed' target. * fabien/igr/check.sh: Update. * fabien/igr/fun_labels.cc: Update. * fabien/igr/fun_labels.sh: Update. * fabien/igr/med.cc: Update. * fabien/igr/norm.cc: Update. * fabien/igr/seg_fixed.cc: New. * fabien/igr/space_smooth/Makefile: Update. * fabien/igr/space_smooth/linear.cc: Update. * fabien/igr/thres.cc: Update. * fabien/igr/time_max_norm.cc: New tool for tmax map. * fabien/igr/time_smooth/Makefile: Update. * fabien/igr/time_smooth/linear.cc: Update. --- TODO | 18 +++++- igr/Makefile | 12 +++- igr/check.sh | 11 ++- igr/fun_labels.cc | 36 ++++++------ igr/fun_labels.sh | 36 +++++++++--- igr/med.cc | 15 ++--- igr/norm.cc | 14 +--- igr/seg_fixed.cc | 135 +++++++++++++++++++++++++++++++++++++++++++++ igr/space_smooth/Makefile | 2 igr/space_smooth/linear.cc | 21 ++++--- igr/thres.cc | 2 igr/time_max_norm.cc | 116 ++++++++++++++++++++++++++++++++++++++ igr/time_smooth/Makefile | 2 igr/time_smooth/linear.cc | 42 ++++++++++---- 14 files changed, 388 insertions(+), 74 deletions(-) Index: trunk/milena/sandbox/fabien/igr/seg_fixed.cc =================================================================== --- trunk/milena/sandbox/fabien/igr/seg_fixed.cc (revision 0) +++ trunk/milena/sandbox/fabien/igr/seg_fixed.cc (revision 3695) @@ -0,0 +1,135 @@ +#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/routine/duplicate.hh> + +#include <mln/io/dump/all.hh> + +#include <mln/value/int_u12.hh> + +#include <mln/accu/sum.hh> +#include <mln/data/fill.hh> +#include <mln/convert/from_to.hh> +#include <mln/level/compute.hh> +#include <mln/util/array.hh> + + +using namespace mln; +using value::int_u12; + + + +inline +point2d +get_edge_location(point2d p, point2d n) +{ + point2d res(p); + + res.to_vec()[0] *= 2; + res.to_vec()[1] *= 2; + + if (n.to_vec()[0] > p.to_vec()[0]) + ++(res.to_vec()[0]); + if (n.to_vec()[0] < p.to_vec()[0]) + --(res.to_vec()[0]); + + if (n.to_vec()[1] > p.to_vec()[1]) + ++(res.to_vec()[1]); + if (n.to_vec()[1] < p.to_vec()[1]) + --(res.to_vec()[1]); + + return res; +} + + +template <typename I> +inline +float +compute_dist(image2d<util::array<I> > ima_arr, + image2d<float> ima_sum, + point2d p, point2d n) +{ + float res = 0.f; + + for (unsigned i = 0; i < ima_arr(p).nelements(); ++i) + res += std::min(ima_arr(p)[i], ima_arr(n)[i]); + res /= std::max(ima_sum(p), ima_sum(n)); + + return res; +} + +template <typename I> +inline +void +compute_sum_arrays(image2d<float> ima_sum, image2d<util::array<I> > ima_arr) +{ + mln_piter(image2d<float>) p(ima_sum.domain()); + for_all(p) + { + image1d<I> tmp_ima; + convert::from_to(ima_arr(p), tmp_ima); + accu::sum<I> accu_sum; + ima_sum(p) = level::compute(accu_sum, tmp_ima); + } +} + +template <typename I> +image2d<float> +dist_on_edges(image2d<util::array<I> > ima_arr) +{ + image2d<float> edges(2 * ima_arr.nrows(), 2 * ima_arr.ncols()); + data::fill(edges, -1.f); + image2d<float> ima_sum; + initialize(ima_sum, ima_arr); + compute_sum_arrays(ima_sum, ima_arr); + + mln_piter(image2d<util::array<I> >) p(ima_arr.domain()); + mln_niter(neighb2d) n(c4(), p); + for_all(p) + for_all(n) + { + point2d location = get_edge_location(p, n); + if (edges(location) != -1) + edges(location) = compute_dist(ima_arr, ima_sum, p, n); + } + + return edges; +} + + + + + +int usage(const char* bin) +{ + std::cout << "Usage: " << bin << " input.dump" << std::endl; + return 1; +} + +int main(int argc, char* argv[]) +{ + typedef int_u12 I; + + if (argc != 2) + return usage(argv[0]); + + image3d<I> input; + io::dump::save(input, argv[1]); + image2d<util::array<I> > ima_arr; + initialize(ima_arr, slice(input, 0)); + for (unsigned int i = 0; i < input.nslices(); ++i) + { + image2d<I> tmp_slice = duplicate(slice(input, i)); + mln_piter_(image2d<I>) p(tmp_slice.domain()); + for_all(p) + ima_arr(p).append(tmp_slice(p)); + } + + image2d<float> edges = dist_on_edges(ima_arr); + + return 0; +} Index: trunk/milena/sandbox/fabien/igr/time_max_norm.cc =================================================================== --- trunk/milena/sandbox/fabien/igr/time_max_norm.cc (revision 0) +++ trunk/milena/sandbox/fabien/igr/time_max_norm.cc (revision 3695) @@ -0,0 +1,116 @@ +#include <sstream> + +#include <mln/core/image/image2d.hh> +#include <mln/core/image/image3d.hh> +#include <mln/core/image/image_if.hh> +#include <mln/core/image/cast_image.hh> +#include <mln/core/image/slice_image.hh> +#include <mln/core/routine/duplicate.hh> + +#include <mln/value/int_u8.hh> +#include <mln/value/int_u12.hh> + +#include <mln/io/dump/load.hh> +#include <mln/io/pgm/save.hh> + +#include <mln/accu/count.hh> +#include <mln/accu/mean.hh> +#include <mln/accu/sum.hh> +#include <mln/accu/image/all.hh> + +#include <mln/arith/minus.hh> +#include <mln/arith/all.hh> + +#include <mln/data/fill.hh> +#include <mln/data/paste.hh> + +#include <mln/level/compute.hh> +#include <mln/level/stretch.hh> + +#include <mln/math/abs.hh> +#include <mln/pw/all.hh> +#include <mln/trait/concrete.hh> +#include <mln/util/array.hh> + +#include <cmath> + +using namespace mln; +using value::int_u8; + + + +// FIXME: Protoype is wrong. Should be Image<I>. +template <typename I> +inline +void +save_tmax_map(util::array<image2d<I> >& arr_ima, unsigned dim3, const char* desc) +{ + image2d<float> ima_c; + initialize(ima_c, arr_ima[0]); + data::fill(ima_c, 0.0); + image2d<unsigned> ima_t; + initialize(ima_t, ima_c); + data::fill(ima_t, 0); + + mln_piter(image2d<float>) p(ima_c.domain()); + for_all(p) + for (unsigned k = 0; k < dim3; ++k) + if (ima_c(p) < arr_ima[k](p)) + { + ima_c(p) = arr_ima[k](p); + ima_t(p) = k; + } + + std::ostringstream smax; + smax << desc << "_max.pgm"; + std::ostringstream stime; + stime << desc << "_time.pgm"; + + image2d<int_u8> result_c = level::stretch(int_u8(), ima_c); + image2d<int_u8> result_t = level::stretch(int_u8(), ima_t); + io::pgm::save(result_c, smax.str()); + io::pgm::save(result_t, stime.str()); +} + + +int main(int argc, char* argv[]) +{ + if (argc != 2) + { + std::cout << "Usage: " << argv[0] << " input" << std::endl; + return 1; + } + + image3d<float> input; + io::dump::load(input, argv[1]); + util::array<image2d<float> > arr_ima; + for (unsigned int i = 0; i < input.nslices(); ++i) + arr_ima.append(duplicate(cast_image<float>(slice(input, i)))); + + unsigned dim3 = arr_ima.nelements(); + + + ///////////// + // // + // Lissage // + // // + ///////////// + + util::array<image2d<double> > arr_smooth; + arr_smooth.append(arr_ima[0] * 1.0); + for (unsigned k = 1; k < dim3 - 1; ++k) + arr_smooth.append(arr_ima[k] * 0.5 + arr_ima[k - 1] * 0.25 + arr_ima[k + 1] * 0.25); + arr_smooth.append(arr_ima[dim3 - 1] * 1.0); + + + /////////////////////////////////// + // // + // Calcul image max et temps max // + // // + /////////////////////////////////// + + save_tmax_map(arr_ima, dim3, "tmax"); + save_tmax_map(arr_smooth, dim3, "tmax_smooth"); + + return 0; +} Index: trunk/milena/sandbox/fabien/igr/check.sh =================================================================== --- trunk/milena/sandbox/fabien/igr/check.sh (revision 3694) +++ trunk/milena/sandbox/fabien/igr/check.sh (revision 3695) @@ -2,19 +2,20 @@ process_file () { - echo "Processing $3..." + echo "Processing $1..." | cowsay dist_max=10 input=$1 dim=$2 - ./grad $input $dim + ./crop $input 0 50 90 149 230 170 crop.dump + ./grad crop.dump $dim for lambda_closing in 50 100 500 1000 5000 10000 50000; do echo " for lambda_closing = ${lambda_closing}"; ./clo_vol grad.dump $dim ${lambda_closing} nbasins=`./wst clo_vol.dump $dim` echo " nbasins = $nbasins" - ../bin/dumpl32_to_colorize wst.dump $dim $nbasins results/colorize_${3}_${lambda_closing}.ppm - median=`./med wst.dump $dim $input $nbasins` + ../bin/dumpl16_to_colorize wst.dump $dim $nbasins results/colorize_${3}_${lambda_closing}.ppm + median=`./med wst.dump $dim crop.dump $nbasins` echo " median = $median" threshold=$(($median / 2)) ../bin/dumpi12_to_pgm med.dump $dim results/median_${3}_${lambda_closing}.pgm @@ -38,6 +39,8 @@ # rm *.dump } +make crop grad clo_vol wst med thres + #process_file "/Users/HiSoKa/Work/IGR/souris18/irm/IM_0049.dcm" 2 "49" process_file "/Users/HiSoKa/Work/IGR/souris18/irm/IM_0052.dcm" 3 "52" #process_file "/Users/HiSoKa/Work/IGR/souris18/irm/IM_0055.dcm" 2 "55" Index: trunk/milena/sandbox/fabien/igr/fun_labels.cc =================================================================== --- trunk/milena/sandbox/fabien/igr/fun_labels.cc (revision 3694) +++ trunk/milena/sandbox/fabien/igr/fun_labels.cc (revision 3695) @@ -71,7 +71,7 @@ box3d slice = make::box3d(sli, min_row, min_col, sli, max_row, max_col); mln_VAR(slice_label, vol_label | slice); - accu::mean<int_u12> accu_mean; + accu::mean<mln_value(I)> accu_mean; float mean = level::compute(accu_mean, slice_label); arr.append(mean); } @@ -148,14 +148,15 @@ void plot_point(Image<I>& ima, Image<L>& ima_labels, point2d point, const char* desc) { util::array<float> arr; - label_16 prev_lbl; + mln_value(L) prev_lbl; int start = 0; int count = 1; + int nslices = geom::nslis(ima); - for (unsigned sli = 0; sli < geom::nslis(ima); ++sli) + for (unsigned sli = 0; sli < nslices; ++sli) { - image2d<int_u12> ima_slice = duplicate(slice(ima, sli)); - image2d<label_16> lbl_slice = duplicate(slice(ima_labels, sli)); + image2d<mln_value(I)> ima_slice = duplicate(slice(ima, sli)); + image2d<mln_value(L)> lbl_slice = duplicate(slice(ima_labels, sli)); if (sli == 0) prev_lbl = lbl_slice(point); if (lbl_slice(point) != prev_lbl) @@ -166,13 +167,13 @@ start = sli + 1; } // Taking the median value of the region. - accu::median_h<int_u12> accu_med; - int_u12 median = level::compute(accu_med, ima_slice | pw::value(lbl_slice) == pw::cst(lbl_slice(point))); - arr.append(median); + accu::mean<mln_value(I)> accu_mean; + mln_value(I) mean = level::compute(accu_mean, ima_slice | pw::value(lbl_slice) == pw::cst(lbl_slice(point))); + arr.append(mean); prev_lbl = lbl_slice(point); // Saving a image of the selected label in the current slice for debug. - data::fill((ima_slice | pw::value(lbl_slice) == pw::cst(prev_lbl)).rw(), 1750); + /*data::fill((ima_slice | pw::value(lbl_slice) == pw::cst(prev_lbl)).rw(), 1750); std::ostringstream str_ima; str_ima << "debug_" << desc << "_"; if (sli < 100) @@ -180,7 +181,7 @@ if (sli < 10) str_ima << "0"; str_ima << sli << ".pgm"; - io::pgm::save(level::stretch(int_u8(), ima_slice), str_ima.str()); + io::pgm::save(level::stretch(int_u8(), ima_slice), str_ima.str());*/ } if (!arr.is_empty()) @@ -198,6 +199,7 @@ int main(int argc, char *argv[]) { typedef label_16 L; + typedef float I; if (argc != 4) { @@ -208,8 +210,8 @@ L nlabels = atoi(argv[3]); - point2d p_tumeur(156, 114); - point2d p_air(34, 94); + point2d p_tumeur(163, 114); + point2d p_air(54, 94); point2d p_poumon(122, 115); image3d<L> ima_labels; io::dump::load(ima_labels, argv[1]); @@ -220,15 +222,15 @@ //plot_all_labels(ima, ima_labels, nlabels); - L l = 0; + /*L l = 0; for (unsigned i = 0; i < nlabels; ++i, l = i) - plot_label(ima, ima_labels, l); + plot_label(ima, ima_labels, l);*/ io::dump::save(ima_labels, "labels.dump"); - //plot_point(ima, ima_labels, p_tumeur, "tumeur"); - //plot_point(ima, ima_labels, p_air, "air"); - //plot_point(ima, ima_labels, p_poumon, "poumon"); + plot_point(ima, ima_labels, p_tumeur, "tumeur"); + plot_point(ima, ima_labels, p_air, "air"); + plot_point(ima, ima_labels, p_poumon, "poumon"); /*util::set<L> lbl_set; for (int sli = 0; sli < geom::nslis(ima_labels); ++sli) Index: trunk/milena/sandbox/fabien/igr/norm.cc =================================================================== --- trunk/milena/sandbox/fabien/igr/norm.cc (revision 3694) +++ trunk/milena/sandbox/fabien/igr/norm.cc (revision 3695) @@ -18,6 +18,8 @@ #include <mln/data/paste.hh> // DEBUG +#include <mln/core/var.hh> +#include <mln/estim/min_max.hh> /*#include <mln/accu/min.hh> #include <mln/accu/max.hh> #include <mln/level/compute.hh>*/ @@ -60,18 +62,10 @@ image2d<float> ima_ini = mean_slices(ima_f, first, last); image3d<float> ima_result; - initialize(ima_result, ima_f); + initialize(ima_result, ima); for (int i = min_sli; i <= max_sli; ++i) - data::paste((slice(ima_f, i) - ima_ini), slice(ima_result, i).rw()); - - // DEBUG - /*accu::min<float> accu_min; - accu::max<float> accu_max; - float min = level::compute(accu_min, ima_ini); - float max = level::compute(accu_max, ima_ini); - std::cout << "min = " << min << std::endl; - std::cout << "max = " << max << std::endl;*/ + data::paste((slice(ima_f, i) - ima_ini) / ima_ini, slice(ima_result, i).rw()); return ima_result; } Index: trunk/milena/sandbox/fabien/igr/thres.cc =================================================================== --- trunk/milena/sandbox/fabien/igr/thres.cc (revision 3694) +++ trunk/milena/sandbox/fabien/igr/thres.cc (revision 3695) @@ -34,7 +34,7 @@ using value::int_u12; using value::label_16; using value::label_32; - typedef label_32 L; + typedef label_16 L; if (argc != 4) { Index: trunk/milena/sandbox/fabien/igr/Makefile =================================================================== --- trunk/milena/sandbox/fabien/igr/Makefile (revision 3694) +++ trunk/milena/sandbox/fabien/igr/Makefile (revision 3695) @@ -28,7 +28,7 @@ ${CXX} -I../../../ ${DICOM} ${CXXFLAGS} $^ -o graph med: med.cc - ${CXX} -I../../../ ${DICOM} ${CXXFLAGS} $^ -o med + ${CXX} -I../../../ ${CXXFLAGS} $^ -o med thres: thres.cc ${CXX} -I../../../ ${CXXFLAGS} $^ -o thres @@ -39,6 +39,9 @@ time_max: time_max.cc ${CXX} -I../../../ ${DICOM} ${MAGICK} ${CXXFLAGS} -lm $^ -o time_max +time_max_norm: time_max_norm.cc + ${CXX} -I../../../ ${CXXFLAGS} -lm $^ -o time_max_norm + first_slice_dicom: first_slice_dicom.cc ${CXX} -I../../../ ${DICOM} ${MAGICK} ${CXXFLAGS} -lm $^ -o first_slice_dicom @@ -57,6 +60,13 @@ norm: norm.cc ${CXX} -I../../../ ${CXXFLAGS} $^ -o norm +##################### + +seg_fixed: seg_fixed.cc + ${CXX} -I../../../ ${CXXFLAGS} $^ -o seg_fixed + +##################### + 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/fun_labels.sh =================================================================== --- trunk/milena/sandbox/fabien/igr/fun_labels.sh (revision 3694) +++ trunk/milena/sandbox/fabien/igr/fun_labels.sh (revision 3695) @@ -1,5 +1,9 @@ #!/bin/zsh +######### +# Plots # +######### + reconstruct_plot () { rm -f ${1}_${2}.plot @@ -10,11 +14,16 @@ rename_label_plots () { - for i in label_*.plot; do + for i in *_label_*.plot; do mv $i ${1}_$i done } + +############# +# Animation # +############# + create_anim () { echo " Creating ${1} animation..." @@ -43,15 +52,25 @@ rm debug_${1}_*.png } + + + + + + + + + process_file () { - echo "Processing $3..." + echo "Processing $1..." | cowsay input=$1 dim=$2 ./crop $input 0 50 90 149 230 170 crop.dump + ./norm crop.dump norm.dump ./grad crop.dump $dim - for lambda_closing in 10000; do + for lambda_closing in 1000; do echo " for lambda_closing = ${lambda_closing}"; ./clo_vol grad.dump $dim ${lambda_closing} nbasins=`./wst clo_vol.dump $dim` @@ -61,24 +80,25 @@ #../bin/dumpi12_to_png mean_slices.dump $dim mean_slices_${3}_${lambda_closing}.png #../bin/dumpi12_to_pgm mean_slices.dump $dim mean_slices_${3}_${lambda_closing}.pgm - ./norm crop.dump norm.dump ./fun_labels wst.dump norm.dump $nbasins - rename_label_plots ${lambda_closing} #./all_labels2gif.sh crop.dump labels.dump $nbasins ${lambda_closing} #mv *.gif results/ #mv *.plot results/plots/ -#reconstruct_plot tumeur ${lambda_closing} + reconstruct_plot tumeur ${lambda_closing} + reconstruct_plot air ${lambda_closing} + reconstruct_plot poumon ${lambda_closing} + rename_label_plots ${lambda_closing} #create_anim tumeur ${lambda_closing} -#reconstruct_plot air ${lambda_closing} #create_anim air ${lambda_closing} -#reconstruct_plot poumon ${lambda_closing} #create_anim poumon ${lambda_closing} done } +make crop grad clo_vol fun_labels norm label2gif + # 3D (2D + t) images only process_file "/Users/HiSoKa/Work/IGR/souris18/irm/IM_0052.dcm" 3 52 Index: trunk/milena/sandbox/fabien/igr/space_smooth/Makefile =================================================================== --- trunk/milena/sandbox/fabien/igr/space_smooth/Makefile (revision 3694) +++ trunk/milena/sandbox/fabien/igr/space_smooth/Makefile (revision 3695) @@ -2,7 +2,7 @@ linear: linear.cc - ${CXX} -I../../../../ ${DICOM} ${CXXFLAGS} $^ -o linear + ${CXX} -I../../../../ ${CXXFLAGS} $^ -o linear median: median.cc ${CXX} -I../../../../ ${DICOM} ${CXXFLAGS} $^ -o median Index: trunk/milena/sandbox/fabien/igr/space_smooth/linear.cc =================================================================== --- trunk/milena/sandbox/fabien/igr/space_smooth/linear.cc (revision 3694) +++ trunk/milena/sandbox/fabien/igr/space_smooth/linear.cc (revision 3695) @@ -7,7 +7,7 @@ #include <mln/value/int_u12.hh> -#include <mln/io/dicom/load.hh> +#include <mln/io/dump/load.hh> #include <mln/io/plot/save.hh> #include <mln/accu/median_h.hh> @@ -29,17 +29,19 @@ return 1; } + typedef float I; + /////////////////// // // // Image loading // // // /////////////////// - image3d<int_u12> input; - io::dicom::load(input, argv[1]); - util::array<image2d<int_u12> > arr_ima; - for (int i = 0; i < input.nslices(); ++i) + image3d<I> input; + io::dump::load(input, argv[1]); + util::array<image2d<I> > arr_ima; + for (unsigned int i = 0; i < input.nslices(); ++i) { - image2d<int_u12> tmp_slice = duplicate(slice(input, i)); + image2d<I> tmp_slice = duplicate(slice(input, i)); arr_ima.append(tmp_slice); } @@ -61,14 +63,15 @@ // Outputs // // // ///////////// - image2d<util::array<float> > ima_result(input.nrows(), input.ncols()); + image2d<util::array<float> > ima_result; + initialize(ima_result, slice(input, 0)); mln_piter_(image2d<util::array<float> >) p(ima_linear[0].domain()); for_all(p) - for (int i = 0; i < ima_linear.nelements(); ++i) + for (unsigned int i = 0; i < ima_linear.nelements(); ++i) ima_result(p).append(ima_linear[i](p)); io::plot::save(ima_result(point2d(156, 114)), "linear_tumeur.plot"); - io::plot::save(ima_result(point2d(34, 94)), "linear_air.plot"); + io::plot::save(ima_result(point2d(54, 94)), "linear_air.plot"); io::plot::save(ima_result(point2d(122, 115)), "linear_poumon.plot"); return 0; Index: trunk/milena/sandbox/fabien/igr/time_smooth/Makefile =================================================================== --- trunk/milena/sandbox/fabien/igr/time_smooth/Makefile (revision 3694) +++ trunk/milena/sandbox/fabien/igr/time_smooth/Makefile (revision 3695) @@ -2,7 +2,7 @@ linear: linear.cc - ${CXX} -I../../../../ ${DICOM} ${CXXFLAGS} $^ -o linear + ${CXX} -I../../../../ ${CXXFLAGS} $^ -o linear median: median.cc ${CXX} -I../../../../ ${DICOM} ${CXXFLAGS} $^ -o median Index: trunk/milena/sandbox/fabien/igr/time_smooth/linear.cc =================================================================== --- trunk/milena/sandbox/fabien/igr/time_smooth/linear.cc (revision 3694) +++ trunk/milena/sandbox/fabien/igr/time_smooth/linear.cc (revision 3695) @@ -7,11 +7,13 @@ #include <mln/value/int_u12.hh> -#include <mln/io/dicom/load.hh> +#include <mln/io/dump/all.hh> #include <mln/io/plot/save.hh> #include <mln/accu/median_h.hh> #include <mln/util/array.hh> +#include <mln/linear/convolve.hh> +#include <mln/make/w_window3d.hh> using namespace mln; @@ -26,33 +28,48 @@ return 1; } + typedef float I; + /////////////////// // // // Image loading // // // /////////////////// - image3d<int_u12> input; - io::dicom::load(input, argv[1]); - image2d<util::array<int_u12> > ima_arr(input.nrows(), input.ncols()); - for (int i = 0; i < input.nslices(); ++i) + image3d<I> input; + io::dump::load(input, argv[1]); + image2d<util::array<I> > ima_arr; + initialize(ima_arr, duplicate(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()); + image2d<I> tmp_slice = duplicate(slice(input, i)); + mln_piter_(image2d<I>) p(tmp_slice.domain()); for_all(p) { ima_arr(p).append(tmp_slice(p)); } } + /*image3d<I> output; + initialize(output, input);*/ //////////////////////// // // // Linear convolution // // // //////////////////////// - image2d<util::array<int_u12> > ima_linear; + /*float ws[][] = {{0, 0, 0, + 0, 0.25, 0, + 0, 0, 0}, + {0, 0, 0, + 0, 0.5, 0, + 0, 0, 0}, + {0, 0, 0, + 0, 0.25, 0, + 0, 0, 0}}; + + output = linear::convolve(input, make::w_window3d(ws));*/ + image2d<util::array<I> > ima_linear; initialize(ima_linear, ima_arr); - mln_piter_(image2d<int_u12>) p(ima_linear.domain()); - accu::median_h<int_u12> accu_med; + mln_piter_(image2d<I>) p(ima_linear.domain()); for_all(p) { ima_linear(p).append(ima_arr(p)[0]); @@ -66,10 +83,11 @@ // Outputs // // // ///////////// + //io::dump::save(output, "time_linear.dump"); io::plot::save(ima_arr(point2d(156, 114)), "ref_tumeur.plot"); io::plot::save(ima_linear(point2d(156, 114)), "linear_tumeur.plot"); - io::plot::save(ima_arr(point2d(34, 94)), "ref_air.plot"); - io::plot::save(ima_linear(point2d(34, 94)), "linear_air.plot"); + io::plot::save(ima_arr(point2d(54, 94)), "ref_air.plot"); + io::plot::save(ima_linear(point2d(54, 94)), "linear_air.plot"); io::plot::save(ima_arr(point2d(122, 115)), "ref_poumon.plot"); io::plot::save(ima_linear(point2d(122, 115)), "linear_poumon.plot"); Index: trunk/milena/sandbox/fabien/igr/med.cc =================================================================== --- trunk/milena/sandbox/fabien/igr/med.cc (revision 3694) +++ trunk/milena/sandbox/fabien/igr/med.cc (revision 3695) @@ -9,7 +9,6 @@ #include <mln/core/alias/window3d.hh> #include <mln/io/dump/all.hh> -#include <mln/io/dicom/load.hh> #include <mln/value/int_u8.hh> #include <mln/value/int_u12.hh> @@ -45,7 +44,7 @@ using value::int_u12; using value::label_16; using value::label_32; - typedef label_32 L; + typedef label_16 L; if (argc != 5) { @@ -70,12 +69,12 @@ { image2d<L> labels; io::dump::load(labels, argv[1]); - image2d<int_u12> dcm; - io::dicom::load(dcm, argv[3]); + image2d<int_u12> input; + io::dump::load(input, argv[3]); mln_VAR(wst_dilate, morpho::elementary::dilation(extend(labels | (pw::value(labels) == 0u), labels), c8())); data::fill((labels | (pw::value(labels) == 0u)).rw(), wst_dilate); - mln_VAR(wst_mean, labeling::mean_values(dcm, labels, nbasins)); + mln_VAR(wst_mean, labeling::mean_values(input, labels, nbasins)); histo::array<int_u12> histogram = histo::compute(wst_mean); int j = 0; @@ -106,12 +105,12 @@ { image3d<L> labels; io::dump::load(labels, argv[1]); - image3d<int_u12> dcm; - io::dicom::load(dcm, argv[3]); + image3d<int_u12> input; + io::dump::load(input, argv[3]); mln_VAR(wst_dilate, morpho::elementary::dilation(extend(labels | (pw::value(labels) == 0u), labels), c26())); data::fill((labels | (pw::value(labels) == 0u)).rw(), wst_dilate); - mln_VAR(wst_mean, labeling::mean_values(dcm, labels, nbasins)); + mln_VAR(wst_mean, labeling::mean_values(input, labels, nbasins)); histo::array<int_u12> histogram = histo::compute(wst_mean); int j = 0; Index: trunk/milena/sandbox/fabien/TODO =================================================================== --- trunk/milena/sandbox/fabien/TODO (revision 3694) +++ trunk/milena/sandbox/fabien/TODO (revision 3695) @@ -47,6 +47,20 @@ [ ] Fix mean slices values [X] Compatibility Windows [X] Fix spatial smooth -[ ] Crop volume 52 -[ ] Plot all labels (3, 4 labels for tumeur) +[X] Crop volume 52 +[X] Plot all labels (3, 4 labels for tumeur) [ ] Prepare data for IGR + [X] crop->norm->tmax + [X] crop->norm->space_smooth->tmax + + (comparo normalisé) + 1)brut + 2)time_smooth + 3)space_smooth + 4)current_label_smooth (lambda faible, pas de ligne watershed) + + [X] plot label + [X] gif animés labels + + [X] fausses couleurs watershed + [X] images moyennes

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r3694: Closure with flat element
by Etienne FOLIO 21 Apr '09

21 Apr '09

URL: https://svn.lrde.epita.fr/svn/oln/trunk/milena/sandbox ChangeLog: 2009-04-21 Etienne FOLIO <folio(a)lrde.epita.fr> Closure with flat element. * inim/2010/morpho/morpho.cc: New test algorithm. * inim/2010/morpho/test.sh: New build tests file. * inim/2010/morpho: New directory for mini-project. --- morpho.cc | 71 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ test.sh | 5 ++++ 2 files changed, 76 insertions(+) Index: trunk/milena/sandbox/inim/2010/morpho/morpho.cc =================================================================== --- trunk/milena/sandbox/inim/2010/morpho/morpho.cc (revision 0) +++ trunk/milena/sandbox/inim/2010/morpho/morpho.cc (revision 3694) @@ -0,0 +1,71 @@ +#include <iostream> +#include <sstream> +#include <string> +#include <mln/debug/println.hh> + +#include <mln/io/pbm/load.hh> +#include <mln/io/pgm/save.hh> + +#include <mln/data/fill.hh> +#include <mln/literal/all.hh> +#include <mln/arith/revert.hh> +#include <mln/level/convert.hh> +#include <mln/level/stretch.hh> +#include <mln/morpho/closing/structural.hh> +#include <mln/core/alias/window2d.hh> +#include <mln/make/win_chamfer.hh> + +int main(int argc, char** argv) +{ + using namespace mln; + + // check arguments + if (argc != 4) + { + std::cerr << "Usage:" << std::endl + << " ./a.out <in.pbm> <k> <out.pbm>" << std::endl; + exit(1); + } + + // build test image + std::cout << " => loading " << argv[1] << "..." << std::endl; + image2d<bool> in; + io::pbm::load(in, argv[1]); + + value::int_u8 k = 1; + image2d<value::int_u8> out = level::convert(k, in); + out = level::stretch(k, out); + + std::cout << " => revert image..." << std::endl; + out = arith::revert(out); + + // closure +/* int ws[] = { 0, 1, 0, + 1, 0, 1, + 0, 1, 0 }; +*/ + // w_window2d_int == w_window<dpoint2d, int> + + + for (unsigned j = 20; j <= 40; j += 10) + { + window2d it; + it.insert(0, 0); + + for (unsigned i = 0; i < j; ++i) + { + it.insert(0, -i); + it.insert(0, i); + } + + out = morpho::closing::structural(out, it); + + // export out image + std::stringstream ss; + ss << "../" << j << '/' << argv[3]; + std::string s; + ss >> s; + std::cout << " => saving " << s << "..." << std::endl; + io::pgm::save(out, s.c_str()); + } +} Index: trunk/milena/sandbox/inim/2010/morpho/test.sh =================================================================== --- trunk/milena/sandbox/inim/2010/morpho/test.sh (revision 0) +++ trunk/milena/sandbox/inim/2010/morpho/test.sh (revision 3694) @@ -0,0 +1,5 @@ +#!/bin/sh + +for i in `ls *.tif`; do + ../closure $i.pbm 1 $i.pbm ; +done Property changes on: trunk/milena/sandbox/inim/2010/morpho/test.sh ___________________________________________________________________ Name: svn:executable + *

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Re: [Olena-patches] [Olena] #3: Migrate Olena 0.11 (and previous revisions) from PRCS to Git
by Olena Trac 21 Apr '09

21 Apr '09

#3: Migrate Olena 0.11 (and previous revisions) from PRCS to Git -----------------------+---------------------------------------------------- Reporter: levill_r | Owner: levill_r Type: task | Status: reopened Priority: blocker | Milestone: Olena 0.11.1 Component: other | Version: 0.11 Resolution: | Keywords: prcs subversion svn git -----------------------+---------------------------------------------------- Changes (by levill_r): * type: enhancement => task -- Ticket URL: <https://trac.lrde.org/olena/ticket/3#comment:9> Olena <http://olena.lrde.epita.fr> Olena, a generic and efficient C++ image processing library.

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3692: Update use of transposition.
by Thierry Geraud 20 Apr '09

20 Apr '09

https://svn.lrde.epita.fr/svn/oln/trunk/milena/sandbox Index: ChangeLog from Thierry Geraud <thierry.geraud(a)lrde.epita.fr> Update use of transposition. * icdar/2009/hsc/input_to_lines.hh: Update. * icdar/2009/hsc/input_to_ws.hh: Add log. Update. * icdar/2009/hsc/ws_to_wsl.hh: Likewise. * jardonnet/registration/cov.hh: Update. * jardonnet/registration/quat7.hh: Update. icdar/2009/hsc/input_to_lines.hh | 5 ++- icdar/2009/hsc/input_to_ws.hh | 51 ++++++++++++++++++++++++++++++++++++++- icdar/2009/hsc/ws_to_wsl.hh | 48 ++++++++++++------------------------ jardonnet/registration/cov.hh | 2 - jardonnet/registration/quat7.hh | 4 +-- 5 files changed, 72 insertions(+), 38 deletions(-) Index: icdar/2009/hsc/input_to_lines.hh --- icdar/2009/hsc/input_to_lines.hh (revision 3691) +++ icdar/2009/hsc/input_to_lines.hh (working copy) @@ -6,9 +6,10 @@ #include <mln/world/binary_2d/subsample.hh> #include <mln/value/int_u8.hh> #include <mln/value/label.hh> -#include <mln/labeling/relabel.hh> +#include <mln/labeling/pack.hh> #include <mln/core/image/violent_cast_image.hh> +#include <mln/io/pgm/save.hh> namespace mln @@ -38,7 +39,7 @@ // Clean lines wsl = clean_lines(input, wsl, tau); - return labeling::relabel(violent_cast_image_<L>(wsl), + return labeling::pack(violent_cast_image_<L>(wsl), n_lines); } Index: icdar/2009/hsc/input_to_ws.hh --- icdar/2009/hsc/input_to_ws.hh (revision 3691) +++ icdar/2009/hsc/input_to_ws.hh (working copy) @@ -10,10 +10,18 @@ #include <sandbox/theo/exec/gaussian_directional_2d.hh> #include <mln/win/rectangle2d.hh> - #include <mln/morpho/closing/structural.hh> #include <mln/morpho/watershed/flooding.hh> +#include <mln/io/pgm/save.hh> +#include <mln/io/ppm/save.hh> +#include <mln/literal/colors.hh> +#include <mln/debug/colorize.hh> +#include <mln/level/convert.hh> +#include <mln/labeling/wrap.hh> +#include <mln/pw/all.hh> +#include <mln/core/image/image_if.hh> + namespace mln { @@ -52,6 +60,12 @@ out = linear::gaussian_directional_2d(out, 0, v_sigma, 0); fuzzy = level::saturate(value::int_u8(), out); + +#ifdef LOG + io::pgm::save(small, "temp_small.pgm"); + io::pgm::save(fuzzy, "temp_fuzzy.pgm"); +#endif // LOG + } // Closing. @@ -60,6 +74,41 @@ // Watershed transform. image2d<L> ws = morpho::watershed::flooding(clo, c4(), n_lines); + +# ifdef LOG + { + // Watershed line (red) over small image. + image2d<value::rgb8> cool = level::convert(value::rgb8(), small); + data::fill((cool | (pw::value(ws) == pw::cst(0))).rw(), + literal::red); + io::ppm::save(cool, "temp_small_ws.ppm"); + } + { + // Watershed line (red) over fuzzy image. + image2d<value::rgb8> cool = level::convert(value::rgb8(), fuzzy); + data::fill((cool | (pw::value(ws) == pw::cst(0))).rw(), + literal::red); + io::ppm::save(cool, "temp_fuzzy_ws.ppm"); + } + { + // Watershed basins colorize the small image. + image2d<value::rgb8> cool = debug::colorize(value::rgb8(), ws, n_lines); + data::fill((cool | (pw::value(ws) == pw::cst(0))).rw(), + literal::white); + mln_piter(box2d) p(small.domain()); + for_all(p) + { + if (small(p) == 255) + continue; + float f = float(small(p)) / 255; + cool(p).red() = cool(p).red() * f; + cool(p).green() = cool(p).green() * f; + cool(p).blue() = cool(p).blue() * f; + } + io::ppm::save(cool, "temp_ws.ppm"); + } +# endif + return ws; } Index: icdar/2009/hsc/ws_to_wsl.hh --- icdar/2009/hsc/ws_to_wsl.hh (revision 3691) +++ icdar/2009/hsc/ws_to_wsl.hh (working copy) @@ -44,25 +44,6 @@ { - algebra::mat<1,2,float> - trans(const algebra::vec<2,float>& v) - { - algebra::mat<1,2,float> tmp; - tmp(0,0) = v[0]; - tmp(0,1) = v[1]; - return tmp; - } - - algebra::mat<2,1,float> - to_mat(const algebra::vec<2,float>& v) - { - algebra::mat<2,1,float> tmp; - tmp(0,0) = v[0]; - tmp(1,0) = v[1]; - return tmp; - } - - struct mahalanobis : public mln::accu::internal::base< unsigned , mahalanobis > { typedef point2d argument; @@ -113,7 +94,7 @@ if (n_ == 0) return; mean_ /= n_; - cov_ = cov_ / n_ - to_mat(mean_) * trans(mean_); + cov_ = cov_ / n_ - mean_ * mean_.t(); float a = cov_(0, 0), b = cov_(0, 1), @@ -174,7 +155,7 @@ { mln_invariant(valid_); algebra::vec<2,float> v_ = v - mean_; - return (trans(v_) * cov_1_ * v_)[0]; + return v_.t() * cov_1_ * v_; } /// Get the number of items. @@ -397,29 +378,32 @@ #ifdef LOG { - io::pgm::save(small, "tmp_small.pgm"); - io::pgm::save(ws, "tmp_ws.pgm"); - using value::rgb8; - image2d<rgb8> small_ws = level::convert(rgb8(), small); - data::fill((small_ws | (pw::value(ws) == pw::cst(0))).rw(), - literal::red); - io::ppm::save(small_ws, "tmp_small_ws.ppm"); - fun::i2v::array<L> f_relab(n_basins + 1); f_relab(0) = 0; for (L l = 1; l <= n_basins; ++l) f_relab(l) = parent[l]; image2d<L> ws_ = level::transform(ws, f_relab); - io::ppm::save(debug::colorize(rgb8(), ws_, n_basins), "tmp_ws.ppm"); + image2d<rgb8> cool = debug::colorize(rgb8(), ws_, n_basins); + data::fill((cool | (pw::value(ws) == pw::cst(0))).rw(), + literal::white); + mln_piter(box2d) p(small.domain()); + for_all(p) + { + if (small(p) == 255) + continue; + float f = float(small(p)) / 255; + cool(p).red() = cool(p).red() * f; + cool(p).green() = cool(p).green() * f; + cool(p).blue() = cool(p).blue() * f; + } + io::ppm::save(cool, "temp_wsl.ppm"); } #endif // LOG - - // Outputing. image2d<L> output(input.domain()); Index: jardonnet/registration/cov.hh --- jardonnet/registration/cov.hh (revision 3691) +++ jardonnet/registration/cov.hh (working copy) @@ -66,7 +66,7 @@ // FIXME: ugly cast. algebra::vec<P::dim,float> a1i = a1[i]; algebra::vec<P::dim,float> a2i = a2[i]; - Mk += make::mat(a1i - mu_a1) * trans(make::mat(a2i - mu_a2)); + Mk += (a1i - mu_a1) * (a2i - mu_a2).t(); } return Mk / a1.nsites(); Index: jardonnet/registration/quat7.hh --- jardonnet/registration/quat7.hh (revision 3691) +++ jardonnet/registration/quat7.hh (working copy) @@ -145,8 +145,8 @@ algebra::vec<P::dim,float> Ci = C[i]; algebra::vec<P::dim,float> Xki = map(Ck[i]); - Mk += make::mat(Ci - mu_C) * trans(make::mat(Xki - mu_Xk)); - // or Mk += make::mat(Ci) * trans(make::mat(Xki)) - make::mat(mu_C) * trans(make::mat(mu_Xk)) + Mk += (Ci - mu_C) * (Xki - mu_Xk).t(); + // or Mk += Ci * Xki.t() - mu_C * mu_Xk.t() } Mk /= c_length;

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