- Olena-patches

branch next updated: last-svn-commit-178-g71c9c14
by git＠lrde.epita.fr 24 Jun '10

24 Jun '10

This is an automated email from the git hooks/post-receive script. It was generated because a ref change was pushed to the repository containing the project "Olena, a generic and efficient image processing platform". The branch next has been updated via 71c9c144f233770f1b9652ba98d6137053e8ab47 (commit) from 0d502d0cf9f3571471768db4f3833b0701ef39a0 (commit) Those revisions listed above that are new to this repository have not appeared on any other notification email; so we list those revisions in full, below. - Log ----------------------------------------------------------------- No new revisions were added by this update. ----------------------------------------------------------------------- Summary of changes: ChangeLog | 6 ++++++ lrde-upload.sh | 2 +- 2 files changed, 7 insertions(+), 1 deletions(-) hooks/post-receive -- Olena, a generic and efficient image processing platform

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last-svn-commit-181-gb359f8b Revive, fix and update application mesh-segm.
by Roland Levillain 24 Jun '10

24 Jun '10

* apps/mesh-segm-skel/mesh-segm.cc: Catch up with the new interface of graphs. Use mln::edge_image instead of mln::line_graph_image. Turn a test into an invariant. Use mln::morpho::watershed::flooding instead of mln::morpho::meyer_wst. * apps/mesh-segm-skel/Makefile.am (bin_PROGRAMS): Re-enable mesg-segm. (mesh_segm_SOURCES, mesh_segm_CPPFLAGS) (mesh_segm_LDFLAGS, mesh_segm_LDADD): Re-enable. (TESTS): Reenable test-mesh-segm. (MOSTLYCLEANFILES): Reenable socket-segm.off and teapot-segm.off. --- milena/ChangeLog | 18 +++++ milena/apps/mesh-segm-skel/Makefile.am | 28 +++++---- milena/apps/mesh-segm-skel/mesh-segm.cc | 110 +++++++++++++++++++------------ 3 files changed, 103 insertions(+), 53 deletions(-) diff --git a/milena/ChangeLog b/milena/ChangeLog index 2d28537..b2f2330 100644 --- a/milena/ChangeLog +++ b/milena/ChangeLog @@ -1,3 +1,21 @@ +2010-05-11 Roland Levillain <roland(a)lrde.epita.fr> + + Revive, fix and update application mesh-segm. + + * apps/mesh-segm-skel/mesh-segm.cc: Catch up with the new + interface of graphs. + Use mln::edge_image instead of mln::line_graph_image. + Turn a test into an invariant. + Use mln::morpho::watershed::flooding instead of + mln::morpho::meyer_wst. + * apps/mesh-segm-skel/Makefile.am (bin_PROGRAMS): + Re-enable mesg-segm. + (mesh_segm_SOURCES, mesh_segm_CPPFLAGS) + (mesh_segm_LDFLAGS, mesh_segm_LDADD): + Re-enable. + (TESTS): Reenable test-mesh-segm. + (MOSTLYCLEANFILES): Reenable socket-segm.off and teapot-segm.off. + 2010-05-10 Roland Levillain <roland(a)lrde.epita.fr> Fix a bug in the reimplementation of Trimesh algorithms. diff --git a/milena/apps/mesh-segm-skel/Makefile.am b/milena/apps/mesh-segm-skel/Makefile.am index 9768f25..501dec0 100644 --- a/milena/apps/mesh-segm-skel/Makefile.am +++ b/milena/apps/mesh-segm-skel/Makefile.am @@ -1,4 +1,5 @@ -# Copyright (C) 2008, 2009 EPITA Research and Development Laboratory (LRDE). +# Copyright (C) 2008, 2009, 2010 EPITA Research and Development +# Laboratory (LRDE). # # This file is part of Olena. # @@ -49,19 +50,22 @@ MOSTLYCLEANFILES = ## ------------------------------------------------ ## if ENABLE_TRIMESH -# bin_PROGRAMS += mesh-segm mesh-skel -# -# mesh_segm_SOURCES = mesh-segm.cc io.hh -# mesh_segm_CPPFLAGS = $(AM_CPPFLAGS) $(CPPFLAGS_trimesh) -# mesh_segm_LDFLAGS = $(LDFLAGS_trimesh) -# mesh_segm_LDADD = $(LDADD_trimesh) -# -# TESTS += test-mesh-segm -# MOSTLYCLEANFILES += socket-segm.off teapot-segm.off - -# FIXME: mesh_skel is unfinished. Anyway, it should be superseded by -# another program, using no Trimesh code. - +## FIXME: Rename as mesh-trimesh-graph-{max,pinv}-curv-segm? +bin_PROGRAMS += mesh-segm +mesh_segm_SOURCES = mesh-segm.cc io.hh +mesh_segm_CPPFLAGS = $(AM_CPPFLAGS) $(CPPFLAGS_trimesh) +mesh_segm_LDFLAGS = $(LDFLAGS_trimesh) +mesh_segm_LDADD = $(LDADD_trimesh) + +TESTS += test-mesh-segm +# FIXME: Likewise. +MOSTLYCLEANFILES += socket-segm.off teapot-segm.off + +# FIXME: mesh_skel is unfinished. Anyway, it has been be superseded +# by `mesh-complex-skel' (see below), using no Trimesh code. + +## FIXME: Rename as mesh-trimesh-graph-{max,pinv}-curv-skel? +# bin_PROGRAMS += mesh-skel # mesh_skel_SOURCES = mesh-skel.cc io.hh # mesh_skel_CPPFLAGS = $(AM_CPPFLAGS) $(CPPFLAGS_trimesh) # mesh_skel_LDFLAGS = $(LDFLAGS_trimesh) diff --git a/milena/apps/mesh-segm-skel/mesh-segm.cc b/milena/apps/mesh-segm-skel/mesh-segm.cc index bf87249..06ddc93 100644 --- a/milena/apps/mesh-segm-skel/mesh-segm.cc +++ b/milena/apps/mesh-segm-skel/mesh-segm.cc @@ -1,4 +1,5 @@ -// Copyright (C) 2008, 2009 EPITA Research and Development Laboratory (LRDE) +// Copyright (C) 2008, 2009, 2010 EPITA Research and Development +// Laboratory (LRDE) // // This file is part of the Milena Library. This library is free // software; you can redistribute it and/or modify it under the terms @@ -40,14 +41,18 @@ #include <TriMesh.h> #include <mln/core/alias/point3d.hh> -#include <mln/core/alias/point3d.hh> + +#include <mln/fun/i2v/array.hh> +#include <mln/convert/from_to.hh> #include <mln/util/graph.hh> -#include <mln/core/image/line_graph_image.hh> -#include <mln/core/image/line_graph_elt_neighborhood.hh> +#include <mln/util/line_graph.hh> +#include <mln/util/site_pair.hh> +#include <mln/core/image/edge_image.hh> +#include <mln/make/edge_image.hh> #include <mln/morpho/closing/area.hh> -#include <mln/morpho/meyer_wst.hh> +#include <mln/morpho/watershed/flooding.hh> #include "io.hh" @@ -116,12 +121,9 @@ int main(int argc, char* argv[]) std::vector<curv_t> vertex_values (mesh.faces.size(), 0.f); std::vector<curv_t> edge_values; - /* FIXME: We don't have the required site type yet. Simulate with a - dummy type (point3d). */ - mln::util::graph<mln::point3d> g; + mln::util::graph g; // Populate the graph with vertices. - for (unsigned i = 0; i < mesh.faces.size(); ++i) - g.add_vertex (mln::point3d(i, i, i)); + g.add_vertices(mesh.faces.size()); // Populate the graph with edges. mesh.need_across_edge(); @@ -132,25 +134,26 @@ int main(int argc, char* argv[]) if (f_adj != -1) { // Add an edge into the graph. - if (g.add_edge(f, f_adj) != mln_max(mln::util::edge_id::equiv)) - { - // Find the edge (i.e., the two vertices) common to faces - // F and F_ADJ. - /* FIXME: We lack a proper interface from the TriMesh - structure to do this elegantly. */ - std::vector<int> adj_vertices; - adj_vertices.reserve(2); - for (unsigned i = 0; i < 3; ++i) - for (unsigned j = 0; j < 3; ++j) - if (mesh.faces[f][i] == mesh.faces[f_adj][j]) - adj_vertices.push_back(mesh.faces[f][i]); - mln_assertion(adj_vertices.size() == 2); - - // Compute the mean curvature on the edge. - edge_values.push_back((vertex_h_inv[adj_vertices[0]] + - vertex_h_inv[adj_vertices[1]]) - / 2); - } + mln::util::edge_id_t new_edge = g.add_edge(f, f_adj); + mln_invariant(new_edge.is_valid()); + + /* Among the edges adjacent to F and F_ADJ, find the one + they share. In practice, find the two vertices shared + by F and F_ADJ. */ + /* FIXME: We lack a proper interface from the TriMesh + structure to do this elegantly. */ + std::vector<int> adj_vertices; + adj_vertices.reserve(2); + for (unsigned i = 0; i < 3; ++i) + for (unsigned j = 0; j < 3; ++j) + if (mesh.faces[f][i] == mesh.faces[f_adj][j]) + adj_vertices.push_back(mesh.faces[f][i]); + mln_assertion(adj_vertices.size() == 2); + + // Compute the mean curvature on the edge. + edge_values.push_back((vertex_h_inv[adj_vertices[0]] + + vertex_h_inv[adj_vertices[1]]) + / 2); // Check the consistency of the two arrays. mln_assertion(g.edges().size() == edge_values.size()); @@ -161,19 +164,38 @@ int main(int argc, char* argv[]) | Line graph image. | `-------------------*/ - mln::p_line_graph<mln::point3d> plg(g); + // Points associated to the line graph vertices (edges in the graph). + typedef mln::util::site_pair<mln::point3df> P; + typedef mln::fun::i2v::array<P> fsite_t; + fsite_t sites(g.e_nmax()); + for (unsigned i = 0; i < g.e_nmax(); ++i) + /* FIXME: Add a dummy location information for the moment. This + doesn't really matter as we won't use it to produce the output. + However, we may need it later: do not forget to add relevant + locations (obtained from the mesh) in a future version of this + program. */ + sites(i) = P(mln::point3df(0, 0, 0), mln::point3df(1, 1, 1)); + + // FIXME: This intermediate structure costs us a copy. + typedef mln::fun::i2v::array<curv_t> values_t; + values_t values; + mln::convert::from_to(edge_values, values); + + typedef mln::edge_image<P, curv_t, mln::util::graph> ima_t; + ima_t graph_ima(g, sites, values); - typedef mln::line_graph_image<mln::point3d, curv_t> ima_t; - ima_t lg_ima(plg, vertex_values, edge_values); /*-----------------. | Simplification. | `-----------------*/ - typedef mln::line_graph_elt_neighborhood<mln::point3d> nbh_t; + typedef ima_t::nbh_t nbh_t; nbh_t nbh; - ima_t closed_lg_ima = mln::morpho::closing::area(lg_ima, nbh, lambda); + // ``Area'' is not a proper term here, since it is defined to the + // number of edges in the graph. Taking into account the actual + // area of triangles would be a more clever choice. + ima_t closed_graph_ima = mln::morpho::closing::area(graph_ima, nbh, lambda); /*------. | WST. | @@ -181,24 +203,30 @@ int main(int argc, char* argv[]) typedef unsigned wst_val_t; wst_val_t nbasins; - typedef mln::line_graph_image<mln::point3d, wst_val_t> wst_ima_t; - wst_ima_t wshed = mln::morpho::meyer_wst(closed_lg_ima, nbh, nbasins); + typedef mln_ch_value_(ima_t, wst_val_t) wst_ima_t; + wst_ima_t wshed = + mln::morpho::watershed::flooding(closed_graph_ima, nbh, nbasins); std::cout << "nbasins = " << nbasins << std::endl; /*------------------------------------------. | Label graph vertices (i.e., mesh faces). | `------------------------------------------*/ - /* FIXME: We should be using wshed.vertex_values_ if - mln::line_graph_image were fully functional... */ - std::vector<unsigned> vertex_label(wshed.domain().nvertices(), 0); + // FIXME: Use a vertex_image and a e2v neighborhood instead? + + /* FIXME: p_edges does not provide nvertices(), so we cannot write + + std::vector<unsigned> vertex_label(wshed.domain().nvertices(), 0); + + Likewise, p_vertices does not provide n_edges(). */ + std::vector<unsigned> vertex_label(wshed.domain().graph().v_nmax(), 0); mln_piter_(wst_ima_t) pw(wshed.domain()); for_all(pw) if (wshed(pw) != 0) { mln_psite_(wst_ima_t) pp(pw); - vertex_label[pp.first_id().to_equiv()] = wshed(pw); - vertex_label[pp.second_id().to_equiv()] = wshed(pw); + vertex_label[pp.v1().id()] = wshed(pw); + vertex_label[pp.v2().id()] = wshed(pw); } /*---------. -- 1.5.6.5

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last-svn-commit-180-g0d9aa9c Fix a bug in the reimplementation of Trimesh algorithms.
by Roland Levillain 24 Jun '10

24 Jun '10

* apps/mesh-segm-skel/trimesh/misc.hh (mln::geom::mesh_curvature): Always call algebra::ldlt_decomp, even when NDEBUG is defined. Typo. Avoid a warning about an undefined variable when NDEBUG is not defined. --- milena/ChangeLog | 10 ++++++++++ milena/apps/mesh-segm-skel/trimesh/misc.hh | 15 +++++++++------ 2 files changed, 19 insertions(+), 6 deletions(-) diff --git a/milena/ChangeLog b/milena/ChangeLog index f1c1386..2d28537 100644 --- a/milena/ChangeLog +++ b/milena/ChangeLog @@ -1,3 +1,13 @@ +2010-05-10 Roland Levillain <roland(a)lrde.epita.fr> + + Fix a bug in the reimplementation of Trimesh algorithms. + + * apps/mesh-segm-skel/trimesh/misc.hh (mln::geom::mesh_curvature): + Always call algebra::ldlt_decomp, even when NDEBUG is defined. + Typo. + Avoid a warning about an undefined variable when NDEBUG is not + defined. + 2010-05-04 Roland Levillain <roland(a)lrde.epita.fr> Improve topo::skeleton::breadth_first_thinning. diff --git a/milena/apps/mesh-segm-skel/trimesh/misc.hh b/milena/apps/mesh-segm-skel/trimesh/misc.hh index 5084632..79eea14 100644 --- a/milena/apps/mesh-segm-skel/trimesh/misc.hh +++ b/milena/apps/mesh-segm-skel/trimesh/misc.hh @@ -1,5 +1,5 @@ -// Copyright (C) 2008, 2009 EPITA Research and Development Laboratory -// (LRDE) +// Copyright (C) 2008, 2009, 2010 EPITA Research and Development +// Laboratory (LRDE) // // This file is part of the Milena Library. This library is free // software; you can redistribute it and/or modify it under the terms @@ -623,10 +623,13 @@ namespace mln // Least squares solution. vec3f diag; -#ifndef NDEBUG - bool ldlt_decomp_sucess_p = algebra::ldlt_decomp(w, diag); -#endif // ! NDEBUG - mln_assertion(ldlt_decomp_sucess_p); + // Note that algebra::ldlt_decomp has side effects on its + // arguments; this call is not ``just an assertion''. + bool ldlt_decomp_success_p = algebra::ldlt_decomp(w, diag); + mln_assertion(ldlt_decomp_success_p); + // Avoid a warning about an undefined variable when NDEBUG + // is not defined. + (void) ldlt_decomp_success_p; algebra::ldlt_solve(w, diag, m, m); // Push it back out to the vertices -- 1.5.6.5

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last-svn-commit-179-g7bfa2cb Improve topo::skeleton::breadth_first_thinning.
by Roland Levillain 24 Jun '10

24 Jun '10

* mln/topo/skeleton/breadth_first_thinning.hh (mln::topo::skeleton::breadth_first_thinning): Fix a bias in the algorithm due to a buggy predicate. Introduce a temporary psite to help the compiler. Fix the type of `output'. --- milena/ChangeLog | 10 ++++++++++ milena/mln/topo/skeleton/breadth_first_thinning.hh | 20 ++++++++++++++------ 2 files changed, 24 insertions(+), 6 deletions(-) diff --git a/milena/ChangeLog b/milena/ChangeLog index 214b7e6..f1c1386 100644 --- a/milena/ChangeLog +++ b/milena/ChangeLog @@ -1,3 +1,13 @@ +2010-05-04 Roland Levillain <roland(a)lrde.epita.fr> + + Improve topo::skeleton::breadth_first_thinning. + + * mln/topo/skeleton/breadth_first_thinning.hh + (mln::topo::skeleton::breadth_first_thinning): + Fix a bias in the algorithm due to a buggy predicate. + Introduce a temporary psite to help the compiler. + Fix the type of `output'. + 2010-04-26 Roland Levillain <roland(a)lrde.epita.fr> Clean Milena's tests' outputs during `make mostlyclean'. diff --git a/milena/mln/topo/skeleton/breadth_first_thinning.hh b/milena/mln/topo/skeleton/breadth_first_thinning.hh index 42e1bef..8039ffb 100644 --- a/milena/mln/topo/skeleton/breadth_first_thinning.hh +++ b/milena/mln/topo/skeleton/breadth_first_thinning.hh @@ -1,4 +1,4 @@ -// Copyright (C) 2009 EPITA Research and Development Laboratory (LRDE) +// Copyright (C) 2009, 2010 EPITA Research and Development Laboratory (LRDE) // // This file is part of Olena. // @@ -90,7 +90,7 @@ namespace mln F& is_simple = exact(is_simple_); const H& constraint = exact(constraint_); - I output = duplicate(input); + mln_concrete(I) output = duplicate(input); // Attach the work image to IS_SIMPLE. is_simple.set_image(output); @@ -133,15 +133,23 @@ namespace mln /* FIXME: We compute the cell and attachment of P twice: during the call to is_simple() and within detach(). How could we reuse this elegantly, without breaking - the genericity of the skeleton algorithm? */ + the genericity of the skeleton algorithm? + Also, keep in mind that functors can maintain an + internal state and make side effects, meaning that + e.g. constraint(p) might not be constant for a + given p during the thinning. */ if (constraint(p) && is_simple(p)) { detach(p, output); - mln_niter(N) n(nbh, p); - for_all(n) + mln_niter(N) n_(nbh, p); + for_all(n_) + { + // Same remark as above regarding P and P_. + psite n = n_; if (output.domain().has(n) - && output(n) && constraint(p) && is_simple(n)) + && output(n) && constraint(n) && is_simple(n)) next_set.insert(n); + } } } set.clear(); -- 1.5.6.5

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branch mesh-segm-skel updated: last-svn-commit-188-gf36081f
by git＠lrde.epita.fr 24 Jun '10

24 Jun '10

This is an automated email from the git hooks/post-receive script. It was generated because a ref change was pushed to the repository containing the project "Olena, a generic and efficient image processing platform". The branch mesh-segm-skel has been updated discards 300322ef688a1f38cd1e5918774f21b93b912e6e (commit) discards c9b58ad8fbaa27a3eeeb4ab4167114ccdfe762ec (commit) discards e4978ab662c8a70fdee99977032300c142235ccb (commit) discards 47481b45cfb4e5c687596a52c3cb334e79f163d5 (commit) discards 2da010175cca88a13c231da1007b98e16fca75c1 (commit) discards 3cdb8bbd851688b0678ceeb5746cfe1d8353262b (commit) discards 7c9b5a325426ee398304c873db49fc015e86d516 (commit) discards 679f73c895982eee5b77c2ce1492474ac5957ff7 (commit) discards 40ba1ad80da1ed71f7bccd589ff8aa4d82149d6e (commit) discards 9a842d1a96866d1d54442fc9f582f8551e5e1a2b (commit) via f36081f28428672f81cbb700a0a52da51b10d7ff (commit) via 3f6e1c50761b9ca2c8c8f5403c9236c45d04e969 (commit) via b5e8235b7e417cd015a4978999d1d51540645b7e (commit) via f1c3f6a489dfa9606ce6fa0d13020ea314acd1e7 (commit) via ead83a9b2e0b7269825675cb0a769c119d92ff16 (commit) via 45fcb1970125f5bba8b68ecff943188234caf1ca (commit) via 56c4e2c3c79bec09c11003e222f480443c1288c5 (commit) via b359f8b1bcc79c8f7d1e4f6e22d49d09b82fd983 (commit) via 0d9aa9caa5fe3bb69389b3d67bb53381f8b807f5 (commit) via 7bfa2cb0923ff4103685c7c76feaf44fe8165b06 (commit) via 71c9c144f233770f1b9652ba98d6137053e8ab47 (commit) via 0d502d0cf9f3571471768db4f3833b0701ef39a0 (commit) via ba369b62ba9d59fb093d4247284f2c437f42754e (commit) via 165770feeac77f1dfab40f3173c3e6e483709df1 (commit) This update added new revisions after undoing existing revisions. That is to say, the old revision is not a strict subset of the new revision. This situation occurs when you --force push a change and generate a repository containing something like this: * -- * -- B -- O -- O -- O (300322ef688a1f38cd1e5918774f21b93b912e6e) \ N -- N -- N (f36081f28428672f81cbb700a0a52da51b10d7ff) When this happens we assume that you've already had alert emails for all of the O revisions, and so we here report only the revisions in the N branch from the common base, B. Those revisions listed above that are new to this repository have not appeared on any other notification email; so we list those revisions in full, below. - Log ----------------------------------------------------------------- f36081f Actually use the maximal curvature in mesh-complex-max-curv-segm. 3f6e1c5 Improve the precision of some mesh-segm-skel apps. b5e8235 Configure milena/apps/mesh-segm-skel/test-mesh-complex-max-curv-skel. f1c3f6a New application: mesh-complex-max-curv-skel. ead83a9 Clean up and new FIXMES in in apps/mesh-segm-skel. 45fcb19 Configure milena/apps/mesh-segm-skel/test-mesh-complex-max-curv-extrema. 56c4e2c New application: mesh-complex-max-curv-extrema. b359f8b Revive, fix and update application mesh-segm. 0d9aa9c Fix a bug in the reimplementation of Trimesh algorithms. 7bfa2cb Improve topo::skeleton::breadth_first_thinning. 71c9c14 Add `mesh-segm-skel' to the branches to be uploaded (as snapshot). ----------------------------------------------------------------------- Summary of changes: ChangeLog | 6 + lrde-upload.sh | 2 +- milena/ChangeLog | 105 +++++++++++++++++++- milena/apps/mesh-segm-skel/Makefile.am | 14 ++-- milena/apps/papers/levillain.09.ismm/Makefile.am | 2 +- milena/tests/binarization/Makefile.am | 12 +-- milena/tests/binarization/threshold.cc | 7 +- milena/tests/data/Makefile.am | 13 +-- milena/tests/data/approx/Makefile.am | 9 +- milena/tests/data/approx/median.cc | 7 +- milena/tests/data/median.cc | 7 +- milena/tests/data/median_fast.cc | 5 +- milena/tests/data/naive/Makefile.am | 6 +- milena/tests/data/naive/median.cc | 5 +- milena/tests/io/dump/Makefile.am | 12 ++- milena/tests/io/dump/dump.cc | 24 +++-- milena/tests/io/fits/Makefile.am | 13 +-- milena/tests/io/fits/fits.cc | 11 +- milena/tests/io/magick/Makefile.am | 12 +-- milena/tests/io/magick/save.cc | 9 +- milena/tests/io/off/Makefile.am | 10 +-- milena/tests/io/off/load_save_bin.cc | 5 +- milena/tests/io/pbm/Makefile.am | 14 ++-- milena/tests/io/pbm/pbm.cc | 7 +- milena/tests/io/pbm/pbm_ascii.cc | 6 +- milena/tests/io/pbms/Makefile.am | 6 +- milena/tests/io/pbms/load.cc | 6 +- milena/tests/io/pgm/Makefile.am | 33 ++++--- milena/tests/io/pgm/pgm.cc | 11 +- milena/tests/io/pgm/pgm16.cc | 13 ++- milena/tests/io/pgm/pgm19.cc | 9 +- milena/tests/io/pgm/pgm27.cc | 9 +- milena/tests/io/pgm/pgm_ascii.cc | 10 +- milena/tests/io/pgms/Makefile.am | 7 +- milena/tests/io/pgms/load.cc | 6 +- milena/tests/io/ppm/Makefile.am | 24 ++--- milena/tests/io/ppm/ppm.cc | 7 +- milena/tests/io/ppm/ppm16.cc | 11 +- milena/tests/io/ppm/ppm23.cc | 11 +- milena/tests/io/ppms/Makefile.am | 7 +- milena/tests/io/ppms/load.cc | 8 +- milena/tests/linear/Makefile.am | 13 ++- milena/tests/linear/convolve.cc | 5 +- milena/tests/linear/convolve_2x1d.cc | 5 +- milena/tests/linear/convolve_directional.cc | 5 +- milena/tests/linear/gaussian.cc | 5 +- milena/tests/linear/gaussian/Makefile.am | 4 +- milena/tests/linear/gaussian/filter.cc | 5 +- milena/tests/linear/lap.cc | 5 +- milena/tests/linear/log.cc | 5 +- milena/tests/linear/sobel_2d.cc | 5 +- milena/tests/morpho/Makefile.am | 32 ++++--- milena/tests/morpho/approx/Makefile.am | 13 +-- milena/tests/morpho/approx/dilation.cc | 6 +- milena/tests/morpho/approx/erosion.cc | 6 +- .../morpho/artificial_line_graph_image_wst.cc | 5 +- milena/tests/morpho/closing/Makefile.am | 38 ++++---- milena/tests/morpho/closing/algebraic.cc | 6 +- milena/tests/morpho/closing/approx/Makefile.am | 11 +-- milena/tests/morpho/closing/approx/structural.cc | 6 +- milena/tests/morpho/closing/height.cc | 5 +- milena/tests/morpho/closing/leveling.cc | 6 +- milena/tests/morpho/closing/structural.cc | 4 +- milena/tests/morpho/closing/sum.cc | 5 +- milena/tests/morpho/closing/volume.cc | 7 +- milena/tests/morpho/complex_image_wst.cc | 5 +- milena/tests/morpho/contrast.cc | 5 +- milena/tests/morpho/dilation.cc | 13 ++- milena/tests/morpho/general.cc | 5 +- milena/tests/morpho/gradient.cc | 7 +- milena/tests/morpho/hit_or_miss.cc | 10 +-- milena/tests/morpho/laplacian.cc | 7 +- milena/tests/morpho/lena_line_graph_image_wst1.cc | 5 +- milena/tests/morpho/lena_line_graph_image_wst2.cc | 5 +- milena/tests/morpho/meyer_wst.cc | 5 +- milena/tests/morpho/meyer_wst_long.cc | 6 +- milena/tests/morpho/opening/Makefile.am | 37 ++++--- milena/tests/morpho/opening/algebraic.cc | 6 +- milena/tests/morpho/opening/approx/Makefile.am | 6 +- milena/tests/morpho/opening/approx/structural.cc | 6 +- milena/tests/morpho/opening/area.cc | 5 +- milena/tests/morpho/opening/height.cc | 5 +- milena/tests/morpho/opening/leveling.cc | 6 +- milena/tests/morpho/opening/structural.cc | 4 +- milena/tests/morpho/opening/sum.cc | 5 +- milena/tests/morpho/opening/volume.cc | 5 +- milena/tests/morpho/thinning.cc | 7 +- milena/tests/morpho/watershed/Makefile.am | 13 +-- milena/tests/morpho/watershed/flooding.cc | 13 ++- milena/tests/morpho/watershed/topological.cc | 5 +- swilena/ChangeLog | 12 +++ swilena/python/Makefile.am | 26 +++--- swilena/python/morpho-fun.py | 23 +++-- swilena/python/morpho-segm.py | 7 +- 94 files changed, 567 insertions(+), 405 deletions(-) hooks/post-receive -- Olena, a generic and efficient image processing platform

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last-svn-commit-178-g71c9c14 Add `mesh-segm-skel' to the branches to be uploaded (as snapshot).
by Roland Levillain 24 Jun '10

24 Jun '10

* lrde-upload.sh: Here. --- ChangeLog | 6 ++++++ lrde-upload.sh | 2 +- 2 files changed, 7 insertions(+), 1 deletions(-) diff --git a/ChangeLog b/ChangeLog index 57df1c6..44386d3 100644 --- a/ChangeLog +++ b/ChangeLog @@ -1,3 +1,9 @@ +2010-06-24 Roland Levillain <roland(a)lrde.epita.fr> + + Add `mesh-segm-skel' to the branches to be uploaded (as snapshot). + + * lrde-upload.sh: Here. + 2010-04-23 Roland Levillain <roland(a)lrde.epita.fr> Add variables for C++ compiler flags for Scribo. diff --git a/lrde-upload.sh b/lrde-upload.sh index 5f61ef2..3ed1aa6 100755 --- a/lrde-upload.sh +++ b/lrde-upload.sh @@ -45,7 +45,7 @@ branch=$1 case "$branch" in # Consider these branches only. - master|next|swilena) ;; + master|next|swilena|mesh-segm-skel) ;; # Don't upload other branches. *) exit ;; esac -- 1.5.6.5

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branch exp/green updated: last-svn-commit-46-gcfc3ef7
by git＠lrde.epita.fr 24 Jun '10

24 Jun '10

This is an automated email from the git hooks/post-receive script. It was generated because a ref change was pushed to the repository containing the project "Olena, a generic and efficient image processing platform". The branch exp/green has been updated discards b6f36911eb58513cfceafe871dc5a3cdfd1791bc (commit) discards 2fa459f44c6c7c938c48f4dd53a3210e885be1ac (commit) discards d26549180bf35357fa14783fb99d60108896009f (commit) discards 6e896e2214587d64f2d54a877c41b7cb1451c612 (commit) discards de3450dd6da34b7380382928582f8e8dd6f8f0d6 (commit) discards 9895c32ead3335ff6037eee9c900bc910cb4d74f (commit) via cfc3ef76083def2e08adf726a633919cfd86bd9d (commit) via d2a2a435da3435562e098fb267ecbeae19059b90 (commit) via d602c29a1ebc23c841c0748226af2da193d9dd5e (commit) via 0da8c6375445d82cadb5a4880af9bc8c6770a09a (commit) via 0bf1f8f03ef32c05fe402e6559eacbfe1c8f068a (commit) This update added new revisions after undoing existing revisions. That is to say, the old revision is not a strict subset of the new revision. This situation occurs when you --force push a change and generate a repository containing something like this: * -- * -- B -- O -- O -- O (b6f36911eb58513cfceafe871dc5a3cdfd1791bc) \ N -- N -- N (cfc3ef76083def2e08adf726a633919cfd86bd9d) When this happens we assume that you've already had alert emails for all of the O revisions, and so we here report only the revisions in the N branch from the common base, B. Those revisions listed above that are new to this repository have not appeared on any other notification email; so we list those revisions in full, below. - Log ----------------------------------------------------------------- cfc3ef7 Define documentation files. d2a2a43 Define gnuplot shell export format. d602c29 Import files from milena/sandbox/green. 0da8c63 Define accumulator which computes histogram view as image. 0bf1f8f Import files from milena/sandbox/green. ----------------------------------------------------------------------- Summary of changes: scribo/sandbox/green/ChangeLog | 51 ++ .../sandbox/green/ok/mln/accu/histo}/histo1d.hh | 100 ++-- .../sandbox/green/ok/mln/accu/histo}/histo2d.hh | 0 .../sandbox/green/ok/mln/accu/histo/histo3d.hh | 0 .../sandbox/green/ok}/mln/img_path.hh | 0 .../sandbox/green/ok/test/accu/histo}/gaussian.sh | 0 scribo/sandbox/green/ok/test/accu/histo/histo1d | Bin 0 -> 802920 bytes scribo/sandbox/green/ok/test/accu/histo/histo1d.cc | 726 ++++++++++++++++++++ 8 files changed, 820 insertions(+), 57 deletions(-) copy {milena/sandbox/green/mln/accu/stat => scribo/sandbox/green/ok/mln/accu/histo}/histo1d.hh (74%) copy {milena/sandbox/green/mln/accu/stat => scribo/sandbox/green/ok/mln/accu/histo}/histo2d.hh (100%) copy milena/sandbox/green/mln/accu/stat/histo3d_rgb.hh => scribo/sandbox/green/ok/mln/accu/histo/histo3d.hh (100%) copy {milena/sandbox/green => scribo/sandbox/green/ok}/mln/img_path.hh (100%) copy {milena/sandbox/green/tests/accu/stat/histo1d => scribo/sandbox/green/ok/test/accu/histo}/gaussian.sh (100%) create mode 100755 scribo/sandbox/green/ok/test/accu/histo/histo1d create mode 100644 scribo/sandbox/green/ok/test/accu/histo/histo1d.cc hooks/post-receive -- Olena, a generic and efficient image processing platform

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branch exp/scribo-z updated: last-svn-commit-164-g91b2059
by git＠lrde.epita.fr 24 Jun '10

24 Jun '10

This is an automated email from the git hooks/post-receive script. It was generated because a ref change was pushed to the repository containing the project "Olena, a generic and efficient image processing platform". The branch exp/scribo-z has been updated via 91b205927506a09d3c921c4980da3b114617775d (commit) from 966f8d64839b0d13bdc608ef7f4c4247e984391a (commit) Those revisions listed above that are new to this repository have not appeared on any other notification email; so we list those revisions in full, below. - Log ----------------------------------------------------------------- 91b2059 Delete files ----------------------------------------------------------------------- Summary of changes: scribo/sandbox/green/ko/mln/accu/stat/histo1d.hh | 348 ---------- scribo/sandbox/green/ko/mln/accu/stat/histo2d.hh | 346 ---------- .../sandbox/green/ko/mln/accu/stat/histo3d_hsl.hh | 380 ---------- .../sandbox/green/ko/mln/accu/stat/histo3d_rgb.hh | 349 ---------- scribo/sandbox/green/ok/mln/accu/histo/histo1d.hh | 334 --------- scribo/sandbox/green/ok/mln/accu/histo/histo2d.hh | 346 ---------- scribo/sandbox/green/ok/mln/accu/histo/histo3d.hh | 349 ---------- scribo/sandbox/green/ok/mln/img_path.hh | 239 ------- .../sandbox/green/ok/test/accu/histo/gaussian.sh | 12 - scribo/sandbox/green/ok/test/accu/histo/histo1d | Bin 808312 -> 0 bytes scribo/sandbox/green/ok/test/accu/histo/histo1d.cc | 726 -------------------- 11 files changed, 0 insertions(+), 3429 deletions(-) delete mode 100644 scribo/sandbox/green/ko/mln/accu/stat/histo1d.hh delete mode 100644 scribo/sandbox/green/ko/mln/accu/stat/histo2d.hh delete mode 100644 scribo/sandbox/green/ko/mln/accu/stat/histo3d_hsl.hh delete mode 100644 scribo/sandbox/green/ko/mln/accu/stat/histo3d_rgb.hh delete mode 100644 scribo/sandbox/green/ok/mln/accu/histo/histo1d.hh delete mode 100644 scribo/sandbox/green/ok/mln/accu/histo/histo2d.hh delete mode 100644 scribo/sandbox/green/ok/mln/accu/histo/histo3d.hh delete mode 100644 scribo/sandbox/green/ok/mln/img_path.hh delete mode 100755 scribo/sandbox/green/ok/test/accu/histo/gaussian.sh delete mode 100755 scribo/sandbox/green/ok/test/accu/histo/histo1d delete mode 100644 scribo/sandbox/green/ok/test/accu/histo/histo1d.cc hooks/post-receive -- Olena, a generic and efficient image processing platform

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last-svn-commit-44-gd602c29 Import files from milena/sandbox/green.
by Yann Jacquelet 24 Jun '10

24 Jun '10

* gaussian.sh: New gnuplot shell file. * guassian2d.sh: New gnuplot shell file. * test_labelling.cc: New source. * tests/clustering/k_mean/Makefile.am: New makefile. * tests/clustering/k_mean/k_mean.cc: New source. * tests/clustering/kmean1d/Makefile.am: New makefile. * tests/clustering/kmean1d/kmean1d.cc: New source. * tests/io/plot/save_image_sh/Makefile.am: New makefile. * tests/io/plot/save_image_sh/save_image_sh.cc: New source. --- scribo/sandbox/green/ChangeLog | 14 + .../histo1d => scribo/sandbox/green}/gaussian.sh | 0 .../histo2d => scribo/sandbox/green}/gaussian2d.sh | 0 scribo/sandbox/green/test_labelling.cc | 336 ++++++++++++++++++++ .../green/tests/clustering/k_mean/Makefile.am | 0 .../green/tests/clustering/k_mean/k_mean.cc | 0 .../green/tests/clustering/kmean1d/Makefile.am | 0 .../green/tests/clustering/kmean1d/kmean1d.cc | 0 .../green/tests/io/plot/save_image_sh}/Makefile.am | 0 .../tests/io/plot/save_image_sh/save_image_sh.cc | 0 10 files changed, 350 insertions(+), 0 deletions(-) copy {milena/sandbox/green/tests/accu/stat/histo1d => scribo/sandbox/green}/gaussian.sh (100%) copy {milena/sandbox/green/tests/accu/stat/histo2d => scribo/sandbox/green}/gaussian2d.sh (100%) create mode 100644 scribo/sandbox/green/test_labelling.cc copy {milena => scribo}/sandbox/green/tests/clustering/k_mean/Makefile.am (100%) copy {milena => scribo}/sandbox/green/tests/clustering/k_mean/k_mean.cc (100%) copy {milena => scribo}/sandbox/green/tests/clustering/kmean1d/Makefile.am (100%) copy {milena => scribo}/sandbox/green/tests/clustering/kmean1d/kmean1d.cc (100%) copy {milena/sandbox/green/doc/examples/frac => scribo/sandbox/green/tests/io/plot/save_image_sh}/Makefile.am (100%) copy {milena => scribo}/sandbox/green/tests/io/plot/save_image_sh/save_image_sh.cc (100%) diff --git a/scribo/sandbox/green/ChangeLog b/scribo/sandbox/green/ChangeLog index 8f5101b..db589a1 100644 --- a/scribo/sandbox/green/ChangeLog +++ b/scribo/sandbox/green/ChangeLog @@ -2,6 +2,20 @@ Import files from milena/sandbox/green. + * gaussian.sh: New gnuplot shell file. + * guassian2d.sh: New gnuplot shell file. + * test_labelling.cc: New source. + * tests/clustering/k_mean/Makefile.am: New makefile. + * tests/clustering/k_mean/k_mean.cc: New source. + * tests/clustering/kmean1d/Makefile.am: New makefile. + * tests/clustering/kmean1d/kmean1d.cc: New source. + * tests/io/plot/save_image_sh/Makefile.am: New makefile. + * tests/io/plot/save_image_sh/save_image_sh.cc: New source. + +2010-06-24 Yann Jacquelet <jacquelet(a)lrde.epita.fr> + + Import files from milena/sandbox/green. + * mln/accu/stat/histo1d.hh: New header file. * mln/accu/stat/histo2d.hh: New header file. * mln/accu/stat/histo3d_hsl.hh: New header file. diff --git a/milena/sandbox/green/tests/accu/stat/histo1d/gaussian.sh b/scribo/sandbox/green/gaussian.sh similarity index 100% copy from milena/sandbox/green/tests/accu/stat/histo1d/gaussian.sh copy to scribo/sandbox/green/gaussian.sh diff --git a/milena/sandbox/green/tests/accu/stat/histo2d/gaussian2d.sh b/scribo/sandbox/green/gaussian2d.sh similarity index 100% copy from milena/sandbox/green/tests/accu/stat/histo2d/gaussian2d.sh copy to scribo/sandbox/green/gaussian2d.sh diff --git a/scribo/sandbox/green/test_labelling.cc b/scribo/sandbox/green/test_labelling.cc new file mode 100644 index 0000000..6238d2b --- /dev/null +++ b/scribo/sandbox/green/test_labelling.cc @@ -0,0 +1,336 @@ +// Copyright (C) 2007, 2008, 2009, 2010 EPITA LRDE +// +// This file is part of Olena. +// +// Olena is free software: you can redistribute it and/or modify it under +// the terms of the GNU General Public License as published by the Free +// Software Foundation, version 2 of the License. +// +// Olena 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 Olena. If not, see <http://www.gnu.org/licenses/>. +// +// As a special exception, you may use this file as part of a free +// software project 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 <mln/io/plot/save_histo_sh.hh> +#include <mln/value/rgb8.hh> +#include <mln/value/label_8.hh> +#include <mln/core/alias/neighb1d.hh> +#include <mln/core/image/dmorph/image_if.hh> +#include <mln/labeling/colorize.hh> +#include <mln/labeling/mean_values.hh> +#include <mln/labeling/regional_maxima.hh> +#include <mln/make/w_window1d.hh> +#include <mln/math/pi.hh> +#include <mln/morpho/watershed/flooding.hh> +#include <mln/morpho/elementary/dilation.hh> +#include <mln/morpho/elementary/closing.hh> +#include <mln/pw/value.hh> +#include <mln/linear/convolve.hh> +#include <mln/linear/gaussian.hh> + + +/// ... to complete + +/// \brief Compute the gaussian probability to obtain a given value. +/// +/// \param[in] x the value from which we want the probability. +/// \param[in] mean the mean parameter of the gaussian distribution. +/// \param[in] sigma the sqrt(variance) parameter of the gaussian. +/// \return the probability to obtain the x value. +/// +/// Implements the standard equation of the gaussian. + +double gaussian_distribution(const double x, + const double mean, + const double sigma) +{ + double num = exp(-0.5*mln::math::sqr((x - mean)/sigma)); + double denom = sigma*mln::math::sqrt(2*mln::math::pi); + double result = num/denom; + + return result; +} + +/// \brief Make a 1d gaussian filter. +/// +/// \param[out] ws the window (filter) where to put the probability values. +/// \param[in] size the size of the filter. +/// \param[in] sigma the gaussian parameter for the standard deviation. +/// \return the probability to obtain the x value. +/// +/// Approach the gaussian distribution for a few discrete sites, and +/// then normilize the results to be sure that the sum obtain 1. + +void gaussian_filter(double ws[], const unsigned size, const double sigma) +{ + int h = size/2; + + for (int i = -h; i <= h; ++i) + { + ws[i+h] = gaussian_distribution(i, 0.0, sigma); + } + + double sum = 0.0; + + for (unsigned i = 0; i < size; ++i) + sum += ws[i]; + + for (unsigned i = 0; i < size; ++i) + ws[i] /= sum; +} + +/// \brief Make a 1d gaussian filter. +/// +/// \param[out] ws the window (filter) where to put the probability values. +/// \param[in] size the size of the filter. +/// \param[in] sigma the gaussian parameter for the standard deviation. +/// \return the probability to obtain the x value. +/// +/// Approach the gaussian distribution for a few discrete sites, and +/// then normilize the results to be sure that the sum obtain 1. + +/// The aim of this function is to rebuild an label image2d from the segmenting +/// image of the histogram (label) and the original image (input). +/// label_image2d / for each grey tone, associate its label. + +mln::image2d<mln::value::label_8> +build_8bits(const mln::image2d<mln::value::int_u8>& input, + const mln::image1d<mln::value::label_8>& label) +{ + mln::trace::entering("build_8bits"); + mln_precondition(label.is_valid()); + mln_precondition(input.is_valid()); + + mln::image2d<mln::value::label_8> output; + + mln::initialize(output, input); + + mln_piter_(mln::image2d<mln::value::int_u8>) pi(input.domain()); + mln_piter_(mln::image2d<mln::value::label_8>) po(output.domain()); + + for_all_2(pi, po) + { + mln::value::int_u8 val = input(pi); + unsigned grp = label(mln::point1d(val)); + + output(po) = grp; + } + + mln::trace::exiting("build_8bits"); + return output; +} + + +void test_8bits_classifying() +{ + typedef mln::value::int_u8 int_u8; + typedef mln::value::label_8 label_8; + typedef mln::value::rgb8 rgb8; + typedef mln::accu::stat::mean<double> mean; + + mln::image2d<int_u8> img_ref; + mln::image2d<int_u8> img_out; + mln::image2d<rgb8> img_rgb; + mln::image1d<unsigned> img_res; + mln::image1d<double> img_smooth; + mln::image1d<label_8> labels; + label_8 nlabels; + + //----------------------------------------------------- + // Loading the scribo image and computing its histogram + //----------------------------------------------------- + + std::cout << "(08 bits) LOADING HISTOGRAM" << std::endl; + + // mln::io::pgm::load(img_ref, OLENA_IMG_PATH"/lena.pgm"); + mln::io::pgm::load(img_ref, SCRIBO_IMG_PATH"/mp00082c_50p_8bits.pgm"); + img_res = mln::data::compute(mln::accu::stat::histo1d<int_u8>(), img_ref); + mln::io::plot::save_histo_sh(img_res, "histo0_8bits.sh"); + + + //----------------------------------------------------- + // Smoothing the histogram with a gaussian filter + //----------------------------------------------------- + + std::cout << "(08 bits) SMOOTHING HISTOGRAM" << std::endl; + + double ws[41]; + gaussian_filter(ws, 41, 6.0); + img_smooth = mln::linear::convolve(img_res, mln::make::w_window1d(ws)); + mln::io::plot::save_histo_sh(img_smooth, "histo1_8bits.sh"); + + + //----------------------------------------------------- + // Segmenting the histogram with the watershed method + //----------------------------------------------------- + + std::cout << "SEGMENTING HISTOGRAM" << std::endl; + + /* + labels = mln::labeling::regional_maxima(img_smooth, mln::c2(), nlabels); + std::cout << "N labels : " << nlabels << std::endl; + mln::io::plot::save_histo_sh(labels, "histo2_8bits.sh"); + */ + + // need to revert the histogram + labels = mln::morpho::watershed::flooding(img_smooth, mln::c2(), nlabels); + std::cout << "N labels : " << nlabels << std::endl; + mln::io::plot::save_histo_sh(labels, "histo2_8bits.sh"); + + + //----------------------------------------------------- + // Rebuilding the image with the mean of each region + //----------------------------------------------------- + + std::cout << "(08 bits) BUILDING OUTPUT" << std::endl; + + mln::image2d<label_8>img_label = build_8bits(img_ref, labels); + + std::cout << "(08 bits) COLORING OUTPUT" << std::endl; + + img_out = mln::labeling::mean_values(img_ref, img_label, nlabels); + img_rgb = mln::labeling::colorize(rgb8(), img_label); + + mln::io::pgm::save(img_out, "out_8bits.pgm"); + mln::io::ppm::save(img_rgb, "color_8bits.pgm"); + + //labels = mln::morpho::elementary::dilation(labels, mln::c2()); + //mln::io::plot::save_histo_sh(labels, "histo3.sh"); + //mln::io::plot::save(labels, "labelized.data"); +} + + +/// The aim of this function is to rebuild an label image2d from the segmenting +/// image of the histogram (label) and the original image (input). +/// label_image2d / for each grey tone, associate its label. + +mln::image2d<mln::value::label_8> +build_14bits(const mln::image2d<mln::value::int_u<14> >& input, + const mln::image1d<mln::value::label_8>& label) +{ + mln::trace::entering("build_14bits"); + mln_precondition(label.is_valid()); + mln_precondition(input.is_valid()); + + mln::image2d<mln::value::label_8> output; + + mln::initialize(output, input); + + mln_piter_(mln::image2d<mln::value::int_u<14> >) pi(input.domain()); + mln_piter_(mln::image2d<mln::value::label_8>) po(output.domain()); + + for_all_2(pi, po) + { + mln::value::int_u<14> val = input(pi); + unsigned grp = label(mln::point1d(val)); + + output(po) = grp; + } + + mln::trace::exiting("build_14bits"); + return output; +} + + +void test_14bits_classifying() +{ + typedef mln::value::int_u16 int_u16; + typedef mln::value::int_u<14> int_u14; + typedef mln::value::label_8 label_8; + typedef mln::value::rgb8 rgb8; + typedef mln::accu::stat::mean<double> mean; + + mln::image2d<int_u16> img_fst; + mln::image2d<int_u14> img_ref; + mln::image2d<int_u14> img_out; + mln::image2d<rgb8> img_rgb; + mln::image1d<unsigned> img_res; + mln::image1d<double> img_smooth; + mln::image1d<label_8> labels; + label_8 nlabels; + + //----------------------------------------------------- + // Loading the scribo image and computing its histogram + //----------------------------------------------------- + + std::cout << "(14 bits) LOADING HISTOGRAM" << std::endl; + + //mln::io::pgm::load(img_fst, OLENA_IMG_PATH"/lena_16.pgm"); + mln::io::pgm::load(img_fst, SCRIBO_IMG_PATH"/mp00082c_50p_16bits.pgm"); + img_ref = mln::data::transform(img_fst, mln::fun::v2v::int_u16_to_int_u14()); + img_res = mln::data::compute(mln::accu::stat::histo1d<int_u14>(), img_ref); + mln::io::plot::save_histo_sh(img_res, "histo0_14bits.sh"); + + + //----------------------------------------------------- + // Smoothing the histogram with a gaussian filter + //----------------------------------------------------- + + std::cout << "(14 bits) SMOOTHING HISTOGRAM" << std::endl; + + double ws[401]; + gaussian_filter(ws, 401, 50.0); + img_smooth = mln::linear::convolve(img_res, mln::make::w_window1d(ws)); + mln::io::plot::save_histo_sh(img_smooth, "histo1_14bits.sh"); + + + //----------------------------------------------------- + // Segmenting the histogram with the watershed method + //----------------------------------------------------- + + std::cout << "(14 bits) SEGMENTING HISTOGRAM" << std::endl; + + /* + labels = mln::labeling::regional_maxima(img_smooth, mln::c2(), nlabels); + std::cout << "N labels : " << nlabels << std::endl; + mln::io::plot::save_histo_sh(labels, "histo2.sh"); + */ + + + labels = mln::morpho::watershed::flooding(img_smooth, mln::c2(), nlabels); + std::cout << "N labels : " << nlabels << std::endl; + mln::io::plot::save_histo_sh(labels, "histo2_14bits.sh"); + + + //----------------------------------------------------- + // Rebuilding the image with the mean of each region + //----------------------------------------------------- + + std::cout << "(14 bits) BUILDING OUTPUT" << std::endl; + + mln::image2d<label_8>img_label = build_14bits(img_ref, labels); + + std::cout << "(14 bits) COLORING OUTPUT" << std::endl; + + img_out = mln::labeling::mean_values(img_ref, img_label, nlabels); + img_rgb = mln::labeling::colorize(rgb8(), img_label); + + mln::io::pgm::save(img_out, "out_14bits.pgm"); + mln::io::ppm::save(img_rgb, "color_14bits.pgm"); + + //labels = mln::morpho::elementary::dilation(labels, mln::c2()); + //mln::io::plot::save_histo_sh(labels, "histo3.sh"); + //mln::io::plot::save(labels, "labelized.data"); +} + +int main() +{ + test_8bits_classifying(); + + test_14bits_classifying(); + + return 0; +} diff --git a/milena/sandbox/green/tests/clustering/k_mean/Makefile.am b/scribo/sandbox/green/tests/clustering/k_mean/Makefile.am similarity index 100% copy from milena/sandbox/green/tests/clustering/k_mean/Makefile.am copy to scribo/sandbox/green/tests/clustering/k_mean/Makefile.am diff --git a/milena/sandbox/green/tests/clustering/k_mean/k_mean.cc b/scribo/sandbox/green/tests/clustering/k_mean/k_mean.cc similarity index 100% copy from milena/sandbox/green/tests/clustering/k_mean/k_mean.cc copy to scribo/sandbox/green/tests/clustering/k_mean/k_mean.cc diff --git a/milena/sandbox/green/tests/clustering/kmean1d/Makefile.am b/scribo/sandbox/green/tests/clustering/kmean1d/Makefile.am similarity index 100% copy from milena/sandbox/green/tests/clustering/kmean1d/Makefile.am copy to scribo/sandbox/green/tests/clustering/kmean1d/Makefile.am diff --git a/milena/sandbox/green/tests/clustering/kmean1d/kmean1d.cc b/scribo/sandbox/green/tests/clustering/kmean1d/kmean1d.cc similarity index 100% copy from milena/sandbox/green/tests/clustering/kmean1d/kmean1d.cc copy to scribo/sandbox/green/tests/clustering/kmean1d/kmean1d.cc diff --git a/milena/sandbox/green/doc/examples/frac/Makefile.am b/scribo/sandbox/green/tests/io/plot/save_image_sh/Makefile.am similarity index 100% copy from milena/sandbox/green/doc/examples/frac/Makefile.am copy to scribo/sandbox/green/tests/io/plot/save_image_sh/Makefile.am diff --git a/milena/sandbox/green/tests/io/plot/save_image_sh/save_image_sh.cc b/scribo/sandbox/green/tests/io/plot/save_image_sh/save_image_sh.cc similarity index 100% copy from milena/sandbox/green/tests/io/plot/save_image_sh/save_image_sh.cc copy to scribo/sandbox/green/tests/io/plot/save_image_sh/save_image_sh.cc -- 1.5.6.5

1 0

last-svn-commit-167-gb3416b2 Import files from milena/sandbox/green.
by Yann Jacquelet 24 Jun '10

24 Jun '10

* gaussian.sh: New gnuplot shell file. * guassian2d.sh: New gnuplot shell file. * test_labelling.cc: New source. * tests/clustering/k_mean/Makefile.am: New makefile. * tests/clustering/k_mean/k_mean.cc: New source. * tests/clustering/kmean1d/Makefile.am: New makefile. * tests/clustering/kmean1d/kmean1d.cc: New source. * tests/io/plot/save_image_sh/Makefile.am: New makefile. * tests/io/plot/save_image_sh/save_image_sh.cc: New source. --- scribo/sandbox/green/ChangeLog | 14 + .../histo1d => scribo/sandbox/green}/gaussian.sh | 0 .../histo2d => scribo/sandbox/green}/gaussian2d.sh | 0 scribo/sandbox/green/test_labelling.cc | 336 ++++++++++++++++++++ .../green/tests/clustering/k_mean/Makefile.am | 0 .../green/tests/clustering/k_mean/k_mean.cc | 0 .../green/tests/clustering/kmean1d/Makefile.am | 0 .../green/tests/clustering/kmean1d/kmean1d.cc | 0 .../green/tests/io/plot/save_image_sh}/Makefile.am | 0 .../tests/io/plot/save_image_sh/save_image_sh.cc | 0 10 files changed, 350 insertions(+), 0 deletions(-) copy {milena/sandbox/green/tests/accu/stat/histo1d => scribo/sandbox/green}/gaussian.sh (100%) copy {milena/sandbox/green/tests/accu/stat/histo2d => scribo/sandbox/green}/gaussian2d.sh (100%) create mode 100644 scribo/sandbox/green/test_labelling.cc copy {milena => scribo}/sandbox/green/tests/clustering/k_mean/Makefile.am (100%) copy {milena => scribo}/sandbox/green/tests/clustering/k_mean/k_mean.cc (100%) copy {milena => scribo}/sandbox/green/tests/clustering/kmean1d/Makefile.am (100%) copy {milena => scribo}/sandbox/green/tests/clustering/kmean1d/kmean1d.cc (100%) copy {milena/sandbox/green/doc/examples/frac => scribo/sandbox/green/tests/io/plot/save_image_sh}/Makefile.am (100%) copy {milena => scribo}/sandbox/green/tests/io/plot/save_image_sh/save_image_sh.cc (100%) diff --git a/scribo/sandbox/green/ChangeLog b/scribo/sandbox/green/ChangeLog index 8f5101b..db589a1 100644 --- a/scribo/sandbox/green/ChangeLog +++ b/scribo/sandbox/green/ChangeLog @@ -2,6 +2,20 @@ Import files from milena/sandbox/green. + * gaussian.sh: New gnuplot shell file. + * guassian2d.sh: New gnuplot shell file. + * test_labelling.cc: New source. + * tests/clustering/k_mean/Makefile.am: New makefile. + * tests/clustering/k_mean/k_mean.cc: New source. + * tests/clustering/kmean1d/Makefile.am: New makefile. + * tests/clustering/kmean1d/kmean1d.cc: New source. + * tests/io/plot/save_image_sh/Makefile.am: New makefile. + * tests/io/plot/save_image_sh/save_image_sh.cc: New source. + +2010-06-24 Yann Jacquelet <jacquelet(a)lrde.epita.fr> + + Import files from milena/sandbox/green. + * mln/accu/stat/histo1d.hh: New header file. * mln/accu/stat/histo2d.hh: New header file. * mln/accu/stat/histo3d_hsl.hh: New header file. diff --git a/milena/sandbox/green/tests/accu/stat/histo1d/gaussian.sh b/scribo/sandbox/green/gaussian.sh similarity index 100% copy from milena/sandbox/green/tests/accu/stat/histo1d/gaussian.sh copy to scribo/sandbox/green/gaussian.sh diff --git a/milena/sandbox/green/tests/accu/stat/histo2d/gaussian2d.sh b/scribo/sandbox/green/gaussian2d.sh similarity index 100% copy from milena/sandbox/green/tests/accu/stat/histo2d/gaussian2d.sh copy to scribo/sandbox/green/gaussian2d.sh diff --git a/scribo/sandbox/green/test_labelling.cc b/scribo/sandbox/green/test_labelling.cc new file mode 100644 index 0000000..6238d2b --- /dev/null +++ b/scribo/sandbox/green/test_labelling.cc @@ -0,0 +1,336 @@ +// Copyright (C) 2007, 2008, 2009, 2010 EPITA LRDE +// +// This file is part of Olena. +// +// Olena is free software: you can redistribute it and/or modify it under +// the terms of the GNU General Public License as published by the Free +// Software Foundation, version 2 of the License. +// +// Olena 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 Olena. If not, see <http://www.gnu.org/licenses/>. +// +// As a special exception, you may use this file as part of a free +// software project 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 <mln/io/plot/save_histo_sh.hh> +#include <mln/value/rgb8.hh> +#include <mln/value/label_8.hh> +#include <mln/core/alias/neighb1d.hh> +#include <mln/core/image/dmorph/image_if.hh> +#include <mln/labeling/colorize.hh> +#include <mln/labeling/mean_values.hh> +#include <mln/labeling/regional_maxima.hh> +#include <mln/make/w_window1d.hh> +#include <mln/math/pi.hh> +#include <mln/morpho/watershed/flooding.hh> +#include <mln/morpho/elementary/dilation.hh> +#include <mln/morpho/elementary/closing.hh> +#include <mln/pw/value.hh> +#include <mln/linear/convolve.hh> +#include <mln/linear/gaussian.hh> + + +/// ... to complete + +/// \brief Compute the gaussian probability to obtain a given value. +/// +/// \param[in] x the value from which we want the probability. +/// \param[in] mean the mean parameter of the gaussian distribution. +/// \param[in] sigma the sqrt(variance) parameter of the gaussian. +/// \return the probability to obtain the x value. +/// +/// Implements the standard equation of the gaussian. + +double gaussian_distribution(const double x, + const double mean, + const double sigma) +{ + double num = exp(-0.5*mln::math::sqr((x - mean)/sigma)); + double denom = sigma*mln::math::sqrt(2*mln::math::pi); + double result = num/denom; + + return result; +} + +/// \brief Make a 1d gaussian filter. +/// +/// \param[out] ws the window (filter) where to put the probability values. +/// \param[in] size the size of the filter. +/// \param[in] sigma the gaussian parameter for the standard deviation. +/// \return the probability to obtain the x value. +/// +/// Approach the gaussian distribution for a few discrete sites, and +/// then normilize the results to be sure that the sum obtain 1. + +void gaussian_filter(double ws[], const unsigned size, const double sigma) +{ + int h = size/2; + + for (int i = -h; i <= h; ++i) + { + ws[i+h] = gaussian_distribution(i, 0.0, sigma); + } + + double sum = 0.0; + + for (unsigned i = 0; i < size; ++i) + sum += ws[i]; + + for (unsigned i = 0; i < size; ++i) + ws[i] /= sum; +} + +/// \brief Make a 1d gaussian filter. +/// +/// \param[out] ws the window (filter) where to put the probability values. +/// \param[in] size the size of the filter. +/// \param[in] sigma the gaussian parameter for the standard deviation. +/// \return the probability to obtain the x value. +/// +/// Approach the gaussian distribution for a few discrete sites, and +/// then normilize the results to be sure that the sum obtain 1. + +/// The aim of this function is to rebuild an label image2d from the segmenting +/// image of the histogram (label) and the original image (input). +/// label_image2d / for each grey tone, associate its label. + +mln::image2d<mln::value::label_8> +build_8bits(const mln::image2d<mln::value::int_u8>& input, + const mln::image1d<mln::value::label_8>& label) +{ + mln::trace::entering("build_8bits"); + mln_precondition(label.is_valid()); + mln_precondition(input.is_valid()); + + mln::image2d<mln::value::label_8> output; + + mln::initialize(output, input); + + mln_piter_(mln::image2d<mln::value::int_u8>) pi(input.domain()); + mln_piter_(mln::image2d<mln::value::label_8>) po(output.domain()); + + for_all_2(pi, po) + { + mln::value::int_u8 val = input(pi); + unsigned grp = label(mln::point1d(val)); + + output(po) = grp; + } + + mln::trace::exiting("build_8bits"); + return output; +} + + +void test_8bits_classifying() +{ + typedef mln::value::int_u8 int_u8; + typedef mln::value::label_8 label_8; + typedef mln::value::rgb8 rgb8; + typedef mln::accu::stat::mean<double> mean; + + mln::image2d<int_u8> img_ref; + mln::image2d<int_u8> img_out; + mln::image2d<rgb8> img_rgb; + mln::image1d<unsigned> img_res; + mln::image1d<double> img_smooth; + mln::image1d<label_8> labels; + label_8 nlabels; + + //----------------------------------------------------- + // Loading the scribo image and computing its histogram + //----------------------------------------------------- + + std::cout << "(08 bits) LOADING HISTOGRAM" << std::endl; + + // mln::io::pgm::load(img_ref, OLENA_IMG_PATH"/lena.pgm"); + mln::io::pgm::load(img_ref, SCRIBO_IMG_PATH"/mp00082c_50p_8bits.pgm"); + img_res = mln::data::compute(mln::accu::stat::histo1d<int_u8>(), img_ref); + mln::io::plot::save_histo_sh(img_res, "histo0_8bits.sh"); + + + //----------------------------------------------------- + // Smoothing the histogram with a gaussian filter + //----------------------------------------------------- + + std::cout << "(08 bits) SMOOTHING HISTOGRAM" << std::endl; + + double ws[41]; + gaussian_filter(ws, 41, 6.0); + img_smooth = mln::linear::convolve(img_res, mln::make::w_window1d(ws)); + mln::io::plot::save_histo_sh(img_smooth, "histo1_8bits.sh"); + + + //----------------------------------------------------- + // Segmenting the histogram with the watershed method + //----------------------------------------------------- + + std::cout << "SEGMENTING HISTOGRAM" << std::endl; + + /* + labels = mln::labeling::regional_maxima(img_smooth, mln::c2(), nlabels); + std::cout << "N labels : " << nlabels << std::endl; + mln::io::plot::save_histo_sh(labels, "histo2_8bits.sh"); + */ + + // need to revert the histogram + labels = mln::morpho::watershed::flooding(img_smooth, mln::c2(), nlabels); + std::cout << "N labels : " << nlabels << std::endl; + mln::io::plot::save_histo_sh(labels, "histo2_8bits.sh"); + + + //----------------------------------------------------- + // Rebuilding the image with the mean of each region + //----------------------------------------------------- + + std::cout << "(08 bits) BUILDING OUTPUT" << std::endl; + + mln::image2d<label_8>img_label = build_8bits(img_ref, labels); + + std::cout << "(08 bits) COLORING OUTPUT" << std::endl; + + img_out = mln::labeling::mean_values(img_ref, img_label, nlabels); + img_rgb = mln::labeling::colorize(rgb8(), img_label); + + mln::io::pgm::save(img_out, "out_8bits.pgm"); + mln::io::ppm::save(img_rgb, "color_8bits.pgm"); + + //labels = mln::morpho::elementary::dilation(labels, mln::c2()); + //mln::io::plot::save_histo_sh(labels, "histo3.sh"); + //mln::io::plot::save(labels, "labelized.data"); +} + + +/// The aim of this function is to rebuild an label image2d from the segmenting +/// image of the histogram (label) and the original image (input). +/// label_image2d / for each grey tone, associate its label. + +mln::image2d<mln::value::label_8> +build_14bits(const mln::image2d<mln::value::int_u<14> >& input, + const mln::image1d<mln::value::label_8>& label) +{ + mln::trace::entering("build_14bits"); + mln_precondition(label.is_valid()); + mln_precondition(input.is_valid()); + + mln::image2d<mln::value::label_8> output; + + mln::initialize(output, input); + + mln_piter_(mln::image2d<mln::value::int_u<14> >) pi(input.domain()); + mln_piter_(mln::image2d<mln::value::label_8>) po(output.domain()); + + for_all_2(pi, po) + { + mln::value::int_u<14> val = input(pi); + unsigned grp = label(mln::point1d(val)); + + output(po) = grp; + } + + mln::trace::exiting("build_14bits"); + return output; +} + + +void test_14bits_classifying() +{ + typedef mln::value::int_u16 int_u16; + typedef mln::value::int_u<14> int_u14; + typedef mln::value::label_8 label_8; + typedef mln::value::rgb8 rgb8; + typedef mln::accu::stat::mean<double> mean; + + mln::image2d<int_u16> img_fst; + mln::image2d<int_u14> img_ref; + mln::image2d<int_u14> img_out; + mln::image2d<rgb8> img_rgb; + mln::image1d<unsigned> img_res; + mln::image1d<double> img_smooth; + mln::image1d<label_8> labels; + label_8 nlabels; + + //----------------------------------------------------- + // Loading the scribo image and computing its histogram + //----------------------------------------------------- + + std::cout << "(14 bits) LOADING HISTOGRAM" << std::endl; + + //mln::io::pgm::load(img_fst, OLENA_IMG_PATH"/lena_16.pgm"); + mln::io::pgm::load(img_fst, SCRIBO_IMG_PATH"/mp00082c_50p_16bits.pgm"); + img_ref = mln::data::transform(img_fst, mln::fun::v2v::int_u16_to_int_u14()); + img_res = mln::data::compute(mln::accu::stat::histo1d<int_u14>(), img_ref); + mln::io::plot::save_histo_sh(img_res, "histo0_14bits.sh"); + + + //----------------------------------------------------- + // Smoothing the histogram with a gaussian filter + //----------------------------------------------------- + + std::cout << "(14 bits) SMOOTHING HISTOGRAM" << std::endl; + + double ws[401]; + gaussian_filter(ws, 401, 50.0); + img_smooth = mln::linear::convolve(img_res, mln::make::w_window1d(ws)); + mln::io::plot::save_histo_sh(img_smooth, "histo1_14bits.sh"); + + + //----------------------------------------------------- + // Segmenting the histogram with the watershed method + //----------------------------------------------------- + + std::cout << "(14 bits) SEGMENTING HISTOGRAM" << std::endl; + + /* + labels = mln::labeling::regional_maxima(img_smooth, mln::c2(), nlabels); + std::cout << "N labels : " << nlabels << std::endl; + mln::io::plot::save_histo_sh(labels, "histo2.sh"); + */ + + + labels = mln::morpho::watershed::flooding(img_smooth, mln::c2(), nlabels); + std::cout << "N labels : " << nlabels << std::endl; + mln::io::plot::save_histo_sh(labels, "histo2_14bits.sh"); + + + //----------------------------------------------------- + // Rebuilding the image with the mean of each region + //----------------------------------------------------- + + std::cout << "(14 bits) BUILDING OUTPUT" << std::endl; + + mln::image2d<label_8>img_label = build_14bits(img_ref, labels); + + std::cout << "(14 bits) COLORING OUTPUT" << std::endl; + + img_out = mln::labeling::mean_values(img_ref, img_label, nlabels); + img_rgb = mln::labeling::colorize(rgb8(), img_label); + + mln::io::pgm::save(img_out, "out_14bits.pgm"); + mln::io::ppm::save(img_rgb, "color_14bits.pgm"); + + //labels = mln::morpho::elementary::dilation(labels, mln::c2()); + //mln::io::plot::save_histo_sh(labels, "histo3.sh"); + //mln::io::plot::save(labels, "labelized.data"); +} + +int main() +{ + test_8bits_classifying(); + + test_14bits_classifying(); + + return 0; +} diff --git a/milena/sandbox/green/tests/clustering/k_mean/Makefile.am b/scribo/sandbox/green/tests/clustering/k_mean/Makefile.am similarity index 100% copy from milena/sandbox/green/tests/clustering/k_mean/Makefile.am copy to scribo/sandbox/green/tests/clustering/k_mean/Makefile.am diff --git a/milena/sandbox/green/tests/clustering/k_mean/k_mean.cc b/scribo/sandbox/green/tests/clustering/k_mean/k_mean.cc similarity index 100% copy from milena/sandbox/green/tests/clustering/k_mean/k_mean.cc copy to scribo/sandbox/green/tests/clustering/k_mean/k_mean.cc diff --git a/milena/sandbox/green/tests/clustering/kmean1d/Makefile.am b/scribo/sandbox/green/tests/clustering/kmean1d/Makefile.am similarity index 100% copy from milena/sandbox/green/tests/clustering/kmean1d/Makefile.am copy to scribo/sandbox/green/tests/clustering/kmean1d/Makefile.am diff --git a/milena/sandbox/green/tests/clustering/kmean1d/kmean1d.cc b/scribo/sandbox/green/tests/clustering/kmean1d/kmean1d.cc similarity index 100% copy from milena/sandbox/green/tests/clustering/kmean1d/kmean1d.cc copy to scribo/sandbox/green/tests/clustering/kmean1d/kmean1d.cc diff --git a/milena/sandbox/green/doc/examples/frac/Makefile.am b/scribo/sandbox/green/tests/io/plot/save_image_sh/Makefile.am similarity index 100% copy from milena/sandbox/green/doc/examples/frac/Makefile.am copy to scribo/sandbox/green/tests/io/plot/save_image_sh/Makefile.am diff --git a/milena/sandbox/green/tests/io/plot/save_image_sh/save_image_sh.cc b/scribo/sandbox/green/tests/io/plot/save_image_sh/save_image_sh.cc similarity index 100% copy from milena/sandbox/green/tests/io/plot/save_image_sh/save_image_sh.cc copy to scribo/sandbox/green/tests/io/plot/save_image_sh/save_image_sh.cc -- 1.5.6.5

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