- Olena-patches

3602: Add some code for ICDAR.
by Guillaume Lazzara 02 Apr '09

02 Apr '09

* lazzara/icdar/binarization.cc: Use graphes and gradient for binarization. --- milena/sandbox/ChangeLog | 7 + milena/sandbox/lazzara/icdar/binarization.cc | 273 ++++++++++++++++++++++++++ 2 files changed, 280 insertions(+), 0 deletions(-) create mode 100644 milena/sandbox/lazzara/icdar/binarization.cc diff --git a/milena/sandbox/ChangeLog b/milena/sandbox/ChangeLog index 2f10d6b..70acc5a 100644 --- a/milena/sandbox/ChangeLog +++ b/milena/sandbox/ChangeLog @@ -1,3 +1,10 @@ +2009-04-01 Guillaume Lazzara <z(a)lrde.epita.fr> + + Add some code for ICDAR. + + * lazzara/icdar/binarization.cc: Use graphes and gradient for + binarization. + 2009-04-01 Thierry Geraud <thierry.geraud(a)lrde.epita.fr> Add a 1st threshold code. diff --git a/milena/sandbox/lazzara/icdar/binarization.cc b/milena/sandbox/lazzara/icdar/binarization.cc new file mode 100644 index 0000000..ade1695 --- /dev/null +++ b/milena/sandbox/lazzara/icdar/binarization.cc @@ -0,0 +1,273 @@ +#include <mln/core/image/image2d.hh> +#include <mln/core/site_set/box.hh> +#include <mln/data/fill.hh> +#include <mln/core/alias/dpoint2d.hh> +#include <mln/core/macros.hh> +#include <mln/core/concept/function.hh> +#include <mln/core/alias/neighb2d.hh> +#include <mln/core/site_set/p_edges.hh> +#include <mln/core/site_set/p_vertices.hh> +#include <mln/io/essential.hh> +#include <mln/value/int_u8.hh> +#include <mln/value/int_u16.hh> +#include <mln/value/label_16.hh> +#include <mln/value/rgb8.hh> +#include <mln/morpho/elementary/gradient_internal.hh> +#include <mln/morpho/closing/volume.hh> +#include <mln/morpho/watershed/flooding.hh> +#include <mln/make/rag_and_labeled_wsl.hh> +#include <mln/util/graph.hh> +#include <mln/util/couple.hh> +#include <mln/debug/colorize.hh> +#include <mln/fun/i2v/array.hh> +#include <mln/labeling/compute.hh> +#include <mln/accu/center.hh> +#include <mln/accu/median_h.hh> +#include <mln/accu/mean.hh> +#include <mln/pw/cst.hh> +#include <mln/math/abs.hh> +#include <mln/literal/colors.hh> +#include <mln/debug/draw_graph.hh> + +namespace mln +{ + + struct edge_values : Function_vv2v<edge_values> + { + typedef value::int_u8 result; + typedef void mutable_result; + + value::int_u8 operator()(const value::int_u8& v1, + const value::int_u8& v2) const + { return math::abs(v1 - v2); } + + }; + + + template <typename I, typename V> + class edge_to_color : public Function_p2v< edge_to_color<I,V> > + { + public: + typedef V result; + + edge_to_color(const I& ima_e) : ima_e_(ima_e) + {} + + V + operator()(const unsigned& e) const + { return convert::to<V>(ima_e_.function()(e)); } + + private: + const I& ima_e_; + }; + + + namespace make + { + + template <typename G, typename P> + p_edges<G,pw::cst_<P> > + dummy_pedges(const Graph<G>& g_, const P& dummy_value) + { + trace::entering("dummy_pedges"); + + const G& g = exact(g_); + mln_precondition(g.is_valid()); + p_edges<G,pw::cst_<P> > pe(g, pw::cst(dummy_value)); + + trace::exiting("dummy_pedges"); + return pe; + } + + template <typename FVV, typename G, typename V2P, typename E2P, typename FVE> + pw::image<fun::i2v::array<mln_result(FVE)>,p_edges<G,E2P> > + edge_image(const pw::image<FVV,p_vertices<G,V2P> >& vertex_image, + const p_edges<G,E2P>& pe, + const Function_vv2v<FVE>& edge_value_) + { + trace::entering("edge_image"); + + const FVE& edge_value = exact(edge_value_); + mln_precondition(vertex_image.is_valid()); + mln_precondition(pe.is_valid()); + + typedef fun::i2v::array<mln_result(FVE)> edge_values_t; + edge_values_t edge_values(pe.nsites()); + + // image on graph edges + typedef pw::image<edge_values_t, p_edges<G,E2P> > ima_e_t; + ima_e_t ima_e = (edge_values | pe); + + mln_piter(ima_e_t) e(ima_e.domain()); + for_all(e) + ima_e(e) = edge_value(vertex_image.function()(e.element().v1()), + vertex_image.function()(e.element().v2())); + + trace::exiting("edge_image"); + return ima_e; + } + + + template <typename W, typename G> + inline + p_vertices<util::graph, fun::i2v::array<mln_site(W)> > + common_pvertices(const Image<W>& wst, const mln_value(W)& nbasins, + const Graph<G>& g_) + { + trace::entering("common_pvertices"); + + const G& g = exact(g_); + mln_precondition(g.is_valid()); + + typedef fun::i2v::array<mln_site(W)> vertex_sites_t; + vertex_sites_t vertex_sites; + convert::from_to(labeling::compute(accu::center<mln_site(W)>(), wst, nbasins), + vertex_sites); + + p_vertices<util::graph, vertex_sites_t> pv(g, vertex_sites); + + trace::exiting("common_pvertices"); + return pv; + } + + + template <typename A, typename G, typename F, typename I, typename W> + pw::image<fun::i2v::array<mln_value(I)>, p_vertices<G,F> > + vertex_image(const Accumulator<A>& accu, + const p_vertices<G,F>& pv, + const Image<I>& input_, + const Image<W>& wst_, + const mln_value(W)& nbasins) + { + trace::entering("vertex_image"); + + const I& input = exact(input_); + const W& wst = exact(wst_); + mln_precondition(input.is_valid()); + mln_precondition(wst.is_valid()); + mln_precondition(pv.is_valid()); + + typedef fun::i2v::array<mln_value(I)> vertex_values_t; + vertex_values_t vertex_values; + convert::from_to(labeling::compute(accu, input, wst, nbasins), + vertex_values); + + pw::image<fun::i2v::array<mln_value(I)>, + p_vertices<util::graph, fun::i2v::array<mln_site(I)> > > + ima_vertex = vertex_values | pv; + + trace::exiting("vertex_image"); + return ima_vertex; + } + + + template <typename I, typename V, typename E> + inline + mln_concrete(I) + debug_graph_image(const Image<I>& input_, + const Image<V>& ima_v_, const Image<E>& ima_e_, + unsigned box_size, const mln_value(I)& bg) + { + trace::entering("debug_graph_image"); + + const I& input = exact(input_); + const V& ima_v = exact(ima_v_); + const E& ima_e = exact(ima_e_); + + mln_precondition(input.is_valid()); + mln_precondition(ima_v.is_valid()); + mln_precondition(ima_e.is_valid()); + + mln_concrete(I) output; + initialize(output, input); + + data::fill(output, bg); + debug::draw_graph(output, ima_v.domain(), + pw::cst(150u), + edge_to_color<E, mln_value(I)>(ima_e)); + + dpoint2d tl(-box_size,-box_size); + dpoint2d br(box_size,box_size); + mln_piter(V) p(ima_v.domain()); + for_all(p) + { + box<mln_site(I)> b(p + tl, p + br); + b.crop_wrt(output.domain()); + data::fill((output | b).rw(), convert::to<mln_value(I)>(ima_v(p))); + } + + trace::exiting("debug_graph_image"); + return output; + } + + } // end of namespace mln::make + +} // end of namespace mln + + + +int main(int argc, char *argv[]) +{ + using namespace mln; + using namespace value; + + if (argc < 2) + { + std::cout << argv[0] << " <input.pgm> " << std::endl; + return 1; + } + + image2d<int_u8> input; + io::pgm::load(input, argv[1]); + + image2d<int_u8> grad = morpho::elementary::gradient_internal(input, c4()); + io::pgm::save(grad, "binarization_grad.pgm"); + + image2d<int_u8> clo_vol = morpho::closing::volume(grad, c4(), 500); + io::pgm::save(clo_vol, "binarization_clo.pgm"); + + label_16 nbasins; + image2d<label_16> wst = morpho::watershed::flooding(clo_vol, c4(), nbasins); + io::ppm::save(debug::colorize(rgb8(), wst, nbasins), "binarization_wst.ppm"); + + + util::couple<util::graph, image2d<label_16> > + rag_data = make::rag_and_labeled_wsl(wst, c4(), nbasins); + + io::pgm::save(rag_data.second(), "binarization_lwsl.pgm"); + io::ppm::save(debug::colorize(rgb8(), rag_data.second(), nbasins), "binarization_lwsl.ppm"); + + p_vertices<util::graph, fun::i2v::array<point2d> > + pv = make::common_pvertices(wst, nbasins, rag_data.first()); + + pw::image<fun::i2v::array<int_u8>, + p_vertices<util::graph, fun::i2v::array<point2d> > > + ima_v = make::vertex_image(accu::mean<int_u8>(), pv, input, wst, nbasins); + + pw::image<fun::i2v::array<int_u8>, + p_edges<util::graph,pw::cst_<literal::origin_t> > > + ima_e = make::edge_image(ima_v, + make::dummy_pedges(rag_data.first(),literal::origin), + edge_values()); + + + io::pgm::save(make::debug_graph_image(input,ima_v, ima_e, 4, 0), "binarization_graph.ppm"); + + // FIXME: we should use the following line instead. We cannot since currently + // graph edges are numbered from 0 and we must use mln_max() - 1 as + // background id. + // + //label_16 nelts = rag.first().e_nmax(); + label_16 nelts = mln_max(label_16).prev(); + + util::array<int_u8> median_grad = labeling::compute(accu::meta::median_h(), + grad, + rag_data.second(), + nelts); + fun::i2v::array<int_u8> f; + convert::from_to(median_grad, f); + + image2d<int_u8> med = level::transform(rag_data.second(), f); + + io::pgm::save(med, "binarization_median_grad.pgm"); +} -- 1.5.6.5

1 0

3601: Add labeling::wrap routine.
by Guillaume Lazzara 02 Apr '09

02 Apr '09

* mln/labeling/wrap.hh: new routine. * tests/labeling/Makefile.am, * tests/labeling/wrap.cc: new test. --- milena/ChangeLog | 9 ++++ milena/mln/labeling/wrap.hh | 86 +++++++++++++++++++++++++++++++++++++ milena/tests/labeling/Makefile.am | 4 +- milena/tests/labeling/wrap.cc | 64 +++++++++++++++++++++++++++ 4 files changed, 162 insertions(+), 1 deletions(-) create mode 100644 milena/mln/labeling/wrap.hh create mode 100644 milena/tests/labeling/wrap.cc diff --git a/milena/ChangeLog b/milena/ChangeLog index 7334d37..76e8920 100644 --- a/milena/ChangeLog +++ b/milena/ChangeLog @@ -1,5 +1,14 @@ 2009-04-01 Guillaume Lazzara <lazzara(a)lrde.epita.fr> + Add labeling::wrap routine. + + * mln/labeling/wrap.hh: new routine. + + * tests/labeling/Makefile.am, + * tests/labeling/wrap.cc: new test. + +2009-04-01 Guillaume Lazzara <lazzara(a)lrde.epita.fr> + Add a new routine to create a region adjacency graph. * mln/make/rag_and_labeled_wsl.hh: new routine. diff --git a/milena/mln/labeling/wrap.hh b/milena/mln/labeling/wrap.hh new file mode 100644 index 0000000..aa6478f --- /dev/null +++ b/milena/mln/labeling/wrap.hh @@ -0,0 +1,86 @@ +// Copyright (C) 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 MLN_LABELING_WRAP_HH +# define MLN_LABELING_WRAP_HH + +/// \file mln/labeling/wrap.hh +/// +/// Wrap labels such as 0 -> 0 and [1, lmax] maps to [1, +/// Lmax] (using modulus). + +# include <mln/core/concept/image.hh> +# include <mln/level/transform.hh> +# include <mln/fun/l2l/wrap.hh> +# include <mln/metal/converts_to.hh> +# include <mln/metal/is_a.hh> + +namespace mln +{ + + namespace labeling + { + + /// Wrap labels such as 0 -> 0 and [1, lmax] maps to [1, + /// Lmax] (using modulus). + /// + /// \param[in] value_type The type used to wrap the label type. + /// \param[in] input The label image. + /// + /// \return A new image with values wrapped with type V. + template <typename V, typename I> + mln_ch_value(I,V) + wrap(const V& value_type, const Image<I>& input); + + + +# ifndef MLN_INCLUDE_ONLY + + template <typename V, typename I> + inline + mln_ch_value(I,V) + wrap(const V& value_type, const Image<I>& input) + { + trace::entering("labeling::wrap"); + +// mlc_is_a(mln_value(I), value::Symbolic)::check(); + mln_precondition(exact(input).is_valid()); + + mln_ch_value(I,V) output = level::transform(input, fun::l2l::wrap<V>()); + + trace::exiting("labeling::wrap"); + return output; + } + +# endif // ! MLN_INCLUDE_ONLY + + } // end of namespace mln::labeling + +} // end of namespace mln + +#endif // ! MLN_LABELING_WRAP_HH diff --git a/milena/tests/labeling/Makefile.am b/milena/tests/labeling/Makefile.am index 6b3231f..f436f63 100644 --- a/milena/tests/labeling/Makefile.am +++ b/milena/tests/labeling/Makefile.am @@ -14,7 +14,8 @@ check_PROGRAMS = \ n_max \ regional_maxima \ regional_minima \ - relabel + relabel \ + wrap background_SOURCES = background.cc blobs_SOURCES = blobs.cc @@ -28,5 +29,6 @@ n_max_SOURCES = n_max.cc regional_maxima_SOURCES = regional_maxima.cc regional_minima_SOURCES = regional_minima.cc relabel_SOURCES = relabel.cc +wrap_SOURCES = wrap.cc TESTS = $(check_PROGRAMS) diff --git a/milena/tests/labeling/wrap.cc b/milena/tests/labeling/wrap.cc new file mode 100644 index 0000000..b5e8a71 --- /dev/null +++ b/milena/tests/labeling/wrap.cc @@ -0,0 +1,64 @@ +// Copyright (C) 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. + +/// \file tests/labeling/wrap.cc +/// +/// Test on mln::labeling::wrap. + +#include <mln/core/image/image2d.hh> +#include <mln/core/alias/neighb2d.hh> +#include <mln/value/int_u8.hh> +#include <mln/value/int_u16.hh> +#include <mln/make/image2d.hh> +#include <mln/labeling/wrap.hh> +#include <mln/level/compare.hh> + +#include <mln/debug/println.hh> + +#include "tests/data.hh" + + +int main() +{ + using namespace mln; + using value::int_u8; + using value::int_u16; + + int_u16 values[] = { 1, 1000, + 0, 65534 }; + + int_u8 ref_values[] = { 1, 235, + 0, 254 }; + + image2d<int_u16> ima = make::image2d(values); + image2d<int_u8> ima_ref = make::image2d(ref_values); + + image2d<int_u8> ima_wrapped = labeling::wrap(int_u8(), ima); + + mln_assertion(ima_ref == ima_wrapped); +} -- 1.5.6.5

1 0

3600: Add a new routine to create a region adjacency graph.
by Guillaume Lazzara 02 Apr '09

02 Apr '09

* mln/make/rag_and_labeled_wsl.hh: new routine. * tests/make/Makefile.am, * tests/make/rag_and_labeled_wsl.cc: new test. --- milena/ChangeLog | 9 ++ milena/mln/make/rag_and_labeled_wsl.hh | 230 ++++++++++++++++++++++++++++++ milena/tests/make/Makefile.am | 2 + milena/tests/make/rag_and_labeled_wsl.cc | 90 ++++++++++++ 4 files changed, 331 insertions(+), 0 deletions(-) create mode 100644 milena/mln/make/rag_and_labeled_wsl.hh create mode 100644 milena/tests/make/rag_and_labeled_wsl.cc diff --git a/milena/ChangeLog b/milena/ChangeLog index e7cf8d9..7334d37 100644 --- a/milena/ChangeLog +++ b/milena/ChangeLog @@ -1,3 +1,12 @@ +2009-04-01 Guillaume Lazzara <lazzara(a)lrde.epita.fr> + + Add a new routine to create a region adjacency graph. + + * mln/make/rag_and_labeled_wsl.hh: new routine. + + * tests/make/Makefile.am, + * tests/make/rag_and_labeled_wsl.cc: new test. + 2009-04-01 Thierry Geraud <thierry.geraud(a)lrde.epita.fr> Several fixes. diff --git a/milena/mln/make/rag_and_labeled_wsl.hh b/milena/mln/make/rag_and_labeled_wsl.hh new file mode 100644 index 0000000..d80b954 --- /dev/null +++ b/milena/mln/make/rag_and_labeled_wsl.hh @@ -0,0 +1,230 @@ +// Copyright (C) 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. +// reasons why the executable file might be covered by the GNU General +// Public License. + +#ifndef MLN_MAKE_RAG_AND_ALBL_HH +# define MLN_MAKE_RAG_AND_ALBL_HH + +/// \file mln/make/rag_and_labeled_wsl.hh +/// +/// Create a region adjacency graph and a label image of the watershed line +/// from a watershed image. +/// +/// \sa morpho::watershed::flooding. +/// +/// \todo Do not use mln_max() as background label! + +# include <map> + +# include <mln/core/concept/image.hh> +# include <mln/core/concept/neighborhood.hh> +# include <mln/core/image/image2d.hh> +# include <mln/core/alias/box2d.hh> +# include <mln/extension/adjust_fill.hh> +# include <mln/util/graph.hh> +# include <mln/util/couple.hh> + + +namespace mln +{ + + namespace make + { + + /// Create a region adjacency graph and a label image of the watershed line + /// from a watershed image. + /// + /// \param[in] wshd Watershed image. + /// \param[in] nbh Neighborhood + /// \param[in] nbasins Number of influence zone in \p wshd. + /// + /// \return A couple. First element is the graph, second element is an + /// image with a labeled watershed line. + template <typename I, typename N> + util::couple<util::graph,mln_concrete(I)> + rag_and_labeled_wsl(const Image<I>& wshd_, + const Neighborhood<N>& nbh_, + const mln_value(I)& nbasins); + + + +# ifndef MLN_INCLUDE_ONLY + + + namespace internal + { + + template <typename I, typename N> + inline + void + rag_and_labeled_wsl_tests(const Image<I>& wshd, + const Neighborhood<N>& nbh, + const mln_value(I)&) + { + mln_precondition(exact(wshd).is_valid()); + mln_precondition(exact(nbh).is_valid()); + (void) wshd; + (void) nbh; + } + + } // end of namespace mln::make::internal + + + namespace impl + { + + namespace generic + { + + template <typename I, typename N> + inline + util::couple<util::graph,mln_concrete(I)> + rag_and_labeled_wsl(const Image<I>& wshd_, + const Neighborhood<N>& nbh_, + const mln_value(I)& nbasins) + { + trace::entering("make::impl::generic::rag_and_labeled_wsl"); + + internal::rag_and_labeled_wsl_tests(wshd_, nbh_, nbasins); + const I& wshd = exact(wshd_); + const N& nbh = exact(nbh_); + typedef mln_value(I) L; + + mln::image2d<bool> adj(mln::box2d(nbasins.next(), nbasins.next())); + data::fill(adj, false); + extension::adjust_fill(wshd, nbh, 0u); + + mln_concrete(I) output(wshd.domain()); + + // FIXME: we would like to not use mln_value() but 0 instead. + // We can't do that because graph edges are numbered from 0. + data::fill(output, mln_max(mln_value(I)).prev()); + + std::map<util::couple<L,L>, mln_value(I)> c2la; + util::array<util::couple<L,L> > la2c; + mln_value(I) nlabels = literal::zero; + + L l1, l2; + mln_piter(I) p(wshd.domain()); + mln_niter(N) n(nbh, p); + for_all(p) + { + if (wshd(p) != 0u) + continue; + // p is in the watershed line. + l1 = l2 = 0; + for_all(n) + if (wshd.has(n) && wshd(n) != 0u) + { + if (l1 == 0u) // First label to be stored. + l1 = wshd(n); + else + if (wshd(n) != l1) // Useless: && l2 == 0) + { // Second label to be stored. + mln_invariant(l2 == 0u); + l2 = wshd(n); + break; + } + } + if (l2 == 0u || l1 == 0u) + continue; + if (l2 < l1) + std::swap(l1, l2); + + // adjacency l1 l2 + util::couple<L,L> c = make::couple(l2,l1); + if (c2la.find(c) == c2la.end()) + { + c2la[c] = nlabels++; + la2c.append(c); + } + output(p) = c2la[c]; + + } + + // Construct graph. + util::graph g; + g.add_vertices(nbasins.next()); + for (unsigned i = 0; i < la2c.nelements(); ++i) + g.add_edge(la2c[i].first(), la2c[i].second()); + + trace::exiting("make::impl::generic::rag_and_labeled_wsl"); + return make::couple(g, output); + } + + } // end of namespace mln::make::impl::generic + + } // end of namespace mln::make::impl + + + + namespace internal + { + + template <typename I, typename N> + inline + util::couple<util::graph,mln_concrete(I)> + rag_and_labeled_wsl_dispatch(const Image<I>& wshd, + const Neighborhood<N>& nbh, + const mln_value(I)& nbasins) + { + return make::impl::generic::rag_and_labeled_wsl(wshd, nbh, nbasins); + } + + } // end of namespace mln::make::internal + + + + // Facade + + template <typename I, typename N> + inline + util::couple<util::graph,mln_concrete(I)> + rag_and_labeled_wsl(const Image<I>& wshd, + const Neighborhood<N>& nbh, + const mln_value(I)& nbasins) + { + trace::entering("make::rag_and_labeled_wsl"); + + internal::rag_and_labeled_wsl_tests(wshd, nbh, nbasins); + + util::couple<util::graph,mln_concrete(I)> + result = internal::rag_and_labeled_wsl_dispatch(wshd, nbh, nbasins); + + trace::exiting("make::rag_and_labeled_wsl"); + return result; + } + + +# endif // ! MLN_INCLUDE_ONLY + + + } // end of namespace mln::make + +} // end of namespace mln + + +#endif // ! MLN_MAKE_RAG_AND_ALBL_HH diff --git a/milena/tests/make/Makefile.am b/milena/tests/make/Makefile.am index bf96093..7e4c12b 100644 --- a/milena/tests/make/Makefile.am +++ b/milena/tests/make/Makefile.am @@ -10,6 +10,7 @@ check_PROGRAMS = \ image3d \ mat \ region_adjacency_graph \ + rag_and_labeled_wsl \ w_window \ w_window_directional @@ -20,6 +21,7 @@ image2d_SOURCES = image2d.cc image3d_SOURCES = image3d.cc mat_SOURCES = mat.cc region_adjacency_graph_SOURCES = region_adjacency_graph.cc +rag_and_labeled_wsl_SOURCES = rag_and_labeled_wsl.cc w_window_SOURCES = w_window.cc w_window_directional_SOURCES = w_window_directional.cc diff --git a/milena/tests/make/rag_and_labeled_wsl.cc b/milena/tests/make/rag_and_labeled_wsl.cc new file mode 100644 index 0000000..5abb031 --- /dev/null +++ b/milena/tests/make/rag_and_labeled_wsl.cc @@ -0,0 +1,90 @@ +// Copyright (C) 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. + +/// \file tests/make/rag_and_labeled_wsl.cc +/// +/// Tests on mln::make::rag_and_labeled_wsl + +#include <mln/core/alias/neighb2d.hh> + +#include <mln/util/graph.hh> + +#include <mln/value/label_8.hh> + +#include <mln/make/image2d.hh> +#include <mln/make/rag_and_labeled_wsl.hh> + +# include <mln/debug/println.hh> + +int main() +{ + using namespace mln; + + value::label_8 vals[16] = { 1, 0, 3, 3, + 1, 0, 0, 0, + 0, 0, 4, 4, + 2, 2, 0, 4 }; + + typedef image2d<value::label_8> wst_t; + wst_t ima = make::image2d(vals); + + util::couple<util::graph, wst_t> + res = make::rag_and_labeled_wsl(ima, c4(), 4u); + + // check that adjacency labels map edge labels. + mln_piter_(wst_t) p(res.second().domain()); + mln_niter_(neighb2d) n(c4(),p); + for_all(p) + if (res.second()(p) != mln_max(value::label_8)) + { + value::label_8 l1 = 0, l2 = 0; + for_all(n) + if (ima.has(n) && ima(n) != 0u) + { + if (l1 == 0u) // First label to be stored. + l1 = ima(n); + else + if (ima(n) != l1) // Useless: && l2 == 0) + { // Second label to be stored. + mln_invariant(l2 == 0u); + l2 = ima(n); + break; + } + } + if (l2 < l1) + std::swap(l1, l2); + mln_assertion(res.first().v1(res.second()(p)) == l1); + mln_assertion(res.first().v2(res.second()(p)) == l2); + } + + mln_assertion(res.first().e_nmax() == 4u); + mln_assertion(res.first().v_nmax() == 5u); + mln_assertion(res.first().v_nmax_nbh_edges(0) == 0); + for (unsigned i = 1; i < 4; ++i) + mln_assertion(res.first().v_nmax_nbh_edges(i) == 2); +} + -- 1.5.6.5

1 0

3599: Several fixes.
by Thierry Geraud 01 Apr '09

01 Apr '09

https://svn.lrde.epita.fr/svn/oln/trunk/milena Index: ChangeLog from Thierry Geraud <thierry.geraud(a)lrde.epita.fr> Several fixes. * mln/morpho/leveling_filter.hh: Layout. (leveling_filter): Fix trace naming. Call facade instead of dispatch. * mln/canvas/morpho/attribute_filter.hh: Layout. (attribute_filter_fastest): Fix deja_vu border value. canvas/morpho/attribute_filter.hh | 7 ++++++- morpho/leveling_filter.hh | 30 ++++++++++++++++++++---------- 2 files changed, 26 insertions(+), 11 deletions(-) Index: mln/morpho/leveling_filter.hh --- mln/morpho/leveling_filter.hh (revision 3598) +++ mln/morpho/leveling_filter.hh (working copy) @@ -1,5 +1,5 @@ -// Copyright (C) 2007, 2008, 2009 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 @@ -26,8 +26,8 @@ // reasons why the executable file might be covered by the GNU General // Public License. -#ifndef MLN_MORPHO_LEVELING_FILTER_HH_ -# define MLN_MORPHO_LEVELING_FILTER_HH_ +#ifndef MLN_MORPHO_LEVELING_FILTER_HH +# define MLN_MORPHO_LEVELING_FILTER_HH /// \file mln/morpho/leveling_filter.hh /// @@ -44,8 +44,13 @@ # include <mln/canvas/morpho/attribute_filter.hh> -namespace mln { - namespace morpho { + +namespace mln +{ + + namespace morpho + { + template <typename I, typename N, typename A> mln_concrete(I) @@ -56,8 +61,10 @@ bool increasing); + # ifndef MLN_INCLUDE_ONLY + template <typename I, typename N, typename A> mln_concrete(I) leveling_filter(const Image<I>& input, @@ -66,7 +73,7 @@ const typename A::result& lambda, bool increasing) { - trace::entering("morpho::opening::leveling_filter"); + trace::entering("morpho::leveling_filter"); mln_precondition(exact(input).is_valid()); @@ -76,16 +83,19 @@ trait::accumulator::when_pix::use_v))::check(); mln_concrete(I) output; - output = canvas::morpho::internal::attribute_filter_dispatch(input, nbh, a, lambda, increasing); + output = canvas::morpho::attribute_filter(input, nbh, a, lambda, increasing); - trace::exiting("morpho::opening::leveling_filter"); + trace::exiting("morpho::leveling_filter"); return output; } + # endif // ! MLN_INCLUDE_ONLY + } // end of namespace mln::morpho + } // end of namespace mln -#endif /* !MLN_MORPHO_LEVELING_FILTER_HH_ */ +#endif // ! MLN_MORPHO_LEVELING_FILTER_HH Index: mln/canvas/morpho/attribute_filter.hh --- mln/canvas/morpho/attribute_filter.hh (revision 3598) +++ mln/canvas/morpho/attribute_filter.hh (working copy) @@ -313,7 +313,7 @@ { initialize(deja_vu, input); data::fill(deja_vu, false); - extension::fill(deja_vu, true); // So the border is neutral. + extension::fill(deja_vu, false); // So the border is neutral. initialize(activity, input); data::fill(activity, true); @@ -381,6 +381,7 @@ trace::exiting("canvas::morpho::impl::attribute_filter_fastest"); return output; } + } // end of namespace mln::canvas::morpho::impl @@ -391,7 +392,9 @@ namespace internal { + // Dispatch to generic. + template <typename I, typename N, typename A> inline mln_concrete(I) @@ -409,7 +412,9 @@ return impl::generic::attribute_filter(input, nbh, s, a, lambda); } + // Dispatch to fastest. + template <typename I, typename N, typename A> inline mln_concrete(I)

1 0

3598: Add a 1st threshold code.
by Thierry Geraud 01 Apr '09

01 Apr '09

https://svn.lrde.epita.fr/svn/oln/trunk/milena/sandbox Index: ChangeLog from Thierry Geraud <thierry.geraud(a)lrde.epita.fr> Add a 1st threshold code. * theo/icdar/dibco/main.cc: New. First threshold attempt. * theo/icdar/hsc/boxes.cc (param): Set to a reasonable value. (tmp_pgm): Save this temp image. * theo/exec/subsample.cc: New. exec/subsample.cc | 43 ++++++++++++ icdar/dibco/main.cc | 184 ++++++++++++++++++++++++++++++++++++++++++++++++++++ icdar/hsc/boxes.cc | 11 ++- 3 files changed, 236 insertions(+), 2 deletions(-) Index: theo/icdar/dibco/main.cc --- theo/icdar/dibco/main.cc (revision 0) +++ theo/icdar/dibco/main.cc (revision 0) @@ -0,0 +1,184 @@ +// Copyright (C) 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. + +/// \file theo/icdar/dibco/main.cc +/// +/// Simple thresholding of a gray-level document. + +# include <mln/io/pgm/load.hh> +# include <mln/io/pgm/save.hh> +# include <mln/io/pbm/save.hh> + +# include <mln/debug/println.hh> +# include <mln/fun/l2l/wrap.hh> +# include <mln/level/transform.hh> + +# include <mln/core/image/image1d.hh> +# include <mln/core/alias/neighb1d.hh> + +# include <mln/core/image/image2d.hh> +# include <mln/core/alias/neighb2d.hh> + +# include <mln/core/routine/duplicate.hh> +# include <mln/core/image/image_if.hh> +# include <mln/pw/all.hh> + +# include <mln/histo/compute.hh> +# include <mln/debug/histo.hh> +# include <mln/convert/from_to.hh> + +# include <mln/morpho/elementary/gradient_internal.hh> +# include <mln/morpho/elementary/gradient_external.hh> +# include <mln/morpho/closing/height.hh> +# include <mln/morpho/closing/volume.hh> +# include <mln/morpho/watershed/flooding.hh> + +# include <mln/linear/gaussian_1d.hh> +# include <mln/labeling/regional_minima.hh> +# include <mln/labeling/compute.hh> +# include <mln/value/label_8.hh> +# include <mln/accu/center.hh> + + + +void usage(char* argv[]) +{ + std::cerr << "usage: " << argv[0] << " input.pgm output.pbm" << std::endl + << " ICDAR'2009: DIBCO." << std::endl; + std::abort(); +} + + +namespace mln +{ + + int + find_threshold(const histo::array<value::int_u8>& h) + { + + const float sigma = 5; // FIXME: hard-coded! + + util::array<point1d> c; + value::label_8 n; + + { + image1d<unsigned> h_, hs_; + image1d<value::label_8> l; + + convert::from_to(h, h_); + hs_ = linear::gaussian_1d(h_, sigma, 0); + l = labeling::regional_minima(hs_, c2(), n); + + { +// debug::println("l", l); +// debug::histo(h, "tmp_h.txt"); + +// std::ofstream file("tmp_hs.txt"); +// mln_piter_(box1d) p(h_.domain()); +// for_all(p) +// file << p.ind() << ' ' << hs_(p) << std::endl; +// file.close(); + } + + accu::center<point1d, point1d> a; + c = labeling::compute(a, l, n); + + c[0] = point1d(0); // Force a neutral value for the non-label value (0). + + // std::cout << "c = " << c << std::endl; + } + + + int threshold; + + { + std::vector<int> v; + for (unsigned i = 0; i <= n; ++i) + v.push_back(c[i].ind()); + std::sort(v.begin(), v.end()); + + for (unsigned i = 0; i <= n; ++i) + if (v[i] != 0) + { + threshold = v[i]; + break; + } + + std::cout << "threshold = " << threshold << std::endl; + } + + return threshold; + } + + +} // ! mln + + + +int main(int argc, char* argv[]) +{ + using namespace mln; + using value::int_u8; + + if (argc != 3) + usage(argv); + + image2d<int_u8> input; + io::pgm::load(input, argv[1]); + + typedef int_u8 V; + histo::array<V> h; + + image2d<int_u8> g; + g = morpho::elementary::gradient_internal(input, c4()); + io::pgm::save(g, "tmp_g.pgm"); + + g = morpho::closing::height(g, c4(), 3); // FIXME: hard-coded! + + unsigned nbasins; + image2d<unsigned> w = morpho::watershed::flooding(g, c4(), nbasins); + + io::pgm::save(level::transform(w, + fun::l2l::wrap<int_u8>()), + "tmp_w.pgm"); + + h = histo::compute(g | (pw::value(w) == pw::cst(0))); + + unsigned threshold = find_threshold(h); + +// output = duplicate((pw::value(g) > pw::cst(threshold)) | input.domain()); + + io::pbm::save((pw::value(g) > pw::cst(threshold)) | input.domain(), + "tmp_g.pbm"); + + image2d<bool> output; + output = duplicate((pw::value(g) > pw::cst(threshold) + && pw::value(w) == pw::cst(0)) | input.domain()); + + io::pbm::save(output, argv[2]); +} Index: theo/icdar/hsc/boxes.cc --- theo/icdar/hsc/boxes.cc (revision 3597) +++ theo/icdar/hsc/boxes.cc (working copy) @@ -44,6 +44,9 @@ #include <mln/logical/not.hh> #include <mln/io/dump/save.hh> +#include <mln/io/pgm/save.hh> +#include <mln/fun/l2l/wrap.hh> + int usage(const char *name) { @@ -74,8 +77,8 @@ text = filter::small_components(text,4); mln::util::array<unsigned> - left_link = text::grouping::group_with_single_left_link(text, 100), - right_link = text::grouping::group_with_single_right_link(text, 100); + left_link = text::grouping::group_with_single_left_link(text, 30), + right_link = text::grouping::group_with_single_right_link(text, 30); std::cout << "BEFORE - nbboxes = " << nbboxes << std::endl; @@ -94,6 +97,10 @@ io::dump::save(grouped_text.label_image(), argv[2]); + io::pgm::save(level::transform(grouped_text.label_image(), + fun::l2l::wrap<value::int_u8>()), + "tmp.pgm"); + scribo::debug::save_textbboxes_image(input, grouped_text.bboxes(), literal::red, scribo::make::debug_filename("boxes.ppm")); Index: theo/exec/subsample.cc --- theo/exec/subsample.cc (revision 0) +++ theo/exec/subsample.cc (revision 0) @@ -0,0 +1,43 @@ +#include "filetype.hh" + +#include <mln/world/binary_2d/subsample.hh> + + + +void usage(char* argv[]) +{ + std::cerr << "usage: " << argv[0] << " input.pbm n output.pgm" << std::endl + << " Subsampling." << std::endl + << " n >= 2." << std::endl; + std::abort(); +} + + + +int main(int argc, char* argv[]) +{ + using namespace mln; + using value::int_u8; + + if (argc != 4) + usage(argv); + + + trace::entering("main"); + + int n = std::atoi(argv[2]); + if (n < 2) + { + std::cerr << "bad n!" << std::endl; + usage(argv); + } + + + image2d<bool> ima; + io::pbm::load(ima, argv[1]); + io::pgm::save(world::binary_2d::subsample(ima, + n), + argv[3]); + + trace::exiting("main"); +}

1 0

r3597: Update spatial smoothing
by Fabien Freling 31 Mar '09

31 Mar '09

URL: https://svn.lrde.epita.fr/svn/oln/trunk/milena/sandbox ChangeLog: 2009-03-31 Fabien Freling <fabien.freling(a)lrde.epita.fr> Update spatial smoothing. * fabien/igr/Makefile: Update. * fabien/igr/space_smooth/linear.cc: Fix spatial smoothing. * fabien/igr/space_smooth/median.cc: Implement spatial smoothing. * fabien/igr/space_smooth/morpho.cc: Draft. * fabien/igr/time_smooth/linear.cc: Small fix. --- Makefile | 5 +- space_smooth/linear.cc | 8 +-- space_smooth/median.cc | 111 +++++++++++++++++++++++++++++++------------------ space_smooth/morpho.cc | 12 +---- time_smooth/linear.cc | 2 5 files changed, 83 insertions(+), 55 deletions(-) Index: trunk/milena/sandbox/fabien/igr/space_smooth/median.cc =================================================================== --- trunk/milena/sandbox/fabien/igr/space_smooth/median.cc (revision 3596) +++ trunk/milena/sandbox/fabien/igr/space_smooth/median.cc (revision 3597) @@ -11,6 +11,7 @@ #include <mln/io/plot/save.hh> #include <mln/accu/median_h.hh> +#include <mln/core/alias/window2d.hh> #include <mln/util/array.hh> @@ -33,15 +34,11 @@ /////////////////// image3d<int_u12> input; io::dicom::load(input, argv[1]); - image2d<util::array<int_u12> > ima_arr(input.nrows(), input.ncols()); + util::array<image2d<int_u12> > arr_ima; for (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()); - for_all(p) - { - ima_arr(p).append(tmp_slice(p)); - } + arr_ima.append(tmp_slice); } //////////// @@ -49,41 +46,52 @@ // Median // // // //////////// - image2d<util::array<int_u12> > ima_median3; - image2d<util::array<int_u12> > ima_median5; - initialize(ima_median3, ima_arr); - initialize(ima_median5, ima_arr); - mln_piter_(image2d<int_u12>) p(ima_median3.domain()); - accu::median_h<int_u12> accu_med; + window2d win_c12p; + win_c12p + .insert(-1, -1) + .insert( 0, -1) + .insert(+1, -1) + .insert(-1, 0) + .insert( 0, 0) + .insert(+1, 0) + .insert(-1, +1) + .insert( 0, +1) + .insert(+1, +1) + .insert(+2, +2) + .insert(-2, -2) + .insert(+2, -2) + .insert(-2, +2); + window2d win_c4 = win_c4p(); + util::array<image2d<int_u12> > ima_median3; + util::array<image2d<int_u12> > ima_median5; + accu::median_h<int_u12> accu_med3; + accu::median_h<int_u12> accu_med5; + image2d<int_u12> tmp; + initialize(tmp, arr_ima[0]); + mln_piter_(image2d<int_u12>) p(arr_ima[0].domain()); + mln_qiter_(window2d) q3(win_c4, p); + mln_qiter_(window2d) q5(win_c12p, p); + for (unsigned i = 0; i < arr_ima.nelements(); ++i) + { for_all(p) { // Median 3 - ima_median3(p).append(ima_arr(p)[0]); - for (unsigned i = 1; i < ima_arr(p).nelements() - 1; ++i) - { - accu_med.init(); - accu_med.take(ima_arr(p)[i - 1]); - accu_med.take(ima_arr(p)[i]); - accu_med.take(ima_arr(p)[i + 1]); - ima_median3(p).append(accu_med.to_result()); + accu_med3.init(); + for_all(q3) if (arr_ima[i].domain().has(q3)) + accu_med3.take(arr_ima[i](q3)); + tmp(p) = accu_med3.to_result(); } - ima_median3(p).append(ima_arr(p)[ima_arr(p).nelements() - 1]); + ima_median3.append(duplicate(tmp)); + for_all(p) + { // Median 5 - ima_median5(p).append(ima_arr(p)[0]); - ima_median5(p).append(ima_arr(p)[1]); - for (unsigned i = 2; i < ima_arr(p).nelements() - 2; ++i) - { - accu_med.init(); - accu_med.take(ima_arr(p)[i - 2]); - accu_med.take(ima_arr(p)[i - 1]); - accu_med.take(ima_arr(p)[i]); - accu_med.take(ima_arr(p)[i + 1]); - accu_med.take(ima_arr(p)[i + 2]); - ima_median5(p).append(accu_med.to_result()); + accu_med5.init(); + for_all(q5) if (arr_ima[i].domain().has(q5)) + accu_med5.take(arr_ima[i](q5)); + tmp(p) = accu_med5.to_result(); } - ima_median5(p).append(ima_arr(p)[ima_arr(p).nelements() - 2]); - ima_median5(p).append(ima_arr(p)[ima_arr(p).nelements() - 1]); + ima_median5.append(duplicate(tmp)); } ///////////// @@ -91,12 +99,35 @@ // Outputs // // // ///////////// - io::plot::save(ima_median3(point2d(160, 120)), "median3_tumeur.plot"); - io::plot::save(ima_median3(point2d(34, 94)), "median3_air.plot"); - io::plot::save(ima_median3(point2d(122, 115)), "median3_poumon.plot"); - io::plot::save(ima_median5(point2d(160, 120)), "median5_tumeur.plot"); - io::plot::save(ima_median5(point2d(34, 94)), "median5_air.plot"); - io::plot::save(ima_median5(point2d(122, 115)), "median5_poumon.plot"); + util::array<int_u12> arr_tumeur3; + util::array<int_u12> arr_tumeur5; + for (unsigned i = 0; i < ima_median3.nelements(); ++i) + { + arr_tumeur3.append(ima_median3[i](point2d(160, 120))); + arr_tumeur5.append(ima_median5[i](point2d(160, 120))); + } + io::plot::save(arr_tumeur3, "median3_tumeur.plot"); + io::plot::save(arr_tumeur5, "median5_tumeur.plot"); + + util::array<int_u12> arr_air3; + util::array<int_u12> arr_air5; + for (unsigned i = 0; i < ima_median3.nelements(); ++i) + { + arr_air3.append(ima_median3[i](point2d(34, 94))); + arr_air5.append(ima_median5[i](point2d(34, 94))); + } + io::plot::save(arr_air3, "median3_air.plot"); + io::plot::save(arr_air5, "median5_air.plot"); + + util::array<int_u12> arr_poumon3; + util::array<int_u12> arr_poumon5; + for (unsigned i = 0; i < ima_median3.nelements(); ++i) + { + arr_poumon3.append(ima_median3[i](point2d(122, 115))); + arr_poumon5.append(ima_median5[i](point2d(122, 115))); + } + io::plot::save(arr_poumon3, "median3_poumon.plot"); + io::plot::save(arr_poumon5, "median5_poumon.plot"); return 0; } Index: trunk/milena/sandbox/fabien/igr/space_smooth/morpho.cc =================================================================== --- trunk/milena/sandbox/fabien/igr/space_smooth/morpho.cc (revision 3596) +++ trunk/milena/sandbox/fabien/igr/space_smooth/morpho.cc (revision 3597) @@ -48,15 +48,11 @@ /////////////////// image3d<int_u12> input; io::dicom::load(input, argv[1]); - image2d<util::array<int_u12> > ima_arr(input.nrows(), input.ncols()); + util::array<image2d<int_u12> > arr_ima; for (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()); - for_all(p) - { - ima_arr(p).append(tmp_slice(p)); - } + arr_ima.append(tmp_slice); } //////////// @@ -64,10 +60,8 @@ // Morpho // // // //////////// - image2d<image1d<int_u12> > ima_morpho; - initialize(ima_morpho, ima_arr); + util::array<image2d<int_u12> > ima_morpho; mln_piter_(image2d<int_u12>) p(ima_morpho.domain()); - accu::median_h<int_u12> accu_med; for_all(p) { image1d<int_u12> tmp_ima; Index: trunk/milena/sandbox/fabien/igr/space_smooth/linear.cc =================================================================== --- trunk/milena/sandbox/fabien/igr/space_smooth/linear.cc (revision 3596) +++ trunk/milena/sandbox/fabien/igr/space_smooth/linear.cc (revision 3597) @@ -48,12 +48,12 @@ // Linear convolution // // // //////////////////////// - float ws[] = { 0, 1/8, 0, - 1/8, 1/2, 1/8, - 0, 1/8, 0 }; + float ws[] = { 0, 1/8.f, 0, + 1/8.f, 1/2.f, 1/8.f, + 0, 1/8.f, 0 }; util::array<image2d<float> > ima_linear; - for (unsigned i = 1; i < arr_ima.nelements(); ++i) + for (unsigned i = 0; i < arr_ima.nelements(); ++i) ima_linear.append(linear::convolve(arr_ima[i], make::w_window2d(ws))); ///////////// Index: trunk/milena/sandbox/fabien/igr/time_smooth/linear.cc =================================================================== --- trunk/milena/sandbox/fabien/igr/time_smooth/linear.cc (revision 3596) +++ trunk/milena/sandbox/fabien/igr/time_smooth/linear.cc (revision 3597) @@ -52,7 +52,7 @@ image2d<util::array<int_u12> > ima_linear; initialize(ima_linear, ima_arr); mln_piter_(image2d<int_u12>) p(ima_linear.domain()); - accu::median<int_u12> accu_med; + accu::median_h<int_u12> accu_med; for_all(p) { ima_linear(p).append(ima_arr(p)[0]); Index: trunk/milena/sandbox/fabien/igr/Makefile =================================================================== --- trunk/milena/sandbox/fabien/igr/Makefile (revision 3596) +++ trunk/milena/sandbox/fabien/igr/Makefile (revision 3597) @@ -47,6 +47,9 @@ time_max: time_max.cc ${CXX} -I../../../ ${DICOM} ${MAGICK} ${CXXFLAGS} -lm $^ -o time_max +first_slice_dicom: first_slice_dicom.cc + ${CXX} -I../../../ ${DICOM} ${MAGICK} ${CXXFLAGS} -lm $^ -o first_slice_dicom + 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 + rm seg2d seg3d wsd2d wsd3d nbasins_finder grad clo_vol wst graph med thres matlab time_max first_slice_dicom

1 0

3596: Several bug fixes.
by Thierry Geraud 30 Mar '09

30 Mar '09

https://svn.lrde.epita.fr/svn/oln/trunk/milena Index: ChangeLog from Thierry Geraud <thierry.geraud(a)lrde.epita.fr> Several bug fixes. * mln/histo/array.hh: Layout. * mln/core/image/image1d.hh (from_to_): Remove border setting to 0. Add some hints of future code. (todo): New. * mln/core/alias/point1d.hh: Upgrade doc style. (row, row_t): Fix naming as... (ind, ind_t): ...those. * mln/linear/gaussian_directional_2d.hh: New. * mln/linear/gaussian_1d.hh: New. Both files have been copied from my sandbox. * mln/linear/all.hh: Update. * mln/accu/center.hh (to_result): Make it work when invalid. (todo): New. * mln/value/label.hh (prev): New. * mln/canvas/morpho/attribute_filter.hh (lambda): Use macro for this arg type. (attribute_filter_dispatch): Fix missing border adjustment for the fastest version. (attribute_filter_fastest): New precondition. Fix missing border initialization so that it is neutral. * tests/morpho/closing/volume.cc: Force no border to test that the border is correctly adapted to nbh. * mln/labeling/compute.hh: Move code intro trace. mln/accu/center.hh | 18 ++--- mln/canvas/morpho/attribute_filter.hh | 42 ++++++++----- mln/core/alias/point1d.hh | 48 +++++++------- mln/core/image/image1d.hh | 12 +++ mln/histo/array.hh | 1 mln/labeling/compute.hh | 15 +++- mln/linear/all.hh | 11 ++- mln/linear/gaussian_1d.hh | 109 ++++++++++++++++++++++++++++++++++ mln/linear/gaussian_directional_2d.hh | 98 ++++++++++++++++++++++++------ mln/value/label.hh | 11 +++ tests/morpho/closing/volume.cc | 5 + 11 files changed, 291 insertions(+), 79 deletions(-) Index: mln/histo/array.hh --- mln/histo/array.hh (revision 3595) +++ mln/histo/array.hh (working copy) @@ -81,6 +81,7 @@ + # ifndef MLN_INCLUDE_ONLY template <typename T> Index: mln/core/image/image1d.hh --- mln/core/image/image1d.hh (revision 3595) +++ mln/core/image/image1d.hh (working copy) @@ -32,6 +32,8 @@ /// \file mln/core/image/image1d.hh /// /// Definition of the basic mln::image1d class. +/// +/// \todo Rewrite from_to(histo, image1d) after Etienne's work. # include <mln/core/internal/fixme.hh> # include <mln/core/internal/image_primary.hh> @@ -576,7 +578,13 @@ void from_to_(const histo::array<V>& from, image1d<T>& to) { - to.init_(make::box1d(from.nvalues()), 0); + // FIXME: The code should looks like: + +// box1d b(point1d(mln_min(V)), point1d(mln_max(V))); +// ima.init_(b, 0); +// for_all(v) +// from_to(h(v), ima.at_( index_of(v) )); + to.init_(make::box1d(from.nvalues())); for (unsigned i = 0; i < from.nvalues(); ++i) from_to(from[i], to(point1d(i))); } @@ -587,7 +595,7 @@ void from_to_(const util::array<V>& from, image1d<T>& to) { - to.init_(make::box1d(from.nelements()), 0); + to.init_(make::box1d(from.nelements())); for (unsigned i = 0; i < from.nelements(); ++i) from_to(from[i], to(point1d(i))); } Index: mln/core/alias/point1d.hh --- mln/core/alias/point1d.hh (revision 3595) +++ mln/core/alias/point1d.hh (working copy) @@ -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 @@ -29,25 +29,26 @@ #ifndef MLN_CORE_ALIAS_POINT1D_HH # define MLN_CORE_ALIAS_POINT1D_HH -/*! \file mln/core/alias/point1d.hh - * - * \brief Definition of the mln::point1d alias and of its construction - * routine. - */ +/// \file mln/core/alias/point1d.hh +/// +/// Definition of the mln::point1d alias and of its construction +/// routine. # include <mln/core/point.hh> // For site_const_impl and site_mutable_impl. # include <mln/core/concept/site_proxy.hh> # include <mln/core/internal/force_exact.hh> + namespace mln { - /*! \brief Type alias for a point defined on the 1D square grid with - * integer coordinates. - */ + /// Type alias for a point defined on the 1D square grid with + /// integer coordinates. + // typedef point<grid::tick, def::coord> point1d; + namespace internal { @@ -59,8 +60,8 @@ typedef C coord; enum { dim = 1 }; - typedef const C& row_t; - const C& row() const; + typedef const C& ind_t; + const C& ind() const; const C& operator[](unsigned i) const; const C& last_coord() const; @@ -79,8 +80,8 @@ typedef subject_impl< const point<grid::tick, C>, E > super_; E& exact_(); public: - using super_::row; - C& row(); + using super_::ind; + C& ind(); using super_::operator[]; C& operator[](unsigned i); }; @@ -94,9 +95,9 @@ template <typename C, typename E> inline const C& - subject_impl< const point<grid::tick, C>, E >::row() const + subject_impl< const point<grid::tick, C>, E >::ind() const { - return exact_().get_subject().row(); + return exact_().get_subject().ind(); } template <typename C, typename E> @@ -104,8 +105,9 @@ const C& subject_impl< const point<grid::tick, C>, E >::operator[](unsigned i) const { - mln_precondition(i < 1); - return exact_().get_subject()[i]; + mln_precondition(i == 0); + (void)i; + return exact_().get_subject()[0]; } template <typename C, typename E> @@ -121,9 +123,9 @@ template <typename C, typename E> inline C& - subject_impl< point<grid::tick, C>, E >::row() + subject_impl< point<grid::tick, C>, E >::ind() { - return exact_().get_subject().row(); + return exact_().get_subject().ind(); } template <typename C, typename E> @@ -131,15 +133,15 @@ C& subject_impl< point<grid::tick, C>, E >::operator[](unsigned i) { - mln_precondition(i < 2); - return exact_().get_subject()[i]; + mln_precondition(i == 0); + (void)i; + return exact_().get_subject()[0]; } # endif // ! MLN_INCLUDE_ONLY } // end of namespace mln::internal - } // end of namespace mln Index: mln/linear/all.hh --- mln/linear/all.hh (revision 3595) +++ mln/linear/all.hh (working copy) @@ -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 @@ -50,8 +50,7 @@ { /// Namespace of local linear routines implementation details. - namespace impl - {} + namespace impl {} } } @@ -62,7 +61,11 @@ # include <mln/linear/convolve.hh> # include <mln/linear/convolve_2x1d.hh> # include <mln/linear/convolve_directional.hh> + # include <mln/linear/gaussian.hh> +# include <mln/linear/gaussian_directional_2d.hh> +# include <mln/linear/gaussian_1d.hh> + # include <mln/linear/lap.hh> # include <mln/linear/log.hh> //# include <mln/linear/sobel.hh> Index: mln/linear/gaussian_directional_2d.hh --- mln/linear/gaussian_directional_2d.hh (revision 3588) +++ mln/linear/gaussian_directional_2d.hh (working copy) @@ -1,3 +1,38 @@ +// Copyright (C) 2009 EPITA Research and 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, Inc., 51 Franklin Street, Fifth Floor, +// Boston, MA 02110-1301, 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 MLN_LINEAR_GAUSSIAN_DIRECTIONAL_2D_HH +# define MLN_LINEAR_GAUSSIAN_DIRECTIONAL_2D_HH + +/// \file mln/linear/gaussian_directional_2d.hh +/// +/// Directional Gaussian filter for 2D images. +/// +/// \todo This is experimental code to be merged with regular code... #include <mln/core/image/image2d.hh> #include <mln/extension/adjust_fill.hh> @@ -11,6 +46,17 @@ namespace linear { + + template <typename I> + mln_concrete(I) + gaussian_directional_2d(const Image<I>& input, + unsigned dir, double sigma, + const mln_value(I)& bdr); + + + +# ifndef MLN_INCLUDE_ONLY + namespace my { @@ -20,14 +66,14 @@ DericheGaussianFirstDerivative, DericheGaussianSecondDerivative }; - std::vector<MLN_FLOAT> n, d, nm, dm; - MLN_FLOAT sumA, sumC; + std::vector<double> n, d, nm, dm; + double sumA, sumC; - recursivefilter_coef_(MLN_FLOAT a0, MLN_FLOAT a1, - MLN_FLOAT b0, MLN_FLOAT b1, - MLN_FLOAT c0, MLN_FLOAT c1, - MLN_FLOAT w0, MLN_FLOAT w1, - MLN_FLOAT s, FilterType filter_type) + recursivefilter_coef_(double a0, double a1, + double b0, double b1, + double c0, double c1, + double w0, double w1, + double s, FilterType filter_type) { n.reserve(5); d.reserve(5); @@ -39,10 +85,10 @@ w0 /= s; w1 /= s; - MLN_FLOAT sin0 = sin(w0); - MLN_FLOAT sin1 = sin(w1); - MLN_FLOAT cos0 = cos(w0); - MLN_FLOAT cos1 = cos(w1); + double sin0 = sin(w0); + double sin1 = sin(w1); + double cos0 = cos(w0); + double cos1 = cos(w1); switch (filter_type) { @@ -81,7 +127,7 @@ case DericheGaussianSecondDerivative : { - MLN_FLOAT aux; + double aux; aux = 12.0 * cos0 * exp( 3.0 * b0 ) - 3.0 * exp( 2.0 * b0 ) + 8.0 * cos0 * cos0 * cos0 * exp( 3.0 * b0 ) - 12.0 * cos0 * cos0 * @@ -197,15 +243,15 @@ template <typename I, typename C> inline void - recursivefilter_directional_2d_generic(I& ima, + recursivefilter_directional_generic(I& ima, const C& c, const mln_psite(I)& start, const mln_psite(I)& finish, int len, const mln_deduce(I, psite, delta)& d) { - std::vector<MLN_FLOAT> tmp1(len); - std::vector<MLN_FLOAT> tmp2(len); + std::vector<double> tmp1(len); + std::vector<double> tmp2(len); tmp1[0] = c.n[0]*ima(start); @@ -292,7 +338,7 @@ template <typename I, typename C> inline void - recursivefilter_directional_2d_fastest(I& ima, + recursivefilter_directional_fastest(I& ima, const C& c, const mln_psite(I)& start, const mln_psite(I)& finish, @@ -303,8 +349,8 @@ // extension::adjust_fill(ima, 5 * int(151 + .50001) + 1, bdr); // extension::fill(ima, bdr); - std::vector<MLN_FLOAT> tmp1(len); - std::vector<MLN_FLOAT> tmp2(len); + std::vector<double> tmp1(len); + std::vector<double> tmp2(len); unsigned delta_offset = ima.delta_index(d); unsigned @@ -418,9 +464,14 @@ inline mln_concrete(I) gaussian_directional_2d(const Image<I>& input_, - unsigned dir, MLN_FLOAT sigma, + unsigned dir, double sigma, const mln_value(I)& bdr) { + trace::entering("linear::gaussian_directional_2d"); + + typedef mln_site(I) P; + mlc_bool(P::dim == 2)::check(); + const I& input = exact(input_); mln_precondition(dir == 0 || dir == 1); @@ -447,7 +498,7 @@ if (dir == 0) { for (int j = 0; j < ncols; ++j) - recursivefilter_directional_2d_fastest(output, coef, + recursivefilter_directional_fastest(output, coef, point2d(- b, j), point2d(nrows - 1 + b, j), nrows + 2 * b, @@ -458,7 +509,7 @@ if (dir == 1) { for (int i = 0; i < nrows; ++i) - recursivefilter_directional_2d_fastest(output, coef, + recursivefilter_directional_fastest(output, coef, point2d(i, - b), point2d(i, ncols - 1 + b), ncols + 2 * b, @@ -466,10 +517,15 @@ bdr); } + trace::exiting("linear::gaussian_directional_2d"); return output; } +# endif // ! MLN_INCLUDE_ONLY } // end of namespace mln::linear } // end of namespace mln + + +#endif // ! MLN_LINEAR_GAUSSIAN_DIRECTIONAL_2D_HH Property changes on: mln/linear/gaussian_directional_2d.hh ___________________________________________________________________ Added: svn:mergeinfo Index: mln/linear/gaussian_1d.hh --- mln/linear/gaussian_1d.hh (revision 0) +++ mln/linear/gaussian_1d.hh (revision 0) @@ -0,0 +1,109 @@ +// Copyright (C) 2009 EPITA Research and 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, Inc., 51 Franklin Street, Fifth Floor, +// Boston, MA 02110-1301, 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 MLN_LINEAR_GAUSSIAN_1D_HH +# define MLN_LINEAR_GAUSSIAN_1D_HH + +/// \file mln/linear/gaussian_1d.hh +/// +/// Gaussian filter for fastest 1D images. +/// +/// \todo This is experimental code to be merged with regular code... + +#include <mln/core/image/image1d.hh> +#include <mln/linear/gaussian_directional_2d.hh> + + + +namespace mln +{ + + namespace linear + { + + + template <typename I> + mln_concrete(I) + gaussian_1d(const Image<I>& input, + double sigma, + const mln_value(I)& bdr); + + + +# ifndef MLN_INCLUDE_ONLY + + template <typename I> + inline + mln_concrete(I) + gaussian_1d(const Image<I>& input_, + double sigma, + const mln_value(I)& bdr) + { + trace::entering("linear::gaussian_1d"); + + typedef mln_site(I) P; + mlc_bool(P::dim == 1)::check(); + + const I& input = exact(input_); + mln_precondition(input.is_valid()); + + my::recursivefilter_coef_ coef(1.68f, 3.735f, + 1.783f, 1.723f, + -0.6803f, -0.2598f, + 0.6318f, 1.997f, + sigma, + my::recursivefilter_coef_::DericheGaussian); + + extension::adjust_fill(input, 5 * int(sigma + .50001) + 1, bdr); + mln_concrete(I) output = duplicate(input); + + if (sigma < 0.006) + return output; + + int + ninds = geom::ninds(input), + b = input.border(); + + recursivefilter_directional_fastest(output, coef, + point1d(- b), + point1d(ninds - 1 + b), + ninds + 2 * b, + dpoint1d(1), + bdr); + + trace::exiting("linear::gaussian_1d"); + return output; + } + +# endif // ! MLN_INCLUDE_ONLY + + } // end of namespace mln::linear + +} // end of namespace mln + + +#endif // ! MLN_LINEAR_GAUSSIAN_1D_HH Index: mln/accu/center.hh --- mln/accu/center.hh (revision 3595) +++ mln/accu/center.hh (working copy) @@ -1,4 +1,5 @@ -// Copyright (C) 2008, 2009 EPITA Research and Development Laboratory (LRDE) +// Copyright (C) 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 @@ -31,7 +32,8 @@ /// \file mln/accu/center.hh /// /// Define an accumulator that computes the mass center of a site set. - +/// +/// \todo Fix to_result() value when invalid... # include <mln/accu/internal/base.hh> # include <mln/accu/bbox.hh> @@ -66,7 +68,6 @@ /// Get the value of the accumulator. V to_result() const; - operator V() const; operator P() const; /// Check whether this accu is able to return a result. @@ -136,19 +137,14 @@ V center<P,V>::to_result() const { - mln_precondition(is_valid()); + // mln_precondition(is_valid()); + if (! is_valid()) + return V(); return center_ / nsites_; } template <typename P, typename V> inline - center<P,V>::operator V() const - { - return to_result(); - } - - template <typename P, typename V> - inline center<P,V>::operator P() const { return P(to_result()); Index: mln/value/label.hh --- mln/value/label.hh (revision 3595) +++ mln/value/label.hh (working copy) @@ -155,6 +155,9 @@ /// Return the next value. label<n> next() const; + /// Return the previous value. + label<n> prev() const; + }; @@ -279,6 +282,14 @@ template <unsigned n> inline + label<n> + label<n>::prev() const + { + return label<n>(this->v_ - 1); + } + + template <unsigned n> + inline std::ostream& operator<<(std::ostream& ostr, const label<n>& i) { return ostr << debug::format(i.to_equiv()); Index: mln/canvas/morpho/attribute_filter.hh --- mln/canvas/morpho/attribute_filter.hh (revision 3595) +++ mln/canvas/morpho/attribute_filter.hh (working copy) @@ -1,5 +1,5 @@ -// Copyright (C) 2007, 2008, 2009 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 @@ -39,14 +39,15 @@ # include <mln/core/concept/accumulator.hh> # include <mln/level/sort_offsets.hh> - # include <mln/trait/accumulators.hh> - # include <mln/util/pix.hh> +# include <mln/border/get.hh> # include <mln/data/fill.hh> +# include <mln/extension/adjust_fill.hh> # include <mln/level/sort_psites.hh> + namespace mln { @@ -56,16 +57,20 @@ namespace morpho { - // Facade Fwd Declaration + // FIXME: Doc! + template <typename I, typename N, typename A> mln_concrete(I) attribute_filter(const Image<I>& input, const Neighborhood<N>& nbh, - const Accumulator<A>& a, const typename A::result& lambda, + const Accumulator<A>& a, const mln_result(A)& lambda, bool increasing); + + # ifndef MLN_INCLUDE_ONLY - namespace impl { + namespace impl + { template <typename A, typename I> void take_as_init_fastest (trait::accumulator::when_pix::use_none, A& accu, @@ -128,8 +133,9 @@ } - namespace generic { + namespace generic + { //////////////////////// /// Generic version. /// @@ -153,7 +159,7 @@ const Neighborhood<N>& nbh_, const Site_Set<S>& s_, const Accumulator<A>& a_, - const typename A::result& lambda) + const mln_result(A)& lambda) { trace::entering("canvas::morpho::impl::generic::attribute_filter"); // FIXME: Test?! @@ -278,7 +284,7 @@ const Neighborhood<N>& nbh_, const util::array<unsigned>& s, const Accumulator<A>& a_, - const typename A::result& lambda) + const mln_result(A)& lambda) { trace::entering("canvas::morpho::impl::attribute_filter_fastest"); // FIXME: Tests? @@ -287,6 +293,10 @@ const N& nbh = exact(nbh_); (void)a_; + // The border adaptation is performed in the calling scope since + // we want offsets of 's' to match the image structure / dimensions. + mln_precondition(border::get(input) >= nbh.delta()); + mln_concrete(I) output; initialize(output, input); @@ -303,6 +313,8 @@ { initialize(deja_vu, input); data::fill(deja_vu, false); + extension::fill(deja_vu, true); // So the border is neutral. + initialize(activity, input); data::fill(activity, true); initialize(parent, input); @@ -387,7 +399,7 @@ const Image<I>& input, const Neighborhood<N>& nbh, const Accumulator<A>& a, - const typename A::result& lambda, + const mln_result(A)& lambda, bool increasing) { p_array<mln_psite(I)> s = increasing ? @@ -405,9 +417,11 @@ const Image<I>& input, const Neighborhood<N>& nbh, const Accumulator<A>& a, - const typename A::result& lambda, + const mln_result(A)& lambda, bool increasing) { + extension::adjust(input, nbh); + util::array<unsigned> s = increasing ? level::sort_offsets_increasing(input) : @@ -424,7 +438,7 @@ attribute_filter_dispatch(const Image<I>& input, const Neighborhood<N>& nbh, const Accumulator<A>& a, - const typename A::result& lambda, + const mln_result(A)& lambda, bool increasing) { enum { @@ -451,7 +465,7 @@ attribute_filter(const Image<I>& input, const Neighborhood<N>& nbh, const Accumulator<A>& a, - const typename A::result& lambda, + const mln_result(A)& lambda, bool increasing) { return internal::attribute_filter_dispatch(input, nbh, a, lambda, increasing); Index: mln/labeling/compute.hh --- mln/labeling/compute.hh (revision 3595) +++ mln/labeling/compute.hh (working copy) @@ -1,4 +1,5 @@ -// Copyright (C) 2008 EPITA Research and Development Laboratory (LRDE) +// Copyright (C) 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 @@ -39,7 +40,7 @@ # include <mln/core/concept/accumulator.hh> # include <mln/core/concept/meta_accumulator.hh> # include <mln/util/array.hh> -# include <mln/convert/to.hh> +# include <mln/convert/from_to.hh> namespace mln @@ -180,8 +181,11 @@ for_all(p) accus[label(p)].take(p); + util::array<mln_result(A)> res; + convert::from_to(accus, res); + trace::exiting("labeling::impl::generic::compute"); - return convert::to< util::array<mln_result(A)> >(accus); + return res; } @@ -206,8 +210,11 @@ for_all(p) accus[label(p)].take(input(p)); + util::array<mln_result(A)> res; + convert::from_to(accus, res); + trace::exiting("labeling::impl::generic::compute"); - return convert::to< util::array<mln_result(A)> >(accus); + return res; } } // end of namespace mln::labeling::impl::generic Index: tests/morpho/closing/volume.cc --- tests/morpho/closing/volume.cc (revision 3595) +++ tests/morpho/closing/volume.cc (working copy) @@ -40,6 +40,8 @@ #include <mln/morpho/closing/volume.hh> #include <mln/morpho/attribute/volume.hh> +#include <mln/border/resize.hh> + #include "tests/data.hh" @@ -51,6 +53,9 @@ typedef image2d<int_u8> I; I lena; io::pgm::load(lena, MLN_IMG_DIR "/tiny.pgm"); + + border::resize(lena, 0); + io::pgm::save(morpho::closing::volume(lena, c4(), 10000), "ref.pgm");

1 0

3595: Add into scribo a simple binarization.
by Thierry Geraud 30 Mar '09

30 Mar '09

https://svn.lrde.epita.fr/svn/oln/trunk/milena/sandbox Index: ChangeLog from Thierry Geraud <thierry.geraud(a)lrde.epita.fr> Add into scribo a simple binarization. * scribo/binarization: New directory. * scribo/binarization/simple.hh: New. * scribo/src/binarization: New directory. * scribo/src/Makefile.am: Update. * scribo/src/binarization/Makefile.am: New. * scribo/src/binarization/simple.cc: New. binarization/simple.hh | 178 +++++++++++++++++++++++++++++++++++++++++++ src/Makefile.am | 3 src/binarization/Makefile.am | 9 ++ src/binarization/simple.cc | 36 ++++++++ 4 files changed, 226 insertions(+) Index: scribo/src/binarization/Makefile.am --- scribo/src/binarization/Makefile.am (revision 0) +++ scribo/src/binarization/Makefile.am (revision 0) @@ -0,0 +1,9 @@ +## Process this file through Automake to create Makefile.in -*- Makefile -*- + +include $(top_srcdir)/milena/sandbox/scribo/scribo.mk + +bin_PROGRAMS = \ + simple + +simple_SOURCES = simple.cc + Index: scribo/src/binarization/simple.cc --- scribo/src/binarization/simple.cc (revision 0) +++ scribo/src/binarization/simple.cc (revision 0) @@ -0,0 +1,36 @@ +#include <scribo/binarization/simple.hh> + +#include <mln/io/pgm/load.hh> +#include <mln/io/pbm/save.hh> + + + +void usage(char* argv[]) +{ + std::cerr << "usage: " << argv[0] << " input.pgm output.pbm" << std::endl + << " Simple binarization in SCRIBO." << std::endl; + std::abort(); +} + + + +int main(int argc, char *argv[]) +{ + using namespace mln; + using value::int_u8; + + if (argc != 3) + usage(argv); + + trace::entering("main"); + + image2d<int_u8> input; + io::pgm::load(input, argv[1]); + + + io::pbm::save(scribo::binarization::simple(input), + argv[2]); + + + trace::exiting("main"); +} Index: scribo/src/Makefile.am --- scribo/src/Makefile.am (revision 3594) +++ scribo/src/Makefile.am (working copy) @@ -2,6 +2,9 @@ include $(top_srcdir)/milena/sandbox/scribo/scribo.mk +SUBDIRS = \ + binarization + bin_PROGRAMS = \ dmap \ extract_text_single_link \ Index: scribo/binarization/simple.hh --- scribo/binarization/simple.hh (revision 0) +++ scribo/binarization/simple.hh (revision 0) @@ -0,0 +1,178 @@ +// Copyright (C) 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 SCRIBO_BINARIZATION_SIMPLE_HH +# define SCRIBO_BINARIZATION_SIMPLE_HH + +/// \file scribo/binarization/simple.hh +/// +/// Simple binarization of a gray-level document. + +# include <mln/core/image/image1d.hh> +# include <mln/core/alias/neighb1d.hh> + +# include <mln/core/image/image2d.hh> +# include <mln/core/alias/neighb2d.hh> + +# include <mln/core/routine/duplicate.hh> +# include <mln/core/image/image_if.hh> +# include <mln/pw/all.hh> + +# include <mln/histo/compute.hh> +# include <mln/debug/histo.hh> +# include <mln/convert/from_to.hh> + +# include <mln/morpho/elementary/gradient_external.hh> +# include <mln/morpho/closing/height.hh> +# include <mln/morpho/closing/volume.hh> +# include <mln/morpho/watershed/flooding.hh> + +# include <mln/linear/gaussian_1d.hh> +# include <mln/labeling/regional_minima.hh> +# include <mln/labeling/compute.hh> +# include <mln/value/label_8.hh> +# include <mln/accu/center.hh> + + + +namespace scribo +{ + + namespace binarization + { + + using namespace mln; + + /// Simple binarization of a gray-level document. + /*! + * + * \param[in] input_ A binary image. + * \param[in] nbh_ The neighborhood used for labeling image components. + * \param[out] nlines The number of lines found. + * \param[in] vwin Window used to extract the vertical lines in a morphological + * opening + * \param[in] hwin Window used to extract the horizontal lines in a morphological + * opening + * + * \return pair of array of bounding boxes. The first array holds the + * vertical lines bounding boxes and the second one the + * horizontal lines bounding boxes. + */ + template <typename I> + mln_ch_value(I, bool) + simple(const Image<I>& input); + + + +# ifndef MLN_INCLUDE_ONLY + + template <typename I> + inline + mln_ch_value(I, bool) + simple(const Image<I>& input_) + { + trace::entering("scribo::binarization::simple"); + + const I& input = exact(input_); + mln_precondition(input.is_valid()); + + const float sigma = 5; // FIXME: hard-coded! + + typedef mln_value(I) V; + histo::array<V> h; + + { + mln_concrete(I) g; + g = morpho::elementary::gradient_external(input, c4()); + g = morpho::closing::height(g, c4(), 5); // FIXME: hard-coded! + + unsigned nbasins; + mln_ch_value(I, unsigned) w = morpho::watershed::flooding(g, c4(), nbasins); + h = histo::compute(input | (pw::value(w) == pw::cst(0))); + } + + + util::array<point1d> c; + value::label_8 n; + + { + image1d<unsigned> h_, hs_; + image1d<value::label_8> l; + + convert::from_to(h, h_); + hs_ = linear::gaussian_1d(h_, sigma, 0); + l = labeling::regional_minima(hs_, c2(), n); + + if (n < 3) + { + std::cerr << "This method has not worked properly!" << std::endl; + + debug::histo(h, "tmp_h.txt"); + + std::ofstream file("tmp_hs.txt"); + mln_piter(box1d) p(h_.domain()); + for_all(p) + file << p.ind() << ' ' << hs_(p) << std::endl; + file.close(); + + std::abort(); + } + + accu::center<point1d, point1d> a; + c = labeling::compute(a, l, n); + c[0] = point1d(0); // Force a neutral value for the non-label value (0). + } + + int threshold; + + { + std::vector<int> v; + for (unsigned i = 0; i <= n; ++i) + v.push_back(c[i].ind()); + std::sort(v.begin(), v.end()); + threshold = v[n.prev()]; + + // std::cout << "threshold = " << threshold << std::endl; + } + + mln_ch_value(I, bool) output; + output = duplicate((pw::value(input) > pw::cst(threshold)) | input.domain()); + + trace::exiting("scribo::binarization::simple"); + return output; + } + +# endif // !MLN_INCLUDE_ONLY + + } // end of namespace scribo::binarization + +} // end of namespace scribo + + +#endif // ! SCRIBO_BINARIZATION_SIMPLE_HH

1 0

r3594: Add time smoothing in IGR and drafts of space smoothing
by Fabien Freling 30 Mar '09

30 Mar '09

URL: https://svn.lrde.epita.fr/svn/oln/trunk/milena/sandbox ChangeLog: 2009-03-30 Fabien Freling <fabien.freling(a)lrde.epita.fr> Add time smoothing in IGR and drafts of space smoothing. * fabien/igr/Makefile.rules: New file to centralize rules. * fabien/igr/img/slice_7.pgm: Remove. * fabien/igr/img: Remove. * fabien/igr/space_smooth/Makefile: New. * fabien/igr/space_smooth/linear.cc: Implements linear space smoothing. * fabien/igr/space_smooth/median.cc: Draft. * fabien/igr/space_smooth/morpho.cc: Draft. * fabien/igr/time_smooth/Makefile: New. * fabien/igr/time_smooth/linear.cc: Implements linear time smoothing. * fabien/igr/time_smooth/median.cc: Implements median time smoothing. * fabien/igr/time_smooth/morpho.cc: Implements morpho time smoothing. --- Makefile.rules | 9 ++++ space_smooth/Makefile | 15 +++++++ space_smooth/linear.cc | 75 ++++++++++++++++++++++++++++++++++++ space_smooth/median.cc | 102 +++++++++++++++++++++++++++++++++++++++++++++++++ space_smooth/morpho.cc | 102 +++++++++++++++++++++++++++++++++++++++++++++++++ time_smooth/Makefile | 15 +++++++ time_smooth/linear.cc | 77 ++++++++++++++++++++++++++++++++++++ time_smooth/median.cc | 102 +++++++++++++++++++++++++++++++++++++++++++++++++ time_smooth/morpho.cc | 102 +++++++++++++++++++++++++++++++++++++++++++++++++ 9 files changed, 599 insertions(+) Index: trunk/milena/sandbox/fabien/igr/space_smooth/median.cc =================================================================== --- trunk/milena/sandbox/fabien/igr/space_smooth/median.cc (revision 0) +++ trunk/milena/sandbox/fabien/igr/space_smooth/median.cc (revision 3594) @@ -0,0 +1,102 @@ +#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_u12.hh> + +#include <mln/io/dicom/load.hh> +#include <mln/io/plot/save.hh> + +#include <mln/accu/median_h.hh> +#include <mln/util/array.hh> + + +using namespace mln; +using value::int_u12; + + +int main(int argc, char* argv[]) +{ + if (argc != 2) + { + std::cout << "Usage: " << argv[0] << "input" << std::endl; + return 1; + } + + /////////////////// + // // + // 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) + { + 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)); + } + } + + //////////// + // // + // Median // + // // + //////////// + image2d<util::array<int_u12> > ima_median3; + image2d<util::array<int_u12> > ima_median5; + initialize(ima_median3, ima_arr); + initialize(ima_median5, ima_arr); + mln_piter_(image2d<int_u12>) p(ima_median3.domain()); + accu::median_h<int_u12> accu_med; + for_all(p) + { + // Median 3 + ima_median3(p).append(ima_arr(p)[0]); + for (unsigned i = 1; i < ima_arr(p).nelements() - 1; ++i) + { + accu_med.init(); + accu_med.take(ima_arr(p)[i - 1]); + accu_med.take(ima_arr(p)[i]); + accu_med.take(ima_arr(p)[i + 1]); + ima_median3(p).append(accu_med.to_result()); + } + ima_median3(p).append(ima_arr(p)[ima_arr(p).nelements() - 1]); + + // Median 5 + ima_median5(p).append(ima_arr(p)[0]); + ima_median5(p).append(ima_arr(p)[1]); + for (unsigned i = 2; i < ima_arr(p).nelements() - 2; ++i) + { + accu_med.init(); + accu_med.take(ima_arr(p)[i - 2]); + accu_med.take(ima_arr(p)[i - 1]); + accu_med.take(ima_arr(p)[i]); + accu_med.take(ima_arr(p)[i + 1]); + accu_med.take(ima_arr(p)[i + 2]); + ima_median5(p).append(accu_med.to_result()); + } + ima_median5(p).append(ima_arr(p)[ima_arr(p).nelements() - 2]); + ima_median5(p).append(ima_arr(p)[ima_arr(p).nelements() - 1]); + } + + ///////////// + // // + // Outputs // + // // + ///////////// + io::plot::save(ima_median3(point2d(160, 120)), "median3_tumeur.plot"); + io::plot::save(ima_median3(point2d(34, 94)), "median3_air.plot"); + io::plot::save(ima_median3(point2d(122, 115)), "median3_poumon.plot"); + io::plot::save(ima_median5(point2d(160, 120)), "median5_tumeur.plot"); + io::plot::save(ima_median5(point2d(34, 94)), "median5_air.plot"); + io::plot::save(ima_median5(point2d(122, 115)), "median5_poumon.plot"); + + return 0; +} Index: trunk/milena/sandbox/fabien/igr/space_smooth/morpho.cc =================================================================== --- trunk/milena/sandbox/fabien/igr/space_smooth/morpho.cc (revision 0) +++ trunk/milena/sandbox/fabien/igr/space_smooth/morpho.cc (revision 3594) @@ -0,0 +1,102 @@ +#include <mln/core/image/image1d.hh> +#include <mln/core/alias/neighb1d.hh> +#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_u12.hh> + +#include <mln/io/dicom/load.hh> +#include <mln/io/plot/save.hh> + +#include <mln/accu/median_h.hh> +#include <mln/convert/from_to.hh> +#include <mln/morpho/closing/area.hh> +#include <mln/morpho/opening/area.hh> +#include <mln/util/array.hh> + +/*#include <mln/draw/line.hh> +#include <mln/io/magick/save.hh> +#include <mln/level/convert.hh> +#include <mln/level/stretch.hh> +#include <mln/value/int_u8.hh> +#include <mln/value/rgb8.hh> +#include <mln/literal/all.hh> +using mln::value::rgb8; +using mln::value::int_u8;*/ + + +using namespace mln; +using value::int_u12; + + +int main(int argc, char* argv[]) +{ + if (argc != 2) + { + std::cout << "Usage: " << argv[0] << "input" << std::endl; + return 1; + } + + /////////////////// + // // + // 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) + { + 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)); + } + } + + //////////// + // // + // Morpho // + // // + //////////// + image2d<image1d<int_u12> > ima_morpho; + initialize(ima_morpho, ima_arr); + mln_piter_(image2d<int_u12>) p(ima_morpho.domain()); + accu::median_h<int_u12> accu_med; + for_all(p) + { + image1d<int_u12> tmp_ima; + convert::from_to(ima_arr(p), tmp_ima); + tmp_ima = morpho::closing::area(tmp_ima, c2(), 3); + tmp_ima = morpho::opening::area(tmp_ima, c2(), 3); + ima_morpho(p) = tmp_ima; + } + + ///////////// + // // + // Outputs // + // // + ///////////// + /*image2d<rgb8> ima_color = level::convert(rgb8(), level::stretch(int_u8(), slice(input, 0))); + algebra::vec<2, unsigned int> vmin; + algebra::vec<2, unsigned int> vmax; + vmin[0] = 160; + vmin[1] = 120; + vmax[0] = 122; + vmax[1] = 115; + mln_site_(image2d<bool>) pbeg(vmin); + mln_site_(image2d<bool>) pend(vmax); + draw::line(ima_color, pbeg, pend, literal::red); + io::magick::save(ima_color, "test.png");*/ + + io::plot::save(ima_morpho(point2d(160, 120)), "morpho_tumeur.plot"); + io::plot::save(ima_morpho(point2d(34, 94)), "morpho_air.plot"); + io::plot::save(ima_morpho(point2d(122, 115)), "morpho_poumon.plot"); + + return 0; +} Index: trunk/milena/sandbox/fabien/igr/space_smooth/Makefile =================================================================== --- trunk/milena/sandbox/fabien/igr/space_smooth/Makefile (revision 0) +++ trunk/milena/sandbox/fabien/igr/space_smooth/Makefile (revision 3594) @@ -0,0 +1,15 @@ +include ../Makefile.rules + + +linear: linear.cc + ${CXX} -I../../../../ ${DICOM} ${CXXFLAGS} $^ -o linear + +median: median.cc + ${CXX} -I../../../../ ${DICOM} ${CXXFLAGS} $^ -o median + +morpho: morpho.cc + ${CXX} -I../../../../ ${DICOM} ${MAGICK} ${CXXFLAGS} $^ -o morpho + +clean: + rm -rf *.dump *.p?m *.plot *.log *.csv *.dSYM + rm linear median morpho Index: trunk/milena/sandbox/fabien/igr/space_smooth/linear.cc =================================================================== --- trunk/milena/sandbox/fabien/igr/space_smooth/linear.cc (revision 0) +++ trunk/milena/sandbox/fabien/igr/space_smooth/linear.cc (revision 3594) @@ -0,0 +1,75 @@ +#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_u12.hh> + +#include <mln/io/dicom/load.hh> +#include <mln/io/plot/save.hh> + +#include <mln/accu/median_h.hh> +#include <mln/linear/convolve.hh> +#include <mln/make/w_window2d.hh> +#include <mln/util/array.hh> + + +using namespace mln; +using value::int_u12; + + + +int main(int argc, char* argv[]) +{ + if (argc != 2) + { + std::cout << "Usage: " << argv[0] << "input" << std::endl; + return 1; + } + + /////////////////// + // // + // 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) + { + image2d<int_u12> tmp_slice = duplicate(slice(input, i)); + arr_ima.append(tmp_slice); + } + + //////////////////////// + // // + // Linear convolution // + // // + //////////////////////// + float ws[] = { 0, 1/8, 0, + 1/8, 1/2, 1/8, + 0, 1/8, 0 }; + + util::array<image2d<float> > ima_linear; + for (unsigned i = 1; i < arr_ima.nelements(); ++i) + ima_linear.append(linear::convolve(arr_ima[i], make::w_window2d(ws))); + + ///////////// + // // + // Outputs // + // // + ///////////// + image2d<util::array<float> > ima_result(input.nrows(), input.ncols()); + mln_piter_(image2d<util::array<float> >) p(ima_linear[0].domain()); + for_all(p) + for (int i = 0; i < ima_linear.nelements(); ++i) + ima_result(p).append(ima_linear[i](p)); + + io::plot::save(ima_result(point2d(160, 120)), "linear_tumeur.plot"); + io::plot::save(ima_result(point2d(34, 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/median.cc =================================================================== --- trunk/milena/sandbox/fabien/igr/time_smooth/median.cc (revision 0) +++ trunk/milena/sandbox/fabien/igr/time_smooth/median.cc (revision 3594) @@ -0,0 +1,102 @@ +#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_u12.hh> + +#include <mln/io/dicom/load.hh> +#include <mln/io/plot/save.hh> + +#include <mln/accu/median_h.hh> +#include <mln/util/array.hh> + + +using namespace mln; +using value::int_u12; + + +int main(int argc, char* argv[]) +{ + if (argc != 2) + { + std::cout << "Usage: " << argv[0] << "input" << std::endl; + return 1; + } + + /////////////////// + // // + // 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) + { + 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)); + } + } + + //////////// + // // + // Median // + // // + //////////// + image2d<util::array<int_u12> > ima_median3; + image2d<util::array<int_u12> > ima_median5; + initialize(ima_median3, ima_arr); + initialize(ima_median5, ima_arr); + mln_piter_(image2d<int_u12>) p(ima_median3.domain()); + accu::median_h<int_u12> accu_med; + for_all(p) + { + // Median 3 + ima_median3(p).append(ima_arr(p)[0]); + for (unsigned i = 1; i < ima_arr(p).nelements() - 1; ++i) + { + accu_med.init(); + accu_med.take(ima_arr(p)[i - 1]); + accu_med.take(ima_arr(p)[i]); + accu_med.take(ima_arr(p)[i + 1]); + ima_median3(p).append(accu_med.to_result()); + } + ima_median3(p).append(ima_arr(p)[ima_arr(p).nelements() - 1]); + + // Median 5 + ima_median5(p).append(ima_arr(p)[0]); + ima_median5(p).append(ima_arr(p)[1]); + for (unsigned i = 2; i < ima_arr(p).nelements() - 2; ++i) + { + accu_med.init(); + accu_med.take(ima_arr(p)[i - 2]); + accu_med.take(ima_arr(p)[i - 1]); + accu_med.take(ima_arr(p)[i]); + accu_med.take(ima_arr(p)[i + 1]); + accu_med.take(ima_arr(p)[i + 2]); + ima_median5(p).append(accu_med.to_result()); + } + ima_median5(p).append(ima_arr(p)[ima_arr(p).nelements() - 2]); + ima_median5(p).append(ima_arr(p)[ima_arr(p).nelements() - 1]); + } + + ///////////// + // // + // Outputs // + // // + ///////////// + io::plot::save(ima_median3(point2d(160, 120)), "median3_tumeur.plot"); + io::plot::save(ima_median3(point2d(34, 94)), "median3_air.plot"); + io::plot::save(ima_median3(point2d(122, 115)), "median3_poumon.plot"); + io::plot::save(ima_median5(point2d(160, 120)), "median5_tumeur.plot"); + io::plot::save(ima_median5(point2d(34, 94)), "median5_air.plot"); + io::plot::save(ima_median5(point2d(122, 115)), "median5_poumon.plot"); + + return 0; +} Index: trunk/milena/sandbox/fabien/igr/time_smooth/morpho.cc =================================================================== --- trunk/milena/sandbox/fabien/igr/time_smooth/morpho.cc (revision 0) +++ trunk/milena/sandbox/fabien/igr/time_smooth/morpho.cc (revision 3594) @@ -0,0 +1,102 @@ +#include <mln/core/image/image1d.hh> +#include <mln/core/alias/neighb1d.hh> +#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_u12.hh> + +#include <mln/io/dicom/load.hh> +#include <mln/io/plot/save.hh> + +#include <mln/accu/median_h.hh> +#include <mln/convert/from_to.hh> +#include <mln/morpho/closing/area.hh> +#include <mln/morpho/opening/area.hh> +#include <mln/util/array.hh> + +/*#include <mln/draw/line.hh> +#include <mln/io/magick/save.hh> +#include <mln/level/convert.hh> +#include <mln/level/stretch.hh> +#include <mln/value/int_u8.hh> +#include <mln/value/rgb8.hh> +#include <mln/literal/all.hh> +using mln::value::rgb8; +using mln::value::int_u8;*/ + + +using namespace mln; +using value::int_u12; + + +int main(int argc, char* argv[]) +{ + if (argc != 2) + { + std::cout << "Usage: " << argv[0] << "input" << std::endl; + return 1; + } + + /////////////////// + // // + // 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) + { + 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)); + } + } + + //////////// + // // + // Morpho // + // // + //////////// + image2d<image1d<int_u12> > ima_morpho; + initialize(ima_morpho, ima_arr); + mln_piter_(image2d<int_u12>) p(ima_morpho.domain()); + accu::median_h<int_u12> accu_med; + for_all(p) + { + image1d<int_u12> tmp_ima; + convert::from_to(ima_arr(p), tmp_ima); + tmp_ima = morpho::closing::area(tmp_ima, c2(), 3); + tmp_ima = morpho::opening::area(tmp_ima, c2(), 3); + ima_morpho(p) = tmp_ima; + } + + ///////////// + // // + // Outputs // + // // + ///////////// + /*image2d<rgb8> ima_color = level::convert(rgb8(), level::stretch(int_u8(), slice(input, 0))); + algebra::vec<2, unsigned int> vmin; + algebra::vec<2, unsigned int> vmax; + vmin[0] = 160; + vmin[1] = 120; + vmax[0] = 122; + vmax[1] = 115; + mln_site_(image2d<bool>) pbeg(vmin); + mln_site_(image2d<bool>) pend(vmax); + draw::line(ima_color, pbeg, pend, literal::red); + io::magick::save(ima_color, "test.png");*/ + + io::plot::save(ima_morpho(point2d(160, 120)), "morpho_tumeur.plot"); + io::plot::save(ima_morpho(point2d(34, 94)), "morpho_air.plot"); + io::plot::save(ima_morpho(point2d(122, 115)), "morpho_poumon.plot"); + + return 0; +} Index: trunk/milena/sandbox/fabien/igr/time_smooth/Makefile =================================================================== --- trunk/milena/sandbox/fabien/igr/time_smooth/Makefile (revision 0) +++ trunk/milena/sandbox/fabien/igr/time_smooth/Makefile (revision 3594) @@ -0,0 +1,15 @@ +include ../Makefile.rules + + +linear: linear.cc + ${CXX} -I../../../../ ${DICOM} ${CXXFLAGS} $^ -o linear + +median: median.cc + ${CXX} -I../../../../ ${DICOM} ${CXXFLAGS} $^ -o median + +morpho: morpho.cc + ${CXX} -I../../../../ ${DICOM} ${MAGICK} ${CXXFLAGS} $^ -o morpho + +clean: + rm -rf *.dump *.p?m *.plot *.log *.csv *.dSYM + rm linear median morpho Index: trunk/milena/sandbox/fabien/igr/time_smooth/linear.cc =================================================================== --- trunk/milena/sandbox/fabien/igr/time_smooth/linear.cc (revision 0) +++ trunk/milena/sandbox/fabien/igr/time_smooth/linear.cc (revision 3594) @@ -0,0 +1,77 @@ +#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_u12.hh> + +#include <mln/io/dicom/load.hh> +#include <mln/io/plot/save.hh> + +#include <mln/accu/median_h.hh> +#include <mln/util/array.hh> + + +using namespace mln; +using value::int_u12; + + +int main(int argc, char* argv[]) +{ + if (argc != 2) + { + std::cout << "Usage: " << argv[0] << "input" << std::endl; + return 1; + } + + /////////////////// + // // + // 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) + { + 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)); + } + } + + //////////////////////// + // // + // Linear convolution // + // // + //////////////////////// + image2d<util::array<int_u12> > ima_linear; + initialize(ima_linear, ima_arr); + mln_piter_(image2d<int_u12>) p(ima_linear.domain()); + accu::median<int_u12> accu_med; + for_all(p) + { + ima_linear(p).append(ima_arr(p)[0]); + for (unsigned i = 1; i < ima_arr(p).nelements() - 1; ++i) + ima_linear(p).append(0.25 * ima_arr(p)[i - 1] + 0.5 * ima_arr(p)[i] + 0.25 * ima_arr(p)[i + 1]); + ima_linear(p).append(ima_arr(p)[ima_arr(p).nelements() - 1]); + } + + ///////////// + // // + // Outputs // + // // + ///////////// + io::plot::save(ima_arr(point2d(160, 120)), "ref_tumeur.plot"); + io::plot::save(ima_linear(point2d(160, 120)), "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(122, 115)), "ref_poumon.plot"); + io::plot::save(ima_linear(point2d(122, 115)), "linear_poumon.plot"); + + return 0; +} Index: trunk/milena/sandbox/fabien/igr/Makefile.rules =================================================================== --- trunk/milena/sandbox/fabien/igr/Makefile.rules (revision 0) +++ trunk/milena/sandbox/fabien/igr/Makefile.rules (revision 3594) @@ -0,0 +1,9 @@ +CXX = llvm-g++ +CXXFLAGS = -DNDEBUG -O4 + +DICOM_INC = -I/usr/local/include/gdcm-2.0 +DICOM_LIBS = -lgdcmCommon -lgdcmDICT -lgdcmDSED -lgdcmIOD -lgdcmMSFF -lgdcmexpat -lgdcmjpeg12 -lgdcmjpeg16 -lgdcmjpeg8 -lgdcmopenjpeg -lgdcmuuid -lgdcmzlib \ + -framework CoreFoundation +DICOM = ${DICOM_INC} ${DICOM_LIBS} + +MAGICK = `Magick++-config --cppflags --ldflags --libs`

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3593: Avoid invalid assigments with image concept.
by Guillaume Lazzara 30 Mar '09

30 Mar '09

* mln/core/concept/image.hh: Add an invalid operator= in order to avoid wrong assignment. See sandbox/bug/concept_and_assignment.cc. --- milena/ChangeLog | 7 +++++++ milena/mln/core/concept/image.hh | 19 ++++++++++++++++++- 2 files changed, 25 insertions(+), 1 deletions(-) diff --git a/milena/ChangeLog b/milena/ChangeLog index 3ece40a..8753025 100644 --- a/milena/ChangeLog +++ b/milena/ChangeLog @@ -1,5 +1,12 @@ 2009-03-30 Guillaume Lazzara <lazzara(a)lrde.epita.fr> + Avoid invalid assigments with image concept. + + * mln/core/concept/image.hh: Add an invalid operator= in order to + avoid wrong assignment. See sandbox/bug/concept_and_assignment.cc. + +2009-03-30 Guillaume Lazzara <lazzara(a)lrde.epita.fr> + Add math::sin and math::pi. * mln/math/all.hh: add new includes. diff --git a/milena/mln/core/concept/image.hh b/milena/mln/core/concept/image.hh index e2bc4f8..6b23192 100644 --- a/milena/mln/core/concept/image.hh +++ b/milena/mln/core/concept/image.hh @@ -43,6 +43,7 @@ # include <mln/trait/concrete.hh> // FIXME: Should be in all.hh! # include <mln/trait/images.hh> +# include <mln/metal/abort.hh> # include <mln/metal/is_a.hh> # include <mln/metal/equal.hh> @@ -73,6 +74,9 @@ namespace mln { typedef Image<void> category; + template <typename J> + Image<E>& operator=(const J& rhs); + /* // provided by internal::image_base: @@ -110,7 +114,6 @@ namespace mln }; - namespace convert { @@ -176,6 +179,20 @@ namespace mln } // end of namespace mln::internal + template <typename E> + template <typename J> + inline + Image<E>& + Image<E>::operator=(const J&) + { + /// You are assigning an image of a concrete type to + /// an image with a concept type. It does NOT work. + /// + /// You forgot a call to exact() on the left operand! + mlc_abort(E)::check(); + return *this; + } + template <typename E> inline -- 1.5.6.5

1 0