[Olena-patches] 1818: Add personal folder in sandbox with prototype of najman component tree.

https://svn.lrde.epita.fr/svn/oln/trunk/milena Index: ChangeLog from Alexandre Abraham &lt;abraham(a)lrde.epita.fr&gt; Add personal folder in sandbox with prototype of najman component tree. * sandbox/abraham: New. * sandbox/abraham/morpho: New. * sandbox/abraham/morpho/basic_najman.hh: New, contains Najman component tree. * sandbox/abraham/morpho/test.cc: New. * sandbox/abraham/morpho/images: New. * sandbox/abraham/morpho/images/test_component_tree.pgm: New. * sandbox/abraham/morpho/topo_wst.hh: New, draft of topological watershed. * sandbox/abraham/morpho/Makefile: New. Makefile | 8 + basic_najman.hh | 287 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++ test.cc | 43 ++++++++ topo_wst.hh | 130 +++++++++++++++++++++++++ 4 files changed, 468 insertions(+) Index: sandbox/abraham/morpho/basic_najman.hh --- sandbox/abraham/morpho/basic_najman.hh (revision 0) +++ sandbox/abraham/morpho/basic_najman.hh (revision 0) @@ -0,0 +1,287 @@ +#include <mln/level/sort_psites.hh> +#include <mln/level/fill.hh> +#include <mln/core/image2d.hh> + +namespace mln +{ + + namespace morpho + { + + template <class I, class N> + struct basic_najman + { + + typedef mln_psite(I) psite; + + struct node { + int level; + int area; + int highest; + p_array<mln_psite(I)> children; + + void addChildren(const node& n) + { + typename p_array<mln_psite(I)>::fwd_piter it(n.children); + for (it.start(); + it.is_valid(); + it.next()) + children.append(it.to_psite()); + } + void addChild(const psite n) + { + children.append(n); + } + }; // struct node + + + const Image<I>& ima; + const Neighborhood<N>& nbh; + mln_ch_value(I, psite) par; + + mln_ch_value(I, psite) Par_tree; + // Par_node is handled by par (from ap_maxtree) + mln_ch_value(I, int) Rnk_tree; + mln_ch_value(I, int) Rnk_node; + mln_ch_value(I, psite) lowestNode; + mln_ch_value(I, node) nodes; + mln_ch_value(I, bool) isproc; + psite Root; + p_array<mln_psite(I)> S; + // std::map<psite,psite> M; // to keep the root of any point. + + basic_najman(const Image<I>& i, + const Neighborhood<N>& n) + : ima(i), + nbh(n), + par(exact(i).domain(), exact(i).border()), + Par_tree(exact(i).domain(), exact(i).border()), + Rnk_tree(exact(i).domain(), exact(i).border()), + Rnk_node(exact(i).domain(), exact(i).border()), + lowestNode(exact(i).domain(), exact(i).border()), + nodes(exact(i).domain(), exact(i).border()), + isproc(exact(i).domain(), exact(i).border()) + { + } + + + void MakeSet_tree(psite x) + { + Par_tree(x) = x; + Rnk_tree(x) = 0; + } + + void MakeSet_node(psite x) + { + par(x) = x; // was Par_node(x) = x; + Rnk_node(x) = 0; + } + + psite Find_tree(psite x) + { + if (Par_tree(x) != x) + Par_tree(x) = Find_tree(Par_tree(x)); + return Par_tree(x); + } + + void swap(psite& x, psite& y) + { + psite memo = x; + x = y; + y = memo; + } + + bool is_root(const psite& x) const + { + return par(x) == x; + } + + bool is_level_root(const psite& x) const + { + return is_root(x) || exact(ima)(par(x)) < exact(ima)(x); + } + + psite find_level_root(const psite& x) + { + if (is_level_root(x)) + return x; + else + return par(x) = find_level_root(par(x)); + } + + psite Find_node(psite x) + { + if (par(x) != x) + par(x) = Find_node(par(x)); + return par(x); + } + + void go() + { + init(); + BuildComponentTree(); + } + + + void init() + { + // Sort the points in increasing order + S = level::sort_psites_increasing(ima); + + // Clear the marker map + level::fill(isproc, false); + for (int ip = 0; ip < int(S.npoints()); ++ip) + { + psite p = S[ip]; + MakeSet_node(p); + MakeSet_tree(p); + // if (lowestNode.hold(p)) + lowestNode(p) = p; + // if (nodes.hold(p)) + nodes(p) = MakeNode(exact(ima)(p)); + } + } + + + void BuildComponentTree() + { + for (int ip = 0; ip < int(S.npoints()); ++ip) + { + psite p = S[ip]; + isproc(p) = true; + + psite curTree = Find_tree(p); + psite curNode = Find_node(lowestNode(curTree)); + + mln_niter(N) q(nbh, p); + + for_all(q) + if (exact(ima).has(q) and isproc(q) and exact(ima)(q) >= exact(ima)(p)) // f[q] >= f[p] parce qu'on prend l'ordre de l'histogramme + { + psite adjTree = Find_tree(q); + psite adjNode = Find_node(lowestNode(adjTree)); + if (curNode != adjNode) + { + if (nodes(curNode).level == nodes(adjNode).level) + curNode = MergeNode(adjNode, curNode); + else + { + // we have nodes[curNode].level < nodes[adjNode].level + nodes(curNode).addChild(adjNode); + //apparemment NON :Par_node[adjNode] = curNode; // car adjNode devient fils de curNode + nodes(curNode).area += nodes(adjNode).area; + nodes(curNode).highest += nodes(adjNode).highest; + } + } + curTree = Link_tree(adjTree, curTree); + lowestNode(curTree) = curNode; + } + } + Root = lowestNode(Find_tree(Find_node(psite(0, 0)))); + // Pour garder une map de correspondance point <-> local_root + // for (int ip = 0; ip < int(S.size()); ++ip) + // { + // psite p = S[ip]; + // M(p) = Find_node(p); + // } + + mln_piter(I) r(par.domain()); + for_all(r) + par(r) = Find_node(r); + } + + + psite MergeNode(psite& node1, psite& node2) + { + psite tmpNode = Link_node(node1, node2); + psite tmpNode2; + if (tmpNode == node2) + { + nodes(node2).addChildren(nodes(node1)); + tmpNode2 = node1; + } + else + { + nodes(node1).addChildren(nodes(node2)); + tmpNode2 = node2; + } + nodes(tmpNode).area += nodes(tmpNode2).area; + nodes(tmpNode).highest += nodes(tmpNode2).highest; + return tmpNode; + } + + psite Link_tree(psite x, psite y) + { + if (Rnk_tree(x) > Rnk_tree(y)) + swap(x, y); + else + if (Rnk_tree(x) == Rnk_tree(y)) + Rnk_tree(y) += 1; + Par_tree(x) = y; + return y; + } + + psite Link_node(psite x, psite y) + { + if (Rnk_node(x) > Rnk_node(y)) + swap(x, y); + else + if (Rnk_node(x) == Rnk_node(y)) + Rnk_node(y) += 1; + par(x) = y; // was Par_node(x) = y; + return y; + } + + node MakeNode(int level) + { + node n; + n.level = level; + n.area = 1; + n.highest = level; + return n; + } + + template <typename C> + void image_output(image2d<C>& img) + { + for(unsigned int i = 0; i < img.domain().len(0); ++i) + { + for(unsigned int j = 0; j < img.domain().len(1); ++j) + { + C l = (img(psite(i, j)));//.row() * img.domain().len(1) + (img(psite(i, j))).col(); + std::cout << " " << l << " "; + } + std::cout << std::endl; + } + } + + + + void print_tree(psite p) + { + node& n = nodes(p); + std::cout << "psite " << p << "=" << (p.row() * exact(lowestNode).domain().len(1) + p.col()) << " : "; + + typename p_array<mln_psite(I)>::fwd_piter it(n.children); + for (it.start(); + it.is_valid(); + it.next()) + { + psite q = it.to_psite(); + std::cout << q << "=" << (q.row() * lowestNode.domain().len(2) + q.col()) << " "; + } + std::cout << std::endl; + + for (it.start(); + it.is_valid(); + it.next()) + { + print_tree(it.to_psite()); + } + } + + }; // struct basic_najman + + }; // namespace morpho + +}; // namespace mln Index: sandbox/abraham/morpho/test.cc --- sandbox/abraham/morpho/test.cc (revision 0) +++ sandbox/abraham/morpho/test.cc (revision 0) @@ -0,0 +1,43 @@ +#include <mln/core/image2d.hh> +#include <mln/core/window2d.hh> +#include <mln/core/neighb2d.hh> + +#include <mln/value/int_u8.hh> + +//#include <mln/morpho/meyer_wst.hh> + +#include <mln/io/pgm/load.hh> +#include <mln/io/pgm/save.hh> + +# include "basic_najman.hh" +// # include "topo_wst.hh" + +int main () +{ + using namespace mln; + using value::int_u8; + + // component_tree< image2d<int_u8> > c; + + using namespace mln; + using value::int_u8; + + image2d<int_u8> input; + io::pgm::load(input, "./images/test_component_tree.pgm"); + + morpho::basic_najman< image2d<int_u8>, neighb2d> n(input, c8()); + n.image_output(input); + n.go(); + n.image_output(n.Par_tree); + n.print_tree(n.Root); + n.image_output(n.par); + std::cout << " --------------------------- " << std::endl; + n.image_output(n.Rnk_tree); + std::cout << " --------------------------- " << std::endl; + n.image_output(n.Rnk_node); + + // image2d<int_u8> output = morpho::topo_wst(input, c4()); + // io::pgm::save(output, "out.pgm"); + + return 0; +} Index: sandbox/abraham/morpho/images/test_component_tree.pgm Cannot display: file marked as a binary type. svn:mime-type = application/octet-stream Property changes on: sandbox/abraham/morpho/images/test_component_tree.pgm ___________________________________________________________________ Name: svn:mime-type + application/octet-stream Index: sandbox/abraham/morpho/topo_wst.hh --- sandbox/abraham/morpho/topo_wst.hh (revision 0) +++ sandbox/abraham/morpho/topo_wst.hh (revision 0) @@ -0,0 +1,130 @@ +// Copyright (C) 2008 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_MORPHO_TOPO_WST_HH +# define MLN_MORPHO_TOPO_WST_HH + +/** \file mln/morpho/topo_wst.hh + \brief Topological Watershed Transform (WST) algorithm. + + Reference: + Quasi-linear algorithms for the topological watershed. Michel + Courie and Laurent Najman and Gilles Bertrand. +*/ + +# include <mln/trait/ch_value.hh> + +//# include <mln/util/greater_psite.hh> +# include <mln/morpho/includes.hh> +//# include <mln/morpho/extrema_components.hh> + +# include "component_tree.hh" + +namespace mln +{ + + namespace morpho + { + + /** \brief Topological Watershed Transform (WST) algorithm. + + \param[in] input The input image. + \param[in] nbh The connexity of markers. + \param[out] nbasins The number of basins. + + \li \p L is the type of labels, used to number the watershed + itself (with the minimal value), and the basins. + \li \p I is the exact type of the input image. + \li \p N is the exact type of the neighborhood used to express + \a input's connexity. */ + template <typename L, typename I, typename N> + mln_ch_value(I, L) + topo_wst(const Image<I>& input, const Neighborhood<N>& nbh); + + template <typename I, typename P> + bool is_m_destructible(const Image<I>& ima, const Point<P>& point, component_tree c); + + template <typename L, typename I, typename N> + mln_ch_value(I, L) + m_wst(const Image<I>& input, const Neighborhood<N>& nbh); + + +# ifndef MLN_INCLUDE_ONLY + + template <typename I, typename P> + int is_m_destructible(const Image<I>& ima, const mln_psite(I) p, const Neighborhood<N>& nbh, component_tree c) + { + p_set<P> v; + + mln_niter(N) n(nbh, p); + for_all(n) + if (n < p) + v = uni(V, c(n)); + if (v.is_empty()) + return -1; + + p_set<P>::fwd_piter p = v.begin(); + if (c(*p).children.size() != 0) + return -1; + + component_tree highest_fork = c.highest_fork(v); + if (highest_fork.level == -1) + return -1; + + return highest_fork.level; + } + + template <typename L, typename I, typename N> + mln_ch_value(I, L) + m_wst(const Image<I>& input, const Neighborhood<N>& nbh); + { + typedef + std::priority_queue< psite, std::vector<psite>, util::greater_psite<I> > + ordered_queue_type; + + ordered_queue_type queue(); + component_tree c(input); + + mln_piter(I) p(input.domain()); + + for_all(p) + { + if (is_m_destructible(input, p, c4(), c + } + + } + + + +# endif // ! MLN_INCLUDE_ONLY + + } // end of namespace mln::morpho + +} // end of namespace mln + + +#endif // ! MLN_MORPHO_TOPOLOGICAL_WST_HH Index: sandbox/abraham/morpho/Makefile --- sandbox/abraham/morpho/Makefile (revision 0) +++ sandbox/abraham/morpho/Makefile (revision 0) @@ -0,0 +1,8 @@ +SOURCE=test.cc +OBJECTS=test.o +CXXFLAGS=-Wall -W -I ../../.. -g + +all:${OBJECTS} + g++ ${FLAGS} ${OBJECTS} -o test + +test.o: basic_najman.hh \ No newline at end of file