renaming

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/bottleneckDistance@1240 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 53bcbf20e176a21dc41ef3c4d4295b1e9aa959b0

1 files changed, 233 insertions, 0 deletions

diff --git a/src/Bottleneck_distance/include/gudhi/Graph_matching.h b/src/Bottleneck_distance/include/gudhi/Graph_matching.h
new file mode 100644
index 00000000..d8860841
--- /dev/null
+++ b/src/Bottleneck_distance/include/gudhi/Graph_matching.h
@@ -0,0 +1,233 @@
+/*    This file is part of the Gudhi Library. The Gudhi library
+ *    (Geometric Understanding in Higher Dimensions) is a generic C++
+ *    library for computational topology.
+ *
+ *    Author(s):       Francois Godi
+ *
+ *    Copyright (C) 2015  INRIA Sophia-Antipolis (France)
+ *
+ *    This program is free software: you can redistribute it and/or modify
+ *    it under the terms of the GNU General Public License as published by
+ *    the Free Software Foundation, either version 3 of the License, or
+ *    (at your option) any later version.
+ *
+ *    This program 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 program.  If not, see <http://www.gnu.org/licenses/>.
+ */
+
+#ifndef SRC_BOTTLENECK_INCLUDE_GUDHI_GRAPH_MATCHING_H_
+#define SRC_BOTTLENECK_INCLUDE_GUDHI_GRAPH_MATCHING_H_
+
+#include <deque>
+
+#include <gudhi/Neighbors_finder.h>
+
+namespace Gudhi {
+
+namespace Bottleneck_distance {
+
+/** \brief Function to use in order to compute the Bottleneck distance between two persistence diagrams.
+ *
+ *
+ *
+ * \ingroup bottleneck_distance
+ */
+template<typename Persistence_diagram1, typename Persistence_diagram2>
+double compute(const Persistence_diagram1& diag1, const Persistence_diagram2& diag2, double e = 0.);
+
+/** \internal \brief Structure representing a graph matching. The graph is a Persistence_diagrams_graph.
+ *
+ * \ingroup bottleneck_distance
+ */
+class Graph_matching {
+public:
+    /** \internal \brief Constructor constructing an empty matching. */
+    explicit Graph_matching();
+    /** \internal \brief Copy operator. */
+    Graph_matching& operator=(const Graph_matching& m);
+    /** \internal \brief Is the matching perfect ? */
+    bool perfect() const;
+    /** \internal \brief Augments the matching with a maximal set of edge-disjoint shortest augmenting paths. */
+    bool multi_augment();
+    /** \internal \brief Sets the maximum length of the edges allowed to be added in the matching, 0 initially. */
+    void set_r(double r);
+
+private:
+    double r;
+    /** \internal \brief Given a point from V, provides its matched point in U, null_point_index() if there isn't. */
+    std::vector<int> v_to_u;
+    /** \internal \brief All the unmatched points in U. */
+    std::list<int> unmatched_in_u;
+
+    /** \internal \brief Provides a Layered_neighbors_finder dividing the graph in layers. Basically a BFS. */
+    std::shared_ptr<Layered_neighbors_finder> layering() const;
+    /** \internal \brief Augments the matching with a simple path no longer than max_depth. Basically a DFS. */
+    bool augment(Layered_neighbors_finder & layered_nf, int u_start_index, int max_depth);
+    /** \internal \brief Update the matching with the simple augmenting path given as parameter. */
+    void update(std::deque<int> & path);
+};
+
+inline Graph_matching::Graph_matching()
+    : r(0.), v_to_u(G::size(), null_point_index()), unmatched_in_u() {
+    for (int u_point_index = 0; u_point_index < G::size(); ++u_point_index)
+        unmatched_in_u.emplace_back(u_point_index);
+}
+
+inline Graph_matching& Graph_matching::operator=(const Graph_matching& m) {
+    r = m.r;
+    v_to_u = m.v_to_u;
+    unmatched_in_u = m.unmatched_in_u;
+    return *this;
+}
+
+inline bool Graph_matching::perfect() const {
+    return unmatched_in_u.empty();
+}
+
+inline bool Graph_matching::multi_augment() {
+    if (perfect())
+        return false;
+    Layered_neighbors_finder layered_nf = *layering();
+    int max_depth = layered_nf.vlayers_number()*2 - 1;
+    double rn = sqrt(G::size());
+    // verification of a necessary criterion in order to shortcut if possible
+    if (max_depth <0 || (unmatched_in_u.size() > rn && max_depth >= rn))
+        return false;
+    bool successful = false;
+    std::list<int> tries(unmatched_in_u);
+    for (auto it = tries.cbegin(); it != tries.cend(); it++)
+        // 'augment' has side-effects which have to be always executed, don't change order
+        successful =  augment(layered_nf, *it, max_depth) || successful;
+    return successful;
+}
+
+inline void Graph_matching::set_r(double r) {
+    this->r = r;
+}
+
+inline bool Graph_matching::augment(Layered_neighbors_finder & layered_nf, int u_start_index, int max_depth) {
+    //V vertices have at most one successor, thus when we backtrack from U we can directly pop_back 2 vertices.
+    std::deque<int> path;
+    path.emplace_back(u_start_index);
+    do {
+        if (static_cast<int>(path.size()) > max_depth) {
+            path.pop_back();
+            path.pop_back();
+        }
+        if (path.empty())
+            return false;
+        path.emplace_back(layered_nf.pull_near(path.back(), static_cast<int>(path.size())/2));
+        while (path.back() == null_point_index()) {
+            path.pop_back();
+            path.pop_back();
+            if (path.empty())
+                return false;
+            path.pop_back();
+            path.emplace_back(layered_nf.pull_near(path.back(), path.size() / 2));
+        }
+        path.emplace_back(v_to_u.at(path.back()));
+    } while (path.back() != null_point_index());
+    //if v_to_u.at(path.back()) has no successor, path.back() is an exposed vertex
+    path.pop_back();
+    update(path);
+    return true;
+}
+
+inline std::shared_ptr<Layered_neighbors_finder> Graph_matching::layering() const {
+    std::list<int> u_vertices(unmatched_in_u);
+    std::list<int> v_vertices;
+    Neighbors_finder nf(r);
+    for (int v_point_index = 0; v_point_index < G::size(); ++v_point_index)
+        nf.add(v_point_index);
+    std::shared_ptr<Layered_neighbors_finder> layered_nf(new Layered_neighbors_finder(r));
+    for(int layer = 0; !u_vertices.empty(); layer++) {
+        // one layer is one step in the BFS
+        for (auto it1 = u_vertices.cbegin(); it1 != u_vertices.cend(); ++it1) {
+            std::shared_ptr<std::list<int>> u_succ(nf.pull_all_near(*it1));
+            for (auto it2 = u_succ->begin(); it2 != u_succ->end(); ++it2) {
+                layered_nf->add(*it2, layer);
+                v_vertices.emplace_back(*it2);
+            }
+        }
+        // When the above for finishes, we have progress of one half-step (from U to V) in the BFS
+        u_vertices.clear();
+        bool end = false;
+        for (auto it = v_vertices.cbegin(); it != v_vertices.cend(); it++)
+            if (v_to_u.at(*it) == null_point_index())
+                // we stop when a nearest exposed V vertex (from U exposed vertices) has been found
+                end = true;
+            else
+                u_vertices.emplace_back(v_to_u.at(*it));
+        // When the above for finishes, we have progress of one half-step (from V to U) in the BFS
+        if (end)
+            return layered_nf;
+        v_vertices.clear();
+    }
+    return layered_nf;
+}
+
+inline void Graph_matching::update(std::deque<int>& path) {
+    unmatched_in_u.remove(path.front());
+    for (auto it = path.cbegin(); it != path.cend(); ++it) {
+        // Be careful, the iterator is incremented twice each time
+        int tmp = *it;
+        v_to_u[*(++it)] = tmp;
+    }
+}
+
+template<typename Persistence_diagram1, typename Persistence_diagram2>
+double compute_exactly(const Persistence_diagram1 &diag1, const Persistence_diagram2 &diag2) {
+    G::initialize(diag1, diag2, 0.);
+    std::shared_ptr< std::vector<double> > sd(G::sorted_distances());
+    int idmin = 0;
+    int idmax = sd->size() - 1;
+    // alpha can be modified, this will change the complexity
+    double alpha = pow(sd->size(), 0.25);
+    Graph_matching m;
+    Graph_matching biggest_unperfect;
+    while (idmin != idmax) {
+        int step = static_cast<int>((idmax - idmin) / alpha);
+        m.set_r(sd->at(idmin + step));
+        while (m.multi_augment());
+        //The above while compute a maximum matching (according to the r setted before)
+        if (m.perfect()) {
+            idmax = idmin + step;
+            m = biggest_unperfect;
+        } else {
+            biggest_unperfect = m;
+            idmin = idmin + step + 1;
+        }
+    }
+    return sd->at(idmin);
+}
+
+template<typename Persistence_diagram1, typename Persistence_diagram2>
+double compute(const Persistence_diagram1 &diag1, const Persistence_diagram2 &diag2, double e) {
+    if(e< std::numeric_limits<double>::min())
+        return compute_exactly(diag1, diag2);
+    G::initialize(diag1, diag2, e);
+    double d = 0.;
+    double f = G::diameter();
+    while (f-d > e){
+        Graph_matching m;
+        m.set_r((d+f)/2.);
+        while (m.multi_augment());
+        //The above while compute a maximum matching (according to the r setted before)
+        if (m.perfect()) 
+            f = (d+f)/2.;
+         else 
+            d= (d+f)/2.;
+    }
+    return d;
+}
+
+}  // namespace Bottleneck_distance
+
+}  // namespace Gudhi
+
+#endif  // SRC_BOTTLENECK_INCLUDE_GUDHI_GRAPH_MATCHING_H_