new alpha shapes persistence example

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/TDA_dev_1.1.0@407 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: c261b88e39db9a910d90dccbcb1798287b0ed6da

2 files changed, 312 insertions, 0 deletions

diff --git a/src/Persistent_cohomology/example/CMakeLists.txt b/src/Persistent_cohomology/example/CMakeLists.txt
index ae4b3be9..5255988a 100644
--- a/src/Persistent_cohomology/example/CMakeLists.txt
+++ b/src/Persistent_cohomology/example/CMakeLists.txt
@@ -24,4 +24,13 @@ if(GMPXX_FOUND AND GMP_FOUND)
 
    add_executable ( performance_rips_persistence performance_rips_persistence.cpp )
    target_link_libraries(performance_rips_persistence ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES})
+
+   if(CGAL_FOUND)
+      add_definitions(-DDEBUG_TRACES)
+      add_executable(alpha_shapes_persistence alpha_shapes_persistence.cpp)
+      target_link_libraries(alpha_shapes_persistence ${Boost_SYSTEM_LIBRARY} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES} ${CGAL_LIBRARY})
+      #add_test(persistence_from_file_3_2_0 ${CMAKE_CURRENT_BINARY_DIR}/persistence_from_file ${CMAKE_SOURCE_DIR}/data/points/bunny_5000.st -p 2 -m 0)
+      #add_test(persistence_from_file_3_3_100 ${CMAKE_CURRENT_BINARY_DIR}/persistence_from_file ${CMAKE_SOURCE_DIR}/data/points/bunny_5000.st -p 3 -m 100)
+   endif()
+
 endif()
diff --git a/src/Persistent_cohomology/example/alpha_shapes_persistence.cpp b/src/Persistent_cohomology/example/alpha_shapes_persistence.cpp
new file mode 100644
index 00000000..02baf1b0
--- /dev/null
+++ b/src/Persistent_cohomology/example/alpha_shapes_persistence.cpp
@@ -0,0 +1,303 @@
+ /*    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):       Vincent Rouvreau
+  *
+  *    Copyright (C) 2014  INRIA Saclay (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/>.
+  */
+
+#include <CGAL/Exact_predicates_inexact_constructions_kernel.h>
+#include <CGAL/Delaunay_triangulation_3.h>
+#include <CGAL/Alpha_shape_3.h>
+#include <CGAL/iterator.h>
+
+#include <fstream>
+#include <cmath>
+
+#include "gudhi/graph_simplicial_complex.h"
+#include "gudhi/Simplex_tree.h"
+#include "gudhi/Persistent_cohomology.h"
+#include <boost/variant.hpp>
+
+using namespace Gudhi;
+using namespace Gudhi::persistent_cohomology;
+
+// Alpha_shape_3 templates type definitions
+typedef CGAL::Exact_predicates_inexact_constructions_kernel Kernel;
+typedef CGAL::Alpha_shape_vertex_base_3<Kernel>             Vb;
+typedef CGAL::Alpha_shape_cell_base_3<Kernel>               Fb;
+typedef CGAL::Triangulation_data_structure_3<Vb,Fb>         Tds;
+typedef CGAL::Delaunay_triangulation_3<Kernel,Tds>          Triangulation_3;
+typedef CGAL::Alpha_shape_3<Triangulation_3>                Alpha_shape_3;
+
+// From file type definition
+typedef Kernel::Point_3                                     Point;
+
+// filtration with alpha values needed type definition
+typedef Alpha_shape_3::FT Alpha_value_type;
+typedef CGAL::Object      Object;
+typedef CGAL::Dispatch_output_iterator<
+  CGAL::cpp11::tuple<Object, Alpha_value_type>,
+  CGAL::cpp11::tuple<std::back_insert_iterator< std::vector<Object> >, std::back_insert_iterator< std::vector<Alpha_value_type> >
+                     > > Dispatch;
+typedef Alpha_shape_3::Cell_handle   Cell_handle;
+typedef Alpha_shape_3::Facet         Facet;
+typedef Alpha_shape_3::Edge          Edge;
+typedef std::list<Alpha_shape_3::Vertex_handle> Vertex_list;
+
+// gudhi type definition
+typedef Simplex_tree<>::Vertex_handle Simplex_tree_vertex;
+typedef std::map<Alpha_shape_3::Vertex_handle, Simplex_tree_vertex > Alpha_shape_simplex_tree_map;
+typedef std::pair<Alpha_shape_3::Vertex_handle, Simplex_tree_vertex> Alpha_shape_simplex_tree_pair;
+typedef std::vector< Simplex_tree_vertex > Simplex_tree_vector_vertex;
+
+//#define DEBUG_TRACES
+
+Vertex_list from (const Cell_handle& ch)
+{
+  Vertex_list the_list;
+  for (auto i = 0; i < 4; i++)
+  {
+#ifdef DEBUG_TRACES
+    std::cout << "from cell[" << i << "]=" << ch->vertex(i)->point() << std::endl;
+#endif // DEBUG_TRACES
+    the_list.push_back(ch->vertex(i));
+  }
+  return the_list;
+}
+Vertex_list from (const Facet& fct)
+{
+  Vertex_list the_list;
+  for (auto i = 0; i < 4; i++)
+  {
+    if (fct.second != i)
+    {
+#ifdef DEBUG_TRACES
+      std::cout << "from facet=[" << i << "]" << fct.first->vertex(i)->point() << std::endl;
+#endif // DEBUG_TRACES
+      the_list.push_back(fct.first->vertex(i));
+    }
+  }
+  return the_list;
+}
+Vertex_list from (const Edge& edg)
+{
+  Vertex_list the_list;
+  for (auto i = 0; i < 4; i++)
+  {
+    if ((edg.second == i) ||(edg.third == i))
+    {
+#ifdef DEBUG_TRACES
+      std::cout << "from edge[" << i << "]=" << edg.first->vertex(i)->point() << std::endl;
+#endif // DEBUG_TRACES
+      the_list.push_back(edg.first->vertex(i));
+    }
+  }
+  return the_list;
+}
+Vertex_list from (const Alpha_shape_3::Vertex_handle& vh)
+{
+  Vertex_list the_list;
+#ifdef DEBUG_TRACES
+  std::cout << "from vertex=" << vh->point() << std::endl;
+#endif // DEBUG_TRACES
+  the_list.push_back(vh);
+  return the_list;
+}
+
+void usage(char * const progName)
+{
+  std::cerr << "Usage: " << progName << " path_to_file_graph coeff_field_characteristic min_persistence\n";
+  exit(-1); // ----- >>
+}
+
+int main (int argc, char * const argv[])
+{
+
+  int coeff_field_characteristic=0;
+  int returnedScanValue = sscanf(argv[2], "%d", &coeff_field_characteristic);
+  if ((returnedScanValue == EOF) || (coeff_field_characteristic <= 0)) {
+    std::cerr << "Error: " << argv[2] << " is not correct\n";
+    usage(argv[0]);
+  }
+
+  int min_persist_int = 0;
+  returnedScanValue = sscanf(argv[3], "%d", &min_persist_int);
+  if ((returnedScanValue == EOF) || (min_persist_int < -1)) {
+    std::cerr << "Error: " << argv[3] << " is not correct\n";
+    usage(argv[0]);
+  }
+  Filtration_value min_persistence = (Filtration_value)min_persist_int;
+
+  // program args management
+  if (argc != 4) {
+    std::cerr << "Error: Number of arguments (" << argc << ") is not correct\n";
+    usage(argv[0]);
+  }
+
+  // Read points from file
+  std::string filegraph   = argv[1];
+  std::list<Point> lp;
+  std::ifstream is(filegraph.c_str());
+  int n;
+  is >> n;
+#ifdef DEBUG_TRACES
+  std::cout << "Reading " << n << " points " << std::endl;
+#endif // DEBUG_TRACES
+  Point p;
+  for( ; n>0 ; n--)    {
+    is >> p;
+    lp.push_back(p);
+  }
+
+  // alpha shape construction from points. CGAL has a strange behavior in REGULARIZED mode.
+  Alpha_shape_3 as(lp.begin(),lp.end(),0,Alpha_shape_3::GENERAL);
+#ifdef DEBUG_TRACES
+  std::cout << "Alpha shape computed in GENERAL mode" << std::endl;
+#endif // DEBUG_TRACES
+
+  // filtration with alpha values from alpha shape
+  std::vector<Object> the_objects;
+  std::vector<Alpha_value_type> the_alpha_values;
+
+  Dispatch disp = CGAL::dispatch_output<Object, Alpha_value_type>( std::back_inserter(the_objects), std::back_inserter(the_alpha_values));
+
+  as.filtration_with_alpha_values(disp);
+#ifdef DEBUG_TRACES
+  std::cout << "filtration_with_alpha_values returns : " << the_objects.size() << " objects" << std::endl;
+#endif // DEBUG_TRACES
+
+  Alpha_shape_3::size_type count_vertices = 0;
+  Alpha_shape_3::size_type count_edges    = 0;
+  Alpha_shape_3::size_type count_facets   = 0;
+  Alpha_shape_3::size_type count_cells    = 0;
+
+  // Loop on objects vector
+  Vertex_list vertex_list;
+  Simplex_tree<> simplex_tree;
+  Alpha_shape_simplex_tree_map map_cgal_simplex_tree;
+  std::vector<Alpha_value_type>::iterator the_alpha_value_iterator = the_alpha_values.begin();
+  int dim_max=0;
+  Filtration_value filtration_max=0.0;
+  for(auto object_iterator: the_objects)
+  {
+    // Retrieve Alpha shape vertex list from object
+    if (const Cell_handle* cell = CGAL::object_cast<Cell_handle>(&object_iterator))
+    {
+      vertex_list = from(*cell);
+      count_cells++;
+      if (dim_max < 3) {
+        dim_max=3; // Cell is of dim 3
+      }
+    }
+    else if (const Facet* facet = CGAL::object_cast<Facet>(&object_iterator))
+    {
+      vertex_list = from(*facet);
+      count_facets++;
+      if (dim_max < 2) {
+        dim_max=2; // Facet is of dim 2
+      }
+    }
+    else if (const Edge* edge = CGAL::object_cast<Edge>(&object_iterator))
+    {
+      vertex_list = from(*edge);
+      count_edges++;
+      if (dim_max < 1) {
+        dim_max=1; // Edge is of dim 1
+      }
+    }
+    else if (const Alpha_shape_3::Vertex_handle* vertex = CGAL::object_cast<Alpha_shape_3::Vertex_handle>(&object_iterator))
+    {
+      count_vertices++;
+      vertex_list = from(*vertex);
+    }
+    // Construction of the vector of simplex_tree vertex from list of alpha_shapes vertex
+    Simplex_tree_vector_vertex the_simplex_tree;
+    for (auto the_alpha_shape_vertex:vertex_list)
+    {
+      Alpha_shape_simplex_tree_map::iterator the_map_iterator = map_cgal_simplex_tree.find(the_alpha_shape_vertex);
+      if (the_map_iterator == map_cgal_simplex_tree.end())
+      {
+        // alpha shape not found
+        Simplex_tree_vertex vertex = map_cgal_simplex_tree.size();
+#ifdef DEBUG_TRACES
+        std::cout << "vertex [" << the_alpha_shape_vertex->point() << "] not found - insert " << vertex << std::endl;
+#endif // DEBUG_TRACES
+        the_simplex_tree.push_back(vertex);
+        map_cgal_simplex_tree.insert(Alpha_shape_simplex_tree_pair(the_alpha_shape_vertex,vertex));
+      } else
+      {
+        // alpha shape found
+        Simplex_tree_vertex vertex = the_map_iterator->second;
+#ifdef DEBUG_TRACES
+        std::cout << "vertex [" << the_alpha_shape_vertex->point() << "] found in " << vertex << std::endl;
+#endif // DEBUG_TRACES
+        the_simplex_tree.push_back(vertex);
+      }
+    }
+    // Construction of the simplex_tree
+    Filtration_value filtr = std::sqrt(*the_alpha_value_iterator);
+#ifdef DEBUG_TRACES
+    std::cout << "filtration = " << filtr << std::endl;
+#endif // DEBUG_TRACES
+    if (filtr > filtration_max) {
+      filtration_max = filtr;
+    }
+    simplex_tree.insert(the_simplex_tree, std::sqrt(*the_alpha_value_iterator));
+    if (the_alpha_value_iterator != the_alpha_values.end())
+      ++the_alpha_value_iterator;
+    else
+      std::cout << "This shall not happen" << std::endl;
+  }
+  simplex_tree.set_filtration(filtration_max);
+  simplex_tree.set_num_simplices(count_vertices + count_edges + count_facets + count_cells);
+  simplex_tree.set_dimension(dim_max);
+
+#ifdef DEBUG_TRACES
+  std::cout << "vertices \t\t" << count_vertices << std::endl;
+  std::cout << "edges \t\t"    << count_edges << std::endl;
+  std::cout << "facets \t\t"   << count_facets << std::endl;
+  std::cout << "cells \t\t"    << count_cells << std::endl;
+
+
+  std::cout << "Information of the Simplex Tree: " << std::endl;
+  std::cout << "  Number of vertices = " << simplex_tree.num_vertices() << " ";
+  std::cout << "  Number of simplices = " << simplex_tree.num_simplices() << std::endl << std::endl;
+  std::cout << "  Dimension = " << simplex_tree.dimension() << " ";
+  std::cout << "  filtration = " << simplex_tree.filtration() << std::endl << std::endl;
+#endif // DEBUG_TRACES
+
+#ifdef DEBUG_TRACES
+  std::cout << "Iterator on vertices: " << std::endl;
+  for( auto vertex : simplex_tree.complex_vertex_range() )
+  { std::cout << vertex << " "; }
+#endif // DEBUG_TRACES
+
+  // Sort the simplices in the order of the filtration
+  simplex_tree.initialize_filtration();
+
+  std::cout << "Simplex_tree dim: " << simplex_tree.dimension() << std::endl;
+  // Compute the persistence diagram of the complex
+  Persistent_cohomology< Simplex_tree<>, Field_Zp > pcoh( simplex_tree );
+  pcoh.init_coefficients( coeff_field_characteristic ); //initializes the coefficient field for homology
+
+  pcoh.compute_persistent_cohomology( min_persistence );
+
+  pcoh.output_diagram();
+
+  return 0;
+}