Added everything missing

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/relaxed-witness@1265 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: c148ce9136bb0786acc1c9ae49827cb3958326c6

1 files changed, 305 insertions, 0 deletions

diff --git a/src/Witness_complex/example/output.h b/src/Witness_complex/example/output.h
new file mode 100644
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--- /dev/null
+++ b/src/Witness_complex/example/output.h
@@ -0,0 +1,305 @@
+#ifndef OUTPUT_H
+#define OUTPUT_H
+
+#include <fstream>
+#include <vector>
+#include <string>
+
+#include <gudhi/Simplex_tree.h>
+
+#include <CGAL/Epick_d.h>
+#include <CGAL/Delaunay_triangulation.h>
+
+//typename Gudhi::Witness_complex<> Witness_complex;
+
+typedef CGAL::Epick_d<CGAL::Dynamic_dimension_tag> K;
+typedef K::Point_d Point_d;
+typedef std::vector<Point_d> Point_Vector;
+typedef CGAL::Delaunay_triangulation<K> Delaunay_triangulation;
+
+/** \brief Write the table of the nearest landmarks to each witness
+ *  to a file.
+ */
+template <class Value>
+void write_wl( std::string file_name, std::vector< std::vector <Value> > & WL)
+{
+  std::ofstream ofs (file_name, std::ofstream::out);
+  for (auto w : WL)
+    {
+      for (auto l: w)
+        ofs << l << " ";
+      ofs << "\n";
+    }
+  ofs.close();
+}
+
+/** \brief Write the coordinates of points in points to a file. 
+ *
+ */
+void write_points( std::string file_name, std::vector< Point_d > & points)
+{
+  std::ofstream ofs (file_name, std::ofstream::out);
+  for (auto w : points)
+    {
+      for (auto it = w.cartesian_begin(); it != w.cartesian_end(); ++it)
+        ofs << *it << " ";
+      ofs << "\n";
+    }
+  ofs.close();
+}
+
+/** Write edges of a witness complex in a file.
+ *  The format of an edge is coordinates of u \n coordinates of v \n\n\n
+ *  This format is compatible with gnuplot
+ */
+template< typename STree >
+void write_edges(std::string file_name, STree& witness_complex, Point_Vector& landmarks)
+{
+  std::ofstream ofs (file_name, std::ofstream::out);
+  for (auto u: witness_complex.complex_vertex_range())
+    for (auto v: witness_complex.complex_vertex_range())
+      {
+        std::vector<int> edge = {u,v};
+        if (u < v && witness_complex.find(edge) != witness_complex.null_simplex())   
+          {
+            for (auto it = landmarks[u].cartesian_begin(); it != landmarks[u].cartesian_end(); ++it)
+              ofs << *it << " ";
+            ofs << "\n";
+            for (auto it = landmarks[v].cartesian_begin(); it != landmarks[v].cartesian_end(); ++it)
+              ofs << *it << " ";
+            ofs << "\n\n\n";
+          }
+      }
+  ofs.close();
+}
+
+/** \brief Write triangles (tetrahedra in 3d) of a witness
+ *  complex in a file, compatible with medit.
+ *  l_is_v = landmark is vertex
+ */
+template <typename SimplexHandleRange,
+          typename STree >
+void write_witness_mesh(Point_Vector& W, std::vector<int>& landmarks_ind, STree& st, SimplexHandleRange const & shr, bool is2d, bool l_is_v, std::string file_name = "witness.mesh")
+{
+  std::ofstream ofs (file_name, std::ofstream::out);
+  if (is2d)
+    ofs << "MeshVersionFormatted 1\nDimension 2\n";
+  else
+    ofs << "MeshVersionFormatted 1\nDimension 3\n";
+  
+  if (!l_is_v)
+    ofs << "Vertices\n" << W.size() << "\n";
+  else
+    ofs << "Vertices\n" << landmarks_ind.size() << "\n";
+  
+  if (l_is_v)
+    for (auto p_it : landmarks_ind) {
+      for (auto coord = W[p_it].cartesian_begin(); coord != W[p_it].cartesian_end() && coord != W[p_it].cartesian_begin()+3 ; ++coord)
+        ofs << *coord << " ";
+      ofs << "508\n";
+    }
+  else
+    for (auto p_it : W) {
+      for (auto coord = p_it.cartesian_begin(); coord != p_it.cartesian_end() && coord != p_it.cartesian_begin()+3 ; ++coord)
+        ofs << *coord << " ";
+      ofs << "508\n";
+    }
+
+  //  int num_triangles = W.size(), num_tetrahedra = 0;
+  int num_edges = 0, num_triangles = 0, num_tetrahedra = 0;
+  if (!l_is_v) {
+      for (auto sh_it : shr)
+        if (st.dimension(sh_it) == 1)
+          num_edges++;
+        else if (st.dimension(sh_it) == 2)
+          num_triangles++;
+        else if (st.dimension(sh_it) == 3)
+          num_tetrahedra++;
+      ofs << "Edges " << num_edges << "\n";
+      for (auto sh_it : shr) {
+           if (st.dimension(sh_it) == 1) {
+            for (auto v_it : st.simplex_vertex_range(sh_it))
+              ofs << landmarks_ind[v_it]+1 << " ";
+           ofs << "200\n";
+          }
+        }
+      ofs << "Triangles " << num_triangles << "\n";
+      for (unsigned i = 0; i < W.size(); ++i)
+        ofs << i << " " << i << " " << i << " " << "508\n";
+      for (auto sh_it : shr)
+        {
+           if (st.dimension(sh_it) == 2) {
+            for (auto v_it : st.simplex_vertex_range(sh_it))
+              ofs << landmarks_ind[v_it]+1 << " ";
+           ofs << "508\n";
+          }
+        }
+      ofs << "Tetrahedra " << num_tetrahedra << "\n";
+      for (auto sh_it : shr)
+        {
+           if (st.dimension(sh_it) == 3) {
+            for (auto v_it : st.simplex_vertex_range(sh_it))
+              ofs << landmarks_ind[v_it]+1 << " ";
+           ofs << "250\n";
+          }
+        }
+  }
+  else {
+      for (auto sh_it : shr)
+        if (st.dimension(sh_it) == 1)
+          num_edges++;
+        else if (st.dimension(sh_it) == 2)
+          num_triangles++;
+        else if (st.dimension(sh_it) == 3)
+          num_tetrahedra++;
+      ofs << "Edges " << num_edges << "\n";
+      for (auto sh_it : shr) {
+           if (st.dimension(sh_it) == 1) {
+            for (auto v_it : st.simplex_vertex_range(sh_it))
+              ofs << v_it+1 << " ";
+           ofs << "200\n";
+          }
+        }
+      ofs << "Triangles " << num_triangles << "\n";
+      for (auto sh_it : shr)
+        {
+           if (st.dimension(sh_it) == 2) {
+            for (auto v_it : st.simplex_vertex_range(sh_it))
+              ofs << v_it+1 << " ";
+           ofs << "508\n";
+          }
+        }
+      ofs << "Tetrahedra " << num_tetrahedra << "\n";
+      for (auto sh_it : shr)
+        {
+           if (st.dimension(sh_it) == 3) {
+            for (auto v_it : st.simplex_vertex_range(sh_it))
+              ofs << v_it+1 << " ";
+           ofs << "250\n";
+          }
+        }
+  }
+    
+  ofs << "End\n";
+  /*
+  else
+    {
+      ofs << "Tetrahedra " << t.number_of_finite_full_cells()+1 << "\n";
+      for (auto fc_it = t.full_cells_begin(); fc_it != t.full_cells_end(); ++fc_it)
+        {
+          if (t.is_infinite(fc_it))
+            continue;
+          for (auto vh_it = fc_it->vertices_begin(); vh_it != fc_it->vertices_end(); ++vh_it)
+            ofs << index_of_vertex[*vh_it] << " ";
+          ofs << "508\n";
+        }
+      ofs << nbV << " " << nbV << " " << nbV << " " << nbV << " " << 208 << "\n";
+      ofs << "End\n";
+    }
+  */
+  ofs.close();
+}
+
+void write_witness_mesh(Point_Vector& W, std::vector<int>& landmarks_ind, Gudhi::Simplex_tree<>& st, bool is2d, bool l_is_v, std::string file_name = "witness.mesh")
+{
+  write_witness_mesh(W, landmarks_ind, st, st.complex_simplex_range(), is2d, l_is_v, file_name);
+}
+
+/** \brief Write triangles (tetrahedra in 3d) of a Delaunay
+ *  triangulation in a file, compatible with medit.
+ */
+void write_delaunay_mesh(Delaunay_triangulation& t, const Point_d& p, bool is2d)
+{
+  std::ofstream ofs ("delaunay.mesh", std::ofstream::out);
+  int nbV = t.number_of_vertices()+1;
+  if (is2d)
+    ofs << "MeshVersionFormatted 1\nDimension 2\n";
+  else
+    ofs << "MeshVersionFormatted 1\nDimension 3\n";
+  ofs << "Vertices\n" << nbV << "\n";
+  int ind = 1; //index of a vertex
+  std::map<Delaunay_triangulation::Vertex_handle, int> index_of_vertex;
+  for (auto v_it = t.vertices_begin(); v_it != t.vertices_end(); ++v_it)
+    {
+      if (t.is_infinite(v_it))
+        continue;
+      // Add maximum 3 coordinates
+      for (auto coord = v_it->point().cartesian_begin(); coord != v_it->point().cartesian_end() && coord != v_it->point().cartesian_begin()+3; ++coord)
+        ofs << *coord << " ";
+      ofs << "508\n";
+      index_of_vertex[v_it] = ind++;
+    }
+  for (auto coord = p.cartesian_begin(); coord != p.cartesian_end(); ++coord)
+    ofs << *coord << " ";
+  ofs << "208\n";
+  if (is2d)
+    {
+      ofs << "Triangles " << t.number_of_finite_full_cells()+1 << "\n";
+      for (auto fc_it = t.full_cells_begin(); fc_it != t.full_cells_end(); ++fc_it)
+        {
+          if (t.is_infinite(fc_it))
+            continue;
+          for (auto vh_it = fc_it->vertices_begin(); vh_it != fc_it->vertices_end(); ++vh_it)
+            ofs << index_of_vertex[*vh_it] << " ";
+          ofs << "508\n";
+        }
+      ofs << nbV << " " << nbV << " " << nbV << " " << 208 << "\n";
+      ofs << "End\n";
+    }
+  else if (p.size() == 3)
+    {
+      ofs << "Tetrahedra " << t.number_of_finite_full_cells()+1 << "\n";
+      for (auto fc_it = t.full_cells_begin(); fc_it != t.full_cells_end(); ++fc_it)
+        {
+          if (t.is_infinite(fc_it))
+            continue;
+          for (auto vh_it = fc_it->vertices_begin(); vh_it != fc_it->vertices_end(); ++vh_it)
+            ofs << index_of_vertex[*vh_it] << " ";
+          ofs << "508\n";
+        }
+      ofs << nbV << " " << nbV << " " << nbV << " " << nbV << " " << 208 << "\n";
+      ofs << "End\n";
+    }
+  else if (p.size() == 4)
+    {
+      ofs << "Tetrahedra " << 5*(t.number_of_finite_full_cells())+1 << "\n";
+      for (auto fc_it = t.full_cells_begin(); fc_it != t.full_cells_end(); ++fc_it)
+        {
+          if (t.is_infinite(fc_it))
+            continue;
+          for (auto vh_it = fc_it->vertices_begin(); vh_it != fc_it->vertices_end(); ++vh_it)
+            {
+              for (auto vh_it2 = fc_it->vertices_begin(); vh_it2 != fc_it->vertices_end(); ++vh_it2)
+                if (vh_it != vh_it2)
+                  ofs << index_of_vertex[*vh_it2] << " ";
+              ofs << "508\n"; 
+            }
+        }
+      ofs << nbV << " " << nbV << " " << nbV << " " << nbV << " " << 208 << "\n";
+      ofs << "End\n";
+    }
+  ofs.close();
+}
+
+///////////////////////////////////////////////////////////////////////
+// PRINT VECTOR
+///////////////////////////////////////////////////////////////////////
+
+template <typename T>
+void print_vector(std::vector<T> v)
+{
+  std::cout << "[";
+  if (!v.empty())
+    {
+      std::cout << *(v.begin());
+      for (auto it = v.begin()+1; it != v.end(); ++it)
+        {
+          std::cout << ",";
+          std::cout << *it;
+        }
+    }
+  std::cout << "]";
+}
+
+
+#endif