Merge VR_bitmap

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/bitmap@1074 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 4c9ac225ffcfb924371c72fccc44cbd6ecb3d6e3

4 files changed, 193 insertions, 218 deletions

diff --git a/src/Bitmap_cubical_complex/example/Bitmap_cubical_complex.cpp b/src/Bitmap_cubical_complex/example/Bitmap_cubical_complex.cpp
index 4c30ee85..7c7e8ac5 100644
--- a/src/Bitmap_cubical_complex/example/Bitmap_cubical_complex.cpp
+++ b/src/Bitmap_cubical_complex/example/Bitmap_cubical_complex.cpp
@@ -1,73 +1,72 @@
- /*    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):       Pawel Dlotko
-  *
-  *    Copyright (C) 2015  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/>.
-  */
+/*    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):       Pawel Dlotko
+ *
+ *    Copyright (C) 2015  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 <gudhi/reader_utils.h>
-#include <gudhi/Bitmap_cubical_complex_base.h>
 #include <gudhi/Bitmap_cubical_complex.h>
 #include <gudhi/Persistent_cohomology.h>
 
-
-using namespace Gudhi;
-using namespace Gudhi::Cubical_complex;
-using namespace Gudhi::persistent_cohomology;
-
-//standard stuff
+// standard stuff
 #include <iostream>
 #include <sstream>
 #include <vector>
 
-using namespace std;
+int main(int argc, char** argv) {
+  std::cout << "This program computes persistent homology, by using bitmap_cubical_complex class, of cubical " <<
+      "complexes provided in text files in Perseus style (the only numbered in the first line is a dimension D of a" <<
+      "bitmap. In the lines I between 2 and D+1 there are numbers of top dimensional cells in the direction I. Let " <<
+      "N denote product of the numbers in the lines between 2 and D. In the lines D+2 to D+2+N there are " <<
+      "filtrations of top dimensional cells. We assume that the cells are in the lexicographical order. See " <<
+      "CubicalOneSphere.txt or CubicalTwoSphere.txt for example.\n" << std::endl;
 
+  int p = 2;
+  double min_persistence = 0;
 
-int main( int argc , char** argv )
-{
-    cout << "This program computes persistent homology, by using bitmap_cubical_complex class, of cubical complexes provided in text files in Perseus style (the only numbered in \
-the first line is a dimension D of a bitmap. In the lines I between 2 and D+1 there are numbers of top dimensional cells in the direction I. Let N denote product \
-of the numbers in the lines between 2 and D. In the lines D+2 to D+2+N there are filtrations of top dimensional cells. We assume that the cells are in the \
-lexicographical order. See CubicalOneSphere.txt or CubicalTwoSphere.txt for example." << endl;
+  if (argc != 2) {
+    std::cerr << "Wrong number of parameters. Please provide the name of a file with a Perseus style bitmap at " <<
+        "the input. The program will now terminate.\n";
+    return 1;
+  }
 
-    int p = 2;
-    double min_persistence = 0;
+  typedef Gudhi::Cubical_complex::Bitmap_cubical_complex_base<double> Bitmap_cubical_complex_base;
+  typedef Gudhi::Cubical_complex::Bitmap_cubical_complex<Bitmap_cubical_complex_base> Bitmap_cubical_complex;
+  typedef Gudhi::persistent_cohomology::Field_Zp Field_Zp;
+  typedef Gudhi::persistent_cohomology::Persistent_cohomology<Bitmap_cubical_complex, Field_Zp> Persistent_cohomology;
 
-    if ( argc != 2 )
-    {
-        cout << "Wrong number of parameters. Please provide the name of a file with a Perseus style bitmap at the input. The program will now terminate.\n";
-        return 1;
-    }
+  Bitmap_cubical_complex b(argv[1]);
 
-    Bitmap_cubical_complex< Bitmap_cubical_complex_base<double> > b( argv[1] );
+  // Compute the persistence diagram of the complex
+  Persistent_cohomology pcoh(b);
+  pcoh.init_coefficients(p);  // initializes the coefficient field for homology
+  pcoh.compute_persistent_cohomology(min_persistence);
 
-    // Compute the persistence diagram of the complex
-    persistent_cohomology::Persistent_cohomology< Bitmap_cubical_complex< Bitmap_cubical_complex_base<double> >, Field_Zp > pcoh(b);
-    pcoh.init_coefficients( p ); //initilizes the coefficient field for homology
+  std::stringstream ss;
+  ss << argv[1] << "_persistence";
+  std::ofstream out(ss.str().c_str());
+  pcoh.output_diagram(out);
+  out.close();
 
-    pcoh.compute_persistent_cohomology( min_persistence );
+  std::cout << "Result in file: " << ss.str().c_str() << "\n";
 
-    stringstream ss;
-    ss << argv[1] << "_persistence";
-    std::ofstream out((char*)ss.str().c_str());
-    pcoh.output_diagram(out);
-    out.close();
-
-    return 0;
+  return 0;
 }
+
diff --git a/src/Bitmap_cubical_complex/example/Bitmap_cubical_complex_periodic_boundary_conditions.cpp b/src/Bitmap_cubical_complex/example/Bitmap_cubical_complex_periodic_boundary_conditions.cpp
index df01240b..2c5d7fd3 100644
--- a/src/Bitmap_cubical_complex/example/Bitmap_cubical_complex_periodic_boundary_conditions.cpp
+++ b/src/Bitmap_cubical_complex/example/Bitmap_cubical_complex_periodic_boundary_conditions.cpp
@@ -1,24 +1,24 @@
- /*    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):       Pawel Dlotko
-  *
-  *    Copyright (C) 2015  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/>.
-  */
+/*    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):       Pawel Dlotko
+ *
+ *    Copyright (C) 2015  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 <gudhi/reader_utils.h>
@@ -26,59 +26,49 @@
 #include <gudhi/Bitmap_cubical_complex_periodic_boundary_conditions_base.h>
 #include <gudhi/Persistent_cohomology.h>
 
-using namespace Gudhi;
-using namespace Gudhi::Cubical_complex;
-using namespace Gudhi::persistent_cohomology;
-
-//standard stuff
+// standard stuff
 #include <iostream>
 #include <sstream>
 #include <vector>
 
-using namespace std;
-
-int main( int argc , char** argv )
-{
-    clock_t beginOfProgram = clock();
-
-    cout << "This program computes persistent homology, by using Bitmap_cubical_complex_periodic_boundary_conditions class, of cubical complexes provided in text files in Perseus style (the only numbered in \
-the first line is a dimension D of a bitmap. In the lines I between 2 and D+1 there are numbers of top dimensional cells in the direction I. Let N denote product \
-of the numbers in the lines between 2 and D. In the lines D+2 to D+2+N there are filtrations of top dimensional cells. We assume that the cells are in the \
-lexicographical order. See CubicalOneSphere.txt or CubicalTwoSphere.txt for example." << endl;
-
-    int p = 2;
-    double min_persistence = 0;
-
-    if ( argc != 2 )
-    {
-        cout << "Wrong number of parameters. Please provide the name of a file with a Perseus style bitmap at the input. The program will now terminate.\n";
-        return 1;
-    }
-
-    Bitmap_cubical_complex< Bitmap_cubical_complex_periodic_boundary_conditions_base<float> > b( argv[1] );
-
-    cerr << "Here \n";
-
-    clock_t endCreateBitmap = clock();
-    double elapsed_secsCreateBitmap = double(endCreateBitmap - beginOfProgram) / CLOCKS_PER_SEC;
-    cerr << "Time of creation of bitmap : " << elapsed_secsCreateBitmap << endl;
-    
-
-
-    // Compute the persistence diagram of the complex
-    persistent_cohomology::Persistent_cohomology< Bitmap_cubical_complex< Bitmap_cubical_complex_periodic_boundary_conditions_base<float> >, Field_Zp > pcoh(b,true);
-    pcoh.init_coefficients( p ); //initilizes the coefficient field for homology
-    pcoh.compute_persistent_cohomology( min_persistence );
-
-
-    stringstream ss;
-    ss << argv[1] << "_persistence";
-    std::ofstream out((char*)ss.str().c_str());
-    pcoh.output_diagram(out);
-    out.close();
-
-    clock_t endOfProgram = clock();
-    double elapsed_secsOfProgram = double(endOfProgram - beginOfProgram) / CLOCKS_PER_SEC;
-    cerr << "Overall execution time : " << elapsed_secsOfProgram << endl;
-    return 0;
+int main(int argc, char** argv) {
+  std::cout << "This program computes persistent homology, by using " <<
+      "Bitmap_cubical_complex_periodic_boundary_conditions class, of cubical complexes provided in text files in " <<
+      "Perseus style (the only numbered in the first line is a dimension D of a bitmap. In the lines I between 2 " <<
+      "and D+1 there are numbers of top dimensional cells in the direction I. Let N denote product of the numbers " <<
+      "in the lines between 2 and D. In the lines D+2 to D+2+N there are filtrations of top dimensional cells. We " <<
+      "assume that the cells are in the lexicographical order. See CubicalOneSphere.txt or CubicalTwoSphere.txt for" <<
+      " example.\n" << std::endl;
+
+  int p = 2;
+  double min_persistence = 0;
+
+  if (argc != 2) {
+    std::cerr << "Wrong number of parameters. Please provide the name of a file with a Perseus style bitmap at " <<
+        "the input. The program will now terminate.\n";
+    return 1;
+  }
+
+  typedef Gudhi::Cubical_complex::Bitmap_cubical_complex_periodic_boundary_conditions_base<double> Bitmap_base;
+  typedef Gudhi::Cubical_complex::Bitmap_cubical_complex< Bitmap_base > Bitmap_cubical_complex;
+
+  Bitmap_cubical_complex b(argv[1]);
+
+  typedef Gudhi::persistent_cohomology::Field_Zp Field_Zp;
+  typedef Gudhi::persistent_cohomology::Persistent_cohomology<Bitmap_cubical_complex, Field_Zp> Persistent_cohomology;
+  // Compute the persistence diagram of the complex
+  Persistent_cohomology pcoh(b, true);
+  pcoh.init_coefficients(p);  // initializes the coefficient field for homology
+  pcoh.compute_persistent_cohomology(min_persistence);
+
+  std::stringstream ss;
+  ss << argv[1] << "_persistence";
+  std::ofstream out(ss.str().c_str());
+  pcoh.output_diagram(out);
+  out.close();
+
+  std::cout << "Result in file: " << ss.str().c_str() << "\n";
+
+  return 0;
 }
+
diff --git a/src/Bitmap_cubical_complex/example/CMakeLists.txt b/src/Bitmap_cubical_complex/example/CMakeLists.txt
index 088e6fbd..8f9cfa80 100644
--- a/src/Bitmap_cubical_complex/example/CMakeLists.txt
+++ b/src/Bitmap_cubical_complex/example/CMakeLists.txt
@@ -3,8 +3,8 @@ project(GUDHIBitmap)
 
 add_executable ( Bitmap_cubical_complex Bitmap_cubical_complex.cpp )
 target_link_libraries(Bitmap_cubical_complex ${Boost_SYSTEM_LIBRARY})	
-add_test(Bitmap_cubical_complex ${CMAKE_CURRENT_BINARY_DIR}/Bitmap_cubical_complex ${CMAKE_SOURCE_DIR}/data/bitmap/CubicalOneSphere.txt)
-add_test(Bitmap_cubical_complex ${CMAKE_CURRENT_BINARY_DIR}/Bitmap_cubical_complex ${CMAKE_SOURCE_DIR}/data/bitmap/CubicalTwoSphere.txt)
+add_test(Bitmap_cubical_complex_one_sphere ${CMAKE_CURRENT_BINARY_DIR}/Bitmap_cubical_complex ${CMAKE_SOURCE_DIR}/data/bitmap/CubicalOneSphere.txt)
+add_test(Bitmap_cubical_complex_two_sphere ${CMAKE_CURRENT_BINARY_DIR}/Bitmap_cubical_complex ${CMAKE_SOURCE_DIR}/data/bitmap/CubicalTwoSphere.txt)
 
 add_executable ( Random_bitmap_cubical_complex Random_bitmap_cubical_complex.cpp )
 target_link_libraries(Random_bitmap_cubical_complex ${Boost_SYSTEM_LIBRARY})	
@@ -12,9 +12,6 @@ add_test(Random_bitmap_cubical_complex ${CMAKE_CURRENT_BINARY_DIR}/Random_bitmap
 
 add_executable ( Bitmap_cubical_complex_periodic_boundary_conditions Bitmap_cubical_complex_periodic_boundary_conditions.cpp )
 target_link_libraries(Bitmap_cubical_complex_periodic_boundary_conditions ${Boost_SYSTEM_LIBRARY})	
+add_test(Bitmap_cubical_complex_periodic_2d_torus ${CMAKE_CURRENT_BINARY_DIR}/Bitmap_cubical_complex_periodic_boundary_conditions ${CMAKE_SOURCE_DIR}/data/bitmap/2d_torus.txt)
+add_test(Bitmap_cubical_complex_periodic_3d_torus ${CMAKE_CURRENT_BINARY_DIR}/Bitmap_cubical_complex_periodic_boundary_conditions ${CMAKE_SOURCE_DIR}/data/bitmap/3d_torus.txt)
 
-#add_executable ( Compute_persistence_with_phat Compute_persistence_with_phat.cpp )
-#target_link_libraries(Compute_persistence_with_phat ${Boost_SYSTEM_LIBRARY})
-
-#add_executable ( periodic_boundary_conditions_phat periodic_boundary_conditions_phat.cpp )
-#target_link_libraries(periodic_boundary_conditions_phat ${Boost_SYSTEM_LIBRARY})
\ No newline at end of file
diff --git a/src/Bitmap_cubical_complex/example/Random_bitmap_cubical_complex.cpp b/src/Bitmap_cubical_complex/example/Random_bitmap_cubical_complex.cpp
index 8b7f6a04..416ad8f2 100644
--- a/src/Bitmap_cubical_complex/example/Random_bitmap_cubical_complex.cpp
+++ b/src/Bitmap_cubical_complex/example/Random_bitmap_cubical_complex.cpp
@@ -1,94 +1,83 @@
- /*    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):       Pawel Dlotko
-  *
-  *    Copyright (C) 2015  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/>.
-  */
-
-
-//for persistence algorithm
+/*    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):       Pawel Dlotko
+ *
+ *    Copyright (C) 2015  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/>.
+ */
+
+
+// for persistence algorithm
 #include <gudhi/reader_utils.h>
 #include <gudhi/Bitmap_cubical_complex.h>
 #include <gudhi/Persistent_cohomology.h>
 
-
-using namespace Gudhi;
-using namespace Gudhi::Cubical_complex;
-using namespace Gudhi::persistent_cohomology;
-
-//standard stuff
+// standard stuff
 #include <iostream>
 #include <sstream>
 #include <vector>
 
-using namespace std;
-
-int main( int argc , char** argv )
-{
-    srand( time(0) );
-
-    cout << "This program computes persistent homology, by using bitmap_cubical_complex class, of cubical complexes. \
-The first parameter of the program is the dimension D of the bitmap. \
-The next D parameters are number of top dimensional cubes in each dimension of the bitmap.\
-The program will create random cubical complex of that sizes and compute persistent homology of it." << endl;
-
-    int p = 2;
-    double min_persistence = 0;
-
-    if ( argc < 3 )
-    {
-        cerr << "Wrong number of parameters, the program will now terminate\n";
-        return 1;
-    }
-
-    size_t dimensionOfBitmap = (size_t)atoi( argv[1] );
-    std::vector< unsigned > sizes;
-    size_t multipliers = 1;
-    for ( size_t dim = 0 ; dim != dimensionOfBitmap ; ++dim )
-    {
-        unsigned sizeInThisDimension = (unsigned)atoi( argv[2+dim] );
-        sizes.push_back( sizeInThisDimension );
-        multipliers *= sizeInThisDimension;
-    }
-
-    std::vector< double > data;
-    for ( size_t i = 0 ; i != multipliers ; ++i )
-    {
-        data.push_back( rand()/(double)RAND_MAX );
-    }

-
-    Bitmap_cubical_complex< Bitmap_cubical_complex_base<double> > b( sizes , data );

-

-

-
-
-
-    // Compute the persistence diagram of the complex
-    persistent_cohomology::Persistent_cohomology< Bitmap_cubical_complex< Bitmap_cubical_complex_base<double> >, Field_Zp > pcoh(b);
-    pcoh.init_coefficients( p ); //initilizes the coefficient field for homology
-    pcoh.compute_persistent_cohomology( min_persistence );
-
-
-    stringstream ss;
-    ss << "randomComplex_persistence";
-    std::ofstream out(ss.str().c_str());
-    pcoh.output_diagram(out);
-    out.close();
-
-    return 0;
+int main(int argc, char** argv) {
+  srand(time(0));
+
+  std::cout << "This program computes persistent homology, by using bitmap_cubical_complex class, of cubical " <<
+      "complexes. The first parameter of the program is the dimension D of the bitmap. The next D parameters are " <<
+      "number of top dimensional cubes in each dimension of the bitmap. The program will create random cubical " <<
+      "complex of that sizes and compute persistent homology of it." << std::endl;
+
+  int p = 2;
+  double min_persistence = 0;
+
+  if (argc < 3) {
+    std::cerr << "Wrong number of parameters, the program will now terminate\n";
+    return 1;
+  }
+
+  size_t dimensionOfBitmap = (size_t) atoi(argv[1]);
+  std::vector< unsigned > sizes;
+  size_t multipliers = 1;
+  for (size_t dim = 0; dim != dimensionOfBitmap; ++dim) {
+    unsigned sizeInThisDimension = (unsigned) atoi(argv[2 + dim]);
+    sizes.push_back(sizeInThisDimension);
+    multipliers *= sizeInThisDimension;
+  }
+
+  std::vector< double > data;
+  for (size_t i = 0; i != multipliers; ++i) {
+    data.push_back(rand() / static_cast<double>(RAND_MAX));
+  }
+
+  typedef Gudhi::Cubical_complex::Bitmap_cubical_complex_base<double> Bitmap_cubical_complex_base;
+  typedef Gudhi::Cubical_complex::Bitmap_cubical_complex<Bitmap_cubical_complex_base> Bitmap_cubical_complex;
+  Bitmap_cubical_complex b(sizes, data);
+
+  // Compute the persistence diagram of the complex
+  typedef Gudhi::persistent_cohomology::Field_Zp Field_Zp;
+  typedef Gudhi::persistent_cohomology::Persistent_cohomology<Bitmap_cubical_complex, Field_Zp> Persistent_cohomology;
+  Persistent_cohomology pcoh(b);
+  pcoh.init_coefficients(p);  // initializes the coefficient field for homology
+  pcoh.compute_persistent_cohomology(min_persistence);
+
+  std::stringstream ss;
+  ss << "randomComplex_persistence";
+  std::ofstream out(ss.str().c_str());
+  pcoh.output_diagram(out);
+  out.close();
+
+  return 0;
 }
+