Move 2 examples from Bitmap_cubical_complex to utilities

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/add_utils_in_gudhi_v2@2492 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 40e5f550edb48780d2cf1fe322a5c1d7dd5c80b0

3 files changed, 192 insertions, 0 deletions

diff --git a/src/Bitmap_cubical_complex/utilities/Bitmap_cubical_complex.cpp b/src/Bitmap_cubical_complex/utilities/Bitmap_cubical_complex.cpp
new file mode 100644
index 00000000..67735ba1
--- /dev/null
+++ b/src/Bitmap_cubical_complex/utilities/Bitmap_cubical_complex.cpp
@@ -0,0 +1,80 @@
+/*    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.h>
+#include <gudhi/Persistent_cohomology.h>
+
+// standard stuff
+#include <iostream>
+#include <string>
+#include <vector>
+#include <cstddef>
+
+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;
+
+  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_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;
+
+  Bitmap_cubical_complex b(argv[1]);
+
+  // Compute the persistence diagram of the complex
+  Persistent_cohomology pcoh(b);
+  int p = 2;
+  double min_persistence = 0;
+
+  pcoh.init_coefficients(p);  // initializes the coefficient field for homology
+  pcoh.compute_persistent_cohomology(min_persistence);
+
+  std::string output_file_name(argv[1]);
+  output_file_name += "_persistence";
+
+  std::size_t last_in_path = output_file_name.find_last_of("/\\");
+
+  if (last_in_path != std::string::npos) {
+    output_file_name = output_file_name.substr(last_in_path+1);
+  }
+
+  std::ofstream out(output_file_name.c_str());
+  pcoh.output_diagram(out);
+  out.close();
+
+  std::cout << "Result in file: " << output_file_name << "\n";
+
+  return 0;
+}
+
diff --git a/src/Bitmap_cubical_complex/utilities/Bitmap_cubical_complex_periodic_boundary_conditions.cpp b/src/Bitmap_cubical_complex/utilities/Bitmap_cubical_complex_periodic_boundary_conditions.cpp
new file mode 100644
index 00000000..f8754345
--- /dev/null
+++ b/src/Bitmap_cubical_complex/utilities/Bitmap_cubical_complex_periodic_boundary_conditions.cpp
@@ -0,0 +1,81 @@
+/*    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.h>
+#include <gudhi/Bitmap_cubical_complex_periodic_boundary_conditions_base.h>
+#include <gudhi/Persistent_cohomology.h>
+
+// standard stuff
+#include <iostream>
+#include <sstream>
+#include <vector>
+
+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;
+
+  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);
+
+  int p = 2;
+  double min_persistence = 0;
+  pcoh.init_coefficients(p);  // initializes the coefficient field for homology
+  pcoh.compute_persistent_cohomology(min_persistence);
+
+  std::string output_file_name(argv[1]);
+  output_file_name += "_persistence";
+
+  std::size_t last_in_path = output_file_name.find_last_of("/\\");
+
+  if (last_in_path != std::string::npos) {
+    output_file_name = output_file_name.substr(last_in_path+1);
+  }
+
+  std::ofstream out(output_file_name.c_str());
+  pcoh.output_diagram(out);
+  out.close();
+
+  std::cout << "Result in file: " << output_file_name << "\n";
+
+  return 0;
+}
+
diff --git a/src/Bitmap_cubical_complex/utilities/CMakeLists.txt b/src/Bitmap_cubical_complex/utilities/CMakeLists.txt
new file mode 100644
index 00000000..43fb8c86
--- /dev/null
+++ b/src/Bitmap_cubical_complex/utilities/CMakeLists.txt
@@ -0,0 +1,31 @@
+cmake_minimum_required(VERSION 2.6)
+project(Bitmap_cubical_complex_utilities)
+
+add_executable ( Bitmap_cubical_complex Bitmap_cubical_complex.cpp )
+target_link_libraries(Bitmap_cubical_complex ${Boost_SYSTEM_LIBRARY})
+if (TBB_FOUND)
+  target_link_libraries(Bitmap_cubical_complex ${TBB_LIBRARIES})
+endif()
+
+add_test(NAME Bitmap_cubical_complex_utility_persistence_one_sphere COMMAND $<TARGET_FILE:Bitmap_cubical_complex>
+    "${CMAKE_SOURCE_DIR}/data/bitmap/CubicalOneSphere.txt")
+
+add_test(NAME Bitmap_cubical_complex_utility_persistence_two_sphere COMMAND $<TARGET_FILE:Bitmap_cubical_complex>
+    "${CMAKE_SOURCE_DIR}/data/bitmap/CubicalTwoSphere.txt")
+
+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})
+if (TBB_FOUND)
+  target_link_libraries(Bitmap_cubical_complex_periodic_boundary_conditions ${TBB_LIBRARIES})
+endif()
+
+add_test(NAME Bitmap_cubical_complex_utility_periodic_boundary_conditions_2d_torus
+    COMMAND $<TARGET_FILE:Bitmap_cubical_complex_periodic_boundary_conditions>
+    "${CMAKE_SOURCE_DIR}/data/bitmap/2d_torus.txt")
+
+add_test(NAME Bitmap_cubical_complex_utility_periodic_boundary_conditions_3d_torus
+    COMMAND $<TARGET_FILE:Bitmap_cubical_complex_periodic_boundary_conditions>
+    "${CMAKE_SOURCE_DIR}/data/bitmap/3d_torus.txt")
+
+install(TARGETS Bitmap_cubical_complex DESTINATION bin)
+install(TARGETS Bitmap_cubical_complex_periodic_boundary_conditions DESTINATION bin)