4 files changed, 203 insertions, 0 deletions
diff --git a/src/Bitmap_cubical_complex/utilities/CMakeLists.txt b/src/Bitmap_cubical_complex/utilities/CMakeLists.txt
new file mode 100644
index 00000000..416db67f
--- /dev/null
+++ b/src/Bitmap_cubical_complex/utilities/CMakeLists.txt
@@ -0,0 +1,28 @@
+project(Bitmap_cubical_complex_utilities)
+
+add_executable ( cubical_complex_persistence cubical_complex_persistence.cpp )
+if (TBB_FOUND)
+  target_link_libraries(cubical_complex_persistence ${TBB_LIBRARIES})
+endif()
+
+add_test(NAME Bitmap_cubical_complex_utility_persistence_one_sphere COMMAND $<TARGET_FILE:cubical_complex_persistence>
+    "${CMAKE_SOURCE_DIR}/data/bitmap/CubicalOneSphere.txt")
+
+add_test(NAME Bitmap_cubical_complex_utility_persistence_two_sphere COMMAND $<TARGET_FILE:cubical_complex_persistence>
+    "${CMAKE_SOURCE_DIR}/data/bitmap/CubicalTwoSphere.txt")
+
+add_executable ( periodic_cubical_complex_persistence periodic_cubical_complex_persistence.cpp )
+if (TBB_FOUND)
+  target_link_libraries(periodic_cubical_complex_persistence ${TBB_LIBRARIES})
+endif()
+
+add_test(NAME Bitmap_cubical_complex_utility_periodic_boundary_conditions_2d_torus
+    COMMAND $<TARGET_FILE:periodic_cubical_complex_persistence>
+    "${CMAKE_SOURCE_DIR}/data/bitmap/2d_torus.txt")
+
+add_test(NAME Bitmap_cubical_complex_utility_periodic_boundary_conditions_3d_torus
+    COMMAND $<TARGET_FILE:periodic_cubical_complex_persistence>
+    "${CMAKE_SOURCE_DIR}/data/bitmap/3d_torus.txt")
+
+install(TARGETS cubical_complex_persistence DESTINATION bin)
+install(TARGETS periodic_cubical_complex_persistence DESTINATION bin)
diff --git a/src/Bitmap_cubical_complex/utilities/cubical_complex_persistence.cpp b/src/Bitmap_cubical_complex/utilities/cubical_complex_persistence.cpp
new file mode 100644
index 00000000..a9792c2d
--- /dev/null
+++ b/src/Bitmap_cubical_complex/utilities/cubical_complex_persistence.cpp
@@ -0,0 +1,68 @@
+/*    This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT.
+ *    See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details.
+ *    Author(s):       Pawel Dlotko
+ *
+ *    Copyright (C) 2015 Inria
+ *
+ *    Modification(s):
+ *      - YYYY/MM Author: Description of the modification
+ */
+
+#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 = 11;
+  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/cubicalcomplex.md b/src/Bitmap_cubical_complex/utilities/cubicalcomplex.md
new file mode 100644
index 00000000..5b0404c3
--- /dev/null
+++ b/src/Bitmap_cubical_complex/utilities/cubicalcomplex.md
@@ -0,0 +1,37 @@
+---
+layout: page
+title: "Cubical complex"
+meta_title: "Cubical complex"
+teaser: ""
+permalink: /cubicalcomplex/
+---
+{::comment}
+Leave the lines above as it is required by the web site generator 'Jekyll'
+{:/comment}
+
+
+## cubical_complex_persistence ##
+This program computes persistent homology, by using the Bitmap_cubical_complex class, of cubical complexes provided in text files in Perseus style.
+See [here](/doc/latest/fileformats.html#FileFormatsPerseus) for a description of the file format.
+
+**Example**
+
+```
+   cubical_complex_persistence data/bitmap/CubicalTwoSphere.txt
+```
+
+* Creates a Cubical Complex from the Perseus style file `CubicalTwoSphere.txt`,
+computes Persistence cohomology from it and writes the results in a persistence file `CubicalTwoSphere.txt_persistence`.
+
+## periodic_cubical_complex_persistence ##
+
+Same as above, but with periodic boundary conditions.
+
+**Example**
+
+```
+   periodic_cubical_complex_persistence data/bitmap/3d_torus.txt
+```
+
+* Creates a Periodical Cubical Complex from the Perseus style file `3d_torus.txt`,
+computes Persistence cohomology from it and writes the results in a persistence file `3d_torus.txt_persistence`.
diff --git a/src/Bitmap_cubical_complex/utilities/periodic_cubical_complex_persistence.cpp b/src/Bitmap_cubical_complex/utilities/periodic_cubical_complex_persistence.cpp
new file mode 100644
index 00000000..fa97bac0
--- /dev/null
+++ b/src/Bitmap_cubical_complex/utilities/periodic_cubical_complex_persistence.cpp
@@ -0,0 +1,70 @@
+/*    This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT.
+ *    See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details.
+ *    Author(s):       Pawel Dlotko
+ *
+ *    Copyright (C) 2015 Inria
+ *
+ *    Modification(s):
+ *      - YYYY/MM Author: Description of the modification
+ */
+
+#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>
+#include <string>
+
+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 = 11;
+  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;
+}