Add bitmap cubical complex

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/bitmap@794 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 50d9b8eb80e0fe99f871afa5bdbb853add97e25e

3 files changed, 166 insertions, 0 deletions

diff --git a/src/Bitmap_cubical_complex/example/Bitmap_cubical_complex.cpp b/src/Bitmap_cubical_complex/example/Bitmap_cubical_complex.cpp
new file mode 100644
index 00000000..c0dbaf36
--- /dev/null
+++ b/src/Bitmap_cubical_complex/example/Bitmap_cubical_complex.cpp
@@ -0,0 +1,69 @@
+/*    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 Sophia-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"

+

+#include <boost/program_options.hpp>

+

+using namespace Gudhi;

+using namespace Gudhi::persistent_cohomology;

+

+//standard stuff

+#include <iostream>

+#include <sstream>

+

+using namespace std;

+

+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 numbed in \

+the first line is a dimension D of a cubical complex. 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 cubical complex at the input. The program will now terminate.\n";

+    return 1;

+  }

+

+  Bitmap_cubical_complex<double> b(argv[1]);

+

+

+  // Compute the persistence diagram of the complex

+  persistent_cohomology::Persistent_cohomology< Bitmap_cubical_complex<double>, Field_Zp > pcoh(b);

+  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();

+

+  return 0;

+}

diff --git a/src/Bitmap_cubical_complex/example/CMakeLists.txt b/src/Bitmap_cubical_complex/example/CMakeLists.txt
new file mode 100644
index 00000000..05ef1319
--- /dev/null
+++ b/src/Bitmap_cubical_complex/example/CMakeLists.txt
@@ -0,0 +1,12 @@
+cmake_minimum_required(VERSION 2.6)
+project(GUDHISimplexTreeFromFile)
+
+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_executable ( Random_bitmap_cubical_complex Random_bitmap_cubical_complex.cpp )
+target_link_libraries(Random_bitmap_cubical_complex ${Boost_SYSTEM_LIBRARY})	
+add_test(Random_bitmap_cubical_complex ${CMAKE_CURRENT_BINARY_DIR}/Random_bitmap_cubical_complex 2 100 100)
+
diff --git a/src/Bitmap_cubical_complex/example/Random_bitmap_cubical_complex.cpp b/src/Bitmap_cubical_complex/example/Random_bitmap_cubical_complex.cpp
new file mode 100644
index 00000000..de9d96e0
--- /dev/null
+++ b/src/Bitmap_cubical_complex/example/Random_bitmap_cubical_complex.cpp
@@ -0,0 +1,85 @@
+/*    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"

+

+#include <boost/program_options.hpp>

+

+using namespace Gudhi;

+using namespace Gudhi::persistent_cohomology;

+

+//standard stuff

+#include <iostream>

+#include <sstream>

+#include <vector>

+#include <cstdlib>

+#include <ctime>

+

+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 cubical complex. The next D parameters are number of top dimensional cubes in each dimension of the cubical complex.\

+The program will create random cubical complex of that sizes and compute persistent homology of it." << endl;

+

+  int p = 2;

+  double min_persistence = 0;

+

+  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<double> b(sizes, data);

+

+

+  // Compute the persistence diagram of the complex

+  persistent_cohomology::Persistent_cohomology< Bitmap_cubical_complex<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((char*) ss.str().c_str());

+  pcoh.output_diagram(out);

+  out.close();

+

+  return 0;

+}