Adding a first vesion of a functionality that provide periodic boundary codnitions.

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/bitmap@955 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: ae60d98a6b2c15c2f7152663c3b05d40f0a56e86

3 files changed, 148 insertions, 73 deletions

diff --git a/src/Bitmap_cubical_complex/example/Bitmap_cubical_complex.cpp b/src/Bitmap_cubical_complex/example/Bitmap_cubical_complex.cpp
index e56428b6..ed141ed9 100644
--- a/src/Bitmap_cubical_complex/example/Bitmap_cubical_complex.cpp
+++ b/src/Bitmap_cubical_complex/example/Bitmap_cubical_complex.cpp
@@ -1,73 +1,73 @@
- /*    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
-#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 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<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(ss.str().c_str());
-    pcoh.output_diagram(out);
-    out.close();
-
-    return 0;
-}
+ /*    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>

+

+

+using namespace Gudhi;

+using namespace Gudhi::Cubical_complex;

+using namespace Gudhi::persistent_cohomology;

+

+//standard stuff

+#include <iostream>

+#include <sstream>

+#include <vector>

+

+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 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<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/Bitmap_cubical_complex_periodic_boundary_conditions.cpp b/src/Bitmap_cubical_complex/example/Bitmap_cubical_complex_periodic_boundary_conditions.cpp
new file mode 100644
index 00000000..fa60d4f3
--- /dev/null
+++ b/src/Bitmap_cubical_complex/example/Bitmap_cubical_complex_periodic_boundary_conditions.cpp
@@ -0,0 +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/>.

+  */

+

+

+#include <gudhi/reader_utils.h>

+#include <gudhi/Bitmap_cubical_complex_periodic_boundary_conditions.h>

+#include <gudhi/Persistent_cohomology.h>

+

+

+using namespace Gudhi;

+using namespace Gudhi::Cubical_complex;

+using namespace Gudhi::persistent_cohomology;

+

+//standard stuff

+#include <iostream>

+#include <sstream>

+#include <vector>

+

+using namespace std;

+

+int main( int argc , char** argv )

+{

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

+

+

+    // Compute the persistence diagram of the complex

+    persistent_cohomology::Persistent_cohomology< Bitmap_cubical_complex_periodic_boundary_conditions<double>, 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();

+

+    return 0;

+}

diff --git a/src/Bitmap_cubical_complex/example/CMakeLists.txt b/src/Bitmap_cubical_complex/example/CMakeLists.txt
index dd252a79..26796e9d 100644
--- a/src/Bitmap_cubical_complex/example/CMakeLists.txt
+++ b/src/Bitmap_cubical_complex/example/CMakeLists.txt
@@ -10,3 +10,6 @@ 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)
 
+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})	
+