Over here I have linkd phat with Gudhi. So far it is done only for cubical complexes, but since I am ONLY using Filtration_simplex_iterator, there should be no problem to have it run with any other class we have.

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/bitmap@1004 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: ddb3e2c5fa0c2a816e7435c57d32c0644f8163d2

3 files changed, 146 insertions, 75 deletions

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 3d80c96d..df01240b 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
@@ -1,75 +1,84 @@
- /*    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>

-

-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< Bitmap_cubical_complex_periodic_boundary_conditions_base<double> > b( argv[1] );

-

-

-    // Compute the persistence diagram of the complex

-    persistent_cohomology::Persistent_cohomology<

-    Bitmap_cubical_complex< Bitmap_cubical_complex_periodic_boundary_conditions_base<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;

-}

+ /*    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>
+
+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 )
+{
+    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;
+}
diff --git a/src/Bitmap_cubical_complex/example/CMakeLists.txt b/src/Bitmap_cubical_complex/example/CMakeLists.txt
index 26796e9d..fbd1b28b 100644
--- a/src/Bitmap_cubical_complex/example/CMakeLists.txt
+++ b/src/Bitmap_cubical_complex/example/CMakeLists.txt
@@ -13,3 +13,5 @@ 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_executable ( Compute_persistence_with_phat Compute_persistence_with_phat.cpp )
+target_link_libraries(Compute_persistence_with_phat ${Boost_SYSTEM_LIBRARY})
\ No newline at end of file
diff --git a/src/Bitmap_cubical_complex/example/Compute_persistence_with_phat.cpp b/src/Bitmap_cubical_complex/example/Compute_persistence_with_phat.cpp
new file mode 100644
index 00000000..fe9be33e
--- /dev/null
+++ b/src/Bitmap_cubical_complex/example/Compute_persistence_with_phat.cpp
@@ -0,0 +1,60 @@
+

+ /*    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_periodic_boundary_conditions_base.h>

+#include <gudhi/Bitmap_cubical_complex.h>

+#include <gudhi/Compute_persistence_with_phat.h>

+

+using namespace Gudhi;

+using namespace Gudhi::Cubical_complex;

+

+//standard stuff

+#include <iostream>

+#include <sstream>

+#include <vector>

+

+using namespace std;

+

+

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

+{

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

+    cerr << "Cubical complex created \n";

+

+

+    Compute_persistence_with_phat< Bitmap_cubical_complex< Bitmap_cubical_complex_base<double> > , double > phat(&b);

+    phat::persistence_pairs pairs = phat.compute_persistence_pairs_dualized_chunk_reduction();

+    std::pair< std::vector< std::vector<double> > , std::vector< std::vector< std::pair<double,double> > > > persistence = phat.get_the_intervals( pairs );

+    writeBettiNumbersAndPersistenceIntervalsToFile( "phat_persistence" , persistence );

+

+    return 0;

+}