diff options
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;
+}
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