Typo

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/persistence_representation_integration@2472 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 457b970258b8a99519db664358c19d0dee80d879

7 files changed, 410 insertions, 0 deletions

diff --git a/src/Persistence_representations/utilities/persistence_vectors/CMakeLists.txt b/src/Persistence_representations/utilities/persistence_vectors/CMakeLists.txt
new file mode 100644
index 00000000..8033e27a
--- /dev/null
+++ b/src/Persistence_representations/utilities/persistence_vectors/CMakeLists.txt
@@ -0,0 +1,25 @@
+cmake_minimum_required(VERSION 2.6)
+project(GUDHI_STAT)
+
+#persitence vectors
+add_executable ( create_persistence_vectors create_persistence_vectors.cpp )
+target_link_libraries(create_persistence_vectors ${Boost_SYSTEM_LIBRARY})
+add_test ( create_persistence_vectors ${CMAKE_CURRENT_BINARY_DIR}/create_persistence_vectors -1 "${CMAKE_SOURCE_DIR}/data/persistence_diagram/simple_diagram.txt" )
+
+add_executable ( average_persistence_vectors average_persistence_vectors.cpp )
+target_link_libraries(average_persistence_vectors ${Boost_SYSTEM_LIBRARY})
+add_test ( average_persistence_vectors ${CMAKE_CURRENT_BINARY_DIR}/average_persistence_vectors "${CMAKE_SOURCE_DIR}/data/persistence_diagram/simple_diagram.txt.vect" "${CMAKE_SOURCE_DIR}/data/persistence_diagram/simple_diagram.txt.vect" )
+
+add_executable ( compute_distance_of_persistence_vectors compute_distance_of_persistence_vectors.cpp )
+target_link_libraries(compute_distance_of_persistence_vectors ${Boost_SYSTEM_LIBRARY})
+add_test ( compute_distance_of_persistence_vectors ${CMAKE_CURRENT_BINARY_DIR}/compute_distance_of_persistence_vectors -1 "${CMAKE_SOURCE_DIR}/data/persistence_diagram/simple_diagram.txt.vect" "${CMAKE_SOURCE_DIR}/data/persistence_diagram/simple_diagram.txt.vect" )
+
+add_executable ( compute_scalar_product_of_persistence_vectors compute_scalar_product_of_persistence_vectors.cpp )
+target_link_libraries(compute_scalar_product_of_persistence_vectors ${Boost_SYSTEM_LIBRARY})
+add_test ( compute_scalar_product_of_persistence_vectors ${CMAKE_CURRENT_BINARY_DIR}/compute_scalar_product_of_persistence_vectors "${CMAKE_SOURCE_DIR}/data/persistence_diagram/simple_diagram.txt.vect" "${CMAKE_SOURCE_DIR}/data/persistence_diagram/simple_diagram.txt.vect" )
+
+add_executable ( plot_persistence_vectors plot_persistence_vectors.cpp )
+target_link_libraries(plot_persistence_vectors ${Boost_SYSTEM_LIBRARY})
+add_test ( plot_persistence_vectors ${CMAKE_CURRENT_BINARY_DIR}/plot_persistence_vectors "${CMAKE_SOURCE_DIR}/data/persistence_diagram/simple_diagram.txt.vect" )
+
+
diff --git a/src/Persistence_representations/utilities/persistence_vectors/average_persistence_vectors.cpp b/src/Persistence_representations/utilities/persistence_vectors/average_persistence_vectors.cpp
new file mode 100644
index 00000000..320d1f63
--- /dev/null
+++ b/src/Persistence_representations/utilities/persistence_vectors/average_persistence_vectors.cpp
@@ -0,0 +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 (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/Persistence_vectors.h>
+
+
+
+using namespace Gudhi;
+using namespace Gudhi::Persistence_representations;
+
+#include <iostream>
+
+
+int main( int argc , char** argv )
+{
+	std::cout << "This program computes average persistence vector of persistence vectors created based on persistence diagrams provided as an input. \n";
+	std::cout << "Please call this program with the names of files with persistence diagrams \n";
+	std::vector< const char* > filenames;
+	
+	if ( argc == 1 )
+	{
+		std::cout << "No input files given, the program will now terminate \n";
+		return 1;
+	}
+	
+	for ( int i = 1 ; i < argc ; ++i )
+	{
+		filenames.push_back( argv[i] );
+	}
+	
+	std::cout << "Reading persistence vectors...\n";
+	std::vector< Vector_distances_in_diagram< Euclidean_distance >* > lands;
+	for ( size_t i = 0 ; i != filenames.size() ; ++i )
+	{		
+		Vector_distances_in_diagram< Euclidean_distance >* l = new Vector_distances_in_diagram< Euclidean_distance >;
+		l->load_from_file( filenames[i] );
+		lands.push_back(l );
+	}
+	
+	Vector_distances_in_diagram< Euclidean_distance > av;
+	av.compute_average( lands );
+	
+	av.print_to_file( "average.vect" );
+	
+	for ( size_t i = 0 ; i != filenames.size() ; ++i )
+	{
+		delete lands[i];
+	}
+	
+	std::cout << "Done \n";
+
+	return 0;
+}
diff --git a/src/Persistence_representations/utilities/persistence_vectors/compute_distance_of_persistence_vectors.cpp b/src/Persistence_representations/utilities/persistence_vectors/compute_distance_of_persistence_vectors.cpp
new file mode 100644
index 00000000..39e24cd7
--- /dev/null
+++ b/src/Persistence_representations/utilities/persistence_vectors/compute_distance_of_persistence_vectors.cpp
@@ -0,0 +1,111 @@
+/*    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 (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/Persistence_vectors.h>
+
+
+
+using namespace Gudhi;
+using namespace Gudhi::Persistence_representations;
+
+#include <iostream>
+#include <sstream>
+
+
+int main( int argc , char** argv )
+{
+	std::cout << "This program compute distance of persistence vectors stored in a file (the file needs to be created beforehand). \n";	
+	std::cout << "The first parameter of a program is an interger p. The program compute l^p distance of the vectors. For l^infty distance choose p = -1. \n";
+	std::cout << "The remaining parameters of this programs are names of files with persistence vectors.\n";
+	
+	if ( argc < 3 )
+	{
+		std::cout << "Wrong number of parameters, the program will now terminate \n";
+		return 1;
+	}
+	
+	int pp = atoi( argv[1] );
+	double p = std::numeric_limits<double>::max();
+	if ( pp != -1 )
+	{
+		p = pp;
+	}
+	
+
+	std::vector< const char* > filenames;
+	for ( int i = 2 ; i < argc ; ++i )
+	{
+		filenames.push_back( argv[i] );
+	}
+	std::vector< Vector_distances_in_diagram< Euclidean_distance > > vectors;
+	vectors.reserve( filenames.size() );
+	for ( size_t file_no = 0 ; file_no != filenames.size() ; ++file_no )
+	{
+		//cerr << filenames[file_no] << endl;
+		Vector_distances_in_diagram< Euclidean_distance > l;
+		l.load_from_file( filenames[file_no] );
+		vectors.push_back( l );
+	}
+		
+	//and now we will compute the scalar product of landscapes.
+	
+	//first we prepare an array:
+	std::vector< std::vector< double > > distance( filenames.size() );
+	for ( size_t i = 0 ; i != filenames.size() ; ++i )
+	{
+		std::vector< double > v( filenames.size() , 0 );
+		distance[i] = v;
+	}
+		
+	//and now we can compute the distances:
+	for ( size_t i = 0 ; i != vectors.size() ; ++i )
+	{
+		for ( size_t j = i+1 ; j != vectors.size() ; ++j )
+		{
+			distance[i][j] = distance[j][i] = vectors[i].distance( vectors[j] , p ) ;
+		}
+	}
+	
+	//and now output the result to the screen and a file:
+	std::ofstream out;
+	out.open( "distance" );
+	for ( size_t i = 0 ; i != distance.size() ; ++i )
+	{
+		for ( size_t j = 0 ; j != distance.size() ; ++j )
+		{
+			std::cout << distance[i][j] << " ";
+			out << distance[i][j] << " ";
+		}
+		std::cout << std::endl;
+		out << std::endl;
+	}
+	out.close();
+		
+	return 0;
+}
+
+
+
+
+
+
+	
diff --git a/src/Persistence_representations/utilities/persistence_vectors/compute_scalar_product_of_persistence_vectors.cpp b/src/Persistence_representations/utilities/persistence_vectors/compute_scalar_product_of_persistence_vectors.cpp
new file mode 100644
index 00000000..7a1bbaf0
--- /dev/null
+++ b/src/Persistence_representations/utilities/persistence_vectors/compute_scalar_product_of_persistence_vectors.cpp
@@ -0,0 +1,87 @@
+/*    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 (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/Persistence_vectors.h>
+
+
+
+using namespace Gudhi;
+using namespace Gudhi::Persistence_representations;
+
+#include <iostream>
+#include <sstream>
+
+
+int main( int argc , char** argv )
+{
+	std::cout << "This program compute scalar product of persistence vectors stored in a file (the file needs to be created beforehand). \n";	
+	std::cout << "The parameters of this programs are names of files with persistence vectors.\n";
+
+	std::vector< const char* > filenames;
+	for ( int i = 1 ; i < argc ; ++i )
+	{
+		filenames.push_back( argv[i] );
+	}
+	std::vector< Vector_distances_in_diagram< Euclidean_distance > > vectors;
+	vectors.reserve( filenames.size() );
+	for ( size_t file_no = 0 ; file_no != filenames.size() ; ++file_no )
+	{
+		Vector_distances_in_diagram< Euclidean_distance > l;
+		l.load_from_file( filenames[file_no] );
+		vectors.push_back( l );
+	}
+		
+	//and now we will compute the scalar product of landscapes.
+	
+	//first we prepare an array:
+	std::vector< std::vector< double > > scalar_product( filenames.size() );
+	for ( size_t i = 0 ; i != filenames.size() ; ++i )
+	{
+		std::vector< double > v( filenames.size() , 0 );
+		scalar_product[i] = v;
+	}
+	
+	//and now we can compute the scalar product:
+	for ( size_t i = 0 ; i != vectors.size() ; ++i )
+	{
+		for ( size_t j = i ; j != vectors.size() ; ++j )
+		{
+			scalar_product[i][j] = scalar_product[j][i] = vectors[i].compute_scalar_product( vectors[j] ) ;
+		}
+	}
+	
+	//and now output the result to the screen and a file:
+	std::ofstream out;
+	out.open( "scalar_product" );
+	for ( size_t i = 0 ; i != scalar_product.size() ; ++i )
+	{
+		for ( size_t j = 0 ; j != scalar_product.size() ; ++j )
+		{
+			std::cout << scalar_product[i][j] << " ";
+			out << scalar_product[i][j] << " ";
+		}
+		std::cout << std::endl;
+		out << std::endl;
+	}
+	out.close();	
+	return 0;
+}
diff --git a/src/Persistence_representations/utilities/persistence_vectors/create_persistence_vectors.cpp b/src/Persistence_representations/utilities/persistence_vectors/create_persistence_vectors.cpp
new file mode 100644
index 00000000..634bcb13
--- /dev/null
+++ b/src/Persistence_representations/utilities/persistence_vectors/create_persistence_vectors.cpp
@@ -0,0 +1,65 @@
+/*    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 (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/Persistence_vectors.h>
+
+
+
+using namespace Gudhi;
+using namespace Gudhi::Persistence_representations;
+
+#include <iostream>
+#include <sstream>
+
+
+int main( int argc , char** argv )
+{
+	std::cout << "This program creates persistence vectors of diagrams provided as an input. The first parameter of this program is a dimension of persistence ";
+	std::cout << " that will be used in creation of the persistence vectors. If our input files contain persistence pairs of various dimension, as a second parameter of the ";
+	std::cout << " procedure please provide the dimension of persistence you want to use. If in your file there are only birth-death pairs of the same dimension, set the first parameter to -1." << std::endl;
+	std::cout << "The remaining parameters are the names of files with persistence diagrams. \n";
+	int dim = atoi( argv[1] );
+	unsigned dimension = std::numeric_limits<unsigned>::max();
+	if ( dim >= 0 )
+	{
+		dimension = (unsigned)dim;
+	}
+	
+	std::vector< const char* > filenames;
+	for ( int i = 2 ; i < argc ; ++i )
+	{
+		filenames.push_back( argv[i] );
+	}
+	
+	for ( size_t i = 0 ; i != filenames.size() ; ++i )
+	{
+		std::cerr << "Creatign persistence vectors based on a file : " << filenames[i] << std::endl;
+		//std::vector< std::pair< double , double > > persistence_pairs = read_gudhi_persistence_file_in_one_dimension( filenames[i] , size_t dimension = 0 )
+		Vector_distances_in_diagram< Euclidean_distance > l( filenames[i] , dimension );				
+		std::stringstream ss;
+		ss << filenames[i] << ".vect";
+		l.print_to_file( ss.str().c_str() );
+	}
+	std::cout << "Done \n";
+	return 0;
+}
+
diff --git a/src/Persistence_representations/utilities/persistence_vectors/plot_persistence_vectors.cpp b/src/Persistence_representations/utilities/persistence_vectors/plot_persistence_vectors.cpp
new file mode 100644
index 00000000..c72fc1ee
--- /dev/null
+++ b/src/Persistence_representations/utilities/persistence_vectors/plot_persistence_vectors.cpp
@@ -0,0 +1,48 @@
+/*    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 (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/Persistence_vectors.h>
+
+
+
+using namespace Gudhi;
+using namespace Gudhi::Persistence_representations;
+
+#include <iostream>
+#include <sstream>
+
+
+int main( int argc , char** argv )
+{
+	std::cout << "This program create a Gnuplot script to plot persistence vector. Please call this program with the name of file with persistence vector. \n";
+	if ( argc != 2 )
+	{
+		std::cout << "Wrong number of parameters, the program will now terminate. \n";
+		return 1;
+	}
+	Vector_distances_in_diagram< Euclidean_distance > l;
+	l.load_from_file( argv[1] );
+	l.plot( argv[1] );
+	
+	return 0;
+}
+
diff --git a/src/Persistence_representations/utilities/persistence_vectors/simple_diagram.txt.vect b/src/Persistence_representations/utilities/persistence_vectors/simple_diagram.txt.vect
new file mode 100644
index 00000000..1d4eeaaf
--- /dev/null
+++ b/src/Persistence_representations/utilities/persistence_vectors/simple_diagram.txt.vect
@@ -0,0 +1 @@
+0.707107 0.707107 0.707107 0.707107 0.707107 0.707107 0.707107 0.707107 0.707107 0.707107 
\ No newline at end of file