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, 539 insertions, 0 deletions

diff --git a/src/Persistence_representations/utilities/persistence_landscapes_on_grid/CMakeLists.txt b/src/Persistence_representations/utilities/persistence_landscapes_on_grid/CMakeLists.txt
new file mode 100644
index 00000000..f1ef144b
--- /dev/null
+++ b/src/Persistence_representations/utilities/persistence_landscapes_on_grid/CMakeLists.txt
@@ -0,0 +1,27 @@
+cmake_minimum_required(VERSION 2.6)
+project(GUDHI_STAT)
+
+
+
+
+#persitence landscapes on a grid
+add_executable ( create_landscapes_on_grid create_landscapes_on_grid.cpp )
+target_link_libraries(create_landscapes_on_grid ${Boost_SYSTEM_LIBRARY})
+add_test ( create_landscapes_on_grid ${CMAKE_CURRENT_BINARY_DIR}/create_landscapes_on_grid 100 -1 -1 -1 "${CMAKE_SOURCE_DIR}/data/persistence_diagram/simple_diagram.txt" )
+
+add_executable ( average_landscapes_on_grid average_landscapes_on_grid.cpp )
+target_link_libraries(average_landscapes_on_grid ${Boost_SYSTEM_LIBRARY})
+add_test ( average_landscapes_on_grid ${CMAKE_CURRENT_BINARY_DIR}/average_landscapes_on_grid "${CMAKE_SOURCE_DIR}/data/persistence_diagram/simple_diagram.txt.g_land" "${CMAKE_SOURCE_DIR}/data/persistence_diagram/simple_diagram.txt.g_land" )
+
+add_executable ( plot_landscapes_on_grid plot_landscapes_on_grid.cpp )
+target_link_libraries(plot_landscapes_on_grid ${Boost_SYSTEM_LIBRARY})
+add_test ( plot_landscapes_on_grid ${CMAKE_CURRENT_BINARY_DIR}/plot_landscapes_on_grid "${CMAKE_SOURCE_DIR}/data/persistence_diagram/simple_diagram.txt.g_land" )
+
+add_executable ( compute_distance_of_landscapes_on_grid compute_distance_of_landscapes_on_grid.cpp )
+target_link_libraries(compute_distance_of_landscapes_on_grid ${Boost_SYSTEM_LIBRARY})
+add_test ( compute_distance_of_landscapes_on_grids ${CMAKE_CURRENT_BINARY_DIR}/compute_distance_of_landscapes_on_grid "${CMAKE_SOURCE_DIR}/data/persistence_diagram/simple_diagram.txt.g_land" "${CMAKE_SOURCE_DIR}/data/persistence_diagram/simple_diagram.txt.g_land" )
+
+add_executable ( compute_scalar_product_of_landscapes_on_grid compute_scalar_product_of_landscapes_on_grid.cpp )
+target_link_libraries(compute_scalar_product_of_landscapes_on_grid ${Boost_SYSTEM_LIBRARY})
+add_test ( compute_scalar_product_of_landscapes_on_grid ${CMAKE_CURRENT_BINARY_DIR}/compute_scalar_product_of_landscapes_on_grid "${CMAKE_SOURCE_DIR}/data/persistence_diagram/simple_diagram.txt.g_land" "${CMAKE_SOURCE_DIR}/data/persistence_diagram/simple_diagram.txt.g_land" )	
+
diff --git a/src/Persistence_representations/utilities/persistence_landscapes_on_grid/average_landscapes_on_grid.cpp b/src/Persistence_representations/utilities/persistence_landscapes_on_grid/average_landscapes_on_grid.cpp
new file mode 100644
index 00000000..10d9e7ac
--- /dev/null
+++ b/src/Persistence_representations/utilities/persistence_landscapes_on_grid/average_landscapes_on_grid.cpp
@@ -0,0 +1,71 @@
+/*    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_landscape_on_grid.h>
+
+
+
+using namespace Gudhi;
+using namespace Gudhi::Persistence_representations;
+
+#include <iostream>
+
+
+int main( int argc , char** argv )
+{
+	std::cout << "This program computes average persistence landscape on grid of persistence landscapes on grid created based on persistence diagrams provided as an input. 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 << "Creating persistence landscapes...\n";
+	std::vector< Persistence_landscape_on_grid* > lands;
+	for ( size_t i = 0 ; i != filenames.size() ; ++i )
+	{
+		Persistence_landscape_on_grid* l = new Persistence_landscape_on_grid;
+		l->load_landscape_from_file( filenames[i] );
+		lands.push_back( l );
+	}
+	
+	Persistence_landscape_on_grid av;
+	av.compute_average( lands );
+	
+	av.print_to_file( "average.g_land" );
+	
+	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_landscapes_on_grid/compute_distance_of_landscapes_on_grid.cpp b/src/Persistence_representations/utilities/persistence_landscapes_on_grid/compute_distance_of_landscapes_on_grid.cpp
new file mode 100644
index 00000000..4ecbd548
--- /dev/null
+++ b/src/Persistence_representations/utilities/persistence_landscapes_on_grid/compute_distance_of_landscapes_on_grid.cpp
@@ -0,0 +1,110 @@
+/*    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_landscape_on_grid.h>
+
+
+
+using namespace Gudhi;
+using namespace Gudhi::Persistence_representations;
+
+#include <iostream>
+#include <sstream>
+
+
+int main( int argc , char** argv )
+{
+	std::cout << "This program compute dsitance of persistence landscapes on grid 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 the landscapes on grid. For L^infty distance choose p = -1. \n";
+	std::cout << "The remaining parameters of this programs are names of files with persistence landscapes on grid.\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< Persistence_landscape_on_grid > landscaspes;
+	landscaspes.reserve( filenames.size() );
+	for ( size_t file_no = 0 ; file_no != filenames.size() ; ++file_no )
+	{
+		Persistence_landscape_on_grid l;
+		l.load_landscape_from_file( filenames[file_no] );
+		landscaspes.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 scalar product:
+	for ( size_t i = 0 ; i != landscaspes.size() ; ++i )
+	{
+		for ( size_t j = i ; j != landscaspes.size() ; ++j )
+		{
+			distance[i][j] = distance[j][i] = compute_distance_of_landscapes_on_grid( landscaspes[i], landscaspes[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_landscapes_on_grid/compute_scalar_product_of_landscapes_on_grid.cpp b/src/Persistence_representations/utilities/persistence_landscapes_on_grid/compute_scalar_product_of_landscapes_on_grid.cpp
new file mode 100644
index 00000000..342613b4
--- /dev/null
+++ b/src/Persistence_representations/utilities/persistence_landscapes_on_grid/compute_scalar_product_of_landscapes_on_grid.cpp
@@ -0,0 +1,89 @@
+/*    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_landscape_on_grid.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 landscapes on grid 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 landscapes on grid.\n";
+
+	std::vector< const char* > filenames;
+	for ( int i = 1 ; i < argc ; ++i )
+	{
+		filenames.push_back( argv[i] );
+	}
+	std::vector< Persistence_landscape_on_grid > landscaspes;
+	landscaspes.reserve( filenames.size() );
+	for ( size_t file_no = 0 ; file_no != filenames.size() ; ++file_no )
+	{
+		Persistence_landscape_on_grid l;
+		l.load_landscape_from_file( filenames[file_no] );
+		landscaspes.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 != landscaspes.size() ; ++i )
+	{
+		for ( size_t j = i ; j != landscaspes.size() ; ++j )
+		{
+			scalar_product[i][j] = scalar_product[j][i] = compute_inner_product( landscaspes[i], landscaspes[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_landscapes_on_grid/create_landscapes_on_grid.cpp b/src/Persistence_representations/utilities/persistence_landscapes_on_grid/create_landscapes_on_grid.cpp
new file mode 100644
index 00000000..a033362c
--- /dev/null
+++ b/src/Persistence_representations/utilities/persistence_landscapes_on_grid/create_landscapes_on_grid.cpp
@@ -0,0 +1,86 @@
+/*    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_landscape_on_grid.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 landscape on grid of diagrams provided as an input.\n";
+	std::cout << "The first parameter of a program is an integer, a size of a grid.\n";
+	std::cout << "The second and third parameters are min and max of the grid. If you want those numbers to be computed based on the data, set them both to -1 \n";
+	std::cout << "The fourth parameter of the program is the dimension of persistence to be used to construct persistence landscape on a grid. If your file contains ";
+	std::cout << "the information about dimension of birth-death pairs, please provide here the dimension of intervals you want to use. If your input files consist only ";
+	std::cout << "of birth-death pairs, please set the fourth parameter to -1 \n";
+	std::cout << "The remaining parameters are the names of files with persistence diagrams. \n";
+	
+	if ( argc < 5 )
+	{
+		std::cout << "Wrong parameter list, the program will now terminate \n";
+		return 1;
+	}
+	
+	size_t size_of_grid = (size_t)atoi( argv[1] );
+	double min_ = atof( argv[2] );
+	double max_ = atof( argv[3] );
+	int dim = atoi( argv[4] );
+	unsigned dimension = std::numeric_limits<unsigned>::max();
+	if ( dim >= 0 )
+	{
+		dimension = (unsigned)dim;
+	}
+	
+	std::vector< const char* > filenames;
+	for ( int i = 5 ; i < argc ; ++i )
+	{
+		filenames.push_back( argv[i] );
+	}
+	
+	std::cout << "Creating persistence landscapes...\n";	
+	for ( size_t i = 0 ; i != filenames.size() ; ++i )
+	{
+		std::cout << "Creating persistence landscape on a grid based on a file : " << filenames[i] << std::endl;
+		Persistence_landscape_on_grid l;
+		if ( (min_ != -1) || (max_ != -1) )
+		{
+			l = Persistence_landscape_on_grid( filenames[i] , min_ , max_ , size_of_grid , dimension );
+		}
+		else
+		{
+			//(min_ == -1) && (max_ == -1), in this case the program will find min_ and max_ based on the data.
+			l = Persistence_landscape_on_grid( filenames[i] , size_of_grid , dimension );
+		}		
+		std::stringstream ss;
+		ss << filenames[i] << ".g_land";
+		l.print_to_file( ss.str().c_str() );
+	}
+	std::cout << "Done \n";
+	return 0;
+}
diff --git a/src/Persistence_representations/utilities/persistence_landscapes_on_grid/plot_landscapes_on_grid.cpp b/src/Persistence_representations/utilities/persistence_landscapes_on_grid/plot_landscapes_on_grid.cpp
new file mode 100644
index 00000000..700b2f1f
--- /dev/null
+++ b/src/Persistence_representations/utilities/persistence_landscapes_on_grid/plot_landscapes_on_grid.cpp
@@ -0,0 +1,52 @@
+/*    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_landscape_on_grid.h>
+
+
+
+using namespace Gudhi;
+using namespace Gudhi::Persistence_representations;
+
+#include <iostream>
+#include <sstream>
+
+
+int main( int argc , char** argv )
+{
+	std::cout << "This program plot persistence landscape on grid stored in a file (the file needs to be created beforehand). Please call the code with the name of a landsape on grid file \n";	
+	if ( argc == 1 )
+	{
+		std::cout << "Wrong parameters of a program call, the program will now terminate \n";
+		return 1;
+	}
+	Persistence_landscape_on_grid l;
+	l.load_landscape_from_file( argv[1] );
+	
+	std::stringstream ss;
+	ss << argv[1] << "_gnuplot_script";
+	l.plot( ss.str().c_str() );
+	
+	std::cout << "Done \n";
+		
+	return 0;
+}
diff --git a/src/Persistence_representations/utilities/persistence_landscapes_on_grid/simple_diagram.txt.g_land b/src/Persistence_representations/utilities/persistence_landscapes_on_grid/simple_diagram.txt.g_land
new file mode 100644
index 00000000..dc53b932
--- /dev/null
+++ b/src/Persistence_representations/utilities/persistence_landscapes_on_grid/simple_diagram.txt.g_land
@@ -0,0 +1,104 @@
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