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, 521 insertions, 0 deletions

diff --git a/src/Persistence_representations/utilities/persistence_intervals/CMakeLists.txt b/src/Persistence_representations/utilities/persistence_intervals/CMakeLists.txt
new file mode 100644
index 00000000..b5c5928d
--- /dev/null
+++ b/src/Persistence_representations/utilities/persistence_intervals/CMakeLists.txt
@@ -0,0 +1,32 @@
+cmake_minimum_required(VERSION 2.6)
+project(GUDHI_STAT)
+
+#persitence diagrams
+add_executable ( plot_persistence_intervals plot_persistence_intervals.cpp )
+target_link_libraries( plot_persistence_intervals ${Boost_SYSTEM_LIBRARY})
+add_test ( plot_persistence_intervals ${CMAKE_CURRENT_BINARY_DIR}/plot_persistence_intervals "${CMAKE_SOURCE_DIR}/data/persistence_diagram/simple_diagram.txt" )
+
+add_executable ( compute_birth_death_range_in_persistence_diagram compute_birth_death_range_in_persistence_diagram.cpp )
+target_link_libraries( compute_birth_death_range_in_persistence_diagram ${Boost_SYSTEM_LIBRARY})
+add_test ( compute_birth_death_range_in_persistence_diagram ${CMAKE_CURRENT_BINARY_DIR}/compute_birth_death_range_in_persistence_diagram -1 "${CMAKE_SOURCE_DIR}/data/persistence_diagram/simple_diagram.txt" )
+
+add_executable ( compute_number_of_dominant_intervals compute_number_of_dominant_intervals.cpp )
+target_link_libraries( compute_number_of_dominant_intervals ${Boost_SYSTEM_LIBRARY})
+add_test ( compute_number_of_dominant_intervals ${CMAKE_CURRENT_BINARY_DIR}/compute_number_of_dominant_intervals "${CMAKE_SOURCE_DIR}/data/persistence_diagram/simple_diagram.txt" -1 2 )
+
+add_executable ( plot_histogram_of_intervals_lengths plot_histogram_of_intervals_lengths.cpp )
+target_link_libraries( plot_histogram_of_intervals_lengths ${Boost_SYSTEM_LIBRARY})
+add_test ( plot_histogram_of_intervals_lengths ${CMAKE_CURRENT_BINARY_DIR}/plot_histogram_of_intervals_lengths "${CMAKE_SOURCE_DIR}/data/persistence_diagram/simple_diagram.txt" 2 )
+
+add_executable ( plot_persistence_Betti_numbers plot_persistence_Betti_numbers.cpp )
+target_link_libraries( plot_persistence_Betti_numbers ${Boost_SYSTEM_LIBRARY})
+add_test ( plot_persistence_Betti_numbers ${CMAKE_CURRENT_BINARY_DIR}/plot_persistence_Betti_numbers "${CMAKE_SOURCE_DIR}/data/persistence_diagram/simple_diagram.txt" )
+
+if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
+add_executable ( compute_bottleneck_distance compute_bottleneck_distance.cpp )
+target_link_libraries( compute_bottleneck_distance ${Boost_SYSTEM_LIBRARY})
+if (TBB_FOUND)
+target_link_libraries(compute_bottleneck_distance ${TBB_LIBRARIES})
+endif(TBB_FOUND)
+add_test ( compute_bottleneck_distance ${CMAKE_CURRENT_BINARY_DIR}/compute_bottleneck_distance "${CMAKE_SOURCE_DIR}/data/persistence_diagram/simple_diagram.txt" "${CMAKE_SOURCE_DIR}/data/persistence_diagram/simple_diagram.txt" )
+endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
diff --git a/src/Persistence_representations/utilities/persistence_intervals/compute_birth_death_range_in_persistence_diagram.cpp b/src/Persistence_representations/utilities/persistence_intervals/compute_birth_death_range_in_persistence_diagram.cpp
new file mode 100644
index 00000000..2e0d680f
--- /dev/null
+++ b/src/Persistence_representations/utilities/persistence_intervals/compute_birth_death_range_in_persistence_diagram.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/reader_utils.h>
+#include <gudhi/Persistence_intervals.h>
+
+#include <iostream>
+#include <vector>
+#include <limits>
+
+
+
+using namespace Gudhi;
+using namespace Gudhi::Persistence_representations;
+
+
+int main( int argc , char** argv )
+{
+	std::cout << "This program compute the range of birth and death times of persistence pairs in diagrams provided as an input. \n";
+	std::cout << "The first parameter of the program is the dimension of persistence to be used. If your file contains ";
+	std::cout << "the information about dimension of persistence pairs, please provide here the dimension of persistence pairs you want to use. If your input files consist only ";
+	std::cout << "of birth-death pairs, please set this first parameter to -1 \n";	
+	std::cout << "The remaining parameters of the program 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] );
+	}
+	
+	double min_ = std::numeric_limits<double>::max();
+	double max_ = -std::numeric_limits<double>::max();
+	
+	for ( size_t file_no = 0 ; file_no != filenames.size() ; ++file_no )
+	{
+		std::cout << "Creating diagram based on a file : " << filenames[file_no] << std::endl;
+		Persistence_intervals p( filenames[file_no] , dimension );
+		std::pair<double,double> min_max_ = p.get_x_range();
+		if ( min_max_.first < min_ )min_ = min_max_.first;
+		if ( min_max_.second > max_ )max_ = min_max_.second;
+	}
+	std::cout << "Birth-death range : min: " <<  min_ << ", max: " << max_ << std::endl;
+	return 0;
+}
diff --git a/src/Persistence_representations/utilities/persistence_intervals/compute_bottleneck_distance.cpp b/src/Persistence_representations/utilities/persistence_intervals/compute_bottleneck_distance.cpp
new file mode 100644
index 00000000..19e49bbb
--- /dev/null
+++ b/src/Persistence_representations/utilities/persistence_intervals/compute_bottleneck_distance.cpp
@@ -0,0 +1,113 @@
+/*    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_intervals_with_distances.h>
+#include <gudhi/read_persistence_from_file.h>
+
+
+
+using namespace Gudhi;
+using namespace Gudhi::Persistence_representations;
+
+#include <iostream>
+#include <sstream>
+
+
+int main( int argc , char** argv )
+{
+	std::cout << "This program compute the bottleneck distance of persistence diarams stored in a files. \n";
+	std::cout << "The first parameter of the program is the dimension of persistence to be used to construct persistence landscapes. If your file contains ";
+	std::cout << "the information about dimension of persistence pairs, please provide here the dimension of persistence pairs you want to use. If your input files consist only ";
+	std::cout << "of birth-death pairs, please set this first parameter to -1 \n";	
+	std::cout << "The remaining parameters of this programs are names of files with persistence diagrams.\n";
+
+	if ( argc < 3 )
+	{
+		std::cout << "Wrong number of parameters, the program will now terminate \n";
+		return 1;
+	}
+
+	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] );
+	}
+	
+	//reading the persistence intervals:
+	std::vector< Persistence_intervals_with_distances > persistence_intervals;
+	for ( size_t i = 0 ; i != filenames.size() ; ++i )
+	{
+		Persistence_intervals_with_distances pers(filenames[i] , dimension );	
+		persistence_intervals.push_back( pers );
+	}
+	
+	//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 != persistence_intervals.size() ; ++i )
+	{
+		for ( size_t j = i+1 ; j != persistence_intervals.size() ; ++j )
+		{
+			distance[i][j] = distance[j][i] = persistence_intervals[i].distance( persistence_intervals[j] );
+		}
+	}
+
+	//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_intervals/compute_number_of_dominant_intervals.cpp b/src/Persistence_representations/utilities/persistence_intervals/compute_number_of_dominant_intervals.cpp
new file mode 100644
index 00000000..c099befc
--- /dev/null
+++ b/src/Persistence_representations/utilities/persistence_intervals/compute_number_of_dominant_intervals.cpp
@@ -0,0 +1,59 @@
+/*    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/reader_utils.h>
+#include <gudhi/Persistence_intervals.h>
+
+#include <iostream>
+
+
+
+using namespace Gudhi;
+using namespace Gudhi::Persistence_representations;
+
+
+int main( int argc , char** argv )
+{
+	std::cout << "This program compute the dominant intervals. A number of intervals to be displayed is a parameter of this program. \n";
+	if ( argc != 4 )
+	{
+		std::cout << "To run this program, please provide the name of a file with persistence diagram, dimension of intervals that should be taken into account (if your file contains only persistence pairs in a single dimension, set it up to -1) and number of dominant intervals you would like to get \n";
+		return 1;
+	}
+	int dim = atoi( argv[2] );
+	unsigned dimension = std::numeric_limits<unsigned>::max();
+	if ( dim >= 0 )
+	{
+		dimension = (unsigned)dim;
+	}
+	Persistence_intervals p( argv[1] , dimension );
+	std::vector< std::pair<double,double> > dominant_intervals = p.dominant_intervals( atoi( argv[3] ) );
+	std::cout << "Here are the dominant intervals : " << std::endl;
+	for ( size_t i = 0 ; i != dominant_intervals.size() ; ++i )
+	{
+		std::cout << " " << dominant_intervals[i].first<< "," << dominant_intervals[i].second  << " "<< std::endl;
+	}
+	
+	return 0;
+}
diff --git a/src/Persistence_representations/utilities/persistence_intervals/plot_histogram_of_intervals_lengths.cpp b/src/Persistence_representations/utilities/persistence_intervals/plot_histogram_of_intervals_lengths.cpp
new file mode 100644
index 00000000..b2cbac70
--- /dev/null
+++ b/src/Persistence_representations/utilities/persistence_intervals/plot_histogram_of_intervals_lengths.cpp
@@ -0,0 +1,77 @@
+/*    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/reader_utils.h>
+#include <gudhi/Persistence_intervals.h>
+
+#include <iostream>
+
+
+
+using namespace Gudhi;
+using namespace Gudhi::Persistence_representations;
+
+
+int main( int argc , char** argv )
+{
+	std::cout << "This program compute a histogram of barcode's length. A number of bins in the histogram is a parameter of this program. \n";
+	if ( argc != 3 )
+	{
+		std::cout << "To run this program, please provide the name of a file with persistence diagram and number of dominant intervals you would like to get \n";
+		std::cout << "The third parameter of a program is the dimension of the persistence that is to be used. If your file contains only birth-death pairs, you can skip this parameter\n";
+		return 1;
+	}
+	unsigned dimension = std::numeric_limits<unsigned>::max();
+	int dim = -1;
+	if ( argc > 2 )
+	{
+		dim = atoi( argv[2] );
+	} 
+	if ( dim >= 0 )
+	{
+		dimension = (unsigned)dim;
+	}
+
+	Persistence_intervals p( argv[1] , dimension );
+	std::vector< std::pair<double,double> > dominant_intervals = p.dominant_intervals( atoi( argv[2] ) );
+	std::vector< size_t > histogram = p.histogram_of_lengths( 10  );
+	
+	std::stringstream gnuplot_script;
+	gnuplot_script << argv[1] << "_Gnuplot_script";
+	std::ofstream out;
+	out.open( gnuplot_script.str().c_str() );
+	
+	out << "set style data histogram" << std::endl;
+	out << "set style histogram cluster gap 1" << std::endl;
+	out << "set style fill solid border -1" << std::endl;
+	out << "plot '-' notitle" << std::endl;    
+	for ( size_t i = 0 ; i != histogram.size() ; ++i )
+	{
+		out << histogram[i]  << std::endl;
+	}		
+	out << std::endl;
+	std::cout << "To vizualize, open gnuplot and type: load \'" << gnuplot_script.str().c_str() << "\'" <<  std::endl;	
+	out.close();	
+	return 0;
+}
diff --git a/src/Persistence_representations/utilities/persistence_intervals/plot_persistence_Betti_numbers.cpp b/src/Persistence_representations/utilities/persistence_intervals/plot_persistence_Betti_numbers.cpp
new file mode 100644
index 00000000..e20f85c0
--- /dev/null
+++ b/src/Persistence_representations/utilities/persistence_intervals/plot_persistence_Betti_numbers.cpp
@@ -0,0 +1,100 @@
+/*    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/reader_utils.h>
+#include <gudhi/Persistence_intervals.h>
+
+#include <iostream>
+
+
+
+using namespace Gudhi;
+using namespace Gudhi::Persistence_representations;
+
+
+int main( int argc , char** argv )
+{
+	std::cout << "This program compute a plot of persistence Betti numbers. The input parameter is a file with persistence intervals. \n";
+	std::cout << "The second optional parameter of a program is the dimension of the persistence that is to be used. If your file contains only birth-death pairs, you can skip this parameter\n";
+	if ( argc < 2 )
+	{
+		std::cout << "To run this program, please provide the name of a file with persistence diagram and number of dominant intervals you would like to get \n";
+		return 1;
+	}
+	unsigned dimension = std::numeric_limits<unsigned>::max();
+	int dim = -1;
+	if ( argc > 2 )
+	{
+		dim = atoi( argv[2] );
+	} 
+	if ( dim >= 0 )
+	{
+		dimension = (unsigned)dim;
+	}
+	
+	
+	std::stringstream gnuplot_script;
+	gnuplot_script << argv[1] << "_Gnuplot_script";
+	std::ofstream out;
+	out.open( gnuplot_script.str().c_str() );
+	
+	Persistence_intervals p( argv[1] , dimension );
+	std::vector< std::pair< double , size_t > > pbns = p.compute_persistent_betti_numbers();	
+	
+	//set up the ranges so that we see the image well.
+	double xRangeBegin = pbns[0].first;
+	double xRangeEnd = pbns[ pbns.size()-1 ].first;
+	double yRangeBegin = 0;
+	double yRangeEnd = 0;
+	for ( size_t i = 0 ; i != pbns.size() ; ++i )
+	{
+		if ( pbns[i].second > yRangeEnd )yRangeEnd = pbns[i].second;
+	}
+	xRangeBegin -= (xRangeEnd -xRangeBegin)/100.0;
+	xRangeEnd += (xRangeEnd -xRangeBegin)/100.0;
+	yRangeEnd += yRangeEnd/100;
+	
+	
+	out << "set xrange [" << xRangeBegin << " : " << xRangeEnd << "]" << std::endl;
+    out << "set yrange [" << yRangeBegin << " : " << yRangeEnd << "]" << std::endl;	
+	out << "plot '-' using 1:2 notitle with lp " << std::endl;    
+	double previous_y = 0;
+	for ( size_t i = 0 ; i != pbns.size() ; ++i )
+	{
+		out << pbns[i].first << " " << previous_y << std::endl;
+		out << pbns[i].first << " " << pbns[i].second << std::endl;
+		previous_y = pbns[i].second;
+	}		
+	out << std::endl;
+	out.close();
+	
+	//for ( size_t i = 0 ; i != pbns.size() ; ++i )
+	//{
+	//	std::cout << pbns[i].first << " " << pbns[i].second << std::endl;
+	//}	
+	
+	std::cout << "To vizualize, open gnuplot and type: load \'" << gnuplot_script.str().c_str() << "\'" << std::endl;
+			
+	return 0;
+}
diff --git a/src/Persistence_representations/utilities/persistence_intervals/plot_persistence_intervals.cpp b/src/Persistence_representations/utilities/persistence_intervals/plot_persistence_intervals.cpp
new file mode 100644
index 00000000..ed03459b
--- /dev/null
+++ b/src/Persistence_representations/utilities/persistence_intervals/plot_persistence_intervals.cpp
@@ -0,0 +1,69 @@
+/*    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/reader_utils.h>
+#include <gudhi/Persistence_intervals.h>
+#include <gudhi/read_persistence_from_file.h>
+
+#include <iostream>
+
+
+
+using namespace Gudhi;
+using namespace Gudhi::Persistence_representations;
+
+
+double epsilon = 0.0000005;
+
+	
+int main( int argc , char** argv )
+{
+	if ( argc < 2 )
+	{
+		std::cout << "To run this program, please provide the name of a file with persistence diagram \n";
+		std::cout << "The second optional parameter of a program is the dimension of the persistence that is to be used. If your file contains only birth-death pairs, you can skip this parameter\n";		
+		return 1;
+	}
+	unsigned dimension = std::numeric_limits<unsigned>::max();
+	int dim = -1;
+	if ( argc > 2 )
+	{
+		dim = atoi( argv[2] );
+	} 
+	if ( dim >= 0 )
+	{
+		dimension = (unsigned)dim;
+	}			
+	std::vector< std::pair< double , double > > intervals = read_persistence_intervals_in_one_dimension_from_file( argv[1] , dimension );
+	Persistence_intervals b( intervals );
+	b.plot( argv[1] );
+	return 0;
+}
+
+
+
+
+
+
+