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, 499 insertions, 0 deletions

diff --git a/src/Persistence_representations/example/CMakeLists.txt b/src/Persistence_representations/example/CMakeLists.txt
new file mode 100644
index 00000000..3c783d36
--- /dev/null
+++ b/src/Persistence_representations/example/CMakeLists.txt
@@ -0,0 +1,31 @@
+cmake_minimum_required(VERSION 2.6)
+project(GUDHI_STAT)
+
+file(COPY "simple_diagram.txt" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
+add_executable ( persistence_landscape_on_grid persistence_landscape_on_grid.cpp )
+target_link_libraries(persistence_landscape_on_grid ${Boost_SYSTEM_LIBRARY})
+add_test ( persistence_landscape_on_grid ${CMAKE_CURRENT_BINARY_DIR}/persistence_landscape_on_grid )
+
+file(COPY "simple_diagram.txt" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
+add_executable ( persistence_landscape persistence_landscape.cpp )
+target_link_libraries(persistence_landscape ${Boost_SYSTEM_LIBRARY})
+add_test ( persistence_landscape ${CMAKE_CURRENT_BINARY_DIR}/persistence_landscape )
+
+file(COPY "simple_diagram.txt" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
+add_executable ( persistence_intervals persistence_intervals.cpp )
+target_link_libraries(persistence_intervals ${Boost_SYSTEM_LIBRARY})
+add_test ( persistence_intervals ${CMAKE_CURRENT_BINARY_DIR}/persistence_intervals simple_diagram.txt )
+
+file(COPY "simple_diagram.txt" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
+add_executable ( persistence_vectors persistence_vectors.cpp )
+target_link_libraries(persistence_vectors ${Boost_SYSTEM_LIBRARY})
+add_test ( persistence_vectors ${CMAKE_CURRENT_BINARY_DIR}/persistence_vectors )
+
+file(COPY "simple_diagram.txt" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
+add_executable ( persistence_heat_maps persistence_heat_maps.cpp )
+target_link_libraries(persistence_heat_maps ${Boost_SYSTEM_LIBRARY})
+add_test ( persistence_heat_maps ${CMAKE_CURRENT_BINARY_DIR}/persistence_heat_maps )
+
+
+
+
diff --git a/src/Persistence_representations/example/persistence_heat_maps.cpp b/src/Persistence_representations/example/persistence_heat_maps.cpp
new file mode 100644
index 00000000..da87486d
--- /dev/null
+++ b/src/Persistence_representations/example/persistence_heat_maps.cpp
@@ -0,0 +1,93 @@
+/*    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_heat_maps.h>
+
+#include <iostream>
+#include <vector>
+
+
+
+using namespace Gudhi;
+using namespace Gudhi::Persistence_representations;
+
+
+double epsilon = 0.0000005;
+
+
+	
+int main( int argc , char** argv )
+{	
+	//create two simple vectors with birth--death pairs:
+	
+	std::vector< std::pair< double , double > > persistence1;
+	std::vector< std::pair< double , double > > persistence2;
+	
+	persistence1.push_back( std::make_pair(1,2) );
+	persistence1.push_back( std::make_pair(6,8) );
+	persistence1.push_back( std::make_pair(0,4) );
+	persistence1.push_back( std::make_pair(3,8) );
+	
+	persistence2.push_back( std::make_pair(2,9) );
+	persistence2.push_back( std::make_pair(1,6) );
+	persistence2.push_back( std::make_pair(3,5) );
+	persistence2.push_back( std::make_pair(6,10) );
+	
+	//over here we define a function we sill put on a top on every birth--death pair in the persistence interval. It can be anything. Over here we will use standarg Gaussian
+	std::vector< std::vector<double> > filter = create_Gaussian_filter(5,1);
+			
+	//creating two heat maps. 
+	Persistence_heat_maps<constant_scaling_function> hm1( persistence1 , filter , false , 20 , 0 , 11 );		
+	Persistence_heat_maps<constant_scaling_function> hm2( persistence2 , filter , false , 20 , 0 , 11 );
+	
+	std::vector<Persistence_heat_maps<constant_scaling_function>*> vector_of_maps;
+	vector_of_maps.push_back( &hm1 );
+	vector_of_maps.push_back( &hm2 );
+	
+	//compute median/mean of a vector of heat maps:	
+	Persistence_heat_maps<constant_scaling_function> mean;
+	mean.compute_mean( vector_of_maps );	
+	Persistence_heat_maps<constant_scaling_function> median;
+	median.compute_median( vector_of_maps );
+	
+	//to compute L^1 disance between hm1 and hm2:
+	std::cout << "The L^1 distance is : " << hm1.distance( hm2 , 1 ) << std::endl;
+	
+	//to average of hm1 and hm2:
+	std::vector< Persistence_heat_maps<constant_scaling_function>* > to_average;
+	to_average.push_back( &hm1 );
+	to_average.push_back( &hm2 );
+	Persistence_heat_maps<constant_scaling_function> av;	
+	av.compute_average( to_average );	
+	
+	//to compute scalar product of hm1 and hm2:
+	std::cout << "Scalar product is : " << hm1.compute_scalar_product( hm2 ) << std::endl;
+	
+	return 0;
+}
+
+
+
+
diff --git a/src/Persistence_representations/example/persistence_intervals.cpp b/src/Persistence_representations/example/persistence_intervals.cpp
new file mode 100644
index 00000000..ed5b4e34
--- /dev/null
+++ b/src/Persistence_representations/example/persistence_intervals.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/reader_utils.h>
+#include <gudhi/Persistence_intervals.h>
+
+#include <iostream>
+
+
+
+using namespace Gudhi;
+using namespace Gudhi::Persistence_representations;
+
+	
+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";
+		return 1;
+	}
+	
+	Persistence_intervals p( argv[1] );
+	std::pair<double,double> min_max_ = p.get_x_range();	
+	std::cout << "Birth-death range : " <<  min_max_.first << " " << min_max_.second << std::endl;
+	
+	
+	std::vector<double> dominant_ten_intervals_length = p.length_of_dominant_intervals(10);
+	std::cout << "Lendth of ten dominant intervals : " <<std::endl;	
+	for ( size_t i = 0 ; i != dominant_ten_intervals_length.size() ; ++i )
+	{
+		std::cout << dominant_ten_intervals_length[i] <<std::endl;
+	}
+	
+	std::vector< std::pair<double,double> > ten_dominant_intervals = p.dominant_intervals( 10 );	
+	std::cout << "Here are the dominant intervals : " <<std::endl;
+	for ( size_t i = 0 ; i != ten_dominant_intervals.size() ; ++i )
+	{
+		std::cout << "( " << ten_dominant_intervals[i].first<< "," << ten_dominant_intervals[i].second <<std::endl;
+	}
+	
+	std::vector< size_t > histogram = p.histogram_of_lengths( 10  );
+	std::cout << "Here is the histogram of barcode's length : " <<std::endl;
+	for ( size_t i = 0 ; i != histogram.size() ; ++i )
+	{
+		std::cout << histogram[i]  << " ";
+	}		
+	std::cout <<std::endl;
+
+	
+	std::vector< size_t > cumulative_histogram = p.cumulative_histogram_of_lengths( 10  );
+	std::cout<< "Cumuative histogram : " <<std::endl;	
+	for ( size_t i = 0 ; i != cumulative_histogram.size() ; ++i )
+	{
+		std::cout << cumulative_histogram[i] << " ";
+	}		
+	std::cout <<std::endl;
+
+	std::vector< double  > char_funct_diag = p.characteristic_function_of_diagram( min_max_.first , min_max_.second );	
+	std::cout << "Characteristic function of diagram : " <<std::endl;
+	for ( size_t i = 0 ; i != char_funct_diag.size() ; ++i )
+	{
+		std::cout << char_funct_diag[i] << " ";
+	}		
+	std::cout <<std::endl;
+
+	std::vector< double  > cumul_char_funct_diag = p.cumulative_characteristic_function_of_diagram( min_max_.first , min_max_.second );
+	std::cout << "Cumulative characteristic function of diagram : " <<std::endl;
+	for ( size_t i = 0 ; i != cumul_char_funct_diag.size() ; ++i )
+	{		
+		std::cout << cumul_char_funct_diag[i] << " ";
+	}	
+	std::cout <<std::endl;
+
+	std::cout << "Persistence Betti numbers \n";
+	std::vector< std::pair< double , size_t > > pbns = p.compute_persistent_betti_numbers();	
+	for ( size_t i = 0 ; i != pbns.size() ; ++i )
+	{
+		std::cout <<  pbns[i].first << " " << pbns[i].second <<std::endl;	
+	}
+	
+	return 0;
+}
+
+
+
+
+
+
+
diff --git a/src/Persistence_representations/example/persistence_landscape.cpp b/src/Persistence_representations/example/persistence_landscape.cpp
new file mode 100644
index 00000000..40fb7d32
--- /dev/null
+++ b/src/Persistence_representations/example/persistence_landscape.cpp
@@ -0,0 +1,92 @@
+/*    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.h>
+
+
+
+using namespace Gudhi;
+using namespace Gudhi::Persistence_representations;
+
+#include <iostream>
+
+
+int main( int argc , char** argv )
+{	
+	//create two simple vectors with birth--death pairs:
+	
+	std::vector< std::pair< double , double > > persistence1;
+	std::vector< std::pair< double , double > > persistence2;
+	
+	persistence1.push_back( std::make_pair(1,2) );
+	persistence1.push_back( std::make_pair(6,8) );
+	persistence1.push_back( std::make_pair(0,4) );
+	persistence1.push_back( std::make_pair(3,8) );
+	
+	persistence2.push_back( std::make_pair(2,9) );
+	persistence2.push_back( std::make_pair(1,6) );
+	persistence2.push_back( std::make_pair(3,5) );
+	persistence2.push_back( std::make_pair(6,10) );
+	
+	//create two persistence landscapes based on persistence1 and persistence2:
+	Persistence_landscape l1( persistence1 );
+	Persistence_landscape l2( persistence2 );
+	
+	//This is how to compute integral of landscapes:
+	std::cout << "Integral of the first landscape : " << l1.compute_integral_of_landscape() << std::endl;
+	std::cout << "Integral of the second landscape : " << l2.compute_integral_of_landscape() << std::endl;
+	
+	//And here how to write landscapes to stream:
+	std::cout << "l1 : " << l1 << std::endl;
+	std::cout << "l2 : " << l2 << std::endl;
+	
+	//Arythmetic operations on landscapes:
+	Persistence_landscape sum = l1+l2;
+	std::cout << "sum : " << sum << std::endl;
+	
+	//here are the maxima of the functions:
+	std::cout << "Maximum of l1 : " << l1.compute_maximum() << std::endl;
+	std::cout << "Maximum of l2 : " << l2.compute_maximum() << std::endl;
+	
+	//here are the norms of landscapes:
+	std::cout << "L^1 Norm of l1 : " << l1.compute_norm_of_landscape( 1. ) << std::endl;
+	std::cout << "L^1 Norm of l2 : " << l2.compute_norm_of_landscape( 1. ) << std::endl;
+	
+	//here is the average of landscapes:
+	Persistence_landscape average;
+	average.compute_average( {&l1,&l2} );
+	std::cout << "average : " << average << std::endl;
+	
+	//here is the distance of landscapes:
+	std::cout << "Distance : " << l1.distance( l2 ) << std::endl;
+	
+	//here is the scalar product of landscapes:
+	std::cout << "Scalar product : " << l1.compute_scalar_product( l2 ) << std::endl;
+	
+	//here is how to create a file which is suitable for vizualization via gnuplot:
+	average.plot( "average_landscape" );
+		
+	return 0;
+}
+
diff --git a/src/Persistence_representations/example/persistence_landscape_on_grid.cpp b/src/Persistence_representations/example/persistence_landscape_on_grid.cpp
new file mode 100644
index 00000000..b38ac3d9
--- /dev/null
+++ b/src/Persistence_representations/example/persistence_landscape_on_grid.cpp
@@ -0,0 +1,88 @@
+/*    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 )
+{
+	//create two simple vectors with birth--death pairs:
+	
+	std::vector< std::pair< double , double > > persistence1;
+	std::vector< std::pair< double , double > > persistence2;
+	
+	persistence1.push_back( std::make_pair(1,2) );
+	persistence1.push_back( std::make_pair(6,8) );
+	persistence1.push_back( std::make_pair(0,4) );
+	persistence1.push_back( std::make_pair(3,8) );
+	
+	persistence2.push_back( std::make_pair(2,9) );
+	persistence2.push_back( std::make_pair(1,6) );
+	persistence2.push_back( std::make_pair(3,5) );
+	persistence2.push_back( std::make_pair(6,10) );
+	
+	//create two persistence landscapes based on persistence1 and persistence2:
+	Persistence_landscape_on_grid l1( persistence1 , 0 , 11 , 20 );
+	Persistence_landscape_on_grid l2( persistence2 , 0 , 11 , 20 );
+	
+	//This is how to compute integral of landscapes:
+	std::cout << "Integral of the first landscape : " << l1.compute_integral_of_landscape() << std::endl;
+	std::cout << "Integral of the second landscape : " << l2.compute_integral_of_landscape() << std::endl;
+	
+	//And here how to write landscapes to stream:
+	std::cout << "l1 : " << l1 << std::endl;
+	std::cout << "l2 : " << l2 << std::endl;
+	
+	//here are the maxima of the functions:
+	std::cout << "Maximum of l1 : " << l1.compute_maximum() << std::endl;
+	std::cout << "Maximum of l2 : " << l2.compute_maximum() << std::endl;
+	
+	//here are the norms of landscapes:
+	std::cout << "L^1 Norm of l1 : " << l1.compute_norm_of_landscape( 1. ) << std::endl;
+	std::cout << "L^1 Norm of l2 : " << l2.compute_norm_of_landscape( 1. ) << std::endl;
+	
+	//here is the average of landscapes:
+	Persistence_landscape_on_grid average;	
+	average.compute_average( {&l1,&l2} );
+	std::cout << "average : " << average << std::endl;
+	
+	//here is the distance of landscapes:
+	std::cout << "Distance : " << l1.distance( l2 ) << std::endl;
+	
+	//here is the scalar product of landscapes:
+	std::cout << "Scalar product : " << l1.compute_scalar_product( l2 ) << std::endl;
+	
+	//here is how to create a file which is suitable for vizualization via gnuplot:
+	average.plot( "average_landscape" );
+		
+		
+	return 0;
+}
diff --git a/src/Persistence_representations/example/persistence_vectors.cpp b/src/Persistence_representations/example/persistence_vectors.cpp
new file mode 100644
index 00000000..028d95eb
--- /dev/null
+++ b/src/Persistence_representations/example/persistence_vectors.cpp
@@ -0,0 +1,80 @@
+/*    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>
+#include <iostream>
+
+
+#include <gudhi/reader_utils.h>
+#include <vector>
+#include <cmath>
+#include <iomanip>
+
+using namespace Gudhi;
+using namespace Gudhi::Persistence_representations;
+
+
+
+
+int main( int argc , char** argv )
+{
+	//create two simple vectors with birth--death pairs:
+	
+	std::vector< std::pair< double , double > > persistence1;
+	std::vector< std::pair< double , double > > persistence2;
+	
+	persistence1.push_back( std::make_pair(1,2) );
+	persistence1.push_back( std::make_pair(6,8) );
+	persistence1.push_back( std::make_pair(0,4) );
+	persistence1.push_back( std::make_pair(3,8) );
+	
+	persistence2.push_back( std::make_pair(2,9) );
+	persistence2.push_back( std::make_pair(1,6) );
+	persistence2.push_back( std::make_pair(3,5) );
+	persistence2.push_back( std::make_pair(6,10) );
+	
+	//create two persistence vectors based on persistence1 and persistence2:
+	Vector_distances_in_diagram<Euclidean_distance > v1 = Vector_distances_in_diagram<Euclidean_distance >( persistence1 , std::numeric_limits<size_t>::max() );
+	Vector_distances_in_diagram<Euclidean_distance > v2 = Vector_distances_in_diagram<Euclidean_distance >( persistence2 , std::numeric_limits<size_t>::max() );
+	
+	//writing to a stream:
+	std::cout << "v1 : " << v1 << std::endl;
+	std::cout << "v2 : " << v2 << std::endl;
+	
+	//averages:
+	Vector_distances_in_diagram<Euclidean_distance > average;
+	average.compute_average( {&v1,&v2} );
+	std::cout << "Average : " << average << std::endl;
+	
+	//computations of distances:
+	std::cout << "l^1 distance : " << v1.distance( v2 ) << std::endl;
+    
+   //computations of scalar product:
+    std::cout << "Scalar product of l1 and l2 : " << v1.compute_scalar_product( v2 ) << std::endl;
+    
+    //create a file with a gnuplot script:
+    v1.plot( "plot_of_vector_representation" );
+
+	return 0;
+}
diff --git a/src/Persistence_representations/example/simple_diagram.txt b/src/Persistence_representations/example/simple_diagram.txt
new file mode 100644
index 00000000..2f199fd4
--- /dev/null
+++ b/src/Persistence_representations/example/simple_diagram.txt
@@ -0,0 +1,4 @@
+1 2
+3 4
+5 6
+7 8
\ No newline at end of file