Answers to Vincent's comments.

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/gudhi_stat@2383 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 67e837dc1620294b3538c6f4a0515be5bde53fa9

15 files changed, 203 insertions, 28 deletions

diff --git a/src/Gudhi_stat/include/gudhi/Persistence_heat_maps.h b/src/Gudhi_stat/include/gudhi/Persistence_heat_maps.h
index 78cbed20..59e58e41 100644
--- a/src/Gudhi_stat/include/gudhi/Persistence_heat_maps.h
+++ b/src/Gudhi_stat/include/gudhi/Persistence_heat_maps.h
@@ -487,6 +487,8 @@ public:
 	
 	/**	 
 	 * This function is required by the Real_valued_topological_data concept. It returns various projections od the persistence heat map to a real line.
+         * At the moment this function is not tested, since it is quite likelly to be changed in the future. Given this, when using it, keep in mind that it
+         * will be most likelly changed in the next versions.
 	**/ 	
 	double project_to_R( int number_of_function )const;	
 	/**
diff --git a/src/Gudhi_stat/include/gudhi/Persistence_intervals.h b/src/Gudhi_stat/include/gudhi/Persistence_intervals.h
index 95e6ae91..539d38e5 100644
--- a/src/Gudhi_stat/include/gudhi/Persistence_intervals.h
+++ b/src/Gudhi_stat/include/gudhi/Persistence_intervals.h
@@ -223,6 +223,8 @@ public:
 	/**
 	 * This is a simple function projectig the persistence intervals to a real number. The function we use here is a sum of squared lendgths of intervals. It can be naturally interpreted as
 	 * sum of step function, where the step hight it equal to the length of the interval.
+         * At the moment this function is not tested, since it is quite likelly to be changed in the future. Given this, when using it, keep in mind that it
+         * will be most likelly changed in the next versions.
 	 **/ 
 	double project_to_R( int number_of_function )const;   
 	/**
diff --git a/src/Gudhi_stat/include/gudhi/Persistence_intervals_with_distances.h b/src/Gudhi_stat/include/gudhi/Persistence_intervals_with_distances.h
index 60343dc1..7ef711e9 100644
--- a/src/Gudhi_stat/include/gudhi/Persistence_intervals_with_distances.h
+++ b/src/Gudhi_stat/include/gudhi/Persistence_intervals_with_distances.h
@@ -24,7 +24,7 @@
 #define Persistence_intervals_WITH_DISTANCES_H_
 
 
-#include <gudhi/persistence_representations/Persistence_intervals.h>
+#include <gudhi/Persistence_intervals.h>
 #include <gudhi/Bottleneck.h>
 
 namespace Gudhi 
@@ -44,7 +44,7 @@ public:
      * exception will be thrown.
      * The last parameter, tolerance, it is an additiv error of the approimation, set by default to zero.
     **/
-     double distance( const Persistence_intervals_with_distances& second , double power = std::numeric_limits< double >::max() , double tolerance = 0) const
+    double distance( const Persistence_intervals_with_distances& second , double power = std::numeric_limits< double >::max() , double tolerance = 0) const
     {
 		if ( power >= std::numeric_limits< double >::max() )
 		{
diff --git a/src/Gudhi_stat/include/gudhi/Persistence_landscape.h b/src/Gudhi_stat/include/gudhi/Persistence_landscape.h
index 9150e507..9a177b60 100644
--- a/src/Gudhi_stat/include/gudhi/Persistence_landscape.h
+++ b/src/Gudhi_stat/include/gudhi/Persistence_landscape.h
@@ -347,6 +347,8 @@ public:
 	/**
 	 * The number of projections to R is defined to the number of nonzero landscape functions. I-th projection is an integral of i-th landscape function over whole R.
 	 * This function is required by the Real_valued_topological_data concept.
+         * At the moment this function is not tested, since it is quite likelly to be changed in the future. Given this, when using it, keep in mind that it
+         * will be most likelly changed in the next versions.
 	**/
     double project_to_R( int number_of_function )const
     {
@@ -543,24 +545,17 @@ protected:
 
 
 
-
 Persistence_landscape::Persistence_landscape(const char* filename , size_t dimension)
-{
-    bool dbg = false;
-
-    if ( dbg )
+{    
+    std::vector< std::pair< double , double > > barcode;    
+    if ( dimension < std::numeric_limits<double>::max() )
     {
-        std::cerr << "Using constructor : Persistence_landscape(char* filename)" << std::endl;
-    }
-    std::vector< std::pair< double , double > > barcode;
-    if ( dimension == std::numeric_limits<unsigned>::max() )
-    {
-     barcode = read_persistence_intervals_in_one_dimension_from_file( filename );
-    }
+		barcode = read_persistence_intervals_in_one_dimension_from_file( filename , dimension );	
+	}
     else
     {
-     barcode = read_persistence_intervals_in_one_dimension_from_file( filename , dimension );
-    }
+		barcode = read_persistence_intervals_in_one_dimension_from_file( filename );
+    }    
     this->construct_persistence_landscape_from_barcode( barcode );
     this->set_up_numbers_of_functions_for_vectorization_and_projections_to_reals();
 }
diff --git a/src/Gudhi_stat/include/gudhi/Persistence_landscape_on_grid.h b/src/Gudhi_stat/include/gudhi/Persistence_landscape_on_grid.h
index de5c74ac..ed9c14ea 100644
--- a/src/Gudhi_stat/include/gudhi/Persistence_landscape_on_grid.h
+++ b/src/Gudhi_stat/include/gudhi/Persistence_landscape_on_grid.h
@@ -865,7 +865,9 @@ public:
 
 	/**
 	 * The number of projections to R is defined to the number of nonzero landscape functions. I-th projection is an integral of i-th landscape function over whole R.
-	 * This function is required by the Real_valued_topological_data concept. 
+	 * This function is required by the Real_valued_topological_data concept.
+         * At the moment this function is not tested, since it is quite likelly to be changed in the future. Given this, when using it, keep in mind that it
+         * will be most likelly changed in the next versions.
 	**/
     double project_to_R( int number_of_function )const
     {
diff --git a/src/Gudhi_stat/include/gudhi/persistence_vectors.h b/src/Gudhi_stat/include/gudhi/persistence_vectors.h
index 9ed32fc1..d623dd0d 100644
--- a/src/Gudhi_stat/include/gudhi/persistence_vectors.h
+++ b/src/Gudhi_stat/include/gudhi/persistence_vectors.h
@@ -177,6 +177,8 @@ public:
     //Implementations of functions for various concepts.  
      /**
      * Compute projection to real numbers of persistence vector. This function is required by the Real_valued_topological_data concept
+     * At the moment this function is not tested, since it is quite likelly to be changed in the future. Given this, when using it, keep in mind that it
+     * will be most likelly changed in the next versions.
     **/
     double project_to_R( int number_of_function )const;
     /**
diff --git a/src/Gudhi_stat/test/CMakeLists.txt b/src/Gudhi_stat/test/CMakeLists.txt
index 35231e83..62335c77 100644
--- a/src/Gudhi_stat/test/CMakeLists.txt
+++ b/src/Gudhi_stat/test/CMakeLists.txt
@@ -85,3 +85,31 @@ add_test(NAME read_persistence_from_file_test
   file(COPY data DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/read_persistence_from_file_test/data")
   # XML format for Jenkins xUnit plugin
   --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/read_persistence_from_file_UT.xml --log_level=test_suite --report_level=no)
+
+file(COPY data DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
+add_executable ( additional_tests additional_tests.cpp )
+target_link_libraries(additional_tests ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
+
+# Unitary tests
+add_test(NAME additional_tests
+  COMMAND ${CMAKE_CURRENT_BINARY_DIR}/additional_tests
+  file(COPY data DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/additional_tests/data")
+  # XML format for Jenkins xUnit plugin
+  --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/additional_tests_UT.xml --log_level=test_suite --report_level=no)
+
+
+
+if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
+file(COPY data DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
+add_executable ( persistence_intervals_with_distances_test persistence_intervals_with_distances_test.cpp )
+target_link_libraries(persistence_intervals_with_distances_test ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
+if (TBB_FOUND)
+target_link_libraries(persistence_intervals_with_distances_test ${TBB_LIBRARIES})
+endif(TBB_FOUND)
+# Unitary tests
+add_test(NAME persistence_intervals_with_distances_test
+  COMMAND ${CMAKE_CURRENT_BINARY_DIR}/persistence_intervals_with_distances_test
+  file(COPY data DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/persistence_intervals_with_distances_test/data")
+  # XML format for Jenkins xUnit plugin
+  --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/persistence_intervals_with_distances_test_UT.xml --log_level=test_suite --report_level=no)
+endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
diff --git a/src/Gudhi_stat/test/data/persistence_file_with_four_entries_per_line_landscape b/src/Gudhi_stat/test/data/persistence_file_with_four_entries_per_line_landscape
new file mode 100644
index 00000000..33fae63e
--- /dev/null
+++ b/src/Gudhi_stat/test/data/persistence_file_with_four_entries_per_line_landscape
@@ -0,0 +1,8 @@
+#lambda_0
+0  0
+1  1
+2  0
+4  0
+10  0
+50  40
+90  0
diff --git a/src/Gudhi_stat/test/persistence_heat_maps_test.cpp b/src/Gudhi_stat/test/persistence_heat_maps_test.cpp
index c7b36688..b997382e 100644
--- a/src/Gudhi_stat/test/persistence_heat_maps_test.cpp
+++ b/src/Gudhi_stat/test/persistence_heat_maps_test.cpp
@@ -23,7 +23,7 @@
 
 
 #define BOOST_TEST_DYN_LINK
-#define BOOST_TEST_MODULE "gudhi_stat"
+#define BOOST_TEST_MODULE "Persistence_representations"
 #include <boost/test/unit_test.hpp>
 #include <gudhi/reader_utils.h>
 #include <gudhi/Persistence_heat_maps.h>
@@ -254,8 +254,24 @@ BOOST_AUTO_TEST_CASE(check_arythmetic_operations_for_heat_maps)
 	Persistence_heat_maps<constant_scaling_function> multiply_by_scalar_template;
 	multiply_by_scalar_template.load_from_file( "data/heat_map_multiply_by_scalar" );
 	
-	BOOST_CHECK( sum == sum_template );
+	BOOST_CHECK( sum == sum_template );	
+}
+
+BOOST_AUTO_TEST_CASE(check_distance_of_heat_maps_infinite_power_parameters) 
+{	
+	std::vector< std::vector<double> > filter = create_Gaussian_filter(100,1);		
+	Persistence_heat_maps<constant_scaling_function> p( "data/file_with_diagram" , filter , false , 1000 , 0 , 1 );
+	
+	std::vector< std::vector<double> > filter_2 = create_Gaussian_filter(150,1);
+	Persistence_heat_maps<constant_scaling_function> q( "data/file_with_diagram" , filter_2 , true , 1000 , 0 , 1 );
 	
+	double distance_max_double_parameter = p.distance( q , std::numeric_limits<double>::max() );
+	double distance_inf_double_parameter = p.distance( q , std::numeric_limits<double>::infinity() );	
+		
+	//std::cerr << "distance_max_double_parameter: " << distance_max_double_parameter << std::endl;
+	//std::cerr << "distance_inf_double_parameter: " << distance_inf_double_parameter << std::endl;
+		
+	BOOST_CHECK( distance_max_double_parameter == distance_inf_double_parameter );
 }
 
 
diff --git a/src/Gudhi_stat/test/persistence_intervals_test.cpp b/src/Gudhi_stat/test/persistence_intervals_test.cpp
index dae270ed..8bad499a 100644
--- a/src/Gudhi_stat/test/persistence_intervals_test.cpp
+++ b/src/Gudhi_stat/test/persistence_intervals_test.cpp
@@ -23,7 +23,7 @@
 
 
 #define BOOST_TEST_DYN_LINK
-#define BOOST_TEST_MODULE "gudhi_stat"
+#define BOOST_TEST_MODULE "Persistence_representations"
 #include <boost/test/unit_test.hpp>
 #include <gudhi/reader_utils.h>
 #include "gudhi/Persistence_intervals.h"
diff --git a/src/Gudhi_stat/test/persistence_intervals_with_distances_test.cpp b/src/Gudhi_stat/test/persistence_intervals_with_distances_test.cpp
new file mode 100644
index 00000000..703b5011
--- /dev/null
+++ b/src/Gudhi_stat/test/persistence_intervals_with_distances_test.cpp
@@ -0,0 +1,70 @@
+/*    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/>.
+ */
+
+#define BOOST_TEST_DYN_LINK
+#define BOOST_TEST_MODULE "Persistence_representations"
+#include <boost/test/unit_test.hpp>
+#include <gudhi/reader_utils.h>
+#include "gudhi/Persistence_intervals_with_distances.h"
+#include "gudhi/common_persistence_representations.h"
+
+#include <iostream>
+
+
+
+using namespace Gudhi;
+using namespace Gudhi::Persistence_representations;
+
+
+BOOST_AUTO_TEST_CASE(check_bottleneck_distances_computation) 
+{
+	Persistence_intervals_with_distances p( "data/file_with_diagram" );
+	Persistence_intervals_with_distances q( "data/file_with_diagram_1" );
+	
+	double dist = p.distance( q );
+	
+	//std::cout << "dist : " << dist << std::endl;
+	
+	BOOST_CHECK( almost_equal(dist,0.389043) );
+}
+
+
+BOOST_AUTO_TEST_CASE(check_default_parameters_in_distance) 
+{
+	Persistence_intervals_with_distances p( "data/file_with_diagram" );
+	Persistence_intervals_with_distances q( "data/file_with_diagram_1" );
+	
+	double default_parameter_distance = p.distance( q );
+	double max_parameter_distance = p.distance( q , std::numeric_limits< double >::max() );
+	double inf_parameter_distance = p.distance( q , std::numeric_limits<double>::infinity() );
+	
+	//std::cout << "default_parameter_distance : " << default_parameter_distance << std::endl;
+	//std::cout << "max_parameter_distance : " << max_parameter_distance << std::endl;
+	//std::cout << "inf_parameter_distance : " << inf_parameter_distance << std::endl;
+	
+	BOOST_CHECK( default_parameter_distance == max_parameter_distance );
+	BOOST_CHECK( inf_parameter_distance == max_parameter_distance );
+	BOOST_CHECK( inf_parameter_distance == max_parameter_distance );
+}
+
+
+
diff --git a/src/Gudhi_stat/test/persistence_lanscapes_on_grid_test.cpp b/src/Gudhi_stat/test/persistence_lanscapes_on_grid_test.cpp
index e935cb97..971993ed 100644
--- a/src/Gudhi_stat/test/persistence_lanscapes_on_grid_test.cpp
+++ b/src/Gudhi_stat/test/persistence_lanscapes_on_grid_test.cpp
@@ -23,7 +23,7 @@
 
 
 #define BOOST_TEST_DYN_LINK
-#define BOOST_TEST_MODULE "gudhi_stat"
+#define BOOST_TEST_MODULE "Persistence_representations"
 #include <boost/test/unit_test.hpp>
 #include <gudhi/reader_utils.h>
 #include <gudhi/Persistence_landscape_on_grid.h>
@@ -36,10 +36,6 @@ using namespace Gudhi;
 using namespace Gudhi::Persistence_representations;
 
 
-double epsilon = 0.0000005;
-
-
-
 	
 
 BOOST_AUTO_TEST_CASE(check_construction_of_landscape) 
@@ -231,6 +227,20 @@ BOOST_AUTO_TEST_CASE(check_computations_of_maxima_and_norms)
 	BOOST_CHECK( fabs(compute_distance_of_landscapes_on_grid(p,sum,std::numeric_limits<double>::max()) - 0.45 ) <= 0.00001 );		
 }
 
+BOOST_AUTO_TEST_CASE(check_default_parameters_of_distances ) 
+{	
+	std::vector< std::pair< double , double > > diag = read_standard_persistence_file( "data/file_with_diagram" );	
+	Persistence_landscape_on_grid p( diag , 0. , 1. , 100 );
+	
+	std::vector< std::pair< double , double > > diag1 = read_standard_persistence_file( "data/file_with_diagram_1" );	
+	Persistence_landscape_on_grid q( diag1 , 0. , 1. , 100 );
+	
+	double dist_numeric_limit_max = p.distance( q,std::numeric_limits<double>::max()  );
+	double dist_infinity = p.distance( q,std::numeric_limits<double>::infinity() );
+	
+	BOOST_CHECK( dist_numeric_limit_max == dist_infinity );	
+}
+
 
 
 
diff --git a/src/Gudhi_stat/test/persistence_lanscapes_test.cpp b/src/Gudhi_stat/test/persistence_lanscapes_test.cpp
index 684c50ff..e401e075 100644
--- a/src/Gudhi_stat/test/persistence_lanscapes_test.cpp
+++ b/src/Gudhi_stat/test/persistence_lanscapes_test.cpp
@@ -23,12 +23,13 @@
 
 
 #define BOOST_TEST_DYN_LINK
-#define BOOST_TEST_MODULE "gudhi_stat"
+#define BOOST_TEST_MODULE "Persistence_representations"
 #include <boost/test/unit_test.hpp>
 #include <gudhi/reader_utils.h>
 #include <gudhi/Persistence_landscape.h>
 
 #include <iostream>
+#include <limits>
 
 
 
@@ -51,6 +52,16 @@ BOOST_AUTO_TEST_CASE(check_construction_of_landscape)
 }
 
 
+BOOST_AUTO_TEST_CASE(check_construction_of_landscape_form_gudhi_style_file) 
+{		
+	Persistence_landscape p( "data/persistence_file_with_four_entries_per_line" , 1 );	
+	//p.print_to_file("persistence_file_with_four_entries_per_line_landscape");
+	Persistence_landscape q;
+	q.load_landscape_from_file( "data/persistence_file_with_four_entries_per_line_landscape" );		
+	BOOST_CHECK( p == q );
+}
+
+
 BOOST_AUTO_TEST_CASE(check_computations_of_integrals) 
 {
 	std::vector< std::pair< double , double > > diag = read_standard_persistence_file( "data/file_with_diagram" );
@@ -190,6 +201,21 @@ BOOST_AUTO_TEST_CASE(check_computations_of_maxima_and_norms)
 	BOOST_CHECK( fabs(compute_distance_of_landscapes( p , sum , std::numeric_limits<double>::max() ) - 0.464478 ) <= 0.00001 );		
 }
 
+
+BOOST_AUTO_TEST_CASE(check_default_parameters_of_distances ) 
+{	
+	std::vector< std::pair< double , double > > diag = read_standard_persistence_file( "data/file_with_diagram" );	
+	Persistence_landscape p( diag );
+	
+	std::vector< std::pair< double , double > > diag1 = read_standard_persistence_file( "data/file_with_diagram_1" );	
+	Persistence_landscape q( diag1 );
+	
+	double dist_numeric_limit_max = p.distance( q,std::numeric_limits<double>::max()  );
+	double dist_infinity = p.distance( q,std::numeric_limits<double>::infinity() );
+	
+	BOOST_CHECK( dist_numeric_limit_max == dist_infinity );	
+}
+
 BOOST_AUTO_TEST_CASE(check_computations_of_averages) 
 {
 	std::vector< std::pair< double , double > > diag = read_standard_persistence_file( "data/file_with_diagram" );
diff --git a/src/Gudhi_stat/test/read_persistence_from_file_test.cpp b/src/Gudhi_stat/test/read_persistence_from_file_test.cpp
index d4dc7f89..69493efb 100644
--- a/src/Gudhi_stat/test/read_persistence_from_file_test.cpp
+++ b/src/Gudhi_stat/test/read_persistence_from_file_test.cpp
@@ -23,7 +23,7 @@
 
 
 #define BOOST_TEST_DYN_LINK
-#define BOOST_TEST_MODULE "gudhi_stat"
+#define BOOST_TEST_MODULE "Persistence_representations"
 #include <boost/test/unit_test.hpp>
 #include <gudhi/reader_utils.h>
 #include <gudhi/read_persistence_from_file.h>
diff --git a/src/Gudhi_stat/test/vector_representation_test.cpp b/src/Gudhi_stat/test/vector_representation_test.cpp
index 2c1ef1f8..3ef3427c 100644
--- a/src/Gudhi_stat/test/vector_representation_test.cpp
+++ b/src/Gudhi_stat/test/vector_representation_test.cpp
@@ -26,7 +26,7 @@
 #include <iostream>
 
 #define BOOST_TEST_DYN_LINK
-#define BOOST_TEST_MODULE "gudhi_stat"
+#define BOOST_TEST_MODULE "Persistence_representations"
 #include <boost/test/unit_test.hpp>
 #include <gudhi/reader_utils.h>
 #include <vector>
@@ -317,6 +317,20 @@ BOOST_AUTO_TEST_CASE(check_distance_computations)
 	BOOST_CHECK( almost_equal ( p_prime.distance( p_bis , 1 ) , 1.86428 ) );		
 }
 
+BOOST_AUTO_TEST_CASE(check_default_parameters_of_distances ) 
+{	
+	std::vector< std::pair< double , double > > diag = read_standard_persistence_file( "data/file_with_diagram" );	
+	Vector_distances_in_diagram< Euclidean_distance > p( diag , 100 );
+	
+	std::vector< std::pair< double , double > > diag1 = read_standard_persistence_file( "data/file_with_diagram_1" );	
+	Vector_distances_in_diagram< Euclidean_distance > q( diag1 , 100 );
+	
+	double dist_numeric_limit_max = p.distance( q,std::numeric_limits<double>::max()  );
+	double dist_infinity = p.distance( q,std::numeric_limits<double>::infinity() );
+	
+	BOOST_CHECK( dist_numeric_limit_max == dist_infinity );	
+}
+
 
 
 BOOST_AUTO_TEST_CASE(check_compute_average)