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authorpdlotko <pdlotko@636b058d-ea47-450e-bf9e-a15bfbe3eedb>2017-08-14 19:43:45 +0000
committerpdlotko <pdlotko@636b058d-ea47-450e-bf9e-a15bfbe3eedb>2017-08-14 19:43:45 +0000
commite2c0166fcbf17e91cf5ed7b6159f80d64b49cc0b (patch)
tree8b406841de67ed77647a9c4153bbb88dee90a60a /src/Persistence_representations/include
parent871bf8d781f88536942a92f9003509eaaa4e2e12 (diff)
Adding a code that use Clement's procedure to read files. Correcting some samll errors. Now the code is ready.
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/persistence_representation_integration@2610 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: b2947d1c484d661eca6c32fe5386461e741b76f9
Diffstat (limited to 'src/Persistence_representations/include')
-rw-r--r--src/Persistence_representations/include/gudhi/Persistence_intervals_with_distances.h1
-rw-r--r--src/Persistence_representations/include/gudhi/Persistence_landscape.h28
-rw-r--r--src/Persistence_representations/include/gudhi/read_persistence_from_file.h192
3 files changed, 91 insertions, 130 deletions
diff --git a/src/Persistence_representations/include/gudhi/Persistence_intervals_with_distances.h b/src/Persistence_representations/include/gudhi/Persistence_intervals_with_distances.h
index e476d28a..d5ab04b4 100644
--- a/src/Persistence_representations/include/gudhi/Persistence_intervals_with_distances.h
+++ b/src/Persistence_representations/include/gudhi/Persistence_intervals_with_distances.h
@@ -26,6 +26,7 @@
#include <gudhi/Persistence_intervals.h>
#include <gudhi/Bottleneck.h>
+
#include <limits>
namespace Gudhi {
diff --git a/src/Persistence_representations/include/gudhi/Persistence_landscape.h b/src/Persistence_representations/include/gudhi/Persistence_landscape.h
index c86e68d3..63e45bc9 100644
--- a/src/Persistence_representations/include/gudhi/Persistence_landscape.h
+++ b/src/Persistence_representations/include/gudhi/Persistence_landscape.h
@@ -77,16 +77,16 @@ class Persistence_landscape {
Persistence_landscape() { this->set_up_numbers_of_functions_for_vectorization_and_projections_to_reals(); }
/**
- * Constructor that takes as an input a vector of birth-death pairs.
- **/
- Persistence_landscape(const std::vector<std::pair<double, double> >& p);
+ * Constructor that takes as an input a vector of birth-death pairs.
+ **/
+ Persistence_landscape(const std::vector<std::pair<double, double> >& p, size_t number_of_levels = std::numeric_limits<size_t>::max() );
/**
* Constructor that reads persistence intervals from file and creates persistence landscape. The format of the
*input file is the following: in each line we put birth-death pair. Last line is assumed
* to be empty. Even if the points within a line are not ordered, they will be ordered while the input is read.
**/
- Persistence_landscape(const char* filename, size_t dimension = std::numeric_limits<unsigned>::max());
+ Persistence_landscape(const char* filename, size_t dimension = std::numeric_limits<unsigned>::max() , size_t number_of_levels = std::numeric_limits<size_t>::max() );
/**
* This procedure loads a landscape from file. It erase all the data that was previously stored in this landscape.
@@ -451,7 +451,7 @@ class Persistence_landscape {
size_t number_of_functions_for_vectorization;
size_t number_of_functions_for_projections_to_reals;
- void construct_persistence_landscape_from_barcode(const std::vector<std::pair<double, double> >& p);
+ void construct_persistence_landscape_from_barcode(const std::vector<std::pair<double, double> >& p , size_t number_of_levels = std::numeric_limits<size_t>::max());
Persistence_landscape multiply_lanscape_by_real_number_not_overwrite(double x) const;
void multiply_lanscape_by_real_number_overwrite(double x);
friend double compute_maximal_distance_non_symmetric(const Persistence_landscape& pl1,
@@ -464,14 +464,14 @@ class Persistence_landscape {
}
};
-Persistence_landscape::Persistence_landscape(const char* filename, size_t dimension) {
+Persistence_landscape::Persistence_landscape(const char* filename, size_t dimension, size_t number_of_levels) {
std::vector<std::pair<double, double> > barcode;
if (dimension < std::numeric_limits<double>::max()) {
barcode = read_persistence_intervals_in_one_dimension_from_file(filename, dimension);
} else {
barcode = read_persistence_intervals_in_one_dimension_from_file(filename);
}
- this->construct_persistence_landscape_from_barcode(barcode);
+ this->construct_persistence_landscape_from_barcode(barcode,number_of_levels);
this->set_up_numbers_of_functions_for_vectorization_and_projections_to_reals();
}
@@ -504,13 +504,14 @@ bool Persistence_landscape::operator==(const Persistence_landscape& rhs) const {
return true;
}
-Persistence_landscape::Persistence_landscape(const std::vector<std::pair<double, double> >& p) {
- this->construct_persistence_landscape_from_barcode(p);
+Persistence_landscape::Persistence_landscape(const std::vector<std::pair<double, double> >& p,size_t number_of_levels) {
+ this->construct_persistence_landscape_from_barcode(p,number_of_levels);
this->set_up_numbers_of_functions_for_vectorization_and_projections_to_reals();
}
void Persistence_landscape::construct_persistence_landscape_from_barcode(
- const std::vector<std::pair<double, double> >& p) {
+ const std::vector<std::pair<double, double> >& p, size_t number_of_levels)
+ {
bool dbg = false;
if (dbg) {
std::cerr << "Persistence_landscape::Persistence_landscape( const std::vector< std::pair< double , double > >& p )"
@@ -536,6 +537,7 @@ void Persistence_landscape::construct_persistence_landscape_from_barcode(
std::make_pair((bars[i].first + bars[i].second) / 2.0, (bars[i].second - bars[i].first) / 2.0);
}
std::vector<std::vector<std::pair<double, double> > > Persistence_landscape;
+ size_t number_of_levels_in_the_landscape = 0;
while (!characteristicPoints.empty()) {
if (dbg) {
for (size_t i = 0; i != characteristicPoints.size(); ++i) {
@@ -644,6 +646,12 @@ void Persistence_landscape::construct_persistence_landscape_from_barcode(
lambda_n.erase(std::unique(lambda_n.begin(), lambda_n.end()), lambda_n.end());
this->land.push_back(lambda_n);
+
+ ++number_of_levels_in_the_landscape;
+ if ( number_of_levels == number_of_levels_in_the_landscape )
+ {
+ break;
+ }
}
}
diff --git a/src/Persistence_representations/include/gudhi/read_persistence_from_file.h b/src/Persistence_representations/include/gudhi/read_persistence_from_file.h
index ad3d4e83..770da15b 100644
--- a/src/Persistence_representations/include/gudhi/read_persistence_from_file.h
+++ b/src/Persistence_representations/include/gudhi/read_persistence_from_file.h
@@ -30,6 +30,7 @@
#include <algorithm>
#include <string>
#include <utility>
+#include <gudhi/reader_utils.h>
namespace Gudhi {
namespace Persistence_representations {
@@ -49,130 +50,81 @@ namespace Persistence_representations {
* The procedure returns vector of persistence pairs.
**/
std::vector<std::pair<double, double> > read_persistence_intervals_in_one_dimension_from_file(
- std::string const& filename, int dimension = -1, double what_to_substitute_for_infinite_bar = -1) {
+ std::string const& filename, int dimension = -1, double what_to_substitute_for_infinite_bar = -1) {
bool dbg = false;
- std::ifstream in;
- in.open(filename);
- // checking if the file exist:
- if (!in.good()) {
- std::cerr << "The file : " << filename << " do not exist. The program will now terminate \n";
- throw "The persistence landscape file do not exist. The program will now terminate \n";
- }
std::string line;
- std::vector<std::pair<double, double> > barcode;
-
- int number_of_entries_per_line = -1;
-
- while (!in.eof()) {
- getline(in, line);
- if (dbg) std::cerr << "Reading line : " << line << std::endl;
- if (!(line.length() == 0 || line[0] == '#')) {
- // If we do not know how many entries per line we have, we check it in below.
- if (number_of_entries_per_line == -1) {
- number_of_entries_per_line = 0;
- std::string line_copy(line);
- if (line_copy.find("inf") != std::string::npos) {
- size_t np = line_copy.find("inf");
- // replace symbols 'inf' in line_copy with white spaces:
- line_copy[np] = ' ';
- line_copy[np + 1] = ' ';
- line_copy[np + 2] = ' ';
- number_of_entries_per_line = 1;
- }
- // check how many entries we have in the line.
- std::stringstream ss(line_copy);
- double number;
- std::vector<double> this_line;
- while (ss >> number) {
- this_line.push_back(number);
- }
- number_of_entries_per_line += static_cast<int>(this_line.size());
- if (dbg) {
- std::cerr << "number_of_entries_per_line : " << number_of_entries_per_line
- << ". This number was obtained by analyzing this line : " << line << std::endl;
- }
- if ((number_of_entries_per_line < 2) || (number_of_entries_per_line > 4)) {
- std::cerr << "The input file you have provided have wrong number of numerical entries per line. The program "
- "will now terminate. \n";
- throw "Wrong number of numerical entries per line in the input file. The program will now terminate. \n";
- }
- }
- // In case there is an 'inf' string in this line, we are dealing with this situation in below.
- if (line.find("inf") != std::string::npos) {
- if (dbg) {
- std::cerr << "This line: " << line << " contains infinite interval. \n";
- }
- // first we substitute inf by white spaces:
- size_t np = line.find("inf");
- line[np] = ' ';
- line[np + 1] = ' ';
- line[np + 2] = ' ';
- if (what_to_substitute_for_infinite_bar != -1) {
- double beginn, field, dim;
- std::stringstream lineSS(line);
- if (number_of_entries_per_line == 4) lineSS >> field;
- if (number_of_entries_per_line >= 3) {
- lineSS >> dim;
- } else {
- dim = dimension;
- }
- lineSS >> beginn;
- if (dim == dimension) {
- if (beginn > what_to_substitute_for_infinite_bar) {
- barcode.push_back(std::make_pair(what_to_substitute_for_infinite_bar, beginn));
- } else {
- barcode.push_back(std::make_pair(beginn, what_to_substitute_for_infinite_bar));
- }
- if (dbg) {
- std::cerr << "this is the line that is going to the output : " << beginn << " , "
- << what_to_substitute_for_infinite_bar << std::endl;
- }
- }
- } else {
- // this is a line with infinity. Since the variable what_to_substitute_for_infinite_bar have not been set up,
- // it means that this line will be skipped.
- if (dbg) {
- std::cerr << "We will skip it \n";
- }
- }
- continue;
- } else {
- // Then, we read the content of the line. We know that it do not contain 'inf' substring.
- std::stringstream lineSS(line);
- double beginn, endd, field, dim;
- if (number_of_entries_per_line == 4) lineSS >> field;
- if (number_of_entries_per_line >= 3) {
- lineSS >> dim;
- } else {
- dim = dimension;
- }
- lineSS >> beginn;
- lineSS >> endd;
- if (beginn > endd) {
- std::swap(beginn, endd);
- }
- if (dim == dimension) {
- barcode.push_back(std::make_pair(beginn, endd));
- if (dbg) {
- std::cerr << "This is a line that is going to the output : " << beginn << " , " << endd << std::endl;
- }
- } else {
- if ((number_of_entries_per_line == 3) && (dimension == -1)) {
- barcode.push_back(std::make_pair(beginn, endd));
- }
- }
- }
- } else {
- if (dbg) {
- std::cerr << "This is a comment line \n";
- }
- }
+ std::vector<std::pair<double, double> > barcode_initial = read_persistence_intervals_in_dimension(filename,(int)dimension);
+ std::vector<std::pair<double, double> > final_barcode;
+ final_barcode.reserve( barcode_initial.size() );
+
+ if ( dbg )
+ {
+ std::cerr << "Here are the intervals that we read from the file : \n";
+ for ( size_t i = 0 ; i != barcode_initial.size() ; ++i )
+ {
+ std::cout << barcode_initial[i].first << " " << barcode_initial[i].second << std::endl;
+ }
+ getchar();
}
- in.close();
- if (dbg) std::cerr << "End of reading \n";
-
- return barcode;
+
+ for ( size_t i = 0 ; i != barcode_initial.size() ; ++i )
+ {
+ if ( dbg )
+ {
+ std::cout << "COnsidering interval : " << barcode_initial[i].first << " " << barcode_initial[i].second << std::endl;
+ }
+ // if ( barcode_initial[i].first == barcode_initial[i].second )
+ //{
+ // if ( dbg )std::cout << "It has zero length \n";
+ // continue;//zero length intervals are not relevant, so we skip all of them.
+ //}
+
+ if ( barcode_initial[i].first > barcode_initial[i].second )//note that in this case barcode_initial[i].second != std::numeric_limits<double>::infinity()
+ {
+ if ( dbg )std::cout << "Swap and enter \n";
+ //swap them to make sure that birth < death
+ final_barcode.push_back( std::pair<double,double>( barcode_initial[i].second , barcode_initial[i].first ) );
+ continue;
+ }
+ else
+ {
+ if ( barcode_initial[i].second != std::numeric_limits<double>::infinity() )
+ {
+ if ( dbg )std::cout << "Simply enters\n";
+ //in this case, due to the previous conditions we know that barcode_initial[i].first < barcode_initial[i].second, so we put them as they are
+ final_barcode.push_back( std::pair<double,double>( barcode_initial[i].first , barcode_initial[i].second ) );
+ }
+ }
+
+ if ( (barcode_initial[i].second == std::numeric_limits<double>::infinity() ) && ( what_to_substitute_for_infinite_bar != -1 ) )
+ {
+ if ( barcode_initial[i].first < what_to_substitute_for_infinite_bar )//if only birth < death.
+ {
+ final_barcode.push_back( std::pair<double,double>( barcode_initial[i].first , what_to_substitute_for_infinite_bar ) );
+ }
+ }
+ else
+ {
+ //if the variable what_to_substitute_for_infinite_bar is not set, then we ignore all the infinite bars.
+ }
+ }
+
+
+ if ( dbg )
+ {
+ std::cerr << "Here are the final bars that we are sending further : \n";
+ for ( size_t i = 0 ; i != final_barcode.size() ; ++i )
+ {
+ std::cout << final_barcode[i].first << " " << final_barcode[i].second << std::endl;
+ }
+ std::cerr << "final_barcode.size() : " << final_barcode.size() << std::endl;
+ getchar();
+ }
+
+
+
+ return final_barcode;
} // read_persistence_intervals_in_one_dimension_from_file
} // namespace Persistence_representations