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+/* 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/>.
+ */
+
+
+#ifndef Read_Persitence_From_File_H
+#define Read_Persitence_From_File_H
+
+#include <iostream>
+#include <fstream>
+#include <sstream>
+#include <vector>
+#include <algorithm>
+#include <unistd.h>
+
+
+namespace Gudhi
+{
+namespace Gudhi_stat
+{
+
+
+/**
+ * This procedure reads birth-death dagta from a file. We assume that in the file, there may be one type of string 'inf' or 'Inf'. If the second parameter of the program is set to -1,
+ * then those vales are ignored. If the second parameter of this program is set to a positive value, then the infinite intervals will be substituted by that number.
+**/
+std::vector< std::pair< double,double > > read_persistence_file_that_may_contain_inf_string( const char* filename , double what_to_substitute_for_infinite_bar = -1 )
+{
+
+ bool dbg = true;
+
+ if ( !( access( filename, F_OK ) != -1 ) )
+ {
+ std::cerr << "The file : " << filename << " do not exist. The program will now terminate \n";
+ throw "The file from which you are trying to read do not exist. The program will now terminate \n";
+ }
+
+ std::string line;
+ std::vector< std::pair<double,double> > barcode;
+
+ std::ifstream in;
+ in.open( filename );
+ while (!in.eof())
+ {
+ getline(in,line);
+ if ( !(line.length() == 0 || line[0] == '#') )
+ {
+ std::stringstream lineSS(line);
+ double beginn, endd;
+ if ( (line.find("inf") != std::string::npos) || (line.find("Inf") != std::string::npos) )
+ {
+ if ( dbg )
+ {
+ std::cerr << "This line: " << line << " contains infinite interval. We will skip it. \n";
+ }
+ if ( what_to_substitute_for_infinite_bar != -1 )
+ {
+ lineSS >> beginn;
+ endd = what_to_substitute_for_infinite_bar;
+ }
+ else
+ {
+ continue;
+ }
+ }
+ else
+ {
+ lineSS >> beginn;
+ lineSS >> endd;
+ }
+ if ( beginn > endd )
+ {
+ std::swap(beginn,endd);
+ }
+ if ( dbg )
+ {
+ std::cerr << "Getting an interval : " << beginn << "," << endd << std::endl;
+ }
+ barcode.push_back( std::make_pair( beginn , endd ) );
+ }
+ }
+ return barcode;
+}//readFileNames
+
+
+/**
+ * This procedure reads names of files which are stored in a file.
+**/
+std::vector< std::string > readFileNames( const char* filenameWithFilenames )
+{
+ bool dbg = false;
+
+ if ( !( access( filenameWithFilenames, F_OK ) != -1 ) )
+ {
+ std::cerr << "The file : " << filenameWithFilenames << " do not exist. The program will now terminate \n";
+ throw "The file from which you are trying to read do not exist. The program will now terminate \n";
+ }
+
+ std::vector< std::string > result;
+ std::ifstream in;
+ in.open( filenameWithFilenames );
+ std::string line;
+ while (!in.eof())
+ {
+ getline(in,line);
+ line.erase( std::remove_if( line.begin(), line.end(), ::isspace) , line.end() );
+
+ if (dbg){std::cerr << "line : " << line << std::endl;}
+
+ if ( (line.length() == 0) || (line[0] == '#') )
+ {
+ //in this case we have a file name. First we should remove all the white spaces.
+ if ( dbg ){std::cerr << "This is a line with comment, it will be ignored n";}
+ }
+ else
+ {
+ result.push_back( line.c_str() );
+ if (dbg){std::cerr << "Line after removing white spaces : " << line << std::endl;}
+ }
+ }
+ in.close();
+
+ return result;
+}//readFileNames
+
+
+/**
+ * This method reads persistence from standalone file. The format of the file is as follows:
+ * In every line there are two numbers which denotes birth and death of a persistence interval. The file is not supposed to contains any nonwhite characters excet from digits. In particular symbols
+ * like 'inf' are not allowed.
+ * If begin of the interval is greater than the end of the interval, those two numbers are swapped.
+**/
+std::vector< std::pair< double , double > > read_standard_persistence_file( const char* filename )
+{
+ bool dbg = false;
+
+ std::ifstream in;
+ in.open( filename );
+ if ( !( access( filename, F_OK ) != -1 ) )
+ {
+ std::cerr << "The file : " << filename << " do not exist. The program will now terminate \n";
+ throw "The file from which you are trying to read the persistence landscape do not exist. The program will now terminate \n";
+ }
+
+ std::string line;
+ std::vector< std::pair<double,double> > barcode;
+
+ while (!in.eof())
+ {
+ getline(in,line);
+ if ( !(line.length() == 0 || line[0] == '#') )
+ {
+ std::stringstream lineSS(line);
+ double beginn, endd;
+ lineSS >> beginn;
+ lineSS >> endd;
+ if ( beginn == endd )continue;
+ if ( beginn > endd )
+ {
+ std::swap(beginn,endd);
+ }
+ barcode.push_back( std::make_pair( beginn , endd ) );
+ if (dbg)
+ {
+ std::cerr << beginn << " , " << endd << std::endl;
+ }
+ }
+ }
+ in.close();
+ return barcode;
+}//read_standard_file
+
+
+
+/**
+ * This procedure reads Gudhi style file. The format of a Gudhi style file is as follows:
+ * Each line consist of the following information:
+ * A prime number p indicating that the class is nontrivial over Z_p field.
+ * A positive numebr, being a dimension of a persistence class
+ * A birth and a death time of a class.
+ * Death time may be infitnity, in which case a string 'inf' is used.
+ * If begin of the interval is greater than the end of the interval, those two numbers are swapped.
+ * Note that this procedure reads persistence in a single dimension. The dimension of intervals that
+ * are to be read are determined by the second parameter of the function.
+**/
+std::vector< std::pair< double , double > > read_gudhi_persistence_file_in_one_dimension( const char* filename , size_t dimension = 0 , double what_to_substitute_for_infinite_bar = -1)
+{
+ bool dbg = false;
+ if ( !( access( filename, F_OK ) != -1 ) )
+ {
+ std::cerr << "The file : " << filename << " do not exist. The program will now terminate \n";
+ throw "The file from which you are trying to read the persistence landscape do not exist. The program will now terminate \n";
+ }
+ std::ifstream in;
+ in.open( filename );
+
+ std::string line;
+ std::vector< std::pair<double,double> > barcode;
+
+ while (!in.eof())
+ {
+ getline(in,line);
+ if ( !(line.length() == 0 || line[0] == '#') )
+ {
+ if ( line.find("inf") != std::string::npos )
+ {
+ if ( dbg )
+ {
+ std::cerr << "This line: " << line << " contains infinite interval. We will skip it. \n";
+ }
+ if ( what_to_substitute_for_infinite_bar != -1 )
+ {
+ double beginn, field, dim;
+ std::stringstream lineSS(line);
+ lineSS >> field;
+ lineSS >> dim;
+ 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 << beginn << " , " << what_to_substitute_for_infinite_bar << std::endl;
+ }
+ }
+ }
+ continue;
+ }
+ std::stringstream lineSS(line);
+ double beginn, endd, field, dim;
+ lineSS >> field;
+ lineSS >> dim;
+ 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 << beginn << " , " << endd << std::endl;
+ }
+ }
+ }
+ }
+ in.close();
+ return barcode;
+}//read_gudhi_file
+
+
+std::vector< std::vector< double > > read_numbers_from_file_line_by_line( const char* filename )
+{
+ bool dbg = false;
+ if ( !( access( filename, F_OK ) != -1 ) )
+ {
+ std::cerr << "The file : " << filename << " do not exist. The program will now terminate \n";
+ throw "The file from which you are trying to read the persistence landscape do not exist. The program will now terminate \n";
+ }
+
+ std::vector< std::vector< double > > result;
+ double number;
+
+ std::ifstream in(filename);
+ std::string line;
+ while ( in.good() )
+ {
+ std::getline(in,line);
+ std::stringstream ss(line);
+
+ if ( dbg )std::cerr << "\n Reading line : " << line << std::endl;
+
+ std::vector< double > this_line;
+ while ( ss.good() )
+ {
+ ss >> number;
+ this_line.push_back( number );
+ if ( dbg )std::cerr << number << " ";
+ }
+ if ( this_line.size() && in.good() ) result.push_back( this_line );
+ }
+ in.close();
+
+ return result;
+}//read_numbers_from_file_line_by_line
+
+
+/**
+ * Universal procedure to read files with persistence. It ignores the lines starting from # (treat them as comments).
+ * It reads the fist line which is not a comment and assume that there are some numerical entries over there. The program assume
+ * that each other line in the file, which is not a comment, have the same number of numerical entries.
+ * If there are two numerical entries per line, then the function assume that they are birth/death coordinates.
+ * If there are three numerical entries per line, then the function assume that they are: dimension and birth/death coordinates.
+ * If there are four numerical entries per line, then the function assume that they are: thc characteristic of a filed over which
+ * persistence was computed, dimension and birth/death coordinates.
+ * 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 )
+{
+ bool dbg = false;
+
+ //checking if the file exist:
+ if ( !( access( filename.c_str() , F_OK ) != -1 ) )
+ {
+ std::cerr << "The file : " << filename << " do not exist. The program will now terminate \n";
+ throw "The file from which you are trying to read the persistence landscape do not exist. The program will now terminate \n";
+ }
+
+
+ std::ifstream in;
+ in.open( filename );
+
+ 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 ( number_of_entries_per_line == -1 )
+ {
+ //check how many entries we have in the line.
+ std::stringstream ss( line );
+ int number;
+ std::vector<int> this_line;
+ while ( ss >> number )
+ {
+ this_line.push_back( number );
+ }
+ number_of_entries_per_line = (int)this_line.size();
+ //if thie line contains 'inf' string, then we need to increment number_of_entries_per_line
+ if ( line.find("inf") != std::string::npos )++number_of_entries_per_line;
+ 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 "The input file you have provided have wrong number of numerical entries per line. The program will now terminate. \n";
+ }
+ }
+ if ( line.find("inf") != std::string::npos )
+ {
+ if ( dbg )
+ {
+ std::cerr << "This line: " << line << " contains infinite interval. \n";
+ }
+ 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
+ {
+ if ( dbg )
+ {
+ std::cerr << "We will skip it \n";
+ }
+ }
+ continue;
+ }
+ 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 ( dbg )
+ {
+ std::cerr << "This is a comment line \n";
+ }
+ }
+ }
+ in.close();
+ if ( dbg )std::cerr << "End of reading \n";
+
+ return barcode;
+}//read_persistence_intervals_in_one_dimension_from_file
+
+}//namespace Gudhi_stat
+}//namespace Gudhi
+
+
+
+
+#endif
+
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