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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>
namespace Gudhi
{
namespace Persistence_representations
{
/**
* This procedure reads names of files which are stored in a file.
**/
std::vector< std::string > readFileNames( const char* filenameWithFilenames )
{
bool dbg = false;
std::ifstream in(filenameWithFilenames);
if ( !in.good() )
{
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::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 );
if (dbg){std::cerr << "Line after removing white spaces : " << line << std::endl;}
}
}
in.close();
return result;
}//readFileNames
std::vector< std::vector< double > > read_numbers_from_file_line_by_line( const char* filename )
{
bool dbg = false;
std::ifstream in(filename);
if ( !in.good() )
{
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::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 (2, 3 or 4).
* 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 'inf' string can appear only as a last element of a line.
* 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;
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 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;
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 whilespaces:
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 += (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 "The input file you have provided have wrong number of numerical entries per line. 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 whitespaces:
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";
}
}
}
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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