diff options
Diffstat (limited to 'src/Gudhi_stat/include/gudhi/read_persitence_from_file.h')
| -rw-r--r-- | src/Gudhi_stat/include/gudhi/read_persitence_from_file.h | 154 |
1 files changed, 152 insertions, 2 deletions
diff --git a/src/Gudhi_stat/include/gudhi/read_persitence_from_file.h b/src/Gudhi_stat/include/gudhi/read_persitence_from_file.h index 38cdecd5..a340b40c 100644 --- a/src/Gudhi_stat/include/gudhi/read_persitence_from_file.h +++ b/src/Gudhi_stat/include/gudhi/read_persitence_from_file.h @@ -42,7 +42,7 @@ 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( char* filename , double what_to_substitute_for_infinite_bar = -1 ) +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; @@ -203,7 +203,12 @@ std::vector< std::pair< double , double > > read_standard_persistence_file( cons **/ 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; + 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 ); @@ -306,6 +311,151 @@ std::vector< std::vector< double > > read_numbers_from_file_line_by_line( const 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 |