diff options
Diffstat (limited to 'src/Gudhi_stat/include/gudhi/read_persistence_from_file.h')
| -rw-r--r-- | src/Gudhi_stat/include/gudhi/read_persistence_from_file.h | 211 |
1 files changed, 13 insertions, 198 deletions
diff --git a/src/Gudhi_stat/include/gudhi/read_persistence_from_file.h b/src/Gudhi_stat/include/gudhi/read_persistence_from_file.h index 39b3ca7b..f869f8e2 100644 --- a/src/Gudhi_stat/include/gudhi/read_persistence_from_file.h +++ b/src/Gudhi_stat/include/gudhi/read_persistence_from_file.h @@ -38,67 +38,6 @@ namespace Persistence_representations { -/** - * 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; - - 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 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; - 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. @@ -130,7 +69,7 @@ std::vector< std::string > readFileNames( const char* filenameWithFilenames ) } else { - result.push_back( line.c_str() ); + result.push_back( line ); if (dbg){std::cerr << "Line after removing white spaces : " << line << std::endl;} } } @@ -140,140 +79,6 @@ std::vector< std::string > readFileNames( const char* filenameWithFilenames ) }//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 ( !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; - - 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; - std::ifstream in; - in.open( 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::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 ) { @@ -315,14 +120,14 @@ std::vector< std::vector< double > > read_numbers_from_file_line_by_line( const /** * 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. + * 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 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::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; @@ -348,6 +153,7 @@ std::vector<std::pair<double,double>> read_persistence_intervals_in_one_dimensio 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 ) { //check how many entries we have in the line. @@ -371,6 +177,7 @@ std::vector<std::pair<double,double>> read_persistence_intervals_in_one_dimensio 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 ) @@ -416,6 +223,7 @@ std::vector<std::pair<double,double>> read_persistence_intervals_in_one_dimensio } continue; } + //Then, we read the content of the line: std::stringstream lineSS(line); double beginn, endd, field, dim; if ( number_of_entries_per_line == 4 )lineSS >> field; @@ -441,6 +249,13 @@ std::vector<std::pair<double,double>> read_persistence_intervals_in_one_dimensio 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 { |