Typo

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/persistence_representation_integration@2472 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 457b970258b8a99519db664358c19d0dee80d879

1 files changed, 300 insertions, 0 deletions

diff --git a/src/Persistence_representations/include/gudhi/read_persistence_from_file.h b/src/Persistence_representations/include/gudhi/read_persistence_from_file.h
new file mode 100644
index 00000000..058c77a4
--- /dev/null
+++ b/src/Persistence_representations/include/gudhi/read_persistence_from_file.h
@@ -0,0 +1,300 @@
+/*    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
+