Add trim_cr utility function and apply it to CSV parsing in multiple files

BioFVM/BioFVM_microenvironment.cpp

@@ -47,6 +47,7 @@
 */
 
 #include "BioFVM_microenvironment.h"
+#include "BioFVM_utilities.h"
 #include "BioFVM_solvers.h"
 #include "BioFVM_vector.h"
 #include <cmath>
@@ -1467,6 +1468,7 @@ void load_initial_conditions_from_csv(std::string filename)
 	// determine if header row exists 
 	std::string line; 
 	std::getline( file , line );
+	trim_cr(line);
 	char c = line.c_str()[0];
 	std::vector<int> substrate_indices;
 	bool header_provided = false;
@@ -1515,13 +1517,15 @@ void load_initial_conditions_from_csv(std::string filename)
 		file.close();
 		std::ifstream file(filename, std::ios::in);
 		std::getline(file, line);
+		trim_cr(line);
 	}
 
 	std::cout << "Loading substrate initial conditions from CSV file " << filename << " ... " << std::endl;
 	std::vector<int> voxel_set = {}; // set to check that no voxel value is set twice
 
 	while (std::getline(file, line))
 	{
+		trim_cr(line);
 		get_row_from_substrate_initial_condition_csv(voxel_set, line, substrate_indices, header_provided);
 	}
 

BioFVM/BioFVM_utilities.h

@@ -78,9 +78,12 @@ void seed_random( void );
 double uniform_random( void );
 
 double compute_mean( std::vector<double>& values );
-double compute_variance( std::vector<double>& values, double mean ); 
-double compute_variance( std::vector<double>& values ); 
-
+double compute_variance( std::vector<double>& values, double mean );
+double compute_variance( std::vector<double>& values );
+
+inline void trim_cr( std::string& line )
+{ if (!line.empty() && line.back() == '\r') { line.pop_back(); } }
+
 };
 
 #endif 

core/PhysiCell_rules.cpp

@@ -1535,8 +1535,9 @@ void parse_csv_rules_v0( std::string filename )
 
 	while( fs.eof() == false )
 	{
-		std::string line; 	
-		std::getline( fs , line, '\n'); 
+		std::string line;
+		std::getline( fs , line, '\n');
+		trim_cr(line);
 		if( line.size() > 0 )
 		{ parse_csv_rule_v0(line); }
 	}
@@ -1671,8 +1672,9 @@ void parse_csv_rules_v1( std::string filename )
 
 	while( fs.eof() == false )
 	{
-		std::string line; 	
-		std::getline( fs , line, '\n'); 
+		std::string line;
+		std::getline( fs , line, '\n');
+		trim_cr(line);
 		if( line.size() > 0 )
 		{ parse_csv_rule_v1(line); }
 	}
@@ -1804,8 +1806,9 @@ void parse_csv_rules_v3( std::string filename )
 
 	while( fs.eof() == false )
 	{
-		std::string line; 	
-		std::getline( fs , line, '\n'); 
+		std::string line;
+		std::getline( fs , line, '\n');
+		trim_cr(line);
 		if( line.size() > 0 )
 		{ parse_csv_rule_v3(line); }
 	}

modules/PhysiCell_geometry.cpp

@@ -308,6 +308,7 @@ void load_cells_csv_v1( std::string filename )
 	std::string line;
 	while (std::getline(file, line))
 	{
+		trim_cr(line);
 		std::vector<double> data;
 		csv_to_vector( line.c_str() , data ); 
 
@@ -840,6 +841,7 @@ void load_cells_csv_v2( std::string filename )
 
 	std::string line; 
 	std::getline( file , line ); 
+	trim_cr(line);
 
 	// tokenize the labels 
 
@@ -848,7 +850,10 @@ void load_cells_csv_v2( std::string filename )
 	// process all remaining lines 
 
 	while (std::getline(file, line))
-	{ process_csv_v2_line(line,labels); }	
+	{
+		trim_cr(line);
+		process_csv_v2_line(line,labels);
+	}
 
 	// close the file 
 
@@ -871,6 +876,7 @@ void load_cells_csv( std::string filename )
 	// determine version 
 	std::string line; 
 	std::getline( file , line );
+	trim_cr(line);
 	char c = line.c_str()[0]; 
 
 	file.close();