Merge pull request MathCancer#276 from drbergman/copy-inputs-to-outpu…

…t-folder

copy cell ic file and substrate ic file to output

core/PhysiCell_rules.cpp

@@ -1940,31 +1940,6 @@ void parse_rules_from_pugixml( void )
 		node = node.next_sibling( "ruleset"); 		
 	}
 	return; 
-
-	exit(0); 
-
-	// enabled? 
-	if( node.attribute("enabled").as_bool() == false )
-	{ return; }
-
-	// get filename 
-
-	std::string folder = xml_get_string_value( node, "folder" ); 
-	std::string filename = xml_get_string_value( node, "filename" ); 
-	std::string input_filename = folder + "/" + filename; 
-
-	std::string filetype = node.attribute("type").value() ; 
-
-	// what kind? 
-	if( filetype == "csv" || filetype == "CSV" )
-	{
-		std::cout << "Loading rules from CSV file " << input_filename << " ... " << std::endl; 
-		// load_cells_csv( input_filename );
-		parse_csv_rules_v0( input_filename ); 
-		return; 
-	}
-
-	return; 
 }
 
 void parse_rules_from_parameters_v0( void )

core/PhysiCell_utilities.cpp

@@ -359,4 +359,24 @@ int choose_event( std::vector<double>& probabilities )
 	return probabilities.size(); 
 }
 
+void copy_file_to_output(std::string filename)
+{
+	std::cout << "Copying " << filename << " to output folder." << std::endl;
+	// copy the file to the output folder
+	std::string basename = filename;
+	size_t found = basename.find_last_of("/"); // find the end of the path
+	if (found != std::string::npos)
+	{
+		basename = basename.substr(found + 1);
+	}
+
+	std::string output_filename = PhysiCell_settings.folder + "/" + basename;
+
+	// copy filename to output_filename
+	char copy_command[1024];
+	sprintf(copy_command, "cp %s %s", filename.c_str(), output_filename.c_str());
+	std::cout << "Copy command: " << copy_command << std::endl;
+	system(copy_command);
+}
+
 };

core/PhysiCell_utilities.h

@@ -111,6 +111,7 @@ void add_software_citation( std::string name , std::string version, std::string
 
 int choose_event( std::vector<double>& probabilities ); 
 
+void copy_file_to_output( std::string filename );
 };
 
 #endif

modules/PhysiCell_geometry.cpp

@@ -373,31 +373,30 @@ bool load_cells_from_pugixml( pugi::xml_node root )
 		std::cout << "Loading cells from CSV file " << input_filename << " ... " << std::endl; 
 		load_cells_csv( input_filename );
 		system("sleep 1");
-		return true; 
 	}
-	if( filetype == "matlab" || filetype == "mat" || filetype == "MAT" )
+	else if( filetype == "matlab" || filetype == "mat" || filetype == "MAT" )
 	{
 		std::cout << "Error: Load cell positions from matlab not yet supported. Try CSV." << std::endl; 
 		exit(-1); 
-		std::cout << "Loading cells from matlab file " << input_filename << " ... " << std::endl; 
-		return false; 
 	}
-	if( filetype == "scene" )
+	else if( filetype == "scene" )
 	{
 		std::cout << "Error: load cell positions from scene not yet supported. Try CSV." << std::endl; 
 		exit(-1); 
-		std::cout << "Loading cells from scene file " << input_filename << " ... " << std::endl; 
-		return false; 
 	}
-	if( filetype == "physicell" || filetype == "PhysiCell" )
+	else if( filetype == "physicell" || filetype == "PhysiCell" )
 	{
 		std::cout << "Error: load cell positions from PhysiCell snapshot not yet supported. Try CSV." << std::endl; 
 		exit(-1); 
-		std::cout << "Loading cells from PhysiCell file " << input_filename << " ... " << std::endl; 
-		return false; 
+	}
+	else
+	{
+		std::cout << "Error: Unknown cell position filetype " << filetype << " in XML. Try CSV." << std::endl; 
+		exit(-1);
 	}
 
-	return false; 
+	copy_file_to_output(input_filename);
+	return true; 
 }
 
 bool load_cells_from_pugixml( void )

modules/PhysiCell_settings.cpp

@@ -901,6 +901,8 @@ bool setup_microenvironment_from_XML( pugi::xml_node root_node )
 		{
 			default_microenvironment_options.initial_condition_file_type = node.attribute("type").as_string();
 			default_microenvironment_options.initial_condition_file = xml_get_string_value(node, "filename");
+
+			copy_file_to_output(default_microenvironment_options.initial_condition_file);
 		}
 	}