DC initialization from file

.gitignore

@@ -49,3 +49,5 @@ Studio.zip
 /unit_tests
 /test_custom_DCs
 /test_voxel_values
+
+.vscode

BioFVM/BioFVM_microenvironment.h

@@ -254,6 +254,9 @@ class Microenvironment
 	void set_substrate_dirichlet_activation( int index, std::vector<bool>& new_value ); 
 	bool get_substrate_dirichlet_activation( int substrate_index, int index );  
 
+	// only change dirichlet_activation_vector, not the activation_vectors for each voxel
+	void set_only_substrate_dirichlet_activation( int substrate_index , bool new_value );
+
     double get_substrate_dirichlet_value( int substrate_index, int index );
 
 	bool& is_dirichlet_node( int voxel_index ); 
@@ -341,9 +344,13 @@ class Microenvironment_Options
 
 	std::vector<double> initial_condition_vector; 
 
-	bool initial_condition_from_file_enabled;
+	bool initial_condition_from_file_enabled = false;
 	std::string initial_condition_file_type;
 	std::string initial_condition_file;
+
+	bool dirichlet_condition_from_file_enabled = false;
+	std::string dirichlet_condition_file_type;
+	std::string dirichlet_condition_file;
 
 	bool simulate_2D; 
 	std::vector<double> X_range; 
@@ -368,6 +375,13 @@ void set_microenvironment_initial_condition( void );
 void load_initial_conditions_from_matlab( std::string filename );
 void load_initial_conditions_from_csv( std::string filename );
 void get_row_from_substrate_initial_condition_csv(std::vector<int> &voxel_set, const std::string line, const std::vector<int> substrate_indices, const bool header_provided);
+
+void set_dirichlet_initial_condition( void );
+void set_dirichlet_boundaries_from_XML( void );
+void set_dirichlet_boundaries_from_file( void );
+void load_dirichlet_conditions_from_matlab( std::string filename );
+void load_dirichlet_conditions_from_csv(std::string filename);
+void get_row_from_dirichlet_condition_csv(std::vector<int> &voxel_set, const std::string line, const std::vector<int> substrate_indices, const bool header_provided, int n_cols);
 };
 
 #endif

BioFVM/BioFVM_vector.cpp

@@ -47,6 +47,8 @@
 */
 
 #include "BioFVM_vector.h" 
+#include <stdexcept>
+#include <string>
 
 /* some global BioFVM strings */ 
 
@@ -376,6 +378,88 @@ void csv_to_vector( const char* buffer , std::vector<double>& vect )
 	return; 
 }
 
+// store one field of a dirichlet-condition csv row. The bounds check matters: a row carrying more
+// fields than the header established would otherwise write past the end of both vectors.
+static void store_dirichlet_csv_entry( const char* buffer , const std::string& entry , std::vector<bool>& is_missing , std::vector<double>& data , const size_t ind )
+{
+	if (ind >= is_missing.size())
+	{
+		std::cerr << "Error: Too many data supplied in a row of the .csv file specifying BioFVM dirichlet conditions." << std::endl;
+		std::cerr << "\tExpected: " << is_missing.size() << ". Found: " << ind + 1 << " or more." << std::endl;
+		std::cerr << "\tRow: " << buffer << std::endl;
+		exit(-1);
+	}
+
+	// a field holding nothing but whitespace is omitted, so that " , " reads the same as ","
+	size_t first = entry.find_first_not_of(" \t\r");
+	if (first == std::string::npos)
+	{
+		is_missing[ind] = true;
+		return;
+	}
+	std::string trimmed = entry.substr(first, entry.find_last_not_of(" \t\r") - first + 1);
+
+	double value = 0.0;
+	size_t parsed = 0;
+	try
+	{
+		value = std::stod(trimmed, &parsed);
+	}
+	catch (const std::logic_error&) // std::stod throws invalid_argument on no conversion, out_of_range on overflow
+	{
+		parsed = 0;
+	}
+	if (parsed != trimmed.size()) // no conversion, or trailing garbage as in "1.5abc"
+	{
+		std::cerr << "Error: Column " << ind + 1 << " of a row of the .csv file specifying BioFVM dirichlet conditions is not a number." << std::endl;
+		std::cerr << "\tOffending value: " << trimmed << std::endl;
+		std::cerr << "\tRow: " << buffer << std::endl;
+		exit(-1);
+	}
+
+	data[ind] = value;
+	is_missing[ind] = false;
+}
+
+void dirichlet_csv_to_vector( const char* buffer , std::vector<bool>& is_missing , std::vector<double>& data )
+{
+	size_t ind = 0;
+    unsigned int i=0;
+    std::string entry;
+    while( i < strlen( buffer ) )
+    {
+        if(buffer[i] == ',')
+        {
+			store_dirichlet_csv_entry(buffer, entry, is_missing, data, ind);
+            entry.clear();
+			ind++;
+        }
+        else
+        {
+            entry += buffer[i];
+        }
+        i++;
+    }
+    // Handle the last entry
+	store_dirichlet_csv_entry(buffer, entry, is_missing, data, ind);
+
+	if (is_missing[0] || is_missing[1] || is_missing[2])
+	{
+		std::cerr << "Error: x, y, and z data must be provided for each row in the .csv file specifying BioFVM dirichlet conditions." << std::endl;
+		exit(-1);
+	}
+
+	if (ind < is_missing.size() - 1)
+	{
+		std::cerr << "Error: Wrong number of data supplied in a row of the .csv file specifying BioFVM dirichlet conditions." << std::endl;
+		std::cerr << "\tExpected: " << is_missing.size() << ". Found: " << ind + 1 << std::endl;
+		std::cerr << "\tRow: " << buffer << std::endl;
+		exit(-1);
+	}
+    return; 
+}
+
+
 char* vector_to_csv( const std::vector<double>& vect )
 { 
 	static int datum_size = 16;  // format = %.7e, 1 (sign) + 1 (lead) + 1 (decimal) + 7 (figs) + 2 (e, sign) + 3 (exponent) + 1 (delimiter) = 16

BioFVM/BioFVM_vector.h

@@ -130,6 +130,7 @@ void double_axpy_div( std::vector<double>* y, std::vector<double>& a1 , std::vec
 // turn a delimited character array (e.g., csv) into a vector of doubles
 
 void csv_to_vector( const char* buffer , std::vector<double>& vect ); 
+void dirichlet_csv_to_vector( const char* buffer , std::vector<bool>& missings , std::vector<double>& values );
 char* vector_to_csv( const std::vector<double>& vect );
 void vector_to_csv_safe( const std::vector<double>& vect , char*& buffer );
 void vector_to_csv( const std::vector<double>& vect , char*& buffer );

Makefile

@@ -92,7 +92,7 @@ template:
 	cp Makefile Makefile-backup
 	cp ./sample_projects/template/Makefile .
 	cp -r ./sample_projects/template/config/* ./config 
-	
+
 # sample projects 
 
 # ---- non-intracellular projects 
@@ -238,6 +238,14 @@ episode-sample:
 	cp ./sample_projects/episode/Makefile .
 	cp -r ./sample_projects/episode/config/* ./config
 
+dirichlet-from-file-sample:
+	cp -r ./sample_projects/dirichlet_from_file/custom_modules/* ./custom_modules/
+	touch main.cpp && cp main.cpp main-backup.cpp
+	cp ./sample_projects/dirichlet_from_file/main.cpp ./main.cpp 
+	cp Makefile Makefile-backup
+	cp ./sample_projects/dirichlet_from_file/Makefile .
+	cp -r ./sample_projects/dirichlet_from_file/config/* ./config 
+
 # ---- intracellular projects 
 ode-energy-sample:
 	cp ./sample_projects_intracellular/ode/ode_energy/custom_modules/* ./custom_modules/

modules/PhysiCell_settings.cpp

@@ -987,6 +987,21 @@ bool setup_microenvironment_from_XML( pugi::xml_node root_node )
 		}
 	}
 
+	node = xml_find_node( root_node , "microenvironment_setup" );
+	node = xml_find_node( node , "options" );
+	node = xml_find_node(node, "dirichlet_nodes");
+	if (node)
+	{
+		default_microenvironment_options.dirichlet_condition_from_file_enabled = node.attribute("enabled").as_bool();
+		if (default_microenvironment_options.dirichlet_condition_from_file_enabled)
+		{
+			default_microenvironment_options.dirichlet_condition_file_type = node.attribute("type").as_string();
+			default_microenvironment_options.dirichlet_condition_file = xml_get_string_value(node, "filename");
+
+			copy_file_to_output(default_microenvironment_options.dirichlet_condition_file);
+		}
+	}
+
 	// not yet supported : read initial conditions 
 	/*
 	// read in initial conditions from an external file 

sample_projects/Makefile-default

@@ -92,7 +92,7 @@ template:
 	cp Makefile Makefile-backup
 	cp ./sample_projects/template/Makefile .
 	cp -r ./sample_projects/template/config/* ./config 
-	
+
 # sample projects 
 
 # ---- non-intracellular projects 
@@ -238,6 +238,14 @@ episode-sample:
 	cp ./sample_projects/episode/Makefile .
 	cp -r ./sample_projects/episode/config/* ./config
 
+dirichlet-from-file-sample:
+	cp -r ./sample_projects/dirichlet_from_file/custom_modules/* ./custom_modules/
+	touch main.cpp && cp main.cpp main-backup.cpp
+	cp ./sample_projects/dirichlet_from_file/main.cpp ./main.cpp 
+	cp Makefile Makefile-backup
+	cp ./sample_projects/dirichlet_from_file/Makefile .
+	cp -r ./sample_projects/dirichlet_from_file/config/* ./config 
+
 # ---- intracellular projects 
 ode-energy-sample:
 	cp ./sample_projects_intracellular/ode/ode_energy/custom_modules/* ./custom_modules/