Updated PhysiBoSS sample projects

Author: vincent-noel

sample_projects_intracellular/boolean/cancer_invasion/custom_modules/custom.cpp

@@ -129,24 +129,24 @@ void create_cell_types( void )
 	   This is a good place to set custom functions. 
 	*/ 
 
-	cell_defaults.functions.pre_update_intracellular = pre_update_intracellular;
-	cell_defaults.functions.post_update_intracellular = post_update_intracellular;
+	cell_defaults.phenotype.intracellulars[0]->pre_update_intracellular = pre_update_intracellular;
+	cell_defaults.phenotype.intracellulars[0]->post_update_intracellular = post_update_intracellular;
 
 	cell_defaults.functions.update_phenotype = phenotype_function; 
 	cell_defaults.functions.custom_cell_rule = custom_function; 
 	cell_defaults.functions.contact_function = contact_function; 
 
 	Cell_Definition* pCD = find_cell_definition( "epithelial");
 
-	pCD->functions.pre_update_intracellular = pre_update_intracellular;
-	pCD->functions.post_update_intracellular = post_update_intracellular;
+	pCD->phenotype.intracellulars[0]->pre_update_intracellular = pre_update_intracellular;
+	pCD->phenotype.intracellulars[0]->post_update_intracellular = post_update_intracellular;
 	pCD->functions.custom_cell_rule = custom_function; 
 	pCD->functions.contact_function = contact_function; 
 	pCD->functions.update_velocity = standard_update_cell_velocity; 
 
 	pCD = find_cell_definition( "mesenchymal");
-	pCD->functions.pre_update_intracellular = pre_update_intracellular;
-	pCD->functions.post_update_intracellular = post_update_intracellular;
+	pCD->phenotype.intracellulars[0]->pre_update_intracellular = pre_update_intracellular;
+	pCD->phenotype.intracellulars[0]->post_update_intracellular = post_update_intracellular;
 	pCD->functions.custom_cell_rule = custom_function; 
 	pCD->functions.contact_function = contact_function;
 	pCD->functions.update_velocity = standard_update_cell_velocity; 
@@ -301,11 +301,11 @@ void contact_function( Cell* pMe, Phenotype& phenoMe , Cell* pOther, Phenotype&
 	return; 
 } 
 
-void pre_update_intracellular(Cell* pCell, Phenotype& phenotype, double dt){
+void pre_update_intracellular(Cell* pCell, Phenotype& phenotype, Intracellular* intracellular, double dt){
 	return;
 }
 
-void post_update_intracellular(Cell* pCell, Phenotype& phenotype, double dt){
+void post_update_intracellular(Cell* pCell, Phenotype& phenotype, Intracellular* intracellular, double dt){
 	return;
 }
 

sample_projects_intracellular/boolean/cancer_invasion/custom_modules/custom.h

@@ -97,8 +97,8 @@ inline double get_motility_amplitude( double percent )
 void contact_function( Cell* pMe, Phenotype& phenoMe , Cell* pOther, Phenotype& phenoOther , double dt ); 
 
 void add_ecm_interaction( Cell* pCell, int index_ecm, int index_voxel );
-void pre_update_intracellular(Cell* pCell, Phenotype& phenotype, double dt);
-void post_update_intracellular(Cell* pCell, Phenotype& phenotype, double dt);
+void pre_update_intracellular(Cell* pCell, Phenotype& phenotype, Intracellular* intracellular, double dt);
+void post_update_intracellular(Cell* pCell, Phenotype& phenotype, Intracellular* intracellular, double dt);
 
 std::string my_coloring_function_for_stroma( double concentration, double max_conc, double min_conc );
 void color_node(Cell* pCell);

sample_projects_intracellular/boolean/physiboss_cell_lines/custom_modules/custom.cpp

@@ -95,8 +95,6 @@ void create_cell_types( void )
 	cell_defaults.functions.update_velocity = NULL;
 	cell_defaults.functions.update_phenotype = NULL; 
 	cell_defaults.functions.update_migration_bias = NULL; 
-	cell_defaults.functions.pre_update_intracellular = pre_update_intracellular; 
-	cell_defaults.functions.post_update_intracellular = post_update_intracellular; 
 	cell_defaults.functions.custom_cell_rule = NULL; 
 
 	cell_defaults.functions.add_cell_basement_membrane_interactions = NULL; 
@@ -115,6 +113,8 @@ void create_cell_types( void )
 	   
 	   This is a good place to set custom functions. 
 	*/ 
+	PhysiCell::cell_definitions_by_name["last_one"]->phenotype.intracellulars[0]->pre_update_intracellular = pre_update_intracellular; 
+	PhysiCell::cell_definitions_by_name["last_one"]->phenotype.intracellulars[0]->post_update_intracellular = post_update_intracellular; 
 
 	/*
 	   This builds the map of cell definitions and summarizes the setup. 
@@ -158,26 +158,26 @@ void setup_tissue( void )
 	load_cells_from_pugixml(); 	
 }
 
-void pre_update_intracellular( Cell* pCell, Phenotype& phenotype, double dt )
+void pre_update_intracellular( Cell* pCell, Phenotype& phenotype, Intracellular* intracellular, double dt )
 {
 	if (PhysiCell::PhysiCell_globals.current_time >= 100.0 
-		&& pCell->phenotype.intracellular->get_parameter_value("$time_scale") == 0.0
+		&& intracellular->get_parameter_value("$time_scale") == 0.0
 	){
-		pCell->phenotype.intracellular->set_parameter_value("$time_scale", 0.1);
+		intracellular->set_parameter_value("$time_scale", 0.1);
 	}
 
 }
 
-void post_update_intracellular( Cell* pCell, Phenotype& phenotype, double dt )
+void post_update_intracellular( Cell* pCell, Phenotype& phenotype, Intracellular* intracellular, double dt )
 {
-	color_node(pCell);
+	color_node(pCell, intracellular);
 }
 
 std::vector<std::string> my_coloring_function( Cell* pCell )
 {
 	std::vector< std::string > output( 4 , "rgb(0,0,0)" );
 
-	if ( !pCell->phenotype.intracellular->get_boolean_variable_value( parameters.strings("node_to_visualize") ) )
+	if ( !pCell->phenotype.intracellulars[0]->get_boolean_variable_value( parameters.strings("node_to_visualize") ) )
 	{
 		output[0] = "rgb(255,0,0)";
 		output[2] = "rgb(125,0,0)";
@@ -191,7 +191,7 @@ std::vector<std::string> my_coloring_function( Cell* pCell )
 	return output;
 }
 
-void color_node(Cell* pCell){
+void color_node(Cell* pCell, Intracellular* intracellular){
 	std::string node_name = parameters.strings("node_to_visualize");
-	pCell->custom_data[node_name] = pCell->phenotype.intracellular->get_boolean_variable_value(node_name);
+	pCell->custom_data[node_name] = intracellular->get_boolean_variable_value(node_name);
 }

sample_projects_intracellular/boolean/physiboss_cell_lines/custom_modules/custom.h

@@ -84,8 +84,8 @@ void setup_microenvironment( void );
 std::vector<std::string> my_coloring_function( Cell* );
 
 // custom cell phenotype functions could go here 
-void pre_update_intracellular( Cell* pCell, Phenotype& phenotype, double dt );
-void post_update_intracellular( Cell* pCell, Phenotype& phenotype, double dt );
-void color_node(Cell* pCell);
+void pre_update_intracellular( Cell* pCell, Phenotype& phenotype, Intracellular* intracellular, double dt );
+void post_update_intracellular( Cell* pCell, Phenotype& phenotype, Intracellular* intracellular, double dt );
+void color_node(Cell* pCell, Intracellular* intracellular);
 
 #endif