Custom division

core/PhysiCell_cell.cpp

@@ -418,6 +418,8 @@ Cell::Cell()
 
 	is_movable = true;
 	is_out_of_domain = false;
+    generation = 0;
+    parentID = -1;   // overridden in create_cell() and divide()
 	displacement.resize(3,0.0); // state? 
 
 	assign_orientation();
@@ -563,6 +565,13 @@ Cell* Cell::divide( )
 
 	Cell* child = create_cell(functions.instantiate_cell);
 	child->copy_data( this );	
+    // lineage tracking
+    generation = generation + 1;     // this (parent) cell has its generation incremented
+    child->generation = generation;  // daughter cell has the same generation
+    // child->generation = generation + 1;
+    // child->parentID = parentID;
+    parentID = ID;
+    child->parentID = ID;
 	child->copy_function_pointers(this);
 	child->parameters = parameters;
 
@@ -649,6 +658,9 @@ Cell* Cell::divide( )
 	child->state.damage = 0.0; 
 	child->state.total_attack_time = 0.0; 
 
+    if( this->functions.cell_division_function )
+        { this->functions.cell_division_function( this, child); }
+
 	return child;
 }
 
@@ -1066,6 +1078,7 @@ Cell* create_cell( Cell* (*custom_instantiate)())
 	} else {
 		pNew = standard_instantiate_cell();
 	}
+    pNew->parentID = pNew->ID;
 
 	(*all_cells).push_back( pNew ); 
 	pNew->index=(*all_cells).size()-1;
@@ -1306,6 +1319,7 @@ void Cell::ingest_cell( Cell* pCell_to_eat )
 		pCell_to_eat->functions.custom_cell_rule = NULL; 
 		pCell_to_eat->functions.update_phenotype = NULL; 
 		pCell_to_eat->functions.contact_function = NULL; 
+		pCell_to_eat->functions.cell_division_function = NULL; 
 
 		// should set volume fuction to NULL too! 
 		pCell_to_eat->functions.volume_update_function = NULL; 
@@ -1531,6 +1545,7 @@ void Cell::fuse_cell( Cell* pCell_to_fuse )
 		pCell_to_fuse->functions.custom_cell_rule = NULL; 
 		pCell_to_fuse->functions.update_phenotype = NULL; 
 		pCell_to_fuse->functions.contact_function = NULL; 
+		pCell_to_fuse->functions.cell_division_function = NULL; 
 		pCell_to_fuse->functions.volume_update_function = NULL; 
 
 		// remove all adhesions 
@@ -1570,6 +1585,7 @@ void Cell::lyse_cell( void )
 	functions.custom_cell_rule = NULL; 
 	functions.update_phenotype = NULL; 
 	functions.contact_function = NULL; 
+	functions.cell_division_function = NULL; 
 
 	// remove all adhesions 
 
@@ -1660,6 +1676,14 @@ void display_ptr_as_bool( void (*ptr)(Cell*,Phenotype&,Cell*,Phenotype&,double),
 	return;
 }
 
+void display_ptr_as_bool( void (*ptr)(Cell*,Cell*), std::ostream& os )
+{
+	if( ptr )
+	{ os << "true"; return; }
+	os << "false"; 
+	return;
+}
+
 void display_cell_definitions( std::ostream& os )
 {
 	for( int n=0; n < cell_definitions_by_index.size() ; n++ )
@@ -1743,6 +1767,8 @@ void display_cell_definitions( std::ostream& os )
 		os << std::endl;
 		os << "\t\t contact function: "; display_ptr_as_bool( pCF->contact_function , std::cout ); 
 		os << std::endl; 
+		os << "\t\t cell division function: "; display_ptr_as_bool( pCF->cell_division_function , std::cout ); 
+		os << std::endl; 
 
 		// summarize motility 
 

core/PhysiCell_cell.h

@@ -188,6 +188,9 @@ class Cell : public Basic_Agent
 
 	bool is_out_of_domain;
 	bool is_movable;
+
+    int generation;   // for lineage tracking
+    int parentID;   // for lineage tracking
 
 	void flag_for_division( void ); // done 
 	void flag_for_removal( void ); // done 

core/PhysiCell_phenotype.h

@@ -496,6 +496,8 @@ class Cell_Functions
 
 	void (*contact_function)(Cell* pMyself, Phenotype& my_phenotype, 
 		Cell* pOther, Phenotype& other_phenotype, double dt ); 
+
+    void (*cell_division_function)(Cell* pCell1, Cell* pCell2 );
 
 	/* prototyping / beta in 1.5.0 */ 
 /*	

modules/PhysiCell_MultiCellDS.cpp

@@ -890,6 +890,29 @@ void add_PhysiCell_cells_to_open_xml_pugi_v2( pugi::xml_document& xml_dom, std::
 		data_start_indices.push_back( index ); 
 		cell_data_size += size; 
 		index += size; 
+
+        // generation
+		name = "generation"; 
+		size = 1; 
+		units="none";
+		data_names.push_back( name ); 
+		data_units.push_back(units); 
+		data_sizes.push_back( size ); 
+		data_start_indices.push_back( index ); 
+		cell_data_size += size; 
+		index += size; 
+
+        // parentID
+		name = "parentID"; 
+		size = 1; 
+		units="none";
+		data_names.push_back( name ); 
+		data_units.push_back(units); 
+		data_sizes.push_back( size ); 
+		data_start_indices.push_back( index ); 
+		cell_data_size += size; 
+		index += size; 
+
 		//					<label index="1" size="3">position</label>
 		name = "position"; 
 		size = 3; 
@@ -1754,6 +1777,12 @@ void add_PhysiCell_cells_to_open_xml_pugi_v2( pugi::xml_document& xml_dom, std::
 		// name = "ID"; 
 		dTemp = (double) pCell->ID;
 		std::fwrite( &( dTemp ) , sizeof(double) , 1 , fp ); 
+        // name = "generation"; 
+		dTemp = (double) pCell->generation;
+		std::fwrite( &( dTemp ) , sizeof(double) , 1 , fp ); 
+        // name = "parentID"; 
+		dTemp = (double) pCell->parentID;
+		std::fwrite( &( dTemp ) , sizeof(double) , 1 , fp ); 
 		// name = "position";    NOTE very different syntax for writing vectors!
         std::fwrite( pCell->position.data() , sizeof(double) , 3 , fp );
 		// name = "total_volume"; 

sample_projects/Makefile-default

@@ -73,7 +73,7 @@ name:
 list-projects:
 	@echo "Sample projects: template biorobots-sample cancer-biorobots-sample cancer-immune-sample"
 	@echo "                 celltypes3-sample heterogeneity-sample pred-prey-farmer virus-macrophage-sample"
-	@echo "                 worm-sample interaction-sample mechano-sample rules-sample physimess-sample"
+	@echo "                 worm-sample interaction-sample mechano-sample rules-sample physimess-sample custom-division-sample"
 	@echo ""
 	@echo "Sample intracellular projects: template_BM ode-energy-sample physiboss-cell-lines-sample"
 	@echo "                 cancer-metabolism-sample physiboss-tutorial physiboss-tutorial-invasion"
@@ -198,6 +198,15 @@ physimess-sample:
 	cp ./config/PhysiCell_settings.xml ./config/PhysiCell_settings-backup.xml 
 	cp -r ./sample_projects/physimess/config/* ./config/
 
+custom-division-sample:
+	cp ./sample_projects/custom_division/custom_modules/* ./custom_modules/
+	touch main.cpp && cp main.cpp main-backup.cpp
+	cp ./sample_projects/custom_division/main.cpp ./main.cpp 
+	cp Makefile Makefile-backup
+	cp ./sample_projects/custom_division/Makefile .
+	cp ./config/PhysiCell_settings.xml ./config/PhysiCell_settings-backup.xml 
+	cp -r ./sample_projects/custom_division/config/* ./config/
+
 # ---- intracellular projects 
 ode-energy-sample:
 	cp ./sample_projects_intracellular/ode/ode_energy/custom_modules/* ./custom_modules/