updated XML input and output. way better.

MathCancer · Jul 16, 2024 · 9a7d006 · 9a7d006
1 parent d5809c3
commit 9a7d006
Show file tree

Hide file tree

Showing 7 changed files with 2,040 additions and 140 deletions.
diff --git a/config/PhysiCell_settings.xml b/config/PhysiCell_settings.xml
@@ -214,6 +214,7 @@
                     <attachment_elastic_constant units="1/min">0.01</attachment_elastic_constant>
                     <attachment_rate units="1/min">0.0</attachment_rate>
                     <detachment_rate units="1/min">0.0</detachment_rate>
+                    <maximum_number_of_attachments units="none">6</maximum_number_of_attachments>
                 </mechanics>
                 <motility>
                     <speed units="micron/min">0.1</speed>
@@ -274,6 +275,9 @@
                 </secretion>
                 <cell_interactions>
                     <dead_phagocytosis_rate units="1/min">0</dead_phagocytosis_rate>
+                    <apoptotic_phagocytosis_rate units="1/min">0</apoptotic_phagocytosis_rate>
+                    <necrotic_phagocytosis_rate units="1/min">0</necrotic_phagocytosis_rate>
+
                     <live_phagocytosis_rates>
                         <phagocytosis_rate name="malignant epithelial cell" units="1/min">0</phagocytosis_rate>
                         <phagocytosis_rate name="M0 macrophage" units="1/min">0.0</phagocytosis_rate>
@@ -291,6 +295,8 @@
                         <attack_rate name="exhausted T cell" units="1/min">0.0</attack_rate>
                     </attack_rates>
                     <attack_damage_rate units="1/min">1</attack_damage_rate>
+                    <attack_duration units="min">0.1</attack_duration>
+
                     <fusion_rates>
                         <fusion_rate name="malignant epithelial cell" units="1/min">0</fusion_rate>
                         <fusion_rate name="M0 macrophage" units="1/min">0.0</fusion_rate>
@@ -310,6 +316,10 @@
                         <transformation_rate name="exhausted T cell" units="1/min">0.0</transformation_rate>
                     </transformation_rates>
                 </cell_transformations>
+                <cell_integrity>
+                    <damage_rate units="1/min">0.0</damage_rate>
+                    <damage_repair_rate units="1/min">0.0</damage_repair_rate>
+                </cell_integrity>
             </phenotype>
             <custom_data>
                 <sample conserved="false" units="dimensionless" description="">1.0</sample>
@@ -385,6 +395,7 @@
                     <attachment_elastic_constant units="1/min">0.01</attachment_elastic_constant>
                     <attachment_rate units="1/min">0.0</attachment_rate>
                     <detachment_rate units="1/min">0.0</detachment_rate>
+                    <maximum_number_of_attachments units="none">6</maximum_number_of_attachments>
                 </mechanics>
                 <motility>
                     <speed units="micron/min">1.0</speed>
@@ -445,6 +456,8 @@
                 </secretion>
                 <cell_interactions>
                     <dead_phagocytosis_rate units="1/min">0.01</dead_phagocytosis_rate>
+                    <apoptotic_phagocytosis_rate units="1/min">0</apoptotic_phagocytosis_rate>
+                    <necrotic_phagocytosis_rate units="1/min">0</necrotic_phagocytosis_rate>
                     <live_phagocytosis_rates>
                         <phagocytosis_rate name="malignant epithelial cell" units="1/min">0.0</phagocytosis_rate>
                         <phagocytosis_rate name="M0 macrophage" units="1/min">0.0</phagocytosis_rate>
@@ -462,6 +475,7 @@
                         <attack_rate name="exhausted T cell" units="1/min">0.0</attack_rate>
                     </attack_rates>
                     <attack_damage_rate units="1/min">1.0</attack_damage_rate>
+                    <attack_duration units="min">0.1</attack_duration>
                     <fusion_rates>
                         <fusion_rate name="malignant epithelial cell" units="1/min">0.0</fusion_rate>
                         <fusion_rate name="M0 macrophage" units="1/min">0.0</fusion_rate>
@@ -481,6 +495,10 @@
                         <transformation_rate name="exhausted T cell" units="1/min">0.0</transformation_rate>
                     </transformation_rates>
                 </cell_transformations>
+                <cell_integrity>
+                    <damage_rate units="1/min">0.0</damage_rate>
+                    <damage_repair_rate units="1/min">0.0</damage_repair_rate>
+                </cell_integrity>                
             </phenotype>
             <custom_data>
                 <sample conserved="false" units="dimensionless" description="">0.0</sample>
@@ -556,6 +574,7 @@
                     <attachment_elastic_constant units="1/min">0.01</attachment_elastic_constant>
                     <attachment_rate units="1/min">0.0</attachment_rate>
                     <detachment_rate units="1/min">0.0</detachment_rate>
+                    <maximum_number_of_attachments units="none">6</maximum_number_of_attachments>
                 </mechanics>
                 <motility>
                     <speed units="micron/min">1.0</speed>
@@ -616,6 +635,8 @@
                 </secretion>
                 <cell_interactions>
                     <dead_phagocytosis_rate units="1/min">0.01</dead_phagocytosis_rate>
+                    <apoptotic_phagocytosis_rate units="1/min">0</apoptotic_phagocytosis_rate>
+                    <necrotic_phagocytosis_rate units="1/min">0</necrotic_phagocytosis_rate>
                     <live_phagocytosis_rates>
                         <phagocytosis_rate name="malignant epithelial cell" units="1/min">0.0</phagocytosis_rate>
                         <phagocytosis_rate name="M0 macrophage" units="1/min">0.0</phagocytosis_rate>
@@ -633,6 +654,8 @@
                         <attack_rate name="exhausted T cell" units="1/min">0.0</attack_rate>
                     </attack_rates>
                     <attack_damage_rate units="1/min">1.0</attack_damage_rate>
+                    <attack_duration units="min">0.1</attack_duration>
+
                     <fusion_rates>
                         <fusion_rate name="malignant epithelial cell" units="1/min">0.0</fusion_rate>
                         <fusion_rate name="M0 macrophage" units="1/min">0.0</fusion_rate>
@@ -652,6 +675,10 @@
                         <transformation_rate name="exhausted T cell" units="1/min">0.0</transformation_rate>
                     </transformation_rates>
                 </cell_transformations>
+                <cell_integrity>
+                    <damage_rate units="1/min">0.0</damage_rate>
+                    <damage_repair_rate units="1/min">0.0</damage_repair_rate>
+                </cell_integrity>                
             </phenotype>
             <custom_data>
                 <sample conserved="false" units="dimensionless" description="">0.0</sample>
@@ -727,6 +754,7 @@
                     <attachment_elastic_constant units="1/min">0.01</attachment_elastic_constant>
                     <attachment_rate units="1/min">0.0</attachment_rate>
                     <detachment_rate units="1/min">0.0</detachment_rate>
+                    <maximum_number_of_attachments units="none">6</maximum_number_of_attachments>
                 </mechanics>
                 <motility>
                     <speed units="micron/min">1.0</speed>
@@ -787,6 +815,8 @@
                 </secretion>
                 <cell_interactions>
                     <dead_phagocytosis_rate units="1/min">0.01</dead_phagocytosis_rate>
+                    <apoptotic_phagocytosis_rate units="1/min">0</apoptotic_phagocytosis_rate>
+                    <necrotic_phagocytosis_rate units="1/min">0</necrotic_phagocytosis_rate>
                     <live_phagocytosis_rates>
                         <phagocytosis_rate name="malignant epithelial cell" units="1/min">0.0</phagocytosis_rate>
                         <phagocytosis_rate name="M0 macrophage" units="1/min">0.0</phagocytosis_rate>
@@ -804,6 +834,8 @@
                         <attack_rate name="exhausted T cell" units="1/min">0.0</attack_rate>
                     </attack_rates>
                     <attack_damage_rate units="1/min">1.0</attack_damage_rate>
+                    <attack_duration units="min">0.1</attack_duration>
+
                     <fusion_rates>
                         <fusion_rate name="malignant epithelial cell" units="1/min">0.0</fusion_rate>
                         <fusion_rate name="M0 macrophage" units="1/min">0.0</fusion_rate>
@@ -823,6 +855,10 @@
                         <transformation_rate name="exhausted T cell" units="1/min">0.0</transformation_rate>
                     </transformation_rates>
                 </cell_transformations>
+                <cell_integrity>
+                    <damage_rate units="1/min">0.0</damage_rate>
+                    <damage_repair_rate units="1/min">0.0</damage_repair_rate>
+                </cell_integrity>                
             </phenotype>
             <custom_data>
                 <sample conserved="false" units="dimensionless" description="">0.0</sample>
@@ -898,6 +934,7 @@
                     <attachment_elastic_constant units="1/min">0.01</attachment_elastic_constant>
                     <attachment_rate units="1/min">0.0</attachment_rate>
                     <detachment_rate units="1/min">0.0</detachment_rate>
+                    <maximum_number_of_attachments units="none">6</maximum_number_of_attachments>
                 </mechanics>
                 <motility>
                     <speed units="micron/min">0.1</speed>
@@ -958,6 +995,8 @@
                 </secretion>
                 <cell_interactions>
                     <dead_phagocytosis_rate units="1/min">0</dead_phagocytosis_rate>
+                    <apoptotic_phagocytosis_rate units="1/min">0</apoptotic_phagocytosis_rate>
+                    <necrotic_phagocytosis_rate units="1/min">0</necrotic_phagocytosis_rate>
                     <live_phagocytosis_rates>
                         <phagocytosis_rate name="malignant epithelial cell" units="1/min">0.0</phagocytosis_rate>
                         <phagocytosis_rate name="M0 macrophage" units="1/min">0.0</phagocytosis_rate>
@@ -975,6 +1014,8 @@
                         <attack_rate name="exhausted T cell" units="1/min">0.0</attack_rate>
                     </attack_rates>
                     <attack_damage_rate units="1/min">1.0</attack_damage_rate>
+                    <attack_duration units="min">0.1</attack_duration>
+
                     <fusion_rates>
                         <fusion_rate name="malignant epithelial cell" units="1/min">0.0</fusion_rate>
                         <fusion_rate name="M0 macrophage" units="1/min">0.0</fusion_rate>
@@ -994,6 +1035,10 @@
                         <transformation_rate name="exhausted T cell" units="1/min">0.0</transformation_rate>
                     </transformation_rates>
                 </cell_transformations>
+                <cell_integrity>
+                    <damage_rate units="1/min">0.0</damage_rate>
+                    <damage_repair_rate units="1/min">0.0</damage_repair_rate>
+                </cell_integrity>                
             </phenotype>
             <custom_data>
                 <sample conserved="false" units="dimensionless" description="">0.0</sample>
@@ -1069,6 +1114,7 @@
                     <attachment_elastic_constant units="1/min">0.01</attachment_elastic_constant>
                     <attachment_rate units="1/min">0.0</attachment_rate>
                     <detachment_rate units="1/min">0.0</detachment_rate>
+                    <maximum_number_of_attachments units="none">6</maximum_number_of_attachments>
                 </mechanics>
                 <motility>
                     <speed units="micron/min">0.01</speed>
@@ -1129,6 +1175,8 @@
                 </secretion>
                 <cell_interactions>
                     <dead_phagocytosis_rate units="1/min">0</dead_phagocytosis_rate>
+                    <apoptotic_phagocytosis_rate units="1/min">0</apoptotic_phagocytosis_rate>
+                    <necrotic_phagocytosis_rate units="1/min">0</necrotic_phagocytosis_rate>                    
                     <live_phagocytosis_rates>
                         <phagocytosis_rate name="malignant epithelial cell" units="1/min">0.0</phagocytosis_rate>
                         <phagocytosis_rate name="M0 macrophage" units="1/min">0.0</phagocytosis_rate>
@@ -1146,6 +1194,8 @@
                         <attack_rate name="exhausted T cell" units="1/min">0.0</attack_rate>
                     </attack_rates>
                     <attack_damage_rate units="1/min">1.0</attack_damage_rate>
+                    <attack_duration units="min">0.1</attack_duration>
+
                     <fusion_rates>
                         <fusion_rate name="malignant epithelial cell" units="1/min">0.0</fusion_rate>
                         <fusion_rate name="M0 macrophage" units="1/min">0.0</fusion_rate>
@@ -1165,6 +1215,10 @@
                         <transformation_rate name="exhausted T cell" units="1/min">0.0</transformation_rate>
                     </transformation_rates>
                 </cell_transformations>
+                <cell_integrity>
+                    <damage_rate units="1/min">0.0</damage_rate>
+                    <damage_repair_rate units="1/min">0.0</damage_repair_rate>
+                </cell_integrity>
             </phenotype>
             <custom_data>
                 <sample conserved="false" units="dimensionless" description="">0.0</sample>

diff --git a/core/PhysiCell_cell.cpp b/core/PhysiCell_cell.cpp
@@ -247,7 +247,7 @@ Cell_State::Cell_State()
 	number_of_nuclei = 1; 
 
 	// damage = 0.0; 
-	total_attack_time = 0.0; 
+	// total_attack_time = 0.0; 
 
 	contact_with_basement_membrane = false; 
 
@@ -357,7 +357,7 @@ void Cell::advance_bundled_phenotype_functions( double dt_ )
 	phenotype.geometry.update( this, phenotype, dt_ );
 
 	// update integrity 
-	phenotype.integrity.advance_damage( dt_ );  
+	phenotype.cell_integrity.advance_damage( dt_ );  
 
 	// check for new death events 
 	if( phenotype.death.check_for_death( dt_ ) == true )
@@ -648,8 +648,10 @@ Cell* Cell::divide( )
 
 	// changes for new phenotyp March 2022
 	// state.damage = 0.0; 
+	// phenotype.integrity.damage = 0.0; // leave alone - damage is heritable
 	state.total_attack_time = 0; 
 	// child->state.damage = 0.0; 
+	// child->phenotype.integrity.damage = 0.0; // leave alone - damage is heritable 
 	child->state.total_attack_time = 0.0; 
 
 	return child;
@@ -1408,7 +1410,7 @@ void Cell::attack_cell( Cell* pCell_to_attack , double dt )
 	{ 
 		// std::cout << this->type_name << " attacks " << pCell_to_attack->type_name << std::endl;
 		// 
-		pCell_to_attack->phenotype.integrity.damage += phenotype.cell_interactions.attack_damage_rate * dt; 
+		pCell_to_attack->phenotype.cell_integrity.damage += phenotype.cell_interactions.attack_damage_rate * dt; 
 		pCell_to_attack->state.total_attack_time += dt; 
 	}
 	return; 
@@ -2589,7 +2591,6 @@ Cell_Definition* initialize_cell_definition_from_pugixml( pugi::xml_node cd_node
 		node_mech = node.child( "maximum_number_of_attachments" );
 		if ( node_mech )
 		{ pM->maximum_number_of_attachments = xml_get_my_int_value( node_mech ); }
-
 	}
 
 	// motility 
@@ -2836,6 +2837,19 @@ Cell_Definition* initialize_cell_definition_from_pugixml( pugi::xml_node cd_node
 		pugi::xml_node node_dpr = node.child("dead_phagocytosis_rate");
 		pCI->dead_phagocytosis_rate = xml_get_my_double_value(node_dpr); 
 
+		pCI->apoptotic_phagocytosis_rate = pCI->dead_phagocytosis_rate; 
+		pCI->necrotic_phagocytosis_rate = pCI->dead_phagocytosis_rate; 
+
+		// if specific apoptotic rate is specified, overwrite 
+		pugi::xml_node node_apr = node.child("apoptotic_phagocytosis_rate"); 
+		if( node_apr )
+		{ pCI->apoptotic_phagocytosis_rate = xml_get_my_double_value(node_apr);  }
+
+		// if specific necrotic rate is specified, overwrite 
+		pugi::xml_node node_npr = node.child("necrotic_phagocytosis_rate"); 
+		if( node_npr )
+		{ pCI->necrotic_phagocytosis_rate = xml_get_my_double_value(node_npr);  }
+
 		// live phagocytosis rates 
 		pugi::xml_node node_lpcr = node.child( "live_phagocytosis_rates");
 		if( node_lpcr )
@@ -2967,7 +2981,23 @@ Cell_Definition* initialize_cell_definition_from_pugixml( pugi::xml_node cd_node
 			node_tr = node_tr.next_sibling( "transformation_rate" ); 
 		}
 
-	}	
+	}
+
+	// cell integrity 
+	node = cd_node.child( "phenotype" );
+	node = node.child( "cell_integrity" ); 
+	if( node )
+	{
+		Cell_Integrity *pCI = &(pCD->phenotype.cell_integrity);
+
+		pugi::xml_node node_dr = node.child("damage_rate");
+		if( node_dr )
+		{ pCI->damage_rate = xml_get_my_double_value( node_dr ); }
+
+		pugi::xml_node node_drr = node.child("damage_repair_rate");
+		if( node_drr )
+		{ pCI->damage_repair_rate = xml_get_my_double_value( node_drr ); }
+	}
 
     	// intracellular
 	node = cd_node.child( "phenotype" );

diff --git a/core/PhysiCell_cell.h b/core/PhysiCell_cell.h
@@ -155,7 +155,7 @@ class Cell_State
 	int number_of_nuclei; 
 
 	// double damage; 
-	double total_attack_time; 
+	double total_attack_time; // now in interactions
 	bool contact_with_basement_membrane; // not implemented yet 
 
 	Cell_State(); 

diff --git a/core/PhysiCell_phenotype.cpp b/core/PhysiCell_phenotype.cpp
@@ -1211,7 +1211,7 @@ Phenotype& Phenotype::operator=(const Phenotype &p ) {
 
 	molecular = p.molecular;
 
-	integrity = p.integrity; 
+	cell_integrity = p.cell_integrity; 
 
 	delete intracellular;
 
@@ -1357,7 +1357,7 @@ double& Cell_Transformations::transformation_rate( std::string type_name )
 }
 
 // beta functionality in 1.10.3 
-Integrity::Integrity()
+Cell_Integrity::Cell_Integrity()
 {
  	damage = 0;  
 	damage_rate = 0.0; 
@@ -1377,7 +1377,7 @@ Integrity::Integrity()
 	return; 
 }
 
-void Integrity::advance_damage( double dt )
+void Cell_Integrity::advance_damage( double dt )
 {
 	double temp1;
 	double temp2; 

diff --git a/core/PhysiCell_phenotype.h b/core/PhysiCell_phenotype.h
@@ -713,7 +713,7 @@ class Cell_Transformations
 };
 
 // pre-beta functionality in 1.10.3 
-class Integrity
+class Cell_Integrity
 {
  private:
  public: 
@@ -738,7 +738,7 @@ class Integrity
 	// mitochondrial? spindle? other? 
 */	
 
-	Integrity(); 
+	Cell_Integrity(); 
 
 	void advance_damage( double dt ); 
 };
@@ -760,7 +760,7 @@ class Phenotype
 
 	Molecular molecular; 
 
-	Integrity integrity; 
+	Cell_Integrity cell_integrity; 
 
     // We need it to be a pointer to allow polymorphism
 	// then this object could be a MaBoSSIntracellular, or a RoadRunnerIntracellular