Merge pull request #349 from elmbeech/patch1141_episode

episode sample project

.github/workflows/build_binaries.yml

@@ -20,6 +20,7 @@ jobs:
           {short_name: "rules", project: "rules-sample", name: "PhysiCell Rules", binary: "project", extra_run: ""},
           {short_name: "physimess", project: "physimess-sample", name: "PhysiMeSS", binary: "project", extra_run: ""},
           {short_name: "interaction", project: "interaction-sample", name: "PhysiCell Interaction", binary: "interaction_demo", extra_run: ""},
+          {short_name: "episode", project: "episode-sample", name: "PhysiCell Episode", binary: "project", extra_run: ""},
         ]
 
     runs-on: ubuntu-latest
@@ -32,7 +33,7 @@ jobs:
         make ${{ matrix.projects.project }}
         make clean
         ${{ matrix.projects.extra_run }}
-        make static STATIC_OPENMP=/usr/lib/gcc/x86_64-linux-gnu/11/libgomp.a
+        make static STATIC_OPENMP=/usr/lib/gcc/x86_64-linux-gnu/12/libgomp.a
       
     - name: Checking binary for ${{ matrix.projects.name }}
       run: |
@@ -66,6 +67,7 @@ jobs:
           {short_name: "rules", project: "rules-sample", name: "PhysiCell Rules", binary: "project", extra_run: ""},
           {short_name: "physimess", project: "physimess-sample", name: "PhysiMeSS", binary: "project", extra_run: ""},
           {short_name: "interaction", project: "interaction-sample", name: "PhysiCell Interaction", binary: "interaction_demo", extra_run: ""},
+          {short_name: "episode", project: "episode-sample", name: "PhysiCell Episode", binary: "project", extra_run: ""},
         ]
 
     runs-on: windows-latest
@@ -122,6 +124,7 @@ jobs:
           {short_name: "rules", project: "rules-sample", name: "PhysiCell Rules", binary: "project", extra_run: ""},
           {short_name: "physimess", project: "physimess-sample", name: "PhysiMeSS", binary: "project", extra_run: ""},
           {short_name: "interaction", project: "interaction-sample", name: "PhysiCell Interaction", binary: "interaction_demo", extra_run: ""},
+          {short_name: "episode", project: "episode-sample", name: "PhysiCell Episode", binary: "project", extra_run: ""},
        ]
 
     runs-on: macos-13
@@ -171,6 +174,7 @@ jobs:
           {short_name: "rules", project: "rules-sample", name: "PhysiCell Rules", binary: "project", extra_run: ""},
           {short_name: "physimess", project: "physimess-sample", name: "PhysiMeSS", binary: "project", extra_run: ""},
           {short_name: "interaction", project: "interaction-sample", name: "PhysiCell Interaction", binary: "interaction_demo", extra_run: ""},
+          {short_name: "episode", project: "episode-sample", name: "PhysiCell Episode", binary: "project", extra_run: ""},
         ]
 
     runs-on: macos-14
@@ -220,6 +224,7 @@ jobs:
           {short_name: "rules", project: "rules-sample", name: "PhysiCell Rules", binary: "project", extra_run: ""},
           {short_name: "physimess", project: "physimess-sample", name: "PhysiMeSS", binary: "project", extra_run: ""},
           {short_name: "interaction", project: "interaction-sample", name: "PhysiCell Interaction", binary: "interaction_demo", extra_run: ""},
+          {short_name: "episode", project: "episode-sample", name: "PhysiCell Episode", binary: "project", extra_run: ""},
         ]
 
     runs-on: macos-13
@@ -266,4 +271,4 @@ jobs:
         upload_url: ${{ github.event.release.upload_url }}
         asset_name: ${{ matrix.projects.short_name }}-macos.tar.gz
         asset_path: ${{ github.workspace }}/${{ matrix.projects.short_name }}-macos.tar.gz
-        asset_content_type: application/gzip
+        asset_content_type: application/gzip

.github/workflows/tests.yml

@@ -33,7 +33,8 @@ jobs:
           {project: "interaction-sample", name: "PhysiCell interactions", binary: "interaction_demo", config: "config/PhysiCell_settings.xml", max_time: 120, output_folder: ""},
           {project: "pred-prey-farmer", name: "PhysiCell prey predator", binary: "pred_prey", config: "config/PhysiCell_settings.xml", max_time: 120, output_folder: ""},
           {project: "rules-sample", name: "PhysiCell rules sample", binary: "rules_sample", config: "config/PhysiCell_settings.xml", max_time: 120, output_folder: ""},
-          {project: "asymmetric-division-sample", name: "PhysiCell asymmetric division", binary: "project", config: "config/PhysiCell_settings.xml", max_time: 120, output_folder: ""}
+          {project: "asymmetric-division-sample", name: "PhysiCell asymmetric division", binary: "project", config: "config/PhysiCell_settings.xml", max_time: 120, output_folder: ""},
+          {project: "episode-sample", name: "PhysiCell Episode", binary: "project", max_time: 120, config: "config/PhysiCell_settings.xml", output_folder: ""},
         ]
 
     name: Testing ${{ matrix.projects.name }} on ${{ matrix.os.name }}
@@ -64,4 +65,4 @@ jobs:
     - name: Check ${{ matrix.projects.name }} project simulation results
       if: matrix.projects.output_folder != ''
       run: |
-        python beta/test_diff_svg.py ${{ matrix.projects.output_folder }} tests/cases/output_${{ matrix.projects.project }}
+        python beta/test_diff_svg.py ${{ matrix.projects.output_folder }} tests/cases/output_${{ matrix.projects.project }}

BioFVM/BioFVM_microenvironment.cpp

@@ -253,7 +253,7 @@ bool Microenvironment::get_substrate_dirichlet_activation( int substrate_index )
 // TODO? fix confusing swapped usage of args
 double Microenvironment::get_substrate_dirichlet_value( int substrate_index, int index )
 { 
-    return dirichlet_value_vectors[index][substrate_index]; 
+	return dirichlet_value_vectors[index][substrate_index];
 }  
 
 // new functions for finer-grained control of Dirichlet conditions -- 1.7.0
@@ -487,7 +487,7 @@ void Microenvironment::add_density( std::string name , std::string units )
 
 void Microenvironment::add_density( std::string name , std::string units, double diffusion_constant, double decay_rate )
 {
-	// fix in PhysiCell preview November 2017 
+	// check if density exist
 	if ( find_density_index( name ) != -1 )
 	{
 		std::cout << "ERROR: density named " << name << " already exists. You probably want your substrates all have unique names!" << std::endl;
@@ -1198,7 +1198,11 @@ void initialize_microenvironment( void )
 	}
 
 	// set the initial condition
+	set_microenvironment_initial_condition();
+}
 
+void set_microenvironment_initial_condition( void )
+{
 	if (default_microenvironment_options.initial_condition_from_file_enabled)
 	{
 		if (default_microenvironment_options.initial_condition_file_type=="matlab")
@@ -1389,51 +1393,6 @@ void initialize_microenvironment( void )
 		}
 
 	}
-
-/*
-	if( default_microenvironment_options.outer_Dirichlet_conditions == true ) 
-	{
-		
-		for( unsigned int k=0 ; k < microenvironment.mesh.z_coordinates.size() ; k++ )
-		{
-			// set Dirichlet conditions along the 4 outer edges 
-			for( unsigned int i=0 ; i < microenvironment.mesh.x_coordinates.size() ; i++ )
-			{
-				int J = microenvironment.mesh.y_coordinates.size()-1;
-				microenvironment.add_dirichlet_node( microenvironment.voxel_index(i,0,k) , default_microenvironment_options.Dirichlet_condition_vector );
-				microenvironment.add_dirichlet_node( microenvironment.voxel_index(i,J,k) , default_microenvironment_options.Dirichlet_condition_vector );
-			}
-			int I = microenvironment.mesh.x_coordinates.size()-1;
-			for( unsigned int j=1; j < microenvironment.mesh.y_coordinates.size()-1 ; j++ )
-			{
-				microenvironment.add_dirichlet_node( microenvironment.voxel_index(0,j,k) , default_microenvironment_options.Dirichlet_condition_vector );
-				microenvironment.add_dirichlet_node( microenvironment.voxel_index(I,j,k) , default_microenvironment_options.Dirichlet_condition_vector );
-			}		
-		}
-		// if 3-D, also along the corresponding additional faces 
-		if( default_microenvironment_options.simulate_2D == false )
-		{
-			int K = microenvironment.mesh.z_coordinates.size()-1; 
-			for( unsigned int j=1 ; j < microenvironment.mesh.y_coordinates.size()-1 ; j++ )
-			{
-				for( unsigned int i=1; i < microenvironment.mesh.x_coordinates.size()-1 ; i++ )
-				{
-					microenvironment.add_dirichlet_node( microenvironment.voxel_index(i,j,0) , default_microenvironment_options.Dirichlet_condition_vector );
-					microenvironment.add_dirichlet_node( microenvironment.voxel_index(i,j,K) , default_microenvironment_options.Dirichlet_condition_vector );
-				}	
-			}	
-		}
-		
-	}
-*/
-
-    // April 2023: no longer necessary after flipping our approach and doing an "additive" instead of "subtractive" DCs handling. I.e., we assume DC activation is false by default; make true on-demand.
-
-	// // set the Dirichlet condition activation vector to match the microenvironment options
-	// for( int i=0 ; i < default_microenvironment_options.Dirichlet_activation_vector.size(); i++ )
-	// {
-	// 	microenvironment.set_substrate_dirichlet_activation( i , default_microenvironment_options.Dirichlet_activation_vector[i] );
-	// }
 
 	microenvironment.display_information(std::cout);
 	return;

BioFVM/BioFVM_microenvironment.h

@@ -362,7 +362,8 @@ class Microenvironment_Options
 extern Microenvironment_Options default_microenvironment_options; 
 extern Microenvironment microenvironment;
 
-void initialize_microenvironment( void ); 
+void initialize_microenvironment( void );
+void set_microenvironment_initial_condition( void );
 
 void load_initial_conditions_from_matlab( std::string filename );
 void load_initial_conditions_from_csv( std::string filename );

Makefile

@@ -74,7 +74,7 @@ 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 custom-division-sample"
-	@echo "					asymmetric-division-sample immune-function-sample"
+	@echo "                 asymmetric-division-sample immune-function-sample episode-sample"
 	@echo ""
 	@echo "Sample intracellular projects: template_BM ode-energy-sample physiboss-cell-lines-sample"
 	@echo "                 cancer-metabolism-sample physiboss-tutorial physiboss-tutorial-invasion"
@@ -225,6 +225,14 @@ immune-function-sample:
 	cp ./config/PhysiCell_settings.xml ./config/PhysiCell_settings-backup.xml 
 	cp -r ./sample_projects/immune_function/config/* ./config/
 
+episode-sample:
+	cp -r ./sample_projects/episode/custom_modules/* ./custom_modules/
+	touch main.cpp && cp main.cpp main-backup.cpp
+	cp ./sample_projects/episode/main.cpp ./main.cpp
+	cp Makefile Makefile-backup
+	cp ./sample_projects/episode/Makefile .
+	cp -r ./sample_projects/episode/config/* ./config
+
 # ---- intracellular projects 
 ode-energy-sample:
 	cp ./sample_projects_intracellular/ode/ode_energy/custom_modules/* ./custom_modules/

modules/PhysiCell_settings.cpp

@@ -79,10 +79,12 @@ bool physicell_config_dom_initialized = false;
 pugi::xml_document physicell_config_doc; 	
 pugi::xml_node physicell_config_root; 
 
-bool load_PhysiCell_config_file( std::string filename )
+bool read_PhysiCell_config_file( std::string filename )
 {
+	physicell_config_dom_initialized = false; 
+
 	std::cout << "Using config file " << filename << " ... " << std::endl ; 
-	pugi::xml_parse_result result = physicell_config_doc.load_file( filename.c_str()  );
+	pugi::xml_parse_result result = physicell_config_doc.load_file( filename.c_str() );
 
 	if( result.status != pugi::xml_parse_status::status_ok )
 	{
@@ -92,22 +94,28 @@ bool load_PhysiCell_config_file( std::string filename )
 
 	physicell_config_root = physicell_config_doc.child("PhysiCell_settings");
 	physicell_config_dom_initialized = true; 
-
+	return true;
+}
+
+bool load_PhysiCell_config_file( std::string filename )
+{
+	if (!read_PhysiCell_config_file( filename ))
+	{ return false; }
+
 	PhysiCell_settings.read_from_pugixml(); 
 
 	// now read the microenvironment (optional) 
 
 	if( !setup_microenvironment_from_XML( physicell_config_root ) )
 	{
-		std::cout << std::endl 
-				  << "Warning: microenvironment_setup not found in " << filename << std::endl 
-				  << "         Either manually setup microenvironment in setup_microenvironment() (custom.cpp)" << std::endl
-				  << "         or consult documentation to add microenvironment_setup to your configuration file." << std::endl << std::endl; 
+		std::cout << std::endl
+			<< "Warning: microenvironment_setup not found in " << filename << std::endl
+			<< "         Either manually setup microenvironment in setup_microenvironment() (custom.cpp)" << std::endl
+			<< "         or consult documentation to add microenvironment_setup to your configuration file." << std::endl << std::endl;
 	}
 
 	// now read user parameters
-
-	parameters.read_from_pugixml( physicell_config_root ); 
+	parameters.read_from_pugixml( physicell_config_root );
 
 	create_output_directory( PhysiCell_settings.folder );
 

modules/PhysiCell_settings.h

@@ -89,7 +89,8 @@ namespace PhysiCell{
 
 extern pugi::xml_node physicell_config_root; 
 
-bool load_PhysiCell_config_file( std::string filename );
+bool read_PhysiCell_config_file( std::string filename );
+bool load_PhysiCell_config_file( std::string filename  );
 
 class PhysiCell_Settings
 {

sample_projects/Makefile-default

@@ -74,7 +74,7 @@ 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 custom-division-sample"
-	@echo "					asymmetric-division-sample immune-function-sample"
+	@echo "                 asymmetric-division-sample immune-function-sample episode-sample"
 	@echo ""
 	@echo "Sample intracellular projects: template_BM ode-energy-sample physiboss-cell-lines-sample"
 	@echo "                 cancer-metabolism-sample physiboss-tutorial physiboss-tutorial-invasion"
@@ -225,6 +225,14 @@ immune-function-sample:
 	cp ./config/PhysiCell_settings.xml ./config/PhysiCell_settings-backup.xml 
 	cp -r ./sample_projects/immune_function/config/* ./config/
 
+episode-sample:
+	cp -r ./sample_projects/episode/custom_modules/* ./custom_modules/
+	touch main.cpp && cp main.cpp main-backup.cpp
+	cp ./sample_projects/episode/main.cpp ./main.cpp
+	cp Makefile Makefile-backup
+	cp ./sample_projects/episode/Makefile .
+	cp -r ./sample_projects/episode/config/* ./config
+
 # ---- intracellular projects 
 ode-energy-sample:
 	cp ./sample_projects_intracellular/ode/ode_energy/custom_modules/* ./custom_modules/