Merge pull request #148 from MathCancer/development

Release Version 1.11.0

Author: MathCancer

.github/workflows/test-windows.yml

@@ -19,8 +19,8 @@ jobs:
     - uses: msys2/setup-msys2@v2
       with:
         update: true
-        install: base-devel flex bison gcc make diffutils mingw-w64-x86_64-toolchain
-        
+        install: base-devel flex bison gcc make diffutils mingw-w64-x86_64-toolchain mingw-w64-x86_64-ca-certificates
+    
     - name: Build Virus Macrophage project
       run: |
         make virus-macrophage-sample

.gitignore

@@ -11,4 +11,14 @@ sample_projects/cancer_biorobots/.DS_Store
 sample_projects/cancer_immune/.DS_Store
 sample_projects/celltypes3/.DS_Store
 sample_projects/heterogeneity/.DS_Store
-sample_projects/template/.DS_Store
+sample_projects/template/.DS_Store
+pmb_debug.log
+heterogeneity
+**/.DS_Store
+**/._.DS_Store
+cancer_immune_3D
+biorobots
+project
+initial.svg
+initial.svg
+interaction_demo

BioFVM/BioFVM_MultiCellDS.cpp

@@ -1387,4 +1387,48 @@ void read_microenvironment_from_MultiCellDS_xml( Microenvironment& M_destination
 	return; 
 } 
 
+bool read_microenvironment_from_matlab( std::string mat_filename )
+{
+	std::cout << std::endl << "Attempting to load the microenvironment from " << mat_filename << " ... " << std::endl; 
+
+	std::vector< std::vector<double> > mat = read_matlab( mat_filename ); 
+
+	// row 0 : x
+	// row 1 : y
+	// row 2 : z 
+	// row 3 : vol 
+	// row 4-n : substrate 
+	int num_rows = mat.size(); 
+	int num_cols = mat[0].size(); 
+
+	int number_of_mat_voxels = num_cols; 
+	int number_of_mat_substrates = num_rows - 3 -1; 
+
+	if( number_of_mat_substrates != microenvironment.number_of_densities() )
+	{
+		std::cout << "Error reading microenvironment from " << mat_filename << "! ";  
+		std::cout << "Expected " << microenvironment.number_of_densities() << " substrates but only detected "
+			<< number_of_mat_substrates << std::endl; 
+		return false; 
+	}
+
+	if( number_of_mat_voxels != microenvironment.number_of_voxels() )
+	{
+		std::cout << "Error reading microenvironment from " << mat_filename << "! ";  
+		std::cout << "Expected " << microenvironment.number_of_voxels() << " voxels but only detected "
+			<< number_of_mat_voxels << std::endl; 
+		return false; 
+	}
+
+	for( int n=0 ; n < number_of_mat_voxels ; n++ )
+	{
+		// std::cout << microenvironment.mesh.voxels[n].center << " vs " << mat[0][n] << " " << mat[1][n] << " " << mat[2][n] << std::endl; 	
+		for( int k=4; k < num_rows ; k++ )
+		{ microenvironment(n)[k-4] = mat[k][n]; }
+	}
+
+	std::cout << "done!" << std::endl << std::endl; 
+	return true; 
+}
+
 };

BioFVM/BioFVM_MultiCellDS.h

@@ -188,6 +188,10 @@ void add_BioFVM_to_open_xml_pugi( pugi::xml_document& xml_dom , std::string file
 
 void save_BioFVM_to_MultiCellDS_xml_pugi( std::string filename_base , Microenvironment& M , double current_simulation_time); 
 
+/* beta in PhysiCell 1.11.0 */
+
+bool read_microenvironment_from_matlab( std::string mat_filename ); 
+
 /* future / not yet supported */
 
 void read_BioFVM_from_open_xml_pugi( pugi::xml_document& xml_dom , std::string filename_base, double& current_simulation_time , Microenvironment& M );

CITATION.txt

@@ -1,7 +1,7 @@
 If you use PhysiCell in your project, please cite PhysiCell and the version 
 number, such as below:                                                      
 
-We implemented and solved the model using PhysiCell (Version 1.10.4) [1].    
+We implemented and solved the model using PhysiCell (Version 1.11.0) [1].    
 
 [1] A Ghaffarizadeh, R Heiland, SH Friedman, SM Mumenthaler, and P Macklin, 
     PhysiCell: an Open Source Physics-Based Cell Simulator for Multicellu-  
@@ -11,7 +11,7 @@ We implemented and solved the model using PhysiCell (Version 1.10.4) [1].
 Because PhysiCell extensively uses BioFVM, we suggest you also cite BioFVM  
     as below:                                                               
 
-We implemented and solved the model using PhysiCell (Version 1.10.4) [1],    
+We implemented and solved the model using PhysiCell (Version 1.11.0) [1],    
 with BioFVM [2] to solve the transport equations.                           
 
 [1] A Ghaffarizadeh, R Heiland, SH Friedman, SM Mumenthaler, and P Macklin, 

Makefile

@@ -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"
+	@echo "                 worm-sample interaction-sample mechano-sample"
 	@echo ""
 	@echo "Sample intracellular projects: ode-energy-sample physiboss-cell-lines-sample cancer-metabolism-sample"
 	@echo ""
@@ -93,7 +93,7 @@ template:
 biorobots-sample:
 	cp ./sample_projects/biorobots/custom_modules/* ./custom_modules/
 	touch main.cpp && cp main.cpp main-backup.cpp
-	cp ./sample_projects/biorobots/main-biorobots.cpp ./main.cpp 
+	cp ./sample_projects/biorobots/main.cpp ./main.cpp 
 	cp Makefile Makefile-backup
 	cp ./sample_projects/biorobots/Makefile .
 	cp ./config/PhysiCell_settings.xml ./config/PhysiCell_settings-backup.xml 
@@ -102,7 +102,7 @@ biorobots-sample:
 cancer-biorobots-sample:
 	cp ./sample_projects/cancer_biorobots/custom_modules/* ./custom_modules/
 	touch main.cpp && cp main.cpp main-backup.cpp
-	cp ./sample_projects/cancer_biorobots/main-cancer_biorobots.cpp ./main.cpp 
+	cp ./sample_projects/cancer_biorobots/main.cpp ./main.cpp 
 	cp Makefile Makefile-backup
 	cp ./sample_projects/cancer_biorobots/Makefile .
 	cp ./config/PhysiCell_settings.xml ./config/PhysiCell_settings-backup.xml 
@@ -129,7 +129,7 @@ celltypes3-sample:
 heterogeneity-sample:
 	cp ./sample_projects/heterogeneity/custom_modules/* ./custom_modules/
 	touch main.cpp && cp main.cpp main-backup.cpp
-	cp ./sample_projects/heterogeneity/main-heterogeneity.cpp ./main.cpp 
+	cp ./sample_projects/heterogeneity/main.cpp ./main.cpp 
 	cp Makefile Makefile-backup
 	cp ./sample_projects/heterogeneity/Makefile .
 	cp ./config/PhysiCell_settings.xml ./config/PhysiCell_settings-backup.xml 
@@ -208,6 +208,13 @@ cancer-metabolism-sample:
 	cp ./config/PhysiCell_settings.xml ./config/PhysiCell_settings-backup.xml
 	cp ./sample_projects_intracellular/fba/cancer_metabolism/config/* ./config/
 
+mechano-sample:
+	cp ./sample_projects/mechano/custom_modules/* ./custom_modules/
+	touch main.cpp && cp main.cpp main-backup.cpp
+	cp ./sample_projects/mechano/main.cpp ./main.cpp 
+	cp Makefile Makefile-backup
+	cp ./sample_projects/mechano/Makefile .
+	cp ./sample_projects/mechano/config/* ./config/
 
 # early examples for convergence testing 
 
@@ -422,3 +429,25 @@ upgrade: $(SOURCE)
 	mv -f PhysiCell/documentation/User_Guide.pdf documentation
 	rm -f -r PhysiCell
 	rm -f $(SOURCE) 
+
+# use: make save PROJ=your_project_name
+PROJ := my_project
+
+save: 
+	echo "Saving project as $(PROJ) ... "
+	mkdir -p ./user_projects
+	mkdir -p ./user_projects/$(PROJ)
+	mkdir -p ./user_projects/$(PROJ)/custom_modules
+	mkdir -p ./user_projects/$(PROJ)/config 
+	cp main.cpp ./user_projects/$(PROJ)
+	cp Makefile ./user_projects/$(PROJ)
+	cp VERSION.txt ./user_projects/$(PROJ)
+	cp ./config/* ./user_projects/$(PROJ)/config
+	cp ./custom_modules/* ./user_projects/$(PROJ)/custom_modules
+
+load: 
+	echo "Loading project from $(PROJ) ... "
+	cp ./user_projects/$(PROJ)/main.cpp .
+	cp ./user_projects/$(PROJ)/Makefile .
+	cp ./user_projects/$(PROJ)/config/* ./config/ 
+	cp ./user_projects/$(PROJ)/custom_modules/* ./custom_modules/