Merge pull request MathCancer#122 from rheiland/development

fix fwrite of orientation vec

core/PhysiCell_cell_container.cpp

@@ -337,6 +337,10 @@ void Cell_Container::add_agent_to_outer_voxel(Cell* agent)
 
 void Cell_Container::remove_agent_from_voxel(Cell* agent, int voxel_index)
 {
+	if (voxel_index < 0)
+	{
+		return; 
+	}
 	int delete_index = 0; 
 	while( agent_grid[voxel_index][ delete_index ] != agent )
 	{

modules/PhysiCell_MultiCellDS.cpp

@@ -1776,7 +1776,7 @@ void add_PhysiCell_cells_to_open_xml_pugi_v2( pugi::xml_document& xml_dom, std::
 		// name = "calcified_fraction"; 
 		std::fwrite( &( pCell->phenotype.volume.calcified_fraction ) , sizeof(double) , 1 , fp ); 
 		// name = "orientation"; 
-		std::fwrite( &( pCell->state.orientation ) , sizeof(double) , 3 , fp ); 
+		std::fwrite( pCell->state.orientation.data() , sizeof(double) , 3 , fp ); 
 		// name = "polarity"; 
 		std::fwrite( &( pCell->phenotype.geometry.polarity ) , sizeof(double) , 1 , fp ); 
 

unit_tests/custom_voxel_values/Makefile

@@ -0,0 +1,309 @@
+VERSION := $(shell grep . VERSION.txt | cut -f1 -d:)
+PROGRAM_NAME := test_voxel_values
+
+CC := g++
+# CC := g++-mp-7 # typical macports compiler name
+# CC := g++-7 # typical homebrew compiler name 
+
+# Check for environment definitions of compiler 
+# e.g., on CC = g++-7 on OSX
+ifdef PHYSICELL_CPP 
+	CC := $(PHYSICELL_CPP)
+endif
+
+ARCH := native # best auto-tuning
+# ARCH := core2 # a reasonably safe default for most CPUs since 2007
+# ARCH := corei7
+# ARCH := corei7-avx # earlier i7 
+# ARCH := core-avx-i # i7 ivy bridge or newer 
+# ARCH := core-avx2 # i7 with Haswell or newer
+# ARCH := nehalem
+# ARCH := westmere
+# ARCH := sandybridge # circa 2011
+# ARCH := ivybridge   # circa 2012
+# ARCH := haswell     # circa 2013
+# ARCH := broadwell   # circa 2014
+# ARCH := skylake     # circa 2015
+# ARCH := bonnell
+# ARCH := silvermont
+# ARCH := skylake-avx512
+# ARCH := nocona #64-bit pentium 4 or later 
+
+# CFLAGS := -march=$(ARCH) -Ofast -s -fomit-frame-pointer -mfpmath=both -fopenmp -m64 -std=c++11
+CFLAGS := -march=$(ARCH) -O3 -fomit-frame-pointer -mfpmath=both -fopenmp -m64 -std=c++11
+
+ifeq ($(OS),Windows_NT)
+else
+	UNAME_S := $(shell uname -s)
+	ifeq ($(UNAME_S),Darwin)
+		UNAME_P := $(shell uname -p)
+		var := $(shell which $(CC) | xargs file)
+		ifeq ($(lastword $(var)),arm64)
+		  CFLAGS := -march=$(ARCH) -O3 -fomit-frame-pointer -fopenmp -m64 -std=c++11
+		endif
+	endif
+endif
+
+COMPILE_COMMAND := $(CC) $(CFLAGS) 
+
+BioFVM_OBJECTS := BioFVM_vector.o BioFVM_mesh.o BioFVM_microenvironment.o BioFVM_solvers.o BioFVM_matlab.o \
+BioFVM_utilities.o BioFVM_basic_agent.o BioFVM_MultiCellDS.o BioFVM_agent_container.o 
+
+PhysiCell_core_OBJECTS := PhysiCell_phenotype.o PhysiCell_cell_container.o PhysiCell_standard_models.o \
+PhysiCell_cell.o PhysiCell_custom.o PhysiCell_utilities.o PhysiCell_constants.o PhysiCell_basic_signaling.o \
+PhysiCell_signal_behavior.o 
+
+PhysiCell_module_OBJECTS := PhysiCell_SVG.o PhysiCell_pathology.o PhysiCell_MultiCellDS.o PhysiCell_various_outputs.o \
+PhysiCell_pugixml.o PhysiCell_settings.o PhysiCell_geometry.o
+
+# put your custom objects here (they should be in the custom_modules directory)
+
+PhysiCell_custom_module_OBJECTS := custom.o
+
+pugixml_OBJECTS := pugixml.o
+
+PhysiCell_OBJECTS := $(BioFVM_OBJECTS)  $(pugixml_OBJECTS) $(PhysiCell_core_OBJECTS) $(PhysiCell_module_OBJECTS)
+ALL_OBJECTS := $(PhysiCell_OBJECTS) $(PhysiCell_custom_module_OBJECTS)
+
+# compile the project 
+
+all: main.cpp $(ALL_OBJECTS)
+	$(COMPILE_COMMAND) -o $(PROGRAM_NAME) $(ALL_OBJECTS) main.cpp 
+	make name
+
+name:
+	@echo ""
+	@echo "Executable name is" $(PROGRAM_NAME)
+	@echo ""
+
+# PhysiCell core components	
+
+PhysiCell_phenotype.o: ./core/PhysiCell_phenotype.cpp
+	$(COMPILE_COMMAND) -c ./core/PhysiCell_phenotype.cpp
+
+PhysiCell_digital_cell_line.o: ./core/PhysiCell_digital_cell_line.cpp
+	$(COMPILE_COMMAND) -c ./core/PhysiCell_digital_cell_line.cpp
+
+PhysiCell_cell.o: ./core/PhysiCell_cell.cpp
+	$(COMPILE_COMMAND) -c ./core/PhysiCell_cell.cpp 
+
+PhysiCell_cell_container.o: ./core/PhysiCell_cell_container.cpp
+	$(COMPILE_COMMAND) -c ./core/PhysiCell_cell_container.cpp 
+
+PhysiCell_standard_models.o: ./core/PhysiCell_standard_models.cpp
+	$(COMPILE_COMMAND) -c ./core/PhysiCell_standard_models.cpp 
+
+PhysiCell_utilities.o: ./core/PhysiCell_utilities.cpp
+	$(COMPILE_COMMAND) -c ./core/PhysiCell_utilities.cpp 
+
+PhysiCell_custom.o: ./core/PhysiCell_custom.cpp
+	$(COMPILE_COMMAND) -c ./core/PhysiCell_custom.cpp 
+
+PhysiCell_constants.o: ./core/PhysiCell_constants.cpp
+	$(COMPILE_COMMAND) -c ./core/PhysiCell_constants.cpp 
+
+PhysiCell_signal_behavior.o: ./core/PhysiCell_signal_behavior.cpp
+	$(COMPILE_COMMAND) -c ./core/PhysiCell_signal_behavior.cpp 
+
+# BioFVM core components (needed by PhysiCell)
+
+BioFVM_vector.o: ./BioFVM/BioFVM_vector.cpp
+	$(COMPILE_COMMAND) -c ./BioFVM/BioFVM_vector.cpp 
+
+BioFVM_agent_container.o: ./BioFVM/BioFVM_agent_container.cpp
+	$(COMPILE_COMMAND) -c ./BioFVM/BioFVM_agent_container.cpp 
+
+BioFVM_mesh.o: ./BioFVM/BioFVM_mesh.cpp
+	$(COMPILE_COMMAND) -c ./BioFVM/BioFVM_mesh.cpp 
+
+BioFVM_microenvironment.o: ./BioFVM/BioFVM_microenvironment.cpp
+	$(COMPILE_COMMAND) -c ./BioFVM/BioFVM_microenvironment.cpp 
+
+BioFVM_solvers.o: ./BioFVM/BioFVM_solvers.cpp
+	$(COMPILE_COMMAND) -c ./BioFVM/BioFVM_solvers.cpp 
+
+BioFVM_utilities.o: ./BioFVM/BioFVM_utilities.cpp
+	$(COMPILE_COMMAND) -c ./BioFVM/BioFVM_utilities.cpp 
+
+BioFVM_basic_agent.o: ./BioFVM/BioFVM_basic_agent.cpp
+	$(COMPILE_COMMAND) -c ./BioFVM/BioFVM_basic_agent.cpp 
+
+BioFVM_matlab.o: ./BioFVM/BioFVM_matlab.cpp
+	$(COMPILE_COMMAND) -c ./BioFVM/BioFVM_matlab.cpp
+
+BioFVM_MultiCellDS.o: ./BioFVM/BioFVM_MultiCellDS.cpp
+	$(COMPILE_COMMAND) -c ./BioFVM/BioFVM_MultiCellDS.cpp
+
+pugixml.o: ./BioFVM/pugixml.cpp
+	$(COMPILE_COMMAND) -c ./BioFVM/pugixml.cpp
+
+# standard PhysiCell modules
+
+PhysiCell_SVG.o: ./modules/PhysiCell_SVG.cpp
+	$(COMPILE_COMMAND) -c ./modules/PhysiCell_SVG.cpp
+
+PhysiCell_pathology.o: ./modules/PhysiCell_pathology.cpp
+	$(COMPILE_COMMAND) -c ./modules/PhysiCell_pathology.cpp
+
+PhysiCell_MultiCellDS.o: ./modules/PhysiCell_MultiCellDS.cpp
+	$(COMPILE_COMMAND) -c ./modules/PhysiCell_MultiCellDS.cpp
+
+PhysiCell_various_outputs.o: ./modules/PhysiCell_various_outputs.cpp
+	$(COMPILE_COMMAND) -c ./modules/PhysiCell_various_outputs.cpp
+
+PhysiCell_pugixml.o: ./modules/PhysiCell_pugixml.cpp
+	$(COMPILE_COMMAND) -c ./modules/PhysiCell_pugixml.cpp
+
+PhysiCell_settings.o: ./modules/PhysiCell_settings.cpp
+	$(COMPILE_COMMAND) -c ./modules/PhysiCell_settings.cpp
+
+PhysiCell_basic_signaling.o: ./core/PhysiCell_basic_signaling.cpp
+	$(COMPILE_COMMAND) -c ./core/PhysiCell_basic_signaling.cpp 	
+
+PhysiCell_geometry.o: ./modules/PhysiCell_geometry.cpp
+	$(COMPILE_COMMAND) -c ./modules/PhysiCell_geometry.cpp 
+
+# user-defined PhysiCell modules
+
+custom.o: ./custom_modules/custom.cpp 
+	$(COMPILE_COMMAND) -c ./custom_modules/custom.cpp
+
+# cleanup
+
+reset:
+	rm -f *.cpp 
+	cp ./sample_projects/Makefile-default Makefile 
+	rm -f ./custom_modules/*
+	touch ./custom_modules/empty.txt 
+	touch ALL_CITATIONS.txt 
+	touch ./core/PhysiCell_cell.cpp
+	rm ALL_CITATIONS.txt 
+	cp ./config/PhysiCell_settings-backup.xml ./config/PhysiCell_settings.xml 
+	touch ./config/empty.csv
+	rm -f ./config/*.csv
+
+clean:
+	rm -f *.o
+	rm -f $(PROGRAM_NAME)*
+
+data-cleanup:
+	rm -rf ./output
+	mkdir ./output
+	touch ./output/empty.txt
+
+# archival 
+
+checkpoint: 
+	zip -r $$(date +%b_%d_%Y_%H%M).zip Makefile *.cpp *.h config/*.xml custom_modules/* 
+
+zip:
+	zip -r latest.zip Makefile* *.cpp *.h BioFVM/* config/* core/* custom_modules/* matlab/* modules/* sample_projects/* 
+	cp latest.zip $$(date +%b_%d_%Y_%H%M).zip
+	cp latest.zip VERSION_$(VERSION).zip 
+	mv *.zip archives/
+
+tar:
+	tar --ignore-failed-read -czf latest.tar Makefile* *.cpp *.h BioFVM/* config/* core/* custom_modules/* matlab/* modules/* sample_projects/* 
+	cp latest.tar $$(date +%b_%d_%Y_%H%M).tar
+	cp latest.tar VERSION_$(VERSION).tar
+	mv *.tar archives/
+
+unzip: 
+	cp ./archives/latest.zip . 
+	unzip latest.zip 
+
+untar: 
+	cp ./archives/latest.tar .
+	tar -xzf latest.tar
+
+# easier animation 
+
+FRAMERATE := 24
+OUTPUT := output
+
+jpeg: 
+	@magick identify -format "%h" $(OUTPUT)/initial.svg > __H.txt 
+	@magick identify -format "%w" $(OUTPUT)/initial.svg > __W.txt 
+	@expr 2 \* \( $$(grep . __H.txt) / 2 \) > __H1.txt 
+	@expr 2 \* \( $$(grep . __W.txt) / 2 \) > __W1.txt 
+	@echo "$$(grep . __W1.txt)!x$$(grep . __H1.txt)!" > __resize.txt 
+	@magick mogrify -format jpg -resize $$(grep . __resize.txt) $(OUTPUT)/s*.svg
+	rm -f __H*.txt __W*.txt __resize.txt 
+
+gif: 
+	magick convert $(OUTPUT)/s*.svg $(OUTPUT)/out.gif 
+
+movie:
+	ffmpeg -r $(FRAMERATE) -f image2 -i $(OUTPUT)/snapshot%08d.jpg -vcodec libx264 -pix_fmt yuv420p -strict -2 -tune animation -crf 15 -acodec none $(OUTPUT)/out.mp4
+
+# upgrade rules 
+
+SOURCE := PhysiCell_upgrade.zip 
+get-upgrade: 
+	@echo $$(curl https://raw.githubusercontent.com/MathCancer/PhysiCell/master/VERSION.txt) > VER.txt 
+	@echo https://github.com/MathCancer/PhysiCell/releases/download/$$(grep . VER.txt)/PhysiCell_V.$$(grep . VER.txt).zip > DL_FILE.txt 
+	rm -f VER.txt
+	$$(curl -L $$(grep . DL_FILE.txt) --output PhysiCell_upgrade.zip)
+	rm -f DL_FILE.txt 
+
+PhysiCell_upgrade.zip: 
+	make get-upgrade 
+
+upgrade: $(SOURCE)
+	unzip $(SOURCE) PhysiCell/VERSION.txt
+	mv -f PhysiCell/VERSION.txt . 
+	unzip $(SOURCE) PhysiCell/core/* 
+	cp -r PhysiCell/core/* core 
+	unzip $(SOURCE) PhysiCell/modules/* 
+	cp -r PhysiCell/modules/* modules 
+	unzip $(SOURCE) PhysiCell/sample_projects/* 
+	cp -r PhysiCell/sample_projects/* sample_projects 
+	unzip $(SOURCE) PhysiCell/BioFVM/* 
+	cp -r PhysiCell/BioFVM/* BioFVM
+	unzip $(SOURCE) PhysiCell/documentation/User_Guide.pdf
+	mv -f PhysiCell/documentation/User_Guide.pdf documentation
+	rm -f -r PhysiCell
+	rm -f $(SOURCE) 
+
+#===================================================================
+#-------------  1.10.5 addition to save user projects --------------
+# useage: 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
+
+# useage: make load PROJ=your_project_name
+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/ 
+
+# useage: make share PROJ=your_project_name
+share: 
+	@echo "Preparing your project for sharing from $(PROJ) ... "
+	@echo " " 
+	zip -r $(PROJ)_$$(date +%b_%d_%Y_%H%M).zip ./user_projects/$(PROJ)/* 
+	@echo "Project saved in $(PROJ)_$$(date +%b_%d_%Y_%H%M).zip."
+	@echo "It can be unzipped (or use tar -xvf) in a PhysiCell root directory."
+	@echo " "
+
+# sci_package: make sci_package PROJ=your_project_name
+sci_package: 
+	@echo "Preparing your project for scientific archival from $(PROJ) ... "
+	@echo " " 
+	touch output/empty.txt
+	zip -r $(PROJ)_packaged_$$(date +%b_%d_%Y_%H%M).zip main.cpp Makefile ./config/* ./BioFVM/* VERSION.txt ./custom_modules/* ./core/* ./addons/* ./licenses/* ./modules/* ./output/empty.txt
+	@echo "Project saved in $(PROJ)_packaged_$$(date +%b_%d_%Y_%H%M).zip."
+	@echo "It is fully self-contained and can be distributed as a separate GitHub repository."
+	@echo " "