From c80c5f722366afe6faa044e40bc02ac99e8ec267 Mon Sep 17 00:00:00 2001 From: Randy Heiland Date: Thu, 28 Jul 2022 10:49:25 -0400 Subject: [PATCH 1/3] fix fwrite of orientation vec --- modules/PhysiCell_MultiCellDS.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/PhysiCell_MultiCellDS.cpp b/modules/PhysiCell_MultiCellDS.cpp index 6c8c6d483..4e9e5da7f 100644 --- a/modules/PhysiCell_MultiCellDS.cpp +++ b/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 ); From 187d94a1697ce12ea36466c42b0a3a4814d78128 Mon Sep 17 00:00:00 2001 From: Randy Heiland Date: Wed, 3 Aug 2022 09:10:27 -0400 Subject: [PATCH 2/3] prevent a segfault --- core/PhysiCell_cell_container.cpp | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/core/PhysiCell_cell_container.cpp b/core/PhysiCell_cell_container.cpp index 13fe12008..4614b7c06 100644 --- a/core/PhysiCell_cell_container.cpp +++ b/core/PhysiCell_cell_container.cpp @@ -310,6 +310,10 @@ 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 ) { From e3558e43595487cefe431b3fdf1e7049abb3ccef Mon Sep 17 00:00:00 2001 From: Randy Heiland Date: Tue, 18 Oct 2022 19:07:37 -0600 Subject: [PATCH 3/3] 3x3x3 voxels sequential values --- unit_tests/custom_voxel_values/Makefile | 309 ++++++++++++++++++ .../config/PhysiCell_settings.xml | 229 +++++++++++++ .../custom_modules/custom.cpp | 229 +++++++++++++ .../custom_modules/custom.h | 92 ++++++ unit_tests/custom_voxel_values/main.cpp | 253 ++++++++++++++ 5 files changed, 1112 insertions(+) create mode 100644 unit_tests/custom_voxel_values/Makefile create mode 100644 unit_tests/custom_voxel_values/config/PhysiCell_settings.xml create mode 100644 unit_tests/custom_voxel_values/custom_modules/custom.cpp create mode 100644 unit_tests/custom_voxel_values/custom_modules/custom.h create mode 100644 unit_tests/custom_voxel_values/main.cpp diff --git a/unit_tests/custom_voxel_values/Makefile b/unit_tests/custom_voxel_values/Makefile new file mode 100644 index 000000000..e27362f79 --- /dev/null +++ b/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 " " diff --git a/unit_tests/custom_voxel_values/config/PhysiCell_settings.xml b/unit_tests/custom_voxel_values/config/PhysiCell_settings.xml new file mode 100644 index 000000000..95c58f68b --- /dev/null +++ b/unit_tests/custom_voxel_values/config/PhysiCell_settings.xml @@ -0,0 +1,229 @@ + + + -30 + 30 + -30 + 30 + -30 + 30 + 20 + 20 + 20 + false + + + + 1 + min + micron + + 0.01 + 0.1 + 6 + + + + 1 + + + + output + + + 1 + true + + + + 1 + true + + + + false + + + + + false + false + + + + + + 0 + 0 + + 0 + 0 + + 0 + 0 + 0 + 0 + 0 + 0 + + + + + true + false + + + ./config/initial.mat + + + + ./config/dirichlet.mat + + + + + + + + + + 0.0 + + + + + + 5.31667e-05 + + 516 + + + 0.05 + 0 + 1.66667e-02 + 5.83333e-03 + 0 + 2.0 + + + + 0.0 + + 0 + 86400 + + + 0.05 + 0 + 1.66667e-02 + 5.83333e-03 + 0 + 2.0 + + + + + + 523.6 + 0.75 + 540 + 0.05 + 0.0045 + 0.0055 + 0 + 0 + 2.0 + + + + 0.4 + 10.0 + 1.25 + + 1.0 + + + 1.8 + 15.12 + + 4.0 + 10.0 + 0.01 + 10.0 + 0.0 + + + + 1 + 1 + 1 + + true + false + + true + oxygen + 1 + + + false + false + + 0.01 + + + + + + + + 0 + 1 + 0 + 0 + + + + + 0.0 + + 0.0 + + + + 0.0 + + + 1.0 + + 0.0 + + + + + + + 0.0 + + + + + + 1.0 + + + + + + + + ./config + cells1.csv + + + + + 0 + 0 + + + \ No newline at end of file diff --git a/unit_tests/custom_voxel_values/custom_modules/custom.cpp b/unit_tests/custom_voxel_values/custom_modules/custom.cpp new file mode 100644 index 000000000..74f057adb --- /dev/null +++ b/unit_tests/custom_voxel_values/custom_modules/custom.cpp @@ -0,0 +1,229 @@ +/* +############################################################################### +# 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 x.y.z) [1]. # +# # +# [1] A Ghaffarizadeh, R Heiland, SH Friedman, SM Mumenthaler, and P Macklin, # +# PhysiCell: an Open Source Physics-Based Cell Simulator for Multicellu- # +# lar Systems, PLoS Comput. Biol. 14(2): e1005991, 2018 # +# DOI: 10.1371/journal.pcbi.1005991 # +# # +# See VERSION.txt or call get_PhysiCell_version() to get the current version # +# x.y.z. Call display_citations() to get detailed information on all cite-# +# able software used in your PhysiCell application. # +# # +# Because PhysiCell extensively uses BioFVM, we suggest you also cite BioFVM # +# as below: # +# # +# We implemented and solved the model using PhysiCell (Version x.y.z) [1], # +# with BioFVM [2] to solve the transport equations. # +# # +# [1] A Ghaffarizadeh, R Heiland, SH Friedman, SM Mumenthaler, and P Macklin, # +# PhysiCell: an Open Source Physics-Based Cell Simulator for Multicellu- # +# lar Systems, PLoS Comput. Biol. 14(2): e1005991, 2018 # +# DOI: 10.1371/journal.pcbi.1005991 # +# # +# [2] A Ghaffarizadeh, SH Friedman, and P Macklin, BioFVM: an efficient para- # +# llelized diffusive transport solver for 3-D biological simulations, # +# Bioinformatics 32(8): 1256-8, 2016. DOI: 10.1093/bioinformatics/btv730 # +# # +############################################################################### +# # +# BSD 3-Clause License (see https://opensource.org/licenses/BSD-3-Clause) # +# # +# Copyright (c) 2015-2021, Paul Macklin and the PhysiCell Project # +# All rights reserved. # +# # +# Redistribution and use in source and binary forms, with or without # +# modification, are permitted provided that the following conditions are met: # +# # +# 1. Redistributions of source code must retain the above copyright notice, # +# this list of conditions and the following disclaimer. # +# # +# 2. Redistributions in binary form must reproduce the above copyright # +# notice, this list of conditions and the following disclaimer in the # +# documentation and/or other materials provided with the distribution. # +# # +# 3. Neither the name of the copyright holder nor the names of its # +# contributors may be used to endorse or promote products derived from this # +# software without specific prior written permission. # +# # +# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" # +# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE # +# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE # +# ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE # +# LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR # +# CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF # +# SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS # +# INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN # +# CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) # +# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE # +# POSSIBILITY OF SUCH DAMAGE. # +# # +############################################################################### +*/ + +#include "./custom.h" + +void create_cell_types( void ) +{ + // set the random seed + SeedRandom( parameters.ints("random_seed") ); + + /* + Put any modifications to default cell definition here if you + want to have "inherited" by other cell types. + + This is a good place to set default functions. + */ + + initialize_default_cell_definition(); + cell_defaults.phenotype.secretion.sync_to_microenvironment( µenvironment ); + + cell_defaults.functions.volume_update_function = standard_volume_update_function; + cell_defaults.functions.update_velocity = standard_update_cell_velocity; + + cell_defaults.functions.update_migration_bias = NULL; + cell_defaults.functions.update_phenotype = NULL; // update_cell_and_death_parameters_O2_based; + cell_defaults.functions.custom_cell_rule = NULL; + cell_defaults.functions.contact_function = NULL; + + cell_defaults.functions.add_cell_basement_membrane_interactions = NULL; + cell_defaults.functions.calculate_distance_to_membrane = NULL; + + /* + This parses the cell definitions in the XML config file. + */ + + initialize_cell_definitions_from_pugixml(); + + /* + This builds the map of cell definitions and summarizes the setup. + */ + + build_cell_definitions_maps(); + + /* + This intializes cell signal and response dictionaries + */ + + setup_signal_behavior_dictionaries(); + + /* + Put any modifications to individual cell definitions here. + + This is a good place to set custom functions. + */ + + cell_defaults.functions.update_phenotype = phenotype_function; + // cell_defaults.functions.custom_cell_rule = custom_function; + // cell_defaults.functions.contact_function = contact_function; + + /* + This builds the map of cell definitions and summarizes the setup. + */ + + display_cell_definitions( std::cout ); + + return; +} + +void setup_microenvironment( void ) +{ + // initialize BioFVM + + initialize_microenvironment(); + + int idx_oxygen = 0; + double oxy_value = 40.0; // set voxel values sequentially + + int idx_xmax = microenvironment.mesh.x_coordinates.size() - 1; + int idx_ymax = microenvironment.mesh.y_coordinates.size() - 1; + int idx_zmax = microenvironment.mesh.z_coordinates.size() - 1; + + for (int idz=0; idzname << " ... " << std::endl; + // for( int n = 0 ; n < parameters.ints("number_of_cells") ; n++ ) + // { + // std::vector position = {0,0,0}; + // position[0] = Xmin + UniformRandom()*Xrange; + // position[1] = Ymin + UniformRandom()*Yrange; + // position[2] = Zmin + UniformRandom()*Zrange; + + // pC = create_cell( *pCD ); + // pC->assign_position( position ); + // } + // } + // std::cout << std::endl; + + // single cell at origin + Cell_Definition* pCD = cell_definitions_by_index[0]; + std::vector position = {0,0,0}; + pC = create_cell( *pCD ); + pC->assign_position( position ); + + + // load cells from your CSV file (if enabled) + load_cells_from_pugixml(); + return; +} + +std::vector my_coloring_function( Cell* pCell ) +{ return paint_by_number_cell_coloring(pCell); } + +void phenotype_function( Cell* pCell, Phenotype& phenotype, double dt ) +{ + return; +} + +void custom_function( Cell* pCell, Phenotype& phenotype , double dt ) +{ return; } + +void contact_function( Cell* pMe, Phenotype& phenoMe , Cell* pOther, Phenotype& phenoOther , double dt ) +{ return; } \ No newline at end of file diff --git a/unit_tests/custom_voxel_values/custom_modules/custom.h b/unit_tests/custom_voxel_values/custom_modules/custom.h new file mode 100644 index 000000000..0e6df8d02 --- /dev/null +++ b/unit_tests/custom_voxel_values/custom_modules/custom.h @@ -0,0 +1,92 @@ +/* +############################################################################### +# 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 x.y.z) [1]. # +# # +# [1] A Ghaffarizadeh, R Heiland, SH Friedman, SM Mumenthaler, and P Macklin, # +# PhysiCell: an Open Source Physics-Based Cell Simulator for Multicellu- # +# lar Systems, PLoS Comput. Biol. 14(2): e1005991, 2018 # +# DOI: 10.1371/journal.pcbi.1005991 # +# # +# See VERSION.txt or call get_PhysiCell_version() to get the current version # +# x.y.z. Call display_citations() to get detailed information on all cite-# +# able software used in your PhysiCell application. # +# # +# Because PhysiCell extensively uses BioFVM, we suggest you also cite BioFVM # +# as below: # +# # +# We implemented and solved the model using PhysiCell (Version x.y.z) [1], # +# with BioFVM [2] to solve the transport equations. # +# # +# [1] A Ghaffarizadeh, R Heiland, SH Friedman, SM Mumenthaler, and P Macklin, # +# PhysiCell: an Open Source Physics-Based Cell Simulator for Multicellu- # +# lar Systems, PLoS Comput. Biol. 14(2): e1005991, 2018 # +# DOI: 10.1371/journal.pcbi.1005991 # +# # +# [2] A Ghaffarizadeh, SH Friedman, and P Macklin, BioFVM: an efficient para- # +# llelized diffusive transport solver for 3-D biological simulations, # +# Bioinformatics 32(8): 1256-8, 2016. DOI: 10.1093/bioinformatics/btv730 # +# # +############################################################################### +# # +# BSD 3-Clause License (see https://opensource.org/licenses/BSD-3-Clause) # +# # +# Copyright (c) 2015-2021, Paul Macklin and the PhysiCell Project # +# All rights reserved. # +# # +# Redistribution and use in source and binary forms, with or without # +# modification, are permitted provided that the following conditions are met: # +# # +# 1. Redistributions of source code must retain the above copyright notice, # +# this list of conditions and the following disclaimer. # +# # +# 2. Redistributions in binary form must reproduce the above copyright # +# notice, this list of conditions and the following disclaimer in the # +# documentation and/or other materials provided with the distribution. # +# # +# 3. Neither the name of the copyright holder nor the names of its # +# contributors may be used to endorse or promote products derived from this # +# software without specific prior written permission. # +# # +# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" # +# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE # +# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE # +# ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE # +# LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR # +# CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF # +# SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS # +# INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN # +# CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) # +# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE # +# POSSIBILITY OF SUCH DAMAGE. # +# # +############################################################################### +*/ + +#include "../core/PhysiCell.h" +#include "../modules/PhysiCell_standard_modules.h" + +using namespace BioFVM; +using namespace PhysiCell; + +// setup functions to help us along + +void create_cell_types( void ); +void setup_tissue( void ); + +// set up the BioFVM microenvironment +void setup_microenvironment( void ); + +// custom pathology coloring function + +std::vector my_coloring_function( Cell* ); + +// custom functions can go here + +void phenotype_function( Cell* pCell, Phenotype& phenotype, double dt ); +void custom_function( Cell* pCell, Phenotype& phenotype , double dt ); + +void contact_function( Cell* pMe, Phenotype& phenoMe , Cell* pOther, Phenotype& phenoOther , double dt ); + diff --git a/unit_tests/custom_voxel_values/main.cpp b/unit_tests/custom_voxel_values/main.cpp new file mode 100644 index 000000000..9d26e541d --- /dev/null +++ b/unit_tests/custom_voxel_values/main.cpp @@ -0,0 +1,253 @@ +/* +############################################################################### +# 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 x.y.z) [1]. # +# # +# [1] A Ghaffarizadeh, R Heiland, SH Friedman, SM Mumenthaler, and P Macklin, # +# PhysiCell: an Open Source Physics-Based Cell Simulator for Multicellu- # +# lar Systems, PLoS Comput. Biol. 14(2): e1005991, 2018 # +# DOI: 10.1371/journal.pcbi.1005991 # +# # +# See VERSION.txt or call get_PhysiCell_version() to get the current version # +# x.y.z. Call display_citations() to get detailed information on all cite-# +# able software used in your PhysiCell application. # +# # +# Because PhysiCell extensively uses BioFVM, we suggest you also cite BioFVM # +# as below: # +# # +# We implemented and solved the model using PhysiCell (Version x.y.z) [1], # +# with BioFVM [2] to solve the transport equations. # +# # +# [1] A Ghaffarizadeh, R Heiland, SH Friedman, SM Mumenthaler, and P Macklin, # +# PhysiCell: an Open Source Physics-Based Cell Simulator for Multicellu- # +# lar Systems, PLoS Comput. Biol. 14(2): e1005991, 2018 # +# DOI: 10.1371/journal.pcbi.1005991 # +# # +# [2] A Ghaffarizadeh, SH Friedman, and P Macklin, BioFVM: an efficient para- # +# llelized diffusive transport solver for 3-D biological simulations, # +# Bioinformatics 32(8): 1256-8, 2016. DOI: 10.1093/bioinformatics/btv730 # +# # +############################################################################### +# # +# BSD 3-Clause License (see https://opensource.org/licenses/BSD-3-Clause) # +# # +# Copyright (c) 2015-2022, Paul Macklin and the PhysiCell Project # +# All rights reserved. # +# # +# Redistribution and use in source and binary forms, with or without # +# modification, are permitted provided that the following conditions are met: # +# # +# 1. Redistributions of source code must retain the above copyright notice, # +# this list of conditions and the following disclaimer. # +# # +# 2. Redistributions in binary form must reproduce the above copyright # +# notice, this list of conditions and the following disclaimer in the # +# documentation and/or other materials provided with the distribution. # +# # +# 3. Neither the name of the copyright holder nor the names of its # +# contributors may be used to endorse or promote products derived from this # +# software without specific prior written permission. # +# # +# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" # +# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE # +# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE # +# ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE # +# LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR # +# CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF # +# SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS # +# INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN # +# CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) # +# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE # +# POSSIBILITY OF SUCH DAMAGE. # +# # +############################################################################### +*/ + +#include +#include +#include +#include +#include +#include +#include + +#include "./core/PhysiCell.h" +#include "./modules/PhysiCell_standard_modules.h" + +// put custom code modules here! + +#include "./custom_modules/custom.h" + +using namespace BioFVM; +using namespace PhysiCell; + +int main( int argc, char* argv[] ) +{ + // load and parse settings file(s) + + bool XML_status = false; + char copy_command [1024]; + if( argc > 1 ) + { + XML_status = load_PhysiCell_config_file( argv[1] ); + sprintf( copy_command , "cp %s %s" , argv[1] , PhysiCell_settings.folder.c_str() ); + } + else + { + XML_status = load_PhysiCell_config_file( "./config/PhysiCell_settings.xml" ); + sprintf( copy_command , "cp ./config/PhysiCell_settings.xml %s" , PhysiCell_settings.folder.c_str() ); + } + if( !XML_status ) + { exit(-1); } + + // copy config file to output directry + system( copy_command ); + + // OpenMP setup + omp_set_num_threads(PhysiCell_settings.omp_num_threads); + + // time setup + std::string time_units = "min"; + + /* Microenvironment setup */ + + setup_microenvironment(); // modify this in the custom code + + /* PhysiCell setup */ + + // set mechanics voxel size, and match the data structure to BioFVM + double mechanics_voxel_size = 30; + Cell_Container* cell_container = create_cell_container_for_microenvironment( microenvironment, mechanics_voxel_size ); + + /* Users typically start modifying here. START USERMODS */ + + create_cell_types(); + + setup_tissue(); + + /* Users typically stop modifying here. END USERMODS */ + + // set MultiCellDS save options + + set_save_biofvm_mesh_as_matlab( true ); + set_save_biofvm_data_as_matlab( true ); + set_save_biofvm_cell_data( true ); + set_save_biofvm_cell_data_as_custom_matlab( true ); + + // save a simulation snapshot + + char filename[1024]; + sprintf( filename , "%s/initial" , PhysiCell_settings.folder.c_str() ); + save_PhysiCell_to_MultiCellDS_v2( filename , microenvironment , PhysiCell_globals.current_time ); + + // save a quick SVG cross section through z = 0, after setting its + // length bar to 200 microns + + PhysiCell_SVG_options.length_bar = 200; + + // for simplicity, set a pathology coloring function + + std::vector (*cell_coloring_function)(Cell*) = my_coloring_function; + + sprintf( filename , "%s/initial.svg" , PhysiCell_settings.folder.c_str() ); + SVG_plot( filename , microenvironment, 0.0 , PhysiCell_globals.current_time, cell_coloring_function ); + + sprintf( filename , "%s/legend.svg" , PhysiCell_settings.folder.c_str() ); + create_plot_legend( filename , cell_coloring_function ); + + display_citations(); + + // set the performance timers + + BioFVM::RUNTIME_TIC(); + BioFVM::TIC(); + + std::ofstream report_file; + if( PhysiCell_settings.enable_legacy_saves == true ) + { + sprintf( filename , "%s/simulation_report.txt" , PhysiCell_settings.folder.c_str() ); + + report_file.open(filename); // create the data log file + report_file<<"simulated time\tnum cells\tnum division\tnum death\twall time"<update_all_cells( PhysiCell_globals.current_time ); + + /* + Custom add-ons could potentially go here. + */ + + PhysiCell_globals.current_time += diffusion_dt; + } + + if( PhysiCell_settings.enable_legacy_saves == true ) + { + log_output(PhysiCell_globals.current_time, PhysiCell_globals.full_output_index, microenvironment, report_file); + report_file.close(); + } + } + catch( const std::exception& e ) + { // reference to the base of a polymorphic object + std::cout << e.what(); // information from length_error printed + } + + // save a final simulation snapshot + + sprintf( filename , "%s/final" , PhysiCell_settings.folder.c_str() ); + save_PhysiCell_to_MultiCellDS_v2( filename , microenvironment , PhysiCell_globals.current_time ); + + sprintf( filename , "%s/final.svg" , PhysiCell_settings.folder.c_str() ); + SVG_plot( filename , microenvironment, 0.0 , PhysiCell_globals.current_time, cell_coloring_function ); + + // timer + + std::cout << std::endl << "Total simulation runtime: " << std::endl; + BioFVM::display_stopwatch_value( std::cout , BioFVM::runtime_stopwatch_value() ); + + return 0; +}