def _run(self): """ Start the simulation. """ self.execConfig.parameterStore.addObj(self) for cellType in self.cellTypes: self.execConfig.parameterStore.addObj(cellType) CompuCellSetup.setSimulationXMLDescription(self._configureSimulation()) CompuCellSetup.initializeSimulationObjects(self.sim, self.simthread) pyAttributeDictionaryAdder, dictAdder = CompuCellSetup.attachDictionaryToCells(self.sim) # Add Python steppables here: steppableRegistry = CompuCellSetup.getSteppableRegistry() for steppable in self._getSteppables(): steppableRegistry.registerSteppable(steppable) CompuCellSetup.mainLoop(self.sim, self.simthread, steppableRegistry)
from os import getcwd import string sys.path.append(environ["PYTHON_MODULE_PATH"]) import CompuCellSetup # path for Win (path for Mac may need full path) CompuCellSetup.setSimulationXMLFileName("Simulation/BlHet.xml") #add additional sim, simthread = CompuCellSetup.getCoreSimulationObjects() #add additional attributes # add extra attributes here pyAttributeDictionaryAdder, dictAdder = CompuCellSetup.attachDictionaryToCells( sim) CompuCellSetup.initializeSimulationObjects(sim, simthread) #notice importing CompuCell to main script has to be done after call to getCoreSimulationObjects() import CompuCell #add lattice monitors here #### changeWatcherREgistry is also initialized at start of Python steppables #### CC3D crashes when changeWatcherRegistry in one of these lines is not commented out; changeWatcherRegistry = CompuCellSetup.getChangeWatcherRegistry(sim) stepperRegistry = CompuCellSetup.getStepperRegistry(sim) #Add Python steppables here from PySteppablesExamples import SteppableRegistry #### changeWatcherREgistry is also initialized at start of lattice monitors
import sys from os import environ from os import getcwd import string sys.path.append(environ["PYTHON_MODULE_PATH"]) import CompuCellSetup sim, simthread = CompuCellSetup.getCoreSimulationObjects() # add extra attributes here pyAttributeDictionaryAdder, dictAdder = CompuCellSetup.attachDictionaryToCells( sim) CompuCellSetup.initializeSimulationObjects(sim, simthread) # Definitions of additional Python-managed fields go here #Add Python steppables here steppableRegistry = CompuCellSetup.getSteppableRegistry() from bistabSwitch2Steppables import EMT_switch1Steppable steppableInstance = EMT_switch1Steppable(sim, _frequency=100) steppableRegistry.registerSteppable(steppableInstance) CompuCellSetup.mainLoop(sim, simthread, steppableRegistry)
## MUST INITIALIZE EXTERNAL POTENTIAL PLUGIN extPotential=cc3d.ElementCC3D("Plugin",{"Name":"ExternalPotential"}) ## Initialize cell field from piff file: piffinit = cc3d.ElementCC3D("Steppable",{"Type":"PIFInitializer"}) piffinit.ElementCC3D("PIFName",{},pifName) CompuCellSetup.setSimulationXMLDescription(cc3d) import CompuCellSetup sim,simthread = CompuCellSetup.getCoreSimulationObjects() configureSimulation(sim) import CompuCell CompuCellSetup.initializeSimulationObjects(sim,simthread) pyAttributeAdder,dictAdder=CompuCellSetup.attachDictionaryToCells(sim) #Add Python steppables here steppableRegistry=CompuCellSetup.getSteppableRegistry() changeWatcherRegistry=CompuCellSetup.getChangeWatcherRegistry(sim) stepperRegistry=CompuCellSetup.getStepperRegistry(sim) from GZ_motility_steppables import InitVolSur initVolSur=InitVolSur(_simulator=sim,_frequency=1,_LamV=lambda_V,_LamS=lambda_S,_tV=target_V,_tS=target_S) steppableRegistry.registerSteppable(initVolSur) # from GZ_motility_steppables import CellCounts # cellCounts=CellCounts(_simulator=sim,_frequency=100) # steppableRegistry.registerSteppable(cellCounts) # from GZ_genesis_steppables import CellGrowth
import sys from os import environ from os import getcwd import string ## sys.path.append(environ["PYTHON_MODULE_PATH"]) import CompuCellSetup # Initialize core CompuCell3D simulation objects sim, simthread = CompuCellSetup.getCoreSimulationObjects() #Create extra player fields here or add attributes pyAttributeAdder,listAdder=CompuCellSetup.attachDictionaryToCells(sim) CompuCellSetup.initializeSimulationObjects(sim,simthread) from OscillatingContactEnergiesFlexSteppables import * # Create instances of required steppables oscillatingContactEnergiesSteppable = OscillatingContactEnergiesSteppable( sim ) # Add steppables to the steppable registry steppableRegistry = CompuCellSetup.getSteppableRegistry() steppableRegistry.registerSteppable( oscillatingContactEnergiesSteppable ) CompuCellSetup.mainLoop(sim, simthread, steppableRegistry)
import sys from os import environ from os import getcwd import string sys.path.append(environ["PYTHON_MODULE_PATH"]) import CompuCellSetup sim,simthread = CompuCellSetup.getCoreSimulationObjects() # add extra attributes here pyAttributeDictionaryAdder,dictAdder=CompuCellSetup.attachDictionaryToCells(sim) CompuCellSetup.initializeSimulationObjects(sim,simthread) # Definitions of additional Python-managed fields go here #Add Python steppables here steppableRegistry=CompuCellSetup.getSteppableRegistry() from bistabSwitch2Steppables import EMT_switch1Steppable steppableInstance=EMT_switch1Steppable(sim,_frequency=100) steppableRegistry.registerSteppable(steppableInstance) CompuCellSetup.mainLoop(sim,simthread,steppableRegistry)
from os import environ from os import getcwd import string sys.path.append(environ["PYTHON_MODULE_PATH"]) import CompuCellSetup CompuCellSetup.setSimulationXMLFileName("2D_vasculogenesis_control.xml") sim,simthread = CompuCellSetup.getCoreSimulationObjects() CompuCellSetup.initializeSimulationObjects(sim,simthread) import CompuCell #notice importing CompuCell to main script has to be done after call to getCoreSimulationObjects() pyAttributeAdder,listAdder=CompuCellSetup.attachListToCells(sim) ####Assigns a list to each cell in the cellList inventory. List elements are later attached to each cell. pyAttributeAdderDict,dictAdder=CompuCellSetup.attachDictionaryToCells(sim) ####Assigns a dictionary to each cell in the cellList inventory. Dictionary elements are later attached to each cell. #Add Python steppables here from PySteppablesExamples import SteppableRegistry steppableRegistry=SteppableRegistry() from steppableBasedMitosisSteppables_control import VolumeParamSteppable volumeParamSteppable=VolumeParamSteppable(sim,10) steppableRegistry.registerSteppable(volumeParamSteppable) from steppableBasedMitosisSteppables_control import MitosisSteppable mitosisSteppable=MitosisSteppable(sim,10) steppableRegistry.registerSteppable(mitosisSteppable) # from steppableBasedMitosisSteppables import ProteinExpression # proteinExpression=ProteinExpression(sim,10)