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)
#PUT YOUR CODE HERE
#PUT YOUR CODE HERE
#PUT YOUR CODE HERE
import XMLUtils
steppableList=CompuCellSetup.cc3dXML2ObjConverter.root.getElements("Plugin")
steppableListPy=XMLUtils.CC3DXMLListPy(steppableList)
for element in steppableListPy:
print "Element",element.name
# ," name", element.getNumberOfChildren()
CompuCellSetup.initializeSimulationObjects(sim,simthread)
steppableRegistry=CompuCellSetup.getSteppableRegistry()
#Add Python steppables here
#PUT YOUR CODE HERE
#PUT YOUR CODE HERE
#PUT YOUR CODE HERE
# sim.ps.steppableCC3DXMLElementVector()
CompuCellSetup.mainLoop(sim,simthread,steppableRegistry)#main loop - simulation is invoked inside this function
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() CompuCellSetup.initializeSimulationObjects(sim,simthread) from OscillatingContactEnergiesSteppables 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)
CompuCellSetup.initializeSimulationObjects(sim,simthread)
steppableRegistry = CompuCellSetup.getSteppableRegistry()
from TissueInvasionSteppables import ConstraintInitializerSteppable
ConstraintInitializerSteppableInstance = ConstraintInitializerSteppable(sim,_frequency=1)
steppableRegistry.registerSteppable(ConstraintInitializerSteppableInstance)
from TissueInvasionSteppables import GrowthSteppable
GrowthSteppableInstance = GrowthSteppable(sim,_frequency=1)
steppableRegistry.registerSteppable(GrowthSteppableInstance)
from TissueInvasionSteppables import MitosisSteppable
MitosisSteppableInstance = MitosisSteppable(sim,_frequency=1)
steppableRegistry.registerSteppable(MitosisSteppableInstance)
from TissueInvasionSteppables import DeathSteppable
DeathSteppableInstance = DeathSteppable(sim,_frequency=1)
steppableRegistry.registerSteppable(DeathSteppableInstance)
from TissueInvasionSteppables import ExtraPlotSteppable
ExtraPlotSteppableInstance = ExtraPlotSteppable(sim,_frequency=1)
steppableRegistry.registerSteppable(ExtraPlotSteppableInstance)
from TissueInvasionSteppables import XMLDataSteppable
XMLDataSteppableInstance = XMLDataSteppable(sim,_frequency=1)
steppableRegistry.registerSteppable(XMLDataSteppableInstance)
CompuCellSetup.mainLoop(sim,simthread,steppableRegistry)
# for single run simulation we copy simulation files to the output directory
if singleSimulation:
cc3dSimulationDataHandler.copySimulationDataFiles(
CompuCellSetup.screenshotDirectoryName)
if CompuCellSetup.simulationPaths.simulationPythonScriptName != "":
execfile(CompuCellSetup.simulationPaths.simulationPythonScriptName)
else:
sim, simthread = CompuCellSetup.getCoreSimulationObjects()
# CompuCellSetup.cmlFieldHandler.outputFrequency=cmlParser.outputFrequency
import CompuCell #notice importing CompuCell to main script has to be done after call to getCoreSimulationObjects()
#import CompuCellSetup
CompuCellSetup.initializeSimulationObjects(sim, simthread)
steppableRegistry = CompuCellSetup.getSteppableRegistry()
CompuCellSetup.mainLoop(
sim, simthread, steppableRegistry
) # main loop - simulation is invoked inside this function
sim.cleanAfterSimulation()
sim = None
print 'FINISHED MAIN LOOP'
# if not allowRelanuch:
# break
# jumping out of the loop when running single simulation. Will stay in the loop for e.g. parameter scan
if singleSimulation:
break
else:
consecutiveRunCounter += 1
if consecutiveRunCounter >= maxNumberOfConsecutiveRuns:
relaunch = True
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)
