#sim.getPotts().getTypeTransition().registerTypeChangeWatcher(typeChangeWatcher) CompuCellSetup.initializeSimulationObjects(sim, simthread) dim = sim.getPotts().getCellFieldG().getDim() #Add Python steppables here from PySteppablesExamples import SteppableRegistry steppableRegistry = SteppableRegistry() from PySteppablesExamples import ContactLocalFlexPrinter clfdPrinter = ContactLocalFlexPrinter() steppableRegistry.registerSteppable(clfdPrinter) CompuCellSetup.mainLoop(sim, simthread, steppableRegistry) #def mainfcn(): #import sys #from os import environ #import string #sys.path.append(environ["PYTHON_MODULE_PATH"]) #import SystemUtils #SystemUtils.setSwigPaths() #SystemUtils.initializeSystemResources() #import CompuCell #import CompuCell
sys.path.append(environ["PYTHON_MODULE_PATH"]) sys.path.append(environ["SWIG_LIB_INSTALL_DIR"]) import CompuCellSetup sim, simthread = CompuCellSetup.getCoreSimulationObjects() CompuCellSetup.initializeSimulationObjects(sim, simthread) import CompuCell #notice importing CompuCell to main script has to be done after call to getCoreSimulationObjects() #Add Python steppables here from PySteppablesExamples import SteppableRegistry steppableRegistry = SteppableRegistry() from steppableBasedMitosisSteppables import DifferentiationSteppable differentiationSteppable = DifferentiationSteppable(sim, 1) steppableRegistry.registerSteppable(differentiationSteppable) from steppableBasedMitosisSteppables import MitosisSteppable mitosisSteppable = MitosisSteppable(sim, 1) steppableRegistry.registerSteppable(mitosisSteppable) from ContactSteeringSteppable import ContactSteering contactSteetingSteppable = ContactSteering(sim, 10) steppableRegistry.registerSteppable(contactSteetingSteppable) from steppableBasedMitosisSteppables import IdFieldVisualizationSteppable idFieldSteppable = IdFieldVisualizationSteppable(sim, 10) steppableRegistry.registerSteppable(idFieldSteppable) 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() import CompuCell #notice importing CompuCell to main script has to be done after call to getCoreSimulationObjects() CompuCellSetup.initializeSimulationObjects(sim, simthread) #Add Python steppables here from PySteppablesExamples import SteppableRegistry steppableRegistry = SteppableRegistry() from diffusion_2D_steppables_player import ExtraFieldVisualizationSteppable extraFieldVisualizationSteppable = ExtraFieldVisualizationSteppable( _simulator=sim, _frequency=10) steppableRegistry.registerSteppable(extraFieldVisualizationSteppable) CompuCellSetup.mainLoop(sim, simthread, steppableRegistry)
#### CC3D crashes when changeWatcherRegistry in one of these lines is not commented out; # changeWatcherRegistry=CompuCellSetup.getChangeWatcherRegistry(sim) steppableRegistry=SteppableRegistry() ############################################### STEPPABLES ################################# DRUG DYNAMICS # from steppablesBlHet import DiffusionSolverFESteeringCisplatinIV # diffusionSolverFESteeringCisplatinIV=DiffusionSolverFESteeringCisplatinIV(sim) # steppableRegistry.registerSteppable(diffusionSolverFESteeringCisplatinIV) from steppablesBlHet import DiffusionSolverFESteeringGemcitabineIV diffusionSolverFESteeringGemcitabineIV=DiffusionSolverFESteeringGemcitabineIV(sim) steppableRegistry.registerSteppable(diffusionSolverFESteeringGemcitabineIV) from steppablesBlHet import SecretionSteppableCisplatin secretionSteppableCisplatin=SecretionSteppableCisplatin(sim) steppableRegistry.registerSteppable(secretionSteppableCisplatin) from steppablesBlHet import SecretionSteppableGemcitabine secretionSteppableGemcitabine=SecretionSteppableGemcitabine(sim) steppableRegistry.registerSteppable(secretionSteppableGemcitabine) from steppablesBlHet import ChangeAtGemIC50Steppable changeAtGemIC50Steppable=ChangeAtGemIC50Steppable(sim) steppableRegistry.registerSteppable(changeAtGemIC50Steppable) from steppablesBlHet import ChangeAtCisIC50Steppable changeAtCisIC50Steppable=ChangeAtCisIC50Steppable(sim)
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() import CompuCell #notice importing CompuCell to main script has to be done after call to getCoreSimulationObjects() #Create extra player fields here or add attributes CompuCellSetup.initializeSimulationObjects(sim,simthread) #Add Python steppables here from PySteppablesExamples import SteppableRegistry steppableRegistry=SteppableRegistry() from SecretionSteadyStateSteppables import DiffusionFieldSteppable instanceOfDiffusionFieldSteppable=DiffusionFieldSteppable(_simulator=sim,_frequency=1) steppableRegistry.registerSteppable(instanceOfDiffusionFieldSteppable) 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() CompuCellSetup.initializeSimulationObjects(sim, simthread) import CompuCell #notice importing CompuCell to main script has to be done after call to getCoreSimulationObjects() # add extra attributes here # Definitions of additional Python-managed fields go here #Add Python steppables here from PySteppablesExamples import SteppableRegistry steppableRegistry = SteppableRegistry() from mouseOvarianDevelopmentSteppables import VolumeParamSteppable volumeParamSteppable = VolumeParamSteppable(sim, 10) steppableRegistry.registerSteppable(volumeParamSteppable) from mouseOvarianDevelopmentSteppables import MitosisSteppable mitosisSteppable = MitosisSteppable(sim, 10) steppableRegistry.registerSteppable(mitosisSteppable) 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() CompuCellSetup.initializeSimulationObjects(sim, simthread) import CompuCell #notice importing CompuCell to main script has to be done after call to getCoreSimulationObjects() #Add Python steppables here from PySteppablesExamples import SteppableRegistry steppableRegistry = SteppableRegistry() from CellManipulationSteppables import CellManipulationSteppable cellManipulationSteppable = CellManipulationSteppable(sim, 10) steppableRegistry.registerSteppable(cellManipulationSteppable) # # # from CellManipulationSteppables import CellManipulationSteppableExplained # # # cellManipulationSteppableExplained=CellManipulationSteppableExplained(sim,10) # # # steppableRegistry.registerSteppable(cellManipulationSteppableExplained) CompuCellSetup.mainLoop(sim, simthread, steppableRegistry)
#Add Python steppables here from PySteppablesExamples import SteppableRegistry #### changeWatcherREgistry is also initialized at start of lattice monitors #### CC3D crashes when changeWatcherRegistry in one of these lines is not commented out; # changeWatcherRegistry=CompuCellSetup.getChangeWatcherRegistry(sim) steppableRegistry = SteppableRegistry() ############################################### STEPPABLES ################################# DRUG DYNAMICS from steppablesBlHet import DiffusionSolverFESteeringCisplatinIV diffusionSolverFESteeringCisplatinIV = DiffusionSolverFESteeringCisplatinIV( sim) steppableRegistry.registerSteppable(diffusionSolverFESteeringCisplatinIV) from steppablesBlHet import DiffusionSolverFESteeringGemcitabineIV diffusionSolverFESteeringGemcitabineIV = DiffusionSolverFESteeringGemcitabineIV( sim) steppableRegistry.registerSteppable(diffusionSolverFESteeringGemcitabineIV) from steppablesBlHet import SecretionSteppableCisplatin secretionSteppableCisplatin = SecretionSteppableCisplatin(sim) steppableRegistry.registerSteppable(secretionSteppableCisplatin) from steppablesBlHet import SecretionSteppableGemcitabine secretionSteppableGemcitabine = SecretionSteppableGemcitabine(sim)
#sim.getPotts().getTypeTransition().registerTypeChangeWatcher(typeChangeWatcher) CompuCellSetup.initializeSimulationObjects(sim,simthread) dim=sim.getPotts().getCellFieldG().getDim() #Add Python steppables here from PySteppablesExamples import SteppableRegistry steppableRegistry=SteppableRegistry() from PySteppablesExamples import ContactLocalFlexPrinter clfdPrinter=ContactLocalFlexPrinter() steppableRegistry.registerSteppable(clfdPrinter) CompuCellSetup.mainLoop(sim,simthread,steppableRegistry) #def mainfcn(): #import sys #from os import environ #import string #sys.path.append(environ["PYTHON_MODULE_PATH"]) #import SystemUtils #SystemUtils.setSwigPaths() #SystemUtils.initializeSystemResources()
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() import CompuCell #notice importing CompuCell to main script has to be done after call to getCoreSimulationObjects() #Create extra player fields here or add attributes CompuCellSetup.initializeSimulationObjects(sim,simthread) #Add Python steppables here from PySteppablesExamples import SteppableRegistry steppableRegistry=SteppableRegistry() from FieldSecretionSteppables import FieldSecretionSteppable fieldSecretionSteppable=FieldSecretionSteppable(_simulator=sim,_frequency=10) steppableRegistry.registerSteppable(fieldSecretionSteppable) 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() import CompuCell # notice importing CompuCell to main script has to be done after call to getCoreSimulationObjects() CompuCellSetup.initializeSimulationObjects(sim, simthread) # Add Python steppables here from PySteppablesExamples import SteppableRegistry steppableRegistry = SteppableRegistry() from diffusion_2D_steppables_player import ExtraFieldVisualizationSteppable extraFieldVisualizationSteppable = ExtraFieldVisualizationSteppable(_simulator=sim, _frequency=10) steppableRegistry.registerSteppable(extraFieldVisualizationSteppable) CompuCellSetup.mainLoop(sim, simthread, steppableRegistry)
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) # steppableRegistry.registerSteppable(proteinExpression) from steppableBasedMitosisSteppables_control import SecretionCellSteppable secretionCellSteppable=SecretionCellSteppable(sim,10) steppableRegistry.registerSteppable(secretionCellSteppable) 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() import CompuCell #Create extra player fields here or add attributes CompuCellSetup.initializeSimulationObjects(sim,simthread) #Add Python steppables here from PySteppablesExamples import SteppableRegistry steppableRegistry=SteppableRegistry() from diffusion_2D_steppables import ConcentrationFieldDumperSteppable concentrationFieldDumperSteppable=ConcentrationFieldDumperSteppable(_simulator=sim,_frequency=100) steppableRegistry.registerSteppable(concentrationFieldDumperSteppable) CompuCellSetup.mainLoop(sim,simthread,steppableRegistry)
from os import environ from os import getcwd import string sys.path.append(environ["PYTHON_MODULE_PATH"]) import CompuCellSetup sim,simthread = CompuCellSetup.getCoreSimulationObjects() CompuCellSetup.initializeSimulationObjects(sim,simthread) import CompuCell #notice importing CompuCell to main script has to be done after call to getCoreSimulationObjects() #Add Python steppables here from PySteppablesExamples import SteppableRegistry steppableRegistry=SteppableRegistry() from CellManipulationSteppables import CellManipulationSteppable cellManipulationSteppable=CellManipulationSteppable(sim,10) steppableRegistry.registerSteppable(cellManipulationSteppable) # # # from CellManipulationSteppables import CellManipulationSteppableExplained # # # cellManipulationSteppableExplained=CellManipulationSteppableExplained(sim,10) # # # steppableRegistry.registerSteppable(cellManipulationSteppableExplained) CompuCellSetup.mainLoop(sim,simthread,steppableRegistry)
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 #### CC3D crashes when changeWatcherRegistry in one of these lines is not commented out; # changeWatcherRegistry=CompuCellSetup.getChangeWatcherRegistry(sim) steppableRegistry=SteppableRegistry() from steppables_drugspheroid import CispIC50VisualizationSteppable cispIC50VisualizationSteppable=CispIC50VisualizationSteppable (sim) steppableRegistry.registerSteppable(cispIC50VisualizationSteppable) # from steppables_drugspheroid import VolumeParamSteppable # volumeParamSteppable=VolumeParamSteppable(sim) # steppableRegistry.registerSteppable(volumeParamSteppable) from steppables_drugspheroid import SetCellDictionaries setCellDictionaries=SetCellDictionaries(sim) steppableRegistry.registerSteppable(setCellDictionaries) from steppables_drugspheroid import DiffusionSolverFESteeringCisplatinIV diffusionSolverFESteeringCisplatinIV=DiffusionSolverFESteeringCisplatinIV(sim) steppableRegistry.registerSteppable(diffusionSolverFESteeringCisplatinIV) # from steppables_drugspheroid import DiffusionSolverFESteeringCisplatinIP # diffusionSolverFESteeringCisplatinIP=DiffusionSolverFESteeringCisplatinIP(sim)
sys.path.append(environ["PYTHON_MODULE_PATH"]) import CompuCellSetup sim, simthread = CompuCellSetup.getCoreSimulationObjects() import CompuCell #Create extra player fields here or add attributes CompuCellSetup.initializeSimulationObjects(sim, simthread) #Add Python steppables here from PySteppablesExamples import SteppableRegistry steppableRegistry = SteppableRegistry() from wetFoamDrainageSteppables import FlexCellInitializer fci = FlexCellInitializer(_simulator=sim, _frequency=1) fci.addCellTypeParameters(_type=1, _count=80, _targetVolume=25, _lambdaVolume=10.0) fci.addCellTypeParameters(_type=2, _count=0, _targetVolume=5, _lambdaVolume=2.0) fci.setFractionOfWater(0.25) steppableRegistry.registerSteppable(fci) 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() import CompuCell #Create extra player fields here or add attributes CompuCellSetup.initializeSimulationObjects(sim,simthread) #Add Python steppables here from PySteppablesExamples import SteppableRegistry steppableRegistry=SteppableRegistry() from wetFoamDrainageSteppables import FlexCellInitializer fci=FlexCellInitializer(_simulator=sim,_frequency=1) fci.addCellTypeParameters(_type=1,_count=80,_targetVolume=25,_lambdaVolume=10.0) fci.addCellTypeParameters(_type=2,_count=0,_targetVolume=5,_lambdaVolume=2.0) fci.setFractionOfWater(0.25) steppableRegistry.registerSteppable(fci) 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() CompuCellSetup.initializeSimulationObjects(sim,simthread) import CompuCell #notice importing CompuCell to main script has to be done after call to getCoreSimulationObjects() #Add Python steppables here from PySteppablesExamples import SteppableRegistry steppableRegistry=SteppableRegistry() from clusterMitosisSteppables import VolumeParamSteppable volumeParamSteppable=VolumeParamSteppable(sim,10) steppableRegistry.registerSteppable(volumeParamSteppable) from clusterMitosisSteppables import MitosisSteppableClusters mitosisSteppable=MitosisSteppableClusters(sim,10) steppableRegistry.registerSteppable(mitosisSteppable) CompuCellSetup.mainLoop(sim,simthread,steppableRegistry)
sim,simthread = CompuCellSetup.getCoreSimulationObjects() import CompuCell #notice importing CompuCell to main script has to be done after call to getCoreSimulationObjects() #Create extra player fields here or add attributes CompuCellSetup.initializeSimulationObjects(sim,simthread) #Add Python steppables here from PySteppablesExamples import SteppableRegistry steppableRegistry=SteppableRegistry() from ExtraFieldsSteppables import ExtraFieldVisualizationSteppable extraFieldVisualizationSteppable=ExtraFieldVisualizationSteppable(_simulator=sim,_frequency=10) steppableRegistry.registerSteppable(extraFieldVisualizationSteppable) from ExtraFieldsSteppables import IdFieldVisualizationSteppable idFieldVisualizationSteppable=IdFieldVisualizationSteppable(_simulator=sim,_frequency=10) steppableRegistry.registerSteppable(idFieldVisualizationSteppable) from ExtraFieldsSteppables import VectorFieldVisualizationSteppable vectorFieldVisualizationSteppable=VectorFieldVisualizationSteppable(_simulator=sim,_frequency=10) steppableRegistry.registerSteppable(vectorFieldVisualizationSteppable) from ExtraFieldsSteppables import VectorFieldCellLevelVisualizationSteppable vectorFieldCellLevelVisualizationSteppable=VectorFieldCellLevelVisualizationSteppable(_simulator=sim,_frequency=10) steppableRegistry.registerSteppable(vectorFieldCellLevelVisualizationSteppable)