#typeChangeWatcher=CompuCell.TypeChangeWatcherPyWrapper() #from PyPluginsExamples import TypeChangeWatcherExample #typeChangeWatcherExample=TypeChangeWatcherExample(typeChangeWatcher) #typeChangeWatcher.registerPyTypeChangeWatcher(typeChangeWatcherExample) #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
from os import environ from os import getcwd import string 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)
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)
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 #### 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
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)
#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
#### 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 PyPluginsExamples import TypeChangeWatcherExample #typeChangeWatcherExample=TypeChangeWatcherExample(typeChangeWatcher) #typeChangeWatcher.registerPyTypeChangeWatcher(typeChangeWatcherExample) #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 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)
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)
# steppableRegistry.registerSteppable(proteinExpression)
from steppableBasedMitosisSteppables_control import SecretionCellSteppable
secretionCellSteppable=SecretionCellSteppable(sim,10)
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)
#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 #### 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)
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)
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)
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 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
