1 def configureSimulation(sim):
   2     import CompuCellSetup
   3     from XMLUtils import ElementCC3D
   4 
   5     cc3d=ElementCC3D("CompuCell3D")
   6     potts=cc3d.ElementCC3D("Potts")
   7     potts.ElementCC3D("Dimensions",{"x":100,"y":100,"z":1})
   8     potts.ElementCC3D("Steps",{},1000000)
   9     potts.ElementCC3D("Anneal",{},10)
  10     potts.ElementCC3D("DebugOutputFrequency",{},0)
  11     potts.ElementCC3D("Temperature",{},10)
  12     potts.ElementCC3D("LatticeType",{},"Hexagonal")
  13     potts.ElementCC3D("NeighborOrder",{},2)
  14     
  15 
  16     cellType=cc3d.ElementCC3D("Plugin",{"Name":"CellType"})
  17     cellType.ElementCC3D("CellType", {"TypeName":"Medium", "TypeId":"0"})
  18     cellType.ElementCC3D("CellType", {"TypeName":"CellOfType1", "TypeId":"1"})
  19     cellType.ElementCC3D("CellType", {"TypeName":"Apoptotic", "TypeId":"2"})
  20 
  21 
  22     volume=cc3d.ElementCC3D("Plugin",{"Name":"Volume"})
  23     
  24     surface=cc3d.ElementCC3D("Plugin",{"Name":"Surface"})
  25     
  26     cc3d.ElementCC3D("Plugin",{"Name":"NeighborTracker"})
  27 
  28 
  29     contact=cc3d.ElementCC3D("Plugin",{"Name":"Contact"})
  30     contact.ElementCC3D("Energy", {"Type1":"Medium", "Type2":"Medium"},0)
  31     contact.ElementCC3D("Energy", {"Type1":"CellOfType1", "Type2":"CellOfType1"},15)
  32     contact.ElementCC3D("Energy", {"Type1":"CellOfType1", "Type2":"Medium"},15)
  33     contact.ElementCC3D("Energy",{"Type1":"CellOfType1", "Type2":"Apoptotic"},5)
  34     contact.ElementCC3D("Energy", {"Type1":"Apoptotic", "Type2":"Medium"},7)
  35     contact.ElementCC3D("Energy", {"Type1":"Apoptotic", "Type2":"Apoptotic"},25)
  36     contact.ElementCC3D("NeighborOrder", {}, 2)
  37 
  38 
  39     blobInitializer=cc3d.ElementCC3D("Steppable",{"Type":"BlobInitializer"})
  40     
  41     blobInitializer.ElementCC3D("Width",{},5)
  42     blobInitializer.ElementCC3D("Radius",{},40)
  43 
  44 
  45     CompuCellSetup.setSimulationXMLDescription(cc3d)
  46     
  47 import sys
  48 from os import environ
  49 import string
  50 sys.path.append(environ["PYTHON_MODULE_PATH"])
  51     
  52 import CompuCellSetup
  53 
  54 ##CompuCellSetup.simulationPaths.simulationPythonScriptName = "something"
  55 sim,simthread = CompuCellSetup.getCoreSimulationObjects()
  56 configureSimulation(sim)
  57 
  58 import CompuCell
  59 CompuCellSetup.initializeSimulationObjects(sim,simthread)
  60 
  61 
  62 pyAttributeAdderDict,dictAdder=CompuCellSetup.attachDictionaryToCells(sim)
  63 
  64 from PySteppables import SteppableRegistry
  65 steppableRegistry=SteppableRegistry()
  66 
  67 from SteppablePresentation import CellPropertyandModifier
  68 steppableRegistry.registerSteppable(CellPropertyandModifier(_simulator=sim,_frequency=500))
  69 
  70 ##from SteppablePresentation import CellTypeVisualizer
  71 ##steppableRegistry.registerSteppable(CellTypeVisualizer(_simulator=sim,_frequency=1))
  72 ##
  73 ##from SteppablePresentation import Output
  74 ##steppableRegistry.registerSteppable(Output(_simulator=sim,_frequency=5))
  75 ##
  76 ##from SteppablePresentation import ApoptosisCheck
  77 ##steppableRegistry.registerSteppable(ApoptosisCheck(_simulator=sim,_frequency=1))
  78 ##
  79 ##from SteppablePresentation import Apoptosis
  80 ##steppableRegistry.registerSteppable(Apoptosis(_simulator=sim,_frequency=1))
  81 ##
  82 ##from SteppablePresentation import PropertySwitcher
  83 ##steppableRegistry.registerSteppable(PropertySwitcher(_simulator=sim,_frequency=1))
  84 ##
  85 ##from SteppablePresentation import MassConservationViaMacrophage
  86 ##steppableRegistry.registerSteppable(MassConservationViaMacrophage(_simulator=sim,_frequency=5))
  87 ##
  88 ##from SteppablePresentation import Mitosis
  89 ##steppableRegistry.registerSteppable(Mitosis(_simulator=sim,_frequency=10))
  90 
  91 
  92 CompuCellSetup.mainLoop(sim,simthread,steppableRegistry)