def configureSimulation(sim):
import CompuCellSetup
from XMLUtils import ElementCC3D
cc3d = ElementCC3D("CompuCell3D")
potts = cc3d.ElementCC3D("Potts")
potts.ElementCC3D("Dimensions", {"x": 55, "y": 55, "z": 1})
potts.ElementCC3D("Steps", {}, 1000)
potts.ElementCC3D("Temperature", {}, 0)
potts.ElementCC3D("Flip2DimRatio", {}, 0.0)
cellType = cc3d.ElementCC3D("Plugin", {"Name": "CellType"})
cellType.ElementCC3D("CellType", {"TypeName": "Medium", "TypeId": "0"})
flexDiffSolver = cc3d.ElementCC3D("Steppable",
{"Type": "DiffusionSolverFE"})
diffusionField = flexDiffSolver.ElementCC3D("DiffusionField")
diffusionData = diffusionField.ElementCC3D("DiffusionData")
diffusionData.ElementCC3D("FieldName", {}, "FGF")
diffusionData.ElementCC3D("DiffusionConstant", {}, 0.10)
diffusionData.ElementCC3D("DecayConstant", {}, 0.0)
diffusionData.ElementCC3D("ConcentrationFileName", {},
"Simulation/diffusion_2D.pulse.txt")
CompuCellSetup.setSimulationXMLDescription(cc3d)
def saveAsXML(self, _fileName):
print '_fileName=',_fileName
import XMLUtils
from XMLUtils import ElementCC3D
import Version
xml2ObjConverter = XMLUtils.Xml2Obj()
plSetElem = ElementCC3D('PlayerSettings',{'version':Version.getVersionAsString()})
# print '\n\n\nself.__typeSettingDictDict.keys() = ', self.__typeSettingDictDict.keys()
# print '__typeSettingDictDict=',self.__typeSettingDictDict
for typeName , settingDict in self.__typeSettingDictDict.iteritems():
typeContainerElem = plSetElem.ElementCC3D( 'Settings', {'Type':typeName} )
# print 'typeName=',typeName
# if typeName =='FieldParams':
# print 'typeName=',typeName, ' settingDict=',settingDict
for settingName, setting in sorted(settingDict.iteritems()): # keys are sorted before outputting to XML
# if settingName=='ShowPlotAxes':
#
# try:
# print 'settingName=', settingName, ' setting=', setting, 'typeContainerElem=',typeName
# except:
# pass
setting.toXML(typeContainerElem)
fileFullPath = os.path.abspath(_fileName)
plSetElem.CC3DXMLElement.saveXML(fileFullPath)
def writeScreenshotDescriptionFile(self,_fileName):
from XMLUtils import ElementCC3D
screenshotFileElement=ElementCC3D("CompuCell3DScreenshots")
for name in self.screenshotDataDict:
scrData=self.screenshotDataDict[name]
if scrData.spaceDimension=="2D":
scrDescElement=screenshotFileElement.ElementCC3D("ScreenshotDescription")
scrDescElement.ElementCC3D("Dimension", {}, str(scrData.spaceDimension))
scrDescElement.ElementCC3D("Plot", {"PlotType":str(scrData.plotData[1]),"PlotName":str(scrData.plotData[0])})
scrDescElement.ElementCC3D("Projection", {"ProjectionPlane":scrData.projection,"ProjectionPosition":str(scrData.projectionPosition)})
scrDescElement.ElementCC3D("Size", {"Width":str(scrData.screenshotGraphicsWidget.size().width()),"Height":str(scrData.screenshotGraphicsWidget.size().height())})
if scrData.spaceDimension=="3D":
scrDescElement=screenshotFileElement.ElementCC3D("ScreenshotDescription")
scrDescElement.ElementCC3D("Dimension", {}, str(scrData.spaceDimension))
scrDescElement.ElementCC3D("Plot", {"PlotType":str(scrData.plotData[1]),"PlotName":str(scrData.plotData[0])})
scrDescElement.ElementCC3D("CameraClippingRange", {"Min":str(scrData.clippingRange[0]),"Max":str(scrData.clippingRange[1])})
scrDescElement.ElementCC3D("CameraFocalPoint", {"x":str(scrData.focalPoint[0]),"y":str(scrData.focalPoint[1]),"z":str(scrData.focalPoint[2])})
scrDescElement.ElementCC3D("CameraPosition", {"x":str(scrData.position[0]),"y":str(scrData.position[1]),"z":str(scrData.position[2])})
scrDescElement.ElementCC3D("CameraViewUp", {"x":str(scrData.viewUp[0]),"y":str(scrData.viewUp[1]),"z":str(scrData.viewUp[2])})
scrDescElement.ElementCC3D("Size", {"Width":str(scrData.screenshotGraphicsWidget.size().width()),"Height":str(scrData.screenshotGraphicsWidget.size().height())})
screenshotFileElement.CC3DXMLElement.saveXML(str(_fileName))
def writeXMLDescriptionFile(self,_fileName=""):
from os.path import join
"""
This function will write XML description of the stored fields. It has to be called after
initialization of theCMLFieldHandler is completed
"""
import CompuCellSetup
latticeTypeStr = CompuCellSetup.ExtractLatticeType()
if latticeTypeStr=="":
latticeTypeStr = "Square"
typeIdTypeNameDict = CompuCellSetup.ExtractTypeNamesAndIds()
print "typeIdTypeNameDict",typeIdTypeNameDict
from XMLUtils import ElementCC3D
dim = self.sim.getPotts().getCellFieldG().getDim()
numberOfSteps = self.sim.getNumSteps()
latticeDataXMLElement=ElementCC3D("CompuCell3DLatticeData",{"Version":"1.0"})
latticeDataXMLElement.ElementCC3D("Dimensions",{"x":str(dim.x),"y":str(dim.y),"z":str(dim.z)})
latticeDataXMLElement.ElementCC3D("Lattice",{"Type":latticeTypeStr})
latticeDataXMLElement.ElementCC3D("Output",{"Frequency":str(self.outputFrequency),"NumberOfSteps":str(numberOfSteps),"CoreFileName":self.outputFileCoreName,"Directory":self.outputDirName})
#output information about cell type names and cell ids. It is necessary during generation of the PIF files from VTK output
for typeId in typeIdTypeNameDict.keys():
latticeDataXMLElement.ElementCC3D("CellType",{"TypeName":str(typeIdTypeNameDict[typeId]),"TypeId":str(typeId)})
fieldsXMLElement=latticeDataXMLElement.ElementCC3D("Fields")
for fieldName in self.fieldTypes.keys():
fieldsXMLElement.ElementCC3D("Field",{"Name":fieldName,"Type":self.fieldTypes[fieldName]})
# writing XML description to the disk
if _fileName!="":
latticeDataXMLElement.CC3DXMLElement.saveXML(str(_fileName))
else:
latticeDataFileName = join(self.outputDirName,self.outputFileCoreName+"LDF.dml")
latticeDataXMLElement.CC3DXMLElement.saveXML(str(latticeDataFileName))
def configureSimulation(sim):
import CompuCellSetup
from XMLUtils import ElementCC3D
cc3d = ElementCC3D("CompuCell3D")
potts = cc3d.ElementCC3D("Potts")
potts.ElementCC3D("Dimensions", {"x": 100, "y": 100, "z": 1})
potts.ElementCC3D("Steps", {}, 10000)
potts.ElementCC3D("Temperature", {}, 5)
potts.ElementCC3D("NeighborOrder", {}, 2)
potts.ElementCC3D("Boundary_x", {}, "Periodic")
cellType = cc3d.ElementCC3D("Plugin", {"Name": "CellType"})
cellType.ElementCC3D("CellType", {"TypeName": "Medium", "TypeId": "0"})
cellType.ElementCC3D("CellType", {"TypeName": "Body1", "TypeId": "1"})
cellType.ElementCC3D("CellType", {"TypeName": "Body2", "TypeId": "2"})
cellType.ElementCC3D("CellType", {"TypeName": "Body3", "TypeId": "3"})
volume = cc3d.ElementCC3D("Plugin", {"Name": "Volume"})
volume.ElementCC3D("TargetVolume", {}, 25)
volume.ElementCC3D("LambdaVolume", {}, 4.0)
contact = cc3d.ElementCC3D("Plugin", {"Name": "Contact"})
contact.ElementCC3D("Energy", {"Type1": "Medium", "Type2": "Medium"}, 0)
contact.ElementCC3D("Energy", {"Type1": "Body1", "Type2": "Body1"}, 16)
contact.ElementCC3D("Energy", {"Type1": "Body1", "Type2": "Medium"}, 4)
contact.ElementCC3D("Energy", {"Type1": "Body2", "Type2": "Body2"}, 16)
contact.ElementCC3D("Energy", {"Type1": "Body2", "Type2": "Medium"}, 4)
contact.ElementCC3D("Energy", {"Type1": "Body3", "Type2": "Body3"}, 16)
contact.ElementCC3D("Energy", {"Type1": "Body3", "Type2": "Medium"}, 4)
contact.ElementCC3D("Energy", {"Type1": "Body1", "Type2": "Body2"}, 16)
contact.ElementCC3D("Energy", {"Type1": "Body1", "Type2": "Body3"}, 16)
contact.ElementCC3D("Energy", {"Type1": "Body2", "Type2": "Body3"}, 16)
contact.ElementCC3D("neighborOrder", {}, 2)
centerOfMass = cc3d.ElementCC3D("Plugin", {"Name": "CenterOfMass"})
elasticityTracker = cc3d.ElementCC3D("Plugin",
{"Name": "ElasticityTracker"})
elasticityTracker.ElementCC3D("IncludeType", {}, "Body1")
elasticityTracker.ElementCC3D("IncludeType", {}, "Body2")
elasticityTracker.ElementCC3D("IncludeType", {}, "Body3")
elasticityEnergy = cc3d.ElementCC3D("Plugin", {"Name": "ElasticityEnergy"})
elasticityEnergy.ElementCC3D("Local", {})
# elasticityEnergy.ElementCC3D("LambdaElasticity",{},200.0)
# elasticityEnergy.ElementCC3D("TargetLengthElasticity",{},6)
externalPotential = cc3d.ElementCC3D("Plugin",
{"Name": "ExternalPotential"})
externalPotential.ElementCC3D("Lambda", {"x": -10, "y": 0, "z": 0})
pifInitializer = cc3d.ElementCC3D("Steppable", {"Type": "PIFInitializer"})
pifInitializer.ElementCC3D("PIFName", {}, "Simulation/elasticitytest.piff")
CompuCellSetup.setSimulationXMLDescription(cc3d)
def configureSimulation(sim):
import CompuCellSetup
from XMLUtils import ElementCC3D
cc3d = ElementCC3D("CompuCell3D")
potts = cc3d.ElementCC3D("Potts")
potts.ElementCC3D("Dimensions", {"x": 100, "y": 100, "z": 1})
potts.ElementCC3D("Steps", {}, 1000)
potts.ElementCC3D("Temperature", {}, 10)
potts.ElementCC3D("NeighborOrder", {}, 2)
cellType = cc3d.ElementCC3D("Plugin", {"Name": "CellType"})
cellType.ElementCC3D("CellType", {"TypeName": "Medium", "TypeId": "0"})
cellType.ElementCC3D("CellType", {"TypeName": "Condensing", "TypeId": "1"})
cellType.ElementCC3D("CellType", {
"TypeName": "NonCondensing",
"TypeId": "2"
})
volume = cc3d.ElementCC3D("Plugin", {"Name": "Volume"})
volume.ElementCC3D("TargetVolume", {}, 25)
volume.ElementCC3D("LambdaVolume", {}, 2.0)
contact = cc3d.ElementCC3D("Plugin", {"Name": "Contact"})
contact.ElementCC3D("Energy", {"Type1": "Medium", "Type2": "Medium"}, 0)
contact.ElementCC3D("Energy", {
"Type1": "NonCondensing",
"Type2": "NonCondensing"
}, 16)
contact.ElementCC3D("Energy", {
"Type1": "Condensing",
"Type2": "Condensing"
}, 2)
contact.ElementCC3D("Energy", {
"Type1": "NonCondensing",
"Type2": "Condensing"
}, 11)
contact.ElementCC3D("Energy", {
"Type1": "NonCondensing",
"Type2": "Medium"
}, 16)
contact.ElementCC3D("Energy", {
"Type1": "Condensing",
"Type2": "Medium"
}, 16)
blobInitializer = cc3d.ElementCC3D("Steppable",
{"Type": "BlobInitializer"})
blobInitializer.ElementCC3D("Gap", {}, 0)
blobInitializer.ElementCC3D("Width", {}, 5)
blobInitializer.ElementCC3D("CellSortInit", {}, "yes")
blobInitializer.ElementCC3D("Radius", {}, 40)
CompuCellSetup.setSimulationXMLDescription(cc3d)
def __init__(self, simulationDir, simulationName):
self.simulationDir = simulationDir
self.simulationName = simulationName
self.fileName = os.path.join(str(self.simulationDir), str(self.simulationName) + ".xml")
self.generalPropertiesDict = {}
self.cellTypeTable = [["Medium", False]]
self.cc3d = ElementCC3D("CompuCell3D", {"version": "3.6.0"})
self.afMolecules = []
self.afFormula = 'min(Molecule1,Molecule2)'
self.cmcCadherins = []
self.chemFieldsTable = []
self.secretionTable = {}
self.chemotaxisTable = {}
def saveAsXML(self, _fileName):
import XMLUtils
from XMLUtils import ElementCC3D
import Version
xml2ObjConverter = XMLUtils.Xml2Obj()
plSetElem = ElementCC3D('PlayerSettings',
{'version': Version.getVersionAsString()})
# print '\n\n\nself.__typeSettingDictDict.keys() = ', self.__typeSettingDictDict.keys()
for typeName, settingDict in self.__typeSettingDictDict.iteritems():
typeContainerElem = plSetElem.ElementCC3D('Settings',
{'Type': typeName})
for settingName, setting in sorted(settingDict.iteritems(
)): # keys are sorted before outputting to XML
setting.toXML(typeContainerElem)
fileFullPath = os.path.abspath(_fileName)
plSetElem.CC3DXMLElement.saveXML(fileFullPath)
def configureSimulation(sim):
import CompuCellSetup
from XMLUtils import ElementCC3D
cc3d=ElementCC3D("CompuCell3D")
Globals=cc3d.ElementCC3D("Globals")
for key in sorted(globals(), key=str.lower):
if key not in Old:
Globals.ElementCC3D(key,{},globals()[key])
keys.append(key)
md=cc3d.ElementCC3D("Metadata")
md.ElementCC3D("VirtualProcessingUnits",{"ThreadsPerVPU":2},2)
md.ElementCC3D("DebugOutputFrequency",{},0)
potts=cc3d.ElementCC3D("Potts")
potts.ElementCC3D("Dimensions",{"x":Lx,"y":Ly,"z":Lz})
potts.ElementCC3D("Steps",{},Time)
potts.ElementCC3D("Temperature",{},int(T))
potts.ElementCC3D("NeighborOrder",{},2)
#CELL TYPES:
cellType=cc3d.ElementCC3D("Plugin",{"Name":"CellType"})
cellType.ElementCC3D("CellType", {"TypeName":"Medium","TypeId":"0"})
cellType.ElementCC3D("CellType", {"TypeName":"cyto", "TypeId":"1"})
#CELL COLORS:
playSet=cc3d.ElementCC3D("Plugin",{"Name":"PlayerSettings"})
playSet.ElementCC3D("Cell", {"Type":"0", "Color":"#000000"}) #black
playSet.ElementCC3D("Cell", {"Type":"1", "Color":"#FFFFFF"}) #white
#CONTACT ENERGIES:
contact=cc3d.ElementCC3D("Plugin",{"Name":"Contact"})
contact.ElementCC3D("Energy", {"Type1":"Medium", "Type2":"Medium"},0)
contact.ElementCC3D("Energy", {"Type1":"Medium", "Type2":"cyto" },10)
#
contact.ElementCC3D("Energy", {"Type1":"cyto", "Type2":"cyto"},10)
#-neighbor order
contact.ElementCC3D("NeighborOrder",{},nOrder)
CompuCellSetup.setSimulationXMLDescription(cc3d)
def generateXML(self):
from XMLUtils import ElementCC3D
mElement = ElementCC3D('Potts')
mElement.addComment("newline")
mElement.addComment("Basic properties of CPM (GGH) algorithm")
mElement.ElementCC3D(
"Dimensions", {
"x": self.xDimSB.value(),
"y": self.yDimSB.value(),
"z": self.zDimSB.value()
})
mElement.ElementCC3D("Steps", {}, self.mcsSB.value())
if self.anneal_mcsSB.value() != 0:
mElement.ElementCC3D("Anneal", {}, self.anneal_mcsSB.value())
mElement.ElementCC3D("Temperature", {},
float(str(self.membraneFluctuationsLE.text())))
mElement.ElementCC3D("NeighborOrder", {}, self.neighborOrderSB.value())
if str(self.latticeTypeCB.currentText()) != "Square":
mElement.ElementCC3D("LatticeType", {},
str(self.latticeTypeCB.currentText()))
for dim_name_bc_widget, dim_name in [(self.xbcCB, 'x'),
(self.ybcCB, 'y'),
(self.zbcCB, 'z')]:
try:
if str(dim_name_bc_widget.currentText()) == 'Periodic':
mElement.ElementCC3D('Boundary_' + dim_name, {},
'Periodic')
except KeyError:
pass
# mElement.ElementCC3D('Boundary_' + dim_name, {}, 'NoFlux')
if self.auto_gen_rand_seed_CB.isChecked():
mElement.ElementCC3D('RandomSeed', {}, randint(0, sys.maxint))
return mElement
def writeXMLDescriptionFile(self,_fileName=""):
"""
This function will write XML description of the stored fields. It has to be called after
initializetion of theCMLFieldHandler is completed
"""
from XMLUtils import ElementCC3D
dim=self.sim.getPotts().getCellFieldG().getDim()
latticeDataXMLElement=ElementCC3D("CompuCell3DLatticeData",{"Version":"1.0"})
latticeDataXMLElement.ElementCC3D("Dimensions",{"x":str(dim.x),"y":str(dim.y),"z":str(dim.z)})
latticeDataXMLElement.ElementCC3D("Output",{"Frequency":str(self.outputFrequency),"CoreFileName":self.outputFileCoreName,"Directory":self.outputDirName})
fieldsXMLElement=latticeDataXMLElement.ElementCC3D("Fields")
for fieldName in self.fieldTypes.keys():
fieldsXMLElement.ElementCC3D("Field",{"Name":fieldName,"Type":self.fieldTypes[fieldName]})
# writing XML description to the disk
if _fileName!="":
latticeDataXMLElement.CC3DXMLElement.saveXML(str(_fileName))
else:
latticeDataFileName=os.path.join(self.outputDirName,self.outputFileCoreName+"LDF.dml")
latticeDataXMLElement.CC3DXMLElement.saveXML(str(latticeDataFileName))
def configureSimulation(sim):
import CompuCellSetup
from XMLUtils import ElementCC3D
cc3d = ElementCC3D("CompuCell3D")
potts = cc3d.ElementCC3D("Potts")
potts.ElementCC3D("Dimensions", {"x": 42, "y": 42, "z": 1})
potts.ElementCC3D("Steps", {}, 10000)
potts.ElementCC3D("Anneal", {}, 10)
potts.ElementCC3D("Temperature", {}, 10)
potts.ElementCC3D("NeighborOrder", {}, 2)
potts.ElementCC3D("Boundary_x", {}, "Periodic")
potts.ElementCC3D("Boundary_y", {}, "Periodic")
cellType = cc3d.ElementCC3D("Plugin", {"Name": "CellType"})
cellType.ElementCC3D("CellType", {"TypeName": "Medium", "TypeId": "0"})
cellType.ElementCC3D("CellType", {"TypeName": "TypeA", "TypeId": "1"})
contact = cc3d.ElementCC3D("Plugin", {"Name": "Contact"})
contact.ElementCC3D("Energy", {"Type1": "Medium", "Type2": "Medium"}, 0)
contact.ElementCC3D("Energy", {"Type1": "Medium", "Type2": "TypeA"}, 5)
contact.ElementCC3D("Energy", {"Type1": "TypeA", "Type2": "TypeA"}, 5)
contact.ElementCC3D("NeighborOrder", {}, 4)
vp = cc3d.ElementCC3D("Plugin", {"Name": "Volume"})
vp.ElementCC3D("TargetVolume", {}, 49)
vp.ElementCC3D("LambdaVolume", {}, 5)
ntp = cc3d.ElementCC3D("Plugin", {"Name": "NeighborTracker"})
uipd = cc3d.ElementCC3D("Steppable", {"Type": "UniformInitializer"})
region = uipd.ElementCC3D("Region")
region.ElementCC3D("BoxMin", {"x": 0, "y": 0, "z": 0})
region.ElementCC3D("BoxMax", {"x": 42, "y": 42, "z": 1})
region.ElementCC3D("Types", {}, "TypeA")
region.ElementCC3D("Width", {}, 7)
CompuCellSetup.setSimulationXMLDescription(cc3d)
def writeCC3DFileFormat(self,_fileName):
# print '\n\n\n will write ',_fileName
from XMLUtils import ElementCC3D
csd=self.cc3dSimulationData
simulationElement = ElementCC3D("Simulation",{"version":csd.version})
if csd.xmlScriptResource.path!="":
elName,attributeDict,path = self.formatResourceElement(csd.xmlScriptResource,"XMLScript")
# print 'ADDING XML ',path
simulationElement.ElementCC3D(elName,attributeDict,path)
if csd.pythonScriptResource.path!="":
elName,attributeDict,path = self.formatResourceElement(csd.pythonScriptResource,"PythonScript")
# print 'ADDING PYTHON ',path
simulationElement.ElementCC3D(elName,attributeDict,path)
if csd.pifFileResource.path!="":
elName,attributeDict,path = self.formatResourceElement(csd.pifFileResource,"PIFFile")
# print 'ADDING PIF ',path
simulationElement.ElementCC3D(elName,attributeDict,path)
if csd.windowScriptResource.path!="":
elName,attributeDict,path = self.formatResourceElement(csd.windowScriptResource,"WindowScript")
simulationElement.ElementCC3D(elName,attributeDict,path)
resourcesDict={}
#storing resources in a dictionary using resource type as a key
for resourceKey, resource in csd.resources.iteritems():
if resource.type=="PIFFile" and csd.pifFileResource.path==resource.path:
print MODULENAME,"IGNORING RESOURCE =",resource.path
continue
try:
resourcesDict[resource.type].append(resource)
except LookupError,e:
def configureSimulation(sim, Lx, Ly, Lz, Temp, Time, NOrder, CNOrder,
debugFreq):
import CompuCellSetup
from XMLUtils import ElementCC3D
CompuCell3DElement = ElementCC3D("CompuCell3D", {"Version": "3.7.5"})
# Basic properties of CPM (GGH) algorithm
potts = CompuCell3DElement.ElementCC3D("Potts")
potts.ElementCC3D("Dimensions", {"x": 500, "y": 500, "z": 10})
potts.ElementCC3D("Temperature", {}, 50)
potts.ElementCC3D("Steps", {}, Time)
potts.ElementCC3D("NeighborOrder", {}, 1)
potts.ElementCC3D("DebugOutputFrequency", {}, debugFreq)
# Setting periodic boundary conditions to all directions
potts.ElementCC3D("Boundary_x", {}, "Periodic")
potts.ElementCC3D("Boundary_y", {}, "Periodic")
potts.ElementCC3D("Boundary_z", {}, "Periodic")
# Cell Types -> Epidermis, Progenitors, PPap, QPap, PRet, QRet, Adipocytes, ECM, Lumen
cellType = CompuCell3DElement.ElementCC3D("Plugin", {"Name": "CellType"})
cellType.ElementCC3D("CellType", {"TypeName": "Medium", "TypeId": 0})
cellType.ElementCC3D("CellType", {"TypeName": "Epidermis", "TypeId": 1})
cellType.ElementCC3D("CellType", {"TypeName": "Progenitors", "TypeId": 2})
cellType.ElementCC3D("CellType", {"TypeName": "PPap", "TypeId": 3})
cellType.ElementCC3D("CellType", {"TypeName": "QPap", "TypeId": 4})
cellType.ElementCC3D("CellType", {"TypeName": "PRet", "TypeId": 5})
cellType.ElementCC3D("CellType", {"TypeName": "QRet", "TypeId": 6})
cellType.ElementCC3D("CellType", {"TypeName": "Adipocytes", "TypeId": 7})
cellType.ElementCC3D("CellType", {"TypeName": "ECM", "TypeId": 8})
cellType.ElementCC3D("CellType", {"TypeName": "Lumen", "TypeId": 9})
cellType.ElementCC3D("CellType", {"TypeName": "MyoF", "TypeId": 10})
cellType.ElementCC3D("CellType", {"TypeName": "QMyoF", "TypeId": 11})
cellType.ElementCC3D("CellType", {"TypeName": "BC", "TypeId": 12})
cellType.ElementCC3D("CellType", {"TypeName": "IC", "TypeId": 13})
cellType.ElementCC3D("CellType", {"TypeName": "Fatty", "TypeId": 14})
# CELL COLORS --> not working
cellColor = CompuCell3DElement.ElementCC3D("Plugin",
{"Name": "PlayerSettings"})
cellColor.ElementCC3D("Cell", {
"Type": 0,
"Color": "#000000"
}) # Black -> Medium
cellColor.ElementCC3D("Cell", {
"Type": 1,
"Color": "#008000"
}) # Green -> Epidermis
cellColor.ElementCC3D("Cell", {
"Type": 2,
"Color": "#0000FF"
}) # Blue -> Progenitors
cellColor.ElementCC3D("Cell", {
"Type": 3,
"Color": "#FF0000"
}) # Red -> PPap
cellColor.ElementCC3D("Cell", {
"Type": 4,
"Color": "#990000"
}) # Dark red -> QPap
cellColor.ElementCC3D("Cell", {
"Type": 5,
"Color": "#FFFF00"
}) # Yellow -> PRet
cellColor.ElementCC3D("Cell", {
"Type": 6,
"Color": "#CCCC00"
}) # Dark Yellow -> QRet
cellColor.ElementCC3D("Cell", {
"Type": 7,
"Color": "#00E6E6"
}) # Light blue -> Adipocytes
cellColor.ElementCC3D("Cell", {
"Type": 8,
"Color": "#8B1A89"
}) # Purple -> ECM
cellColor.ElementCC3D("Cell", {
"Type": 9,
"Color": "#D3D3D3"
}) # Light grey -> Lumen
cellColor.ElementCC3D("Cell", {
"Type": 10,
"Color": "#D3D3D3"
}) # Light grey -> MyoF
cellColor.ElementCC3D("Cell", {
"Type": 11,
"Color": "#FF0000"
}) # Red -> BC
cellColor.ElementCC3D("Cell", {
"Type": 12,
"Color": "#FF0000"
}) # Red -> IC
cellColor.ElementCC3D("Cell", {
"Type": 13,
"Color": "#00E6E6"
}) # Light blue -> Fatty
# cellColor.ElementCC3D("TypesInvisibleIn3D",{"Types":"0,9"}) # Don't show Medium and Lumen
cellColor.ElementCC3D("VisualControl", {
"ScreenshotFrequency": 250,
"ScreenUpdateFrequency": 10
})
# # Cell Colors
# cellColor=CompuCell3DElement.ElementCC3D("Plugin",{"Name":"PlayerSettings"})
# cellColor.ElementCC3D("Cell",{"Type":0,"Color":"#000000"}) # Black -> Medium
# cellColor.ElementCC3D("Cell",{"Type":1,"Color":"black"}) # Green -> Epidermis
# cellColor.ElementCC3D("Cell",{"Type":2,"Color":"blue"}) # Blue -> Progenitors
# cellColor.ElementCC3D("Cell",{"Type":3,"Color":"green"}) # Red -> PPap
# cellColor.ElementCC3D("Cell",{"Type":4,"Color":"#990000"}) # Dark red -> QPap
# cellColor.ElementCC3D("Cell",{"Type":5,"Color":"cyan"}) # Yellow -> PRet
# cellColor.ElementCC3D("Cell",{"Type":6,"Color":"#CCCC00"}) # Dark Yellow -> QRet
# cellColor.ElementCC3D("Cell",{"Type":7,"Color":"#00E6E6"}) # Light blue -> Adipocytes
# cellColor.ElementCC3D("Cell",{"Type":8,"Color":"#8B1A89"}) # Purple -> ECM
# cellColor.ElementCC3D("Cell",{"Type":9,"Color":"#D3D3D3"}) # Light grey -> Lumen
# cellColor.ElementCC3D("Cell",{"Type":10,"Color":"#D3D3D3"}) # Light grey -> MyoF
# cellColor.ElementCC3D("Cell",{"Type":11,"Color":"red"}) # Red -> BC
# cellColor.ElementCC3D("Cell",{"Type":12,"Color":"red"}) # Red -> BCtop
# # cellColor.ElementCC3D("TypesInvisibleIn3D",{"Types":"0,9"}) # Don't show Medium and Lumen
# cellColor.ElementCC3D("VisualControl",{"ScreenshotFrequency":250,"ScreenUpdateFrequency":10})
# Specification of adhesion energies
contact = CompuCell3DElement.ElementCC3D("Plugin", {"Name": "Contact"})
# #MEDIUM
# contact.ElementCC3D("Energy",{"Type1":"Medium","Type2":"Medium"},0)
# contact.ElementCC3D("Energy",{"Type1":"Medium","Type2":"Epidermis"},2)
# contact.ElementCC3D("Energy",{"Type1":"Medium","Type2":"Progenitors"},100)
# contact.ElementCC3D("Energy",{"Type1":"Medium","Type2":"PPap"},100)
# contact.ElementCC3D("Energy",{"Type1":"Medium","Type2":"QPap"},100)
# contact.ElementCC3D("Energy",{"Type1":"Medium","Type2":"PRet"},100)
# contact.ElementCC3D("Energy",{"Type1":"Medium","Type2":"QRet"},100)
# contact.ElementCC3D("Energy",{"Type1":"Medium","Type2":"Adipocytes"},100)
# contact.ElementCC3D("Energy",{"Type1":"Medium","Type2":"ECM"},100)
# contact.ElementCC3D("Energy",{"Type1":"Medium","Type2":"Lumen"},100)
# #ECM
# contact.ElementCC3D("Energy",{"Type1":"ECM","Type2":"ECM"},1)
# contact.ElementCC3D("Energy",{"Type1":"ECM","Type2":"Epidermis"},50)
# contact.ElementCC3D("Energy",{"Type1":"ECM","Type2":"Progenitors"},20)
# contact.ElementCC3D("Energy",{"Type1":"ECM","Type2":"PPap"},2)
# contact.ElementCC3D("Energy",{"Type1":"ECM","Type2":"QPap"},20)
# contact.ElementCC3D("Energy",{"Type1":"ECM","Type2":"PRet"},2)
# contact.ElementCC3D("Energy",{"Type1":"ECM","Type2":"QRet"},1)
# contact.ElementCC3D("Energy",{"Type1":"ECM","Type2":"Adipocytes"},50)
# contact.ElementCC3D("Energy",{"Type1":"ECM","Type2":"Lumen"},20)
# #EPIDERMIS
# contact.ElementCC3D("Energy",{"Type1":"Epidermis","Type2":"Epidermis"},2)
# contact.ElementCC3D("Energy",{"Type1":"Epidermis","Type2":"Progenitors"},5)
# contact.ElementCC3D("Energy",{"Type1":"Epidermis","Type2":"PPap"},10)
# contact.ElementCC3D("Energy",{"Type1":"Epidermis","Type2":"QPap"},10)
# contact.ElementCC3D("Energy",{"Type1":"Epidermis","Type2":"PRet"},20)
# contact.ElementCC3D("Energy",{"Type1":"Epidermis","Type2":"QRet"},20)
# contact.ElementCC3D("Energy",{"Type1":"Epidermis","Type2":"Adipocytes"},100)
# contact.ElementCC3D("Energy",{"Type1":"Epidermis","Type2":"Lumen"},100)
# #PROGENITORS
# contact.ElementCC3D("Energy",{"Type1":"Progenitors","Type2":"Progenitors"},10)
# contact.ElementCC3D("Energy",{"Type1":"Progenitors","Type2":"PPap"},10)
# contact.ElementCC3D("Energy",{"Type1":"Progenitors","Type2":"QPap"},10)
# contact.ElementCC3D("Energy",{"Type1":"Progenitors","Type2":"PRet"},10)
# contact.ElementCC3D("Energy",{"Type1":"Progenitors","Type2":"QRet"},10)
# contact.ElementCC3D("Energy",{"Type1":"Progenitors","Type2":"Adipocytes"},10)
# contact.ElementCC3D("Energy",{"Type1":"Progenitors","Type2":"Lumen"},100)
# #PPAP
# contact.ElementCC3D("Energy",{"Type1":"PPap","Type2":"PPap"},20)
# contact.ElementCC3D("Energy",{"Type1":"PPap","Type2":"QPap"},10)
# contact.ElementCC3D("Energy",{"Type1":"PPap","Type2":"PRet"},10)
# contact.ElementCC3D("Energy",{"Type1":"PPap","Type2":"QRet"},20)
# contact.ElementCC3D("Energy",{"Type1":"PPap","Type2":"Adipocytes"},100)
# contact.ElementCC3D("Energy",{"Type1":"PPap","Type2":"Lumen"},100)
# #QPAP
# contact.ElementCC3D("Energy",{"Type1":"QPap","Type2":"QPap"},10)
# contact.ElementCC3D("Energy",{"Type1":"QPap","Type2":"PRet"},20)
# contact.ElementCC3D("Energy",{"Type1":"QPap","Type2":"QRet"},10)
# contact.ElementCC3D("Energy",{"Type1":"QPap","Type2":"Adipocytes"},100)
# contact.ElementCC3D("Energy",{"Type1":"QPap","Type2":"Lumen"},100)
# #PRET
# contact.ElementCC3D("Energy",{"Type1":"PRet","Type2":"PRet"},10)
# contact.ElementCC3D("Energy",{"Type1":"PRet","Type2":"QRet"},10)
# contact.ElementCC3D("Energy",{"Type1":"PRet","Type2":"Adipocytes"},100)
# contact.ElementCC3D("Energy",{"Type1":"PRet","Type2":"Lumen"},100)
# #QRET
# # 24/01/2017: considere increase QRet QRet
# contact.ElementCC3D("Energy",{"Type1":"QRet","Type2":"QRet"},20)
# contact.ElementCC3D("Energy",{"Type1":"QRet","Type2":"Adipocytes"},50)
# contact.ElementCC3D("Energy",{"Type1":"QRet","Type2":"Lumen"},100)
# #ADIPOCYTES
# contact.ElementCC3D("Energy",{"Type1":"Adipocytes","Type2":"Adipocytes"},2)
# contact.ElementCC3D("Energy",{"Type1":"Adipocytes","Type2":"Lumen"},10)
# #LUMEN
# contact.ElementCC3D("Energy",{"Type1":"Lumen","Type2":"Lumen"},1)
############# bellow is the current code ##############
#MEDIUM
contact.ElementCC3D("Energy", {"Type1": "Medium", "Type2": "Medium"}, 0)
contact.ElementCC3D("Energy", {"Type1": "Medium", "Type2": "Epidermis"}, 2)
contact.ElementCC3D("Energy", {
"Type1": "Medium",
"Type2": "Progenitors"
}, 50)
contact.ElementCC3D("Energy", {"Type1": "Medium", "Type2": "PPap"}, 50)
contact.ElementCC3D("Energy", {"Type1": "Medium", "Type2": "QPap"}, 50)
contact.ElementCC3D("Energy", {"Type1": "Medium", "Type2": "PRet"}, 50)
contact.ElementCC3D("Energy", {"Type1": "Medium", "Type2": "QRet"}, 50)
contact.ElementCC3D("Energy", {
"Type1": "Medium",
"Type2": "Adipocytes"
}, 50)
contact.ElementCC3D("Energy", {"Type1": "Medium", "Type2": "ECM"}, 50)
contact.ElementCC3D("Energy", {"Type1": "Medium", "Type2": "Lumen"}, 50)
#ECM
contact.ElementCC3D("Energy", {"Type1": "ECM", "Type2": "ECM"}, 5)
contact.ElementCC3D("Energy", {"Type1": "ECM", "Type2": "Epidermis"}, 10)
contact.ElementCC3D("Energy", {"Type1": "ECM", "Type2": "Progenitors"}, 2)
contact.ElementCC3D("Energy", {"Type1": "ECM", "Type2": "PPap"}, 2)
contact.ElementCC3D("Energy", {"Type1": "ECM", "Type2": "QPap"}, 2)
contact.ElementCC3D("Energy", {"Type1": "ECM", "Type2": "PRet"}, 2)
contact.ElementCC3D("Energy", {"Type1": "ECM", "Type2": "QRet"}, 2)
contact.ElementCC3D("Energy", {
"Type1": "ECM",
"Type2": "Adipocytes"
}, 30) #changed from 50
contact.ElementCC3D("Energy", {"Type1": "ECM", "Type2": "Lumen"}, 30)
#EPIDERMIS
contact.ElementCC3D("Energy", {
"Type1": "Epidermis",
"Type2": "Epidermis"
}, 2)
contact.ElementCC3D("Energy", {
"Type1": "Epidermis",
"Type2": "Progenitors"
}, 5)
contact.ElementCC3D("Energy", {"Type1": "Epidermis", "Type2": "PPap"}, 10)
contact.ElementCC3D("Energy", {"Type1": "Epidermis", "Type2": "QPap"}, 10)
contact.ElementCC3D("Energy", {
"Type1": "Epidermis",
"Type2": "PRet"
}, 10) #changed from 20
contact.ElementCC3D("Energy", {
"Type1": "Epidermis",
"Type2": "QRet"
}, 10) #changed from 20
contact.ElementCC3D("Energy", {
"Type1": "Epidermis",
"Type2": "Adipocytes"
}, 30) #changed from 100
contact.ElementCC3D("Energy", {
"Type1": "Epidermis",
"Type2": "Lumen"
}, 50) #changed from100
#PROGENITORS
contact.ElementCC3D("Energy", {
"Type1": "Progenitors",
"Type2": "Progenitors"
}, 10)
contact.ElementCC3D("Energy", {
"Type1": "Progenitors",
"Type2": "PPap"
}, 10)
contact.ElementCC3D("Energy", {
"Type1": "Progenitors",
"Type2": "QPap"
}, 10)
contact.ElementCC3D("Energy", {
"Type1": "Progenitors",
"Type2": "PRet"
}, 10)
contact.ElementCC3D("Energy", {
"Type1": "Progenitors",
"Type2": "QRet"
}, 10)
contact.ElementCC3D("Energy", {
"Type1": "Progenitors",
"Type2": "Adipocytes"
}, 30) # changed from 10
contact.ElementCC3D("Energy", {
"Type1": "Progenitors",
"Type2": "Lumen"
}, 50)
#PPAP
contact.ElementCC3D("Energy", {
"Type1": "PPap",
"Type2": "PPap"
}, 5) # changed from 20
contact.ElementCC3D("Energy", {"Type1": "PPap", "Type2": "QPap"}, 5)
contact.ElementCC3D("Energy", {
"Type1": "PPap",
"Type2": "PRet"
}, 5) # changed from 10
contact.ElementCC3D("Energy", {
"Type1": "PPap",
"Type2": "QRet"
}, 5) # changed from 20
contact.ElementCC3D("Energy", {
"Type1": "PPap",
"Type2": "Adipocytes"
}, 30) #changed from 100
contact.ElementCC3D("Energy", {
"Type1": "PPap",
"Type2": "Lumen"
}, 50) #changed from 100
#QPAP
contact.ElementCC3D("Energy", {
"Type1": "QPap",
"Type2": "QPap"
}, 5) # changed from 10
contact.ElementCC3D("Energy", {
"Type1": "QPap",
"Type2": "PRet"
}, 5) # changed from 20
contact.ElementCC3D("Energy", {
"Type1": "QPap",
"Type2": "QRet"
}, 5) # changed from 10
contact.ElementCC3D("Energy", {
"Type1": "QPap",
"Type2": "Adipocytes"
}, 30) #changed from 100
contact.ElementCC3D("Energy", {
"Type1": "QPap",
"Type2": "Lumen"
}, 30) #changed from 100
#PRET
contact.ElementCC3D("Energy", {
"Type1": "PRet",
"Type2": "PRet"
}, 5) #changed from 5
contact.ElementCC3D("Energy", {"Type1": "PRet", "Type2": "QRet"}, 5)
contact.ElementCC3D("Energy", {
"Type1": "PRet",
"Type2": "Adipocytes"
}, 30) #changed from 100
contact.ElementCC3D("Energy", {
"Type1": "PRet",
"Type2": "Lumen"
}, 50) #changed from 100
#QRET
contact.ElementCC3D("Energy", {
"Type1": "QRet",
"Type2": "QRet"
}, 5) # changed from 20
contact.ElementCC3D("Energy", {
"Type1": "QRet",
"Type2": "Adipocytes"
}, 30) # changed from 50
contact.ElementCC3D("Energy", {
"Type1": "QRet",
"Type2": "Lumen"
}, 30) # changed from 100
#ADIPOCYTES
contact.ElementCC3D("Energy", {
"Type1": "Adipocytes",
"Type2": "Adipocytes"
}, 2)
contact.ElementCC3D("Energy", {
"Type1": "Adipocytes",
"Type2": "Lumen"
}, 10)
#LUMEN
contact.ElementCC3D("Energy", {"Type1": "Lumen", "Type2": "Lumen"}, 1)
#FATTYs
contact.ElementCC3D("Energy", {"Type1": "Fatty", "Type2": "Fatty"}, 2)
contact.ElementCC3D("Energy", {"Type1": "Fatty", "Type2": "IC"}, 10)
contact.ElementCC3D("Energy", {"Type1": "Fatty", "Type2": "BC"}, 100)
contact.ElementCC3D("Energy", {"Type1": "Fatty", "Type2": "Medium"}, 100)
contact.ElementCC3D("Energy", {"Type1": "Fatty", "Type2": "ECM"}, 5)
contact.ElementCC3D("Energy", {"Type1": "Fatty", "Type2": "Epidermis"}, 30)
contact.ElementCC3D("Energy", {
"Type1": "Fatty",
"Type2": "Progenitors"
}, 10)
contact.ElementCC3D("Energy", {"Type1": "Fatty", "Type2": "PPap"}, 30)
contact.ElementCC3D("Energy", {"Type1": "Fatty", "Type2": "QPap"}, 30)
contact.ElementCC3D("Energy", {"Type1": "Fatty", "Type2": "PRet"}, 30)
contact.ElementCC3D("Energy", {"Type1": "Fatty", "Type2": "QRet"}, 30)
contact.ElementCC3D("Energy", {"Type1": "Fatty", "Type2": "Adipocytes"}, 2)
contact.ElementCC3D("Energy", {"Type1": "Fatty", "Type2": "Lumen"}, 10)
contact.ElementCC3D("Energy", {"Type1": "Fatty", "Type2": "MyoF"}, 20)
contact.ElementCC3D("Energy", {"Type1": "Fatty", "Type2": "QMyoF"}, 20)
#MYOF
contact.ElementCC3D("Energy", {"Type1": "MyoF", "Type2": "MyoF"}, 2)
contact.ElementCC3D("Energy", {"Type1": "MyoF", "Type2": "Medium"}, 100)
contact.ElementCC3D("Energy", {"Type1": "MyoF", "Type2": "ECM"}, 100)
contact.ElementCC3D("Energy", {"Type1": "MyoF", "Type2": "Epidermis"}, 10)
contact.ElementCC3D("Energy", {
"Type1": "MyoF",
"Type2": "Progenitors"
}, 10)
contact.ElementCC3D("Energy", {"Type1": "MyoF", "Type2": "PPap"}, 10)
contact.ElementCC3D("Energy", {"Type1": "MyoF", "Type2": "QPap"}, 10)
contact.ElementCC3D("Energy", {"Type1": "MyoF", "Type2": "PRet"}, 10)
contact.ElementCC3D("Energy", {"Type1": "MyoF", "Type2": "QRet"}, 10)
contact.ElementCC3D("Energy", {"Type1": "MyoF", "Type2": "Adipocytes"}, 20)
contact.ElementCC3D("Energy", {"Type1": "MyoF", "Type2": "Lumen"}, 100)
#QMYOF
contact.ElementCC3D("Energy", {"Type1": "QMyoF", "Type2": "QMyoF"}, 5)
contact.ElementCC3D("Energy", {"Type1": "QMyoF", "Type2": "Medium"}, 50)
contact.ElementCC3D("Energy", {
"Type1": "QMyoF",
"Type2": "ECM"
}, 1) #changed from 100
contact.ElementCC3D("Energy", {"Type1": "QMyoF", "Type2": "Epidermis"}, 10)
contact.ElementCC3D("Energy", {
"Type1": "QMyoF",
"Type2": "Progenitors"
}, 10)
contact.ElementCC3D("Energy", {"Type1": "QMyoF", "Type2": "PPap"}, 10)
contact.ElementCC3D("Energy", {"Type1": "QMyoF", "Type2": "QPap"}, 5)
contact.ElementCC3D("Energy", {"Type1": "QMyoF", "Type2": "PRet"}, 10)
contact.ElementCC3D("Energy", {"Type1": "QMyoF", "Type2": "QRet"}, 5)
contact.ElementCC3D("Energy", {
"Type1": "QMyoF",
"Type2": "Adipocytes"
}, 20)
contact.ElementCC3D("Energy", {"Type1": "QMyoF", "Type2": "Lumen"}, 20)
contact.ElementCC3D("Energy", {"Type1": "QMyoF", "Type2": "MyoF"}, 10)
contact.ElementCC3D("Energy", {"Type1": "QMyoF", "Type2": "BC"}, 100)
contact.ElementCC3D("Energy", {"Type1": "QMyoF", "Type2": "IC"}, 10)
#BLOOD CLOT
contact.ElementCC3D("Energy", {"Type1": "BC", "Type2": "BC"}, 2)
contact.ElementCC3D("Energy", {"Type1": "BC", "Type2": "Medium"}, 2)
contact.ElementCC3D("Energy", {"Type1": "BC", "Type2": "ECM"}, 100)
contact.ElementCC3D("Energy", {"Type1": "BC", "Type2": "Epidermis"}, 30)
contact.ElementCC3D("Energy", {"Type1": "BC", "Type2": "Progenitors"}, 100)
contact.ElementCC3D("Energy", {"Type1": "BC", "Type2": "PPap"}, 100)
contact.ElementCC3D("Energy", {"Type1": "BC", "Type2": "QPap"}, 100)
contact.ElementCC3D("Energy", {"Type1": "BC", "Type2": "PRet"}, 100)
contact.ElementCC3D("Energy", {"Type1": "BC", "Type2": "QRet"}, 100)
contact.ElementCC3D("Energy", {"Type1": "BC", "Type2": "Adipocytes"}, 100)
contact.ElementCC3D("Energy", {"Type1": "BC", "Type2": "Lumen"}, 100)
contact.ElementCC3D("Energy", {"Type1": "BC", "Type2": "MyoF"}, 100)
#IMMUNE CELLS & COMPANY
contact.ElementCC3D("Energy", {"Type1": "IC", "Type2": "IC"}, 5)
contact.ElementCC3D("Energy", {"Type1": "IC", "Type2": "BC"}, 100)
contact.ElementCC3D("Energy", {"Type1": "IC", "Type2": "Medium"}, 100)
contact.ElementCC3D("Energy", {"Type1": "IC", "Type2": "ECM"}, 10)
contact.ElementCC3D("Energy", {"Type1": "IC", "Type2": "Epidermis"}, 30)
contact.ElementCC3D("Energy", {"Type1": "IC", "Type2": "Progenitors"}, 10)
contact.ElementCC3D("Energy", {"Type1": "IC", "Type2": "PPap"}, 10)
contact.ElementCC3D("Energy", {"Type1": "IC", "Type2": "QPap"}, 10)
contact.ElementCC3D("Energy", {"Type1": "IC", "Type2": "PRet"}, 10)
contact.ElementCC3D("Energy", {"Type1": "IC", "Type2": "QRet"}, 10)
contact.ElementCC3D("Energy", {"Type1": "IC", "Type2": "Adipocytes"}, 10)
contact.ElementCC3D("Energy", {"Type1": "IC", "Type2": "Lumen"}, 50)
contact.ElementCC3D("Energy", {"Type1": "IC", "Type2": "MyoF"}, 2)
#Neighbor order
contact.ElementCC3D("NeighborOrder", {},
CNOrder) # changed to CNOrder instead of 5
#OTHER PLUGINS
boundaryPTracker = CompuCell3DElement.ElementCC3D(
"Plugin", {"Name": "BoundaryPixelTracker"})
# boundaryPTracker.ElementCC3D("NeighborOrder",{},"1")
vlFlex = CompuCell3DElement.ElementCC3D("Plugin",
{"Name": "VolumeLocalFlex"})
coMass = CompuCell3DElement.ElementCC3D("Plugin", {"Name": "CenterOfMass"})
neighborTracker = CompuCell3DElement.ElementCC3D(
"Plugin", {"Name": "NeighborTracker"})
SteppableElmnt = CompuCell3DElement.ElementCC3D("Steppable",
{"Type": "BoxWatcher"})
# Module tracing boundaries of the minimal box enclosing all the cells. May speed up calculations. May have no effect for parallel version
SteppableElmnt.ElementCC3D("XMargin", {}, "5")
SteppableElmnt.ElementCC3D("YMargin", {}, "5")
SteppableElmnt.ElementCC3D("ZMargin", {}, "5")
# Secretion
secretion = CompuCell3DElement.ElementCC3D("Plugin", {"Name": "Secretion"})
# secretionchemicalField1=secretion.ElementCC3D("Field", {"Name":"EpidermalGrowthSignal"})
# secretionchemicalField1.ElementCC3D("Secretion",{"Type":"Epidermis"},"10.0")
# secretionchemicalField2=secretion.ElementCC3D("Field", {"Name":"ECMSignal"})
# secretionchemicalField2.ElementCC3D("Secretion",{"Type":"Lumen"},"100.0")
# # secretionchemicalField2.ElementCC3D("Secretion",{"Type":"ECM"},"5.0")
# secretionchemicalField2.ElementCC3D("Secretion",{"Type":"QRet"},"5.0")
# secretionchemicalField2.ElementCC3D("Secretion",{"Type":"QPap"},"5.0")
secretionchemicalField3 = secretion.ElementCC3D(
"Field", {"Name": "WoundHealingSignal"})
secretionchemicalField3.ElementCC3D("Secretion", {"Type": "IC"}, "1.0")
# secretionchemicalField3.ElementCC3D("SecretionOnContact",{"SecreteOnContactWith":"Progenitors, PPap, QRet","Type":"MyoF"},"50.0")
# Chemotaxis
chemotaxis = CompuCell3DElement.ElementCC3D("Plugin",
{"Name": "Chemotaxis"})
# chemicalFieldEGF=chemotaxis.ElementCC3D("ChemicalField", {"Source":"DiffusionSolverFE", "Name":"EpidermalGrowthSignal"})
chemicalFieldWH = chemotaxis.ElementCC3D("ChemicalField", {
"Source": "DiffusionSolverFE",
"Name": "WoundHealingSignal"
})
chemicalFieldWH.ElementCC3D("ChemotaxisByType", {
"Type": "MyoF",
"Lambda": -10
})
chemicalFieldWH.ElementCC3D("ChemotaxisByType", {
"Type": "MyoF",
"Epidermis": -100
})
# Specification of PDE solvers
flexDiffSolver1 = CompuCell3DElement.ElementCC3D(
"Steppable", {"Type": "SteadyStateDiffusionSolver2D"})
diffusionFieldEGF = flexDiffSolver1.ElementCC3D("DiffusionField")
diffusionDataEGF = diffusionFieldEGF.ElementCC3D("DiffusionData")
diffusionDataEGF.ElementCC3D("FieldName", {}, "EpidermalGrowthSignal")
# diffusionDataEGF.ElementCC3D("GlobalDiffusionConstant",{},1e-1)
# diffusionDataEGF.ElementCC3D("GlobalDecayConstant",{},1e-3)
diffusionDataEGF.ElementCC3D("DiffusionConstant", {}, 1e-1)
diffusionDataEGF.ElementCC3D("DecayConstant", {}, 1e-3)
diffusionDataEGF.ElementCC3D("DoNotDiffuseTo", {}, "Medium")
diffusionDataEGF.ElementCC3D("DoNotDiffuseTo", {}, "Lumen")
secretionDataEGF = diffusionFieldEGF.ElementCC3D("SecretionData")
# When secretion is defined inside DissufionSolverFEall secretio nconstants are scaled automaticly to account for extra calls of the solver when handling large diffusion constants
# Uniform secretion Definition
secretionDataEGF.ElementCC3D("Secretion", {"Type": "Epidermis"}, "10.")
BoundaryConditionsEGF = diffusionFieldEGF.ElementCC3D("BoundaryConditions")
BoundaryConditionsEGF_X = BoundaryConditionsEGF.ElementCC3D(
"Plane", {"Axis": "X"})
BoundaryConditionsEGF_X.ElementCC3D("ConstantValue", {
"PlanePosition": "Min",
"Value": "0.0"
})
BoundaryConditionsEGF_X.ElementCC3D("ConstantValue", {
"PlanePosition": "Max",
"Value": "0.0"
})
BoundaryConditionsEGF_Y = BoundaryConditionsEGF.ElementCC3D(
"Plane", {"Axis": "Y"})
BoundaryConditionsEGF_Y.ElementCC3D("ConstantValue", {
"PlanePosition": "Min",
"Value": "0.0"
})
BoundaryConditionsEGF_Y.ElementCC3D("ConstantValue", {
"PlanePosition": "Max",
"Value": "0.0"
})
BoundaryConditionsEGF_Z = BoundaryConditionsEGF.ElementCC3D(
"Plane", {"Axis": "Z"})
BoundaryConditionsEGF_Z.ElementCC3D("ConstantDerivative", {
"PlanePosition": "Min",
"Value": "0.0"
})
BoundaryConditionsEGF_Z.ElementCC3D("ConstantDerivative", {
"PlanePosition": "Max",
"Value": "0.0"
})
flexDiffSolver = CompuCell3DElement.ElementCC3D(
"Steppable", {"Type": "DiffusionSolverFE"})
# diffusionFieldECM=flexDiffSolver.ElementCC3D("DiffusionField")
# diffusionDataECM=diffusionFieldECM.ElementCC3D("DiffusionData")
# diffusionDataECM.ElementCC3D("FieldName",{},"ECMSignal")
# diffusionDataECM.ElementCC3D("DiffusionConstant",{},1e0)
# diffusionDataECM.ElementCC3D("DecayConstant",{},1e-5)
# # diffusionDataECM.ElementCC3D("DoNotDiffuseTo",{},"PPap")
# # diffusionDataECM.ElementCC3D("DoNotDiffuseTo",{},"Epidermis")
# diffusionDataECM.ElementCC3D("DoNotDiffuseTo",{},"Medium")
# diffusionDataECM.ElementCC3D("DoNotDiffuseTo",{},"Lumen")
# # diffusionDataECM.ElementCC3D("DecayConstant",{"CellType":"Lumen"},100)
# secretionDataECM=diffusionFieldEGF.ElementCC3D("SecretionData")
# # When secretion is defined inside DissufionSolverFEall secretio nconstants are scaled automaticly to account for extra calls of the solver when handling large diffusion constants
# # Uniform secretion Definition
# secretionDataECM.ElementCC3D("Secretion",{"Type":"Lumen"},"5.")
# # secretionDataECM.ElementCC3D("Secretion",{"Type":"QRet"},"1.")
# BoundaryConditionsECM=diffusionFieldECM.ElementCC3D("BoundaryConditions")
# BoundaryConditionsECM_X=BoundaryConditionsEGF.ElementCC3D("Plane",{"Axis":"X"})
# BoundaryConditionsECM_X.ElementCC3D("ConstantValue",{"PlanePosition":"Min","Value":"0.0"})
# BoundaryConditionsECM_X.ElementCC3D("ConstantValue",{"PlanePosition":"Max","Value":"0.0"})
# BoundaryConditionsECM_Y=BoundaryConditionsECM.ElementCC3D("Plane",{"Axis":"Y"})
# BoundaryConditionsECM_Y.ElementCC3D("ConstantValue",{"PlanePosition":"Min","Value":"0.0"})
# BoundaryConditionsECM_Y.ElementCC3D("ConstantValue",{"PlanePosition":"Max","Value":"0.0"})
# BoundaryConditionsECM_Z=BoundaryConditionsECM.ElementCC3D("Plane",{"Axis":"Z"})
# BoundaryConditionsECM_Z.ElementCC3D("ConstantDerivative",{"PlanePosition":"Min","Value":"0.0"})
# BoundaryConditionsECM_Z.ElementCC3D("ConstantDerivative",{"PlanePosition":"Max","Value":"0.0"})
diffusionFieldWH = flexDiffSolver.ElementCC3D("DiffusionField")
diffusionDataWH = diffusionFieldWH.ElementCC3D("DiffusionData")
diffusionDataWH.ElementCC3D("FieldName", {}, "WoundHealingSignal")
diffusionDataWH.ElementCC3D("DiffusionConstant", {}, 1e-0)
diffusionDataWH.ElementCC3D("DecayConstant", {}, 1e-2)
# diffusionDataWH.ElementCC3D("DoNotDiffuseTo",{},"Medium")
diffusionDataWH.ElementCC3D("DoNotDiffuseTo", {}, "Lumen")
# pifInitializer=CompuCell3DElement.ElementCC3D("Steppable",{"Type":"PIFInitializer"})
# pifInitializer.ElementCC3D("PIFName",{},"DermisMaturationCurrentConfiguration.piff01700.pif")
# pifDumper=CompuCell3DElement.ElementCC3D("Steppable",{"Type":"PIFDumper","Frequency":100})
# pifDumper.ElementCC3D("PIFName",{},"DermisMaturationCurrentConfiguration.piff")
CompuCellSetup.setSimulationXMLDescription(CompuCell3DElement)
def configureSimulation(sim):
import CompuCellSetup
from XMLUtils import ElementCC3D
CompuCell3DElmnt = ElementCC3D("CompuCell3D", {"version": "3.7.5"})
def configureSimulation(sim):
import CompuCellSetup
from XMLUtils import ElementCC3D
from numpy import sqrt as nsqrt
CompuCell3DElmnt = ElementCC3D("CompuCell3D", {
"Revision": "20190430",
"Version": "3.7.9"
})
PottsElmnt = CompuCell3DElmnt.ElementCC3D("Potts")
PottsElmnt.ElementCC3D("Dimensions", {"x": "256", "y": "256", "z": "1"})
PottsElmnt.ElementCC3D("Steps", {}, "10001")
PottsElmnt.ElementCC3D("Temperature", {}, "10.0")
PottsElmnt.ElementCC3D("NeighborOrder", {}, str(G_interact_range_G))
PluginElmnt = CompuCell3DElmnt.ElementCC3D("Plugin", {"Name": "CellType"})
PluginElmnt.ElementCC3D("CellType", {"TypeId": "0", "TypeName": "Medium"})
PluginElmnt.ElementCC3D("CellType", {"TypeId": "1", "TypeName": "dark"})
PluginElmnt.ElementCC3D("CellType", {"TypeId": "2", "TypeName": "light"})
MetadataElmnt = CompuCell3DElmnt.ElementCC3D("Metadata")
MetadataElmnt.ElementCC3D("DebugOutputFrequency", {}, "100")
PluginElmnt_1 = CompuCell3DElmnt.ElementCC3D("Plugin", {"Name": "Volume"})
PluginElmnt_1.ElementCC3D(
"VolumeEnergyParameters", {
"CellType": "dark",
"LambdaVolume": str(G_lambdaVol_dark_G),
"TargetVolume": str(G_targetVol_dark_G)
})
PluginElmnt_1.ElementCC3D(
"VolumeEnergyParameters", {
"CellType": "light",
"LambdaVolume": str(G_lambdaVol_light_G),
"TargetVolume": str(G_targetVol_light_G)
})
CompuCell3DElmnt.ElementCC3D("Plugin", {"Name": "CenterOfMass"})
CompuCell3DElmnt.ElementCC3D("Plugin", {"Name": "NeighborTracker"})
PluginElmnt_2 = CompuCell3DElmnt.ElementCC3D("Plugin", {"Name": "Contact"})
PluginElmnt_2.ElementCC3D("Energy", {
"Type1": "Medium",
"Type2": "Medium"
}, "10.0")
PluginElmnt_2.ElementCC3D("Energy", {
"Type1": "Medium",
"Type2": "dark"
}, str(G_J_dm_G))
PluginElmnt_2.ElementCC3D("Energy", {
"Type1": "Medium",
"Type2": "light"
}, str(G_J_lm_G))
PluginElmnt_2.ElementCC3D("Energy", {
"Type1": "dark",
"Type2": "dark"
}, str(G_J_dd_G))
PluginElmnt_2.ElementCC3D("Energy", {
"Type1": "dark",
"Type2": "light"
}, str(G_J_dl_G))
PluginElmnt_2.ElementCC3D("Energy", {
"Type1": "light",
"Type2": "light"
}, str(G_J_ll_G))
PluginElmnt_2.ElementCC3D("NeighborOrder", {}, str(G_interact_range_G))
SteppableElmnt = CompuCell3DElmnt.ElementCC3D("Steppable",
{"Type": "BlobInitializer"})
RegionElmnt = SteppableElmnt.ElementCC3D("Region")
RegionElmnt.ElementCC3D("Center", {"x": "128", "y": "128", "z": "0"})
RegionElmnt.ElementCC3D("Radius", {}, "112")
RegionElmnt.ElementCC3D("Gap", {}, "0")
RegionElmnt.ElementCC3D(
"Width", {}, str(int(round(nsqrt(G_targetVol_light_G))))
) #this way they will be about the right size to begin with
RegionElmnt.ElementCC3D("Types", {}, "dark,light")
CompuCellSetup.setSimulationXMLDescription(CompuCell3DElmnt)
def configureSimulation(sim):
import CompuCellSetup
from XMLUtils import ElementCC3D
import NewSimulation_parameters as p
CompuCell3DElmnt = ElementCC3D("CompuCell3D", {
"Revision": "20180621",
"Version": "3.7.8"
})
PottsElmnt = CompuCell3DElmnt.ElementCC3D("Potts")
PottsElmnt.ElementCC3D("Dimensions", {"x": "111", "y": "111", "z": "111"})
PottsElmnt.ElementCC3D("Steps", {}, p.mcs)
PottsElmnt.ElementCC3D("Temperature", {}, "20.0")
PottsElmnt.ElementCC3D("NeighborOrder", {}, "3")
PluginElmnt = CompuCell3DElmnt.ElementCC3D(
"Plugin", {"Name": "CellType"},
" !-- Listing all cell types in the simulation -->")
PluginElmnt.ElementCC3D("CellType", {"TypeId": "0", "TypeName": "Medium"})
PluginElmnt.ElementCC3D("CellType", {"TypeId": "1", "TypeName": "NPCells"})
PluginElmnt.ElementCC3D("CellType", {"TypeId": "2", "TypeName": "ACells"})
PluginElmnt.ElementCC3D("CellType", {
"Freeze": "",
"TypeId": "3",
"TypeName": "Wall"
})
PluginElmnt_1 = CompuCell3DElmnt.ElementCC3D("Plugin", {"Name": "Volume"})
PluginElmnt_1.ElementCC3D("VolumeEnergyParameters", {
"CellType": "NPCells",
"LambdaVolume": "50.0",
"TargetVolume": "300"
})
PluginElmnt_1.ElementCC3D("VolumeEnergyParameters", {
"CellType": "ACells",
"LambdaVolume": "50.0",
"TargetVolume": "300"
})
CompuCell3DElmnt.ElementCC3D("Plugin", {"Name": "CenterOfMass"})
PluginElmnt_2 = CompuCell3DElmnt.ElementCC3D(
"Plugin", {"Name": "Contact"},
" Specification of adhesion energies ")
PluginElmnt_2.ElementCC3D("Energy", {
"Type1": "Medium",
"Type2": "Medium"
}, "0.0")
PluginElmnt_2.ElementCC3D("Energy", {
"Type1": "Medium",
"Type2": "NPCells"
}, "5.0")
PluginElmnt_2.ElementCC3D("Energy", {
"Type1": "Medium",
"Type2": "ACells"
}, "5.0")
PluginElmnt_2.ElementCC3D("Energy", {
"Type1": "NPCells",
"Type2": "NPCells"
}, "5.0")
PluginElmnt_2.ElementCC3D("Energy", {
"Type1": "NPCells",
"Type2": "ACells"
}, p.AED)
PluginElmnt_2.ElementCC3D("Energy", {
"Type1": "ACells",
"Type2": "ACells"
}, "5.0")
PluginElmnt_2.ElementCC3D("Energy", {
"Type1": "Wall",
"Type2": "Wall"
}, "5.0")
PluginElmnt_2.ElementCC3D("Energy", {
"Type1": "Wall",
"Type2": "NPCells"
}, "5.0")
PluginElmnt_2.ElementCC3D("Energy", {
"Type1": "Wall",
"Type2": "ACells"
}, "5.0")
PluginElmnt_2.ElementCC3D("NeighborOrder", {}, "2")
# PluginElmnt_2a=CompuCell3DElmnt.ElementCC3D("Plugin",{"Name":"CenterOfMass"}) # jps needed to get cell's center of mass
PluginElmnt_2b = CompuCell3DElmnt.ElementCC3D(
"Plugin",
{"Name": "NeighborTracker"}) # jps needed to get cell's neighbors
# PluginElmnt_2c=CompuCell3DElmnt.ElementCC3D("Plugin",{"Name":"PixelTracker"}) # jps Module tracking pixels of each cell
# PluginElmnt_2d=CompuCell3DElmnt.ElementCC3D("Plugin",{"Name":"BoundaryPixelTracker"})# jps Module tracking boundary pixels of each cell
# PluginElmnt_2d.ElementCC3D("NeighborOrder",{},"1")
PluginElmnt_3 = CompuCell3DElmnt.ElementCC3D("Plugin",
{"Name": "Chemotaxis"})
ChemicalFieldElmnt = PluginElmnt_3.ElementCC3D(
"ChemicalField", {
"Name": "Wnt9b",
"Source": "DiffusionSolverFE"
})
ChemicalFieldElmnt.ElementCC3D("ChemotaxisByType", {
"Lambda": p.CL,
"Type": "NPCells"
})
PluginElmnt_4 = CompuCell3DElmnt.ElementCC3D("Plugin",
{"Name": "Secretion"})
FieldElmnt = PluginElmnt_4.ElementCC3D("Field", {"Name": "Wnt9b"})
FieldElmnt.ElementCC3D("Secretion", {"Type": "Wall"}, p.SR)
FieldElmnt.ElementCC3D("Secretion", {"Type": "NPCells"}, p.SR)
SteppableElmnt = CompuCell3DElmnt.ElementCC3D(
"Steppable", {"Type": "DiffusionSolverFE"})
DiffusionFieldElmnt = SteppableElmnt.ElementCC3D("DiffusionField",
{"Name": "Wnt9b"})
DiffusionDataElmnt = DiffusionFieldElmnt.ElementCC3D("DiffusionData")
DiffusionDataElmnt.ElementCC3D("FieldName", {}, "Wnt9b")
DiffusionDataElmnt.ElementCC3D("GlobalDiffusionConstant", {}, p.GDC)
DiffusionDataElmnt.ElementCC3D("GlobalDecayConstant", {}, p.decay)
DiffusionDataElmnt.ElementCC3D("ExtraTimesPerMCS", {}, "8")
DiffusionDataElmnt.ElementCC3D("DoNotDiffuseTo", {}, "Wall")
SteppableElmnt_1 = CompuCell3DElmnt.ElementCC3D("Steppable",
{"Type": "PIFInitializer"})
SteppableElmnt_1.ElementCC3D("PIFName", {},
"Simulation/all cells uniform3d_v2.piff")
CompuCellSetup.setSimulationXMLDescription(CompuCell3DElmnt)
def configureSimulation(sim):
import CompuCellSetup
from XMLUtils import ElementCC3D
CompuCell3DElmnt = ElementCC3D("CompuCell3D", {
"Revision": "20190430",
"Version": "3.7.9"
})
PottsElmnt = CompuCell3DElmnt.ElementCC3D("Potts")
# Basic properties of CPM (GGH) algorithm
PottsElmnt.ElementCC3D("Dimensions", {"x": "100", "y": "100", "z": "1"})
PottsElmnt.ElementCC3D("Steps", {}, "1000")
PottsElmnt.ElementCC3D("Temperature", {}, "10.0")
PottsElmnt.ElementCC3D("NeighborOrder", {}, "1")
PluginElmnt = CompuCell3DElmnt.ElementCC3D("Plugin", {"Name": "CellType"})
# Listing all cell types in the simulation
PluginElmnt.ElementCC3D("CellType", {"TypeId": "0", "TypeName": "Medium"})
PluginElmnt.ElementCC3D("CellType", {"TypeId": "1", "TypeName": "cell2"})
PluginElmnt.ElementCC3D("CellType", {"TypeId": "2", "TypeName": "cell1"})
PluginElmnt_1 = CompuCell3DElmnt.ElementCC3D("Plugin", {"Name": "Volume"})
PluginElmnt_1.ElementCC3D("VolumeEnergyParameters", {
"CellType": "cell2",
"LambdaVolume": "2.0",
"TargetVolume": "25"
})
PluginElmnt_1.ElementCC3D("VolumeEnergyParameters", {
"CellType": "cell1",
"LambdaVolume": "2.0",
"TargetVolume": "25"
})
PluginElmnt_2 = CompuCell3DElmnt.ElementCC3D("Plugin",
{"Name": "CenterOfMass"})
# Module tracking center of mass of each cell
PluginElmnt_3 = CompuCell3DElmnt.ElementCC3D("Plugin", {"Name": "Contact"})
# Specification of adhesion energies
PluginElmnt_3.ElementCC3D("Energy", {
"Type1": "Medium",
"Type2": "Medium"
}, "10.0")
PluginElmnt_3.ElementCC3D("Energy", {
"Type1": "Medium",
"Type2": "cell2"
}, "10.0")
PluginElmnt_3.ElementCC3D("Energy", {
"Type1": "Medium",
"Type2": "cell1"
}, "10.0")
PluginElmnt_3.ElementCC3D("Energy", {
"Type1": "cell2",
"Type2": "cell2"
}, "10.0")
PluginElmnt_3.ElementCC3D("Energy", {
"Type1": "cell2",
"Type2": "cell1"
}, "10.0")
PluginElmnt_3.ElementCC3D("Energy", {
"Type1": "cell1",
"Type2": "cell1"
}, "10.0")
PluginElmnt_3.ElementCC3D("NeighborOrder", {}, "1")
SteppableElmnt = CompuCell3DElmnt.ElementCC3D("Steppable",
{"Type": "BlobInitializer"})
# Initial layout of cells in the form of spherical (circular in 2D) blob
RegionElmnt = SteppableElmnt.ElementCC3D("Region")
RegionElmnt.ElementCC3D("Center", {"x": "50", "y": "50", "z": "0"})
RegionElmnt.ElementCC3D("Radius", {}, "20")
RegionElmnt.ElementCC3D("Gap", {}, "0")
RegionElmnt.ElementCC3D("Width", {}, "5")
RegionElmnt.ElementCC3D("Types", {}, "cell2,cell1")
CompuCellSetup.setSimulationXMLDescription(CompuCell3DElmnt)
CompuCellSetup.setSimulationXMLDescription(CompuCell3DElmnt)
def configureSimulation(sim):
import CompuCellSetup
from XMLUtils import ElementCC3D
## ********** Import Parameters Here
print '>>>>>>>>>>>>>>>> Before imports >>>>>>>>>>>>>>>>'
print 'Current directory', os.getcwd()
from Stats import ParamsContainer
global params_container; params_container = ParamsContainer()
params_dict = params_container.inputParamsFromFile('../tcseg/Simulation/params')
global Dx; Dx = params_container.getNumberParam('Dx')
global Dy; Dy = params_container.getNumberParam('Dy')
global speed_up_sim; speed_up_sim = params_container.getBooleanParam('speed_up_sim')
global batch; batch = params_container.getBooleanParam('batch')
global hinder_cells_near_EN; hinder_cells_near_EN = params_container.getBooleanParam('hinder_cells_near_EN')
global y_target_offset; y_target_offset = params_container.getNumberParam('y_target_offset')
global pull_force_magnitude; pull_force_magnitude = params_container.getNumberParam('pull_force_magnitude')
global pinch_force_relative_center; pinch_force_relative_center = params_container.getNumberParam('pinch_force_relative_center')
global pinch_force_mag; pinch_force_mag = params_container.getNumberParam('pinch_force_mag')
global pinch_force_falloff_sharpness; pinch_force_falloff_sharpness = params_container.getNumberParam('pinch_force_falloff_sharpness')
global regional_mitosis; regional_mitosis = params_container.getNumberParam('regional_mitosis')
print '>>>>>>>>>>>>>>>> After imports >>>>>>>>>>>>>>>>'
CompuCell3DElmnt=ElementCC3D("CompuCell3D",{"Revision":"20140724","Version":"3.7.2"})
PottsElmnt=CompuCell3DElmnt.ElementCC3D("Potts")
# Basic properties of CPM (GGH) algorithm
PottsElmnt.ElementCC3D("Dimensions",{"x":Dx,"y":Dy,"z":1})
PottsElmnt.ElementCC3D("Steps",{},"2001")
PottsElmnt.ElementCC3D("Temperature",{},"10.0")
PottsElmnt.ElementCC3D("NeighborOrder",{},"1")
PluginElmnt=CompuCell3DElmnt.ElementCC3D("Plugin",{"Name":"CellType"}) # Listing all cell types in the simulation
PluginElmnt.ElementCC3D("CellType",{"TypeId":"0","TypeName":"Medium"})
PluginElmnt.ElementCC3D("CellType",{"TypeId":"1","TypeName":"AnteriorLobe"})
PluginElmnt.ElementCC3D("CellType",{"TypeId":"2","TypeName":"EN"})
PluginElmnt.ElementCC3D("CellType",{"TypeId":"3","TypeName":"GZ"})
PluginElmnt.ElementCC3D("CellType",{"TypeId":"4","TypeName":"Mitosing"})
PluginElmnt.ElementCC3D("CellType",{"TypeId":"5","TypeName":"Segmented"})
PluginElmnt_1=CompuCell3DElmnt.ElementCC3D("Plugin",{"Name":"Volume"}) # Cell property trackers and manipulators
PluginElmnt_2=CompuCell3DElmnt.ElementCC3D("Plugin",{"Name":"Surface"})
extPotential=CompuCell3DElmnt.ElementCC3D("Plugin",{"Name":"ExternalPotential"})
PluginElmnt_4=CompuCell3DElmnt.ElementCC3D("Plugin",{"Name":"CenterOfMass"})
PluginElmnt_6=CompuCell3DElmnt.ElementCC3D("Plugin",{"Name":"NeighborTracker"})
PluginElmnt_6=CompuCell3DElmnt.ElementCC3D("Plugin",{"Name":"Secretion"})
PluginElmnt_5=CompuCell3DElmnt.ElementCC3D("Plugin",{"Name":"Contact"}) # Specification of adhesion energies
PluginElmnt_5.ElementCC3D("Energy",{"Type1":"Medium","Type2":"Medium"},"100.0")
PluginElmnt_5.ElementCC3D("Energy",{"Type1":"Medium","Type2":"AnteriorLobe"},"100.0")
PluginElmnt_5.ElementCC3D("Energy",{"Type1":"Medium","Type2":"EN"},"100.0")
PluginElmnt_5.ElementCC3D("Energy",{"Type1":"Medium","Type2":"GZ"},"100.0")
PluginElmnt_5.ElementCC3D("Energy",{"Type1":"Medium","Type2":"Mitosing"},"100.0")
PluginElmnt_5.ElementCC3D("Energy",{"Type1":"Medium","Type2":"Segmented"},"100.0")
PluginElmnt_5.ElementCC3D("Energy",{"Type1":"AnteriorLobe","Type2":"AnteriorLobe"},"10.0")
PluginElmnt_5.ElementCC3D("Energy",{"Type1":"AnteriorLobe","Type2":"EN"},"10.0")
PluginElmnt_5.ElementCC3D("Energy",{"Type1":"AnteriorLobe","Type2":"GZ"},"10.0")
PluginElmnt_5.ElementCC3D("Energy",{"Type1":"AnteriorLobe","Type2":"Mitosing"},"10.0")
PluginElmnt_5.ElementCC3D("Energy",{"Type1":"AnteriorLobe","Type2":"Segmented"},"10.0")
PluginElmnt_5.ElementCC3D("Energy",{"Type1":"EN","Type2":"EN"},"10.0")
PluginElmnt_5.ElementCC3D("Energy",{"Type1":"EN","Type2":"GZ"},"10.0")
PluginElmnt_5.ElementCC3D("Energy",{"Type1":"EN","Type2":"Mitosing"},"10.0")
PluginElmnt_5.ElementCC3D("Energy",{"Type1":"EN","Type2":"Segmented"},"10.0")
PluginElmnt_5.ElementCC3D("Energy",{"Type1":"GZ","Type2":"GZ"},"10.0")
PluginElmnt_5.ElementCC3D("Energy",{"Type1":"GZ","Type2":"Mitosing"},"10.0")
PluginElmnt_5.ElementCC3D("Energy",{"Type1":"GZ","Type2":"Segmented"},"10.0")
PluginElmnt_5.ElementCC3D("Energy",{"Type1":"Mitosing","Type2":"Mitosing"},"10.0")
PluginElmnt_5.ElementCC3D("Energy",{"Type1":"Mitosing","Type2":"Segmented"},"10.0")
PluginElmnt_5.ElementCC3D("Energy",{"Type1":"Segmented","Type2":"Segmented"},"10.0")
PluginElmnt_5.ElementCC3D("NeighborOrder",{},"1")
## EN GENE PRODUCT FIELD NOT ACCOMPLISHING ANYTHING MECHANISTIC, AND SLOWING DOWN SIMULATION A LOT
## ***** Define the properties of the Engrailed gene product ***** ##
if hinder_cells_near_EN: # THIS IS TO AVOID SLOWDOWN WHEN FIELD NOT NECESSARY (sdh)
SteppableElmnt=CompuCell3DElmnt.ElementCC3D("Steppable",{"Type":"DiffusionSolverFE"})
DiffusionFieldElmnt=SteppableElmnt.ElementCC3D("DiffusionField",{"Name":"EN_GENE_PRODUCT"})
DiffusionDataElmnt=DiffusionFieldElmnt.ElementCC3D("DiffusionData")
DiffusionDataElmnt.ElementCC3D("FieldName",{},"EN_GENE_PRODUCT")
DiffusionDataElmnt.ElementCC3D("GlobalDiffusionConstant",{},"10.0") # 0.05 for anterior retardation; 0.5 for bidirectional retardation
DiffusionDataElmnt.ElementCC3D("GlobalDecayConstant",{},"0.05") # 0.005 for anterior retardation; 0.05 for bidirectional retardation
## ***** ##
SteppableElmnt=CompuCell3DElmnt.ElementCC3D("Steppable",{"Type":"PIFInitializer"})
# Initial layout of cells using PIFF file. Piff files can be generated using PIFGEnerator
SteppableElmnt.ElementCC3D("PIFName",{},"Simulation/Dec2014_v02.piff")
CompuCellSetup.setSimulationXMLDescription(CompuCell3DElmnt)
def configureSimulation(sim):
import CompuCellSetup
from XMLUtils import ElementCC3D
CompuCell3DElmnt = ElementCC3D("CompuCell3D", {"version": "3.6.0"})
# Basic properties of CPM (GGH) algorithm
PottsElmnt = CompuCell3DElmnt.ElementCC3D("Potts")
PottsElmnt.ElementCC3D("Dimensions", {"x": "50", "y": "50", "z": "50"})
PottsElmnt.ElementCC3D("Steps", {}, "10000")
PottsElmnt.ElementCC3D("Temperature", {}, "20.0")
PottsElmnt.ElementCC3D("NeighborOrder", {}, "3")
PottsElmnt.ElementCC3D("Boundary_x", {}, "Periodic")
PottsElmnt.ElementCC3D("Boundary_y", {}, "Periodic")
PottsElmnt.ElementCC3D("Boundary_z", {}, "Periodic")
# Listing all cell types in the simulation
PluginElmnt = CompuCell3DElmnt.ElementCC3D("Plugin", {"Name": "CellType"})
PluginElmnt.ElementCC3D("CellType", {"TypeId": "0", "TypeName": "Medium"})
PluginElmnt.ElementCC3D("CellType", {
"TypeId": "1",
"TypeName": "Endothelial"
})
# Constraint on cell volume. Each cell type has different constraint.
# For more flexible specification of the constraint (done in Python) please use VolumeLocalFlex plugin
PluginElmnt_1 = CompuCell3DElmnt.ElementCC3D("Plugin", {"Name": "Volume"})
PluginElmnt_1.ElementCC3D("VolumeEnergyParameters", {
"CellType": "Endothelial",
"LambdaVolume": "20.0",
"TargetVolume": "74"
})
# Specification of adhesion energies
PluginElmnt_2 = CompuCell3DElmnt.ElementCC3D("Plugin", {"Name": "Contact"})
PluginElmnt_2.ElementCC3D("Energy", {
"Type1": "Medium",
"Type2": "Medium"
}, "0")
PluginElmnt_2.ElementCC3D("Energy", {
"Type1": "Medium",
"Type2": "Endothelial"
}, "12")
PluginElmnt_2.ElementCC3D("Energy", {
"Type1": "Endothelial",
"Type2": "Endothelial"
}, "5")
PluginElmnt_2.ElementCC3D("NeighborOrder", {}, "4")
# Specification of chemotaxis properties of select cell types.
PluginElmnt_3 = CompuCell3DElmnt.ElementCC3D("Plugin",
{"Name": "Chemotaxis"})
ChemicalFieldElmnt = PluginElmnt_3.ElementCC3D(
"ChemicalField", {
"Name": "VEGF",
"Source": "FlexibleDiffusionSolverFE"
})
ChemicalFieldElmnt.ElementCC3D("ChemotaxisByType", {
"ChemotactTowards": "Medium",
"Lambda": "6000.0",
"Type": "Endothelial"
})
# Specification of secretion properties of select cell types.
# Specification of secretion properties of individual cells can be done in Python
PluginElmnt_4 = CompuCell3DElmnt.ElementCC3D("Plugin",
{"Name": "Secretion"})
FieldElmnt = PluginElmnt_4.ElementCC3D("Field", {"Name": "VEGF"})
FieldElmnt.ElementCC3D("Secretion", {"Type": "Endothelial"}, "0.013")
# Module allowing multiple calls of the PDE solver. By default number of extra calls is set to 0.
# Change these settings to desired values after consulting CC3D manual on how to work with large diffusion constants (>0.16 in 3D with DeltaX=1.0 and DeltaT=1.0)
PluginElmnt_5 = CompuCell3DElmnt.ElementCC3D("Plugin",
{"Name": "PDESolverCaller"})
PluginElmnt_5.ElementCC3D("CallPDE", {
"ExtraTimesPerMC": "0",
"PDESolverName": "FlexibleDiffusionSolverFE"
})
# Specification of PDE solvers
SteppableElmnt = CompuCell3DElmnt.ElementCC3D(
"Steppable", {"Type": "FlexibleDiffusionSolverFE"})
DiffusionFieldElmnt = SteppableElmnt.ElementCC3D("DiffusionField")
DiffusionDataElmnt = DiffusionFieldElmnt.ElementCC3D("DiffusionData")
DiffusionDataElmnt.ElementCC3D("FieldName", {}, "VEGF")
DiffusionDataElmnt.ElementCC3D("DiffusionConstant", {}, "0.16")
DiffusionDataElmnt.ElementCC3D("DecayConstant", {}, "0.016")
# Additional options are:
#DiffusionDataElmnt.ElementCC3D("DoNotDiffuseTo",{},"LIST YOUR CELL TYPES HERE")
DiffusionDataElmnt.ElementCC3D("DoNotDecayIn", {}, "Endothelial")
# DiffusionDataElmnt.ElementCC3D("ConcentrationFileName",{},"INITIAL CONCENTRATION FIELD - typically a file with path Simulation/NAME_OF_THE_FILE.txt")
# To run solver for large diffusion constants you typically call solver multiple times - ExtraTimesPerMCS to specify additional calls to the solver in each MCS
# IMPORTANT: make sure not to mix this setting with the PDESolverCaller module! See manual for more information
# DiffusionDataElmnt.ElementCC3D("ExtraTimesPerMCS",{},"0")
DiffusionDataElmnt.ElementCC3D("DeltaX", {}, "1.0")
DiffusionDataElmnt.ElementCC3D("DeltaT", {}, "1.0")
# Initial layout of cells in the form of rectangular slab
SteppableElmnt_1 = CompuCell3DElmnt.ElementCC3D(
"Steppable", {"Type": "UniformInitializer"})
RegionElmnt = SteppableElmnt_1.ElementCC3D("Region")
RegionElmnt.ElementCC3D("BoxMin", {"x": "15", "y": "15", "z": "15"})
RegionElmnt.ElementCC3D("BoxMax", {"x": "35", "y": "35", "z": "35"})
RegionElmnt.ElementCC3D("Gap", {}, "0")
RegionElmnt.ElementCC3D("Width", {}, "4")
RegionElmnt.ElementCC3D("Types", {}, "Endothelial")
CompuCellSetup.setSimulationXMLDescription(CompuCell3DElmnt)
def writeScreenshotDescriptionFile_XML(self, fileName):
from XMLUtils import ElementCC3D
screenshotFileElement = ElementCC3D("CompuCell3DScreenshots")
for name in self.screenshotDataDict:
scrData = self.screenshotDataDict[name]
scrDescElement = screenshotFileElement.ElementCC3D("ScreenshotDescription")
if scrData.spaceDimension == "2D":
scrDescElement.ElementCC3D("Dimension", {}, str(scrData.spaceDimension))
scrDescElement.ElementCC3D("Plot",
{"PlotType": str(scrData.plotData[1]), "PlotName": str(scrData.plotData[0])})
scrDescElement.ElementCC3D("Projection", {"ProjectionPlane": scrData.projection,
"ProjectionPosition": str(scrData.projectionPosition)})
if scrData.spaceDimension == "3D":
scrDescElement.ElementCC3D("Dimension", {}, str(scrData.spaceDimension))
scrDescElement.ElementCC3D("Plot",
{"PlotType": str(scrData.plotData[1]), "PlotName": str(scrData.plotData[0])})
scrDescElement.ElementCC3D("CameraClippingRange",
{"Min": str(scrData.clippingRange[0]), "Max": str(scrData.clippingRange[1])})
scrDescElement.ElementCC3D("CameraFocalPoint",
{"x": str(scrData.focalPoint[0]), "y": str(scrData.focalPoint[1]),
"z": str(scrData.focalPoint[2])})
scrDescElement.ElementCC3D("CameraPosition",
{"x": str(scrData.position[0]), "y": str(scrData.position[1]),
"z": str(scrData.position[2])})
scrDescElement.ElementCC3D("CameraViewUp", {"x": str(scrData.viewUp[0]), "y": str(scrData.viewUp[1]),
"z": str(scrData.viewUp[2])})
scrDescElement.ElementCC3D("Size", {"Width": str(scrData.win_width),
"Height": str(scrData.win_height)})
# saving complete visulaization gui settings
self.appendBoolChildElement(elem=scrDescElement, elem_label='CellBorders',
elem_value=scrData.cell_borders_on)
self.appendBoolChildElement(elem=scrDescElement, elem_label='Cells',
elem_value=scrData.cells_on)
self.appendBoolChildElement(elem=scrDescElement, elem_label='ClusterBorders',
elem_value=scrData.cluster_borders_on)
self.appendBoolChildElement(elem=scrDescElement, elem_label='CellGlyphs',
elem_value=scrData.cell_glyphs_on)
self.appendBoolChildElement(elem=scrDescElement, elem_label='FPPLinks',
elem_value=scrData.fpp_links_on)
self.appendBoolChildElement(elem=scrDescElement, elem_label='BoundingBox',
elem_value=scrData.bounding_box_on)
self.appendBoolChildElement(elem=scrDescElement, elem_label='LatticeAxes',
elem_value=scrData.lattice_axes_on)
self.appendBoolChildElement(elem=scrDescElement, elem_label='LatticeAxesLabels',
elem_value=scrData.lattice_axes_labels_on)
invisible_types_str = ''
if scrData.invisible_types is not None:
invisible_types_str = ','.join(list(map(lambda x:str(x), scrData.invisible_types)))
scrDescElement.ElementCC3D("TypesInvisible", {},invisible_types_str)
# scrDescElement.ElementCC3D("TypesInvisible", {},
# scrData.invisible_types if scrData.invisible_types is not None and len(scrData.invisible_types) else '')
# scrDescElement.ElementCC3D("CellBorders", {"On": 1 if scrData.cell_borders_on else 0})
screenshotFileElement.CC3DXMLElement.saveXML(str(fileName))
def configureSimulation(sim):
import CompuCellSetup
from XMLUtils import ElementCC3D
cc3d = ElementCC3D("CompuCell3D")
potts = cc3d.ElementCC3D("Potts")
potts.ElementCC3D("Dimensions", {"x": 55, "y": 55, "z": 1})
potts.ElementCC3D("Steps", {}, 1000)
potts.ElementCC3D("Temperature", {}, 15)
potts.ElementCC3D("Boundary_y", {}, "Periodic")
cellType = cc3d.ElementCC3D("Plugin", {"Name": "CellType"})
cellType.ElementCC3D("CellType", {"TypeName": "Medium", "TypeId": "0"})
cellType.ElementCC3D("CellType", {"TypeName": "Amoeba", "TypeId": "1"})
cellType.ElementCC3D("CellType", {"TypeName": "Bacteria", "TypeId": "2"})
volume = cc3d.ElementCC3D("Plugin", {"Name": "Volume"})
volume.ElementCC3D("TargetVolume", {}, 25)
volume.ElementCC3D("LambdaVolume", {}, 15.0)
surface = cc3d.ElementCC3D("Plugin", {"Name": "Surface"})
surface.ElementCC3D("TargetSurface", {}, 25)
surface.ElementCC3D("LambdaSurface", {}, 2.0)
contact = cc3d.ElementCC3D("Plugin", {"Name": "Contact"})
contact.ElementCC3D("Energy", {"Type1": "Medium", "Type2": "Medium"}, 0)
contact.ElementCC3D("Energy", {"Type1": "Amoeba", "Type2": "Amoeba"}, 15)
contact.ElementCC3D("Energy", {"Type1": "Amoeba", "Type2": "Medium"}, 8)
contact.ElementCC3D("Energy", {
"Type1": "Bacteria",
"Type2": "Bacteria"
}, 15)
contact.ElementCC3D("Energy", {"Type1": "Bacteria", "Type2": "Amoeba"}, 15)
contact.ElementCC3D("Energy", {"Type1": "Bacteria", "Type2": "Medium"}, 8)
contact.ElementCC3D("NeighborOrder", {}, 2)
chemotaxis = cc3d.ElementCC3D("Plugin", {"Name": "Chemotaxis"})
chemicalField = chemotaxis.ElementCC3D("ChemicalField", {
"Source": "DiffusionSolverFE",
"Name": "FGF"
})
chemicalField.ElementCC3D("ChemotaxisByType", {
"Type": "Amoeba",
"Lambda": 3
})
chemicalField.ElementCC3D("ChemotaxisByType", {
"Type": "Bacteria",
"Lambda": 2
})
flexDiffSolver = cc3d.ElementCC3D("Steppable",
{"Type": "DiffusionSolverFE"})
diffusionField = flexDiffSolver.ElementCC3D("DiffusionField")
diffusionData = diffusionField.ElementCC3D("DiffusionData")
diffusionData.ElementCC3D("FieldName", {}, "FGF")
diffusionData.ElementCC3D("DiffusionConstant", {}, 0.0)
diffusionData.ElementCC3D("DecayConstant", {}, 0.0)
diffusionData.ElementCC3D("ConcentrationFileName", {},
"Simulation/amoebaConcentrationField_2D.txt")
pifInitializer = cc3d.ElementCC3D("Steppable", {"Type": "PIFInitializer"})
pifInitializer.ElementCC3D("PIFName", {}, "Simulation/amoebae_2D.piff")
CompuCellSetup.setSimulationXMLDescription(cc3d)
def configureSimulation(sim):
import CompuCellSetup
from XMLUtils import ElementCC3D
cc3d = ElementCC3D("CompuCell3D")
potts = cc3d.ElementCC3D("Potts")
potts.ElementCC3D("Dimensions", {"x": 100, "y": 100, "z": 1})
potts.ElementCC3D("Steps", {}, 10000)
potts.ElementCC3D("Temperature", {}, 15)
potts.ElementCC3D("NeighborOrder", {}, 2)
cellType = cc3d.ElementCC3D("Plugin", {"Name": "CellType"})
cellType.ElementCC3D("CellType", {"TypeName": "Medium", "TypeId": "0"})
cellType.ElementCC3D("CellType", {"TypeName": "Bacterium", "TypeId": "1"})
cellType.ElementCC3D("CellType", {"TypeName": "Macrophage", "TypeId": "2"})
cellType.ElementCC3D("CellType", {
"TypeName": "Wall",
"TypeId": "3",
"Freeze": ""
})
volume = cc3d.ElementCC3D("Plugin", {"Name": "Volume"})
volume.ElementCC3D("TargetVolume", {}, 25)
volume.ElementCC3D("LambdaVolume", {}, 15.0)
surface = cc3d.ElementCC3D("Plugin", {"Name": "Surface"})
surface.ElementCC3D("TargetSurface", {}, 20)
surface.ElementCC3D("LambdaSurface", {}, 4.0)
contact = cc3d.ElementCC3D("Plugin", {"Name": "Contact"})
contact.ElementCC3D("Energy", {"Type1": "Medium", "Type2": "Medium"}, 0)
contact.ElementCC3D("Energy", {
"Type1": "Macrophage",
"Type2": "Macrophage"
}, 15)
contact.ElementCC3D("Energy", {
"Type1": "Macrophage",
"Type2": "Medium"
}, 8)
contact.ElementCC3D("Energy", {
"Type1": "Bacterium",
"Type2": "Bacterium"
}, 15)
contact.ElementCC3D("Energy", {
"Type1": "Bacterium",
"Type2": "Macrophage"
}, 15)
contact.ElementCC3D("Energy", {"Type1": "Bacterium", "Type2": "Medium"}, 8)
contact.ElementCC3D("Energy", {"Type1": "Wall", "Type2": "Wall"}, 0)
contact.ElementCC3D("Energy", {"Type1": "Wall", "Type2": "Medium"}, 0)
contact.ElementCC3D("Energy", {"Type1": "Wall", "Type2": "Bacterium"}, 50)
contact.ElementCC3D("Energy", {"Type1": "Wall", "Type2": "Macrophage"}, 50)
chemotaxis = cc3d.ElementCC3D("Plugin", {"Name": "Chemotaxis"})
chemicalField = chemotaxis.ElementCC3D("ChemicalField", {
"Source": "DiffusionSolverFE",
"Name": "ATTR"
})
chemicalField.ElementCC3D("ChemotaxisByType", {
"Type": "Macrophage",
"Lambda": 200
})
flexDiffSolver = cc3d.ElementCC3D("Steppable",
{"Type": "DiffusionSolverFE"})
diffusionField = flexDiffSolver.ElementCC3D("DiffusionField")
diffusionData = diffusionField.ElementCC3D("DiffusionData")
diffusionData.ElementCC3D("FieldName", {}, "ATTR")
diffusionData.ElementCC3D("DiffusionConstant", {}, 0.10)
diffusionData.ElementCC3D("DecayConstant", {}, 0.0)
diffusionData.ElementCC3D("DoNotDiffuseTo", {}, "Wall")
secretionData = diffusionField.ElementCC3D("SecretionData")
secretionData.ElementCC3D("Secretion", {"Type": "Bacterium"}, 200)
pifInitializer = cc3d.ElementCC3D("Steppable", {"Type": "PIFInitializer"})
pifInitializer.ElementCC3D("PIFName", {},
"Simulation/bacterium_macrophage_2D_wall.piff")
CompuCellSetup.setSimulationXMLDescription(cc3d)