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 init_lattice_type(self):
"""
Initializes lattice type and lattice type enum
:return: None
"""
self.lattice_type_str = CompuCellSetup.ExtractLatticeType()
if self.lattice_type_str in Configuration.LATTICE_TYPES.keys():
self.lattice_type = Configuration.LATTICE_TYPES[
self.lattice_type_str]
else:
# default choice
self.lattice_type = Configuration.LATTICE_TYPES["Square"]
