def readSimulationData(self, _i):
# self.counter+=1
# if self.counter>3:
# return
# print "self.drawMutex=",self.drawMutex
self.drawMutex.lock()
# print "self.readFileSem.available()=",self.readFileSem.available()
self.readFileSem.acquire()
self.newFileBeingLoaded = True # this flag is used to prevent calling draw function when new data is read from hard drive
# print "LOCKED self.newFileBeingLoaded=",self.newFileBeingLoaded
# self.drawMutex.lock()
if _i >= len(self.ldsFileList):
return
fileName = self.ldsFileList[_i]
self.simulationDataReader = vtk.vtkStructuredPointsReader()
self.currentFileName = os.path.join(self.ldsDir, fileName)
self.simulationDataReader.SetFileName(self.currentFileName)
# print "path= ", os.path.join(self.ldsDir,fileName)
self.simulationDataReader.Update()
self.simulationData = self.simulationDataReader.GetOutput()
# print "self.simulationData",self.simulationData
# print 'dimensions=',self.simulationData.GetDimensions()
#updating fieldDim each time we read data
import CompuCell
self.fieldDimPrevious = self.fieldDim
# self.fieldDimPrevious=CompuCell.Dim3D()
dimFromVTK = self.simulationData.GetDimensions()
self.fieldDim = CompuCell.Dim3D(dimFromVTK[0], dimFromVTK[1],
dimFromVTK[2])
#
# self.fieldDim.x=dimFromVTK[0]
# self.fieldDim.y=dimFromVTK[1]
# self.fieldDim.z=dimFromVTK[2]
# print 'self.fieldDim=',self.fieldDim
# print "vtkStructuredPointsReader ERROR CODE=",self.simulationDataReader.GetErrorCode()
self.currentStep = self.frequency * _i
self.setCurrentStep(self.currentStep)
# print "self.frequency=",self.frequency," _i=",self.frequency
# print "\n\n\n\n FINISHED RUNNING readSimulationData step ",self.currentStep," \n\n\n"
self.drawMutex.unlock()
self.readFileSem.release()
def readSimulationDataNonBlocking(self, _i):
self.newFileBeingLoaded = True # this flag is used to prevent calling draw function when new data is read from hard drive
# print "LOCKED self.newFileBeingLoaded=",self.newFileBeingLoaded
# self.drawMutex.lock()
if _i >= len(self.ldsFileList):
return False
fileName = self.ldsFileList[_i]
self.simulationDataReader = vtk.vtkStructuredPointsReader()
self.currentFileName = os.path.join(self.ldsDir, fileName)
print 'self.currentFileName=', self.currentFileName
extractedMCS = self.extractMCSNumberFromFileName(self.currentFileName)
if extractedMCS < 0:
extractedMCS = _i
self.simulationDataReader.SetFileName(self.currentFileName)
# print "path= ", os.path.join(self.ldsDir,fileName)
dataReaderIntAddr = self.__ui.extractAddressIntFromVtkObject(
self.simulationDataReader)
self.__ui.fieldExtractor.readVtkStructuredPointsData(
dataReaderIntAddr
) # swig wrapper on top of vtkStructuredPointsReader.Update() - releases GIL, hence can be used in multithreaded program that does not block GUI
# # # self.simulationDataReader.Update() # does not erlease GIL - VTK ISSUE - cannot be used in multithreaded program - blocks GUI
self.simulationData = self.simulationDataReader.GetOutput()
import CompuCell
self.fieldDimPrevious = self.fieldDim
# self.fieldDimPrevious=CompuCell.Dim3D()
dimFromVTK = self.simulationData.GetDimensions()
self.fieldDim = CompuCell.Dim3D(dimFromVTK[0], dimFromVTK[1],
dimFromVTK[2])
self.currentStep = extractedMCS
# # # self.currentStep = self.frequency * _i # this is how we set CMS for CML reading before
self.setCurrentStep(self.currentStep)
return True
def extractLatticeDescriptionInfo(self, _fileName):
import os
import os.path
import CompuCell
import CompuCellSetup
ldsFile = os.path.abspath(_fileName)
self.ldsDir = os.path.dirname(ldsFile)
import XMLUtils
from XMLUtils import CC3DXMLListPy
xml2ObjConverter = XMLUtils.Xml2Obj()
root_element = xml2ObjConverter.Parse(ldsFile)
dimElement = root_element.getFirstElement("Dimensions")
self.fieldDim = CompuCell.Dim3D()
self.fieldDim.x = int(dimElement.getAttribute("x"))
self.fieldDim.y = int(dimElement.getAttribute("y"))
self.fieldDim.z = int(dimElement.getAttribute("z"))
outputElement = root_element.getFirstElement("Output")
self.ldsCoreFileName = outputElement.getAttribute("CoreFileName")
self.frequency = int(outputElement.getAttribute("Frequency"))
self.numberOfSteps = int(outputElement.getAttribute("NumberOfSteps"))
# obtaining list of files in the ldsDir
latticeElement = root_element.getFirstElement("Lattice")
self.latticeType = latticeElement.getAttribute("Type")
#getting information about cell type names and cell ids. It is necessary during generation of the PIF files from VTK output
cellTypesElements = root_element.getElements("CellType")
listCellTypeElements = CC3DXMLListPy(cellTypesElements)
for cellTypeElement in listCellTypeElements:
typeName = ""
typeId = 0
typeName = cellTypeElement.getAttribute("TypeName")
typeId = cellTypeElement.getAttributeAsInt("TypeId")
self.typeIdTypeNameDict[typeId] = typeName
# now will convert python dictionary into C++ map<int, string>
import CC3DXML
self.typeIdTypeNameCppMap = CC3DXML.MapIntStr()
for typeId in self.typeIdTypeNameDict.keys():
self.typeIdTypeNameCppMap[int(
typeId)] = self.typeIdTypeNameDict[typeId]
# print "self.typeIdTypeNameCppMap=",self.typeIdTypeNameCppMap
ldsFileList = os.listdir(self.ldsDir)
import re
for fName in ldsFileList:
if re.match(".*\.vtk$", fName):
self.ldsFileList.append(fName)
self.ldsFileList.sort()
# print " got those files: ",self.ldsFileList
# extracting information about fields in the lds file
fieldsElement = root_element.getFirstElement("Fields")
if fieldsElement:
fieldList = XMLUtils.CC3DXMLListPy(
fieldsElement.getElements("Field"))
# print MODULENAME," fieldList=",fieldList
# print MODULENAME," dir(fieldList)=",dir(fieldList) # ['__doc__', '__init__', '__iter__', '__module__', 'elementList', 'getBaseClass']
## print MODULENAME," fieldList.getAttributes()=",fieldList.getAttributes() # doesnt exist
# print MODULENAME," fieldList.elementList=",fieldList.elementList
for fieldElem in fieldList:
# print MODULENAME," dir(fieldElem) = ",dir(fieldElem)
# print MODULENAME," fieldElem.getAttributes() = ",fieldElem.getAttributes() # <CC3DXML.MapStrStr; proxy of <Swig Object of type 'std::map< std::string,std::string,std::less< std::string >,std::allocator< std::pair< std::string const,std::string > > > *' at 0x1258e0b70> >
fieldName = fieldElem.getAttribute("Name")
# print MODULENAME," fieldsUsed key = fieldElem.getAttribute('Name') =",fieldName # e.g. 'my_field1' w/ a script
# print MODULENAME," fieldsUsed value = fieldElem.getAttribute('Type') =",fieldElem.getAttribute("Type")
self.fieldsUsed[fieldElem.getAttribute(
"Name")] = fieldElem.getAttribute("Type")
if fieldElem.findAttribute(
"Script"): # True or False if present
# ToDo: if a "CustomVis" Type was provided, require that a "Script" was also provided; else warn user
customVisScript = fieldElem.getAttribute("Script")
# print MODULENAME," fieldElem.getAttribute('Script') =",customVisScript
# self.fieldsUsed['Script'] = fieldElem.getAttribute("Script")
# self.customVisScriptDict[fieldName] = customVisScript
self.customVis = CompuCellSetup.createCustomVisPy(
fieldName)
self.customVis.registerVisCallbackFunction(
CompuCellSetup.vtkScriptCallback)
# print MODULENAME,' customVis.addActor: fieldName (->vtkActor) =',fieldName
self.customVis.addActor(fieldName, "vtkActor")
# self.customVis.addActor(customVisScript,"customVTKScript")
self.customVis.addActor(
"customVTKScript",
customVisScript) # we'll piggyback off the actorsDict
