class GraphVTKVisSteppable(SteppableBasePy):
def __init__(self, _simulator, _frequency=10):
SteppableBasePy.__init__(self, _simulator, _frequency)
def start(self):
try:
import networkx
except ImportError, e:
return
self.visData = CompuCellSetup.createCustomVisPy("CustomGraph")
self.visData.registerVisCallbackFunction(self.visualize)
self.visData.addActor("glyph", "vtkActor")
self.visData.addActor("profile", "vtkActor")
self.visData.addActor("nodeColorBar", "vtkScalarBarActor")
self.visData.addActor("nodeSizeText", "vtkTextActor")
self.visData.addActor("edgeColorBar", "vtkScalarBarActor")
self.visData.addActor("edgeSizeText", "vtkTextActor")
self.cellIdDict = {}
self.cellPosDict = {}
self.cellContactNetwork = nx.Graph()
self.updateCellIdDict()
self.makeContactNetwork(self.cellContactNetwork, fillDegrees=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
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
def start(self):
self.visData = CompuCellSetup.createCustomVisPy("CustomCone")
self.visData.registerVisCallbackFunction(self.visualize)
self.visData.addActor("cone", "vtkActor")
def start(self):
self.visData=CompuCellSetup.createCustomVisPy("CustomCone")
self.visData.registerVisCallbackFunction(self.visualize)
self.visData.addActor("cone","vtkActor")