def main():
# set graphs directory
graphPath = str(cur+'/NetworkFiles/')
# create a new window
window = MyDotWindow()
window.connect('destroy',gtk.main_quit)
window.show()
#create the main graph instance of a graph class
mainGraph = Graph()
#START THE MAIN LOOP
menuInput = ""
subMenuInput = ''
# create vascularNetwork instance
vascularNetwork = VascularNetwork()
filename = None
k = None
while menuInput != "q":
menuInput = ""
print ""
print '====================================='
print '# VascularNetworkCreator_v2.3 #'
print '====================================='
print " [a] - add vessel to network"
print " [d] - delete vessel in network"
print " [n] - new network"
print " [b] - set boundary conditions"
print " [f] - set global fluid properties"
print " [l] - load network"
print " [s] - save network"
print " [u] - update XML form CSV file(s)"
print " [g] - print network graph"
print " [p] - print network informations"
print " [q] - quit"
print ""
print ' current network: ', filename
while menuInput not in ("l","b","q","a","s","g","f","d","u",'n','p'):
menuInput = raw_input("what to do? ")
if menuInput == "a":
print "Add new vessel"
existing = False
vesselId = raw_input(" enter the vessel id: ")
while True:
try:
vesselId = int(vesselId)
if vesselId not in vascularNetwork.vessels:
break
else:
existing = True
except ValueError:
print "TYPE-ERROR: vessel id must be type(int) not type(string)"
vesselId = raw_input(" enter non existing id: ")
if existing == True:
print " the vessel id exists already enter a new one"
vesselId = raw_input(" enter non existing id: ")
existing = False
if vascularNetwork.vessels != {}:
existing = False
mother = raw_input(" enter existing mother id: ")
while True:
try:
mother = int(mother)
if mother in vascularNetwork.vessels.keys() and vascularNetwork.vessels[mother].rightDaughter == None:
break
else:
existing = True
except ValueError:
print "TYPE-ERROR: mother id must be type(int) not type(string)"
mother = raw_input(" enter existing mother id: ")
if existing == True:
if mother not in vascularNetwork.vessels: print " there exists no vessel with this id"
else: print " only bifurcations possible!"
mother = raw_input(" enter existing mother id: ")
existing = False
if vascularNetwork.vessels[mother].leftDaughter == None: vascularNetwork.vessels[mother].leftDaughter = vesselId
else: vascularNetwork.vessels[mother].rightDaughter = vesselId
vascularNetwork.addVessel(vesselId)
print " define vessel compliance!"
inputType = '0'
print " available compliance types:"
print ""
# get all defined boundaryConditions from constants-dict save as bcTypes
complianceTypes = vesselComplianceElements.keys()
compTypes = ['default (Hayashi)']
for compType in complianceTypes:
compTypes.append(compType)
# show all compliance types in the compTypes
index = 0
for key in compTypes:
print " [",str(index).rjust(2),"] ",key
index = index+1
# get user input and check if it was correct to define the bcType
existing = False
inputType = raw_input (" choose type ")
while True:
# check if right input
try:
inputType = int(inputType)
if inputType in np.linspace(0,len(compTypes)-1,len(compTypes)):
break
else:
existing = True
# if not int but string
except ValueError:
print " TYPE-ERROR: vessel id must be type(int) not type(string)"
inputType = (raw_input (" choose type "))
# if int but to low or high
if existing == True:
print " the type does not exist"
inputType = (raw_input (" choose type "))
existing = False
compType = compTypes[int(inputType)]
if compType != 'default (Hayashi)':
vesselData = {'complianceType':compType}
vesselComplianceElements[compType]
print ""
print " set values for the Compliance: ", compType
question = True
for arg in vesselComplianceElements[compType]:
if arg != 'complianceType':
currValue = raw_input (str(" set value for "+str(arg)+' '))
test = True
try: float(currValue)
except:
print ' VALUE or TYPE ERROR, set to None'
test = False
if test == True: vesselData[arg] = (float(currValue))
else: vesselData[arg] = None
vascularNetwork.updateNetwork({'vesselData': { vesselId : vesselData}})
mainGraph.update_graph(vascularNetwork, window)
if menuInput == "d":
print "Delete a vessel and all its daugthers"
if vascularNetwork.vessels.keys() != []:
existing = False
vesselId = raw_input(" enter existing vessel id: ")
while True:
try:
vesselId = int(vesselId)
if vesselId in vascularNetwork.vessels:
break
else:
existing = True
except ValueError:
print "TYPE-ERROR: vessel id must be type(int) not type(string)"
vesselId = raw_input(" enter existing vessel id: ")
if existing == True:
print " the vessel does not exist"
vesselId = raw_input(" enter existing vessel id: ")
existing = False
#travers the tree starting with the vessel and collect all ids
toDelete = findAllDaughters(vascularNetwork,vesselId)
toDelete.append(vesselId)
for vesselToDelete in toDelete:
vascularNetwork.deleteVessel(vesselToDelete)
# empty the graph to redraw it
if vascularNetwork.vessels.keys() == []:
mainGraph.update_graph(None, window)
vascularNetwork = VascularNetwork()
else:
mainGraph.update_graph(vascularNetwork, window)
else:
print " there are no vessels to delete"
elif menuInput == "n":
print "new network"
question = raw_input(" are u sure to delete all current data? [y] - yes: ")
if question == 'y':
# delete vascularNetwork
del vascularNetwork
# create vascularNetwork instance
mainGraph.update_graph(None, window)
vascularNetwork = VascularNetwork()
elif menuInput == "p":
vascularNetwork.showVessels()
vascularNetwork.showNetwork()
elif menuInput == "g":
print mainGraph.getGraph()
elif menuInput == "b":
subMenuInput = ''
while subMenuInput not in ['1','2','3','4','5','b']:
if vascularNetwork.getVariableValue('vessels') == {}:
print " there are no vessels defined and thus no boundarys available";break
else:
# evaluate boundarys in Network
boundarys = []
notDefinedBoundarys = []
boundarys.extend(vascularNetwork.boundaryVessels)
if vascularNetwork.root != None and vascularNetwork.root not in boundarys:
boundarys.append(vascularNetwork.root)
boundarysSaved = vascularNetwork.boundaryConditions.keys()
# update saved boundary conditions
for boundarysCurrent in boundarys:
if boundarysCurrent not in boundarysSaved:
print " boundary added to vascularNetwork"
vascularNetwork.boundaryConditions[boundarysCurrent] = []
boundarysSaved.append(boundarysCurrent)
if vascularNetwork.boundaryConditions[boundarysCurrent] == []:
notDefinedBoundarys.append(boundarysCurrent)
nonBoundarys = list(set(boundarys).symmetric_difference(set(boundarysSaved)))
for nonBoundary in nonBoundarys:
print " boundary removed from vacularNetwork"
del(vascularNetwork.boundaryConditions[nonBoundary])
if nonBoundary in notDefinedBoundarys: notDefinedBoundarys.remove(nonBoundary)
vascularNetwork.evaluateConnections()
print ""
print " sub menu: boundary conditions"
print ""
print " [1] - show boundary conditions"
print " [2] - add boundary condition "
print " [3] - del boundary condition "
print " [4] - load boundary conditions from CSV"
print " [5] - write boundary conditions to CSV"
print " [b] - back to the main menu"
print ""
subMenuInput = raw_input(" what to do? ")
if subMenuInput == '1':
print " boundary conditions"
pprint.pprint(vascularNetwork.boundaryConditions)
subMenuInput = ''
elif subMenuInput == '2' and vascularNetwork.root != []:
print " add boundary condition"
print ""
definedBoundarys = list(set(notDefinedBoundarys).symmetric_difference(set(vascularNetwork.boundaryConditions.keys())))
print " vessels with defined boundary condition:"
print " ",' '.join(str(i) for i in definedBoundarys)
print " vessels with undefined boundary condition:"
print " ",' '.join(str(i) for i in notDefinedBoundarys)
print ""
existing = False
vesselId = raw_input(" enter existing vessel id: ")
while True:
try:
vesselId = int(vesselId)
if vesselId in vascularNetwork.vessels:
break
else:
existing = True
except ValueError:
print " TYPE-ERROR: vessel id must be type(int) not type(string)"
vesselId = raw_input(" enter existing vessel id: ")
if existing == True:
print " the vessel does not exist"
vesselId = raw_input(" enter existing vessel id: ")
existing = False
inputType = '0'
print " add boundary condition type:"
print ""
# get all defined boundaryConditions from constants-dict save as bcTypes
bcTypesAll = bcTagsClassReferences.keys()
bcTypes = []
for bcType in bcTypesAll:
if "_" is not bcType[0]:
bcTypes.append(bcType)
bcTypes.sort()
# show all boundaryConditions in the bcTypes
index = 0
for key in bcTypes:
print " [",str(index).rjust(2),"] ",key
index = index+1
# get user input and check if it was correct to define the bcType
existing = False
inputType = raw_input (" choose type ")
while True:
# check if right input
try:
inputType = int(inputType)
if inputType in np.linspace(0,len(bcTypes)-1,len(bcTypes)):
break
else:
existing = True
# if not int but string
except ValueError:
print " TYPE-ERROR: vessel id must be type(int) not type(string)"
inputType = (raw_input (" choose type "))
# if int but to low or high
if existing == True:
print " the type does not exist"
inputType = (raw_input (" choose type "))
existing = False
bcType = bcTypes[int(inputType)]
boundaryInstance = eval(bcTagsClassReferences[bcType])()
boundaryDataDict = {}
boundaryDataDict['name']= bcType
print ""
print " set values for the BC condition: ", bcType
print " enter 'b' for the first value to skip this procedure"
question = True
for arg in bcTags[bcType]:
if question == True:
currValue = raw_input (str(" set value for "+str(arg)+' '))
if currValue == 'b': question=False
test = True
try: float(currValue)
except:
print ' VALUE or TYPE ERROR, set to None'
test = False
if test == True: boundaryDataDict[arg] = (float(currValue))
else: boundaryDataDict[arg] = None
else: boundaryDataDict[arg] = None
if len(vascularNetwork.boundaryConditions.keys()) == 1:
print " set position of the BC condition"
position = '2'
while position not in ['1','0']:
position = raw_input (" enter '0' for the start or '1' for the end of the vessel ")
if position == '1':
#bcType = ''.join(['_',bcType])
boundaryDataDict['name']= ''.join(['_',bcType])
print bcType,boundaryDataDict
boundaryInstances = []
boundaryInstance.update(boundaryDataDict)
boundaryInstances.append(boundaryInstance)
if vesselId not in vascularNetwork.boundaryConditions.keys():
vascularNetwork.boundaryConditions[vesselId] = boundaryInstances
else:
vascularNetwork.boundaryConditions[vesselId].extend(boundaryInstances)
#if vascularNetwork.getVariableValue('root') != None:
mainGraph.update_graph(vascularNetwork, window)
subMenuInput = ''
elif subMenuInput == '3' and vascularNetwork.root != []:
print " delete boundary condition"
print ""
pprint.pprint(vascularNetwork.boundaryConditions)
vesselId = -1
while vesselId not in vascularNetwork.boundaryConditions.keys():
vesselId = int(raw_input (" choose vessel id "))
bcs = vascularNetwork.boundaryConditions[vesselId]
if bcs != []:
print ""
index = 0
for bc in bcs:
print " [",str(index).rjust(2),"] ",bc.name
index = index+1
print ""
inType = '0'
while inType not in np.linspace(0,len(bcs)-1,len(bcs)):
inType = int(raw_input (" choose condition to delete "))
print ""
print " boundary condition ",bcs[inType]," removed!"
print ""
vascularNetwork.boundaryConditions[vesselId].remove(bcs[inType])
mainGraph.update_graph(vascularNetwork, window)
else:
print " nothing to delete!"
subMenuInput = ''
elif subMenuInput == '4' and vascularNetwork.root != []:
print " load boundary conditions from CSV"
print ""
filename = enterFilename(filename,'')
boundaryConditions,boundaryConditionPolyChaos = readBCFromCSV(filename = ''.join([filename,'BC','.csv']))
vascularNetwork.update({'boundaryConditions':boundaryConditions,
'boundaryConditionPolyChaos':boundaryConditionPolyChaos})
mainGraph.update_graph(vascularNetwork, window)
elif subMenuInput == '5' and vascularNetwork.root != []:
print " write boundary conditions to CSV"
print ""
filename = enterFilename(filename,'')
boundaryConditions = vascularNetwork.getVariableValue('boundaryConditions')
boundaryConditionPolyChaos = deepcopy(vascularNetwork.getVariableValue('boundaryConditionPolyChaos'))
writeBCToCSV(boundaryConditions,boundaryConditionPolyChaos,filename = ''.join([filename,'BC','.csv']))
elif subMenuInput == 'b':
break
elif menuInput == "f":
subMenuInput = ''
while subMenuInput not in ["1","2","b"]:
print ""
print " sub menu: set global fluid properties"
print ""
print " [1] - set all"
print " [2] - set individual"
print " [b] - back to the main menu"
print ""
print " current fluid properties:"
for key,value in vascularNetwork.globalFluid.iteritems():
print " {0:20} {1:10} {2:10}".format(key,value,variableUnits[key])
print ""
subMenuInput = raw_input(" what to do? ")
if subMenuInput == '1':
print " set all fluid properties"
for key in vascularNetwork.globalFluid.keys():
inputType = "1"
typeFalse = False
while typeFalse == False:
try:
inputType = raw_input(" type value for property: {} with unit {} : ".format(key,variableUnits[key]))
inputType = float(inputType)
typeFalse = True
vascularNetwork.globalFluid[key] = inputType
except: pass
subMenuInput = ''
elif subMenuInput == '2':
print " set individual fluid property:"
i = 0
properties = vascularNetwork.globalFluid.keys()
for property_i in properties:
print " [",i,'] - ',property_i
i = 1+i
inputType = 0
while inputType not in [str(i) for i in range(0,len(properties))]:
inputType = raw_input(" choose property to set ")
inputProperty = ""
inputFalse = False
while inputFalse == False:
try:
inputProperty = raw_input(" type value for property: {} with unit {} : ".format(properties[int(inputType)],variableUnits[properties[int(inputType)]]))
inputProperty = float(inputProperty)
vascularNetwork.globalFluid[properties[int(inputType)]] = inputProperty
inputFalse = True
except: pass
subMenuInput = ''
elif subMenuInput == 'b':
break
elif menuInput == "l":
try:
FILE = open('.recentFilenames.pickle',"rb")
# store pickle
recentFilenames = cPickle.load(FILE)
FILE.close()
except:
recentFilenames = []
subMenuInput = ''
print ""
print " sub menu: load data"
print ""
print " [1] - load network from XML"
print " [2] - load vessel data from CSV"
print " [3] - load vessel data and boundary conditions from CSV"
print " [4] - load network from SolutionData"
print " [b] - back to the main menu"
print ""
while subMenuInput not in ["1","2","3","b"]:
subMenuInput = raw_input("what to do? ")
print ""
print " resent used networks"
i = 1
for name in recentFilenames:
print " [",i,'] - ',name
i = 1+i
print ""
if subMenuInput == '1':
print " load from XML"
filename = enterFilename(filename,'.xml',recentFilenames = recentFilenames)
if filename == None:break
# delete the old network
del vascularNetwork
#load the new network
vascularNetwork = loadNetworkFromXML(filename= filename)
if vascularNetwork == None:
mainGraph.update_graph(None, window)
vascularNetwork = VascularNetwork()
filename = None
break
mainGraph.update_graph(vascularNetwork, window)
filename, value = filename.split(".",1)
break
elif subMenuInput == '2':
print " load vessel data from CSV - non existing vessels are added automatically"
print ""
filename = enterFilename(filename,'.csv',recentFilenames = recentFilenames)
if filename == None:break
vascularNetwork.updateNetwork(readVesselDataFromCSV(filename=filename))
mainGraph.update_graph(vascularNetwork, window)
filename, value = filename.split(".",1)
break
elif subMenuInput == '3':
print " load vessel data and boundary conditions from CSV"
filename = enterFilename(filename,'.csv',recentFilenames = recentFilenames)
if filename == None:break
vascularNetwork.updateNetwork(readVesselDataFromCSV(filename=filename))
mainGraph.update_graph(vascularNetwork, window)
filename, value = filename.split(".",1)
boundaryConditions,boundaryConditionPolyChaos = readBCFromCSV(filename = ''.join([filename,'BC','.csv']))
vascularNetwork.update({'boundaryConditions':boundaryConditions,
'boundaryConditionPolyChaos':boundaryConditionPolyChaos})
mainGraph.update_graph(vascularNetwork, window)
break
elif subMenuInput == '4':
print " load network from SolutionData"
try:
networkName,dataSetNumber = chooseSolutionDataCase()
vascularNetwork,solData,Description = loadSolutionDataFile(networkName,[dataSetNumber])
mainGraph.update_graph(vascularNetwork, window)
filename, value = filename.split(".",1)
except: " ERROR occured could not open requested network, maybe the class description is out dated"
break
elif subMenuInput == 'b':
break
if filename != None:
if filename not in recentFilenames: recentFilenames.insert(0,filename)
else:
recentFilenames.remove(filename)
recentFilenames.insert(0,filename)
if len(recentFilenames) > 9: recentFilenames.pop(-1)
FILE = open('.recentFilenames.pickle',"w")
# store pickle
cPickle.dump(recentFilenames, FILE, protocol=2)
FILE.close()
elif menuInput == "s":
subMenuInput = ''
print ""
print " sub menu: save data"
print ""
print " [1] - write to XML"
print " [2] - write vessel data to CSV"
print " [3] - write vessel data and boundary conditions to CSV"
print " [4] - write graph to .png and .dot files"
print " [b] - back to the main menu"
print ""
while subMenuInput not in ["1","2","3","b"]:
subMenuInput = raw_input("what to do? ")
if subMenuInput == '1':
print " write to XML"
filename = enterFilename(filename,'.xml')
if filename == None:break
writeNetworkToXML(vascularNetwork,filename = filename)
filename, value = filename.split(".",1)
break
elif subMenuInput == '2':
print " write vessel data to CSV"
filename = enterFilename(filename,'.csv')
if filename == None:break
writeVesselDataToCSV(vessels = vascularNetwork.vessels, filename = filename)
filename, value = filename.split(".",1)
break
elif subMenuInput == '3':
print " write vessel data and boundary conditions to CSV"
filename = enterFilename(filename,'.csv')
if filename == None:break
writeVesselDataToCSV(vessels = vascularNetwork.vessels, filename = filename)
filename, value = filename.split(".",1)
boundaryConditions = vascularNetwork.getVariableValue('boundaryConditions')
boundaryConditionPolyChaos = deepcopy(vascularNetwork.getVariableValue('boundaryConditionPolyChaos'))
writeBCToCSV(boundaryConditions,boundaryConditionPolyChaos,filename = ''.join([filename,'BC','.csv']))
break
elif subMenuInput == '4':
print " write graph to .png and .dot files"
pictureName = str(raw_input(" enter pictureName (only!):"))
if pictureName == "":
pictureName = 'pydotTest'
mainGraph.graph.write(graphPath+filename+'/'+pictureName+'.dot')
mainGraph.graph.write_png(graphPath+filename+'/'+pictureName+'.png')
break
if subMenuInput == 'b':
break
elif menuInput == "u":
subMenuInput = ''
print ""
print " sub menu: update XML from CSV"
print ""
print " load from XML"
filename = enterFilename(filename,'.xml')
if filename == None:break
# delete the old network
del vascularNetwork
#load the new network
vascularNetwork = loadNetworkFromXML(filename= filename)
if vascularNetwork == None:
vascularNetwork = VascularNetwork()
break
mainGraph.update_graph(vascularNetwork, window)
filename, value = filename.split(".",1)
print " load vessel data from CSV - non existing vessels are added automatically"
filenameCSV = ''.join([filename,'.csv'])
vascularNetwork.updateNetwork(readVesselDataFromCSV(filename=filenameCSV))
print " load boundaryData from csv as well? press [u]"
subMenuInput = raw_input("yes [u]? ")
if subMenuInput == 'u':
boundaryConditions,boundaryConditionPolyChaos = readBCFromCSV(filename = ''.join([filename,'BC','.csv']))
vascularNetwork.update({'boundaryConditions':boundaryConditions,
'boundaryConditionPolyChaos':boundaryConditionPolyChaos})
try: mainGraph.update_graph(vascularNetwork, window)
except:mainGraph.update_graph(None, window)
print " write to XML"
filenameXML = ''.join([filename,'.xml'])
writeNetworkToXML(vascularNetwork,filename = filenameXML)
def loadNetworkFromXML(filename = None, update = None, networkPath = str(cur+"/../NetworkFiles/")):
'''
Function laods network from XML-file
version of XML files supported: 4.0
'''
currentVersions = ['4.0']
# read from file
if filename == None:
print 'ERROR: moduleXML.loadNetworkFromXML() : load XML - no filename passed'
return None
if '.xml' not in filename:
filename = ''.join([filename,'.xml'])
networkDirectory = filename.split('.')[0]
if not os.path.exists(str(networkPath+networkDirectory)):
print 'ERROR: moduleXML.loadNetworkFromXML(): directory and file does not exists'
return None
# create vascularNetwork instance
vascularNetwork = VascularNetwork()
# set name
vascularNetwork.name = (filename.split('.'))[0]
try:
parser = etree.XMLParser(encoding='iso-8859-1')
tree = etree.parse(''.join([networkPath,networkDirectory,'/',filename]), parser)
except (etree.ParseError, ImportError) as e:
if isinstance(e, etree.ParseError):
print " ERROR moduleXML.loadNetworkFromXML() on line {} {}: ".format(e.position[0], e)
exit()
# create root
root = tree.getroot()
xmlFileVersion = root.attrib['version']
if xmlFileVersion not in currentVersions:
print "ERROR moduleXML.loadNetworkFromXML(): XML file is outdated file-version {} " \
"current supported version {}, could not parse file! system exit".format(root.attrib['version'],currentVersions); exit()
for xmlElementName in xmlElements:
for xmlElement in root.findall(''.join([".//",xmlElementName])):
if xmlElementName == 'boundaryConditions':
# loop through all boundaryCondition
for boundaryConditionElement in xmlElement.findall(''.join(['.//','boundaryCondition'])):
try: vesselId = int(boundaryConditionElement.attrib['vesselId'])
except: loadingErrorMessageVariableError('vesselId', 'one boundaryCondition', '', variablesDict['vesselId'])
boundaryInstances = []
boundaryIntervals = []
# loop through possible communicator class types
for boundaryType in xmlElementsReference[xmlElementName]:
# find all bcs of this type
for bcElements in boundaryConditionElement.findall(''.join(['.//',boundaryType])):
boundaryInstance = eval(bcTagsClassReferences[boundaryType])()
boundaryDataDict = {}
boundaryDataDict['name'] = boundaryType
boundaryIntervalDataDict = {}
# loop through all variables of this type, convert and save values of these
for variable in xmlElementsReference[xmlElementName][boundaryType]:
# find normal variables
try: element = bcElements.findall(''.join(['.//',variable]))[0]
except: loadingErrorMessageVariableError(variable, 'boundaryCondition', boundaryType, variablesDict[variable])
# get variable value
try: variableValueStr = element.text
except: loadingErrorMessageValueError(variable, 'boundaryCondition', boundaryType, variablesDict[variable])
# get unit
try: variableUnit = element.attrib['unit']
except: variableUnit = None
# save converted XML-value
boundaryDataDict[variable] = loadVariablesConversion(variable, variableValueStr, variableUnit)
# find polynomial chaos variable
try:
# find polychaos variables
element = bcElements.findall(''.join(['.//',variable,'-polyChaos']))[0]
# get variable value
try: variableValueStr = element.text
except: loadingErrorMessageValueError(variable, 'boundaryCondition', boundaryType, variablesDict[variable])
# get unit
try: variableUnit = element.attrib['unit']
except: variableUnit = None
# save converted XML-value
boundaryIntervalDataDict[variable] = loadVariablesConversion(variable, variableValueStr, variableUnit, polychaos = True)
boundaryIntervalDataDict['name'] = boundaryType
except: pass
# adjust path to boundary condition file
if variable == 'filePathName':
path = ''.join([networkDirectory,'/'])
if path not in variableValueStr: variableValueStr = variableValueStr.join([path,''])
boundaryDataDict['filePathName'] = variableValueStr
boundaryInstance.update(boundaryDataDict)
boundaryInstances.append(boundaryInstance)
if boundaryIntervalDataDict != {}:
boundaryIntervals.append(boundaryIntervalDataDict)
# apply read data to vascularNetwork
if vesselId not in vascularNetwork.boundaryConditions.keys():
vascularNetwork.boundaryConditions[vesselId] = boundaryInstances
else:
vascularNetwork.boundaryConditions[vesselId].extend(boundaryInstances)
if boundaryIntervals != []:
vascularNetwork.boundaryConditionPolyChaos[vesselId] = boundaryIntervals
elif xmlElementName == 'vessels':
for vesselXMLnode in xmlElement.findall(''.join(['.//','vessel'])):
vesselData = {}
vesselPolychaosData = {}
# load vessel attributes
for attribute in vesselAttributes:
try: vesselData[attribute] = loadVariablesConversion(attribute, vesselXMLnode.attrib[attribute], '')
except:
try: loadingErrorMessageVariableError(attribute, 'vessel', vesselData['Id'], variablesDict[attribute])
except: loadingErrorMessageVariableError(attribute, 'one vessel', '', variablesDict[attribute])
for vesselElement in xmlElementsReference[xmlElementName]:
# check if compliance and adjust variables
if vesselElement == 'compliance':
try: complianceTypeElement = vesselXMLnode.findall(''.join(['.//','complianceType']))[0]
except: loadingErrorMessageVariableError('complianceType', 'vessel', vesselData['Id'], variablesDict['complianceType'])
complianceType = loadVariablesConversion('complianceType', complianceTypeElement.text, '')
variables = vesselElementReference[vesselElement][complianceType]
else:
variables = vesselElementReference[vesselElement]
# load variables
for variable in variables:
try: element = vesselXMLnode.findall(''.join(['.//',variable]))[0]
except: loadingErrorMessageVariableError(variable, 'vessel', vesselData['Id'], variablesDict[variable])
# get variable value
try: variableValueStr = element.text
except: loadingErrorMessageValueError(variable, 'vessel', vesselData['Id'], variablesDict[variable])
# get unit
try: variableUnit = element.attrib['unit']
except: variableUnit = None
# save converted XML-value
vesselData[variable] = loadVariablesConversion(variable, variableValueStr, variableUnit)
# find polynomial chaos variable
try:
# find polychaos variables
element = vesselXMLnode.findall(''.join(['.//',variable,'-polyChaos']))[0]
# get variable value
try: variableValueStr = element.text
except: loadingErrorMessageValueError(variable, 'vessel', vesselData['Id'], variablesDict[variable])
# get unit
try: variableUnit = element.attrib['unit']
except: variableUnit = None
# save converted XML-value
vesselPolychaosData[variable] = loadVariablesConversion(variable, variableValueStr, variableUnit, polychaos = True)
except: pass
vesselData['polyChaos'] = vesselPolychaosData
vascularNetwork.updateNetwork({'vesselData':{vesselData['Id']:vesselData}})
elif xmlElementName == 'communicators':
# loop through possible communicator class types
for comunicatorType in xmlElementsReference[xmlElementName]:
# find all communicator of this type
for comElements in xmlElement.findall(''.join(['.//',comunicatorType])):
# loop through all variables of this type, convert and save values of these
communicatorData = {}
for variable in xmlElementsReference[xmlElementName][comunicatorType]:
try: element = comElements.findall(''.join(['.//',variable]))[0]
except: loadingErrorMessageVariableError(variable, 'communicator', comunicatorType, variablesDict[variable])
# get variable value
try: variableValueStr = element.text
except: loadingErrorMessageValueError(variable, 'communicator', comunicatorType, variablesDict[variable])
# get unit
try: variableUnit = element.attrib['unit']
except: variableUnit = None
communicatorData[variable] = loadVariablesConversion(variable, variableValueStr, variableUnit)
if variable == 'comId': comId = communicatorData[variable]
vascularNetwork.updateNetwork({'communicators':{comId:communicatorData}})
elif xmlElementName == 'globalFluid':
globalFluidData = {}
globalFluidPolychaosData = {}
for variable in xmlElementsReference[xmlElementName]:
# find normal variables
try: element = xmlElement.findall(''.join(['.//',variable]))[0]
except: loadingErrorMessageVariableError(variable, 'global fluid', '', variablesDict[variable])
# get variable value
try: variableValueStr = element.text
except: loadingErrorMessageValueError(variable, 'global fluid', '', variablesDict[variable])
# get unit
try: variableUnit = element.attrib['unit']
except: variableUnit = None
# save converted XML-value
globalFluidData[variable] = loadVariablesConversion(variable, variableValueStr, variableUnit)
# find polynomial chaos variable
try:
# find polychaos variables
element = xmlElement.findall(''.join(['.//',variable,'-polyChaos']))[0]
# get variable value
try: variableValueStr = element.text
except: loadingErrorMessageValueError(variable, 'global fluid', '', variablesDict[variable])
# get unit
try: variableUnit = element.attrib['unit']
except: variableUnit = None
# save converted XML-value
globalFluidPolychaosData[variable] = loadVariablesConversion(variable, variableValueStr, variableUnit, polychaos = True)
except: pass
vascularNetwork.updateNetwork({'globalFluid':globalFluidData,'globalFluidPolyChaos':globalFluidPolychaosData})
elif xmlElementName in vascularNetworkElements: # vascularNetwork
vascularNetworkData = {}
for variable in xmlElementsReference[xmlElementName]:
try: element = xmlElement.findall(''.join(['.//',variable]))[0]
except: loadingErrorMessageVariableError(variable, xmlElementName, '', variablesDict[variable])
# get variable value
try: variableValueStr = element.text
except: loadingErrorMessageValueError(variable, xmlElementName, '', variablesDict[variable])
# get
try: variableUnit = element.attrib['unit']
except: variableUnit = None
# save converted XML-value
vascularNetworkData[variable] = loadVariablesConversion(variable, variableValueStr, variableUnit)
vascularNetwork.update(vascularNetworkData)
return vascularNetwork
def main():
# set graphs directory
graphPath = str(cur+'/../vascular1Dflow_v0.2/NetworkFiles/')
# create a new window
window = MyDotWindow()
window.connect('destroy',gtk.main_quit)
window.show()
#create the main graph instance of a graph class
mainGraph = Graph()
#START THE MAIN LOOP
menuInput = ""
subMenuInput = ''
# create vascularNetwork instance
vascularNetwork = VascularNetwork()
filename = None
networkTopologyMode = True
networkTopologyModes = {0: 'node Description', 1:'mother-daugther Description'}
k = None
while menuInput != "q":
menuInput = ""
print ""
print "vnc 2.1 - menu"
print ""
print " [a] - add vessel to network"
print " [d] - delete vessel in network"
print " [n] - new network"
print " [b] - set boundary conditions"
print " [l] - load network"
print " [s] - save network"
print " [u] - update XML form CSV file"
print " [g] - print network graph"
print " [f] - print network informations"
print " [m] - change network topology mode; current: ", networkTopologyModes[networkTopologyMode]
print " [q] - quit"
print ""
print ' current network: ', filename
while menuInput not in ("l","b","q","a","s","g","f","d","u",'n','m'): #(menuInput != "l") and (menuInput != "b") and (menuInput != "q") and (menuInput != "a") and (menuInput != "s") and (menuInput != "g") and (menuInput != "d") and (menuInput != "f"):
menuInput = raw_input("what to do? ")
if menuInput == "a":
print "Add new vessel"
existing = False
vesselID = raw_input(" enter the vessel id: ")
while True:
try:
vesselID = int(vesselID)
if vesselID not in vascularNetwork.vessels:
break
else:
existing = True
except ValueError:
print "TYPE-ERROR: vessel id must be type(int) not type(string)"
vesselID = raw_input(" enter non existing id: ")
if existing == True:
print " the vessel id exists already enter a new one"
vesselID = raw_input(" enter non existing id: ")
existing = False
if not networkTopologyMode:
# define start node ony bifurctaion are allowed
startNode = int(raw_input(" enter starting node: "))
while bifTest(vascularNetwork.vessels, startNode) == False:
print " only bifurcations possible!"
startNode = int(raw_input(" enter starting node: "))
# define end node
endNode = int(raw_input (" enter ending node: "))
# create vessel obj and save them in vessels-dict
dataDict = {'end': endNode, 'start': startNode}
vascularNetwork.addVessel(vesselID, dataDict)
else:
if vascularNetwork.vessels != {}:
# mother = int(raw_input(" enter existing mother id: "))
# while mother not in vascularNetwork.vessels or (mother in vascularNetwork.vessels and vascularNetwork.vessels[mother].rightDaughter != None):
# if mother not in vascularNetwork.vessels: print " there exists no vessel with this ID"
# else: print " only bifurcations possible!"
# mother = int(raw_input(" enter existing mother id: "))
existing = False
mother = raw_input(" enter existing mother id: ")
while True:
try:
mother = int(mother)
if mother in vascularNetwork.vessels and vascularNetwork.vessels[mother].rightDaughter == None:
break
else:
existing = True
except ValueError:
print "TYPE-ERROR: mother id must be type(int) not type(string)"
mother = raw_input(" enter existing mother id: ")
if existing == True:
if mother not in vascularNetwork.vessels: print " there exists no vessel with this id"
else: print " only bifurcations possible!"
mother = raw_input(" enter existing mother id: ")
existing = False
if vascularNetwork.vessels[mother].leftDaughter == None: vascularNetwork.vessels[mother].leftDaughter = vesselID
else: vascularNetwork.vessels[mother].rightDaughter = vesselID
vascularNetwork.vessels[mother].end = None
vascularNetwork.addVessel(vesselID)
mainGraph.update_graph(vascularNetwork, window)
if menuInput == "d":
print "Delete a vessel and all its daugthers"
if vascularNetwork.vessels.keys() != []:
# vesselID = int(raw_input(" enter the vessel id: "))
# while (vesselID in vascularNetwork.vessels) == False:
# print " the vessel does not exist"
# vesselID = int(raw_input(" enter existing vessel id: "))
existing = False
vesselID = raw_input(" enter existing vessel id: ")
while True:
try:
vesselID = int(vesselID)
if vesselID in vascularNetwork.vessels:
break
else:
existing = True
except ValueError:
print "TYPE-ERROR: vessel id must be type(int) not type(string)"
vesselID = raw_input(" enter existing vessel id: ")
if existing == True:
print " the vessel does not exist"
vesselID = raw_input(" enter existing vessel id: ")
existing = False
#travers the tree starting with the vessel and collect all ids
toDelete = findAllDaughters(vascularNetwork,vesselID)
toDelete.append(vesselID)
for vesselToDelete in toDelete:
vascularNetwork.deleteVessel(vesselToDelete)
# empty the graph to redraw it
mainGraph.update_graph(vascularNetwork, window)
else:
print " there are no vessels to delete"
elif menuInput == "n":
print "new network"
question = raw_input(" are u sure to delete all current data? [n] - yes: ")
if question == 'n':
# delet vascularNetwork
del vascularNetwork
# create vascularNetwork instance
vascularNetwork = VascularNetwork()
mainGraph.update_graph(vascularNetwork, window)
elif menuInput == "m":
networkTopologyMode = not networkTopologyMode
elif menuInput == "f":
vascularNetwork.showVessels()
vascularNetwork.showNetwork()
vascularNetwork.calculateNetworkResistance()
elif menuInput == "g":
print mainGraph.getGraph()
elif menuInput == "b":
subMenuInput = ''
print 'create/load/save/delete/show BoundaryCondistions, not implemented yet'
#
# while subMenuInput not in ['1','2','3','4','5','b']:
# # evaluate boundarys in Network
# boundarys = []
# notDefinedBoundarys = []
#
# boundarys.extend(vascularNetwork.ends)
# if vascularNetwork.root != [] and vascularNetwork.root[0] not in boundarys:
# boundarys.extend(vascularNetwork.root)
#
# boundarysSaved = vascularNetwork.boundaryConditions.keys()
#
# # update saved boundary conditions
# for boundarysCurrent in boundarys:
# if boundarysCurrent not in boundarysSaved:
# print " boundary added to vascularNetwork"
# vascularNetwork.boundaryConditions[boundarysCurrent] = {}
# boundarysSaved.append(boundarysCurrent)
#
# if vascularNetwork.boundaryConditions[boundarysCurrent] == {}:
# notDefinedBoundarys.append(boundarysCurrent)
#
# nonBoundarys = list(set(boundarys).symmetric_difference(set(boundarysSaved)))
# for nonBoundary in nonBoundarys:
# print " boundary removed from vacularNetwork"
# del(vascularNetwork.boundaryConditions[nonBoundary])
# if nonBoundary in notDefinedBoundarys: notDefinedBoundarys.remove(nonBoundary)
#
# vascularNetwork.evaluateConnections()
# print ""
# print " sub menu: boundary conditions"
# print ""
# print " [1] - show boundary conditions"
# print " [2] - add boundary condition "
# print " [3] - del boundary condition "
# print " [4] - load boundary conditions from CSV"
# print " [5] - write boundary conditions to CSV"
# print " [b] - back to the main menu"
# print ""
# subMenuInput = raw_input(" what to do? ")
#
# if subMenuInput == '1':
# print " boundary conditions"
# pprint.pprint(vascularNetwork.boundaryConditions)
# subMenuInput = ''
#
# elif subMenuInput == '2' and vascularNetwork.root != []:
#
# print " add boundary condition"
# print ""
#
# definedBoundarys = list(set(notDefinedBoundarys).symmetric_difference(set(vascularNetwork.boundaryConditions.keys())))
# print " vessels with defined boundary condition:"
# print " ",' '.join(str(i) for i in definedBoundarys)
#
# print " vessels with undefined boundary condition:"
# print " ",' '.join(str(i) for i in notDefinedBoundarys)
# print ""
#
# existing = False
# vesselID = raw_input(" enter existing vessel id: ")
# while True:
# try:
# vesselID = int(vesselID)
# if vesselID in vascularNetwork.vessels:
# break
# else:
# existing = True
# except ValueError:
# print " TYPE-ERROR: vessel id must be type(int) not type(string)"
# vesselID = raw_input(" enter existing vessel id: ")
# if existing == True:
# print " the vessel does not exist"
# vesselID = raw_input(" enter existing vessel id: ")
# existing = False
#
#
# inType = '0'
# print " add boundary condition type"
# print ""
# print " 'Qa' 'Q2a' 'Qm' 'Q2m' 'Pa' 'P2a' 'Pm' 'P2m' 'Ue' "
# print " [1] [2] [3] [4] [5] [6] [7] [8] [9]"
# print ""
# print " 'Rt' 'R' 'WK2' 'WK3' 'QPhy' 'Lnet' 'Fou' 'D' 'PhyQ' "
# print " [10] [11] [12] [13] [14] [15] [16] [17] [18]"
# print ""
#
# types = ['Qa','Q2a','Qm','Q2m','Pa','P2a','Pm','P2m','Ue','Rt','R','WK2','WK3','QPhy','Lnet','Fou','D','PhyQ']
#
# existing = False
# inType = raw_input (" choose type ")
# while True:
# try:
# inType = int(inType)
# if inType in np.linspace(1,18,18):
# break
# else:
# existing = True
# except ValueError:
# print " TYPE-ERROR: vessel id must be type(int) not type(string)"
# inType = (raw_input (" choose type "))
# if existing == True:
# print " the type does not exist"
# inType = (raw_input (" choose type "))
# existing = False
#
#
# type = types[int(inType)-1]
#
# bcTags = {'Rt':['Rt'],
# 'R':['Rc'],
# 'WK2':['Rc','C'],
# 'WK3':['Rc','C','R1','RT'],
# 'QPhy':['Q0_a','Npulse','freq','Tpulse','Tspace'],
# 'Qa':['Q0_a','Npulse','freq'],
# 'Q2a':['Q0_a','Npulse','freq','Tpulse'],
# 'Qm':['Q0_m','Tmean','Traise'],
# 'Q2m':['Q0_m','Tmean','Traise'],
# 'Ue':['Upeak','C','Traise'],
# 'Pa':['P0_a','Npulse','freq'],
# 'P2a':['P0_a','Npulse','freq','Tpulse'],
# 'Pm':['P0_m','Tmean','Traise'],
# 'P2m':['P0_m','Tmean','Traise'],
# 'Fou':['P0_m','Tmean','Traise','scale','Npulse','Tpulse'],
# 'D':[''],
# 'PhyQ':[''],
# 'Lnet':['Z','C']}
#
#
# bcList = []
# print " set values for the BC condition"
# print " enter 'b' for the first value to skip this procedure"
# question = True
# for arg in bcTags[type]:
# if question == True:
# currValue = raw_input (str(" set value for "+str(arg)+' '))
# if currValue == 'b': question=False
# test = True
# try: float(currValue)
# except:
# print ' VALUE or TYPE ERROR, set to None'
# test = False
# if test == True: bcList.append(float(currValue))
# else: bcList.append(None)
# else: bcList.append(None)
# if len(vascularNetwork.boundaryConditions.keys()) == 1:
# print " set position of the BC condition"
# position = '2'
# while position not in ['1','0']:
# position = raw_input (" enter '0' for the start or '1' for the end of the vessel ")
# if position == '1':
# type = ''.join(['_',type])
#
# vascularNetwork.boundaryConditions[vesselID].update({type : bcList})
# mainGraph.update_graph(vascularNetwork, window)
# subMenuInput = ''
#
# elif subMenuInput == '3' and vascularNetwork.root != []:
# print " delete boundary condition"
# print ""
# pprint.pprint(vascularNetwork.boundaryConditions)
#
# vesselID = -1
# while vesselID not in vascularNetwork.boundaryConditions.keys():
# vesselID = int(raw_input (" choose vessel id "))
#
# bcs = vascularNetwork.boundaryConditions[vesselID].keys()
# if bcs != []:
# print ""
# print ' ',' '.join(str(' '+i+' ') for i in bcs)
# print ' ',' '.join(str('['+str(int(i))+']') for i in np.linspace(1,len(bcs),len(bcs)))
# print ""
# inType = '0'
# while inType not in np.linspace(1,len(bcs),len(bcs)):
# inType = int(raw_input (" choose condition to delete "))
#
# vascularNetwork.boundaryConditions[vesselID].pop(bcs[inType-1])
# print ""
# print " boundary condition ",bcs[inType-1]," removed!"
# print ""
# mainGraph.update_graph(vascularNetwork, window)
# else:
# print " nothing to delete!"
# subMenuInput = ''
#
# elif subMenuInput == '4' and vascularNetwork.root != []:
#
# print " load boundary conditions from CSV"
# print ""
# filename = enterFilename(filename,'')
# vascularNetwork.boundaryConditions = readBCFromCSV(filename = ''.join([filename,'BC','.csv']))
# mainGraph.update_graph(vascularNetwork, window)
#
# elif subMenuInput == '5' and vascularNetwork.root != []:
# print " write boundary conditions to CSV"
# print ""
# filename = enterFilename(filename,'')
# writeBCToCSV(vascularNetwork.boundaryConditions,filename = ''.join([filename,'BC','.csv']))
#
#
# elif subMenuInput == 'b':
# break
elif menuInput == "l":
try:
FILE = open('recentFilenames.pickle',"rb")
# store pickle
recentFilenames = cPickle.load(FILE)
FILE.close()
except:
recentFilenames = []
subMenuInput = ''
print ""
print " sub menu: load data"
print ""
print " [1] - load network from XML"
print " [2] - load vessel data from CSV"
print " [3] - load vessel data and boundary conditions from CSV"
print " [b] - back to the main menu"
print ""
while subMenuInput not in ["1","2","3","b"]:
subMenuInput = raw_input("what to do? ")
print ""
print " resent used networks"
i = 1
for name in recentFilenames:
print " [",i,'] - ',name
i = 1+i
print ""
if subMenuInput == '1':
print " load from XML"
filename = enterFilename(filename,'.xml',recentFilenames = recentFilenames)
if filename == None:break
# delete the old network
del vascularNetwork
#load the new network
vascularNetwork = loadNetworkFromXML(filename= filename)
if vascularNetwork == None:
vascularNetwork = VascularNetwork()
mainGraph.update_graph(vascularNetwork, window)
filename = None
break
mainGraph.update_graph(vascularNetwork, window)
filename, value = filename.split(".",1)
break
elif subMenuInput == '2':
print " load vessel data from CSV - non existing vessels are added automatically"
print ""
filename = enterFilename(filename,'.csv',recentFilenames = recentFilenames)
if filename == None:break
vascularNetwork.updateNetwork(readVesselDataFromCSV(filename=filename))
mainGraph.update_graph(vascularNetwork, window)
filename, value = filename.split(".",1)
break
elif subMenuInput == '3':
print " load vessel data and boundary conditions from CSV"
filename = enterFilename(filename,'.csv',recentFilenames = recentFilenames)
if filename == None:break
vascularNetwork.updateNetwork(readVesselDataFromCSV(filename=filename))
mainGraph.update_graph(vascularNetwork, window)
filename, value = filename.split(".",1)
vascularNetwork.boundaryConditions = readBCFromCSV(filename = ''.join([filename,'BC','.csv']))
mainGraph.update_graph(vascularNetwork, window)
break
elif subMenuInput == 'b':
break
if filename != None:
if filename not in recentFilenames: recentFilenames.insert(0,filename)
else:
recentFilenames.remove(filename)
recentFilenames.insert(0,filename)
if len(recentFilenames) > 5: recentFilenames.pop(-1)
FILE = open('recentFilenames.pickle',"w")
# store pickle
cPickle.dump(recentFilenames, FILE, protocol=2)
FILE.close()
elif menuInput == "s":
subMenuInput = ''
print ""
print " sub menu: save data"
print ""
print " [1] - write to XML"
print " [2] - write vessel data to CSV"
print " [3] - write vessel data and boundary conditions to CSV"
print " [4] - write graph to .png and .dot files"
print " [b] - back to the main menu"
print ""
while subMenuInput not in ["1","2","3","b"]:
subMenuInput = raw_input("what to do? ")
if subMenuInput == '1':
print " write to XML"
filename = enterFilename(filename,'.xml')
if filename == None:break
writeNetworkToXML(vascularNetwork,filename = filename)
filename, value = filename.split(".",1)
break
elif subMenuInput == '2':
print " write vessel data to CSV"
filename = enterFilename(filename,'.csv')
if filename == None:break
writeVesselDataToCSV(vessels = vascularNetwork.vessels, filename = filename)
filename, value = filename.split(".",1)
break
elif subMenuInput == '3':
print " write vessel data and boundary conditions to CSV"
filename = enterFilename(filename,'.csv')
if filename == None:break
writeVesselDataToCSV(vessels = vascularNetwork.vessels, filename = filename)
filename, value = filename.split(".",1)
writeBCToCSV(vascularNetwork.boundaryConditions,filename = ''.join([filename,'BC','.csv']))
break
elif subMenuInput == '4':
print " write graph to .png and .dot files"
pictureName = str(raw_input(" enter pictureName (only!):"))
if pictureName == "":
pictureName = 'pydotTest'
mainGraph.graph.write(graphPath+filename+'/'+pictureName+'.dot')
mainGraph.graph.write_png(graphPath+filename+'/'+pictureName+'.png')
break
if subMenuInput == 'b':
break
elif menuInput == "u":
subMenuInput = ''
print ""
print " sub menu: update XML from CSV"
print ""
print " load from XML"
filename = enterFilename(filename,'.xml')
if filename == None:break
# delete the old network
del vascularNetwork
#load the new network
vascularNetwork = loadNetworkFromXML(filename= filename)
if vascularNetwork == None:
vascularNetwork = VascularNetwork()
break
mainGraph.update_graph(vascularNetwork, window)
filename, value = filename.split(".",1)
print " load vessel data from CSV - non existing vessels are added automatically"
filenameCSV = ''.join([filename,'.csv'])
vascularNetwork.updateNetwork(readVesselDataFromCSV(filename=filenameCSV))
mainGraph.update_graph(vascularNetwork, window)
print " write to XML"
filenameXML = ''.join([filename,'.xml'])
writeNetworkToXML(vascularNetwork,filename = filenameXML)
def loadNetworkFromXML(filename=None,
update=None,
networkPath=str(cur + "/../NetworkFiles/")):
# read from file
if filename == None:
filename = "oldNetwork1.xml"
networkDirectory = filename.split('.')[0]
if not os.path.exists(str(networkPath + networkDirectory)):
print 'Error: file not in the correct directory'
return
# create vascularNetwork instance
if update == None:
vascularNetwork = VascularNetwork()
# set name
vascularNetwork.name = (filename.split('.'))[0]
else:
netBC = {}
netFluid = {}
netSimCon = {}
netSolver = {}
networkDataDict = {
'boundaryConditions': netBC,
'globalFluid': netFluid,
'simulationContext': netSimCon,
'networkSolver': netSolver
}
vesselDataDict = {}
# load the data!
try:
parser = etree.XMLParser(encoding='iso-8859-1')
tree = etree.parse(networkPath + networkDirectory + '/' + filename,
parser)
except:
print " Error: path / file does not exist or error in file"
if update == None:
return
else:
return {
'networkData': networkDataDict,
'vesselData': vesselDataDict
}
# create root
root = tree.getroot()
#SimulationContext
for simContext in root.findall(".//simulationContext"):
for data in simContext:
if data.tag == 'CFL':
if data.text != 'None' and data.text != None:
if update == None:
vascularNetwork.simulationContext['CFL'] = float(
eval(data.text))
else:
netSimCon['CFL'] = float(eval(data.text))
if data.tag == 'totalTime':
if data.text != 'None' and data.text != None:
if update == None:
vascularNetwork.simulationContext[
'totalTime'] = unitConversionToSI(
unitsDict, float(data.text),
data.attrib['unit'])
else:
netSimCon['totalTime'] = unitConversionToSI(
unitsDict, float(data.text), data.attrib['unit'])
if data.tag == 'EqSystem' or data.tag == 'NumScheme':
if data.text != 'None' and data.text != None:
if update == None:
vascularNetwork.networkSolver[data.tag] = str(
data.text)
else:
netSolver[data.tag] = str(data.text)
if data.tag == 'CharSystem':
if data.text != 'None' and data.text != None:
try:
charsys = int(data.text)
except:
raise TypeError(
'Value of %s in simulationContext not convertable to int'
% data.tag)
if update == None:
vascularNetwork.networkSolver[data.tag] = charsys
else:
netSolver[data.tag] = charsys
#load boundary Conditions
for bcs in root.findall(".//boundaryConditions/boundaryCondition"):
bcDict = bcs.attrib
if 'vessel_id' in bcDict:
try:
vessel_id = int(bcDict['vessel_id'])
except:
raise TypeError(
'vessel_id %s in boundaryCondition not convertable to int'
% bcDict['vessel_id'])
typeData2 = {}
boundaryInstances = []
boundaryIntervals = []
for data in bcs:
if data.tag in bcTags.keys():
boundaryInstance = eval(bcTagsClassReferences[data.tag])()
boundaryDataDict = {}
boundaryDataDict['name'] = data.tag
boundaryIntervalDataDict = {}
bcItems = bcTags[data.tag]
for bcItem in bcItems:
# find scalar Data
for value in data.findall(str(".//" + bcItem)):
try:
floatValue = float(eval(value.text))
except:
raise TypeError(
'Value %s in boundaryCondition not convertable to float'
% value.text)
boundaryDataDict[bcItem] = unitConversionToSI(
unitsDict, floatValue, value.attrib['unit'])
# find interval Data for polychaos
for value in data.findall(".//" + bcItem +
"-interval"):
if value.text != 'None' and value.text != None:
interval = []
try:
for number in map(float,
value.text.split(' ')):
interval.append(
unitConversionToSI(
unitsDict, float(number),
value.attrib['unit']))
except:
raise TypeError(
'Value %s in boundaryCondition Interval not convertable to float'
% value.text)
boundaryIntervalDataDict[bcItem] = interval
boundaryIntervalDataDict['name'] = data.tag
# exception for reflection coefficient because the value can stand rigth begind the
if data.tag in ['Rt', '_Rt']:
if type(data.text) != type(None):
if '.' in data.text:
try:
floatValue = float(eval(data.text))
except:
raise TypeError(
'Value %s in boundaryCondition not convertable to float'
% data.text)
# compatibility old xml-version Rt no unit-tag new version <Rt unit=''>..
Rtunit = ''
if 'unit' in data.attrib:
Rtunit = data.attrib['unit']
boundaryDataDict[bcItem] = unitConversionToSI(
unitsDict, floatValue, Rtunit)
#check if enough parameters are given:
if len(boundaryDataDict) != len(bcItems) + 1:
print len(boundaryDataDict)
raise TypeError(
str('boundaryCondition not sufficient defined; check if these attributes are given '
+ str(bcItems)))
# set du-matrix correct for type 1
if data.tag in bcDuMatrix.keys():
boundaryDataDict['duMatrix'] = bcDuMatrix[data.tag]
# update boundarz condition
boundaryInstance.update(boundaryDataDict)
boundaryInstances.append(boundaryInstance)
boundaryIntervals.append(boundaryIntervalDataDict)
if update == None:
vascularNetwork.boundaryConditions[
vessel_id] = boundaryInstances
if boundaryIntervalDataDict != {}:
vascularNetwork.boundaryConditionIntervals[
vessel_id] = boundaryIntervals
else:
netBC[vessel_id] = boundaryInstances
#load global Fluid properties
for my in root.findall(".//globalFluid/my"):
if str(my.text) != 'None':
# find units and convert if needed to SI
if update == None:
vascularNetwork.globalFluid['my'] = unitConversionToSI(
unitsDict, float(eval(my.text)), my.attrib['unit'])
else:
netFluid['my'] = unitConversionToSI(unitsDict,
float(eval(my.text)),
my.attrib['unit'])
for rho in root.findall(".//globalFluid/rho"):
if str(rho.text) != 'None':
# find units and convert if needed to SI
if update == None:
vascularNetwork.globalFluid['rho'] = unitConversionToSI(
unitsDict, float(eval(rho.text)), rho.attrib['unit'])
else:
netFluid['rho'] = unitConversionToSI(unitsDict,
float(eval(rho.text)),
rho.attrib['unit'])
for gamma in root.findall(".//globalFluid/gamma"):
if str(gamma.text) != 'None':
if update == None:
vascularNetwork.globalFluid['gamma'] = float(eval(gamma.text))
else:
netFluid['gamma'] = float(eval(gamma.text))
for dlt in root.findall(".//globalFluid/dlt"):
if str(dlt.text) != 'None':
if update == None:
vascularNetwork.globalFluid['dlt'] = float(eval(dlt.text))
else:
netFluid['dlt'] = float(eval(dlt.text))
elif str(gamma.text) != 'None':
if update == None:
vascularNetwork.globalFluid['dlt'] = (float(eval(
gamma.text)) + 2.) / (float(eval(gamma.text)) + 1.)
else:
netFluid['dlt'] = (float(eval(gamma.text)) +
2.0) / (float(eval(gamma.text)) + 1.)
for pref in root.findall(".//globalFluid/pref"):
if str(pref.text) != 'None':
if update == None:
vascularNetwork.globalFluid['pref'] = unitConversionToSI(
unitsDict, float(eval(pref.text)), pref.attrib['unit'])
else:
netFluid['pref'] = unitConversionToSI(unitsDict,
float(eval(pref.text)),
pref.attrib['unit'])
# find vessel data
for vessel_i in root.findall(".//vessel"):
vesselXMLDict = vessel_i.attrib
vesselID = None
vesselData = {
'name': None,
'start': None,
'end': None,
'leftDaughter': None,
'rightDaughter': None,
'angleToMother': None,
'geom': None,
'length': None,
'lengthInterval': None,
'radiusA': None,
'radiusAInterval': None,
'radiusB': None,
'radiusBInterval': None,
'N': None,
'comp': None,
'Pfunc': None,
'Ps': None,
'As': None,
'wallThickness': None,
'wallThicknessInterval': None,
'youngModulus': None,
'youngModulusInterval': None,
'beta': None,
'betaInterval': None,
'my': None,
'rho': None,
'gamma': None,
'dlt': None,
'pref': None
}
if 'id' in vesselXMLDict and str(vesselXMLDict['id']) != 'None':
vesselID = int(vesselXMLDict['id'])
if 'start_node' in vesselXMLDict and str(
vesselXMLDict['start_node']) != 'None':
vesselData['start'] = int(vesselXMLDict['start_node'])
if 'end_node' in vesselXMLDict and str(
vesselXMLDict['end_node']) != 'None':
vesselData['end'] = int(vesselXMLDict['end_node'])
if 'name' in vesselXMLDict and str(vesselXMLDict['name']) != 'None':
vesselData['name'] = str(vesselXMLDict['name'])
if 'leftDaughter' in vesselXMLDict and str(
vesselXMLDict['leftDaughter']) != 'None':
vesselData['leftDaughter'] = int(vesselXMLDict['leftDaughter'])
if 'rightDaughter' in vesselXMLDict and str(
vesselXMLDict['rightDaughter']) != 'None':
vesselData['rightDaughter'] = int(vesselXMLDict['rightDaughter'])
if 'angleToMother' in vesselXMLDict and str(
vesselXMLDict['angleToMother']) != 'None':
vesselData['angleToMother'] = float(vesselXMLDict['angleToMother'])
## old variable names // only version compatibility delete this for next version 0.3
if 'leftDaugther' in vesselXMLDict and str(
vesselXMLDict['leftDaugther']) != 'None':
vesselData['leftDaughter'] = int(vesselXMLDict['leftDaugther'])
if 'rightDaugther' in vesselXMLDict and str(
vesselXMLDict['rightDaugther']) != 'None':
vesselData['rightDaughter'] = int(vesselXMLDict['rightDaugther'])
# find grid properties
for grid in vessel_i.findall(".//grid"):
for data in grid:
if data.tag == 'geom':
if data.text != 'None' and data.text != None:
vesselData['geom'] = str(data.text)
if data.tag == 'length' or data.tag == 'radiusA' or data.tag == 'radiusB' or data.tag == 'N':
for value in data.findall(".//scalar"):
if value.text != 'None' and value.text != None:
vesselData[data.tag] = unitConversionToSI(
unitsDict, float(eval(value.text)),
value.attrib['unit'])
for value in data.findall(".//interval"):
if value.text != 'None' and value.text != None:
interval = []
for number in map(float, value.text.split(' ')):
interval.append(
unitConversionToSI(unitsDict,
float(number),
value.attrib['unit']))
vesselData[data.tag + 'Interval'] = interval
# find Solid properties
for solid in vessel_i.findall(".//solid"):
for data in solid:
if data.tag == 'comp':
if data.text != 'None' and data.text != None:
vesselData['comp'] = str(data.text)
if data.tag == 'Pfunc':
if data.text != 'None' and data.text != None:
if data.text == 'True': data.text = '1'
if data.text == 'False': data.text = '0'
vesselData['Pfunc'] = bool(int(data.text))
if data.tag == 'Ps' or data.tag == 'As':
if data.text != 'None' and data.text != None:
vesselData[data.tag] = unitConversionToSI(
unitsDict, float(eval(data.text)),
data.attrib['unit'])
if data.tag == 'beta' or data.tag == 'wallThickness' or data.tag == 'youngModulus':
for value in data.findall(".//scalar"):
if value.text != 'None' and value.text != None:
vesselData[data.tag] = unitConversionToSI(
unitsDict, float(eval(value.text)),
value.attrib['unit'])
for value in data.findall(".//interval"):
if value.text != 'None' and value.text != None:
interval = []
for number in map(float, value.text.split(' ')):
interval.append(
unitConversionToSI(unitsDict,
float(number),
value.attrib['unit']))
vesselData[data.tag + 'Interval'] = interval
# find fluid properties
for fluid in vessel_i.findall(".//fluid"):
for data in fluid:
if data.tag == 'my' or data.tag == 'rho' or data.tag == 'pref' or data.tag == 'gamma' or data.tag == 'dlt':
if data.text != 'None' and data.text != None:
vesselData[data.tag] = unitConversionToSI(
unitsDict, float(eval(data.text)),
data.attrib['unit'])
# pre check if vessels data given is consitent:
# warning if not
if vesselData['comp'] == 'Exponential':
if (vesselData['beta'] or vesselData['Ps']
or vesselData['As']) == None:
print "WARNING: not all specifications for %s are met!" % vesselData[
'comp']
elif vesselData['comp'] == 'Laplace':
if (vesselData['wallThickness'] or vesselData['youngModulus']
or vesselData['Ps'] or vesselData['As']) == None:
print "WARNING: not all specifications for %s are met!" % vesselData[
'comp']
# calculate area out of radius
if vesselData['geom'] == 'Uni':
if vesselData['radiusA'] != None and vesselData['As'] == None:
vesselData['As'] = vesselData['radiusA']**2 * pi
if vesselData['radiusA'] == None and vesselData['As'] != None:
data['radiusA'] = sqrt(data['As'] / pi)
if vesselData['geom'] == 'Cone':
if vesselData['radiusA'] != None and vesselData[
'radiusB'] != None and vesselData['As'] == None:
vesselData['As'] = (vesselData['radiusA']**2 +
vesselData['radiusB']**2) / 2.0 * pi
if vesselData['dlt'] == None and vesselData['gamma'] != None:
vesselData['dlt'] = (vesselData['gamma'] +
2.) / (vesselData['gamma'] + 1.)
# add vessel to the network
if update == None:
vascularNetwork.addVessel(Id=vesselID, dataDict=vesselData)
else:
vesselDataDict[vesselID] = vesselData
if update == None:
print " ... loaded successfully"
return vascularNetwork
else:
return {'networkData': networkDataDict, 'vesselData': vesselDataDict}
