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}
