def chooseNetwork(showTemplates=True):
"""
console Interface to choose a VascularNetwork for simulation / vascularPolynomial Chaos
"""
dirNamesTemplate = []
prettyPringOffset = 0
if showTemplates:
# network templates
templatePath = mFPH.getDirectory('networkXmlFileTemplateDirectory', '',
'', 'read')
dirNamesTemplate = [
d for d in os.listdir(templatePath) if '.' not in d
]
prettyPrintList("\n Template Networks: \n", dirNamesTemplate)
prettyPringOffset = len(dirNamesTemplate)
# working directory
workingDirectoryPath = mFPH.getDirectory('workingDirectory', '', '',
'read')
dirWorkingDirectory = [
d for d in os.listdir(workingDirectoryPath) if '.' not in d
]
prettyPrintList("\n WorkingDirectory Networks: \n",
dirWorkingDirectory,
indexOffSet=prettyPringOffset)
dirNames = dirNamesTemplate + dirWorkingDirectory
userInput = userInputEvaluationInt(len(dirNames), 0)
print ""
print '====================================='
return dirNames[userInput]
def __init__(self, networkName = None, dataNumber = None, connect = False):
Visualisation3DGUI.__init__(self)
# load functions
self.networkName = networkName
self.dataNumber = dataNumber
self.connect = connect
# vascularNewtor Instance
self.vascularNetwork = None
# dictionary with 3D vessels
self.vessels3D = {}
self.nPointsPerCircle = 8 # points for the circle at one gridpoint should bee around 8-16-32
# vessel area/wall
self.areaFactor = [2]
self.areaFactorMaximum = 200
self.wallMovement = [True]
# look up table
self.pressureMaxima = None
self.pressureMaximaSplit = None
self.cLUT = None # color look up table class
self.quantityLUT = ['Pressure']
# enable waveSplit LUT
self.waveSplit = [False] # us an array as it is behaving like a pointer
# simulation timing and update
self.updateTime = 1./60.
self.totalTime = 0
self.timeStepsTotal = 50 # get this from solution length e.g. len(area)
self.timeStepCurrent = 0
self.timeStepIncrement = 1 # time step increment from [1, ... self.totalTimeSteps-1 ]
self.timeStepStart = 0
self.timeStepStop = 50
## create movie
self.recordMovieData = False
self.movieCount = 0
self.oneCycle = False
self.templateMovDataDirectory = ''.join([cur,'/.movieTemplateData'])
self.movieSaveDirectory = mFPH.getDirectory('movieDirectory', networkName, dataNumber, 'write')
self.movieNumber = 0
self.movieFileType = '.mp4'
## create screen shot
self.screenShotNumber = 0
self.screenShotDataDirectory = mFPH.getDirectory('screenshotDirectory', networkName, dataNumber, 'write')
self.initialzeVisualisation()
def chooseSolutionDataCase():
"""
console Interface to choose a vascular1DFlow simulation case for e.g. Visualisation
Output:
networkName <string>
dataNumber <string>
"""
workingDirectory = mFPH.getDirectory('workingDirectory', '', '', 'read')
networkCases = [d for d in os.listdir(workingDirectory) if '.' not in d]
fileNameDataNumber = []
indexOffSet = 0
for networkName in networkCases:
simulationCaseDict = mFPH.getSimulationCaseDescriptions(
networkName) #, exception = 'No')
networkDirectory = mFPH.getDirectory('networkXmlFileXXXDirectory',
networkName, 'xxx', 'read')
listToPrint = []
if simulationCaseDict != None:
first = True
for root, dirs, files in os.walk(networkDirectory):
for file in files:
if ".hdf5" in file and "uqsa" not in file:
solutionDataFile = file.split('.')[0]
dataNumber = solutionDataFile.split(
'_SolutionData_')[-1]
if len(dataNumber) == 3:
if dataNumber not in simulationCaseDict:
description = "'{}' not listed in simulation descriptions of network '{}'.".format(
dataNumber, networkName)
else:
description = simulationCaseDict[dataNumber]
listToPrint.append("{} : {}".format(
dataNumber, description))
fileNameDataNumber.append(
[networkName, dataNumber])
prettyPrintList("\n {}".format(networkName),
listToPrint,
indexOffSet=indexOffSet)
indexOffSet = indexOffSet + len(listToPrint)
if len(fileNameDataNumber) == 0:
print "No solutionCases available, system exit"
exit()
question = " Choose simulation case you want to open according to its number, (q)-quit: "
userInput = userInputEvaluationInt(len(fileNameDataNumber), 0, question)
networkName = fileNameDataNumber[userInput][0]
dataNumber = fileNameDataNumber[userInput][1]
return networkName, dataNumber
def findExistingDataNumbers(networkName):
"""
evaluates exiting data numbers of a network
Args: networkName (str) := networkName
Returns: existingDataNumbers (list)
"""
# TODO: better way to handle this case?
destinationNetworkName = networkName
if "_template" in networkName:
destinationNetworkName = ''.join(networkName.split("_template"))
try:
_ = mFPH.getFilePath('simulationDescriptionFile',
destinationNetworkName,
"xxx",
'read',
exception='No')
except:
_ = mFPH.getFilePath('simulationDescriptionFile',
destinationNetworkName, "xxx",
'write') #, exception = 'No')
simulationCaseDict = mFPH.getSimulationCaseDescriptions(
destinationNetworkName) #, exception = 'No')
print(simulationCaseDict)
networkDirectory = mFPH.getDirectory('networkXmlFileXXXDirectory',
destinationNetworkName, 'xxx', 'read')
existingDataNumbers = []
for root, dirs, files in os.walk(networkDirectory):
for file in files:
if ".hdf5" in file and "_SolutionData_" in file:
solutionDataFile = file.split('.')[0]
dataNumber = solutionDataFile.split('_SolutionData_')[-1]
if len(dataNumber) == 3:
existingDataNumbers.append(dataNumber)
return existingDataNumbers
def main():
"""
vnc main function
menu and all options in one big function
need refactoring:
transformed into class
splitted in single member functions
thus give possibility to make gui
xdot on click should call function in class vncMain
vascularNetwork should never be deleted ?!
modules need to be imported as modules !!
"""
# 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()
networkName = None
k = None
while menuInput != "q":
menuInput = ""
print ""
print '====================================='
print '# VascularNetworkCreator_v2.1 #'
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 from CSV file(s)"
print " [g] - print network graph"
print " [p] - print network informations"
print " [q] - quit"
print ""
print '===========Parameter Units==========='
print ' NOTE! All parameter units are in the'
print ' Pa, seconds, and meters system'
print ' i.e. not mmHg, seconds, cm, or dynes,'
print ' seconds, grams'
print '====================================='
print ' current network: ', networkName
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 = nxml.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}
nxml.vesselComplianceElements[compType]
print ""
print " set values for the Compliance: ", compType
question = True
for arg in nxml.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()
vascularNetwork.randomInputManager.printOutInfo()
elif menuInput == "g":
print mainGraph.getGraph()
elif menuInput == "b":
subMenuInput = ''
while subMenuInput not in ['1', '2', '3', '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 = nxml.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(
nxml.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 nxml.boundaryConditionElements[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 ""
# networkName = enterNetworkName(networkName)
# boundaryConditions,boundaryConditionPolyChaos = mCSV.readBCFromCSV(networkName)
# vascularNetwork.update({'boundaryConditions':boundaryConditions,
# 'boundaryConditionPolyChaos':boundaryConditionPolyChaos})
#
# mainGraph.update_graph(vascularNetwork, window)
#
# elif subMenuInput == '5' and vascularNetwork.root != []:
# print " write boundary conditions to CSV"
# print ""
# networkName = enterNetworkName(networkName)
# boundaryConditions = vascularNetwork.getVariableValue('boundaryConditions')
# boundaryConditionPolyChaos = deepcopy(vascularNetwork.getVariableValue('boundaryConditionPolyChaos'))
# mCSV.writeBCToCSV(networkName, boundaryConditions, boundaryConditionPolyChaos)
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:
vncRescentNetworksFile = open(
mFPH.getFilePath('vncRescentNetworksFile', 'networkName',
'xxx', 'read'), 'rb')
recentNetworkNames = cPickle.load(vncRescentNetworksFile)
vncRescentNetworksFile.close()
except:
recentNetworkNames = []
subMenuInput = ''
while subMenuInput not in ["1", "2", "3", '5', '6',
"b"]: #["1","2","3",'4','5','6',"b"]:
print ""
print " sub menu: load data"
print ""
print " [1] - load network from XML"
print " [2] - load template network"
print " [3] - load vessel data from CSV"
#print " [4] - load vessel data and boundary conditions from CSV"
print " [4] - "
print " [5] - load network from SolutionData"
#print " [6] - load random inputs from CSV"
print " [b] - back to the main menu"
print ""
subMenuInput = raw_input("what to do? ")
if subMenuInput in ["1", "2", "3", '5']:
print ""
print " recently used networks"
i = 1
for name in recentNetworkNames:
print " [", i, '] - ', name
i = 1 + i
print ""
if subMenuInput == '1':
print " load from XML\n"
networkName = enterNetworkName(
networkName, recentNetworkNames=recentNetworkNames)
if networkName == None: break
# delete the old network
del vascularNetwork
#load the new network
try:
vascularNetwork = mXML.loadNetworkFromXML(networkName)
except ValueError as e:
mainGraph.update_graph(None, window)
vascularNetwork = VascularNetwork()
print "\n could not load network, it does not exist or the file is not up-to-date! \n"
print(str(e))
#if networkName in recentNetworkNames:
# recentNetworkNames.remove(networkName)
networkName = None
#vncRescentNetworksFile = open(mFPH.getFilePath('vncRescentNetworksFile', 'networkName', 'xxx', 'write'),'wb')
# store pickle
#cPickle.dump(recentNetworkNames, vncRescentNetworksFile, protocol=2)
#vncRescentNetworksFile.close()
break
if networkName != None:
mainGraph.update_graph(vascularNetwork, window)
break
elif subMenuInput == '2':
print "\n load template network:\n"
# network templates
templatePath = mFPH.getDirectory(
'networkXmlFileTemplateDirectory', '', '', 'read')
dirNamesTemplate = [
d for d in os.listdir(templatePath) if '.' not in d
]
for index, dirName in enumerate(dirNamesTemplate):
print " [ {:3} ] - {}".format(index, dirName)
print ""
indexChoosen = None
while indexChoosen not in [
str(i) for i in xrange(len(dirNamesTemplate))
]:
indexChoosen = raw_input(
" Insert index of network: ")
templateNetworkName = dirNamesTemplate[int(indexChoosen)]
#load the new network
del vascularNetwork
# delete the old network
try:
vascularNetwork = mXML.loadNetworkFromXML(
templateNetworkName)
vascularNetwork.name = None
networkName = None
except:
mainGraph.update_graph(None, window)
vascularNetwork = VascularNetwork()
print "\n could not load network, it does not exist! \n"
if networkName in recentNetworkNames:
recentNetworkNames.remove(networkName)
networkName = None
vncRescentNetworksFile = open(
mFPH.getFilePath('vncRescentNetworksFile',
'networkName', 'xxx', 'write'),
'wb')
# store pickle
cPickle.dump(recentNetworkNames,
vncRescentNetworksFile,
protocol=2)
vncRescentNetworksFile.close()
break
mainGraph.update_graph(vascularNetwork, window)
break
elif subMenuInput == '3':
print " load vessel data from CSV - non existing vessels are added automatically"
print ""
networkName = enterNetworkName(
networkName, recentNetworkNames=recentNetworkNames)
if networkName == None: break
vesselData = mCSV.readVesselDataFromCSV(networkName)
if vesselData == None:
print "\n could not load network csv, it does not exist! \n"
else:
vascularNetwork.updateNetwork(vesselData)
mainGraph.update_graph(vascularNetwork, window)
break
# elif subMenuInput == '4':
# print " load vessel data and boundary conditions from CSV"
# networkName = enterNetworkName(networkName, recentNetworkNames = recentNetworkNames)
# if networkName == None:break
#
# vascularNetwork.updateNetwork(mCSV.readVesselDataFromCSV(networkName))
# boundaryConditions,boundaryConditionPolyChaos = mCSV.readBCFromCSV(networkName)
# vascularNetwork.update({'boundaryConditions':boundaryConditions,
# 'boundaryConditionPolyChaos':boundaryConditionPolyChaos})
#
# mainGraph.update_graph(vascularNetwork, window)
# break
elif subMenuInput == '5':
print " load network from SolutionData"
try:
networkName, dataNumber = mStartUp.chooseSolutionDataCase(
)
vascularNetwork = mXML.loadNetworkFromXML(
networkName, dataNumber=dataNumber)
vascularNetwork.name = None
networkName = None
mainGraph.update_graph(vascularNetwork, window)
except:
print "\n ERROR occured could not open requested network, file does not exist or is out dated"
break
# elif subMenuInput == '6':
# print " load random input from CSV"
# networkName = enterNetworkName(networkName)
# mCSV.readRandomInputsfromCSV(networkName, vascularNetwork.randomInputManager)
# vascularNetwork.randomInputManager.linkRandomInputUpdateFunctions(vascularNetwork)
elif subMenuInput == 'b':
break
if networkName != None:
if networkName not in recentNetworkNames:
recentNetworkNames.insert(0, networkName)
else:
recentNetworkNames.remove(networkName)
recentNetworkNames.insert(0, networkName)
if len(recentNetworkNames) > 9: recentNetworkNames.pop(-1)
vncRescentNetworksFile = open(
mFPH.getFilePath('vncRescentNetworksFile', 'networkName',
'xxx', 'write'), 'wb')
# store pickle
cPickle.dump(recentNetworkNames,
vncRescentNetworksFile,
protocol=2)
vncRescentNetworksFile.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 " [3] - "
print " [4] - write graph to .png"
#print " [5] - write random input data to CSV"
print " [b] - back to the main menu"
print ""
while subMenuInput not in ["1", "2", '4',
"b"]: #["1","2","3",'4','5',"b"]:
subMenuInput = raw_input("what to do? ")
if subMenuInput == '1':
print " write to XML"
networkName = enterNetworkName(networkName)
vascularNetwork.name = networkName
if networkName == None: break
mXML.writeNetworkToXML(vascularNetwork)
break
elif subMenuInput == '2':
print " write vessel data to CSV"
networkName = enterNetworkName(networkName)
if networkName == None: break
mCSV.writeVesselDataToCSV(networkName,
vascularNetwork.vessels)
break
# elif subMenuInput == '3':
# print " write vessel data and boundary conditions to CSV"
# networkName = enterNetworkName(networkName)
# if networkName == None:break
# boundaryConditions = vascularNetwork.getVariableValue('boundaryConditions')
# boundaryConditionPolyChaos = deepcopy(vascularNetwork.getVariableValue('boundaryConditionPolyChaos'))
# # write data
# mCSV.writeVesselDataToCSV(networkName, vascularNetwork.vessels)
# mCSV.writeBCToCSV(networkName, boundaryConditions,boundaryConditionPolyChaos)
# break
elif subMenuInput == '4':
print " write graph to .png"
vncNetworkGraphFile = mFPH.getFilePath(
'vncNetworkGraphFile', networkName, 'xxx', 'write')
#mainGraph.graph.write(graphPath+networkName+'/'+pictureName+'.dot')
mainGraph.graph.write_png(vncNetworkGraphFile)
break
# elif subMenuInput == '5':
# print " write random input data to CSV"
# networkName = enterNetworkName(networkName)
# mCSV.writeRandomInputstoCSV(networkName, vascularNetwork.randomInputManager)
# break
if subMenuInput == 'b':
break
elif menuInput == "u":
try:
vncRescentNetworksFile = open(
mFPH.getFilePath('vncRescentNetworksFile', 'networkName',
'xxx', 'read'), 'rb')
recentNetworkNames = cPickle.load(vncRescentNetworksFile)
vncRescentNetworksFile.close()
except:
recentNetworkNames = []
subMenuInput = ''
print ""
print " sub menu: update XML from CSV"
print ""
print " load from XML"
print ""
print " recently used networks"
i = 1
for name in recentNetworkNames:
print " [", i, '] - ', name
i = 1 + i
print ""
networkName = enterNetworkName(
networkName, recentNetworkNames=recentNetworkNames)
if networkName == None: break
# delete the old network
del vascularNetwork
#load the new network
try:
vascularNetwork = mXML.loadNetworkFromXML(networkName)
except ValueError as e:
mainGraph.update_graph(None, window)
vascularNetwork = VascularNetwork()
print "\n could not load network, it does not exist or the file is not up-to-date! \n"
print(str(e))
#if networkName in recentNetworkNames:
# recentNetworkNames.remove(networkName)
networkName = None
if networkName == None:
mainGraph.update_graph(None, window)
else:
mainGraph.update_graph(vascularNetwork, window)
if networkName is not None:
print " load vessel data from CSV - non existing vessels are added automatically"
vesselData = mCSV.readVesselDataFromCSV(networkName)
if vesselData == None:
print "\n could not load network csv, it does not exist! \n"
else:
vascularNetwork.updateNetwork(vesselData)
#print " load boundaryData from csv as well? press [u]"
#subMenuInput = raw_input("yes [u]? ")
#if subMenuInput == 'u':
# boundaryConditions,boundaryConditionPolyChaos = mCSV.readBCFromCSV(networkName)
# vascularNetwork.update({'boundaryConditions':boundaryConditions,
# 'boundaryConditionPolyChaos':boundaryConditionPolyChaos})
mainGraph.update_graph(vascularNetwork, window)
print " write to XML"
vascularNetwork.name = networkName
mXML.writeNetworkToXML(vascularNetwork)
else:
print "\n could not update network \n"
print "bye bye .."
def main():
print ""
print '====================================='
print '# STARFiSh_v0.3_development #'
print '====================================='
optionsDict = mStartUp.parseOptions(
['f', 'e', 'n', 'd', 's', 'v', 'r', 'w', 'p'])
networkName = optionsDict['networkName']
newNetworkName = optionsDict['NewNetworkName']
save = optionsDict['save']
dataNumber = optionsDict['dataNumber']
simulationDescription = optionsDict['simulationDescription']
vizOutput = optionsDict['vizOutput']
resimulate = optionsDict['resimulate']
filename = str(networkName + '.xml')
print '____________Simulation_______________'
print '%-20s %s' % ('Network name', networkName)
print '%-20s %s' % ('Data number', dataNumber)
print '%-20s %s' % ('Save simulation', save)
print '%-20s %s' % ('Case description', simulationDescription)
print '%-20s %s' % ('Resimulate', resimulate)
print '%-20s %s' % ('Visualisationmode', vizOutput)
## check if template
if '_template' in networkName:
networkName = mFPH.createWorkingCopyOfTemplateNetwork(networkName)
# load network from the path!
if resimulate == False:
vascularNetwork = mXML.loadNetworkFromXML(
networkName) # moved to vascularNetowrk constror
else:
# resimulate network
vascularNetwork = mXML.loadNetworkFromXML(networkName,
dataNumber=dataNumber)
if simulationDescription == '':
simulationDescription = vascularNetwork.description
if vascularNetwork == None: exit()
oldNetworkDirectory = mFPH.getDirectory('networkXmlFileXXXDirectory',
networkName, "xxx", 'read')
vascularNetwork.update({
'description': simulationDescription,
'dataNumber': dataNumber
})
New_network = cNred.NetworkReduction(vascularNetwork)
truncateFile = ''.join([oldNetworkDirectory, '/', 'truncate.txt'])
New_network.reduceNetwork(truncateFile)
New_network.name = newNetworkName
newNetworkXmlFile = mFPH.getFilePath('networkXmlFile', newNetworkName,
"xxx", 'write')
mXML.writeNetworkToXML(New_network,
dataNumber=dataNumber,
networkXmlFile=newNetworkXmlFile)
if New_network.initialsationMethod == 'FromSolution':
oldInitialValuePath = mFPH.getDirectory('initialValueFileDirectory',
networkName, dataNumber,
'write')
newInitialValuePath = mFPH.getDirectory('initialValueFileDirectory',
newNetworkName, dataNumber,
'write')
if os.path.isdir(newInitialValuePath):
shutil.rmtree(newInitialValuePath)
shutil.copytree(oldInitialValuePath, newInitialValuePath)
copyFlowFile = True
if copyFlowFile:
oldInflowFile = ''.join([oldNetworkDirectory, '/', 'inflow.csv'])
newNetworkDirectory = mFPH.getDirectory('networkXmlFileXXXDirectory',
newNetworkName, "xxx", 'read')
newInflowFile = ''.join([newNetworkDirectory, '/', 'inflow.csv'])
shutil.copyfile(oldInflowFile, newInflowFile)
copyTruncateFile = True
if copyTruncateFile:
newNetworkDirectory = mFPH.getDirectory('networkXmlFileXXXDirectory',
newNetworkName, "xxx", 'read')
newTruncateFile = ''.join([newNetworkDirectory, '/', 'truncate.txt'])
shutil.copyfile(truncateFile, newTruncateFile)
def chooseUQSACaseFile(networkName):
"""
console Interface to choose a vascularPolynomialChaos Config File
including the possility to create a template Config File
Input:
networkName of VascularNetwork
Output:
networkName,dataNumber of the Config File (networkName should be the same)
"""
from VascularPolynomialChaosLib import classUqsaCase
workingDirectory = mFPH.getDirectory('workingDirectory', '', '', 'read')
networkDirectory = os.path.join(*[workingDirectory, networkName])
filesNetworkDir = os.listdir(networkDirectory)
filenames = []
for fileNetworkDir in filesNetworkDir:
# check if polychaos directory:
if 'vascularPolynomialChaos' in fileNetworkDir:
allFilenames = os.listdir(
os.path.join(*[workingDirectory, networkName, fileNetworkDir]))
for filename in allFilenames:
if ".xml" in filename and "uqsaCase" in filename:
filenames.append(filename)
print "\n No dataNumber for UQSAcase file passed, choose between all available UQSAcase files:"
print " (NB: use -n dataNumber to define a specific UQSAcase you want to open)\n"
print " [ 0 ] - Create new template uqsa case file and exit"
if filenames != []:
prettyPrintList('', filenames, indexOffSet=1)
question = " Choose Option or Config-File you want to open according to its number:, (q)-quit: "
userInput = userInputEvaluationInt(1 + len(filenames), 0, question)
if userInput in [0]:
userInputDataNumber = 'xxxx'
dataNumber = False
while dataNumber == False:
userInputDataNumber = str(
raw_input(
"\n Insert dataNumber for polynomial Chaos case (overwrites if existing): "
))
dataNumber = evaluateDataNumber(userInputDataNumber,
exception="Warning")[0]
# create template configuration
configurationFilePathTemplate = mFPH_VPC.getFilePath(
'uqsaCaseTemplateFile', networkName, dataNumber, 'read')
uqsaCase = classUqsaCase.UqsaCase()
uqsaCase.loadXMLFile(configurationFilePathTemplate)
# TODO: check if file exits and ask if it should be overwritten
configurationFilePath = mFPH_VPC.getFilePath('uqsaCaseXmlFile',
networkName, dataNumber,
'write')
uqsaCase.writeXMLFile(configurationFilePath)
# copy network file
toCopyFile = mFPH.getFilePath('networkXmlFile', networkName, 'xxx',
'write')
destinationFile = mFPH_VPC.getFilePath('vpcNetworkXmlFile',
networkName, dataNumber,
'write')
shutil.copy(toCopyFile, destinationFile)
print "files created!, exit()"
exit()
else:
networkName = filenames[userInput - 1]
dataNumber = networkName.split('.')[0].split('_')[-1]
return dataNumber