def insertWorkingDirectory(optionArgument):
print("Setting new working directory")
if optionArgument == None:
optionArgument = ""
loopQuestion = True
defaultWD = os.path.expanduser(
os.path.join('~', 'starfish_working_directory'))
print(
"Enter an absolute or relative path to set the working directory, or (q) quit"
)
input_prompt = "[Press enter to use the default path {}]: ".format(
defaultWD)
optionArgument = input3(input_prompt) or defaultWD
if optionArgument != "q":
optionArgument = os.path.expanduser(optionArgument)
if os.path.isdir(optionArgument):
saveConfigFile({'WorkingDirectory': optionArgument})
updateKnownWorkingDirectories()
print(" working directory set!")
else:
print(" working directory does not exist! try to create folder")
try:
os.mkdir(optionArgument)
saveConfigFile({'WorkingDirectory': optionArgument})
updateKnownWorkingDirectories()
print(" created working directory folder successfully")
print(" working directory set!")
except:
print(
" WARNING: moduleStartUp.insertWorkingDirectory() could not set WorkingDirectory {} directory does not exists!"
.format(optionArgument))
def main(args=None):
print("")
print('=====================================')
print('# STARFiSh_v0.4.19.10.2016 #')
print('=====================================')
mainMenuInput = ""
while mainMenuInput not in ['q']:
print('\n Main menu:\n')
print(" [1] - run simulation | Main.py")
if NOVNC:
VNCSTR = "(Not Available)"
else:
VNCSTR = ""
print(" [2] -{} run vnc (vascular network creator) | vnc.py".format(
VNCSTR))
if NOVIZ:
VIZSTR = "(Not Available)"
else:
VIZSTR = ""
print(" [3] -{} run visualisation | Visualisation.py".format(VIZSTR))
print(
" [4] - run uncertainty quantification tool box | VascularPolynomialChaos.py"
)
print(" [q] - quit \n")
while mainMenuInput not in ('1', '2', '3', '4', 'q'):
mainMenuInput = input3("what to do? ")
if mainMenuInput == '1':
print("\n .. running simulation \n")
simulator.main()
mainMenuInput = ""
if mainMenuInput == '2' and NOVNC:
print("\n .. vnc not available \n")
mainMenuInput = ""
elif mainMenuInput == '2':
print("\n .. running vnc \n")
vnc.main()
mainMenuInput = ""
if mainMenuInput == '3' and NOVIZ:
print("\n .. visualisation not available \n")
mainMenuInput = ""
elif mainMenuInput == '3':
print("\n .. running visualisation \n")
visualisationToolBox.main()
mainMenuInput = ""
if mainMenuInput == '4':
print("\n .. running uncertainty quantification tool box \n")
uqsaToolBox.uncertaintyPropagation()
mainMenuInput = ""
print("bye bye ..")
def defineSimulationDescription():
simulationDescription = input3(
"\n Type in description of the simulation case: ")
try:
simulationDescription = str(simulationDescription)
except:
print('ERROR: no String Convertable input given, system exit')
exit()
if simulationDescription in ['', ' ']: simulationDescription = '-'
return simulationDescription
def userInputEvaluationInt(maxBound,
minBound=0,
question=" insert your choice, (q)-quit: "):
'''
Question user to isert an integer number between minBound and maxBound
'''
appropriateInputList = [
str(int(i + minBound)) for i in range(maxBound - minBound)
]
userInput = "NONE"
appropriateInputList.append('q')
print("")
while userInput not in appropriateInputList:
userInput = input3(question)
print("")
if userInput == 'q': exit()
else: return int(userInput)
def defineDataNumber(networkName):
print(
"No solution-datanumber defined (3 characters)! It needs to be defined"
)
#TODO CRITICAL this fails for template networks
existingDataNumbers = findExistingDataNumbers(networkName)
correctDataNumber = False
prettyPrintList(
"\n Existing dataNumbers for this network: {}".format(
networkName), existingDataNumbers)
while correctDataNumber == False:
dataNumber = input3("\n Please enter datanumber (3 characters): ")
testedFailed = False
try:
dataNumber, xx = evaluateDataNumber(dataNumber)
except ValueError as e:
print(e)
testedFailed = True
if dataNumber in existingDataNumbers:
listToPrint = [
" keep this datanumber and overwrite simulation case",
" enter new data number"
]
prettyPrintList(
"\n Simulation case with datanumber exits already".
format(networkName), listToPrint)
userInput = userInputEvaluationInt(2, 0, " What to do? ")
if userInput == 0:
correctDataNumber = True
elif userInput == 0:
dataNumber = False
correctDataNumber = False
elif testedFailed == False:
correctDataNumber = True
return dataNumber
def chooseUQSACaseFile(networkName):
"""
console Interface to choose a vascularPolynomialChaos Config File
including the possibility to create a template Config File
Input:
networkName of VascularNetwork
Output:
networkName,dataNumber of the Config File (networkName should be the same)
"""
from starfish.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")
print(" [ 1 ] - Create new template uqsa case file and run")
indexOffset = 2
if filenames != []:
prettyPrintList('', filenames, indexOffset=indexOffset)
question = " Choose Option or Config-File you want to open according to its number:, (q)-quit: "
userInput = userInputEvaluationInt(indexOffset + len(filenames), 0,
question)
if userInput in [0, 1]:
userInputDataNumber = 'xxxx'
dataNumber = False
while dataNumber == False:
userInputDataNumber = input3(
"\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)
if userInput == 0:
print("files created!, exit()")
exit()
else:
networkName = filenames[userInput - indexOffset]
dataNumber = networkName.split('.')[0].split('_')[-1]
return dataNumber
def extremaFinderFunction(self, dataPure, quantityNamePure, sampleSize, simulationTime, searchPointOfInflection):
allDesieredPointsDetected = False
delta = 0.005
colordef = ['r','g','b','m','k','c']
markerdef = ['o','d','x','s','*','v']
colors = colordef*len(markerdef)
markerstyles = [item for sublist in [ [i]*len(colordef) for i in markerdef] for item in sublist]
while allDesieredPointsDetected == False:
amplitudesList = []
timingList = []
numberOfPointsFirst = None
for sampleIndex in range(sampleSize):
dataPureCurr = dataPure[sampleIndex]
if searchPointOfInflection == True:
pointInfAmp,pointInfTime = mProc.calculatePointOfInflection(dataPureCurr, simulationTime, simulationTime[0])
minMaxPoints = [[pointInfAmp],[pointInfTime]]
numberOfPointsCurrent = len(minMaxPoints[0])
if numberOfPointsFirst == None: numberOfPointsFirst = numberOfPointsCurrent
else:
minMaxPoints = mProc.minMaxFunction(dataPureCurr,timeValues=simulationTime,delta=delta, seperateMinMax = False )
numberOfPointsCurrent = len(minMaxPoints[0])
if numberOfPointsFirst == None: numberOfPointsFirst = numberOfPointsCurrent
deltaAltered = delta
while numberOfPointsCurrent != numberOfPointsFirst:
if numberOfPointsCurrent < numberOfPointsFirst:
deltaAltered -= delta*0.1
elif numberOfPointsCurrent > numberOfPointsFirst:
deltaAltered += delta*0.1
dataPureCurr = dataPure[sampleIndex]
minMaxPoints = mProc.minMaxFunction(dataPureCurr,timeValues=simulationTime,delta=deltaAltered, seperateMinMax = False )
numberOfPointsCurrent = len(minMaxPoints[0])
amplitudesList.append(minMaxPoints[0])
timingList.append(minMaxPoints[1])
for c,m,t,x in zip(colors,markerstyles,minMaxPoints[1],minMaxPoints[0]):
plt.plot(t,x,'o',color = c,marker=m, markersize = 5)
if numberOfPointsCurrent == numberOfPointsFirst:
plt.plot(simulationTime,dataPureCurr,'g', alpha = 0.2)
elif numberOfPointsCurrent < numberOfPointsFirst:
plt.plot(simulationTime,dataPureCurr,'m', alpha = 1.0)
elif numberOfPointsCurrent > numberOfPointsFirst:
plt.plot(simulationTime,dataPureCurr,'k', alpha = 1.0)
# break for inflection point
if searchPointOfInflection == True:
allDesieredPointsDetected = True
break
plt.title(quantityNamePure)
plt.show(block = False)
print('\n Extrema detection all simulations are evaluated:')
print(' [0] - Analyse all points')
print(' [1] - Choose points for analysis')
print(' [2] - Not all desiered peaks are detected (redo and adjust search-delta)')
suggestions = [str(i) for i in range(3)]
answer = "nothing"
while answer not in suggestions:
answer =input3("What do you want to do: ")
if answer == '0':
answerSelectionSplit = [str(i) for i in range(numberOfPointsFirst)]
allDesieredPointsDetected = True
if answer == '1':
allDesieredPointsDetected = True
print("\n points found for analysis:")
for i in range(numberOfPointsFirst):
print(" [{}] - color: {}, marker style {}".format(i,colors[i],markerstyles[i]))
answerSelectionSplit = ['']
while sum([item in [str(i) for i in range(numberOfPointsFirst)] for item in answerSelectionSplit]) != len(answerSelectionSplit):
answerSelection =input3(" please enter the numbers of the points (separated with comma): ")
if ',' in answerSelection:
answerSelectionSplit = answerSelection.split(',')
elif ' ' in answerSelection:
answerSelectionSplit = answerSelection.split(' ')
else:
answerSelectionSplit = [answerSelection]
elif answer == '2':
answer2 = "haha"
convertableToFloat = False
while convertableToFloat == False:
answer2 =input3("please redefine delta, current delta value == {} ".format(delta))
try:
delta = float(answer2)
convertableToFloat = True
except ValueError as v:
print("{} not convertable to float!!".format(v))
#TODO: save the figures and close ..
plt.close()
# get the data of the selected points
selectedPoints = np.array([int(i) for i in answerSelectionSplit])
amplitudeData = np.array(amplitudesList)
timingData = np.array(timingList)
return selectedPoints, amplitudeData, timingData