def main():
print ""
print '====================================='
print '# STARFiSh_v0.3 #'
print '====================================='
optionsDict = parseOptions(['f','n','d','s','v','r'])
networkName = optionsDict['networkName']
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)
# load network from the path!
if resimulate == False:
vascularNetwork = loadNetworkFromXML(filename=filename)
else:
vascularNetwork,solutionDataSets,simulationCaseDescriptions = loadSolutionDataFile(networkName, [dataNumber])
simulationDescription = simulationCaseDescriptions[0][0]
print simulationCaseDescriptions
print simulationDescription,type(simulationDescription)
if vascularNetwork == None: exit()
vascularNetwork.evaluateConnections()
timeSolverInitStart = time.clock()
#initialize Solver
flowSolver = FlowSolver(vascularNetwork)
timeSolverInit = time.clock()-timeSolverInitStart
timeSolverSolveStart = time.clock()
#solve the system
P,Q,A,c = flowSolver.solve()
timeSolverSolve = time.clock()-timeSolverSolveStart
minutesInit = int(timeSolverInit/60.)
secsInit = timeSolverInit-minutesInit*60.
minutesSolve = int(timeSolverSolve/60.)
secsSolve = timeSolverSolve-minutesSolve*60.
#print '====================================='
print '____________ Solver time _____________'
print 'Initialisation: {} min {} sec'.format(minutesInit,secsInit)
print 'Solving: {} min {} sec'.format(minutesSolve,secsSolve)
print '====================================='
solutionDataSave = [{'Pressure': P, 'Flow': Q, 'Area': A, 'WaveSpeed':c, 'Name': str('simulation_'+dataNumber) }]
networkName = filename.split('.')[0]
saveSolutionDataFile(networkName,dataNumber,vascularNetwork,solutionDataSave,simulationDescription)
del flowSolver
gc.collect()
updateSimulationDescriptions(networkName,dataNumber)
gc.collect()
if vizOutput == "2D":
string = ' '.join(['python',cur+'/Visualisation/class2dVisualisation.py','-f',vascularNetwork.name, '-n',str(dataNumber)])
subprocess.Popen(string, shell=True)
if vizOutput == "3D":
string = ' '.join(['python',cur+'/Visualisation/class3dVisualisation.py','-f',vascularNetwork.name, '-n',str(dataNumber), '-c True'])
subprocess.Popen(string, shell=True)
if vizOutput == "2D+3D":
string1 = ' '.join(['python',cur+'/Visualisation/class2dVisualisation.py','-f',vascularNetwork.name, '-n',str(dataNumber), '-c True'])
string2 = ' '.join(['python',cur+'/Visualisation/class3dVisualisation.py','-f',vascularNetwork.name, '-n',str(dataNumber), '-c True'])
viz2d = subprocess.Popen(string1, shell = True )
viz3d = subprocess.Popen(string2, shell = True )
while True:
if viz2d.poll() != None:
viz3d.terminate()
exit()
if viz3d.poll() != None:
viz2d.terminate()
exit()
def main():
parser = OptionParser()
parser.add_option("-f", "--file", dest='networkName',
help="open file with networkName", metavar="FILE")
parser.add_option("-s", "--save", dest="save",
help="save solution data, 0 = False, 1 = True")
parser.add_option("-n", "--dataNumber", dest='dataNumber',
help="number of the solution data (last number in filename), default = 1, max 999", metavar = "FILE")
parser.add_option('-v', '--vizBool', dest='vizBool',
help="choose visualisation mode, 0: no visualisation, 1: 2d and 3d, 2: 2d plots, 3: 3d visualisation default = 1")
(options, args) = parser.parse_args()
networkName = 'oldNetwork1'
if options.networkName != None:
networkName = options.networkName
else:
print " no networkName passed, visualisation could not be intialized"
print " use -f networkName to define an file you want to visualize"
exit()
filename = str(networkName+'.xml')
dataNumber = '001'
if options.dataNumber != None:
dataNumber = options.dataNumber
if len(dataNumber) == 1:
dataNumber = '00'+dataNumber
if len(dataNumber) == 2:
dataNumber = '0'+dataNumber
save = False
if options.save != None:
if options.save == '0':
save = False
elif options.save == '1':
save = True
vizBool = '1'
vizBool2d = True
vizBool3d = True
print options.vizBool
if options.vizBool != None:
if options.vizBool == '0':
vizBool2d = False
vizBool3d = False
elif options.vizBool == '1':
vizBool2d = True
vizBool3d = True
elif options.vizBool == '2':
vizBool2d = True
vizBool3d = False
elif options.vizBool == '3':
vizBool2d = False
vizBool3d = True
# load network from the path!
Lstart = time.clock()
vascularNetwork = loadNetworkFromXML(filename=filename)
if vascularNetwork == None: exit()
# update the connections of the network, as they prob weren't saved correct
vascularNetwork.evaluateConnections()
Lend = time.clock()
print" needed %1.3f sec to load" %(Lend-Lstart)
vascularNetwork.initialize()
#create visualisation
if vizBool3d == True:
visualisation = Visualisation(vascularNetwork=vascularNetwork)
#print '====================================='
#print '_________ Simulation Context _________'
#print '%-25s %-20s' % ('Numerical scheme',networkSolver['NumScheme'])
#print '%-25s %4d' % ('Equation system',int(networkSolver['EqSystem']))
#print '%-25s %4d' % ('Characteristic system',int(networkSolver['CharSystem']))
#print '________ Visualisation Context _______'
Cstart = time.clock()
flowSolver = FlowSolver(vascularNetwork)
P,Q,A = flowSolver.solve()
print '\n____________ Solver time _____________'
minutes = int((time.clock()-Cstart)/60.)
secs = (time.clock()-Cstart)-float(minutes)*60.
print '%d %s %f %s' % (minutes ,'min',secs ,'sec')
if save == True:
#save solution data in c pickle
#standart solution path
networkPath = str(cur+"/NetworkFiles/")
networkDirectory = filename.split('.')[0]
solutionPath = str(networkPath+networkDirectory+'/')
# data to save
solutionDataSave = [{'Pressure': P, 'Flow': Q, 'Area': A, 'WaveSpeed':Q,'Name': str('simulation_'+dataNumber) }]
#create file with filename in soultionPath
endName = "_SolutionData_"+dataNumber+".pickle"
FILE = open(str(solutionPath+vascularNetwork.name+endName),"w")
# store pickle
cPickle.dump(solutionDataSave, FILE, protocol=2)
FILE.close()
if vizBool2d == True:
string = ' '.join(['python',cur+'/Visualisation/class2dVisualisationSimple.py','-f',vascularNetwork.name, '-n 1','-i 0'])
subprocess.call(string, shell=True)
if vizBool3d == True:
# create solution data
solutionData = [ {'Pressure': P, 'Flow': Q, 'Area': A, 'Name': str('simulation '+dataNumber) }]
#set the solution data
visualisation.setSolutionData(solutionData)
visualisation.factor = 10
# set the coefficient for the velocity profile
visualisation.powerLawCoefficient = 2
visualisation.visualize()
# clear memory
visualisation.__del__()
del(visualisation)
def main():
parser = OptionParser()
parser.add_option("-f",
"--file",
dest='networkName',
help="open file with networkName",
metavar="FILE")
parser.add_option("-s",
"--save",
dest="save",
help="save solution data, 0 = False, 1 = True")
parser.add_option(
"-n",
"--dataNumber",
dest='dataNumber',
help=
"number of the solution data (last number in filename), default = 1, max 999",
metavar="FILE")
parser.add_option(
'-v',
'--vizBool',
dest='vizBool',
help=
"choose visualisation mode, 0: no visualisation, 1: 2d and 3d, 2: 2d plots, 3: 3d visualisation default = 1"
)
(options, args) = parser.parse_args()
networkName = 'oldNetwork1'
if options.networkName != None:
networkName = options.networkName
else:
print " no networkName passed, visualisation could not be intialized"
print " use -f networkName to define an file you want to visualize"
exit()
filename = str(networkName + '.xml')
dataNumber = '001'
if options.dataNumber != None:
dataNumber = options.dataNumber
if len(dataNumber) == 1:
dataNumber = '00' + dataNumber
if len(dataNumber) == 2:
dataNumber = '0' + dataNumber
save = False
if options.save != None:
if options.save == '0':
save = False
elif options.save == '1':
save = True
vizBool = '1'
vizBool2d = True
vizBool3d = True
print options.vizBool
if options.vizBool != None:
if options.vizBool == '0':
vizBool2d = False
vizBool3d = False
elif options.vizBool == '1':
vizBool2d = True
vizBool3d = True
elif options.vizBool == '2':
vizBool2d = True
vizBool3d = False
elif options.vizBool == '3':
vizBool2d = False
vizBool3d = True
# load network from the path!
Lstart = time.clock()
vascularNetwork = loadNetworkFromXML(filename=filename)
if vascularNetwork == None: exit()
# update the connections of the network, as they prob weren't saved correct
vascularNetwork.evaluateConnections()
Lend = time.clock()
print " needed %1.3f sec to load" % (Lend - Lstart)
vascularNetwork.initialize()
#create visualisation
if vizBool3d == True:
visualisation = Visualisation(vascularNetwork=vascularNetwork)
#print '====================================='
#print '_________ Simulation Context _________'
#print '%-25s %-20s' % ('Numerical scheme',networkSolver['NumScheme'])
#print '%-25s %4d' % ('Equation system',int(networkSolver['EqSystem']))
#print '%-25s %4d' % ('Characteristic system',int(networkSolver['CharSystem']))
#print '________ Visualisation Context _______'
Cstart = time.clock()
flowSolver = FlowSolver(vascularNetwork)
P, Q, A = flowSolver.solve()
print '\n____________ Solver time _____________'
minutes = int((time.clock() - Cstart) / 60.)
secs = (time.clock() - Cstart) - float(minutes) * 60.
print '%d %s %f %s' % (minutes, 'min', secs, 'sec')
if save == True:
#save solution data in c pickle
#standart solution path
networkPath = str(cur + "/NetworkFiles/")
networkDirectory = filename.split('.')[0]
solutionPath = str(networkPath + networkDirectory + '/')
# data to save
solutionDataSave = [{
'Pressure': P,
'Flow': Q,
'Area': A,
'WaveSpeed': Q,
'Name': str('simulation_' + dataNumber)
}]
#create file with filename in soultionPath
endName = "_SolutionData_" + dataNumber + ".pickle"
FILE = open(str(solutionPath + vascularNetwork.name + endName), "w")
# store pickle
cPickle.dump(solutionDataSave, FILE, protocol=2)
FILE.close()
if vizBool2d == True:
string = ' '.join([
'python', cur + '/Visualisation/class2dVisualisationSimple.py',
'-f', vascularNetwork.name, '-n 1', '-i 0'
])
subprocess.call(string, shell=True)
if vizBool3d == True:
# create solution data
solutionData = [{
'Pressure': P,
'Flow': Q,
'Area': A,
'Name': str('simulation ' + dataNumber)
}]
#set the solution data
visualisation.setSolutionData(solutionData)
visualisation.factor = 10
# set the coefficient for the velocity profile
visualisation.powerLawCoefficient = 2
visualisation.visualize()
# clear memory
visualisation.__del__()
del (visualisation)
