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():
# 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 main2Dplot():
parser = OptionParser()
parser.add_option("-f", "--file", dest='networkName',
help="open file with networkName", metavar="FILE")
parser.add_option("-i", "--vesselId", dest="vesselId",
help="id of the vessel to visualize")
parser.add_option("-n", "--dataNumber", dest='dataNumber',
help="number of the solution data (last number in filename), default = 1, max 999", metavar = "FILE")
(options, args) = parser.parse_args()
networkName = 'oldNetwork2'
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
vesselId = 0
updateVesselId = False
if options.vesselId != None:
vesselId = int(options.vesselId)
else:
updateVesselId = True
vascularNetwork = None
vascularNetwork = loadNetworkFromXML(filename=filename)
if vascularNetwork == None: exit()
vascularNetwork.evaluateConnections()
vascularNetwork.initialize()
if vesselId not in vascularNetwork.vessels.keys():
"No vessel with given id in current vascular network"
sys.exit(1)
vesselName = vascularNetwork.vessels[vesselId].name
solutionData = []
endName1 = "_SolutionData_"
endName2 = ".pickle"
networkPath = str(cur+'/../'+"/NetworkFiles/")
filePath= ''.join([networkPath,networkName,'/',networkName,endName1,dataNumber,endName2])
try:
FILE = open(filePath,"rb")
solutionData = cPickle.load(FILE)
except:
print "no solution file with given data number"
exit()
pRef = vascularNetwork.globalFluid['pref']
totalTime = vascularNetwork.simulationContext['totalTime']
save = True
saveDirectory = ''.join([networkPath,networkName,'/2dTimePlots/'])
for dir in [saveDirectory]:
if not os.path.exists(dir): os.makedirs(dir)
nodeID = 0
nNodes = int(vascularNetwork.vessels[vesselId].N)
filenames = []
Pmax = np.max(solutionData[0]['Pressure'][vesselId])/133.32
Pmin = np.min(solutionData[0]['Pressure'][vesselId])/133.32
Qmax = np.max(solutionData[0]['Flow'][vesselId])*1e6*60
Qmin = np.min(solutionData[0]['Flow'][vesselId])*1e6*60
for n in range(0,nNodes):
Psol = solutionData[0]['Pressure'][vesselId][:,[n]]
Qsol = solutionData[0]['Flow'][vesselId][:,[n]]
timeNormal = np.linspace(0,totalTime,len(Psol))
fig = plt.figure(1, edgecolor='k',dpi=80)
fig.subplots_adjust(hspace=0.5)
fig.set_figwidth(8.27)
fig.set_figheight((11.69/3)*2)
ax = plt.subplot(2,1,1)
ax.plot(timeNormal,Psol/133.32,color='b' ,linestyle = '-',label='total', linewidth = 1.5)
ax.set_ylabel('Pressure [mmHg]')
ax.set_xlabel('Time [t]')
ax.set_xlim(0,totalTime)
ax.set_ylim(Pmin,Pmax)
ax2 = plt.subplot(2,1,2)
ax2.plot(timeNormal,Qsol*1e6*60,color='r' ,linestyle = '-',label='total', linewidth = 1.5)
ax2.set_ylabel('Flow [ml/min]')
ax2.set_xlabel('Time [t]')
ax2.set_xlim(0,totalTime)
ax2.set_ylim(Qmin,Qmax)
savePath = ''.join([saveDirectory,str(vesselId).zfill(2),str(n).zfill(2),'.png'])
filenames.append(savePath)
plt.savefig(savePath)
plt.clf()
PyApp(nNodes,filenames,vesselName,updateVesselId)
gtk.main()
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)