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MeshGenerator.py
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MeshGenerator.py
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#!/usr/bin/env python
## Program: PyNS
## Module: MeshGenerator.py
## Language: Python
## Date: $Date: 2012/09/04 10:21:12 $
## Version: $Revision: 0.4.2 $
## Copyright (c) Simone Manini, Luca Antiga. All rights reserved.
## See LICENCE file for details.
## This software is distributed WITHOUT ANY WARRANTY; without even
## the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
## PURPOSE. See the above copyright notices for more information.
## Developed with support from the EC FP7/2007-2013: ARCH, Project n. 224390
import Elements
from NetworkMesh import Entity
from numpy.ma.core import ceil
class MeshGenerator(object):
'''
This Class builds NetworkMesh from NetworkGraph,
providing two different type of meshing (Maximum length
or Radius Tolerance).
This Class provides the following methods:
SetMeshType: A method for setting specific MeshType for each edge.
SetNetworkGraph: a method for setting NetworkGraph input.
SetNetworkMesh: a method for setting NetworkMesh input.
SetTolerance: a method for setting Radius Tolerance % value.
SetMaxLength: a method for setting maximum length for a single mesh.
ParsingEdgeProperties: a method for parsing properties for each edge of the NetworkGraph.
GenerateMesh: a method for generating NetworkMesh from NetworkGraph. If MaxLength is specified,
GenerateMesh uses MaxLengthMeshing method, otherwise ToleranceMeshing method is used.
'''
def __init__(self):
'''
Constructor
'''
self.MeshType = {} # edgeId:elementType (default 0D)
self.NetworkGraph = None
self.NetworkMesh = None
self.MaxLength = None
self.Tolerance = None
def SetMeshType(self, edgeId, elementType):
'''
Setting meshType for each edge
'''
self.MeshType[edgeId] = elementType
def SetNetworkGraph(self,networkGraph):
'''
Setting NetworkGraph
'''
self.NetworkGraph = networkGraph
def SetNetworkMesh(self, networkMesh):
'''
Setting NetworkMesh
'''
self.NetworkMesh = networkMesh
def SetTolerance(self, radiusTolerance):
'''
Setting Tolerance %
'''
self.Tolerance = {'radius':radiusTolerance*1e-2}
def SetMaxLength(self, maxLength):
'''
Setting Maximum segment length
'''
self.MaxLength = maxLength
def ParsingEdgeProperties(self, edge):
'''
Parsing NetworkGraph.Edge properties into
a dictionary edgeproperty {name:value}
'''
edgeProperty = {} #dictionary property:{s:value}
if edge.Type is not None:
self.SetMeshType(edge.Id, edge.Type)
if edge.Length.has_key('array') == False:
length = edge.Length['value']
edgeProperty['length'] = length
if edge.Radius.has_key('array') == False:
try:
radius = edge.Radius['value']
meshradius = {}
meshradius[0.0] = radius
meshradius[1.0] = radius
edgeProperty['radius'] = meshradius
except KeyError:
edgeProperty['radius'] = None
if edge.xRadius.has_key('value') == True:
xradius = edge.xRadius['value']
else:
xradius = None
edgeProperty['xradius'] = {0.0:xradius, 1.0:xradius}
if edge.yRadius.has_key('value') == True:
yradius = edge.yRadius['value']
else:
yradius = None
edgeProperty['yradius'] = {0.0:yradius, 1.0:yradius}
if edge.Radius.has_key('array') == True:
meshradius = {}
s_list = []
for s in edge.Radius['array'].iterkeys():
s_list.append(s)
s_list.sort()
if meshradius.has_key(s):
meshradius[s].append(edge.Radius['array'][s])
else:
meshradius[s]=edge.Radius['array'][s]
edgeProperty['radius'] = meshradius
if edge.xRadius.has_key('array') == True:
meshradius = {}
s_list = []
for s in edge.xRadius['array'].iterkeys():
s_list.append(s)
s_list.sort()
if meshradius.has_key(s):
meshradius[s].append(edge.xRadius['array'][s])
else:
meshradius[s]=edge.xRadius['array'][s]
edgeProperty['xradius'] = meshradius
elif edge.xRadius.has_key('value') == True:
xradius = edge.xRadius['value']
edgeProperty['xradius'] = {0.0:xradius, 1.0:xradius}
else:
xradius = None
edgeProperty['xradius'] = {0.0:xradius, 1.0:xradius}
if edge.yRadius.has_key('array') == True:
meshradius = {}
s_list = []
for s in edge.yRadius['array'].iterkeys():
s_list.append(s)
s_list.sort()
if meshradius.has_key(s):
meshradius[s].append(edge.yRadius['array'][s])
else:
meshradius[s]=edge.yRadius['array'][s]
edgeProperty['yradius'] = meshradius
elif edge.yRadius.has_key('value') == True:
yradius = edge.yRadius['value']
edgeProperty['yradius'] = {0.0:yradius, 1.0:yradius}
else:
yradius = None
edgeProperty['yradius'] = {0.0:yradius, 1.0:yradius}
if edge.WallThickness.has_key('value') == True:
wallThickness = edge.WallThickness['value']
meshwt = {}
meshwt[0.0] = wallThickness
meshwt[1.0] = wallThickness
edgeProperty['wallthickness'] = meshwt
if edge.WallThickness.has_key('array') == True:
meshwt = {}
s_list = []
for s in edge.WallThickness['array'].iterkeys():
s_list.append(s)
s_list.sort()
if meshwt.has_key(s):
meshwt[s].append(edge.WallThickness['array'][s])
else:
meshwt[s]=edge.WallThickness['array'][s]
edgeProperty['wallthickness'] = meshwt
if edge.WallThickness.has_key('expression') == True:
edgeProperty['wallthickness'] = edge.WallThickness['expression']
if edge.YoungModulus.has_key('array') == False:
try:
youngModulus = edge.YoungModulus['value']
except:
youngModulus = 0.0
meshym = {}
meshym[0.0] = youngModulus
meshym[1.0] = youngModulus
edgeProperty['youngmodulus'] = meshym
if edge.ScalarRadius != {}:
edgeProperty['ScalarRadius'] = edge.ScalarRadius
else:
edgeProperty['ScalarRadius'] = {}
if edgeProperty['radius'] is not None:
for rad in edgeProperty['radius'].itervalues():
if type(rad) is not str:
edgeProperty['ScalarRadius'] = edgeProperty['radius']
return edgeProperty
def GenerateMesh(self):
'''
This method generates Network Mesh from Network Graph
'''
self.NetworkMesh.Id = self.NetworkGraph.Id
if self.Tolerance is not None:
self.ToleranceMeshing(self.Tolerance)
else:
if self.MaxLength is not None:
self.MaxLengthMeshing(self.MaxLength)
else:
raise MeshingError
def MaxLengthMeshing(self, maxLength):
'''
This method build NetworkMesh from NetworkGraph using Maximum Length meshing criterium.
If edge's length is greater than maxLength parameter, a new mesh is created.
'''
meshId = 1 #First mesh Id index
self.NetworkMesh.meshToEdges = {} # dict edgenode:meshnode
self.NetworkMesh.s_mesh = {} # dict (s,edge):meshnode
self.NetworkMesh.MeshToGraph = {} # {meshId : edgeId}
self.NetworkMesh.MeshToS = {} # {meshId : [s]}
self.NetworkMesh.Entities = {} # {entity:[mesh]}
self.NetworkMesh.GraphEdgeToMesh = {} #{edge:[meshId:[s0,s1]]}
self.NetworkMesh.ElementIdsToElements = {} # {mesh.Id:mesh}
self.NetworkMesh.GraphNodeToMesh = {} #{edge:[meshId:[s0,s1]]}
nLeak = 0
meshNode1 = None
meshNode2 = None
nodes_list = [] #nodes list
nodes_list_last = len(nodes_list)
meshNodeAnast0 = None
meshNodeAnast1 = None
meshNodeAnast2 = None
done = 0 #if = 1, AVF resistances meshed
for edgeId, edge in self.NetworkGraph.Edges.iteritems():
if self.NetworkMesh.GraphEdgeToMesh.has_key(edge):
pass
else:
edgeProperties = self.ParsingEdgeProperties(edge)
# Searching for anastomosis element (arterial and venous side)
for nodeId, node in self.NetworkGraph.Nodes.iteritems():
if node.Type == 'anastomosis':
if int(nodeId) in edge.NodeIds:
if edge.Side == 'venous':
if done == 0:
try:
meshNode0 = self.NetworkMesh.meshToEdges[edge.NodeIds[0]]
except KeyError:
meshNode0 = nodes_list_last+1
meshNodeAnast0 = meshNode0
if meshNode0 not in nodes_list:
nodes_list.append(meshNode0)
nodes_list_last = len(nodes_list)
meshNode1 = nodes_list_last+1
if meshNode1 not in nodes_list:
nodes_list.append(meshNode1)
nodes_list_last = len(nodes_list)
meshNodeAnast1 = meshNode1
meshNode2 = nodes_list_last+1
if meshNode2 not in nodes_list:
nodes_list.append(meshNode2)
nodes_list_last = len(nodes_list)
meshNodeAnast2 = meshNode2
else:
meshNode0 = meshNodeAnast0
meshNode1 = meshNodeAnast1
meshNode2 = meshNodeAnast2
self.NetworkMesh.meshToEdges[edge.NodeIds[0]] = meshNodeAnast2
if edge.Side == 'arterial' and int(nodeId) == edge.NodeIds[1]:
if done == 0:
try:
meshNode0 = self.NetworkMesh.meshToEdges[edge.NodeIds[1]]
except KeyError:
meshNode0 = nodes_list_last+1
meshNodeAnast0 = meshNode0
if meshNode0 not in nodes_list:
nodes_list.append(meshNode0)
nodes_list_last = len(nodes_list)
meshNode1 = nodes_list_last+1
if meshNode1 not in nodes_list:
nodes_list.append(meshNode1)
nodes_list_last = len(nodes_list)
meshNodeAnast1 = meshNode1
meshNode2 = nodes_list_last+1
if meshNode2 not in nodes_list:
nodes_list.append(meshNode2)
nodes_list_last = len(nodes_list)
meshNodeAnast2 = meshNode2
else:
meshNode0 = meshNodeAnast0
meshNode1 = meshNodeAnast1
meshNode2 = meshNodeAnast2
self.NetworkMesh.meshToEdges[edge.NodeIds[1]] = meshNodeAnast0
if edge.Side == 'arterial' and int(nodeId) == edge.NodeIds[0]:
if done == 0:
try:
meshNode1 = self.NetworkMesh.meshToEdges[edge.NodeIds[0]]
except KeyError:
meshNode1 = nodes_list_last+1
meshNodeAnast1 = meshNode1
if meshNode1 not in nodes_list:
nodes_list.append(meshNode1)
nodes_list_last = len(nodes_list)
meshNode0 = nodes_list_last+1
if meshNode0 not in nodes_list:
nodes_list.append(meshNode0)
nodes_list_last = len(nodes_list)
meshNodeAnast0 = meshNode0
meshNode2 = nodes_list_last+1
if meshNode2 not in nodes_list:
nodes_list.append(meshNode2)
nodes_list_last = len(nodes_list)
meshNodeAnast2 = meshNode2
else:
meshNode0 = meshNodeAnast0
meshNode1 = meshNodeAnast1
meshNode2 = meshNodeAnast2
self.NetworkMesh.meshToEdges[edge.NodeIds[0]] = meshNodeAnast1
#NEW ELEMENT
if done == 0:
anast_res_0_1 = node.Properties['arterial_resistance']
anast_res_0_2 = node.Properties['venous_resistance']
elementParameters = {}
elementParameters['resistance_0_1'] = anast_res_0_1
elementParameters['resistance_0_2'] = anast_res_0_2
newElement = Elements.Anastomosis(str(meshId), [meshNode0,meshNode1,meshNode2], elementParameters, name = 'anastomosis')
self.NetworkMesh.Elements.append(newElement)
self.NetworkMesh.ElementIdsToElements[newElement.Id] = newElement
self.NetworkMesh.GraphNodeToMesh[node] = newElement.Id
meshId+=1
entity = Entity()
entity.SetId(node.Name)
if self.NetworkMesh.Entities.has_key(entity):
self.NetworkMesh.Entities[entity].append(newElement)
else:
self.NetworkMesh.Entities[entity] = [newElement]
done = 1
#MESHNODE1########
if meshNode1 == None:
meshNode1 = 1
else:
try:
meshNode1 = self.NetworkMesh.meshToEdges[edge.NodeIds[0]]
except KeyError:
meshNode1 = nodes_list_last+1
##################
if edgeProperties['length'] <= self.MaxLength:
elementParameters = {}
self.NetworkMesh.meshToEdges[edge.NodeIds[0]] = meshNode1
if meshNode1 not in nodes_list:
nodes_list.append(meshNode1)
nodes_list_last = len(nodes_list)
#MESHNODE2#######
try:
meshNode2 = self.NetworkMesh.meshToEdges[edge.NodeIds[1]]
except KeyError:
meshNode2 = nodes_list_last+1
self.NetworkMesh.meshToEdges[edge.NodeIds[1]] = meshNode2
if meshNode2 not in nodes_list:
nodes_list.append(meshNode2)
nodes_list_last = len(nodes_list)
###############
#parameters####
elementParameters['s1'] = 0.0
elementParameters['s2'] = 1.0
elementParameters['length'] = edgeProperties['length']
if self.MeshType.get(edgeId,None) == "Resistance":
pass
else:
if edgeProperties['radius'] is not None:
if type(edgeProperties['radius'][0]) is str or type(edgeProperties['radius'][1]) is str:
elementParameters['radiusAtRest'] = edgeProperties['ScalarRadius']
elementParameters['radius'] = edgeProperties['radius']
else:
elementParameters['radius'] = edgeProperties['radius']
else:
elementParameters['radius'] = {elementParameters['s1']:edgeProperties['xradius'][elementParameters['s1']]*edgeProperties['yradius'][elementParameters['s1']]**0.5, elementParameters['s2']:edgeProperties['xradius'][elementParameters['s2']]*edgeProperties['yradius'][elementParameters['s2']]**0.5}
elementParameters['wall_thickness'] = edgeProperties['wallthickness']
elementParameters['young_modulus'] = edgeProperties['youngmodulus']
if edgeProperties['xradius'][0.0] is not None:
elementParameters['xradius'] = edgeProperties['xradius']
else:
elementParameters['xradius'] = None
if edgeProperties['yradius'][0.0] is not None:
elementParameters['yradius'] = edgeProperties['yradius']
else:
elementParameters['yradius'] = None
elementParameters["resistance"] = edge.Resistance
if edge.NlCompliance != {}:
elementParameters["compliance"] = edge.NlCompliance['expression']
else:
elementParameters["compliance"] = edge.Compliance
elementParameters["leakage"] = edge.QLeakage
if edge.QLeakage:
nLeak+=1
##############################################
# MESHING AN EDGE ACCORDING TO ITS MESH TYPE #
##############################################
newElement = Elements.NewElement(self.MeshType.get(edgeId,None), str(meshId), [meshNode1,meshNode2], elementParameters, edge.Side, edge.Name)
self.NetworkMesh.Elements.append(newElement)
#Dicts###
self.NetworkMesh.ElementIdsToElements[newElement.Id] = newElement
self.NetworkMesh.s_mesh[(0.0,edge)] = meshNode1
self.NetworkMesh.s_mesh[(1.0,edge)] = meshNode2
self.NetworkMesh.MeshToGraph[str(meshId)] = edge.Id
self.NetworkMesh.MeshToS[meshId] = [0.0,1.0]
if self.NetworkMesh.GraphEdgeToMesh.has_key(edge):
meshtoSappend = {meshId:self.NetworkMesh.MeshToS[meshId]}
self.NetworkMesh.GraphEdgeToMesh[edge].append(meshtoSappend)
else:
meshtoSappend = {meshId:self.NetworkMesh.MeshToS[meshId]}
self.NetworkMesh.GraphEdgeToMesh[edge] = [meshtoSappend]
##############
meshId+=1
else:
elementParameters = {}
numEl = int(ceil(edgeProperties['length'] / self.MaxLength))
i = 0.0
nameId = 1
self.NetworkMesh.meshToEdges[edge.NodeIds[0]] = meshNode1
if meshNode1 not in nodes_list:
nodes_list.append(meshNode1)
nodes_list_last = len(nodes_list)
while i < numEl:
s1 = i / numEl
s2 = (i+1) / numEl
elLength = edgeProperties['length']/numEl
if s2 >= 1.0:
s2 = 1.0
try:
meshNode2 = self.NetworkMesh.meshToEdges[edge.NodeIds[1]]
except KeyError:
meshNode2 = nodes_list_last+1
self.NetworkMesh.meshToEdges[edge.NodeIds[1]] = meshNode2
else:
meshNode2 = nodes_list_last+1
elementParameters['s1'] = s1
elementParameters['s2'] = s2
if edgeProperties['radius'] is not None:
if type(edgeProperties['radius'][0]) is str or type(edgeProperties['radius'][1]) is str:
elementParameters['radiusAtRest'] = {s1:edgeProperties['ScalarRadius'][0]-((edgeProperties['ScalarRadius'][0]-edgeProperties['ScalarRadius'][1])*s1), s2:edgeProperties['ScalarRadius'][0]-((edgeProperties['ScalarRadius'][0]-edgeProperties['ScalarRadius'][1])*s2)}
elementParameters['radius'] = {s1:edgeProperties['radius'][0], s2:edgeProperties['radius'][1]}
else:
elementParameters['radius'] = {s1:edgeProperties['radius'][0]-((edgeProperties['radius'][0]-edgeProperties['radius'][1])*s1), s2:edgeProperties['radius'][0]-((edgeProperties['radius'][0]-edgeProperties['radius'][1])*s2)}
else:
rs1 = ((edgeProperties['xradius'][0]-((edgeProperties['xradius'][0]-edgeProperties['xradius'][1])*s1))*(edgeProperties['yradius'][0]-((edgeProperties['yradius'][0]-edgeProperties['yradius'][1])*s1)))**0.5
rs2 = ((edgeProperties['xradius'][0]-((edgeProperties['xradius'][0]-edgeProperties['xradius'][1])*s2))*(edgeProperties['yradius'][0]-((edgeProperties['yradius'][0]-edgeProperties['yradius'][1])*s2)))**0.5
elementParameters['radius'] = {s1:rs1, s2:rs2}
if edgeProperties['xradius'][0.0] is not None:
elementParameters['xradius'] = {s1:edgeProperties['xradius'][0]-((edgeProperties['xradius'][0]-edgeProperties['xradius'][1])*s1), s2:edgeProperties['xradius'][0]-((edgeProperties['xradius'][0]-edgeProperties['xradius'][1])*s2)}
else:
elementParameters['xradius'] = None
if edgeProperties['yradius'][0.0] is not None:
elementParameters['yradius'] = {s1:edgeProperties['yradius'][0]-((edgeProperties['yradius'][0]-edgeProperties['yradius'][1])*s1), s2:edgeProperties['yradius'][0]-((edgeProperties['yradius'][0]-edgeProperties['yradius'][1])*s2)}
else:
elementParameters['yradius'] = None
if type(edgeProperties['wallthickness']) == dict:
elementParameters['wall_thickness'] = {s1:edgeProperties['wallthickness'][0]-((edgeProperties['wallthickness'][0]-edgeProperties['wallthickness'][1])*s1), s2:edgeProperties['wallthickness'][0]-((edgeProperties['wallthickness'][0]-edgeProperties['wallthickness'][1])*s2)}
else:
elementParameters['wall_thickness']=edgeProperties['wallthickness']
elementParameters['young_modulus'] = {s1:edgeProperties['youngmodulus'][0]-((edgeProperties['youngmodulus'][0]-edgeProperties['youngmodulus'][1])*s1), s2:edgeProperties['youngmodulus'][0]-((edgeProperties['youngmodulus'][0]-edgeProperties['youngmodulus'][1])*s2)}
elementParameters['length'] = elLength
elementParameters["resistance"] = edge.Resistance
if edge.NlCompliance != {}:
elementParameters["compliance"] = edge.NlCompliance['expression']
else:
elementParameters["compliance"] = edge.Compliance
elementParameters["leakage"] = edge.QLeakage
if edge.QLeakage:
nLeak+=2
name = edge.Name + "_" + str(nameId)
#############
newElement= Elements.NewElement(self.MeshType.get(edgeId,None),str(meshId), [meshNode1,meshNode2], elementParameters, edge.Side, name)
self.NetworkMesh.Elements.append(newElement)
self.NetworkMesh.ElementIdsToElements[newElement.Id] = newElement
self.NetworkMesh.s_mesh[(s1,edge)] = meshNode1
self.NetworkMesh.s_mesh[(s2,edge)] = meshNode2
self.NetworkMesh.MeshToGraph[str(meshId)] = edge.Id
self.NetworkMesh.MeshToS[meshId] = [s1,s2]
if self.NetworkMesh.GraphEdgeToMesh.has_key(edge):
meshtoSappend = {meshId:self.NetworkMesh.MeshToS[meshId]}
self.NetworkMesh.GraphEdgeToMesh[edge].append(meshtoSappend)
else:
meshtoSappend = {meshId:self.NetworkMesh.MeshToS[meshId]}
self.NetworkMesh.GraphEdgeToMesh[edge] = [meshtoSappend]
meshId+=1
if meshNode2 not in nodes_list:
nodes_list.append(meshNode2)
nodes_list_last = len(nodes_list)
meshNode1 = meshNode2
nameId+=1
i+=1
#SETTING ANASTOMOSIS CONNECTIONS DICTIONARIES
for nodeId, node in self.NetworkGraph.Nodes.iteritems():
if node.Type == 'anastomosis':
edge = self.NetworkGraph.Edges[node.Properties['proximal']]
for meshlist in self.NetworkMesh.GraphEdgeToMesh[edge]:
for meshId in meshlist:
if self.NetworkMesh.MeshToS[meshId][1] == 1.0:
proximal = self.NetworkMesh.ElementIdsToElements[str(meshId)]
self.NetworkMesh.ElementIdsToElements[self.NetworkMesh.GraphNodeToMesh[node]].SetProximal(proximal)
try:
edge = self.NetworkGraph.Edges[node.Properties['distal']]
for meshlist in self.NetworkMesh.GraphEdgeToMesh[edge]:
for meshId in meshlist:
if self.NetworkMesh.MeshToS[meshId][0] == 0.0:
distal = self.NetworkMesh.ElementIdsToElements[str(meshId)]
self.NetworkMesh.ElementIdsToElements[self.NetworkMesh.GraphNodeToMesh[node]].SetDistal(distal)
except KeyError:
pass
edge = self.NetworkGraph.Edges[node.Properties['vein']]
for meshlist in self.NetworkMesh.GraphEdgeToMesh[edge]:
for meshId in meshlist:
if self.NetworkMesh.MeshToS[meshId][0] == 0.0:
vein = self.NetworkMesh.ElementIdsToElements[str(meshId)]
self.NetworkMesh.ElementIdsToElements[self.NetworkMesh.GraphNodeToMesh[node]].SetVein(vein)
#SETTING LEAKAGES
for el in self.NetworkMesh.Elements:
if el.Type == "WavePropagation":
el.Leakages = nLeak
#ENTITIES DICTIONARY
for sedge in self.NetworkGraph.SuperEdges.values():
entity = Entity()
entity.SetId(sedge.Name)
for edge in sedge.Edges.values():
for key, value in self.NetworkMesh.MeshToGraph.iteritems():
if value == edge.Id:
for el in self.NetworkMesh.Elements:
if el.Type != 'Resistance':
if el.Id == key:
if self.NetworkMesh.Entities.has_key(entity):
self.NetworkMesh.Entities[entity].append(el)
else:
self.NetworkMesh.Entities[entity] = [el]
# MESHING END SEGMENTS (WINDKESSEL ELEMENTS)
entity = Entity()
entity.SetId('end_segment')
nodeslist = []
for nodeId, node in self.NetworkGraph.Nodes.iteritems():
nodeslist.append(int(node.Id))
nodeslist.sort()
nodes_list_last = len(nodes_list)
meshNode2 = nodes_list_last+1
meshEndId = 1
for nd in nodeslist:
for nodeId, node in self.NetworkGraph.Nodes.iteritems():
if nd == int(node.Id):
if node.Type == 'downstream network':
meshNode1 = self.NetworkMesh.meshToEdges[int(node.Id)]
for el in self.NetworkMesh.Elements:
if el.NodeIds[1] == self.NetworkMesh.meshToEdges[int(node.Id)]:
newElement = Elements.WindkesselElement(meshEndId, [meshNode1,meshNode2], node.Name, el.Side)
newId = newElement.Id
newElement.SetLastElement(el)
newElement.RelExpression = node.Properties['windkessel']
self.NetworkMesh.Elements.append(newElement)
if self.NetworkMesh.Entities.has_key(entity):
self.NetworkMesh.Entities[entity].append(newElement)
else:
self.NetworkMesh.Entities[entity] = [newElement]
self.NetworkMesh.s_mesh[(newId, 1.0)] = meshNode2
self.NetworkMesh.ElementIdsToElements[newElement.Id] = newElement
self.NetworkMesh.GraphNodeToMesh[node] = newElement.Id
meshNode2+=1
meshEndId+=1
def ToleranceMeshing(self, Tolerance):
'''
This method build NetworkMesh from NetworkGraph using Radius Tolerance meshing criterium.
If radius along the curvilinear abscissa increases more than Tolerance, a new mesh is created.
'''
meshId = 1 #First mesh Id index
self.NetworkMesh.meshToEdges = {} # dict edgenode:meshnode
self.NetworkMesh.s_mesh = {} # dict (s,edge):meshnode
self.NetworkMesh.MeshToGraph = {} # {meshId : edgeId}
self.NetworkMesh.MeshToS = {} # {meshId : [s]}
self.NetworkMesh.Entities = {} # {entity:[mesh]}
self.NetworkMesh.GraphEdgeToMesh = {} #{edge:[meshId:[s0,s1]]}
self.NetworkMesh.ElementIdsToElements = {} # {mesh.Id:mesh}
self.NetworkMesh.GraphNodeToMesh = {} #{edge:[meshId:[s0,s1]]}
nLeak = 0
meshNode1 = None
meshNode2 = None
nodes_list = [] #nodes list
nodes_list_last = len(nodes_list)
meshNodeAnast0 = None
meshNodeAnast1 = None
meshNodeAnast2 = None
done = 0 #if = 1, AVF resistances meshed
for edgeId, edge in self.NetworkGraph.Edges.iteritems():
if self.NetworkMesh.GraphEdgeToMesh.has_key(edge):
pass
else:
edgeProperties = self.ParsingEdgeProperties(edge)
# Searching for anastomosis element (arterial and venous side)
for nodeId, node in self.NetworkGraph.Nodes.iteritems():
if node.Type == 'anastomosis':
if int(nodeId) in edge.NodeIds:
if edge.Side == 'venous':
if done == 0:
try:
meshNode0 = self.NetworkMesh.meshToEdges[edge.NodeIds[0]]
except KeyError:
meshNode0 = nodes_list_last+1
meshNodeAnast0 = meshNode0
if meshNode0 not in nodes_list:
nodes_list.append(meshNode0)
nodes_list_last = len(nodes_list)
meshNode1 = nodes_list_last+1
if meshNode1 not in nodes_list:
nodes_list.append(meshNode1)
nodes_list_last = len(nodes_list)
meshNodeAnast1 = meshNode1
meshNode2 = nodes_list_last+1
if meshNode2 not in nodes_list:
nodes_list.append(meshNode2)
nodes_list_last = len(nodes_list)
meshNodeAnast2 = meshNode2
else:
meshNode0 = meshNodeAnast0
meshNode1 = meshNodeAnast1
meshNode2 = meshNodeAnast2
self.NetworkMesh.meshToEdges[edge.NodeIds[0]] = meshNodeAnast2
if edge.Side == 'arterial' and int(nodeId) == edge.NodeIds[1]:
if done == 0:
try:
meshNode0 = self.NetworkMesh.meshToEdges[edge.NodeIds[1]]
except KeyError:
meshNode0 = nodes_list_last+1
meshNodeAnast0 = meshNode0
if meshNode0 not in nodes_list:
nodes_list.append(meshNode0)
nodes_list_last = len(nodes_list)
meshNode1 = nodes_list_last+1
if meshNode1 not in nodes_list:
nodes_list.append(meshNode1)
nodes_list_last = len(nodes_list)
meshNodeAnast1 = meshNode1
meshNode2 = nodes_list_last+1
if meshNode2 not in nodes_list:
nodes_list.append(meshNode2)
nodes_list_last = len(nodes_list)
meshNodeAnast2 = meshNode2
else:
meshNode0 = meshNodeAnast0
meshNode1 = meshNodeAnast1
meshNode2 = meshNodeAnast2
self.NetworkMesh.meshToEdges[edge.NodeIds[1]] = meshNodeAnast0
if edge.Side == 'arterial' and int(nodeId) == edge.NodeIds[0]:
if done == 0:
try:
meshNode1 = self.NetworkMesh.meshToEdges[edge.NodeIds[0]]
except KeyError:
meshNode1 = nodes_list_last+1
meshNodeAnast1 = meshNode1
if meshNode1 not in nodes_list:
nodes_list.append(meshNode1)
nodes_list_last = len(nodes_list)
meshNode0 = nodes_list_last+1
if meshNode0 not in nodes_list:
nodes_list.append(meshNode0)
nodes_list_last = len(nodes_list)
meshNodeAnast0 = meshNode0
meshNode2 = nodes_list_last+1
if meshNode2 not in nodes_list:
nodes_list.append(meshNode2)
nodes_list_last = len(nodes_list)
meshNodeAnast2 = meshNode2
else:
meshNode0 = meshNodeAnast0
meshNode1 = meshNodeAnast1
meshNode2 = meshNodeAnast2
self.NetworkMesh.meshToEdges[edge.NodeIds[0]] = meshNodeAnast1
#NEW ELEMENT
if done == 0:
anast_res_0_1 = node.Properties['arterial_resistance']
anast_res_0_2 = node.Properties['venous_resistance']
elementParameters = {}
elementParameters['resistance_0_1'] = anast_res_0_1
elementParameters['resistance_0_2'] = anast_res_0_2
newElement = Elements.Anastomosis(str(meshId), [meshNode0,meshNode1,meshNode2], elementParameters, name = 'anastomosis')
self.NetworkMesh.Elements.append(newElement)
self.NetworkMesh.ElementIdsToElements[newElement.Id] = newElement
self.NetworkMesh.GraphNodeToMesh[node] = newElement.Id
meshId+=1
entity = Entity()
entity.SetId(node.Name)
if self.NetworkMesh.Entities.has_key(entity):
self.NetworkMesh.Entities[entity].append(newElement)
else:
self.NetworkMesh.Entities[entity] = [newElement]
done = 1
#MESHNODE1########
if meshNode1 == None:
meshNode1 = 1
else:
try:
meshNode1 = self.NetworkMesh.meshToEdges[edge.NodeIds[0]]
except KeyError:
meshNode1 = nodes_list_last+1
##################
elementParameters = {}
nameId = 1
self.NetworkMesh.meshToEdges[edge.NodeIds[0]] = meshNode1
if meshNode1 not in nodes_list:
nodes_list.append(meshNode1)
nodes_list_last = len(nodes_list)
i = 0
s_list=[]
for s in edgeProperties['radius'].iterkeys():
s_list.append(s)
s_list.sort()
print edge.Name, s_list
while i < (len(s_list)-1):
radius_1 = edgeProperties['radius'][s_list[i]]
maxVar = radius_1*self.Tolerance['radius']
radius_2 = edgeProperties['radius'][s_list[i+1]]
if edgeProperties['xradius'][0.0] is not None:
elementParameters['xradius'] = {s_list[i]:edgeProperties['xradius'][s_list[i]], s_list[i+1]:edgeProperties['xradius'][s_list[i+1]]}
else:
elementParameters['xradius'] = None
if edgeProperties['yradius'][0.0] is not None:
elementParameters['yradius'] = {s_list[i]:edgeProperties['yradius'][s_list[i]], s_list[i+1]:edgeProperties['yradius'][s_list[i+1]]}
else:
elementParameters['yradius'] = None
if abs(radius_1-radius_2) <= maxVar:
try:
elementParameters['radius'].update({s_list[i]:radius_1})
except KeyError:
elementParameters['radius']={s_list[i]:radius_1}
if s_list[i+1] == 1.0:
elementParameters['radius'].update({s_list[i+1]:radius_2})
if edgeProperties['xradius'][0.0] is not None:
elementParameters['xradius'] = {s_list[i]:edgeProperties['xradius'][s_list[i]], s_list[i+1]:edgeProperties['xradius'][s_list[i+1]]}
else:
elementParameters['xradius'] = None
if edgeProperties['yradius'][0.0] is not None:
elementParameters['yradius'] = {s_list[i]:edgeProperties['yradius'][s_list[i]], s_list[i+1]:edgeProperties['yradius'][s_list[i+1]]}
else:
elementParameters['yradius'] = None
for s in elementParameters['radius'].iterkeys():
if s not in s_list:
s_list.append(s)
try:
elementParameters['wall_thickness'].update({s:edgeProperties['wallthickness'][s]})
except KeyError:
elementParameters['wall_thickness']={s:edgeProperties['wallthickness'][s]}
try:
elementParameters['young_modulus'].update({s:edgeProperties['youngmodulus'][s]})
except KeyError:
elementParameters['young_modulus']={s:edgeProperties['youngmodulus'][s]}
s_start = min(s_list)
s_end = max(s_list)
elementParameters['s1'] = s_start
elementParameters['s2'] = s_end
elementParameters['length'] = (s_end-s_start)*edgeProperties['length']
elementParameters["resistance"] = edge.Resistance
elementParameters["compliance"] = edge.Compliance
elementParameters["leakage"] = edge.QLeakage
if edge.QLeakage:
nLeak+=1
try:
meshNode2 = self.NetworkMesh.meshToEdges[edge.NodeIds[1]]
except KeyError:
meshNode2 = nodes_list_last+1
self.NetworkMesh.meshToEdges[edge.NodeIds[1]] = meshNode2
if meshNode2 not in nodes_list:
nodes_list.append(meshNode2)
nodes_list_last = len(nodes_list)
name = edge.Name + "_" + str(nameId)
newElement = Elements.NewElement(self.MeshType.get(edgeId,None),str(meshId), [meshNode1,meshNode2], elementParameters, edge.Side, name)
self.NetworkMesh.ElementIdsToElements[newElement.Id] = newElement
self.NetworkMesh.Elements.append(newElement)
self.NetworkMesh.s_mesh[(s_start,edge)] = meshNode1
self.NetworkMesh.s_mesh[(s_end,edge)] = meshNode2
self.NetworkMesh.MeshToGraph[str(meshId)] = edge.Id
self.NetworkMesh.MeshToS[meshId] = [s_start,s_end]
if self.NetworkMesh.GraphEdgeToMesh.has_key(edge):
self.NetworkMesh.GraphEdgeToMesh[edge].append((meshId, self.NetworkMesh.MeshToS[meshId]))
else:
self.NetworkMesh.GraphEdgeToMesh[edge] = [(meshId, self.NetworkMesh.MeshToS[meshId])]
meshId+=1
if meshNode2 not in nodes_list:
nodes_list.append(meshNode2)
nodes_list_last = len(nodes_list)
meshNode1 = meshNode2
nameId+=1
i+=1
if abs(radius_1-radius_2) > maxVar:
s1 = s_list[i]
s2 = s_list[i+1]
try:
elementParameters['radius'].update({s1:radius_1, s2:radius_2})
except KeyError:
elementParameters['radius']={s1:radius_1, s2:radius_2}
if edgeProperties['xradius'][0.0] is not None:
elementParameters['xradius'] = {s1:edgeProperties['xradius'][s1], s2:edgeProperties['xradius'][s2]}
else:
elementParameters['xradius'] = None
if edgeProperties['yradius'][0.0] is not None:
elementParameters['yradius'] = {s1:edgeProperties['yradius'][s1], s2:edgeProperties['yradius'][s2]}
else:
elementParameters['yradius'] = None
for s in elementParameters['radius'].iterkeys():
if s not in s_list:
s_list.append(s)
s_list.append(s)
try:
elementParameters['wall_thickness'].update({s:edgeProperties['wallthickness'][s]})
except KeyError:
elementParameters['wall_thickness']={s:edgeProperties['wallthickness'][s]}
try:
elementParameters['young_modulus'].update({s:edgeProperties['youngmodulus'][s]})
except KeyError:
elementParameters['young_modulus']={s:edgeProperties['youngmodulus'][s]}
s_start = min(s_list)
s_end = max(s_list)
elementParameters['s1'] = s1
elementParameters['s2'] = s2
elementParameters['length'] = (s_end-s_start)*edgeProperties['length']
elementParameters["resistance"] = edge.Resistance
elementParameters["compliance"] = edge.Compliance
elementParameters["leakage"] = edge.QLeakage
if edge.QLeakage:
nLeak+=1
try:
meshNode2 = self.NetworkMesh.meshToEdges[edge.NodeIds[1]]
except KeyError:
meshNode2 = nodes_list_last+1
self.NetworkMesh.meshToEdges[edge.NodeIds[1]] = meshNode2
if meshNode2 not in nodes_list:
nodes_list.append(meshNode2)
nodes_list_last = len(nodes_list)
name = edge.Name + "_" + str(nameId)
newElement= newElement.NewElement(self.MeshType.get(edgeId,None), str(meshId), [meshNode1,meshNode2], elementParameters, edge.Side, name)
self.NetworkMesh.ElementIdsToElements[newElement.Id] = newElement
self.NetworkMesh.Elements.append(newElement)
self.NetworkMesh.s_mesh[(s1,edge)] = meshNode1
self.NetworkMesh.s_mesh[(s2,edge)] = meshNode2
self.NetworkMesh.MeshToGraph[str(meshId)] = edge.Id
self.NetworkMesh.MeshToS[meshId] = [s1,s2]
if self.NetworkMesh.GraphEdgeToMesh.has_key(edge):
self.NetworkMesh.GraphEdgeToMesh[edge].append((meshId, self.NetworkMesh.MeshToS[meshId]))
else:
self.NetworkMesh.GraphEdgeToMesh[edge] = [(meshId, self.NetworkMesh.MeshToS[meshId])]
meshId+=1
if meshNode2 not in nodes_list:
nodes_list.append(meshNode2)
nodes_list_last = len(nodes_list)
meshNode1 = meshNode2
nameId+=1
i+=1
#SETTING ANASTOMOSIS CONNECTIONS DICTIONARIES
for nodeId, node in self.NetworkGraph.Nodes.iteritems():
if node.Type == 'anastomosis':
edge = self.NetworkGraph.Edges[node.Properties['proximal']]
for meshlist in self.NetworkMesh.GraphEdgeToMesh[edge]:
for meshId in meshlist:
if self.NetworkMesh.MeshToS[meshId][1] == 1.0:
proximal = self.NetworkMesh.ElementIdsToElements[str(meshId)]
self.NetworkMesh.ElementIdsToElements[self.NetworkMesh.GraphNodeToMesh[node]].SetProximal(proximal)
edge = self.NetworkGraph.Edges[node.Properties['distal']]
for meshlist in self.NetworkMesh.GraphEdgeToMesh[edge]:
for meshId in meshlist:
if self.NetworkMesh.MeshToS[meshId][0] == 0.0:
distal = self.NetworkMesh.ElementIdsToElements[str(meshId)]
self.NetworkMesh.ElementIdsToElements[self.NetworkMesh.GraphNodeToMesh[node]].SetDistal(distal)
edge = self.NetworkGraph.Edges[node.Properties['vein']]
for meshlist in self.NetworkMesh.GraphEdgeToMesh[edge]:
for meshId in meshlist:
if self.NetworkMesh.MeshToS[meshId][0] == 0.0:
vein = self.NetworkMesh.ElementIdsToElements[str(meshId)]
self.NetworkMesh.ElementIdsToElements[self.NetworkMesh.GraphNodeToMesh[node]].SetVein(vein)
#SETTING LEAKAGES
for el in self.NetworkMesh.Elements:
if el.Type == "WavePropagation":
el.Leakages = nLeak
#ENTITIES DICTIONARY
for sedge in self.NetworkGraph.SuperEdges.values():
entity = Entity()
entity.SetId(sedge.Name)
for edge in sedge.Edges.values():
for key, value in self.NetworkMesh.MeshToGraph.iteritems():
if value == edge.Id:
for el in self.NetworkMesh.Elements:
if el.Type != 'Resistance':
if el.Id == key:
if self.NetworkMesh.Entities.has_key(entity):
self.NetworkMesh.Entities[entity].append(el)
else:
self.NetworkMesh.Entities[entity] = [el]
#SETTING ANASTOMOSIS CONNECTIONS DICTIONARIES
for nodeId, node in self.NetworkGraph.Nodes.iteritems():
if node.Type == 'anastomosis':
edge = self.NetworkGraph.Edges[node.Properties['proximal']]
for meshlist in self.NetworkMesh.GraphEdgeToMesh[edge]:
for meshId in meshlist:
if self.NetworkMesh.MeshToS[meshId][1] == 1.0:
proximal = self.NetworkMesh.ElementIdsToElements[str(meshId)]
self.NetworkMesh.ElementIdsToElements[self.NetworkMesh.GraphNodeToMesh[node]].SetProximal(proximal)
edge = self.NetworkGraph.Edges[node.Properties['distal']]
for meshlist in self.NetworkMesh.GraphEdgeToMesh[edge]:
for meshId in meshlist:
if self.NetworkMesh.MeshToS[meshId][0] == 0.0:
distal = self.NetworkMesh.ElementIdsToElements[str(meshId)]
self.NetworkMesh.ElementIdsToElements[self.NetworkMesh.GraphNodeToMesh[node]].SetDistal(distal)
edge = self.NetworkGraph.Edges[node.Properties['vein']]
for meshlist in self.NetworkMesh.GraphEdgeToMesh[edge]:
for meshId in meshlist:
if self.NetworkMesh.MeshToS[meshId][0] == 0.0:
vein = self.NetworkMesh.ElementIdsToElements[str(meshId)]
self.NetworkMesh.ElementIdsToElements[self.NetworkMesh.GraphNodeToMesh[node]].SetVein(vein)
# MESHING END SEGMENTS (WINDKESSEL ELEMENTS)
entity = Entity()
entity.SetId('end_segment')
nodeslist = []
for nodeId, node in self.NetworkGraph.Nodes.iteritems():
nodeslist.append(int(node.Id))
nodeslist.sort()
nodes_list_last = len(nodes_list)
meshNode2 = nodes_list_last+1
meshEndId = 1
for nd in nodeslist:
for nodeId, node in self.NetworkGraph.Nodes.iteritems():
if nd == int(node.Id):
if node.Type == 'downstream network':
meshNode1 = self.NetworkMesh.meshToEdges[int(node.Id)]
for el in self.NetworkMesh.Elements:
if el.NodeIds[1] == self.NetworkMesh.meshToEdges[int(node.Id)]:
newElement = Elements.WindkesselElement(meshEndId, [meshNode1,meshNode2], node.Name, el.Side)
newId = newElement.Id
newElement.SetLastElement(el)
newElement.RelExpression = node.Properties['windkessel']
self.NetworkMesh.Elements.append(newElement)
self.NetworkMesh.ElementIdsToElements[newElement.Id] = newElement
self.NetworkMesh.GraphNodeToMesh[node] = newElement.Id
if self.NetworkMesh.Entities.has_key(entity):
self.NetworkMesh.Entities[entity].append(newElement)
else:
self.NetworkMesh.Entities[entity] = [newElement]
self.NetworkMesh.s_mesh[(newId, 1.0)] = meshNode2
meshNode2+=1
meshEndId+=1
class Error(Exception):
'''
A base class for exceptions defined in this module.
'''
pass
class MeshingError(Error):
'''
Exception raised for Meshing Failure
'''
def __init__(self):
print "Error, Please set MaxLength or Tolerance before meshing the network."