def setPathParameters(region, nodeValueLabels, nodeValues, editGroupName=None):
'''
Set node parameters for coordinates field in path from listed values.
:param nodeValueLabels: List of nodeValueLabels to set e.g. [ Node.VALUE_LABEL_VALUE, Node.VALUE_LABEL_D_DS1 ]
:param nodeValues: List of values for each type e.g. [ xlist, d1list ]
:param editGroupName: Optional name of existing or new Zinc group to record modified nodes in.
'''
fieldmodule = region.getFieldmodule()
coordinates = fieldmodule.findFieldByName('coordinates').castFiniteElement()
componentsCount = coordinates.getNumberOfComponents()
# following requires at least one value label and node, assumes consistent values and components counts
nodeValueLabelsCount = len(nodeValueLabels)
nodesCount = len(nodeValues[0])
nodes = fieldmodule.findNodesetByFieldDomainType(Field.DOMAIN_TYPE_NODES)
assert nodesCount == nodes.getSize()
with ChangeManager(fieldmodule):
if editGroupName:
editGroup = findOrCreateFieldGroup(fieldmodule, editGroupName, managed=True)
editNodeGroup = editGroup.getFieldNodeGroup(nodes)
if not editNodeGroup.isValid():
editNodeGroup = editGroup.createFieldNodeGroup(nodes)
editNodesetGroup = editNodeGroup.getNodesetGroup()
cache = fieldmodule.createFieldcache()
nodeIter = nodes.createNodeiterator()
node = nodeIter.next()
n = 0
while node.isValid():
cache.setNode(node)
for v in range(nodeValueLabelsCount):
coordinates.setNodeParameters(cache, -1, nodeValueLabels[v], 1, nodeValues[v][n])
if editGroupName:
editNodesetGroup.addNode(node)
node = nodeIter.next()
n += 1
def zinc_write_element_xi_marker_file(outFile, region, allMarkers,
nodeIdentifier):
fm = region.getFieldmodule()
fm.beginChange()
nodes = fm.findNodesetByFieldDomainType(Field.DOMAIN_TYPE_NODES)
mesh = fm.findMeshByDimension(3)
cache = fm.createFieldcache()
markerGroup = findOrCreateFieldGroup(fm, "marker")
markerName = findOrCreateFieldStoredString(fm, name="marker_name")
markerLocation = findOrCreateFieldStoredMeshLocation(
fm, mesh, name="marker_location")
markerPoints = findOrCreateFieldNodeGroup(markerGroup,
nodes).getNodesetGroup()
markerTemplate = nodes.createNodetemplate()
markerTemplate.defineField(markerName)
markerTemplate.defineField(markerLocation)
for key in allMarkers:
addMarker = {"name": key + " projected", "xi": allMarkers[key]["xi"]}
markerPoint = markerPoints.createNode(nodeIdentifier, markerTemplate)
cache.setNode(markerPoint)
markerName.assignString(cache, addMarker["name"])
elementID = allMarkers[key]["elementID"]
element = mesh.findElementByIdentifier(elementID)
result = markerLocation.assignMeshLocation(cache, element,
addMarker["xi"])
nodeIdentifier += 1
fm.endChange()
region.writeFile(outFile)
return
def __init__(self,
region,
field,
selectionGroupName=None,
scalingMode=DerivativeScalingMode.ARITHMETIC_MEAN,
editGroupName=None):
'''
:param selectionGroupName: Optional name of group to limit smoothing to nodes in group.
Only element edges including those nodes are included in smoothing.
'''
self._region = region
self._field = field.castFiniteElement()
componentsCount = self._field.getNumberOfComponents()
assert self._field.isValid()
self._selectionGroupName = selectionGroupName
self._selectionGroup = None
self._selectionNodes = None
self._scalingMode = scalingMode
self._editGroupName = editGroupName
self._fieldmodule = self._region.getFieldmodule()
for dimension in range(3, 0, -1):
self._mesh = self._fieldmodule.findMeshByDimension(dimension)
if self._mesh.getSize() > 0:
break
self._nodes = self._fieldmodule.findNodesetByFieldDomainType(
Field.DOMAIN_TYPE_NODES)
# edited nodes are added to the edit nodeset group, if group is supplied
if editGroupName:
editGroup = findOrCreateFieldGroup(self._fieldmodule,
editGroupName,
managed=True)
editNodeGroup = editGroup.getFieldNodeGroup(self._nodes)
if not editNodeGroup.isValid():
editNodeGroup = editGroup.createFieldNodeGroup(self._nodes)
self._editNodesetGroup = editNodeGroup.getNodesetGroup()
else:
self._editNodesetGroup = None
# edges define curves with 4 expressions for x1, d1, x2, d2, followed by the arcLength
# each expression is a list of terms.
# each term contains a list of global node id, value label, version, element identifier, scale factor or None
# edges are mapped from sorted start and end node
self._edgesMap = {}
# map global nodeid, derivative, version to list of EdgeCurve
self._derivativeMap = {}
if selectionGroupName:
self._selectionGroup = self._fieldmodule.findFieldByName(
selectionGroupName).castGroup()
if not self._selectionGroup.isValid():
print('DerivativeSmoothing: Selection group not found')
return
self._selectionNodes = self._selectionGroup.getFieldNodeGroup(
self._nodes).getNodesetGroup()
if (not self._selectionNodes.isValid()) or (
self._selectionNodes.getSize() == 0):
print('DerivativeSmoothing: No nodes selected for smoothing')
return
self.addElementEdges()
def test_field_group(self):
"""
Test creation of group fields.
"""
context = Context("test")
region = context.createRegion()
fieldmodule = region.getFieldmodule()
group_name = "bob"
group = findOrCreateFieldGroup(fieldmodule, group_name)
self.assertTrue(group.isValid())
self.assertTrue(group.isManaged())
nodes = fieldmodule.findNodesetByFieldDomainType(Field.DOMAIN_TYPE_NODES)
node_group = findOrCreateFieldNodeGroup(group, nodes)
self.assertTrue(node_group.isValid())
self.assertFalse(node_group.isManaged())
node_group_name = group_name + "." + nodes.getName()
self.assertEqual(node_group_name, node_group.getName())
def zinc_write_element_xi_file(outFile, xyz, allMarkers):
context = Context("Example")
outputRegion = context.getDefaultRegion()
fm = outputRegion.getFieldmodule()
fm.beginChange()
cache = fm.createFieldcache()
coordinates = findOrCreateFieldCoordinates(fm)
nodes = fm.findNodesetByFieldDomainType(Field.DOMAIN_TYPE_NODES)
nodetemplate = nodes.createNodetemplate()
nodetemplate.defineField(coordinates)
nodetemplate.setValueNumberOfVersions(coordinates, -1,
Node.VALUE_LABEL_VALUE, 1)
markerNodes = fm.findNodesetByFieldDomainType(Field.DOMAIN_TYPE_DATAPOINTS)
markerGroup = findOrCreateFieldGroup(fm, "marker")
markerName = findOrCreateFieldStoredString(fm, name="marker_name")
markerPoints = findOrCreateFieldNodeGroup(markerGroup,
markerNodes).getNodesetGroup()
markerTemplate = markerPoints.createNodetemplate()
markerTemplate.defineField(markerName)
markerTemplate.defineField(coordinates)
nodeIdentifier = 1
for ix in xyz:
node = nodes.createNode(nodeIdentifier, nodetemplate)
cache.setNode(node)
coordinates.setNodeParameters(cache, -1, Node.VALUE_LABEL_VALUE, 1, ix)
nodeIdentifier += 1
nodeIdentifier = 1
for key in allMarkers:
addMarker = {"name": key, "xyz": allMarkers[key]}
node = markerPoints.createNode(nodeIdentifier, markerTemplate)
cache.setNode(node)
coordinates.setNodeParameters(cache, -1, Node.VALUE_LABEL_VALUE, 1,
addMarker['xyz'])
markerName.assignString(cache, addMarker["name"])
nodeIdentifier += 1
fm.endChange()
outputRegion.writeFile(outFile)
def generateBaseMesh(cls, region, options):
"""
Generate the base tricubic Hermite mesh. See also generateMesh().
:param region: Zinc region to define model in. Must be empty.
:param options: Dict containing options. See getDefaultOptions().
:return: None
"""
parameterSetName = options['Base parameter set']
isDefault = 'Default' in parameterSetName
isMouse = 'Mouse' in parameterSetName
isMean = 'mean' in parameterSetName
fm = region.getFieldmodule()
nodes = fm.findNodesetByFieldDomainType(Field.DOMAIN_TYPE_NODES)
coordinates = findOrCreateFieldCoordinates(fm)
mesh = fm.findMeshByDimension(3)
cache = fm.createFieldcache()
nodetemplate = nodes.createNodetemplate()
nodetemplate.defineField(coordinates)
nodetemplate.setValueNumberOfVersions(coordinates, -1,
Node.VALUE_LABEL_VALUE, 1)
nodetemplate.setValueNumberOfVersions(coordinates, -1,
Node.VALUE_LABEL_D_DS1, 1)
nodetemplate.setValueNumberOfVersions(coordinates, -1,
Node.VALUE_LABEL_D_DS2, 1)
armCount = 3
elementLengthCentral = options['Element width central']
elementLengths = [
options['Element length along arm'],
options['Element width across arm'], options['Element thickness']
]
elementsCountsAlongArms = options['Numbers of elements along arms']
elementsCount2 = 2
elementsCount3 = 1
useCrossDerivatives = False
# arm group annotations for user
armTerms, _ = getAutomaticArmFaceTerms(armCount)
armGroups = [AnnotationGroup(region, armTerm) for armTerm in armTerms]
stellateTerm = get_stellate_term(
"cervicothoracic ganglion") if isMouse else ("stellate", None)
stellateGroup = AnnotationGroup(region, stellateTerm)
annotationGroups = [stellateGroup] + armGroups
armMeshGroups = [a.getMeshGroup(mesh) for a in armGroups]
stellateMeshGroup = stellateGroup.getMeshGroup(mesh)
# markers with element number and xi position
allMarkers = {}
if isMouse:
xProportion = {}
xProportion['ICN'] = 0.9
xProportion['VA'] = 0.9
xProportion['DA'] = 0.9
xProportion['C8'] = 0.9
xProportion['T1'] = 0.25
xProportion['T2'] = 0.5
xProportion['T3'] = 0.75
xProportion['TST'] = 1
armNumber = {}
armNumber['ICN'] = 2
armNumber['VA'] = 2
armNumber['DA'] = 3
armNumber['C8'] = 3
armNumber['T1'] = 1
armNumber['T2'] = 1
armNumber['T3'] = 1
armNumber['TST'] = 1
nerveAbbrev = list(xProportion.keys())
elementIndex = {}
xi1 = {}
for nerve in nerveAbbrev:
elementIndex[nerve] = int(
xProportion[nerve] *
elementsCountsAlongArms[armNumber[nerve] - 1])
xi1[nerve] = 1 if xProportion[nerve] == 1 else xProportion[
nerve] * elementsCountsAlongArms[armNumber[nerve] -
1] - elementIndex[nerve]
elementIndex[nerve] += 1 if xProportion[nerve] < 1 else 0
allMarkers = {
"Inferior cardiac nerve": {
"elementID":
elementIndex['ICN'] + 2 * elementsCountsAlongArms[0],
"xi": [xi1['ICN'], 0.0, 0.5]
},
"Ventral ansa subclavia": {
"elementID":
elementIndex['VA'] + 2 * elementsCountsAlongArms[0] +
elementsCountsAlongArms[1],
"xi": [xi1['VA'], 1.0, 0.5]
},
"Dorsal ansa subclavia": {
"elementID":
elementIndex['DA'] + 2 *
(elementsCountsAlongArms[0] + elementsCountsAlongArms[1]),
"xi": [xi1['DA'], 0.0, 0.5]
},
"Cervical spinal nerve 8": {
"elementID":
elementIndex['C8'] + 2 *
(elementsCountsAlongArms[0] + elementsCountsAlongArms[1]) +
elementsCountsAlongArms[2],
"xi": [xi1['C8'], 1.0, 0.5]
},
"Thoracic spinal nerve 1": {
"elementID": elementIndex['T1'],
"xi": [xi1['T1'], 0.0, 0.5]
},
"Thoracic spinal nerve 2": {
"elementID": elementIndex['T2'],
"xi": [xi1['T2'], 0.0, 0.5]
},
"Thoracic spinal nerve 3": {
"elementID": elementIndex['T3'],
"xi": [xi1['T3'], 0.0, 0.5]
},
"Thoracic sympathetic nerve trunk": {
"elementID": elementIndex['TST'],
"xi": [xi1['TST'], 1.0, 0.5]
},
}
markerGroup = findOrCreateFieldGroup(fm, "marker")
markerName = findOrCreateFieldStoredString(fm, name="marker_name")
markerLocation = findOrCreateFieldStoredMeshLocation(
fm, mesh, name="marker_location")
markerPoints = findOrCreateFieldNodeGroup(markerGroup,
nodes).getNodesetGroup()
markerTemplateInternal = nodes.createNodetemplate()
markerTemplateInternal.defineField(markerName)
markerTemplateInternal.defineField(markerLocation)
# Create nodes
nodeIdentifier = 1
minArmAngle = 2 * math.pi / armCount
halfArmArcAngleRadians = minArmAngle / 2
if not isMean:
dipMultiplier = 1
for na in range(armCount):
elementsCount_i = [
elementsCountsAlongArms[na], elementsCount2, elementsCount3
]
x, ds1, ds2, nWheelEdge = createArm(halfArmArcAngleRadians,
elementLengths,
elementLengthCentral,
elementsCount_i,
dipMultiplier, armCount,
na)
for ix in range(len(x)):
if na == 0 or ix not in nWheelEdge:
node = nodes.createNode(nodeIdentifier, nodetemplate)
cache.setNode(node)
coordinates.setNodeParameters(cache, -1,
Node.VALUE_LABEL_VALUE,
1, x[ix])
coordinates.setNodeParameters(cache, -1,
Node.VALUE_LABEL_D_DS1,
1, ds1[ix])
coordinates.setNodeParameters(cache, -1,
Node.VALUE_LABEL_D_DS2,
1, ds2[ix])
nodeIdentifier += 1
else:
x_dx_all = cls.mouseMeanMesh['meshEdits']
xyz_all = [x[0] for x in x_dx_all]
dxyz = [[x[1], x[2]] for x in x_dx_all]
nodeIdentifier = 1
for i, nx in enumerate(xyz_all):
node = nodes.createNode(nodeIdentifier, nodetemplate)
cache.setNode(node)
coordinates.setNodeParameters(cache, -1,
Node.VALUE_LABEL_VALUE, 1, nx)
coordinates.setNodeParameters(cache, -1,
Node.VALUE_LABEL_D_DS1, 1,
dxyz[i][0])
coordinates.setNodeParameters(cache, -1,
Node.VALUE_LABEL_D_DS2, 1,
dxyz[i][1])
nodeIdentifier += 1
nodesCountsPerArm = [0] + [((elementsCount2 + 1) * e + 1) * 2
for e in elementsCountsAlongArms]
# Create elements
bicubichermitelinear = eftfactory_bicubichermitelinear(
mesh, useCrossDerivatives)
eft = bicubichermitelinear.createEftNoCrossDerivatives(
) #createEftBasic()
elementtemplate = mesh.createElementtemplate()
elementtemplate.setElementShapeType(Element.SHAPE_TYPE_CUBE)
elementtemplate.defineField(coordinates, -1, eft)
elementtemplateX = mesh.createElementtemplate()
elementtemplateX.setElementShapeType(Element.SHAPE_TYPE_CUBE)
elementIdentifier = 1
cumNodesCountsPerArm = [
sum(nodesCountsPerArm[:i + 1])
for i in range(len(nodesCountsPerArm))
]
nCentre = [
elementsCountsAlongArms[0] + 1,
int(nodesCountsPerArm[1] / 2) + elementsCountsAlongArms[0] + 1
]
for na in range(armCount):
for e3 in range(elementsCount3):
for e2 in range(elementsCount2):
for e1 in range(elementsCountsAlongArms[na]):
scalefactors = None
### NODES ###
no2 = (elementsCountsAlongArms[na] + 1)
no3 = (elementsCount2 + 1) * no2 - 2
offset = (cumNodesCountsPerArm[na])
bni = e3 * no3 + e2 * no2 + e1 + 1 + offset
if e2 == 0:
if e1 == 0 and na > 0: # and na < armCount -1: # wheelSouth
nWh = cumNodesCountsPerArm[na - 1] + (
2 * elementsCountsAlongArms[na - 1]) + 2
nplUq = int(
nodesCountsPerArm[na + 1] / 2
) - elementsCountsAlongArms[
na] # unused nodes at centre and shared edge
npl = int(
nodesCountsPerArm[na + 1] /
2) # nodes at centre and shared edge
if na < armCount - 1:
cn = cumNodesCountsPerArm[
na] + elementsCountsAlongArms[na] - 2
no2 = cumNodesCountsPerArm[na]
em = elementsCountsAlongArms[na]
nwPrev = [
nWh,
nWh + int(nodesCountsPerArm[na] / 2)
] # previous arm's edge, depends on armCount.
nodeIdentifiers = [
nwPrev[0], no2 + 1, nCentre[0],
no2 + em, nwPrev[1],
no2 + em - 1 + nplUq, nCentre[1],
bni + (4 * em) - 2
]
else:
nplPrev = int(
nodesCountsPerArm[na] / 2) - 2
no2 = elementsCountsAlongArms[na] - 1
no3 = int(
nodesCountsPerArm[na + 1] / 2) - 3
nwPrev = [
cumNodesCountsPerArm[na - 1] + 2 *
(elementsCountsAlongArms[na - 1]),
cumNodesCountsPerArm[na - 1] + 2 *
(elementsCountsAlongArms[na - 1]) +
nplPrev
]
start = cumNodesCountsPerArm[na] - 3
nodeIdentifiers = [
nwPrev[0], start, nCentre[0],
start + no2, nwPrev[1], start + no3,
nCentre[1], start + no2 + no3
]
elif e1 == elementsCountsAlongArms[
na] - 1: # armEnd, south
if na == 0:
nodeIdentifiers = [
bni, bni + no2 - 1, bni + no2,
bni + no3, bni + no2 + no3 - 1,
bni + no2 + no3
]
else:
no3 = armCount * elementsCountsAlongArms[
na] - 1
no2 = elementsCountsAlongArms[na]
if na > 1:
bni -= 4
no3 -= 1
nodeIdentifiers = [
bni - 1, bni + no2 - 2, bni + no2 - 1,
bni + no3 - 1, bni + no2 - 2 + no3,
bni + no2 + no3 - 1
]
elif na > 0 and e1 > 0: # [na=1+, e1=1+, e2=0] for len=3+
bni -= 1 + ((armCount + 1) * (na - 1))
no2 = elementsCountsAlongArms[na]
no3 = armCount * no2 - (na - 1) - 1
nodeIdentifiers = [
bni, bni + 1, bni + no2 - 1, bni + no2,
bni + no3, bni + no3 + 1,
bni + no2 + no3 - 1, bni + no2 + no3
]
else:
nodeIdentifiers = [
bni, bni + 1, bni + no2 - 1, bni + no2,
bni + no3, bni + no3 + 1,
bni + no2 + no3 - 1, bni + no2 + no3
]
else:
if e1 == 0 and na > 0: # and na < armCount -1: # wheelNorth
if na < armCount - 1:
bni -= armCount
npl = int(
nodesCountsPerArm[na + 1] / 2) - 2
no2 = elementsCountsAlongArms[na]
nodeIdentifiers = [
nCentre[0], bni + 1, bni + no2 + 1,
bni + no2 + 2, nCentre[1],
bni + npl + 1, bni + npl + no2 + 1,
bni + npl + no2 + 2
]
else: # last arm
bni = cumNodesCountsPerArm[na] - 2 - (
armCount - elementsCountsAlongArms[na])
nodeIdentifiers = [
nCentre[0], bni + 1, 1, bni + no2,
nCentre[1], bni + no3 - 2,
int(nodesCountsPerArm[1] / 2) + 1,
bni + no2 + no3 - armCount
]
elif e1 == elementsCountsAlongArms[
na] - 1: # armEnd north
if na > 0:
no2 = elementsCountsAlongArms[na]
nplUq = int(
nodesCountsPerArm[na + 1] / 2) - 2
if na > 1:
adj = na - 1
bni -= armCount * na + (
armCount -
elementsCountsAlongArms[na]) + 1
if elementsCountsAlongArms[na] < 3:
bni += 1
if elementsCountsAlongArms[na] > 3:
bni -= elementsCountsAlongArms[
na] - 3
no2 += 1 - adj
no3 = nplUq - adj
nodeIdentifiers = [
bni, bni + 1, bni + no2, bni + no3,
bni + no3 + 1, bni + no2 + no3
]
else:
bni -= armCount
nodeIdentifiers = [
bni, bni + 1, bni + no2 + 1,
bni + nplUq, bni + nplUq + 1,
bni + no2 + nplUq + 1
]
else:
nodeIdentifiers = [
bni - 1, bni, bni + no2 - 1,
bni + no3 - 1, bni + no3,
bni + no2 + no3 - 1
]
elif na > 0 and e1 > 0: # [na=1+, e1=1+, e2=1] for len=3+
adj = na - 1
bni -= armCount * na + adj
no2 -= adj
k = armCount * elementsCountsAlongArms[na] - na
nodeIdentifiers = [
bni, bni + 1, bni + no2, bni + no2 + 1,
bni + k, bni + k + 1, bni + no2 + k,
bni + no2 + k + 1
]
else:
nodeIdentifiers = [
bni - 1, bni, bni + no2 - 1, bni + no2,
bni + no3 - 1, bni + no3,
bni + no2 + no3 - 1, bni + no2 + no3
]
if e1 == 0: # wheel
eft1 = bicubichermitelinear.createEftNoCrossDerivatives(
)
if armCount == 3:
if e2 == 0:
setEftScaleFactorIds(eft1, [1], [])
scalefactors = [-1.0]
scaleEftNodeValueLabels(
eft1, [1, 5], [
Node.VALUE_LABEL_D_DS1,
Node.VALUE_LABEL_D_DS2
], [1])
ns = [3, 7]
else:
ns = [1, 5]
if na == 0:
remapEftNodeValueLabel(
eft1, ns, Node.VALUE_LABEL_D_DS1,
[(Node.VALUE_LABEL_D_DS1, []),
(Node.VALUE_LABEL_D_DS2, [])])
if e2 == 0:
setEftScaleFactorIds(eft1, [1], [])
scalefactors = [-1.0]
remapEftNodeValueLabel(
eft1, ns, Node.VALUE_LABEL_D_DS2,
[(Node.VALUE_LABEL_D_DS1, [1])])
elif na == 1:
setEftScaleFactorIds(eft1, [1], [])
scalefactors = [-1.0]
remapEftNodeValueLabel(
eft1, ns, Node.VALUE_LABEL_D_DS1,
[(Node.VALUE_LABEL_D_DS1, [1])])
if e2 == 0:
remapEftNodeValueLabel(
eft1, ns, Node.VALUE_LABEL_D_DS2,
[(Node.VALUE_LABEL_D_DS2, [1])])
elif e2 == 1:
remapEftNodeValueLabel(
eft1, ns, Node.VALUE_LABEL_D_DS2,
[(Node.VALUE_LABEL_D_DS1, [1]),
(Node.VALUE_LABEL_D_DS2, [1])])
elif na == 2:
setEftScaleFactorIds(eft1, [1], [])
scalefactors = [-1.0]
remapEftNodeValueLabel(
eft1, ns, Node.VALUE_LABEL_D_DS1,
[(Node.VALUE_LABEL_D_DS2, [1])])
if e2 == 0:
remapEftNodeValueLabel(
eft1, ns, Node.VALUE_LABEL_D_DS2,
[(Node.VALUE_LABEL_D_DS1, []),
(Node.VALUE_LABEL_D_DS2, [])])
elif e2 == 1:
remapEftNodeValueLabel(
eft1, ns, Node.VALUE_LABEL_D_DS2,
[(Node.VALUE_LABEL_D_DS1, [])])
elif armCount == 4:
if e2 == 0:
setEftScaleFactorIds(eft1, [1], [])
scalefactors = [-1.0]
scaleEftNodeValueLabels(
eft1, [1, 5], [
Node.VALUE_LABEL_D_DS1,
Node.VALUE_LABEL_D_DS2
], [1])
ns = [3, 7]
else:
ns = [1, 5]
if na == 0:
remapEftNodeValueLabel(
eft1, ns, Node.VALUE_LABEL_D_DS1,
[(Node.VALUE_LABEL_D_DS1, []),
(Node.VALUE_LABEL_D_DS2, [])])
if e2 == 0:
setEftScaleFactorIds(eft1, [1], [])
scalefactors = [-1.0]
remapEftNodeValueLabel(
eft1, ns, Node.VALUE_LABEL_D_DS2,
[(Node.VALUE_LABEL_D_DS1, [1])])
elif na == 1:
setEftScaleFactorIds(eft1, [1], [])
scalefactors = [-1.0]
remapEftNodeValueLabel(
eft1, ns, Node.VALUE_LABEL_D_DS1,
[(Node.VALUE_LABEL_D_DS1, [1]),
(Node.VALUE_LABEL_D_DS2, [])])
if e2 == 0:
remapEftNodeValueLabel(
eft1, ns, Node.VALUE_LABEL_D_DS2,
[(Node.VALUE_LABEL_D_DS2, [1])])
else:
remapEftNodeValueLabel(
eft1, ns, Node.VALUE_LABEL_D_DS2,
[(Node.VALUE_LABEL_D_DS1, [1])])
elif na == 2:
setEftScaleFactorIds(eft1, [1], [])
scalefactors = [-1.0]
remapEftNodeValueLabel(
eft1, ns, Node.VALUE_LABEL_D_DS1,
[(Node.VALUE_LABEL_D_DS1, [1]),
(Node.VALUE_LABEL_D_DS2, [1])])
if e2 == 0:
remapEftNodeValueLabel(
eft1, ns, Node.VALUE_LABEL_D_DS2,
[(Node.VALUE_LABEL_D_DS1, [])])
else:
remapEftNodeValueLabel(
eft1, ns, Node.VALUE_LABEL_D_DS2,
[(Node.VALUE_LABEL_D_DS2, [1])])
elif na == 3:
setEftScaleFactorIds(eft1, [1], [])
scalefactors = [-1.0]
remapEftNodeValueLabel(
eft1, ns, Node.VALUE_LABEL_D_DS1,
[(Node.VALUE_LABEL_D_DS1, []),
(Node.VALUE_LABEL_D_DS2, [1])])
if e2 == 0:
remapEftNodeValueLabel(
eft1, ns, Node.VALUE_LABEL_D_DS2,
[(Node.VALUE_LABEL_D_DS2, [])])
else:
remapEftNodeValueLabel(
eft1, ns, Node.VALUE_LABEL_D_DS2,
[(Node.VALUE_LABEL_D_DS1, [])])
elif e1 < (elementsCountsAlongArms[na] - 1):
eft1 = eft
elementtemplate1 = elementtemplate
else:
# rounded ends of arms. Collapse xi2 at xi1 = 1
eft1 = bicubichermitelinear.createEftNoCrossDerivatives(
)
remapEftNodeValueLabel(eft1, [2, 4, 6, 8],
Node.VALUE_LABEL_D_DS2, [])
if e2 == 0:
remapEftNodeValueLabel(
eft1, [2, 6], Node.VALUE_LABEL_D_DS1,
[(Node.VALUE_LABEL_D_DS2, [])])
nodeIdentifiers = [
nodeIdentifiers[0], nodeIdentifiers[2],
nodeIdentifiers[1], nodeIdentifiers[3],
nodeIdentifiers[5], nodeIdentifiers[4]
]
else: # e2 == 1
setEftScaleFactorIds(eft1, [1], [])
scalefactors = [-1.0]
remapEftNodeValueLabel(
eft1, [4, 8], Node.VALUE_LABEL_D_DS1,
[(Node.VALUE_LABEL_D_DS2, [1])])
ln_map = [1, 2, 3, 2, 4, 5, 6, 5]
remapEftLocalNodes(eft1, 6, ln_map)
if eft1 is not eft:
elementtemplateX.defineField(coordinates, -1, eft1)
elementtemplate1 = elementtemplateX
element = mesh.createElement(elementIdentifier,
elementtemplate1)
result = element.setNodesByIdentifier(
eft1, nodeIdentifiers)
result3 = element.setScaleFactors(
eft1, scalefactors) if scalefactors else None
# add to meshGroup
stellateMeshGroup.addElement(element)
armMeshGroups[na].addElement(element)
elementIdentifier += 1
# annotation fiducial points
if isMouse:
for key in allMarkers:
xi = allMarkers[key]["xi"]
addMarker = {"name": key, "xi": allMarkers[key]["xi"]}
markerPoint = markerPoints.createNode(nodeIdentifier,
markerTemplateInternal)
nodeIdentifier += 1
cache.setNode(markerPoint)
markerName.assignString(cache, addMarker["name"])
elementID = allMarkers[key]["elementID"]
element = mesh.findElementByIdentifier(elementID)
markerLocation.assignMeshLocation(cache, element,
addMarker["xi"])
return annotationGroups
def generateBaseMesh(cls, region, options):
"""
Generate the base tricubic Hermite mesh. See also generateMesh().
:param region: Zinc region to define model in. Must be empty.
:param options: Dict containing options. See getDefaultOptions().
:return: annotationGroups
"""
centralPath = options['Central path']
elementsCountAround = options['Number of elements around']
elementsCountAlong = options['Number of elements along']
elementsCountThroughWall = options['Number of elements through wall']
wallThickness = options['Wall thickness']
mucosaRelThickness = options['Mucosa relative thickness']
submucosaRelThickness = options['Submucosa relative thickness']
circularRelThickness = options[
'Circular muscle layer relative thickness']
longitudinalRelThickness = options[
'Longitudinal muscle layer relative thickness']
useCrossDerivatives = options['Use cross derivatives']
useCubicHermiteThroughWall = not (options['Use linear through wall'])
firstNodeIdentifier = 1
firstElementIdentifier = 1
# Central path
esophagusTermsAlong = [
None, 'cervical part of esophagus', 'thoracic part of esophagus',
'abdominal part of esophagus'
]
arcLengthOfGroupsAlong = []
for i in range(len(esophagusTermsAlong)):
tmpRegion = region.createRegion()
centralPath.generate(tmpRegion)
cxGroup, cd1Group, cd2Group, cd3Group, cd12Group, cd13Group = \
extractPathParametersFromRegion(tmpRegion, [Node.VALUE_LABEL_VALUE, Node.VALUE_LABEL_D_DS1,
Node.VALUE_LABEL_D_DS2, Node.VALUE_LABEL_D_DS3,
Node.VALUE_LABEL_D2_DS1DS2, Node.VALUE_LABEL_D2_DS1DS3],
groupName=esophagusTermsAlong[i])
arcLength = 0.0
for e in range(len(cxGroup) - 1):
arcLength += interp.getCubicHermiteArcLength(
cxGroup[e], cd1Group[e], cxGroup[e + 1], cd1Group[e + 1])
arcLengthOfGroupsAlong.append(arcLength)
if i == 0:
cx = cxGroup
cd1 = cd1Group
cd2 = cd2Group
cd3 = cd3Group
cd12 = cd12Group
cd13 = cd13Group
del tmpRegion
# Sample central path
sx, sd1, se, sxi, ssf = interp.sampleCubicHermiteCurves(
cx, cd1, elementsCountAlong)
sd2, sd12 = interp.interpolateSampleCubicHermite(
cd2, cd12, se, sxi, ssf)
sd3, sd13 = interp.interpolateSampleCubicHermite(
cd3, cd13, se, sxi, ssf)
centralPathLength = arcLengthOfGroupsAlong[0]
elementAlongLength = centralPathLength / elementsCountAlong
elementsCountAlongGroups = []
groupLength = 0.0
e = 0
elementsCount = 1
length = elementAlongLength
for i in range(1, len(esophagusTermsAlong)):
groupLength += arcLengthOfGroupsAlong[i]
if e == elementsCountAlong - 2:
elementsCount += 1
elementsCountAlongGroups.append(elementsCount)
else:
while length < groupLength:
elementsCount += 1
e += 1
length += elementAlongLength
# check which end is grouplength closer to
distToUpperEnd = abs(length - groupLength)
distToLowerEnd = abs(groupLength -
(length - elementsCountAlong))
if distToLowerEnd < distToUpperEnd:
elementsCount -= 1
elementsCountAlongGroups.append(elementsCount)
e -= 1
length -= elementAlongLength
else:
elementsCountAlongGroups.append(elementsCount)
elementsCount = 0
majorRadiusElementList = sd2
minorRadiusElementList = sd3
# Create annotation groups along esophagus
esophagusGroup = AnnotationGroup(region,
get_esophagus_term("esophagus"))
cervicalGroup = AnnotationGroup(
region, get_esophagus_term("cervical part of esophagus"))
thoracicGroup = AnnotationGroup(
region, get_esophagus_term("thoracic part of esophagus"))
abdominalGroup = AnnotationGroup(
region, get_esophagus_term("abdominal part of esophagus"))
annotationGroupAlong = [[esophagusGroup, cervicalGroup],
[esophagusGroup, thoracicGroup],
[esophagusGroup, abdominalGroup]]
annotationGroupsAlong = []
for i in range(len(elementsCountAlongGroups)):
elementsCount = elementsCountAlongGroups[i]
for n in range(elementsCount):
annotationGroupsAlong.append(annotationGroupAlong[i])
annotationGroupsAround = []
for i in range(elementsCountAround):
annotationGroupsAround.append([])
# Groups through wall
longitudinalMuscleGroup = AnnotationGroup(
region,
get_esophagus_term("esophagus smooth muscle longitudinal layer"))
circularMuscleGroup = AnnotationGroup(
region,
get_esophagus_term("esophagus smooth muscle circular layer"))
submucosaGroup = AnnotationGroup(
region, get_esophagus_term("submucosa of esophagus"))
mucosaGroup = AnnotationGroup(region,
get_esophagus_term("esophagus mucosa"))
if elementsCountThroughWall == 1:
relativeThicknessList = [1.0]
annotationGroupsThroughWall = [[]]
else:
relativeThicknessList = [
mucosaRelThickness, submucosaRelThickness,
circularRelThickness, longitudinalRelThickness
]
annotationGroupsThroughWall = [[mucosaGroup], [submucosaGroup],
[circularMuscleGroup],
[longitudinalMuscleGroup]]
xToSample = []
d1ToSample = []
for n2 in range(elementsCountAlong + 1):
# Create inner points
cx = [0.0, 0.0, elementAlongLength * n2]
axis1 = [vector.magnitude(majorRadiusElementList[n2]), 0.0, 0.0]
axis2 = [0.0, vector.magnitude(minorRadiusElementList[n2]), 0.0]
xInner, d1Inner = geometry.createEllipsePoints(cx,
2 * math.pi,
axis1,
axis2,
elementsCountAround,
startRadians=0.0)
xToSample += xInner
d1ToSample += d1Inner
d2ToSample = [[0.0, 0.0, elementAlongLength]
] * (elementsCountAround * (elementsCountAlong + 1))
# Sample along length
xInnerRaw = []
d2InnerRaw = []
xToWarp = []
d1ToWarp = []
d2ToWarp = []
flatWidthList = []
xiList = []
for n1 in range(elementsCountAround):
xForSamplingAlong = []
d2ForSamplingAlong = []
for n2 in range(elementsCountAlong + 1):
idx = n2 * elementsCountAround + n1
xForSamplingAlong.append(xToSample[idx])
d2ForSamplingAlong.append(d2ToSample[idx])
xSampled, d2Sampled = interp.sampleCubicHermiteCurves(
xForSamplingAlong,
d2ForSamplingAlong,
elementsCountAlong,
arcLengthDerivatives=True)[0:2]
xInnerRaw.append(xSampled)
d2InnerRaw.append(d2Sampled)
# Re-arrange sample order & calculate dx_ds1 and dx_ds3 from dx_ds2
for n2 in range(elementsCountAlong + 1):
xAround = []
d2Around = []
for n1 in range(elementsCountAround):
x = xInnerRaw[n1][n2]
d2 = d2InnerRaw[n1][n2]
xAround.append(x)
d2Around.append(d2)
d1Around = []
for n1 in range(elementsCountAround):
v1 = xAround[n1]
v2 = xAround[(n1 + 1) % elementsCountAround]
d1 = d2 = [v2[c] - v1[c] for c in range(3)]
arcLengthAround = interp.computeCubicHermiteArcLength(
v1, d1, v2, d2, True)
dx_ds1 = [c * arcLengthAround for c in vector.normalise(d1)]
d1Around.append(dx_ds1)
d1Smoothed = interp.smoothCubicHermiteDerivativesLoop(
xAround, d1Around)
xToWarp += xAround
d1ToWarp += d1Smoothed
d2ToWarp += d2Around
# Flat width and xi
flatWidth = 0.0
xiFace = []
for n1 in range(elementsCountAround):
v1 = xAround[n1]
d1 = d1Smoothed[n1]
v2 = xAround[(n1 + 1) % elementsCountAround]
d2 = d1Smoothed[(n1 + 1) % elementsCountAround]
flatWidth += interp.getCubicHermiteArcLength(v1, d1, v2, d2)
flatWidthList.append(flatWidth)
for n1 in range(elementsCountAround + 1):
xi = 1.0 / elementsCountAround * n1
xiFace.append(xi)
xiList.append(xiFace)
# Project reference point for warping onto central path
sxRefList, sd1RefList, sd2ProjectedListRef, zRefList = \
tubemesh.getPlaneProjectionOnCentralPath(xToWarp, elementsCountAround, elementsCountAlong,
centralPathLength, sx, sd1, sd2, sd12)
# Warp points
segmentAxis = [0.0, 0.0, 1.0]
closedProximalEnd = False
innerRadiusAlong = []
for n2 in range(elementsCountAlong + 1):
firstNodeAlong = xToWarp[n2 * elementsCountAround]
midptSegmentAxis = [0.0, 0.0, elementAlongLength * n2]
radius = vector.magnitude(firstNodeAlong[c] - midptSegmentAxis[c]
for c in range(3))
innerRadiusAlong.append(radius)
xWarpedList, d1WarpedList, d2WarpedList, d3WarpedUnitList = \
tubemesh.warpSegmentPoints(xToWarp, d1ToWarp, d2ToWarp, segmentAxis, sxRefList, sd1RefList,
sd2ProjectedListRef, elementsCountAround, elementsCountAlong,
zRefList, innerRadiusAlong, closedProximalEnd)
# Create coordinates and derivatives
transitElementList = [0] * elementsCountAround
xList, d1List, d2List, d3List, curvatureList = \
tubemesh.getCoordinatesFromInner(xWarpedList, d1WarpedList, d2WarpedList, d3WarpedUnitList,
[wallThickness]*(elementsCountAlong+1), relativeThicknessList,
elementsCountAround, elementsCountAlong, elementsCountThroughWall,
transitElementList)
# Create flat coordinates
xFlat, d1Flat, d2Flat = tubemesh.createFlatCoordinates(
xiList, flatWidthList, length, wallThickness,
relativeThicknessList, elementsCountAround, elementsCountAlong,
elementsCountThroughWall, transitElementList)
# Create nodes and elements
xOrgan = []
d1Organ = []
d2Organ = []
nodeIdentifier, elementIdentifier, annotationGroups = \
tubemesh.createNodesAndElements(region, xList, d1List, d2List, d3List, xFlat, d1Flat, d2Flat,
xOrgan, d1Organ, d2Organ, None, elementsCountAround, elementsCountAlong,
elementsCountThroughWall, annotationGroupsAround, annotationGroupsAlong,
annotationGroupsThroughWall, firstNodeIdentifier, firstElementIdentifier,
useCubicHermiteThroughWall, useCrossDerivatives, closedProximalEnd)
# annotation fiducial points
fm = region.getFieldmodule()
fm.beginChange()
mesh = fm.findMeshByDimension(3)
cache = fm.createFieldcache()
markerGroup = findOrCreateFieldGroup(fm, "marker")
markerName = findOrCreateFieldStoredString(fm, name="marker_name")
markerLocation = findOrCreateFieldStoredMeshLocation(
fm, mesh, name="marker_location")
nodes = fm.findNodesetByFieldDomainType(Field.DOMAIN_TYPE_NODES)
markerPoints = findOrCreateFieldNodeGroup(markerGroup,
nodes).getNodesetGroup()
markerTemplateInternal = nodes.createNodetemplate()
markerTemplateInternal.defineField(markerName)
markerTemplateInternal.defineField(markerLocation)
markerNames = [
"proximodorsal midpoint on serosa of upper esophageal sphincter",
"proximoventral midpoint on serosa of upper esophageal sphincter",
"distal point of lower esophageal sphincter serosa on the greater curvature of stomach",
"distal point of lower esophageal sphincter serosa on the lesser curvature of stomach"
]
totalElements = elementIdentifier
radPerElementAround = math.pi * 2.0 / elementsCountAround
elementAroundHalfPi = int(0.25 * elementsCountAround)
xi1HalfPi = (math.pi * 0.5 - radPerElementAround *
elementAroundHalfPi) / radPerElementAround
elementAroundPi = int(0.5 * elementsCountAround)
xi1Pi = (math.pi -
radPerElementAround * elementAroundPi) / radPerElementAround
markerElementIdentifiers = [
elementsCountAround * elementsCountThroughWall -
elementAroundHalfPi, elementAroundHalfPi + 1 +
elementsCountAround * (elementsCountThroughWall - 1),
totalElements - elementsCountAround,
totalElements - elementsCountAround + elementAroundPi
]
markerXis = [[1.0 - xi1HalfPi, 0.0, 1.0], [xi1HalfPi, 0.0, 1.0],
[0.0, 1.0, 1.0], [xi1Pi, 1.0, 1.0]]
for n in range(len(markerNames)):
markerGroup = findOrCreateAnnotationGroupForTerm(
annotationGroups, region, get_esophagus_term(markerNames[n]))
markerElement = mesh.findElementByIdentifier(
markerElementIdentifiers[n])
markerXi = markerXis[n]
cache.setMeshLocation(markerElement, markerXi)
markerPoint = markerPoints.createNode(nodeIdentifier,
markerTemplateInternal)
nodeIdentifier += 1
cache.setNode(markerPoint)
markerName.assignString(cache, markerGroup.getName())
markerLocation.assignMeshLocation(cache, markerElement, markerXi)
for group in [esophagusGroup, markerGroup]:
group.getNodesetGroup(nodes).addNode(markerPoint)
fm.endChange()
return annotationGroups
def generateBaseMesh(cls, region, options):
"""
Generate the base tricubic Hermite mesh.
:param region: Zinc region to define model in. Must be empty.
:param options: Dict containing options. See getDefaultOptions().
:return: list of AnnotationGroup
"""
# set dependent outer diameter used in atria2
options['Aorta outer plus diameter'] = options[
'LV outlet inner diameter'] + 2.0 * options[
'LV outlet wall thickness']
elementsCountAroundAtrialSeptum = options[
'Number of elements around atrial septum']
elementsCountAroundLeftAtriumFreeWall = options[
'Number of elements around left atrium free wall']
elementsCountAroundLeftAtrium = elementsCountAroundLeftAtriumFreeWall + elementsCountAroundAtrialSeptum
elementsCountAroundRightAtriumFreeWall = options[
'Number of elements around right atrium free wall']
elementsCountAroundRightAtrium = elementsCountAroundRightAtriumFreeWall + elementsCountAroundAtrialSeptum
useCrossDerivatives = False
fm = region.getFieldmodule()
coordinates = findOrCreateFieldCoordinates(fm)
cache = fm.createFieldcache()
mesh = fm.findMeshByDimension(3)
# generate heartventriclesbase1 model and put atria1 on it
ventriclesAnnotationGroups = MeshType_3d_heartventriclesbase1.generateBaseMesh(
region, options)
atriaAnnotationGroups = MeshType_3d_heartatria1.generateBaseMesh(
region, options)
annotationGroups = mergeAnnotationGroups(ventriclesAnnotationGroups,
atriaAnnotationGroups)
lFibrousRingGroup = findOrCreateAnnotationGroupForTerm(
annotationGroups, region, get_heart_term("left fibrous ring"))
rFibrousRingGroup = findOrCreateAnnotationGroupForTerm(
annotationGroups, region, get_heart_term("right fibrous ring"))
# annotation fiducial points
markerGroup = findOrCreateFieldGroup(fm, "marker")
markerName = findOrCreateFieldStoredString(fm, name="marker_name")
markerLocation = findOrCreateFieldStoredMeshLocation(
fm, mesh, name="marker_location")
nodes = fm.findNodesetByFieldDomainType(Field.DOMAIN_TYPE_NODES)
markerPoints = findOrCreateFieldNodeGroup(markerGroup,
nodes).getNodesetGroup()
markerTemplateInternal = nodes.createNodetemplate()
markerTemplateInternal.defineField(markerName)
markerTemplateInternal.defineField(markerLocation)
##############
# Create nodes
##############
nodeIdentifier = max(1, getMaximumNodeIdentifier(nodes) + 1)
# discover left and right fibrous ring nodes from ventricles and atria
# because nodes are iterated in identifier order, the lowest and first are on the lv outlet cfb, right and left on lower outer layers
# left fibrous ring
lavNodeId = [[[], []], [[], []]] # [n3][n2][n1]
iter = lFibrousRingGroup.getNodesetGroup(nodes).createNodeiterator()
# left fibrous ring, bottom row
cfbNodeId = iter.next().getIdentifier()
cfbLeftNodeId = iter.next().getIdentifier()
for n1 in range(elementsCountAroundLeftAtrium):
lavNodeId[0][0].append(iter.next().getIdentifier())
lavNodeId[1][0].append(cfbNodeId)
lavNodeId[1][0].append(cfbLeftNodeId)
for n1 in range(elementsCountAroundLeftAtriumFreeWall - 1):
lavNodeId[1][0].append(iter.next().getIdentifier())
for n1 in range(elementsCountAroundAtrialSeptum - 1):
lavNodeId[1][0].append(None) # no outer node on interatrial septum
# left fibrous ring, top row
for n1 in range(elementsCountAroundLeftAtrium):
lavNodeId[0][1].append(iter.next().getIdentifier())
for n1 in range(elementsCountAroundLeftAtriumFreeWall + 1):
lavNodeId[1][1].append(iter.next().getIdentifier())
for n1 in range(elementsCountAroundAtrialSeptum - 1):
lavNodeId[1][1].append(None) # no outer node on interatrial septum
# right fibrous ring
ravNodeId = [[[], []], [[], []]] # [n3][n2][n1]
iter = rFibrousRingGroup.getNodesetGroup(nodes).createNodeiterator()
cfbNodeId = iter.next().getIdentifier()
cfbRightNodeId = iter.next().getIdentifier()
# right fibrous ring, bottom row
for n1 in range(elementsCountAroundRightAtrium):
ravNodeId[0][0].append(iter.next().getIdentifier())
for n1 in range(elementsCountAroundRightAtriumFreeWall - 1):
ravNodeId[1][0].append(iter.next().getIdentifier())
ravNodeId[1][0].append(cfbRightNodeId)
ravNodeId[1][0].append(cfbNodeId)
for n1 in range(elementsCountAroundAtrialSeptum - 1):
ravNodeId[1][0].append(None) # no outer node on interatrial septum
# right fibrous ring, top row
for n1 in range(elementsCountAroundRightAtrium):
ravNodeId[0][1].append(iter.next().getIdentifier())
cfbUpperNodeId = iter.next().getIdentifier(
) # cfb from left will be first
for n1 in range(elementsCountAroundRightAtriumFreeWall):
ravNodeId[1][1].append(iter.next().getIdentifier())
ravNodeId[1][1].append(cfbUpperNodeId)
for n1 in range(elementsCountAroundAtrialSeptum - 1):
ravNodeId[1][1].append(None) # no outer node on interatrial septum
#for n2 in range(2):
# print('n2', n2)
# print('lavNodeId[0]', lavNodeId[0][n2])
# print('lavNodeId[1]', lavNodeId[1][n2])
# print('ravNodeId[0]', ravNodeId[0][n2])
# print('ravNodeId[1]', ravNodeId[1][n2])
#################
# Create elements
#################
lFibrousRingMeshGroup = lFibrousRingGroup.getMeshGroup(mesh)
rFibrousRingMeshGroup = rFibrousRingGroup.getMeshGroup(mesh)
elementIdentifier = getMaximumElementIdentifier(mesh) + 1
elementtemplate1 = mesh.createElementtemplate()
elementtemplate1.setElementShapeType(Element.SHAPE_TYPE_CUBE)
# create fibrous ring elements
bicubichermitelinear = eftfactory_bicubichermitelinear(
mesh,
useCrossDerivatives,
linearAxis=2,
d_ds1=Node.VALUE_LABEL_D_DS1,
d_ds2=Node.VALUE_LABEL_D_DS3)
eftFibrousRing = bicubichermitelinear.createEftBasic()
# left fibrous ring, starting at crux / collapsed posterior interatrial sulcus
cruxElementId = None
for e in range(-1, elementsCountAroundLeftAtriumFreeWall):
eft1 = eftFibrousRing
n1 = e
nids = [
lavNodeId[0][0][n1], lavNodeId[0][0][n1 + 1],
lavNodeId[0][1][n1], lavNodeId[0][1][n1 + 1],
lavNodeId[1][0][n1], lavNodeId[1][0][n1 + 1],
lavNodeId[1][1][n1], lavNodeId[1][1][n1 + 1]
]
scalefactors = None
meshGroups = [lFibrousRingMeshGroup]
if e == -1:
# interatrial groove straddles left and right atria, collapsed to 6 node wedge
nids[0] = ravNodeId[0][0][
elementsCountAroundRightAtriumFreeWall]
nids[2] = ravNodeId[0][1][
elementsCountAroundRightAtriumFreeWall]
nids.pop(6)
nids.pop(4)
eft1 = bicubichermitelinear.createEftNoCrossDerivatives()
setEftScaleFactorIds(eft1, [1], [])
scalefactors = [-1.0]
remapEftNodeValueLabel(eft1, [1, 3], Node.VALUE_LABEL_D_DS1,
[(Node.VALUE_LABEL_D_DS1, []),
(Node.VALUE_LABEL_D_DS3, [])])
remapEftNodeValueLabel(eft1, [2, 4], Node.VALUE_LABEL_D_DS1,
[(Node.VALUE_LABEL_D_DS1, []),
(Node.VALUE_LABEL_D_DS3, [1])])
remapEftNodeValueLabel(eft1, [5, 6, 7, 8],
Node.VALUE_LABEL_D_DS1, [])
# reverse d3 on cfb:
remapEftNodeValueLabel(eft1, [5], Node.VALUE_LABEL_D_DS3,
[(Node.VALUE_LABEL_D_DS1, [1]),
(Node.VALUE_LABEL_D_DS3, [1])])
remapEftNodeValueLabel(eft1, [6], Node.VALUE_LABEL_D_DS3,
[(Node.VALUE_LABEL_D_DS1, [0]),
(Node.VALUE_LABEL_D_DS3, [1])])
remapEftNodeValueLabel(eft1, [7], Node.VALUE_LABEL_D_DS3,
[(Node.VALUE_LABEL_D_DS1, []),
(Node.VALUE_LABEL_D_DS3, [])])
remapEftNodeValueLabel(eft1, [8], Node.VALUE_LABEL_D_DS3,
[(Node.VALUE_LABEL_D_DS1, [1]),
(Node.VALUE_LABEL_D_DS3, [])])
ln_map = [1, 2, 3, 4, 5, 5, 6, 6]
remapEftLocalNodes(eft1, 6, ln_map)
meshGroups += [rFibrousRingMeshGroup]
elif e == 0:
# general linear map d3 adjacent to collapsed sulcus
eft1 = bicubichermitelinear.createEftNoCrossDerivatives()
setEftScaleFactorIds(eft1, [1], [])
scalefactors = [-1.0]
# reverse d1, d3 on cfb, left cfb:
scaleEftNodeValueLabels(
eft1, [6],
[Node.VALUE_LABEL_D_DS1, Node.VALUE_LABEL_D_DS3], [1])
remapEftNodeValueLabel(eft1, [5], Node.VALUE_LABEL_D_DS1,
[(Node.VALUE_LABEL_D_DS1, [1])])
remapEftNodeValueLabel(eft1, [5], Node.VALUE_LABEL_D_DS3,
[(Node.VALUE_LABEL_D_DS1, []),
(Node.VALUE_LABEL_D_DS3, [1])])
remapEftNodeValueLabel(eft1, [7], Node.VALUE_LABEL_D_DS3,
[(Node.VALUE_LABEL_D_DS1, [1]),
(Node.VALUE_LABEL_D_DS3, [])])
elif e == 1:
# reverse d1, d3 on left cfb:
eft1 = bicubichermitelinear.createEftNoCrossDerivatives()
setEftScaleFactorIds(eft1, [1], [])
scalefactors = [-1.0]
remapEftNodeValueLabel(eft1, [5], Node.VALUE_LABEL_D_DS1,
[(Node.VALUE_LABEL_D_DS1, [1]),
(Node.VALUE_LABEL_D_DS3, [])])
remapEftNodeValueLabel(eft1, [5], Node.VALUE_LABEL_D_DS3,
[(Node.VALUE_LABEL_D_DS3, [1])])
elif e == (elementsCountAroundLeftAtriumFreeWall - 1):
# general linear map d3 adjacent to collapsed sulcus
eft1 = bicubichermitelinear.createEftNoCrossDerivatives()
setEftScaleFactorIds(eft1, [1], [])
scalefactors = [-1.0]
remapEftNodeValueLabel(eft1, [6, 8], Node.VALUE_LABEL_D_DS3,
[(Node.VALUE_LABEL_D_DS1, []),
(Node.VALUE_LABEL_D_DS3, [])])
result = elementtemplate1.defineField(coordinates, -1, eft1)
element = mesh.createElement(elementIdentifier, elementtemplate1)
result2 = element.setNodesByIdentifier(eft1, nids)
result3 = element.setScaleFactors(
eft1, scalefactors) if scalefactors else None
#print('create element fibrous ring left', elementIdentifier, result, result2, result3, nids)
elementIdentifier += 1
for meshGroup in meshGroups:
meshGroup.addElement(element)
# right fibrous ring, starting at crux / collapsed posterior interatrial sulcus
for e in range(-1, elementsCountAroundRightAtriumFreeWall):
eft1 = eftFibrousRing
n1 = e
nids = [
ravNodeId[0][0][n1], ravNodeId[0][0][n1 + 1],
ravNodeId[0][1][n1], ravNodeId[0][1][n1 + 1],
ravNodeId[1][0][n1], ravNodeId[1][0][n1 + 1],
ravNodeId[1][1][n1], ravNodeId[1][1][n1 + 1]
]
scalefactors = None
meshGroups = [rFibrousRingMeshGroup]
if e == -1:
# interatrial groove straddles left and right atria, collapsed to 6 node wedge
nids[0] = lavNodeId[0][0][
elementsCountAroundLeftAtriumFreeWall]
nids[2] = lavNodeId[0][1][
elementsCountAroundLeftAtriumFreeWall]
nids.pop(6)
nids.pop(4)
eft1 = bicubichermitelinear.createEftNoCrossDerivatives()
setEftScaleFactorIds(eft1, [1], [])
scalefactors = [-1.0]
remapEftNodeValueLabel(eft1, [1, 3], Node.VALUE_LABEL_D_DS1,
[(Node.VALUE_LABEL_D_DS1, []),
(Node.VALUE_LABEL_D_DS3, [])])
remapEftNodeValueLabel(eft1, [2, 4], Node.VALUE_LABEL_D_DS1,
[(Node.VALUE_LABEL_D_DS1, []),
(Node.VALUE_LABEL_D_DS3, [1])])
remapEftNodeValueLabel(eft1, [5, 6, 7, 8],
Node.VALUE_LABEL_D_DS1, [])
remapEftNodeValueLabel(eft1, [5, 7], Node.VALUE_LABEL_D_DS3,
[(Node.VALUE_LABEL_D_DS1, []),
(Node.VALUE_LABEL_D_DS3, [])])
remapEftNodeValueLabel(eft1, [6, 8], Node.VALUE_LABEL_D_DS3,
[(Node.VALUE_LABEL_D_DS1, [1]),
(Node.VALUE_LABEL_D_DS3, [])])
ln_map = [1, 2, 3, 4, 5, 5, 6, 6]
remapEftLocalNodes(eft1, 6, ln_map)
meshGroups += [lFibrousRingMeshGroup]
cruxElementId = elementIdentifier
elif e == 0:
# general linear map d3 adjacent to collapsed crux/posterior sulcus
eft1 = bicubichermitelinear.createEftNoCrossDerivatives()
setEftScaleFactorIds(eft1, [1], [])
scalefactors = [-1.0]
remapEftNodeValueLabel(eft1, [5, 7], Node.VALUE_LABEL_D_DS3,
[(Node.VALUE_LABEL_D_DS1, [1]),
(Node.VALUE_LABEL_D_DS3, [])])
elif e == (elementsCountAroundRightAtriumFreeWall - 2):
# reverse d1, d3 on right cfb:
eft1 = bicubichermitelinear.createEftNoCrossDerivatives()
setEftScaleFactorIds(eft1, [1], [])
scalefactors = [-1.0]
remapEftNodeValueLabel(eft1, [6], Node.VALUE_LABEL_D_DS1,
[(Node.VALUE_LABEL_D_DS1, [1]),
(Node.VALUE_LABEL_D_DS3, [1])])
remapEftNodeValueLabel(eft1, [6], Node.VALUE_LABEL_D_DS3,
[(Node.VALUE_LABEL_D_DS3, [1])])
elif e == (elementsCountAroundRightAtriumFreeWall - 1):
# general linear map d3 adjacent to collapsed cfb/anterior sulcus
eft1 = bicubichermitelinear.createEftNoCrossDerivatives()
setEftScaleFactorIds(eft1, [1], [])
scalefactors = [-1.0]
# reverse d1, d3 on right cfb, cfb:
scaleEftNodeValueLabels(
eft1, [5],
[Node.VALUE_LABEL_D_DS1, Node.VALUE_LABEL_D_DS3], [1])
remapEftNodeValueLabel(eft1, [6], Node.VALUE_LABEL_D_DS1,
[(Node.VALUE_LABEL_D_DS1, [1])])
remapEftNodeValueLabel(eft1, [6], Node.VALUE_LABEL_D_DS3,
[(Node.VALUE_LABEL_D_DS1, [1]),
(Node.VALUE_LABEL_D_DS3, [1])])
remapEftNodeValueLabel(eft1, [8], Node.VALUE_LABEL_D_DS3,
[(Node.VALUE_LABEL_D_DS1, []),
(Node.VALUE_LABEL_D_DS3, [])])
result = elementtemplate1.defineField(coordinates, -1, eft1)
element = mesh.createElement(elementIdentifier, elementtemplate1)
result2 = element.setNodesByIdentifier(eft1, nids)
result3 = element.setScaleFactors(
eft1, scalefactors) if scalefactors else None
#print('create element fibrous ring right', elementIdentifier, result, result2, result3, nids)
elementIdentifier += 1
for meshGroup in meshGroups:
meshGroup.addElement(element)
# fibrous ring septum:
meshGroups = [lFibrousRingMeshGroup, rFibrousRingMeshGroup]
for e in range(elementsCountAroundAtrialSeptum):
eft1 = eftFibrousRing
nlm = e - elementsCountAroundAtrialSeptum
nlp = nlm + 1
nrm = -e
nrp = nrm - 1
nids = [
lavNodeId[0][0][nlm], lavNodeId[0][0][nlp],
lavNodeId[0][1][nlm], lavNodeId[0][1][nlp],
ravNodeId[0][0][nrm], ravNodeId[0][0][nrp],
ravNodeId[0][1][nrm], ravNodeId[0][1][nrp]
]
eft1 = bicubichermitelinear.createEftNoCrossDerivatives()
setEftScaleFactorIds(eft1, [1], [])
scalefactors = [-1.0]
if e == 0:
# general linear map d3 adjacent to collapsed posterior interventricular sulcus
scaleEftNodeValueLabels(eft1, [5, 6, 7, 8],
[Node.VALUE_LABEL_D_DS1], [1])
scaleEftNodeValueLabels(eft1, [6, 8], [Node.VALUE_LABEL_D_DS3],
[1])
remapEftNodeValueLabel(eft1, [1, 3], Node.VALUE_LABEL_D_DS3,
[(Node.VALUE_LABEL_D_DS1, []),
(Node.VALUE_LABEL_D_DS3, [])])
remapEftNodeValueLabel(eft1, [5, 7], Node.VALUE_LABEL_D_DS3,
[(Node.VALUE_LABEL_D_DS1, []),
(Node.VALUE_LABEL_D_DS3, [1])])
elif e == (elementsCountAroundAtrialSeptum - 1):
# general linear map d3 adjacent to cfb
scaleEftNodeValueLabels(eft1, [5, 6, 7, 8],
[Node.VALUE_LABEL_D_DS1], [1])
scaleEftNodeValueLabels(eft1, [5, 7], [Node.VALUE_LABEL_D_DS3],
[1])
remapEftNodeValueLabel(eft1, [2, 4], Node.VALUE_LABEL_D_DS3,
[(Node.VALUE_LABEL_D_DS1, [1]),
(Node.VALUE_LABEL_D_DS3, [])])
remapEftNodeValueLabel(eft1, [6, 8], Node.VALUE_LABEL_D_DS3,
[(Node.VALUE_LABEL_D_DS1, [1]),
(Node.VALUE_LABEL_D_DS3, [1])])
else:
scaleEftNodeValueLabels(
eft1, [5, 6, 7, 8],
[Node.VALUE_LABEL_D_DS1, Node.VALUE_LABEL_D_DS3], [1])
result = elementtemplate1.defineField(coordinates, -1, eft1)
element = mesh.createElement(elementIdentifier, elementtemplate1)
result2 = element.setNodesByIdentifier(eft1, nids)
result3 = element.setScaleFactors(
eft1, scalefactors) if scalefactors else None
#print('create element fibrous ring septum', elementIdentifier, result, result2, result3, nids)
elementIdentifier += 1
for meshGroup in meshGroups:
meshGroup.addElement(element)
# annotation fiducial points
cruxElement = mesh.findElementByIdentifier(cruxElementId)
cruxXi = [0.5, 0.5, 1.0]
cache.setMeshLocation(cruxElement, cruxXi)
result, cruxCoordinates = coordinates.evaluateReal(cache, 3)
markerPoint = markerPoints.createNode(nodeIdentifier,
markerTemplateInternal)
nodeIdentifier += 1
cache.setNode(markerPoint)
markerName.assignString(cache, "crux of heart")
markerLocation.assignMeshLocation(cache, cruxElement, cruxXi)
return annotationGroups
def main_writerotatefile(data_path):
plot = False
concave_hull = True if 'concave_hull' in data_path else False
# fiducial points are in the new xml file with separate marker field
fids_in_xml = False if concave_hull else True
files = os.listdir(data_path)
files = [f for f in files if f.endswith('.ex')]
max_soma = 5
all_nerves = [
'Inferior cardiac nerve', 'Ventral ansa subclavia',
'Dorsal ansa subclavia', 'Cervical spinal nerve 8',
'Thoracic spinal nerve 1', 'Thoracic spinal nerve 2',
'Thoracic spinal nerve 3', 'Thoracic sympathetic nerve trunk',
'Thoracic ansa'
]
bodyname = ['Cervicalganglion', 'stellate']
fdict = {sample: {} for sample in files}
write_this = False
for sample in files:
print(sample)
lr_groups = True
output_suffix = '_LR.exf'
short_name = sample.split('_')[0] if not concave_hull else sample
fmag = sample.split('_')[1].upper()
full_body = True
xyz_sm = []
txt = []
in_file = data_path + sample
if not os.path.exists(data_path + 'exf_output\\'):
os.mkdir(data_path + 'exf_output\\')
mapclient_workflow_path = 'scaffoldfitter_output\\scaffoldfitter_geofit_folder\\exp_data\\'
with open(in_file, 'r') as f_in:
if '10x' not in sample.lower() and not concave_hull:
full_body = False
out_file = data_path + 'exf_output\\' + short_name + (
'_fragment_%s' % (fmag) * (not full_body)) + output_suffix
possibleGroups = [] if concave_hull else all_nerves + [
'Soma %d' % (i) for i in range(1, 6)
] + ['T3 paravertebral ganglion', 'Cervicothoracic ganglion']
all_node_num, xyz_all, _, xyzGroups, _, xyz_marker, marker_names, marker_nodenum, _ = zinc_read_exf_file(
data_path + sample, 2, 0, 1, [], possibleGroups, 3)
xyz_n = {m: xyz_marker[im] for im, m in enumerate(marker_names)}
xyz_all_dict = {n: xyz_all[n - 1] for n in all_node_num}
if not full_body:
nervename = []
for key in xyzGroups.keys():
if key in all_nerves:
nervename.append(key)
for nn in nervename:
xyz_n_0 = xyzGroups[nn]
xyz_n[nn] = xyz_n_0
try:
xyz_st = xyzGroups['Cervicothoracic ganglion']
except:
xyz_st = [xyz_all_dict[key] for key in xyz_all_dict.keys()]
xyz_t3 = []
xyz_t3Rot = []
try:
xyz_t3 = xyzGroups['T3 paravertebral ganglion']
print('T3 paravertebral ganglion present')
except:
pass
# there may be more than one soma
num_soma = 0
if not concave_hull:
for key in xyzGroups:
if 'soma' in key.lower():
num_soma += 1
for i in range(num_soma):
# print('soma '+str(i+1))
crd = xyzGroups['Soma ' + str(i + 1)]
xyz_sm.extend([[c[0], c[1], c[2], i + 1] for c in crd])
if full_body:
if not concave_hull:
x = [(ix[0]) for ix in xyz_st]
y = [(ix[1]) for ix in xyz_st]
z = [(ix[2]) for ix in xyz_st]
centroid = [np.mean(x), np.mean(y), np.mean(z)]
xsm = [[]] * num_soma
ysm = [[]] * num_soma
zsm = [[]] * num_soma
isoma = [[]] * num_soma
for i in range(num_soma):
xsm[i] = [(ix[0]) for ix in xyz_sm if ix[3] == i + 1]
ysm[i] = [(ix[1]) for ix in xyz_sm if ix[3] == i + 1]
zsm[i] = [(ix[2]) for ix in xyz_sm if ix[3] == i + 1]
isoma[i] = i + 1
try:
xy_ICN = xyz_n['Inferior cardiac nerve']
except:
# print('no iCN. using Ventral ansa for system rotation')
xy_ICN = xyz_n['Ventral ansa subclavia']
xy_nerve_fids = [
xyz_n['Dorsal ansa subclavia'], xy_ICN,
xyz_n['Thoracic sympathetic nerve trunk']
]
[
x, y, z, xsm, ysm, zsm, xyz_st, xyz_sm, xyz_t3, fdict,
xyz_n, xy_nerve_end, _
] = flip_system(x, y, z, xsm, ysm, zsm, xy_nerve_fids,
xyz_t3, centroid, num_soma, fdict, xyz_n,
sample, 0)
centroid = [np.mean(x), np.mean(y), np.mean(z)]
[xyz_stRot, theta] = rotate_points(xyz_st, [], [])
[xyz_smRot, theta] = rotate_points(xyz_sm, theta, [])
if xyz_t3:
[xyz_t3Rot, theta] = rotate_points(xyz_t3, theta, [])
xyz_nRot = xyz_n.copy()
for key in xyz_n:
if xyz_n[key]:
[nrot, theta] = rotate_points([xyz_n[key]], theta, [])
xyz_nRot[key] = nrot[0]
try:
[newcoord,
theta] = rotate_points([fdict[sample][key]],
theta, [])
fdict[sample][key] = newcoord[0]
for i in range(num_soma):
[sout, theta] = rotate_points(
[fdict[sample]['Soma%s' % (str(i + 1))]],
theta, [])
fdict[sample]['Soma%s' %
(str(i + 1))] = sout[0]
except:
pass
x = [(ix[0]) for ix in xyz_stRot]
y = [(ix[1]) for ix in xyz_stRot]
z = [(ix[2]) for ix in xyz_stRot]
centroid = [np.mean(x), np.mean(y), np.mean(z)]
xsm = [[]] * num_soma
ysm = [[]] * num_soma
zsm = [[]] * num_soma
isoma = [[]] * num_soma
for i in range(num_soma):
xsm[i] = [(ix[0]) for ix in xyz_smRot if ix[3] == i + 1]
ysm[i] = [(ix[1]) for ix in xyz_smRot if ix[3] == i + 1]
zsm[i] = [(ix[2]) for ix in xyz_smRot if ix[3] == i + 1]
isoma[i] = i + 1
else:
xyz_smRot_2D = xyz_sm # [[xsm[i], ysm[i], zsm[i]] for i in range(len(xsm))]
xyz_stRot = xyz_st.copy()
xyz_nRot = xyz_n.copy()
x = [(ix[0]) for ix in xyz_stRot]
y = [(ix[1]) for ix in xyz_stRot]
z = [(ix[2]) for ix in xyz_stRot]
xsm = [[]] * num_soma
ysm = [[]] * num_soma
zsm = [[]] * num_soma
isoma = [[]] * num_soma
for i in range(num_soma):
xsm[i] = [(ix[0]) for ix in xyz_smRot_2D if ix[3] == i + 1]
ysm[i] = [(ix[1]) for ix in xyz_smRot_2D if ix[3] == i + 1]
zsm[i] = [(ix[2]) for ix in xyz_smRot_2D if ix[3] == i + 1]
isoma[i] = i + 1
lr_groups = False
# soma cx to nerves - INNERVATIONS
cx_soma = {}
if not concave_hull:
xname = sample.split('.ex')[0]
xml_path = data_path + 'xml\\'
cx_soma = parse_xml_find_soma_ID(xml_path + xname)
if lr_groups:
cx = centroid[0]
cy = centroid[1]
if full_body:
# parse through all stellate nodes between selected fiducials of every contour layer
# LEFT: Dorsal ansa / C8 to Ventral ansa / inferior cardiac nerve
# TOP: iCN/VA to trunk (or rightmost top nodes of rotated stellate)
# BOTTOM: C8/DA to trunk or rightmost bottom nodes
[nleft, ntop,
nbottom] = lefttopbottom_by_fiducials(x, y, z, xyz_nRot,
'by_order', sample,
plot)
if lr_groups or not full_body:
# write with zinc
context = Context('Example')
region = context.getDefaultRegion()
fm = region.getFieldmodule()
fm.beginChange()
nodes = fm.findNodesetByFieldDomainType(Field.DOMAIN_TYPE_NODES)
coordinates = findOrCreateFieldCoordinates(fm, 'data_coordinates')
nodetemplate = nodes.createNodetemplate()
nodetemplate.defineField(coordinates)
nodetemplate.setValueNumberOfVersions(coordinates, -1,
Node.VALUE_LABEL_VALUE, 1)
# stellate face groups
armGroup12 = findOrCreateFieldGroup(fm, 'stellate face 1-2')
armGroup23 = findOrCreateFieldGroup(fm, 'stellate face 2-3')
armGroup31 = findOrCreateFieldGroup(fm, 'stellate face 3-1')
armGroup12Name = findOrCreateFieldStoredString(
fm, name='stellate face 1-2')
armGroup23Name = findOrCreateFieldStoredString(
fm, name='stellate face 2-3')
armGroup31Name = findOrCreateFieldStoredString(
fm, name='stellate face 3-1')
armGroup12Nodes = findOrCreateFieldNodeGroup(
armGroup12, nodes).getNodesetGroup()
armGroup23Nodes = findOrCreateFieldNodeGroup(
armGroup23, nodes).getNodesetGroup()
armGroup31Nodes = findOrCreateFieldNodeGroup(
armGroup31, nodes).getNodesetGroup()
markerNodes = fm.findNodesetByFieldDomainType(
Field.DOMAIN_TYPE_DATAPOINTS)
markerGroup = findOrCreateFieldGroup(fm, 'marker')
markerName = findOrCreateFieldStoredString(fm,
name='marker_data_name')
markerPoints = findOrCreateFieldNodeGroup(
markerGroup, markerNodes).getNodesetGroup()
marker_coordinates = findOrCreateFieldCoordinates(
fm, 'marker_data_coordinates')
markerTemplate = markerPoints.createNodetemplate()
markerTemplate.defineField(marker_coordinates)
markerTemplate.setValueNumberOfVersions(marker_coordinates, -1,
Node.VALUE_LABEL_VALUE, 1)
markerTemplate.defineField(markerName)
cache = fm.createFieldcache()
for nID0, xyz in enumerate(xyz_stRot):
nID = nID0 + 1
if nID in nleft:
node = armGroup23Nodes.createNode(nID, nodetemplate)
cache.setNode(node)
coordinates.setNodeParameters(cache, -1,
Node.VALUE_LABEL_VALUE, 1,
xyz)
elif nID in ntop:
node = armGroup12Nodes.createNode(nID, nodetemplate)
cache.setNode(node)
coordinates.setNodeParameters(cache, -1,
Node.VALUE_LABEL_VALUE, 1,
xyz)
elif nID in nbottom:
node = armGroup31Nodes.createNode(nID, nodetemplate)
cache.setNode(node)
coordinates.setNodeParameters(cache, -1,
Node.VALUE_LABEL_VALUE, 1,
xyz)
else: # nothing
node = nodes.createNode(nID, nodetemplate)
cache.setNode(node)
coordinates.setNodeParameters(cache, -1,
Node.VALUE_LABEL_VALUE, 1,
xyz)
nID = 1000001
for i, key in enumerate(xyz_n):
if xyz_n[key] and 'junction' not in key.lower():
if full_body:
xyz = find_closest_end(x, y, z, xyz_nRot[key])
else: # use junction point
for nkey in xyz_nRot:
if 'junction' in nkey.lower() and key.lower(
) in nkey.lower():
xyz = xyz_nRot[nkey]
node = markerPoints.createNode(nID, markerTemplate)
cache.setNode(node)
marker_coordinates.setNodeParameters(
cache, -1, Node.VALUE_LABEL_VALUE, 1, xyz)
markerName.assignString(cache, key)
nID += 1
written_soma_connections = []
for j in range(num_soma):
soma_id = 'Soma ' + str(j + 1)
for key in cx_soma[soma_id]:
possible_nerve = cx_soma[soma_id][key]
if possible_nerve:
soma_nerve = possible_nerve[0]
if (soma_nerve not in written_soma_connections):
soma_inn_name = 'Soma_' + soma_nerve
xys = [
np.mean(xsm[j]),
np.mean(ysm[j]),
np.mean(zsm[j])
]
node = markerPoints.createNode(nID, markerTemplate)
cache.setNode(node)
marker_coordinates.setNodeParameters(
cache, -1, Node.VALUE_LABEL_VALUE, 1, xys)
markerName.assignString(cache, soma_inn_name)
written_soma_connections.append(soma_nerve)
nID += 1
fm.endChange()
region.writeFile(out_file)
# write to mapclient workflow
m_out = mapclient_workflow_path + short_name + output_suffix
shutil.copyfile(out_file, m_out)
else: # do not write anything for files without LR groups
pass
return
def __init__(self, sourceRegion, targetRegion, sourceAnnotationGroups=[]):
'''
Assumes targetRegion is empty.
:param sourceAnnotationGroups: List of AnnotationGroup for source mesh in sourceRegion.
A copy containing the refined elements is created by the MeshRefinement.
'''
self._sourceRegion = sourceRegion
self._sourceFm = sourceRegion.getFieldmodule()
self._sourceCache = self._sourceFm.createFieldcache()
self._sourceCoordinates = findOrCreateFieldCoordinates(self._sourceFm)
# get range of source coordinates for octree range
self._sourceFm.beginChange()
sourceNodes = self._sourceFm.findNodesetByFieldDomainType(
Field.DOMAIN_TYPE_NODES)
minimumsField = self._sourceFm.createFieldNodesetMinimum(
self._sourceCoordinates, sourceNodes)
result, minimums = minimumsField.evaluateReal(self._sourceCache, 3)
assert result == ZINC_OK, 'MeshRefinement failed to get minimum coordinates'
maximumsField = self._sourceFm.createFieldNodesetMaximum(
self._sourceCoordinates, sourceNodes)
result, maximums = maximumsField.evaluateReal(self._sourceCache, 3)
assert result == ZINC_OK, 'MeshRefinement failed to get maximum coordinates'
xrange = [(maximums[i] - minimums[i]) for i in range(3)]
edgeTolerance = 0.5 * (max(xrange))
if edgeTolerance == 0.0:
edgeTolerance = 1.0
minimums = [(minimums[i] - edgeTolerance) for i in range(3)]
maximums = [(maximums[i] + edgeTolerance) for i in range(3)]
minimumsField = None
maximumsField = None
self._sourceMesh = self._sourceFm.findMeshByDimension(3)
self._sourceNodes = self._sourceFm.findNodesetByFieldDomainType(
Field.DOMAIN_TYPE_NODES)
self._sourceElementiterator = self._sourceMesh.createElementiterator()
self._octree = Octree(minimums, maximums)
self._targetRegion = targetRegion
self._targetFm = targetRegion.getFieldmodule()
self._targetFm.beginChange()
self._targetCache = self._targetFm.createFieldcache()
self._targetCoordinates = findOrCreateFieldCoordinates(self._targetFm)
self._targetNodes = self._targetFm.findNodesetByFieldDomainType(
Field.DOMAIN_TYPE_NODES)
self._nodetemplate = self._targetNodes.createNodetemplate()
self._nodetemplate.defineField(self._targetCoordinates)
self._targetMesh = self._targetFm.findMeshByDimension(3)
self._targetBasis = self._targetFm.createElementbasis(
3, Elementbasis.FUNCTION_TYPE_LINEAR_LAGRANGE)
self._targetEft = self._targetMesh.createElementfieldtemplate(
self._targetBasis)
self._targetElementtemplate = self._targetMesh.createElementtemplate()
self._targetElementtemplate.setElementShapeType(
Element.SHAPE_TYPE_CUBE)
result = self._targetElementtemplate.defineField(
self._targetCoordinates, -1, self._targetEft)
self._nodeIdentifier = 1
self._elementIdentifier = 1
# prepare annotation group map
self._sourceAnnotationGroups = sourceAnnotationGroups
self._annotationGroups = []
self._sourceAndTargetMeshGroups = []
self._sourceAndTargetNodesetGroups = []
for sourceAnnotationGroup in sourceAnnotationGroups:
targetAnnotationGroup = AnnotationGroup(
self._targetRegion, sourceAnnotationGroup.getTerm())
self._annotationGroups.append(targetAnnotationGroup)
# assume have only highest dimension element or node/point annotation groups:
if sourceAnnotationGroup.hasMeshGroup(self._sourceMesh):
self._sourceAndTargetMeshGroups.append(
(sourceAnnotationGroup.getMeshGroup(self._sourceMesh),
targetAnnotationGroup.getMeshGroup(self._targetMesh)))
else:
self._sourceAndTargetNodesetGroups.append(
(sourceAnnotationGroup.getNodesetGroup(self._sourceNodes),
targetAnnotationGroup.getNodesetGroup(self._targetNodes)))
# prepare element -> marker point list map
self.elementMarkerMap = {}
sourceMarkerGroup = findOrCreateFieldGroup(self._sourceFm, "marker")
sourceMarkerName = findOrCreateFieldStoredString(self._sourceFm,
name="marker_name")
sourceMarkerLocation = findOrCreateFieldStoredMeshLocation(
self._sourceFm, self._sourceMesh, name="marker_location")
sourceMarkerNodes = findOrCreateFieldNodeGroup(
sourceMarkerGroup, sourceNodes).getNodesetGroup()
nodeIter = sourceMarkerNodes.createNodeiterator()
node = nodeIter.next()
while node.isValid():
self._sourceCache.setNode(node)
element, xi = sourceMarkerLocation.evaluateMeshLocation(
self._sourceCache, self._sourceMesh.getDimension())
if element.isValid():
elementIdentifier = element.getIdentifier()
markerName = sourceMarkerName.evaluateString(self._sourceCache)
markerList = self.elementMarkerMap.get(elementIdentifier)
if not markerList:
markerList = []
self.elementMarkerMap[elementIdentifier] = markerList
markerList.append((markerName, xi, node.getIdentifier()))
node = nodeIter.next()
if self.elementMarkerMap:
self._targetMarkerGroup = findOrCreateFieldGroup(
self._targetFm, "marker")
self._targetMarkerName = findOrCreateFieldStoredString(
self._targetFm, name="marker_name")
self._targetMarkerLocation = findOrCreateFieldStoredMeshLocation(
self._targetFm, self._targetMesh, name="marker_location")
self._targetMarkerNodes = findOrCreateFieldNodeGroup(
self._targetMarkerGroup, self._targetNodes).getNodesetGroup()
self._targetMarkerTemplate = self._targetMarkerNodes.createNodetemplate(
)
self._targetMarkerTemplate.defineField(self._targetMarkerName)
self._targetMarkerTemplate.defineField(self._targetMarkerLocation)
def generateBaseMesh(region, options):
"""
Generate the base tricubic Hermite mesh. See also generateMesh().
:param region: Zinc region to define model in. Must be empty.
:param options: Dict containing options. See getDefaultOptions().
:return: List of AnnotationGroup
"""
baseParameterSetName = options['Base parameter set']
isHuman = 'Human' in baseParameterSetName
isRat = 'Rat' in baseParameterSetName
centralPath = options['Central path']
full = not options['Lower half']
elementsCountAcrossMajor = options['Number of elements across major']
if not full:
elementsCountAcrossMajor //= 2
elementsCountAcrossMinor = options['Number of elements across minor']
elementsCountAcrossShell = options['Number of elements across shell']
elementsCountAcrossTransition = options['Number of elements across transition']
elementsCountAlongAbdomen = options['Number of elements in abdomen']
elementsCountAlongHead = options['Number of elements in head']
elementsCountAlongNeck = options['Number of elements in neck']
elementsCountAlongThorax = options['Number of elements in thorax']
shellRadiusProportion = options['Shell thickness proportion']
shellProportion = 1/(1/shellRadiusProportion-1)*(elementsCountAcrossMajor/2/elementsCountAcrossShell - 1)
discontinuity = options['Discontinuity on the core boundary']
useCrossDerivatives = options['Use cross derivatives']
elementsCountAlong = elementsCountAlongAbdomen + elementsCountAlongThorax + elementsCountAlongNeck + elementsCountAlongHead
fieldmodule = region.getFieldmodule()
coordinates = findOrCreateFieldCoordinates(fieldmodule)
mesh = fieldmodule.findMeshByDimension(3)
bodyGroup = AnnotationGroup(region, get_body_term("body"))
coreGroup = AnnotationGroup(region, get_body_term("core"))
non_coreGroup = AnnotationGroup(region, get_body_term("non core"))
abdomenGroup = AnnotationGroup(region, get_body_term("abdomen"))
thoraxGroup = AnnotationGroup(region, get_body_term("thorax"))
neckGroup = AnnotationGroup(region, get_body_term("neck core"))
headGroup = AnnotationGroup(region, get_body_term("head core"))
annotationGroups = [bodyGroup, coreGroup, non_coreGroup, abdomenGroup, thoraxGroup, neckGroup, headGroup]
cylinderCentralPath = CylinderCentralPath(region, centralPath, elementsCountAlong)
cylinderShape = CylinderShape.CYLINDER_SHAPE_FULL
base = CylinderEnds(elementsCountAcrossMajor, elementsCountAcrossMinor, elementsCountAcrossShell,
elementsCountAcrossTransition, shellProportion,
[0.0, 0.0, 0.0], cylinderCentralPath.alongAxis[0], cylinderCentralPath.majorAxis[0],
cylinderCentralPath.minorRadii[0])
cylinder1 = CylinderMesh(fieldmodule, coordinates, elementsCountAlong, base,
cylinderShape=cylinderShape,
cylinderCentralPath=cylinderCentralPath, useCrossDerivatives=False)
# body coordinates
bodyCoordinates = findOrCreateFieldCoordinates(fieldmodule, name="body coordinates")
tmp_region = region.createRegion()
tmp_fieldmodule = tmp_region.getFieldmodule()
tmp_body_coordinates = findOrCreateFieldCoordinates(tmp_fieldmodule, name="body coordinates")
tmp_cylinder = CylinderMesh(tmp_fieldmodule, tmp_body_coordinates, elementsCountAlong, base,
cylinderShape=cylinderShape,
cylinderCentralPath=cylinderCentralPath, useCrossDerivatives=False)
sir = tmp_region.createStreaminformationRegion()
srm = sir.createStreamresourceMemory()
tmp_region.write(sir)
result, buffer = srm.getBuffer()
sir = region.createStreaminformationRegion()
srm = sir.createStreamresourceMemoryBuffer(buffer)
region.read(sir)
del srm
del sir
del tmp_body_coordinates
del tmp_fieldmodule
del tmp_region
# Groups of different parts of the body
is_body = fieldmodule.createFieldConstant(1)
bodyMeshGroup = bodyGroup.getMeshGroup(mesh)
bodyMeshGroup.addElementsConditional(is_body)
coreMeshGroup = coreGroup.getMeshGroup(mesh)
# core group
e1a = elementsCountAcrossShell
e1z = elementsCountAcrossMinor - elementsCountAcrossShell - 1
e2a = elementsCountAcrossShell
e2b = e2a + elementsCountAcrossTransition
e2z = elementsCountAcrossMajor - elementsCountAcrossShell - 1
e2y = e2z - elementsCountAcrossTransition
e1oc = elementsCountAcrossMinor - 2*elementsCountAcrossShell - 2*elementsCountAcrossTransition
e2oc = elementsCountAcrossMajor - 2*elementsCountAcrossShell - 2*elementsCountAcrossTransition
e2oCore = e2oc * e1oc + 2 * elementsCountAcrossTransition * (e2oc + e1oc)
elementsCountAround = cylinder1.getElementsCountAround()
e2oShell = elementsCountAround * elementsCountAcrossShell
e2o = e2oCore + e2oShell
elementId = cylinder1.getElementIdentifiers()
for e3 in range(elementsCountAlong):
for e2 in range(elementsCountAcrossMajor):
for e1 in range(elementsCountAcrossMinor):
coreElement = ((e2 >= e2a) and (e2 <= e2z)) and ((e1 >= e1a) and (e1 <= e1z))
if coreElement:
elementIdentifier = elementId[e3][e2][e1]
if elementIdentifier:
element = mesh.findElementByIdentifier(elementIdentifier)
coreMeshGroup.addElement(element)
is_non_core = fieldmodule.createFieldNot(coreGroup.getGroup())
non_coreMeshGroup = non_coreGroup.getMeshGroup(mesh)
non_coreMeshGroup.addElementsConditional(is_non_core)
abdomenMeshGroup = abdomenGroup.getMeshGroup(mesh)
thoraxMeshGroup = thoraxGroup.getMeshGroup(mesh)
neckMeshGroup = neckGroup.getMeshGroup(mesh)
headMeshGroup = headGroup.getMeshGroup(mesh)
meshGroups = [abdomenMeshGroup, thoraxMeshGroup, neckMeshGroup, headMeshGroup]
abdomenRange = [1, elementsCountAlongAbdomen*e2o]
thoraxRange = [abdomenRange[1]+1, abdomenRange[1]+elementsCountAlongThorax*e2o]
neckRange = [thoraxRange[1]+1, thoraxRange[1] + elementsCountAlongNeck*e2o]
headRange = [neckRange[1]+1, elementsCountAlong*e2o]
groupsRanges = [abdomenRange, thoraxRange, neckRange, headRange]
totalElements = e2o*elementsCountAlong
for elementIdentifier in range(1, totalElements+1):
element = mesh.findElementByIdentifier(elementIdentifier)
if coreMeshGroup.containsElement(element):
ri = 0
for groupRange in groupsRanges:
if (elementIdentifier >= groupRange[0]) and (elementIdentifier <= groupRange[1]):
meshGroups[ri].addElement(element)
break
ri += 1
if discontinuity:
# create discontinuity in d3 on the core boundary
nodes = fieldmodule.findNodesetByFieldDomainType(Field.DOMAIN_TYPE_NODES)
elementtemplate = mesh.createElementtemplate()
undefineNodetemplate = nodes.createNodetemplate()
undefineNodetemplate.undefineField(coordinates)
nodetemplate = nodes.createNodetemplate()
fieldcache = fieldmodule.createFieldcache()
with ChangeManager(fieldmodule):
localNodeIndexes = [1, 2, 3, 4]
valueLabel = Node.VALUE_LABEL_D_DS3
for e3 in range(elementsCountAlong):
for e2 in range(elementsCountAcrossMajor):
for e1 in range(elementsCountAcrossMinor):
regularRowElement = (((e2 >= e2b) and (e2 <= e2y)) and ((e1 == e1a - 1) or (e1 == e1z + 1)))
non_coreFirstLayerElement = (e2 == e2a - 1) or regularRowElement or (e2 == e2z + 1)
elementIdentifier = elementId[e3][e2][e1]
if elementIdentifier and non_coreFirstLayerElement:
element = mesh.findElementByIdentifier(elementIdentifier)
eft = element.getElementfieldtemplate(coordinates, -1)
nodeIds = get_element_node_identifiers(element, eft)
for localNodeIndex in localNodeIndexes:
node = element.getNode(eft, localNodeIndex)
nodetemplate.defineFieldFromNode(coordinates, node)
versionsCount = nodetemplate.getValueNumberOfVersions(coordinates, -1, valueLabel)
if versionsCount == 1:
fieldcache.setNode(node)
result0, x = coordinates.getNodeParameters(fieldcache, -1, Node.VALUE_LABEL_VALUE, 1, 3)
result0, d1 = coordinates.getNodeParameters(fieldcache, -1, Node.VALUE_LABEL_D_DS1, 1, 3)
result0, d2 = coordinates.getNodeParameters(fieldcache, -1, Node.VALUE_LABEL_D_DS2, 1, 3)
result0, d3 = coordinates.getNodeParameters(fieldcache, -1, valueLabel, 1, 3)
result1 = node.merge(undefineNodetemplate)
result2 = nodetemplate.setValueNumberOfVersions(coordinates, -1, valueLabel, 2)
result3 = node.merge(nodetemplate)
result4 = coordinates.setNodeParameters(fieldcache, -1, Node.VALUE_LABEL_VALUE, 1, x)
result4 = coordinates.setNodeParameters(fieldcache, -1, Node.VALUE_LABEL_D_DS1, 1, d1)
result4 = coordinates.setNodeParameters(fieldcache, -1, Node.VALUE_LABEL_D_DS2, 1, d2)
result4 = coordinates.setNodeParameters(fieldcache, -1, valueLabel, 1, d3)
result5 = coordinates.setNodeParameters(fieldcache, -1, valueLabel, 2, d3)
remapEftNodeValueLabelsVersion(eft, localNodeIndexes, [valueLabel], 2)
result1 = elementtemplate.defineField(coordinates, -1, eft)
result2 = element.merge(elementtemplate)
result3 = element.setNodesByIdentifier(eft, nodeIds)
else:
fieldcache = fieldmodule.createFieldcache()
# Annotation fiducial point
markerGroup = findOrCreateFieldGroup(fieldmodule, "marker")
markerName = findOrCreateFieldStoredString(fieldmodule, name="marker_name")
markerLocation = findOrCreateFieldStoredMeshLocation(fieldmodule, mesh, name="marker_location")
markerBodyCoordinates = findOrCreateFieldCoordinates(fieldmodule, name="marker_body_coordinates")
nodes = fieldmodule.findNodesetByFieldDomainType(Field.DOMAIN_TYPE_NODES)
markerPoints = findOrCreateFieldNodeGroup(markerGroup, nodes).getNodesetGroup()
markerTemplateInternal = nodes.createNodetemplate()
markerTemplateInternal.defineField(markerName)
markerTemplateInternal.defineField(markerLocation)
markerTemplateInternal.defineField(markerBodyCoordinates)
#
middleLeft = elementsCountAcrossMinor//2
topElem = elementsCountAcrossMajor - 1
middleRight = middleLeft - 1
neckFirstElem = elementsCountAlongAbdomen+elementsCountAlongThorax
thoraxFirstElem = elementsCountAlongAbdomen
middleDown = elementsCountAcrossMajor//2 - 1
# organ landmarks groups
apexOfHeart = heart_terms.get_heart_term('apex of heart')
leftAtriumEpicardiumVenousMidpoint = heart_terms.get_heart_term('left atrium epicardium venous midpoint')
rightAtriumEpicardiumVenousMidpoint = heart_terms.get_heart_term('right atrium epicardium venous midpoint')
apexOfUrinaryBladder = bladder_terms.get_bladder_term('apex of urinary bladder')
leftUreterJunctionWithBladder = bladder_terms.get_bladder_term('left ureter junction with bladder')
rightUreterJunctionWithBladder = bladder_terms.get_bladder_term('right ureter junction with bladder')
urethraJunctionWithBladderDorsal = bladder_terms.get_bladder_term('urethra junction of dorsal bladder neck')
urethraJunctionWithBladderVentral = bladder_terms.get_bladder_term('urethra junction of ventral bladder neck')
gastroesophagalJunctionOnLesserCurvature = stomach_terms.get_stomach_term('esophagogastric junction along the lesser curvature on serosa')
limitingRidgeOnGreaterCurvature = stomach_terms.get_stomach_term('limiting ridge at the greater curvature on serosa')
pylorusOnGreaterCurvature = stomach_terms.get_stomach_term('gastroduodenal junction along the greater curvature on serosa')
junctionBetweenFundusAndBodyOnGreaterCurvature = stomach_terms.get_stomach_term("fundus-body junction along the greater curvature on serosa")
apexOfLeftLung = lung_terms.get_lung_term('apex of left lung')
ventralBaseOfLeftLung = lung_terms.get_lung_term('ventral base of left lung')
dorsalBaseOfLeftLung = lung_terms.get_lung_term('dorsal base of left lung')
apexOfRightLung = lung_terms.get_lung_term('apex of right lung')
ventralBaseOfRightLung = lung_terms.get_lung_term('ventral base of right lung')
dorsalBaseOfRightLung = lung_terms.get_lung_term('dorsal base of right lung')
laterodorsalTipOfMiddleLobeOfRightLung = lung_terms.get_lung_term('laterodorsal tip of middle lobe of right lung')
apexOfRightLungAccessoryLobe = lung_terms.get_lung_term('apex of right lung accessory lobe')
ventralBaseOfRightLungAccessoryLobe = lung_terms.get_lung_term('ventral base of right lung accessory lobe')
dorsalBaseOfRightLungAccessoryLobe = lung_terms.get_lung_term('dorsal base of right lung accessory lobe')
medialBaseOfLeftLung = lung_terms.get_lung_term("medial base of left lung")
medialBaseOfRightLung = lung_terms.get_lung_term("medial base of right lung")
brainstemDorsalMidlineCaudalPoint = brainstem_terms.get_brainstem_term('brainstem dorsal midline caudal point')
brainstemDorsalMidlineCranialPoint = brainstem_terms.get_brainstem_term('brainstem dorsal midline cranial point')
brainstemVentralMidlineCaudalPoint = brainstem_terms.get_brainstem_term('brainstem ventral midline caudal point')
brainstemVentralMidlineCranialPoint = brainstem_terms.get_brainstem_term('brainstem ventral midline cranial point')
# marker coordinates. In future we want to have only one table for all species.
if isRat:
bodyMarkerPoints = [
{"group": ("left hip joint", ''), "x": [0.367, 0.266, 0.477]},
{"group": ("right hip joint", ''), "x": [-0.367, 0.266, 0.477]},
{"group": ("left shoulder joint", ''), "x": [0.456, -0.071, 2.705]},
{"group": ("right shoulder joint", ''), "x": [-0.456, -0.071, 2.705]},
{"group": ("along left femur", ''), "x": [0.456, 0.07, 0.633]},
{"group": ("along right femur", ''), "x": [-0.456, 0.07, 0.633]},
{"group": ("along left humerus", ''), "x": [0.423, -0.173, 2.545]},
{"group": ("along right humerus", ''), "x": [-0.423, -0.173, 2.545]},
{"group": apexOfUrinaryBladder, "x": [-0.124, -0.383, 0.434]},
{"group": leftUreterJunctionWithBladder, "x": [-0.111, -0.172, 0.354]},
{"group": rightUreterJunctionWithBladder, "x": [-0.03, -0.196, 0.363]},
{"group": urethraJunctionWithBladderDorsal, "x": [-0.03, -0.26, 0.209]},
{"group": urethraJunctionWithBladderVentral, "x": [-0.037, -0.304, 0.203]},
{"group": brainstemDorsalMidlineCaudalPoint, "x": [-0.032, 0.418, 2.713]},
{"group": brainstemDorsalMidlineCranialPoint, "x": [-0.017, 0.203, 2.941]},
{"group": brainstemVentralMidlineCaudalPoint, "x": [-0.028, 0.388, 2.72]},
{"group": brainstemVentralMidlineCranialPoint, "x": [-0.019, 0.167, 2.95]},
{"group": apexOfHeart, "x": [0.096, -0.128, 1.601]},
{"group": leftAtriumEpicardiumVenousMidpoint, "x": [0.127, -0.083, 2.079]},
{"group": rightAtriumEpicardiumVenousMidpoint, "x": [0.039, -0.082, 2.075]},
{"group": apexOfLeftLung, "x": [0.172, -0.175, 2.337]},
{"group": ventralBaseOfLeftLung, "x": [0.274, -0.285, 1.602]},
{"group": dorsalBaseOfLeftLung, "x": [0.037, 0.31, 1.649]},
{"group": apexOfRightLung, "x": [-0.086, -0.096, 2.311]},
{"group": ventralBaseOfRightLung, "x": [0.14, -0.357, 1.662]},
{"group": dorsalBaseOfRightLung, "x": [-0.054, 0.304, 1.667]},
{"group": laterodorsalTipOfMiddleLobeOfRightLung, "x": [-0.258, -0.173, 2.013]},
{"group": apexOfRightLungAccessoryLobe, "x": [0.041, -0.063, 1.965]},
{"group": ventralBaseOfRightLungAccessoryLobe, "x": [0.143, -0.356, 1.66]},
{"group": dorsalBaseOfRightLungAccessoryLobe, "x": [0.121, -0.067, 1.627]},
{"group": gastroesophagalJunctionOnLesserCurvature, "x": [0.12, 0.009, 1.446]},
{"group": limitingRidgeOnGreaterCurvature, "x": [0.318, 0.097, 1.406]},
{"group": pylorusOnGreaterCurvature, "x": [0.08, -0.111, 1.443]},
]
elif isHuman:
bodyMarkerPoints = [
{"group": urethraJunctionWithBladderDorsal, "x": [-0.0071, -0.2439, 0.1798]},
{"group": urethraJunctionWithBladderVentral, "x": [-0.007, -0.2528, 0.1732]},
{"group": leftUreterJunctionWithBladder, "x": [0.1074, 0.045, 0.1728]},
{"group": rightUreterJunctionWithBladder, "x": [-0.1058, 0.0533, 0.1701]},
{"group": apexOfUrinaryBladder, "x": [0.005, 0.1286, 0.1264]},
{"group": brainstemDorsalMidlineCaudalPoint, "x": [0.0068, 0.427, 2.7389]},
{"group": brainstemDorsalMidlineCranialPoint, "x": [0.008, -0.0231, 3.0778]},
{"group": brainstemVentralMidlineCaudalPoint, "x": [0.0054, 0.3041, 2.7374]},
{"group": brainstemVentralMidlineCranialPoint, "x": [0.0025, -0.2308, 3.091]},
{"group": apexOfHeart, "x": [0.1373, -0.1855, 1.421]},
{"group": leftAtriumEpicardiumVenousMidpoint, "x": [0.0024, 0.1452, 1.8022]},
{"group": rightAtriumEpicardiumVenousMidpoint, "x": [-0.0464, 0.0373, 1.7491]},
{"group": apexOfLeftLung, "x": [0.0655, -0.0873, 2.3564]},
{"group": apexOfRightLung, "x": [-0.088, -0.0363, 2.3518]},
{"group": laterodorsalTipOfMiddleLobeOfRightLung, "x": [-0.2838, -0.0933, 1.9962]},
{"group": ventralBaseOfLeftLung, "x": [0.219, -0.2866, 1.4602]},
{"group": medialBaseOfLeftLung, "x": [0.0426, -0.0201, 1.4109]},
{"group": ventralBaseOfRightLung, "x": [-0.2302, -0.2356, 1.3926]},
{"group": medialBaseOfRightLung, "x": [-0.0363, 0.0589, 1.3984]},
{"group": dorsalBaseOfLeftLung, "x": [0.1544, 0.2603, 1.3691]},
{"group": dorsalBaseOfRightLung, "x": [0.0369, -0.2524, 0.912]},
{"group": gastroesophagalJunctionOnLesserCurvature, "x": [-0.0062, -0.3259, 0.8586]},
{"group": pylorusOnGreaterCurvature, "x": [-0.0761, -0.3189, 0.8663]},
{"group": junctionBetweenFundusAndBodyOnGreaterCurvature, "x": [0.1884, -0.1839, 0.9639]},
]
nodeIdentifier = cylinder1._endNodeIdentifier
findMarkerLocation = fieldmodule.createFieldFindMeshLocation(markerBodyCoordinates, bodyCoordinates, mesh)
findMarkerLocation.setSearchMode(FieldFindMeshLocation.SEARCH_MODE_EXACT)
for bodyMarkerPoint in bodyMarkerPoints:
markerPoint = markerPoints.createNode(nodeIdentifier, markerTemplateInternal)
fieldcache.setNode(markerPoint)
markerBodyCoordinates.assignReal(fieldcache, bodyMarkerPoint["x"])
markerName.assignString(fieldcache, bodyMarkerPoint["group"][0])
element, xi = findMarkerLocation.evaluateMeshLocation(fieldcache, 3)
markerLocation.assignMeshLocation(fieldcache, element, xi)
nodeIdentifier += 1
return annotationGroups
def generateBaseMesh(cls, region, options):
"""
Generate the base tricubic Hermite mesh. See also generateMesh().
:param region: Zinc region to define model in. Must be empty.
:param options: Dict containing options. See getDefaultOptions().
:return: None
"""
parameterSetName = options['Base parameter set']
isCat = 'Cat 1' in parameterSetName
isHuman = 'Human 1' in parameterSetName
isMouse = 'Mouse 1' in parameterSetName
isRat = 'Rat 1' in parameterSetName
isPig = 'Pig 1' in parameterSetName
isSheep = 'Sheep 1' in parameterSetName
centralPath = options['Central path']
brainstemPath = cls.centralPathDefaultScaffoldPackages['Brainstem 1']
elementsCountAcrossMajor = options['Number of elements across major']
elementsCountAcrossMinor = options['Number of elements across minor']
elementsCountAlong = options['Number of elements along']
# Cross section at Z axis
halfBrainStem = False
if halfBrainStem:
elementsCountAcrossMajor //= 2
elementsPerLayer = (
(elementsCountAcrossMajor - 2) *
elementsCountAcrossMinor) + (2 * (elementsCountAcrossMinor - 2))
fm = region.getFieldmodule()
cache = fm.createFieldcache()
coordinates = findOrCreateFieldCoordinates(fm)
mesh = fm.findMeshByDimension(3)
# Annotation groups
brainstemGroup = AnnotationGroup(region,
get_brainstem_term('brainstem'))
brainstemMeshGroup = brainstemGroup.getMeshGroup(mesh)
midbrainGroup = AnnotationGroup(region, get_brainstem_term('midbrain'))
midbrainMeshGroup = midbrainGroup.getMeshGroup(mesh)
ponsGroup = AnnotationGroup(region, get_brainstem_term('pons'))
ponsMeshGroup = ponsGroup.getMeshGroup(mesh)
medullaGroup = AnnotationGroup(region,
get_brainstem_term('medulla oblongata'))
medullaMeshGroup = medullaGroup.getMeshGroup(mesh)
annotationGroups = [
brainstemGroup, midbrainGroup, ponsGroup, medullaGroup
]
annotationGroupAlong = [[brainstemGroup, midbrainGroup],
[brainstemGroup, ponsGroup],
[brainstemGroup, medullaGroup]]
# point markers
# centralCanal = findOrCreateAnnotationGroupForTerm(annotationGroups, region,
# get_brainstem_term('central canal of spinal cord'))
# cerebralAqueduct = findOrCreateAnnotationGroupForTerm(annotationGroups, region,
# get_brainstem_term('cerebral aqueduct'))
# foramenCaecum = findOrCreateAnnotationGroupForTerm(annotationGroups, region,
# get_brainstem_term('foramen caecum of medulla oblongata'))
dorsalMidCaudalGroup = findOrCreateAnnotationGroupForTerm(
annotationGroups, region,
get_brainstem_term('brainstem dorsal midline caudal point'))
ventralMidCaudalGroup = findOrCreateAnnotationGroupForTerm(
annotationGroups, region,
get_brainstem_term('brainstem ventral midline caudal point'))
dorsalMidCranGroup = findOrCreateAnnotationGroupForTerm(
annotationGroups, region,
get_brainstem_term('brainstem dorsal midline cranial point'))
ventralMidCranGroup = findOrCreateAnnotationGroupForTerm(
annotationGroups, region,
get_brainstem_term('brainstem ventral midline cranial point'))
dorsalMidMedullaPonsJunction = findOrCreateAnnotationGroupForTerm(
annotationGroups, region,
get_brainstem_term(
'brainstem dorsal midline pons-medulla junction'))
ventralMidMedullaPonsJunction = findOrCreateAnnotationGroupForTerm(
annotationGroups, region,
get_brainstem_term(
'brainstem ventral midline pons-medulla junction'))
dorsalMidMidbrainPonsJunction = findOrCreateAnnotationGroupForTerm(
annotationGroups, region,
get_brainstem_term(
'brainstem dorsal midline midbrain-pons junction'))
ventralMidMidbrainPonsJunction = findOrCreateAnnotationGroupForTerm(
annotationGroups, region,
get_brainstem_term(
'brainstem ventral midline midbrain-pons junction'))
#######################
# CREATE MAIN BODY MESH
#######################
cylinderShape = CylinderShape.CYLINDER_SHAPE_FULL if not halfBrainStem else CylinderShape.CYLINDER_SHAPE_LOWER_HALF
# Body coordinates
cylinderCentralPath = CylinderCentralPath(region, centralPath,
elementsCountAlong)
base = CylinderEnds(elementsCountAcrossMajor,
elementsCountAcrossMinor,
centre=[0.0, 0.0, 0.0],
alongAxis=cylinderCentralPath.alongAxis[0],
majorAxis=cylinderCentralPath.majorAxis[0],
minorRadius=cylinderCentralPath.minorRadii[0])
cylinder1 = CylinderMesh(fm,
coordinates,
elementsCountAlong,
base,
cylinderShape=cylinderShape,
cylinderCentralPath=cylinderCentralPath,
useCrossDerivatives=False)
brainstem_coordinates = findOrCreateFieldCoordinates(
fm, name="brainstem coordinates")
# Brain coordinates
tmp_region = region.createRegion()
tmp_fm = tmp_region.getFieldmodule()
tmp_brainstem_coordinates = findOrCreateFieldCoordinates(
tmp_fm, name="brainstem coordinates")
cylinderCentralPath1 = CylinderCentralPath(tmp_region, brainstemPath,
elementsCountAlong)
base1 = CylinderEnds(elementsCountAcrossMajor,
elementsCountAcrossMinor,
centre=[0.0, 0.0, 0.0],
alongAxis=cylinderCentralPath1.alongAxis[0],
majorAxis=cylinderCentralPath1.majorAxis[0],
minorRadius=cylinderCentralPath1.minorRadii[0])
cylinder2 = CylinderMesh(tmp_fm,
tmp_brainstem_coordinates,
elementsCountAlong,
base1,
cylinderShape=cylinderShape,
cylinderCentralPath=cylinderCentralPath1,
useCrossDerivatives=False)
# Write two coordinates
sir = tmp_region.createStreaminformationRegion()
srm = sir.createStreamresourceMemory()
tmp_region.write(sir)
result, buffer = srm.getBuffer()
sir = region.createStreaminformationRegion()
srm = sir.createStreamresourceMemoryBuffer(buffer)
region.read(sir)
del srm
del sir
del tmp_fm
del tmp_brainstem_coordinates
del tmp_region
# Annotating groups
iRegionBoundaries = [
int(6 * elementsCountAlong / 15),
int(13 * elementsCountAlong / 15)
]
for elementIdentifier in range(1, mesh.getSize() + 1):
element = mesh.findElementByIdentifier(elementIdentifier)
brainstemMeshGroup.addElement(element)
if elementIdentifier > (iRegionBoundaries[-1] * elementsPerLayer):
midbrainMeshGroup.addElement(element)
elif (elementIdentifier >
(iRegionBoundaries[0] * elementsPerLayer)) and (
elementIdentifier <=
(iRegionBoundaries[-1] * elementsPerLayer)):
ponsMeshGroup.addElement(element)
else:
medullaMeshGroup.addElement(element)
################
# point markers
################
pointMarkers = [
{
"group": dorsalMidCaudalGroup,
"marker_brainstem_coordinates": [0.0, 1.0, 0.0]
},
{
"group": ventralMidCaudalGroup,
"marker_brainstem_coordinates": [0.0, -1.0, 0.0]
},
{
"group": dorsalMidCranGroup,
"marker_brainstem_coordinates": [0.0, 1.0, 8.0]
},
{
"group": ventralMidCranGroup,
"marker_brainstem_coordinates": [0.0, -1.0, 8.0]
},
{
"group": dorsalMidMedullaPonsJunction,
"marker_brainstem_coordinates": [0.0, 1.0, 3.0]
},
{
"group": ventralMidMedullaPonsJunction,
"marker_brainstem_coordinates": [0.0, -1.0, 3.0]
},
{
"group": dorsalMidMidbrainPonsJunction,
"marker_brainstem_coordinates": [0.0, 1.0, 6.0]
},
{
"group": ventralMidMidbrainPonsJunction,
"marker_brainstem_coordinates": [0.0, -1.0, 6.0]
},
]
markerGroup = findOrCreateFieldGroup(fm, "marker")
markerName = findOrCreateFieldStoredString(fm, name="marker_name")
markerLocation = findOrCreateFieldStoredMeshLocation(
fm, mesh, name="marker_location")
nodes = fm.findNodesetByFieldDomainType(Field.DOMAIN_TYPE_NODES)
markerPoints = findOrCreateFieldNodeGroup(markerGroup,
nodes).getNodesetGroup()
markerBrainstemCoordinates = findOrCreateFieldCoordinates(
fm, name="marker_body_coordinates")
markerTemplateInternal = nodes.createNodetemplate()
markerTemplateInternal.defineField(markerName)
markerTemplateInternal.defineField(markerLocation)
markerTemplateInternal.defineField(markerBrainstemCoordinates)
cache = fm.createFieldcache()
brainstemNodesetGroup = brainstemGroup.getNodesetGroup(nodes)
nodeIdentifier = max(1, getMaximumNodeIdentifier(nodes) + 1)
findMarkerLocation = fm.createFieldFindMeshLocation(
markerBrainstemCoordinates, brainstem_coordinates, mesh)
findMarkerLocation.setSearchMode(
FieldFindMeshLocation.SEARCH_MODE_EXACT)
for pointMarker in pointMarkers:
group = pointMarker["group"]
markerPoint = markerPoints.createNode(nodeIdentifier,
markerTemplateInternal)
cache.setNode(markerPoint)
markerBrainstemCoordinates.assignReal(
cache, pointMarker["marker_brainstem_coordinates"])
markerName.assignString(cache, group.getName())
element, xi = findMarkerLocation.evaluateMeshLocation(cache, 3)
markerLocation.assignMeshLocation(cache, element, xi)
group.getNodesetGroup(nodes).addNode(markerPoint)
brainstemNodesetGroup.addNode(markerPoint)
nodeIdentifier += 1
return annotationGroups
def zinc_write_element_xi_marker_file(region,
allMarkers,
xiNodeInfo,
regionD,
nodeIdentifierStart,
coordinates,
outFile=[]):
fm = region.getFieldmodule()
if outFile:
fm.beginChange()
# if xiNodeInfo['nodeType'] == 'nodes':
nodes = fm.findNodesetByFieldDomainType(Field.DOMAIN_TYPE_NODES)
mesh = fm.findMeshByDimension(3)
mesh1d = fm.findMeshByDimension(1)
cache = fm.createFieldcache()
xiNodeName = findOrCreateFieldStoredString(fm, name=xiNodeInfo['nameStr'])
xiNodeLocation = findOrCreateFieldStoredMeshLocation(
fm, mesh, name="elementxi_location")
xiNodeTemplate = nodes.createNodetemplate()
xiNodeTemplate.defineField(xiNodeLocation)
xiNodeTemplate.defineField(coordinates)
xiNodeTemplate.setValueNumberOfVersions(coordinates, -1,
Node.VALUE_LABEL_VALUE, 1)
xiNodeTemplate.setValueNumberOfVersions(coordinates, -1,
Node.VALUE_LABEL_D_DS1, 1)
xiNodeTemplate.setValueNumberOfVersions(coordinates, -1,
Node.VALUE_LABEL_D_DS2, 1)
xiNodeTemplate.setValueNumberOfVersions(coordinates, -1,
Node.VALUE_LABEL_D_DS3, 1)
xiMeshGroup = AnnotationGroup(
region, ('tracts_xi_elements', None)).getMeshGroup(mesh1d)
nodeIdentifier = nodeIdentifierStart
for key in allMarkers:
xiNodeGroup = findOrCreateFieldGroup(
fm, xiNodeInfo['groupName'] + '_' + key)
xiNodePoints = findOrCreateFieldNodeGroup(xiNodeGroup,
nodes).getNodesetGroup()
addxiNode = {"name": key, "xi": allMarkers[key]["xi"]}
xiNodePoint = xiNodePoints.createNode(nodeIdentifier, xiNodeTemplate)
xiNodePoint.merge(xiNodeTemplate)
cache.setNode(xiNodePoint)
elementID = allMarkers[key]["elementID"]
element = mesh.findElementByIdentifier(elementID)
result = xiNodeLocation.assignMeshLocation(cache, element,
addxiNode["xi"])
result = coordinates.setNodeParameters(cache, -1,
Node.VALUE_LABEL_VALUE, 1,
list(regionD[key]['centre']))
try:
result = coordinates.setNodeParameters(
cache, -1, Node.VALUE_LABEL_D_DS1, 1,
list(regionD[key]['axes'][0]))
result = coordinates.setNodeParameters(
cache, -1, Node.VALUE_LABEL_D_DS2, 1,
list(regionD[key]['axes'][1]))
result = coordinates.setNodeParameters(
cache, -1, Node.VALUE_LABEL_D_DS3, 1,
list(regionD[key]['axes'][2]))
except:
result = coordinates.setNodeParameters(cache, -1,
Node.VALUE_LABEL_D_DS1, 1,
[1, 0, 0])
result = coordinates.setNodeParameters(cache, -1,
Node.VALUE_LABEL_D_DS2, 1,
[0, 1, 0])
result = coordinates.setNodeParameters(cache, -1,
Node.VALUE_LABEL_D_DS3, 1,
[0, 0, 1])
nodeIdentifier += 1
# write 1D elements between embedded nodes
if True:
mesh1d = fm.findMeshByDimension(1)
elementIdentifier = 55555555
basis1d = fm.createElementbasis(
1, Elementbasis.FUNCTION_TYPE_CUBIC_HERMITE)
eft1d = mesh1d.createElementfieldtemplate(basis1d)
elementtemplate = mesh1d.createElementtemplate()
elementtemplate.setElementShapeType(Element.SHAPE_TYPE_LINE)
result = elementtemplate.defineField(coordinates, -1, eft1d)
element = mesh1d.createElement(elementIdentifier, elementtemplate)
result = element.setNodesByIdentifier(
eft1d, [nodeIdentifierStart, nodeIdentifier - 1])
xiMeshGroup.addElement(element)
if outFile:
fm.endChange()
region.writeFile(outFile)
return region
nodetemplate.setValueNumberOfVersions(norm, -1,
Node.VALUE_LABEL_VALUE, 1)
# mesh1d = fmCh.findMeshByDimension(1)
mesh2d = fmCh.findMeshByDimension(2)
# basis1d = fmCh.createElementbasis(1, Elementbasis.FUNCTION_TYPE_LINEAR_LAGRANGE)
# eft1d = mesh1d.createElementfieldtemplate(basis1d)
basisTri = fmCh.createElementbasis(
2, Elementbasis.FUNCTION_TYPE_LINEAR_SIMPLEX)
eftTri = mesh2d.createElementfieldtemplate(basisTri)
elementtemplate = mesh2d.createElementtemplate()
elementtemplate.setElementShapeType(Element.SHAPE_TYPE_TRIANGLE)
result = elementtemplate.defineField(coordinates, -1, eftTri)
cache = fmCh.createFieldcache()
# create nodes
if outline:
exteriorGroup = findOrCreateFieldGroup(
fmCh, 'brainstem_exterior_obsolete')
exteriorPoints = findOrCreateFieldNodeGroup(
exteriorGroup, nodes).getNodesetGroup()
medullaGroup = findOrCreateFieldGroup(
fmCh, 'medulla oblongata_exterior')
medullaPoints = findOrCreateFieldNodeGroup(
medullaGroup, nodes).getNodesetGroup()
ponsGroup = findOrCreateFieldGroup(fmCh, 'pons_exterior')
ponsPoints = findOrCreateFieldNodeGroup(
ponsGroup, nodes).getNodesetGroup()
midbrainGroup = findOrCreateFieldGroup(fmCh,
'midbrain_exterior')
midbrainPoints = findOrCreateFieldNodeGroup(
midbrainGroup, nodes).getNodesetGroup()
extNodetemplate = exteriorPoints.createNodetemplate()
extNodetemplate.defineField(coordinates)
def generateBaseMesh(cls, region, options):
'''
Generate the base tricubic Hermite mesh. See also generateMesh().
:param region: Zinc region to define model in. Must be empty.
:param options: Dict containing options. See getDefaultOptions().
:return: annotationGroups
'''
fm = region.getFieldmodule()
coordinates = findOrCreateFieldCoordinates(fm)
nodes = fm.findNodesetByFieldDomainType(Field.DOMAIN_TYPE_NODES)
nodetemplate = nodes.createNodetemplate()
nodetemplate.defineField(coordinates)
nodetemplate.setValueNumberOfVersions(coordinates, -1,
Node.VALUE_LABEL_VALUE, 1)
nodetemplate.setValueNumberOfVersions(coordinates, -1,
Node.VALUE_LABEL_D_DS1, 1)
nodetemplate.setValueNumberOfVersions(coordinates, -1,
Node.VALUE_LABEL_D_DS2, 1)
nodetemplate.setValueNumberOfVersions(coordinates, -1,
Node.VALUE_LABEL_D_DS3, 1)
mesh = fm.findMeshByDimension(3)
cache = fm.createFieldcache()
elementsCount1 = 2
elementsCount2 = 4
elementsCount3 = 4
# Annotation fiducial point
markerGroup = findOrCreateFieldGroup(fm, "marker")
markerName = findOrCreateFieldStoredString(fm, name="marker_name")
markerLocation = findOrCreateFieldStoredMeshLocation(
fm, mesh, name="marker_location")
nodes = fm.findNodesetByFieldDomainType(Field.DOMAIN_TYPE_NODES)
markerPoints = findOrCreateFieldNodeGroup(markerGroup,
nodes).getNodesetGroup()
markerTemplateInternal = nodes.createNodetemplate()
markerTemplateInternal.defineField(markerName)
markerTemplateInternal.defineField(markerLocation)
# Create nodes
nodeIdentifier = 1
lNodeIds = []
d1 = [0.5, 0.0, 0.0]
d2 = [0.0, 0.5, 0.0]
d3 = [0.0, 0.0, 1.0]
for n3 in range(elementsCount3 + 1):
lNodeIds.append([])
for n2 in range(elementsCount2 + 1):
lNodeIds[n3].append([])
for n1 in range(elementsCount1 + 1):
lNodeIds[n3][n2].append([])
if n3 < elementsCount3:
if (n1 == 0) and ((n2 == 0) or (n2 == elementsCount2)):
continue
else:
if (n2 == 0) or (n2 == elementsCount2) or (n1 == 0):
continue
node = nodes.createNode(nodeIdentifier, nodetemplate)
cache.setNode(node)
x = [0.5 * (n1 - 1), 0.5 * (n2 - 1), 1.0 * n3]
coordinates.setNodeParameters(cache, -1,
Node.VALUE_LABEL_VALUE, 1, x)
coordinates.setNodeParameters(cache, -1,
Node.VALUE_LABEL_D_DS1, 1,
d1)
coordinates.setNodeParameters(cache, -1,
Node.VALUE_LABEL_D_DS2, 1,
d2)
coordinates.setNodeParameters(cache, -1,
Node.VALUE_LABEL_D_DS3, 1,
d3)
lNodeIds[n3][n2][n1] = nodeIdentifier
nodeIdentifier += 1
# Create elements
mesh = fm.findMeshByDimension(3)
eftfactory = eftfactory_tricubichermite(mesh, None)
eftRegular = eftfactory.createEftBasic()
elementtemplateRegular = mesh.createElementtemplate()
elementtemplateRegular.setElementShapeType(Element.SHAPE_TYPE_CUBE)
elementtemplateRegular.defineField(coordinates, -1, eftRegular)
elementtemplateCustom = mesh.createElementtemplate()
elementtemplateCustom.setElementShapeType(Element.SHAPE_TYPE_CUBE)
lungGroup = AnnotationGroup(region, get_lung_term("lung"))
leftLungGroup = AnnotationGroup(region, get_lung_term("left lung"))
rightLungGroup = AnnotationGroup(region, get_lung_term("right lung"))
annotationGroups = [leftLungGroup, rightLungGroup, lungGroup]
lungMeshGroup = lungGroup.getMeshGroup(mesh)
leftLungMeshGroup = leftLungGroup.getMeshGroup(mesh)
rightLungMeshGroup = rightLungGroup.getMeshGroup(mesh)
eft1 = eftfactory.createEftWedgeCollapseXi1Quadrant([1, 5])
eft2 = eftfactory.createEftWedgeCollapseXi1Quadrant([3, 7])
eft3 = eftfactory.createEftWedgeCollapseXi2Quadrant([5, 6])
eft4 = eftfactory.createEftWedgeCollapseXi2Quadrant([7, 8])
eft5 = eftfactory.createEftWedgeCollapseXi1Quadrant([5, 7])
eft6 = eftfactory.createEftTetrahedronCollapseXi1Xi2Quadrant(8, 2)
eft7 = eftfactory.createEftTetrahedronCollapseXi1Xi2Quadrant(6, 3)
elementIdentifier = 1
for e3 in range(elementsCount3):
for e2 in range(elementsCount2):
for e1 in range(elementsCount1):
eft = eftRegular
nodeIdentifiers = [
lNodeIds[e3][e2][e1], lNodeIds[e3][e2][e1 + 1],
lNodeIds[e3][e2 + 1][e1], lNodeIds[e3][e2 + 1][e1 + 1],
lNodeIds[e3 + 1][e2][e1], lNodeIds[e3 + 1][e2][e1 + 1],
lNodeIds[e3 + 1][e2 + 1][e1],
lNodeIds[e3 + 1][e2 + 1][e1 + 1]
]
scalefactors = None
if (e3 < elementsCount3 - 1):
if (e2 == 0) and (e1 == 0):
# Back wedge elements
nodeIdentifiers.pop(4)
nodeIdentifiers.pop(0)
eft = eft1
scalefactors = [-1.0]
elif (e2 == elementsCount2 - 1) and (e1 == 0):
# Front wedge elements
nodeIdentifiers.pop(6)
nodeIdentifiers.pop(2)
eft = eft2
else:
if (e2 == 0) and (e1 == 1):
# Top back wedge elements
nodeIdentifiers.pop(5)
nodeIdentifiers.pop(4)
eft = eft3
elif (e2 == elementsCount2 - 1) and (e1 == 1):
# Top front wedge elements
nodeIdentifiers.pop(7)
nodeIdentifiers.pop(6)
eft = eft4
scalefactors = [-1.0]
elif (e2 == 1) and (e1 == 0):
# Top middle back wedge element
nodeIdentifiers.pop(6)
nodeIdentifiers.pop(4)
eft = eft5
elif (e2 == 2) and (e1 == 0):
# Top middle front wedge element
nodeIdentifiers.pop(6)
nodeIdentifiers.pop(4)
eft = eft5
if (e2 == 0) and (e1 == 0):
# Top back tetrahedron element
nodeIdentifiers.pop(6)
nodeIdentifiers.pop(5)
nodeIdentifiers.pop(4)
nodeIdentifiers.pop(0)
eft = eft6
scalefactors = [-1.0]
if (e2 == elementsCount2 - 1) and (e1 == 0):
# Top front tetrahedron element
nodeIdentifiers.pop(7)
nodeIdentifiers.pop(6)
nodeIdentifiers.pop(4)
nodeIdentifiers.pop(2)
eft = eft7
scalefactors = [-1.0]
if eft is eftRegular:
element = mesh.createElement(elementIdentifier,
elementtemplateRegular)
else:
elementtemplateCustom.defineField(coordinates, -1, eft)
element = mesh.createElement(elementIdentifier,
elementtemplateCustom)
element.setNodesByIdentifier(eft, nodeIdentifiers)
if scalefactors:
element.setScaleFactors(eft, scalefactors)
elementIdentifier += 1
leftLungMeshGroup.addElement(element)
lungMeshGroup.addElement(element)
# Apex annotation point
idx = elementsCount1 * elementsCount2 * (
elementsCount3 - 1) + elementsCount1 * (elementsCount2 // 2)
element1 = mesh.findElementByIdentifier(idx)
markerPoint = markerPoints.createNode(nodeIdentifier,
markerTemplateInternal)
nodeIdentifier += 1
cache.setNode(markerPoint)
markerName.assignString(cache, 'apex of left lung')
markerLocation.assignMeshLocation(cache, element1, [1.0, 1.0, 1.0])
return annotationGroups
