def defineFaceAnnotations(cls, region, options, annotationGroups):
"""
Add face annotation groups from the highest dimension mesh.
Must have defined faces and added subelements for highest dimension groups.
:param region: Zinc region containing model.
:param options: Dict containing options. See getDefaultOptions().
:param annotationGroups: List of annotation groups for top-level elements.
New face annotation groups are appended to this list.
"""
# add epicardium of fibrous ring
fm = region.getFieldmodule()
MeshType_3d_heartventriclesbase1.defineFaceAnnotations(
region, options, annotationGroups)
MeshType_3d_heartatria1.defineFaceAnnotations(region, options,
annotationGroups)
lFibrousRingGroup = getAnnotationGroupForTerm(
annotationGroups, get_heart_term("left fibrous ring"))
rFibrousRingGroup = getAnnotationGroupForTerm(
annotationGroups, get_heart_term("right fibrous ring"))
epiGroup = getAnnotationGroupForTerm(annotationGroups,
get_heart_term("epicardium"))
mesh2d = fm.findMeshByDimension(2)
is_exterior_face_xi3_1 = fm.createFieldAnd(
fm.createFieldIsExterior(),
fm.createFieldIsOnFace(Element.FACE_TYPE_XI3_1))
is_non_septal_fibrous_ring = fm.createFieldXor(
lFibrousRingGroup.getFieldElementGroup(mesh2d),
rFibrousRingGroup.getFieldElementGroup(mesh2d))
is_non_septal_fibrous_ring_epi = fm.createFieldAnd(
is_non_septal_fibrous_ring, is_exterior_face_xi3_1)
epiGroup.getMeshGroup(mesh2d).addElementsConditional(
is_non_septal_fibrous_ring_epi)
def test_heart1(self):
"""
Test creation of heart scaffold.
"""
scaffold = MeshType_3d_heart1
parameterSetNames = scaffold.getParameterSetNames()
self.assertEqual(parameterSetNames, [
"Default", "Human 1", "Mouse 1", "Pig 1", "Rat 1", "Unit Human 1",
"Unit Mouse 1", "Unit Pig 1", "Unit Rat 1"
])
options = scaffold.getDefaultOptions("Human 1")
self.assertEqual(123, len(options))
self.assertEqual(0.9, options.get("LV outer height"))
self.assertEqual(80.0, options.get("Unit scale"))
self.assertEqual(7,
options.get("Number of elements around LV free wall"))
self.assertEqual(7,
options.get("Number of elements around RV free wall"))
# simplify atria
self.assertEqual(8, options.get("Number of elements over atria"))
options["Number of elements over atria"] = 6
self.assertEqual(
2, options.get("Number of elements radial pulmonary vein annuli"))
options["Number of elements radial pulmonary vein annuli"] = 1
self.assertFalse(scaffold.checkOptions(options))
context = Context("Test")
region = context.getDefaultRegion()
self.assertTrue(region.isValid())
annotationGroups = scaffold.generateMesh(region, options)
self.assertEqual(32, len(annotationGroups))
fieldmodule = region.getFieldmodule()
mesh3d = fieldmodule.findMeshByDimension(3)
self.assertEqual(332, mesh3d.getSize())
mesh2d = fieldmodule.findMeshByDimension(2)
self.assertEqual(1287, mesh2d.getSize())
mesh1d = fieldmodule.findMeshByDimension(1)
self.assertEqual(1567, mesh1d.getSize())
nodes = fieldmodule.findNodesetByFieldDomainType(
Field.DOMAIN_TYPE_NODES)
self.assertEqual(614, nodes.getSize())
datapoints = fieldmodule.findNodesetByFieldDomainType(
Field.DOMAIN_TYPE_DATAPOINTS)
self.assertEqual(0, datapoints.getSize())
# check coordinates range, epicardium surface area and volume
coordinates = fieldmodule.findFieldByName(
"coordinates").castFiniteElement()
self.assertTrue(coordinates.isValid())
minimums, maximums = evaluateFieldNodesetRange(coordinates, nodes)
assertAlmostEqualList(self, minimums,
[-50.7876375290527, -58.42494589146976, -91.6],
1.0E-6)
assertAlmostEqualList(
self, maximums,
[43.810947610743156, 39.03925080604259, 42.018608492002784],
1.0E-6)
with ChangeManager(fieldmodule):
one = fieldmodule.createFieldConstant(1.0)
epicardiumGroup = fieldmodule.findFieldByName(
'epicardium').castGroup()
self.assertTrue(epicardiumGroup.isValid())
epicardiumMeshGroup = epicardiumGroup.getFieldElementGroup(
mesh2d).getMeshGroup()
self.assertTrue(epicardiumMeshGroup.isValid())
surfaceAreaField = fieldmodule.createFieldMeshIntegral(
one, coordinates, epicardiumMeshGroup)
surfaceAreaField.setNumbersOfPoints(4)
volumeField = fieldmodule.createFieldMeshIntegral(
one, coordinates, mesh3d)
volumeField.setNumbersOfPoints(3)
fieldcache = fieldmodule.createFieldcache()
result, surfaceArea = surfaceAreaField.evaluateReal(fieldcache, 1)
self.assertEqual(result, RESULT_OK)
self.assertAlmostEqual(surfaceArea, 36541.36513577538, delta=1.0E-2)
result, volume = volumeField.evaluateReal(fieldcache, 1)
self.assertEqual(result, RESULT_OK)
self.assertAlmostEqual(volume, 218014.81436425756, delta=1.0E-1)
# check some annotationGroups:
expectedSizes3d = {
"left ventricle myocardium": 110,
"right ventricle myocardium": 95,
"interventricular septum": 37,
"left atrium myocardium": 88,
"right atrium myocardium": 80,
"interatrial septum": 23
}
for name in expectedSizes3d:
group = getAnnotationGroupForTerm(annotationGroups,
get_heart_term(name))
size = group.getMeshGroup(mesh3d).getSize()
self.assertEqual(expectedSizes3d[name], size, name)
expectedSizes2d = {
"endocardium of left ventricle": 88,
"endocardium of right ventricle": 73,
"endocardium of left atrium": 82,
"endocardium of right atrium": 74,
"epicardium": 229
}
for name in expectedSizes2d:
group = getAnnotationGroupForTerm(annotationGroups,
get_heart_term(name))
size = group.getMeshGroup(mesh2d).getSize()
self.assertEqual(expectedSizes2d[name], size, name)
# test finding a marker in scaffold
markerGroup = fieldmodule.findFieldByName("marker").castGroup()
markerNodes = markerGroup.getFieldNodeGroup(nodes).getNodesetGroup()
self.assertEqual(7, markerNodes.getSize())
markerName = fieldmodule.findFieldByName("marker_name")
self.assertTrue(markerName.isValid())
markerLocation = fieldmodule.findFieldByName("marker_location")
self.assertTrue(markerLocation.isValid())
# test apex marker point
cache = fieldmodule.createFieldcache()
node = findNodeWithName(markerNodes, markerName, "apex of heart")
self.assertTrue(node.isValid())
cache.setNode(node)
element, xi = markerLocation.evaluateMeshLocation(cache, 3)
self.assertEqual(1, element.getIdentifier())
assertAlmostEqualList(self, xi, [0.0, 0.0, 1.0], 1.0E-10)
apexGroup = getAnnotationGroupForTerm(annotationGroups,
get_heart_term("apex of heart"))
self.assertTrue(apexGroup.getNodesetGroup(nodes).containsNode(node))
# refine 2x2x2 and check result
# first remove any face (but not point) annotation groups as they are re-added by defineFaceAnnotations
removeAnnotationGroups = []
for annotationGroup in annotationGroups:
if (not annotationGroup.hasMeshGroup(mesh3d)) and (
annotationGroup.hasMeshGroup(mesh2d)
or annotationGroup.hasMeshGroup(mesh1d)):
removeAnnotationGroups.append(annotationGroup)
for annotationGroup in removeAnnotationGroups:
annotationGroups.remove(annotationGroup)
self.assertEqual(23, len(annotationGroups))
refineRegion = region.createRegion()
refineFieldmodule = refineRegion.getFieldmodule()
options['Refine number of elements surface'] = 2
options['Refine number of elements through LV wall'] = 2
options['Refine number of elements through wall'] = 2
meshrefinement = MeshRefinement(region, refineRegion, annotationGroups)
scaffold.refineMesh(meshrefinement, options)
annotationGroups = meshrefinement.getAnnotationGroups()
refineFieldmodule.defineAllFaces()
oldAnnotationGroups = copy.copy(annotationGroups)
for annotationGroup in annotationGroups:
annotationGroup.addSubelements()
scaffold.defineFaceAnnotations(refineRegion, options, annotationGroups)
for annotation in annotationGroups:
if annotation not in oldAnnotationGroups:
annotationGroup.addSubelements()
self.assertEqual(32, len(annotationGroups))
mesh3d = refineFieldmodule.findMeshByDimension(3)
self.assertEqual(2580, mesh3d.getSize())
mesh2d = refineFieldmodule.findMeshByDimension(2)
self.assertEqual(8872, mesh2d.getSize())
mesh1d = refineFieldmodule.findMeshByDimension(1)
self.assertEqual(9983, mesh1d.getSize())
nodes = refineFieldmodule.findNodesetByFieldDomainType(
Field.DOMAIN_TYPE_NODES)
self.assertEqual(3693, nodes.getSize())
datapoints = refineFieldmodule.findNodesetByFieldDomainType(
Field.DOMAIN_TYPE_DATAPOINTS)
self.assertEqual(0, datapoints.getSize())
# check some refined annotationGroups:
for name in expectedSizes3d:
group = getAnnotationGroupForTerm(annotationGroups,
get_heart_term(name))
size = group.getMeshGroup(mesh3d).getSize()
self.assertEqual(expectedSizes3d[name] * 8, size, name)
for name in expectedSizes2d:
group = getAnnotationGroupForTerm(annotationGroups,
get_heart_term(name))
size = group.getMeshGroup(mesh2d).getSize()
if name == "epicardium":
# fibrous ring is only refined by 1 through its thickness
fibrousRingReduction = (
options['Refine number of elements surface'] - 1
) * options['Refine number of elements surface'] * (
options['Number of elements around left atrium free wall']
+
options['Number of elements around right atrium free wall']
)
self.assertEqual(
expectedSizes2d[name] * 4 - fibrousRingReduction, size,
name)
else:
self.assertEqual(expectedSizes2d[name] * 4, size, name)
# test finding a marker in refined scaffold
markerGroup = refineFieldmodule.findFieldByName("marker").castGroup()
refinedNodes = refineFieldmodule.findNodesetByFieldDomainType(
Field.DOMAIN_TYPE_NODES)
markerNodes = markerGroup.getFieldNodeGroup(
refinedNodes).getNodesetGroup()
self.assertEqual(7, markerNodes.getSize())
markerName = refineFieldmodule.findFieldByName("marker_name")
self.assertTrue(markerName.isValid())
markerLocation = refineFieldmodule.findFieldByName("marker_location")
self.assertTrue(markerLocation.isValid())
# test apex marker point
cache = refineFieldmodule.createFieldcache()
node = findNodeWithName(markerNodes, markerName, "apex of heart")
self.assertTrue(node.isValid())
cache.setNode(node)
element, xi = markerLocation.evaluateMeshLocation(cache, 3)
self.assertEqual(5, element.getIdentifier())
assertAlmostEqualList(self, xi, [0.0, 0.0, 1.0], 1.0E-10)
apexGroup = getAnnotationGroupForTerm(annotationGroups,
get_heart_term("apex of heart"))
self.assertTrue(apexGroup.getNodesetGroup(nodes).containsNode(node))
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 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 test_heart1(self):
"""
Test creation of heart scaffold.
"""
scaffold = MeshType_3d_heart1
parameterSetNames = scaffold.getParameterSetNames()
self.assertEqual(parameterSetNames, [
"Default", "Human 1", "Mouse 1", "Pig 1", "Rat 1", "Unit Human 1",
"Unit Mouse 1", "Unit Pig 1", "Unit Rat 1"
])
options = scaffold.getDefaultOptions("Human 1")
self.assertEqual(117, len(options))
self.assertEqual(0.9, options.get("LV outer height"))
self.assertEqual(80.0, options.get("Unit scale"))
self.assertEqual(7,
options.get("Number of elements around LV free wall"))
self.assertEqual(7,
options.get("Number of elements around RV free wall"))
context = Context("Test")
region = context.getDefaultRegion()
self.assertTrue(region.isValid())
annotationGroups = scaffold.generateMesh(region, options)
self.assertEqual(27, len(annotationGroups))
fieldmodule = region.getFieldmodule()
mesh3d = fieldmodule.findMeshByDimension(3)
self.assertEqual(289, mesh3d.getSize())
mesh2d = fieldmodule.findMeshByDimension(2)
self.assertEqual(1117, mesh2d.getSize())
mesh1d = fieldmodule.findMeshByDimension(1)
self.assertEqual(1356, mesh1d.getSize())
nodes = fieldmodule.findNodesetByFieldDomainType(
Field.DOMAIN_TYPE_NODES)
self.assertEqual(528, nodes.getSize())
datapoints = fieldmodule.findNodesetByFieldDomainType(
Field.DOMAIN_TYPE_DATAPOINTS)
self.assertEqual(0, datapoints.getSize())
coordinates = fieldmodule.findFieldByName(
"coordinates").castFiniteElement()
self.assertTrue(coordinates.isValid())
minimums, maximums = evaluateFieldNodesetRange(coordinates, nodes)
assertAlmostEqualList(self, minimums,
[-50.7876375290527, -57.76590573823474, -91.6],
1.0E-6)
assertAlmostEqualList(
self, maximums,
[43.81084359764995, 39.03925080604259, 40.71693637558552], 1.0E-6)
# check some annotationGroups:
expectedSizes3d = {
"left ventricle myocardium": 94,
"right ventricle myocardium": 79,
"interventricular septum": 30,
"left atrium myocardium": 88,
"right atrium myocardium": 62,
"interatrial septum": 17
}
for name in expectedSizes3d:
group = getAnnotationGroupForTerm(annotationGroups,
get_heart_term(name))
size = group.getMeshGroup(mesh3d).getSize()
self.assertEqual(expectedSizes3d[name], size, name)
expectedSizes2d = {
"endocardium of left ventricle": 74,
"endocardium of right ventricle": 59,
"endocardium of left atrium": 82,
"endocardium of right atrium": 56,
"epicardium": 197
}
for name in expectedSizes2d:
group = getAnnotationGroupForTerm(annotationGroups,
get_heart_term(name))
size = group.getMeshGroup(mesh2d).getSize()
self.assertEqual(expectedSizes2d[name], size, name)
# refine 2x2x2 and check result
# first remove any surface annotation groups as they are re-added by defineFaceAnnotations
removeAnnotationGroups = []
for annotationGroup in annotationGroups:
if annotationGroup.getMeshGroup(mesh3d).getSize() == 0:
removeAnnotationGroups.append(annotationGroup)
for annotationGroup in removeAnnotationGroups:
annotationGroups.remove(annotationGroup)
self.assertEqual(18, len(annotationGroups))
refineRegion = region.createRegion()
refineFieldmodule = refineRegion.getFieldmodule()
options['Refine number of elements surface'] = 2
options['Refine number of elements through LV wall'] = 2
options['Refine number of elements through wall'] = 2
meshrefinement = MeshRefinement(region, refineRegion, annotationGroups)
scaffold.refineMesh(meshrefinement, options)
annotationGroups = meshrefinement.getAnnotationGroups()
refineFieldmodule.defineAllFaces()
oldAnnotationGroups = copy.copy(annotationGroups)
for annotationGroup in annotationGroups:
annotationGroup.addSubelements()
scaffold.defineFaceAnnotations(refineRegion, options, annotationGroups)
for annotation in annotationGroups:
if annotation not in oldAnnotationGroups:
annotationGroup.addSubelements()
self.assertEqual(27, len(annotationGroups))
mesh3d = refineFieldmodule.findMeshByDimension(3)
self.assertEqual(2236, mesh3d.getSize())
mesh2d = refineFieldmodule.findMeshByDimension(2)
self.assertEqual(7676, mesh2d.getSize())
mesh1d = refineFieldmodule.findMeshByDimension(1)
self.assertEqual(8623, mesh1d.getSize())
nodes = refineFieldmodule.findNodesetByFieldDomainType(
Field.DOMAIN_TYPE_NODES)
self.assertEqual(3183, nodes.getSize())
datapoints = refineFieldmodule.findNodesetByFieldDomainType(
Field.DOMAIN_TYPE_DATAPOINTS)
self.assertEqual(0, datapoints.getSize())
# check some refined annotationGroups:
for name in expectedSizes3d:
group = getAnnotationGroupForTerm(annotationGroups,
get_heart_term(name))
size = group.getMeshGroup(mesh3d).getSize()
self.assertEqual(expectedSizes3d[name] * 8, size, name)
for name in expectedSizes2d:
group = getAnnotationGroupForTerm(annotationGroups,
get_heart_term(name))
size = group.getMeshGroup(mesh2d).getSize()
if name == "epicardium":
# fibrous ring is only refined by 1 through its thickness
fibrousRingReduction = (
options['Refine number of elements surface'] - 1
) * options['Refine number of elements surface'] * (
options['Number of elements around left atrium free wall']
+
options['Number of elements around right atrium free wall']
)
self.assertEqual(
expectedSizes2d[name] * 4 - fibrousRingReduction, size,
name)
else:
self.assertEqual(expectedSizes2d[name] * 4, size, name)
# test finding a marker in refined scaffold
markerGroup = refineFieldmodule.findFieldByName("marker").castGroup()
refinedNodes = refineFieldmodule.findNodesetByFieldDomainType(
Field.DOMAIN_TYPE_NODES)
markerNodes = markerGroup.getFieldNodeGroup(
refinedNodes).getNodesetGroup()
self.assertEqual(5, markerNodes.getSize())
markerName = refineFieldmodule.findFieldByName("marker_name")
self.assertTrue(markerName.isValid())
markerLocation = refineFieldmodule.findFieldByName("marker_location")
self.assertTrue(markerLocation.isValid())
cache = refineFieldmodule.createFieldcache()
node = findNodeWithName(markerNodes, markerName, "APEX")
self.assertTrue(node.isValid())
cache.setNode(node)
element, xi = markerLocation.evaluateMeshLocation(cache, 3)
self.assertEqual(5, element.getIdentifier())
assertAlmostEqualList(self, xi, [0.0, 0.0, 1.0], 1.0E-10)
def generateBaseMesh(cls, region, options, baseCentre=[ 0.0, 0.0, 0.0 ], axisSide1=[ 0.0, -1.0, 0.0 ], axisUp=[ 0.0, 0.0, 1.0]):
"""
Generate the base bicubic-linear Hermite mesh.
Optional extra parameters allow centre and axes to be set.
:param region: Zinc region to define model in. Must be empty.
:param options: Dict containing options. See getDefaultOptions().
:param baseCentre: Centre of valve on ventriculo-arterial junction.
:param axisSide: Unit vector in first side direction where angle around starts.
:param axisUp: Unit vector in outflow direction of valve.
:return: list of AnnotationGroup
"""
unitScale = options['Unit scale']
outerHeight = unitScale*options['Outer height']
innerDepth = unitScale*options['Inner depth']
cuspHeight = unitScale*options['Cusp height']
innerRadius = unitScale*0.5*options['Inner diameter']
sinusRadialDisplacement = unitScale*options['Sinus radial displacement']
wallThickness = unitScale*options['Wall thickness']
cuspThickness = unitScale*options['Cusp thickness']
aorticNotPulmonary = options['Aortic not pulmonary']
useCrossDerivatives = False
fm = region.getFieldmodule()
fm.beginChange()
coordinates = findOrCreateFieldCoordinates(fm)
cache = fm.createFieldcache()
mesh = fm.findMeshByDimension(3)
if aorticNotPulmonary:
arterialRootGroup = AnnotationGroup(region, get_heart_term("root of aorta"))
cuspGroups = [
AnnotationGroup(region, get_heart_term("posterior cusp of aortic valve")),
AnnotationGroup(region, get_heart_term("right cusp of aortic valve")),
AnnotationGroup(region, get_heart_term("left cusp of aortic valve")) ]
else:
arterialRootGroup = AnnotationGroup(region, get_heart_term("root of pulmonary trunk"))
cuspGroups = [
AnnotationGroup(region, get_heart_term("right cusp of pulmonary valve")),
AnnotationGroup(region, get_heart_term("anterior cusp of pulmonary valve")),
AnnotationGroup(region, get_heart_term("left cusp of pulmonary valve")) ]
allGroups = [ arterialRootGroup ] # groups that all elements in scaffold will go in
annotationGroups = allGroups + cuspGroups
nodes = fm.findNodesetByFieldDomainType(Field.DOMAIN_TYPE_NODES)
#################
# Create 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)
# most nodes in this scaffold do not have a DS3 derivative
nodetemplateLinearS3 = nodes.createNodetemplate()
nodetemplateLinearS3.defineField(coordinates)
nodetemplateLinearS3.setValueNumberOfVersions(coordinates, -1, Node.VALUE_LABEL_VALUE, 1)
nodetemplateLinearS3.setValueNumberOfVersions(coordinates, -1, Node.VALUE_LABEL_D_DS1, 1)
nodetemplateLinearS3.setValueNumberOfVersions(coordinates, -1, Node.VALUE_LABEL_D_DS2, 1)
# several only have a DS1 derivative
nodetemplateLinearS2S3 = nodes.createNodetemplate()
nodetemplateLinearS2S3.defineField(coordinates)
nodetemplateLinearS2S3.setValueNumberOfVersions(coordinates, -1, Node.VALUE_LABEL_VALUE, 1)
nodetemplateLinearS2S3.setValueNumberOfVersions(coordinates, -1, Node.VALUE_LABEL_D_DS1, 1)
nodeIdentifier = max(1, getMaximumNodeIdentifier(nodes) + 1)
elementsCountAround = 6
radiansPerElementAround = 2.0*math.pi/elementsCountAround
axisSide2 = vector.crossproduct3(axisUp, axisSide1)
outerRadius = innerRadius + wallThickness
cuspOuterLength2 = 0.5*getApproximateEllipsePerimeter(innerRadius, cuspHeight)
cuspOuterWallArcLength = cuspOuterLength2*innerRadius/(innerRadius + cuspHeight)
noduleOuterAxialArcLength = cuspOuterLength2 - cuspOuterWallArcLength
noduleOuterRadialArcLength = innerRadius
cuspOuterWalld1 = interp.interpolateLagrangeHermiteDerivative([ innerRadius, outerHeight + innerDepth - cuspHeight ], [ 0.0, 0.0 ], [ -innerRadius, 0.0 ], 0.0)
sin60 = math.sin(math.pi/3.0)
cuspThicknessLowerFactor = 4.5 # GRC fudge factor
cuspInnerLength2 = 0.5*getApproximateEllipsePerimeter(innerRadius - cuspThickness/sin60, cuspHeight - cuspThicknessLowerFactor*cuspThickness)
noduleInnerAxialArcLength = cuspInnerLength2*(cuspHeight - cuspThicknessLowerFactor*cuspThickness)/(innerRadius - cuspThickness/sin60 + cuspHeight - cuspThicknessLowerFactor*cuspThickness)
noduleInnerRadialArcLength = innerRadius - cuspThickness/math.tan(math.pi/3.0)
nMidCusp = 0 if aorticNotPulmonary else 1
# lower points
ix, id1 = createCirclePoints([ (baseCentre[c] - axisUp[c]*innerDepth) for c in range(3) ],
[ axisSide1[c]*innerRadius for c in range(3) ], [ axisSide2[c]*innerRadius for c in range(3) ],
elementsCountAround)
ox, od1 = getSemilunarValveSinusPoints(baseCentre, axisSide1, axisSide2, outerRadius, sinusRadialDisplacement,
startMidCusp=aorticNotPulmonary)
lowerx, lowerd1 = [ ix, ox ], [ id1, od1 ]
# upper points
topCentre = [ (baseCentre[c] + axisUp[c]*outerHeight) for c in range(3) ]
# twice as many on inner:
ix, id1 = createCirclePoints(topCentre,
[ axisSide1[c]*innerRadius for c in range(3) ], [ axisSide2[c]*innerRadius for c in range(3) ],
elementsCountAround*2)
# tweak inner points so elements attached to cusps are narrower
cuspRadiansFactor = 0.25 # GRC fudge factor
midDerivativeFactor = 1.0 + 0.5*(1.0 - cuspRadiansFactor) # GRC test compromise
cuspAttachmentRadians = cuspRadiansFactor*radiansPerElementAround
cuspAttachmentRadialDisplacement = wallThickness*0.333 # GRC fudge factor
cuspAttachmentRadius = innerRadius - cuspAttachmentRadialDisplacement
for cusp in range(3):
n1 = cusp*2 - 1 + nMidCusp
n2 = n1*2
id1[n2 + 2] = [ 2.0*d for d in id1[n2 + 2] ]
# side 1
radiansAround = n1*radiansPerElementAround + cuspAttachmentRadians
rcosRadiansAround = cuspAttachmentRadius*math.cos(radiansAround)
rsinRadiansAround = cuspAttachmentRadius*math.sin(radiansAround)
ix[n2 + 1] = [ (topCentre[c] + rcosRadiansAround*axisSide1[c] + rsinRadiansAround*axisSide2[c]) for c in range(3) ]
id1[n2 + 1] = interp.interpolateLagrangeHermiteDerivative(ix[n2 + 1], ix[n2 + 2], id1[n2 + 2], 0.0)
# side 2
n1 = ((cusp + 1)*2 - 1 + nMidCusp)%elementsCountAround
n2 = n1*2
radiansAround = n1*radiansPerElementAround - cuspAttachmentRadians
rcosRadiansAround = cuspAttachmentRadius*math.cos(radiansAround)
rsinRadiansAround = cuspAttachmentRadius*math.sin(radiansAround)
ix[n2 - 1] = [ (topCentre[c] + rcosRadiansAround*axisSide1[c] + rsinRadiansAround*axisSide2[c]) for c in range(3) ]
id1[n2 - 1] = interp.interpolateHermiteLagrangeDerivative(ix[n2 - 2], id1[n2 - 2], ix[n2 - 1], 1.0)
ox, od1 = createCirclePoints(topCentre,
[ axisSide1[c]*outerRadius for c in range(3) ], [ axisSide2[c]*outerRadius for c in range(3) ],
elementsCountAround)
upperx, upperd1 = [ ix, ox ], [ id1, od1 ]
# get lower and upper derivative 2
zero = [ 0.0, 0.0, 0.0 ]
upperd2factor = outerHeight
upd2 = [ d*upperd2factor for d in axisUp ]
lowerOuterd2 = interp.smoothCubicHermiteDerivativesLine([ lowerx[1][nMidCusp], upperx[1][nMidCusp] ], [ upd2, upd2 ],
fixStartDirection=True, fixEndDerivative=True)[0]
lowerd2factor = 2.0*(outerHeight + innerDepth) - upperd2factor
lowerInnerd2 = [ d*lowerd2factor for d in axisUp ]
lowerd2 = [ [ lowerInnerd2 ]*elementsCountAround, [ lowerOuterd2 ]*elementsCountAround ] # some lowerd2[0] to be fitted below
upperd2 = [ [ upd2 ]*(elementsCountAround*2), [ upd2 ]*elementsCountAround ]
# get lower and upper derivative 1 or 2 pointing to/from cusps
for n1 in range(elementsCountAround):
radiansAround = n1*radiansPerElementAround
cosRadiansAround = math.cos(radiansAround)
sinRadiansAround = math.sin(radiansAround)
if (n1 % 2) == nMidCusp:
lowerd2[0][n1] = [ -cuspOuterWallArcLength*(cosRadiansAround*axisSide1[c] + sinRadiansAround*axisSide2[c]) for c in range(3) ]
else:
upperd1[0][n1*2] = [ (cuspOuterWalld1[0]*(cosRadiansAround*axisSide1[c] + sinRadiansAround*axisSide2[c]) + cuspOuterWalld1[1]*axisUp[c]) for c in range(3) ]
# inner wall and mid sinus points; only every second one is used
sinusDepth = innerDepth - cuspThicknessLowerFactor*cuspThickness # GRC test
sinusCentre = [ (baseCentre[c] - sinusDepth*axisUp[c]) for c in range(3) ]
sinusx, sinusd1 = createCirclePoints(sinusCentre,
[ axisSide1[c]*innerRadius for c in range(3) ], [ axisSide2[c]*innerRadius for c in range(3) ],
elementsCountAround)
# get sinusd2, parallel to lower inclined lines
sd2 = interp.smoothCubicHermiteDerivativesLine([ [ innerRadius, -sinusDepth ], [ innerRadius, outerHeight ] ],
[ [ wallThickness + sinusRadialDisplacement, innerDepth ], [ 0.0, upperd2factor ] ],
fixStartDirection=True, fixEndDerivative=True)[0]
sinusd2 = [ None ]*elementsCountAround
for cusp in range(3):
n1 = cusp*2 + nMidCusp
radiansAround = n1*radiansPerElementAround
cosRadiansAround = math.cos(radiansAround)
sinRadiansAround = math.sin(radiansAround)
sinusd2[n1] = [ (sd2[0]*(cosRadiansAround*axisSide1[c] + sinRadiansAround*axisSide2[c]) + sd2[1]*axisUp[c]) for c in range(3) ]
# get points on arc between mid sinus and upper cusp points
arcx = []
arcd1 = []
scaled1 = 2.5 # GRC fudge factor
for cusp in range(3):
n1 = cusp*2 + nMidCusp
n1m = n1 - 1
n1p = (n1 + 1)%elementsCountAround
n2m = n1m*2 + 1
n2p = n1p*2 - 1
ax, ad1 = interp.sampleCubicHermiteCurves([ upperx[0][n2m], sinusx[n1] ], [ [ -scaled1*d for d in upperd2[0][n2m] ], [ scaled1*d for d in sinusd1[n1] ] ],
elementsCountOut=2, addLengthStart=0.5*vector.magnitude(upperd2[0][n2m]), lengthFractionStart=0.5,
addLengthEnd=0.5*vector.magnitude(sinusd1[n1]), lengthFractionEnd=0.5, arcLengthDerivatives=False)[0:2]
arcx .append(ax [1])
arcd1.append(ad1[1])
ax, ad1 = interp.sampleCubicHermiteCurves([ sinusx[n1], upperx[0][n2p], ], [ [ scaled1*d for d in sinusd1[n1] ], [ scaled1*d for d in upperd2[0][n2p] ] ],
elementsCountOut=2, addLengthStart=0.5*vector.magnitude(sinusd1[n1]), lengthFractionStart=0.5,
addLengthEnd=0.5*vector.magnitude(upperd2[0][n2p]), lengthFractionEnd=0.5, arcLengthDerivatives=False)[0:2]
arcx .append(ax [1])
arcd1.append(ad1[1])
if nMidCusp == 0:
arcx .append(arcx .pop(0))
arcd1.append(arcd1.pop(0))
# cusp nodule points
noduleCentre = [ (baseCentre[c] + axisUp[c]*(cuspHeight - innerDepth)) for c in range(3) ]
nodulex = [ [], [] ]
noduled1 = [ [], [] ]
noduled2 = [ [], [] ]
noduled3 = [ [], [] ]
cuspRadialThickness = cuspThickness/sin60
for i in range(3):
nodulex[0].append(noduleCentre)
n1 = i*2 + nMidCusp
radiansAround = n1*radiansPerElementAround
cosRadiansAround = math.cos(radiansAround)
sinRadiansAround = math.sin(radiansAround)
nodulex[1].append([ (noduleCentre[c] + cuspRadialThickness*(cosRadiansAround*axisSide1[c] + sinRadiansAround*axisSide2[c])) for c in range(3) ])
n1 = i*2 - 1 + nMidCusp
radiansAround = n1*radiansPerElementAround
cosRadiansAround = math.cos(radiansAround)
sinRadiansAround = math.sin(radiansAround)
noduled1[0].append([ noduleOuterRadialArcLength*(cosRadiansAround*axisSide1[c] + sinRadiansAround*axisSide2[c]) for c in range(3) ])
noduled1[1].append(vector.setMagnitude(noduled1[0][i], noduleInnerRadialArcLength))
n1 = i*2 + 1 + nMidCusp
radiansAround = n1*radiansPerElementAround
cosRadiansAround = math.cos(radiansAround)
sinRadiansAround = math.sin(radiansAround)
noduled2[0].append([ noduleOuterRadialArcLength*(cosRadiansAround*axisSide1[c] + sinRadiansAround*axisSide2[c]) for c in range(3) ])
noduled2[1].append(vector.setMagnitude(noduled2[0][i], noduleInnerRadialArcLength))
noduled3[0].append([ noduleOuterAxialArcLength*axisUp[c] for c in range(3) ])
noduled3[1].append([ noduleInnerAxialArcLength*axisUp[c] for c in range(3) ])
# Create nodes
lowerNodeId = [ [], [] ]
for n3 in range(2):
for n1 in range(elementsCountAround):
node = nodes.createNode(nodeIdentifier, nodetemplateLinearS3)
cache.setNode(node)
coordinates.setNodeParameters(cache, -1, Node.VALUE_LABEL_VALUE, 1, lowerx [n3][n1])
coordinates.setNodeParameters(cache, -1, Node.VALUE_LABEL_D_DS1, 1, lowerd1[n3][n1])
coordinates.setNodeParameters(cache, -1, Node.VALUE_LABEL_D_DS2, 1, lowerd2[n3][n1])
lowerNodeId[n3].append(nodeIdentifier)
nodeIdentifier += 1
sinusNodeId = []
for n1 in range(elementsCountAround):
if (n1%2) != nMidCusp:
sinusNodeId.append(None)
continue
node = nodes.createNode(nodeIdentifier, nodetemplateLinearS3)
cache.setNode(node)
coordinates.setNodeParameters(cache, -1, Node.VALUE_LABEL_VALUE, 1, sinusx [n1])
coordinates.setNodeParameters(cache, -1, Node.VALUE_LABEL_D_DS1, 1, sinusd1[n1])
coordinates.setNodeParameters(cache, -1, Node.VALUE_LABEL_D_DS2, 1, sinusd2[n1])
sinusNodeId.append(nodeIdentifier)
nodeIdentifier += 1
arcNodeId = []
for n1 in range(elementsCountAround):
node = nodes.createNode(nodeIdentifier, nodetemplateLinearS2S3)
cache.setNode(node)
coordinates.setNodeParameters(cache, -1, Node.VALUE_LABEL_VALUE, 1, arcx [n1])
coordinates.setNodeParameters(cache, -1, Node.VALUE_LABEL_D_DS1, 1, arcd1[n1])
arcNodeId.append(nodeIdentifier)
nodeIdentifier += 1
noduleNodeId = [ [], [] ]
for n3 in range(2):
for n1 in range(3):
node = nodes.createNode(nodeIdentifier, nodetemplate)
cache.setNode(node)
coordinates.setNodeParameters(cache, -1, Node.VALUE_LABEL_VALUE, 1, nodulex [n3][n1])
coordinates.setNodeParameters(cache, -1, Node.VALUE_LABEL_D_DS1, 1, noduled1[n3][n1])
coordinates.setNodeParameters(cache, -1, Node.VALUE_LABEL_D_DS2, 1, noduled2[n3][n1])
coordinates.setNodeParameters(cache, -1, Node.VALUE_LABEL_D_DS3, 1, noduled3[n3][n1])
noduleNodeId[n3].append(nodeIdentifier)
nodeIdentifier += 1
upperNodeId = [ [], [] ]
for n3 in range(2):
for n1 in range(len(upperx[n3])):
node = nodes.createNode(nodeIdentifier, nodetemplateLinearS3)
cache.setNode(node)
coordinates.setNodeParameters(cache, -1, Node.VALUE_LABEL_VALUE, 1, upperx [n3][n1])
coordinates.setNodeParameters(cache, -1, Node.VALUE_LABEL_D_DS1, 1, upperd1[n3][n1])
coordinates.setNodeParameters(cache, -1, Node.VALUE_LABEL_D_DS2, 1, upperd2[n3][n1])
upperNodeId[n3].append(nodeIdentifier)
nodeIdentifier += 1
#################
# Create elements
#################
allMeshGroups = [ allGroup.getMeshGroup(mesh) for allGroup in allGroups ]
cuspMeshGroups = [ cuspGroup.getMeshGroup(mesh) for cuspGroup in cuspGroups ]
linearHermiteLinearBasis = fm.createElementbasis(3, Elementbasis.FUNCTION_TYPE_LINEAR_LAGRANGE)
linearHermiteLinearBasis.setFunctionType(2, Elementbasis.FUNCTION_TYPE_CUBIC_HERMITE)
hermiteLinearLinearBasis = fm.createElementbasis(3, Elementbasis.FUNCTION_TYPE_LINEAR_LAGRANGE)
hermiteLinearLinearBasis.setFunctionType(1, Elementbasis.FUNCTION_TYPE_CUBIC_HERMITE)
bicubichermitelinear = eftfactory_bicubichermitelinear(mesh, useCrossDerivatives)
eftDefault = bicubichermitelinear.createEftNoCrossDerivatives()
elementIdentifier = max(1, getMaximumElementIdentifier(mesh) + 1)
elementtemplate1 = mesh.createElementtemplate()
elementtemplate1.setElementShapeType(Element.SHAPE_TYPE_CUBE)
# wall elements
for cusp in range(3):
n1 = cusp*2 - 1 + nMidCusp
n2 = n1*2
for e in range(6):
eft1 = None
scalefactors = None
if (e == 0) or (e == 5):
# 6 node linear-hermite-linear collapsed wedge element expanding from zero width on outer wall of root, attaching to vertical part of cusp
eft1 = mesh.createElementfieldtemplate(linearHermiteLinearBasis)
# switch mappings to use DS2 instead of default DS1
remapEftNodeValueLabel(eft1, [ 1, 2, 3, 4, 5, 6, 7, 8 ], Node.VALUE_LABEL_D_DS1, [ ( Node.VALUE_LABEL_D_DS2, [] ) ])
if e == 0:
nids = [ lowerNodeId[0][n1], arcNodeId[n1], upperNodeId[0][n2], upperNodeId[0][n2 + 1], lowerNodeId[1][n1], upperNodeId[1][n1] ]
setEftScaleFactorIds(eft1, [1], [])
scalefactors = [ -1.0 ]
remapEftNodeValueLabel(eft1, [ 2 ], Node.VALUE_LABEL_D_DS2, [ ( Node.VALUE_LABEL_D_DS1, [1] ) ])
else:
nids = [ arcNodeId[n1 + 1], lowerNodeId[0][n1 - 4], upperNodeId[0][n2 + 3], upperNodeId[0][n2 - 8], lowerNodeId[1][n1 - 4], upperNodeId[1][n1 - 4] ]
remapEftNodeValueLabel(eft1, [ 1 ], Node.VALUE_LABEL_D_DS2, [ ( Node.VALUE_LABEL_D_DS1, [] ) ])
ln_map = [ 1, 2, 3, 4, 5, 5, 6, 6 ]
remapEftLocalNodes(eft1, 6, ln_map)
elif (e == 1) or (e == 4):
# 6 node hermite-linear-linear collapsed wedge element on lower wall
eft1 = mesh.createElementfieldtemplate(hermiteLinearLinearBasis)
if e == 1:
nids = [ lowerNodeId[0][n1], lowerNodeId[0][n1 + 1], arcNodeId[n1], sinusNodeId[n1 + 1], lowerNodeId[1][n1], lowerNodeId[1][n1 + 1] ]
else:
nids = [ lowerNodeId[0][n1 + 1], lowerNodeId[0][n1 - 4], sinusNodeId[n1 + 1], arcNodeId[n1 + 1], lowerNodeId[1][n1 + 1], lowerNodeId[1][n1 - 4] ]
ln_map = [ 1, 2, 3, 4, 5, 6, 5, 6 ]
remapEftLocalNodes(eft1, 6, ln_map)
else:
# 8 node elements with wedges on two sides
if e == 2:
eft1 = bicubichermitelinear.createEftNoCrossDerivatives()
setEftScaleFactorIds(eft1, [1], [])
scalefactors = [ -1.0 ]
nids = [ arcNodeId[n1], sinusNodeId[n1 + 1], upperNodeId[0][n2 + 1], upperNodeId[0][n2 + 2],
lowerNodeId[1][n1], lowerNodeId[1][n1 + 1], upperNodeId[1][n1], upperNodeId[1][n1 + 1] ]
remapEftNodeValueLabel(eft1, [ 1 ], Node.VALUE_LABEL_D_DS2, [ ( Node.VALUE_LABEL_D_DS1, [1] ) ])
else:
eft1 = eftDefault
nids = [ sinusNodeId[n1 + 1], arcNodeId[n1 + 1], upperNodeId[0][n2 + 2], upperNodeId[0][n2 + 3],
lowerNodeId[1][n1 + 1], lowerNodeId[1][n1 - 4], upperNodeId[1][n1 + 1], upperNodeId[1][n1 - 4] ]
remapEftNodeValueLabel(eft1, [ 2 ], Node.VALUE_LABEL_D_DS2, [ ( Node.VALUE_LABEL_D_DS1, [] ) ])
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 arterial root wall', cusp, e, 'element',elementIdentifier, result, result2, result3, nids)
elementIdentifier += 1
for meshGroup in allMeshGroups:
meshGroup.addElement(element)
# cusps (leaflets)
for cusp in range(3):
n1 = cusp*2 - 1 + nMidCusp
n2 = n1*2
meshGroups = allMeshGroups + [ cuspMeshGroups[cusp] ]
for e in range(2):
eft1 = bicubichermitelinear.createEftNoCrossDerivatives()
setEftScaleFactorIds(eft1, [1], [])
scalefactors = [ -1.0 ]
if e == 0:
nids = [ lowerNodeId[0][n1], lowerNodeId[0][n1 + 1], upperNodeId[0][n2], noduleNodeId[0][cusp],
arcNodeId[n1], sinusNodeId[n1 + 1], upperNodeId[0][n2 + 1], noduleNodeId[1][cusp] ]
remapEftNodeValueLabel(eft1, [ 4, 8 ], Node.VALUE_LABEL_D_DS1, [ ( Node.VALUE_LABEL_D_DS1, [1] ) ])
remapEftNodeValueLabel(eft1, [ 4, 8 ], Node.VALUE_LABEL_D_DS2, [ ( Node.VALUE_LABEL_D_DS3, [] ) ])
remapEftNodeValueLabel(eft1, [ 5 ], Node.VALUE_LABEL_D_DS2, [ ( Node.VALUE_LABEL_D_DS1, [1] ) ])
remapEftNodeValueLabel(eft1, [ 6 ], Node.VALUE_LABEL_D_DS2, [ ( Node.VALUE_LABEL_D_DS2, [1] ) ])
remapEftNodeValueLabel(eft1, [ 7 ], Node.VALUE_LABEL_D_DS1, [ ( Node.VALUE_LABEL_D_DS1, [1] ) ])
else:
nids = [ lowerNodeId[0][n1 + 1], lowerNodeId[0][n1 - 4], noduleNodeId[0][cusp], upperNodeId[0][n2 - 8],
sinusNodeId[n1 + 1], arcNodeId[n1 + 1], noduleNodeId[1][cusp], upperNodeId[0][n2 + 3] ]
remapEftNodeValueLabel(eft1, [ 3, 7 ], Node.VALUE_LABEL_D_DS2, [ ( Node.VALUE_LABEL_D_DS3, [] ) ])
remapEftNodeValueLabel(eft1, [ 3, 7 ], Node.VALUE_LABEL_D_DS1, [ ( Node.VALUE_LABEL_D_DS2, [] ) ])
remapEftNodeValueLabel(eft1, [ 4, 8 ], Node.VALUE_LABEL_D_DS1, [ ( Node.VALUE_LABEL_D_DS1, [1] ) ])
remapEftNodeValueLabel(eft1, [ 5 ], Node.VALUE_LABEL_D_DS2, [ ( Node.VALUE_LABEL_D_DS2, [1] ) ])
remapEftNodeValueLabel(eft1, [ 6 ], Node.VALUE_LABEL_D_DS2, [ ( Node.VALUE_LABEL_D_DS1, [] ) ])
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 semilunar cusp', cusp, e, 'element',elementIdentifier, result, result2, result3, nids)
elementIdentifier += 1
for meshGroup in meshGroups:
meshGroup.addElement(element)
fm.endChange()
return annotationGroups