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Merge pull request #105 from arti-sukasem/upperleftlobehumanlung
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Update both lower and upper lobes in the left human.
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@rchristie
rchristie authored Nov 25, 2020
2 parents 02b5862 + a048421 commit f7c5306
Showing 1 changed file with 179 additions and 43 deletions.
222 changes: 179 additions & 43 deletions src/scaffoldmaker/meshtypes/meshtype_3d_lung1.py
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Original file line number Diff line number Diff line change
Expand Up @@ -107,8 +107,11 @@ def generateBaseMesh(cls, region, options):

if isHuman:
lowerLeftLungGroup = AnnotationGroup(region, get_lung_term("lower lobe of left lung"))
lowerLeftLungNMeshGroup = lowerLeftLungGroup.getMeshGroup(mesh)
lowerLeftLungMeshGroup = lowerLeftLungGroup.getMeshGroup(mesh)
upperLeftLungGroup = AnnotationGroup(region, get_lung_term("upper lobe of left lung"))
upperLeftLungMeshGroup = upperLeftLungGroup.getMeshGroup(mesh)
annotationGroups.append(lowerLeftLungGroup)
annotationGroups.append(upperLeftLungGroup)

# Annotation fiducial point
markerGroup = findOrCreateFieldGroup(fm, "marker")
Expand All @@ -127,37 +130,44 @@ def generateBaseMesh(cls, region, options):
eftWedgeCollapseXi1_15 = eftfactory.createEftWedgeCollapseXi1Quadrant([1, 5])
eftWedgeCollapseXi1_26 = eftfactory.createEftWedgeCollapseXi1Quadrant([2, 6])
eftWedgeCollapseXi1_37 = eftfactory.createEftWedgeCollapseXi1Quadrant([3, 7])
eftWedgeCollapseXi1_48 = eftfactory.createEftWedgeCollapseXi1Quadrant([4, 8])
eftWedgeCollapseXi1_57 = eftfactory.createEftWedgeCollapseXi1Quadrant([5, 7])
eftWedgeCollapseXi2_34 = eftfactory.createEftWedgeCollapseXi2Quadrant([3, 4])
eftWedgeCollapseXi1_68 = eftfactory.createEftWedgeCollapseXi1Quadrant([6, 8])
eftWedgeCollapseXi2_56 = eftfactory.createEftWedgeCollapseXi2Quadrant([5, 6])
eftWedgeCollapseXi2_78 = eftfactory.createEftWedgeCollapseXi2Quadrant([7, 8])
eftTetCollapseXi1Xi2_71 = eftfactory.createEftTetrahedronCollapseXi1Xi2Quadrant(7, 1)
eftTetCollapseXi1Xi2_82 = eftfactory.createEftTetrahedronCollapseXi1Xi2Quadrant(8, 2)
eftTetCollapseXi1Xi2_63 = eftfactory.createEftTetrahedronCollapseXi1Xi2Quadrant(6, 3)
eftTetCollapseXi1Xi2_53 = eftfactory.createEftTetrahedronCollapseXi1Xi2Quadrant(5, 3)

if isHuman:
elementsCount1 = 2
elementsCount2 = 4
elementsCount3 = 3
lElementsCount1 = 2
lElementsCount2 = 4
lElementsCount3 = 3

uElementsCount1 = 2
uElementsCount2 = 4
uElementsCount3 = 4

# Create nodes
nodeIdentifier = 1
lNodeIds = []
uNodeIds = []
d1 = [1.0, 0.0, 0.0]
d2 = [0.0, 1.0, 0.0]
d3 = [0.0, 0.0, 1.0]

for n3 in range(elementsCount3 + 1):
# Lower lobe nodes
for n3 in range(lElementsCount3 + 1):
lNodeIds.append([])
for n2 in range(elementsCount2 + 1):
for n2 in range(lElementsCount2 + 1):
lNodeIds[n3].append([])
for n1 in range(elementsCount1 + 1):
for n1 in range(lElementsCount1 + 1):
lNodeIds[n3][n2].append(None)
if (n1 == 0 or n1 == elementsCount1) and (n2 == 0 or n2 == elementsCount2):
continue
if (0 < n3 < (elementsCount3 - 1)) and (n2 > (elementsCount2 - 2)):
continue
if (n3 < elementsCount3) and (n2 == elementsCount2):
continue
if ((n1 == 0) or (n1 == lElementsCount1)) and (n2 == 0):
continue
if (n3 > (lElementsCount3 - 2)) and (n2 > (lElementsCount2 - 2)):
continue

node = nodes.createNode(nodeIdentifier, nodetemplate)
cache.setNode(node)
Expand All @@ -169,11 +179,48 @@ def generateBaseMesh(cls, region, options):
lNodeIds[n3][n2][n1] = nodeIdentifier
nodeIdentifier += 1

# Upper lobe nodes
for n3 in range(uElementsCount3 + 1):
uNodeIds.append([])
for n2 in range(uElementsCount2 + 1):
uNodeIds[n3].append([])
for n1 in range(uElementsCount1 + 1):
uNodeIds[n3][n2].append(None)
if ((n1 == 0) or (n1 == uElementsCount1)) and ((n2 == 0) or (n2 == uElementsCount2)):
continue
if (n2 < (uElementsCount2 - 2)) and (n3 < (uElementsCount3 - 2)):
continue
if ((n2 == 0) or (n2 == uElementsCount2)) and (n3 == uElementsCount3):
continue
if ((n1 == 0) or (n1 == uElementsCount1)) and (n3 == uElementsCount3):
continue

# Oblique fissure nodes
if (n2 == (uElementsCount2 - 2)) and (n3 < (uElementsCount3 - 2)):
uNodeIds[n3][n2][n1] = lNodeIds[n3][lElementsCount2][n1]
print('uNodeIds', uNodeIds[n3][n2][n1])
continue
elif (n2 < (uElementsCount2 - 1)) and (n3 == (uElementsCount3 - 2)):
uNodeIds[n3][n2][n1] = lNodeIds[lElementsCount3][n2][n1]
print('uNodeIds', uNodeIds[n3][n2][n1])
continue

node = nodes.createNode(nodeIdentifier, nodetemplate)
cache.setNode(node)
x = [1.0 * (n1 - 1), 1.0 * (n2 - 1) + 2.5, 1.0 * n3 + 2.0]
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)
uNodeIds[n3][n2][n1] = nodeIdentifier
nodeIdentifier += 1

# Create elements
# Lower lobe elements
elementIdentifier = 1
for e3 in range(elementsCount3):
for e2 in range(elementsCount2):
for e1 in range(elementsCount1):
for e3 in range(lElementsCount3):
for e2 in range(lElementsCount2):
for e1 in range(lElementsCount1):
eft = eftRegular
nodeIdentifiers = [
lNodeIds[e3 ][e2][e1], lNodeIds[e3 ][e2][e1 + 1], lNodeIds[e3 ][e2 + 1][e1], lNodeIds[e3 ][e2 + 1][e1 + 1],
Expand All @@ -184,42 +231,131 @@ def generateBaseMesh(cls, region, options):
nodeIdentifiers.pop(4)
nodeIdentifiers.pop(0)
eft = eftWedgeCollapseXi1_15
elif (e2 == 0) and (e1 == elementsCount1-1):
elif (e2 == 0) and (e1 == (lElementsCount1 - 1)):
# Back wedge elements
nodeIdentifiers.pop(5)
nodeIdentifiers.pop(1)
eft = eftWedgeCollapseXi1_26
elif (e2 == (elementsCount2 - 2)) and (e3 == 0):
# Cubes curving over middle wedge
nodeIdentifiers[6] = lNodeIds[elementsCount3 - 1][e2 + 1][e1 ]
nodeIdentifiers[7] = lNodeIds[elementsCount3 - 1][e2 + 1][e1 + 1]
elif (e3 == 1) and (e2 == (lElementsCount2 - 2)):
# Middle wedge
nodeIdentifiers.pop(7)
nodeIdentifiers.pop(6)
eft = eftWedgeCollapseXi2_78
elif (e3 == (lElementsCount3 - 1)) and (e2 == (lElementsCount2 - 3)):
# Remapped cube element 1
eft = eftfactory.createEftBasic()
setEftScaleFactorIds(eft, [1], [])
remapEftNodeValueLabel(eft, [7, 8], Node.VALUE_LABEL_D_DS3, [(Node.VALUE_LABEL_D_DS2, [1])])
remapEftNodeValueLabel(eft, [7, 8], Node.VALUE_LABEL_D_DS2, [(Node.VALUE_LABEL_D_DS3, [])])
elif e3 == 1 and e2 == (elementsCount2 - 2):
# Middle wedge
remapEftNodeValueLabel(eft, [7, 8], Node.VALUE_LABEL_D_DS2, [(Node.VALUE_LABEL_D_DS3, [1])])
remapEftNodeValueLabel(eft, [7, 8], Node.VALUE_LABEL_D_DS3, [(Node.VALUE_LABEL_D_DS2, [])])
elif (e3 == (lElementsCount3 - 1)) and (e2 == (lElementsCount2 - 2)):
# Remapped cube element 2
nodeIdentifiers[2] = lNodeIds[e3 - 1][e2 + 1][e1 ]
nodeIdentifiers[3] = lNodeIds[e3 - 1][e2 + 1][e1 + 1]
nodeIdentifiers[6] = lNodeIds[e3 - 1][e2 + 2][e1 ]
nodeIdentifiers[7] = lNodeIds[e3 - 1][e2 + 2][e1 + 1]
eft = eftfactory.createEftBasic()
setEftScaleFactorIds(eft, [1], [])
remapEftNodeValueLabel(eft, [5, 6], Node.VALUE_LABEL_D_DS2, [(Node.VALUE_LABEL_D_DS3, [1])])
remapEftNodeValueLabel(eft, [5, 6], Node.VALUE_LABEL_D_DS3, [(Node.VALUE_LABEL_D_DS2, [])])
remapEftNodeValueLabel(eft, [3, 4, 7, 8], Node.VALUE_LABEL_D_DS2, [(Node.VALUE_LABEL_D_DS3, [1])])
remapEftNodeValueLabel(eft, [3, 4, 7, 8], Node.VALUE_LABEL_D_DS3, [(Node.VALUE_LABEL_D_DS2, [])])
elif None in nodeIdentifiers:
continue

# print('element ', elementIdentifier, '|| ', nodeIdentifiers)
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 eft.getNumberOfLocalScaleFactors() == 1:
element.setScaleFactors(eft, [-1.0])
elementIdentifier += 1
leftLungMeshGroup.addElement(element)
lungMeshGroup.addElement(element)
lowerLeftLungMeshGroup.addElement(element)

# Upper lobe elements
for e3 in range(uElementsCount3):
for e2 in range(uElementsCount2):
for e1 in range(uElementsCount1):
eft = eftRegular
nodeIdentifiers = [
uNodeIds[e3][e2][e1], uNodeIds[e3][e2][e1 + 1], uNodeIds[e3][e2 + 1][e1],
uNodeIds[e3][e2 + 1][e1 + 1],
uNodeIds[e3 + 1][e2][e1], uNodeIds[e3 + 1][e2][e1 + 1], uNodeIds[e3 + 1][e2 + 1][e1],
uNodeIds[e3 + 1][e2 + 1][e1 + 1]]

if (e3 < (uElementsCount3 - 1)) and (e2 == (uElementsCount2 - 1)) and (e1 == 0):
# Distal-front wedge elements
nodeIdentifiers.pop(6)
nodeIdentifiers.pop(2)
eft = eftWedgeCollapseXi1_37
elif (e3 < (uElementsCount3 - 1)) and (e2 == (uElementsCount2 - 1)) and (e1 == (uElementsCount1 - 1)):
# Distal-back wedge elements
nodeIdentifiers.pop(7)
nodeIdentifiers.pop(3)
eft = eftWedgeCollapseXi1_48
elif (e3 == (uElementsCount3 - 2)) and (e2 == 0) and (e1 == 0):
# Medial-front wedge elements
nodeIdentifiers.pop(4)
nodeIdentifiers.pop(0)
eft = eftWedgeCollapseXi1_15
elif (e3 == (uElementsCount3 - 2)) and (e2 == 0) and (e1 == (uElementsCount1 - 1)):
# Medial-back wedge elements
nodeIdentifiers.pop(5)
nodeIdentifiers.pop(1)
eft = eftWedgeCollapseXi1_26
elif (e3 == (uElementsCount3 - 1)) and (0 < e2 < (uElementsCount2 - 1)) and (e1 == 0):
# Top-front wedge elements
nodeIdentifiers.pop(6)
nodeIdentifiers.pop(4)
eft = eftWedgeCollapseXi1_57
elif (e3 == (uElementsCount3 - 1)) and (0 < e2 < (uElementsCount2 - 1)) and (e1 == (uElementsCount1 - 1)):
# Top-back wedge elements
nodeIdentifiers.pop(7)
nodeIdentifiers.pop(5)
eft = eftWedgeCollapseXi1_68
elif (e3 == (uElementsCount3 - 1)) and (e2 == 0) and (e1 == 0):
# Top-front-medial tetrahedron wedge elements
nodeIdentifiers.pop(6)
nodeIdentifiers.pop(5)
nodeIdentifiers.pop(4)
nodeIdentifiers.pop(0)
eft = eftTetCollapseXi1Xi2_82
elif (e3 == (uElementsCount3 - 1)) and (e2 == 0) and (e1 == (uElementsCount1 - 1)):
# Top-back-medial tetrahedron wedge elements
nodeIdentifiers.pop(7)
nodeIdentifiers.pop(5)
nodeIdentifiers.pop(4)
nodeIdentifiers.pop(1)
eft = eftTetCollapseXi1Xi2_71
elif (e3 == (uElementsCount3 - 1)) and (e2 == (uElementsCount2 - 1)) and (e1 == 0):
# Top-front-distal tetrahedron wedge elements
nodeIdentifiers.pop(7)
nodeIdentifiers.pop(6)
nodeIdentifiers.pop(4)
nodeIdentifiers.pop(2)
eft = eftWedgeCollapseXi2_34
elif (e3 == (elementsCount3 - 1)) and (e2 == (elementsCount2 - 1)):
# 7 node collapsed element at top end
nodeIdentifiers[2] = lNodeIds[0][elementsCount2 - 1][e1 ]
nodeIdentifiers[3] = lNodeIds[0][elementsCount2 - 1][e1 + 1]
eft = eftTetCollapseXi1Xi2_63
elif (e3 == (uElementsCount3 - 1)) and (e2 == (uElementsCount2 - 1)) and (e1 == (uElementsCount1 - 1)):
# Top-front-distal tetrahedron wedge elements
nodeIdentifiers.pop(7)
nodeIdentifiers.pop(6)
nodeIdentifiers.pop(5)
nodeIdentifiers.pop(3)
eft = eftTetCollapseXi1Xi2_53
elif (e3 == (uElementsCount3 - 2)) and (e2 == (uElementsCount2 - 3)):
# Remapped cube element 1
eft = eftfactory.createEftBasic()
setEftScaleFactorIds(eft, [1], [])
remapEftNodeValueLabel(eft, [3, 4], Node.VALUE_LABEL_D_DS2, [(Node.VALUE_LABEL_D_DS3, [1])])
remapEftNodeValueLabel(eft, [3, 4], Node.VALUE_LABEL_D_DS3, [(Node.VALUE_LABEL_D_DS2, [])])
remapEftNodeValueLabel(eft, [7, 8], Node.VALUE_LABEL_D_DS1, [])
if e1 == 0:
nodeIdentifiers.pop(6)
remapEftNodeValueLabel(eft, [7], Node.VALUE_LABEL_D_DS2, [(Node.VALUE_LABEL_D_DS1, [])])
remapEftNodeValueLabel(eft, [7], Node.VALUE_LABEL_D_DS3, [(Node.VALUE_LABEL_D_DS1, [])])
else:
nodeIdentifiers.pop(7)
remapEftNodeValueLabel(eft, [8], Node.VALUE_LABEL_D_DS2, [(Node.VALUE_LABEL_D_DS1, [1])])
remapEftNodeValueLabel(eft, [8], Node.VALUE_LABEL_D_DS3, [(Node.VALUE_LABEL_D_DS1, [1])])
remapEftLocalNodes(eft, 7, [1, 2, 3, 4, 5, 6, 7, 7])
remapEftNodeValueLabel(eft, [3, 4], Node.VALUE_LABEL_D_DS3, [(Node.VALUE_LABEL_D_DS2, []), (Node.VALUE_LABEL_D_DS3, [])])
elif (e3 == (uElementsCount3 - 2)) and (e2 == (uElementsCount2 - 2)):
# Remapped cube element 2
eft = eftfactory.createEftBasic()
setEftScaleFactorIds(eft, [1], [])
remapEftNodeValueLabel(eft, [1, 2], Node.VALUE_LABEL_D_DS3, [(Node.VALUE_LABEL_D_DS2, []), (Node.VALUE_LABEL_D_DS3, [])])
elif None in nodeIdentifiers:
continue

Expand All @@ -235,7 +371,7 @@ def generateBaseMesh(cls, region, options):
elementIdentifier += 1
leftLungMeshGroup.addElement(element)
lungMeshGroup.addElement(element)
lowerLeftLungNMeshGroup.addElement(element)
upperLeftLungMeshGroup.addElement(element)

elif isMouse:
elementsCount1 = 2
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