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Bladder updated #108

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merged 11 commits into from
Dec 10, 2020
Merged

Bladder updated #108

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fd7ae77
Added new terms for bladder.
zekh167 Nov 29, 2020
637d02b
Added bladder lumen and serosa annotations.
zekh167 Nov 29, 2020
20d0ed0
Merge remote-tracking branch 'abi/master' into bladder_updated
zekh167 Nov 29, 2020
c5f7137
Moved urethra's UBERON ID.
zekh167 Nov 29, 2020
7b77eb1
Capitalized U in urinary.
zekh167 Nov 29, 2020
bd93bdb
Added ureter to the bladder terms.
zekh167 Dec 6, 2020
38dd0d4
Separated ostium and vessel mesh groups.
zekh167 Dec 7, 2020
6ffd585
Changed function name and added ureter mesh group.
zekh167 Dec 7, 2020
1087a65
Merge remote-tracking branch 'abi/master' into bladder_updated
zekh167 Dec 10, 2020
c90777d
Changed rowMeshGroup to the previous version.
zekh167 Dec 10, 2020
6b9e570
Changed some parameters of the ostiums for cat and rat.
zekh167 Dec 10, 2020
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11 changes: 7 additions & 4 deletions src/scaffoldmaker/annotation/bladder_terms.py
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Original file line number Diff line number Diff line change
Expand Up @@ -4,16 +4,19 @@

# convention: preferred name, preferred id, followed by any other ids and alternative names
bladder_terms = [
("urinary bladder", "FMA:15900", "UBERON:0001255"),
("neck of urinary bladder", "FMA:15912", "UBERON:0001258"),
("urinary bladder", "UBERON:0001255", "FMA:15900"),
("neck of urinary bladder", "UBERON:0001258", "FMA:15912"),
("Dome of the Bladder", "ILX:0738433"),
("serosa of urinary bladder", "UBERON:0001260"),
("bladder lumen", "UBERON:0009958"),
("serosa of body of urinary bladder", "ILX:0739276"),
("lumen of body of urinary bladder", "ILX:0739252"),
("serosa of neck of urinary bladder", "ILX:0739277"),
("lumen of neck of urinary bladder", "ILX:0739256"),
("urethra", "ILX:0733022"),
("urethra", "UBERON:0000057", "ILX:0733022"),
("lumen of urethra", "ILX:0736762"),
("serosa of urethra", "ILX:0739282")
("serosa of urethra", "ILX:0739282"),
("ureter", "UBERON:0000056", "ILX:0728080")
]

def get_bladder_term(name : str):
Expand Down
44 changes: 30 additions & 14 deletions src/scaffoldmaker/meshtypes/meshtype_3d_bladderurethra1.py
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Original file line number Diff line number Diff line change
Expand Up @@ -107,13 +107,14 @@ class MeshType_3d_bladderurethra1(Scaffold_base):
'scaffoldSettings': {
'Number of vessels': 1,
'Number of elements around ostium': 8, # implemented for 8
'Number of elements along': 2,
'Number of elements along': 1,
'Unit scale': 1.0,
'Outlet': False,
'Ostium diameter': 2.0,
'Ostium length': 1.0,
'Ostium diameter': 2.2,
'Ostium length': 0.5,
'Ostium wall thickness': 0.5,
'Use linear through ostium wall': True,
'Vessel end length factor': 2.0,
'Vessel inner diameter': 0.8,
'Vessel wall thickness': 0.25,
'Vessel angle 1 degrees': 0.0,
Expand All @@ -136,10 +137,11 @@ class MeshType_3d_bladderurethra1(Scaffold_base):
'Unit scale': 1.0,
'Outlet': False,
'Ostium diameter': 1.0,
'Ostium length': 0.5,
'Ostium length': 0.25,
'Ostium wall thickness': 0.02,
'Use linear through ostium wall': True,
'Vessel inner diameter': 0.4,
'Vessel end length factor': 2.0,
'Vessel inner diameter': 0.3,
'Vessel wall thickness': 0.1,
'Vessel angle 1 degrees': 0.0,
'Vessel angle 1 spread degrees': 0.0,
Expand Down Expand Up @@ -654,6 +656,7 @@ def generateBaseMesh(cls, region, options):
neckGroup = AnnotationGroup(region, get_bladder_term("neck of urinary bladder"))
bladderGroup = AnnotationGroup(region, get_bladder_term("urinary bladder"))
urethraGroup = AnnotationGroup(region, get_bladder_term("urethra"))
ureterGroup = AnnotationGroup(region, get_bladder_term("ureter"))
if includeUrethra:
elementsCountAlongGroups = [elementsCountAlongBody, elementsCountAlongNeck, elementsCountAlongUrethra]
annotationGroupAlong = [[bladderGroup, bodyGroup], [bladderGroup, neckGroup], [urethraGroup]]
Expand All @@ -679,6 +682,7 @@ def generateBaseMesh(cls, region, options):
bodyMeshGroup = bodyGroup.getMeshGroup(mesh)
urinaryBladderMeshGroup = bladderGroup.getMeshGroup(mesh)
urethraMeshGroup = urethraGroup. getMeshGroup(mesh)
ureterMeshGroup = ureterGroup. getMeshGroup(mesh)

# Create nodes and elements
nextNodeIdentifier, nextElementIdentifier, annotationGroups = tubemesh.createNodesAndElements(
Expand All @@ -688,6 +692,8 @@ def generateBaseMesh(cls, region, options):
firstNodeIdentifier, firstElementIdentifier,
useCubicHermiteThroughWall, useCrossDerivatives, closedProximalEnd=True)

annotationGroups.append(ureterGroup)

# Define outer layer of the bladder to create the trackSurface on it
outerNodes_x = []
outerNodes_d1 = []
Expand Down Expand Up @@ -736,12 +742,12 @@ def generateBaseMesh(cls, region, options):
ureterElementPositionDown,
(1 - ureter1Position.xi1) if ureter1Position.xi1 > 0 else ureter1Position.xi1,
ureter1Position.xi2)
annulusMeshGroups = [neckMeshGroup, urinaryBladderMeshGroup]
generateUreters(region, nodes, mesh, ureterDefaultOptions, elementsCountAround, elementsCountThroughWall,
bladderMeshGroup = [neckMeshGroup, urinaryBladderMeshGroup]
generateUreterInlets(region, nodes, mesh, ureterDefaultOptions, elementsCountAround, elementsCountThroughWall,
elementsCountAroundUreter, trackSurfaceUreter1, ureter1Position, trackSurfaceUreter2,
ureter2Position, ureterElementPositionDown, ureterElementPositionAround, xFinal, d1Final,
d2Final, nextNodeIdentifier, nextElementIdentifier, elementsCountUreterRadial,
annulusMeshGroups)
ureterMeshGroup, bladderMeshGroup)

fm.endChange()
return annotationGroups
Expand Down Expand Up @@ -791,6 +797,10 @@ def defineFaceAnnotations(cls, region, options, annotationGroups):
is_neck_serosa = fm.createFieldAnd(is_neck, is_exterior_face_xi3_1)
is_neck_lumen = fm.createFieldAnd(is_neck, is_exterior_face_xi3_0)

is_urinaryBladder = urinaryBladderGroup.getFieldElementGroup(mesh2d)
is_urinaryBladder_serosa = fm.createFieldAnd(is_urinaryBladder, is_exterior_face_xi3_1)
is_urinaryBladder_lumen = fm.createFieldAnd(is_urinaryBladder, is_exterior_face_xi3_0)

serosaOfBody = findOrCreateAnnotationGroupForTerm(annotationGroups, region, get_bladder_term("serosa of body of urinary bladder"))
serosaOfBody.getMeshGroup(mesh2d).addElementsConditional(is_body_serosa)
lumenOfBody = findOrCreateAnnotationGroupForTerm(annotationGroups, region, get_bladder_term("lumen of body of urinary bladder"))
Expand All @@ -801,6 +811,11 @@ def defineFaceAnnotations(cls, region, options, annotationGroups):
lumenOfNeck = findOrCreateAnnotationGroupForTerm(annotationGroups, region, get_bladder_term("lumen of neck of urinary bladder"))
lumenOfNeck.getMeshGroup(mesh2d).addElementsConditional(is_neck_lumen)

serosaOfUrinaryBladder = findOrCreateAnnotationGroupForTerm(annotationGroups, region, get_bladder_term("serosa of urinary bladder"))
serosaOfUrinaryBladder.getMeshGroup(mesh2d).addElementsConditional(is_urinaryBladder_serosa)
lumenOfUrinaryBladder = findOrCreateAnnotationGroupForTerm(annotationGroups, region, get_bladder_term("bladder lumen"))
lumenOfUrinaryBladder.getMeshGroup(mesh2d).addElementsConditional(is_urinaryBladder_lumen)

if options['Include urethra'] == True:
urethraGroup = getAnnotationGroupForTerm(annotationGroups, get_bladder_term("urethra"))

Expand All @@ -813,11 +828,11 @@ def defineFaceAnnotations(cls, region, options, annotationGroups):
lumenOfUrethra = findOrCreateAnnotationGroupForTerm(annotationGroups, region, get_bladder_term("lumen of urethra"))
lumenOfUrethra.getMeshGroup(mesh2d).addElementsConditional(is_urethra_lumen)

def generateUreters(region, nodes, mesh, ureterDefaultOptions,elementsCountAround, elementsCountThroughWall,
def generateUreterInlets(region, nodes, mesh, ureterDefaultOptions,elementsCountAround, elementsCountThroughWall,
elementsCountAroundUreter, trackSurfaceUreter1, ureter1Position, trackSurfaceUreter2,
ureter2Position, ureterElementPositionDown, ureterElementPositionAround,
xBladder, d1Bladder, d2Bladder, nextNodeIdentifier, nextElementIdentifier,
elementsCountUreterRadial, annulusMeshGroups = []):
elementsCountUreterRadial, ureterMeshGroup, bladderMeshGroup):

# Create ureters on the surface
# Ureter 1
Expand All @@ -833,7 +848,7 @@ def generateUreters(region, nodes, mesh, ureterDefaultOptions,elementsCountAroun
nodeIdentifier, elementIdentifier, (o1_x, o1_d1, o1_d2, _, o1_NodeId, o1_Positions) = \
generateOstiumMesh(region, ureterDefaultOptions, trackSurfaceUreter1, ureter1Position, ureter1Direction,
startNodeIdentifier=nextNodeIdentifier, startElementIdentifier=nextElementIdentifier,
ostiumMeshGroups=None)
vesselMeshGroups=[[ureterMeshGroup]], ostiumMeshGroups=bladderMeshGroup)

# Ureter 2
centerUreter2_x, centerUreter2_d1, centerUreter2_d2 = trackSurfaceUreter2.evaluateCoordinates(ureter2Position,
Expand All @@ -848,7 +863,8 @@ def generateUreters(region, nodes, mesh, ureterDefaultOptions,elementsCountAroun
ureter2Direction = vector.crossproduct3(ad3, v2)
nodeIdentifier, elementIdentifier, (o2_x, o2_d1, o2_d2, _, o2_NodeId, o2_Positions) = \
generateOstiumMesh(region, ureterDefaultOptions, trackSurfaceUreter2, ureter2Position, ureter2Direction,
startNodeIdentifier=nodeIdentifier, startElementIdentifier=elementIdentifier)
startNodeIdentifier=nodeIdentifier, startElementIdentifier=elementIdentifier,
vesselMeshGroups=[[ureterMeshGroup]], ostiumMeshGroups=bladderMeshGroup)

# Create annulus mesh around ureters
endPoints1_x = [[None] * elementsCountAroundUreter, [None] * elementsCountAroundUreter]
Expand Down Expand Up @@ -965,15 +981,15 @@ def generateUreters(region, nodes, mesh, ureterDefaultOptions,elementsCountAroun
nodes, mesh, nodeIdentifier, elementIdentifier,
o1_x, o1_d1, o1_d2, None, o1_NodeId, None,
endPoints1_x, endPoints1_d1, endPoints1_d2, None, endNode1_Id, endDerivativesMap,
elementsCountRadial=elementsCountUreterRadial, meshGroups=annulusMeshGroups,
elementsCountRadial=elementsCountUreterRadial, meshGroups=bladderMeshGroup,
tracksurface=trackSurfaceUreter1, startProportions=startProportions1, endProportions=endProportions1,
rescaleEndDerivatives=True)

nodeIdentifier, elementIdentifier = createAnnulusMesh3d(
nodes, mesh, nodeIdentifier, elementIdentifier,
o2_x, o2_d1, o2_d2, None, o2_NodeId, None,
endPoints2_x, endPoints2_d1, endPoints2_d2, None, endNode2_Id, endDerivativesMap,
elementsCountRadial=elementsCountUreterRadial, meshGroups=annulusMeshGroups,
elementsCountRadial=elementsCountUreterRadial, meshGroups=bladderMeshGroup,
tracksurface=trackSurfaceUreter2, startProportions=startProportions2, endProportions=endProportions2,
rescaleEndDerivatives=True)

Expand Down