Skip to content

Commit

Permalink
Merge pull request #108 from zekh167/bladder_updated
Browse files Browse the repository at this point in the history 
Bladder updated
  • Loading branch information
@rchristie
rchristie authored Dec 10, 2020
2 parents 618e7cd + 6b9e570 commit eef39f8
Show file tree
Hide file tree
Showing 2 changed files with 37 additions and 18 deletions.
11 changes: 7 additions & 4 deletions src/scaffoldmaker/annotation/bladder_terms.py
View file
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
View file
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

0 comments on commit eef39f8

Please sign in to comment.