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Added four fiducial points. #125

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merged 8 commits into from
May 11, 2021
Merged

Added four fiducial points. #125

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334b3f5
Added four fiducial points.
zekh167 Mar 21, 2021
5007f71
Minor changes in annotation.
zekh167 Mar 22, 2021
0caee72
Minor changes in annotation.
zekh167 Mar 22, 2021
1fb92aa
Applied dic for markers and changed names.
zekh167 Apr 26, 2021
ed7ced7
Added marker annotations to bladder terms.
zekh167 May 11, 2021
46b2149
Added markers to their own group, the marker group and the whole blad…
zekh167 May 11, 2021
b703bc7
Merge remote-tracking branch 'abi/master' into bladder_marker
zekh167 May 11, 2021
fccc9fd
Merge remote-tracking branch 'abi/master' into bladder_marker
zekh167 May 11, 2021
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7 changes: 6 additions & 1 deletion src/scaffoldmaker/annotation/bladder_terms.py
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Original file line number Diff line number Diff line change
Expand Up @@ -36,7 +36,12 @@
("ventral part of serosa of urethra", "ILX:0739306"),
("ventral part of serosa of urinary bladder", "ILX:0739249"),
("ventral part of bladder", "None"),
("ventral part of urethra", "ILX:0739259")
("ventral part of urethra", "ILX:0739259"),
("apex of urinary bladder", "ILX:0774405"),
("left ureter junction with bladder", "None"),
("right ureter junction with bladder", "None"),
("urethra junction with bladder dorsal", "None"),
("urethra junction with bladder ventral", "None")
]

def get_bladder_term(name : str):
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4 changes: 2 additions & 2 deletions src/scaffoldmaker/meshtypes/meshtype_3d_bladder1.py
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Original file line number Diff line number Diff line change
Expand Up @@ -265,7 +265,7 @@ def generateBaseMesh(cls, region, options):
elementtemplate.defineField(coordinates, -1, eft)

neckGroup = AnnotationGroup(region, get_bladder_term("neck of urinary bladder"))
bodyGroup = AnnotationGroup(region, get_bladder_term("Dome of the Bladder"))
bodyGroup = AnnotationGroup(region, get_bladder_term("dome of the bladder"))
urinaryBladderGroup = AnnotationGroup(region, get_bladder_term("urinary bladder"))
annotationGroups = [neckGroup, bodyGroup, urinaryBladderGroup]

Expand Down Expand Up @@ -863,7 +863,7 @@ def defineFaceAnnotations(cls, region, options, annotationGroups):
# create 2d surface mesh groups
fm = region.getFieldmodule()
neckGroup = getAnnotationGroupForTerm(annotationGroups, get_bladder_term("neck of urinary bladder"))
bodyGroup = getAnnotationGroupForTerm(annotationGroups, get_bladder_term("Dome of the Bladder"))
bodyGroup = getAnnotationGroupForTerm(annotationGroups, get_bladder_term("dome of the bladder"))
urinaryBladderGroup = getAnnotationGroupForTerm(annotationGroups, get_bladder_term("urinary bladder"))
mesh2d = fm.findMeshByDimension(2)
is_exterior = fm.createFieldIsExterior()
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134 changes: 85 additions & 49 deletions src/scaffoldmaker/meshtypes/meshtype_3d_bladderurethra1.py
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Expand Up @@ -677,52 +677,53 @@ def generateBaseMesh(cls, region, options):
outerNodes_d1.append(d1List[(2 * n2 + 1) * elementsCountAround + n1])
outerNodes_d2.append(d2List[(2 * n2 + 1) * elementsCountAround + n1])

elementsCount1 = elementsCountAround // 2
elementsCount2 = elementsCountAlongBladder
# Create trackSurface at the outer layer of the bladder for ureter 1
nodesOnTrackSurface_x = []
nodesOnTrackSurface_d1 = []
nodesOnTrackSurface_d2 = []
for n2 in range(elementsCountAlongBladder + 1):
for n1 in range(elementsCountAround // 2 + 1):
nodesOnTrackSurface_x.append(outerNodes_x[n2 * elementsCountAround + n1])
nodesOnTrackSurface_d1.append(outerNodes_d1[n2 * elementsCountAround + n1])
nodesOnTrackSurface_d2.append(outerNodes_d2[n2 * elementsCountAround + n1])
trackSurfaceUreter1 = TrackSurface(elementsCount1, elementsCount2, nodesOnTrackSurface_x,
nodesOnTrackSurface_d1, nodesOnTrackSurface_d2)

ureter1Position = trackSurfaceUreter1.createPositionProportion(ureterPositionAround, ureterPositionDown)
ureterElementPositionAround = ureter1Position.e1
ureterElementPositionDown = ureter1Position.e2
elementToDeleteStartIdx1 = elementsCountThroughWall * elementsCountAround * (ureterElementPositionDown - (0 if ureter1Position.xi2 > 0.5 else 1)) \
+ ureterElementPositionAround + (1 if ureter1Position.xi1 > 0.5 else 0)

elementIndex = elementToDeleteStartIdx1 - elementsCountAround * ureterElementPositionDown

# Create trackSurface at the outer layer of the bladder for ureter 2
nodesOnTrackSurface2_x = []
nodesOnTrackSurface2_d1 = []
nodesOnTrackSurface2_d2 = []
for n2 in range(elementsCountAlongBladder + 1):
for n1 in range(elementsCountAround // 2, elementsCountAround):
nodesOnTrackSurface2_x.append(outerNodes_x[n2 * elementsCountAround + n1])
nodesOnTrackSurface2_d1.append(outerNodes_d1[n2 * elementsCountAround + n1])
nodesOnTrackSurface2_d2.append(outerNodes_d2[n2 * elementsCountAround + n1])
nodesOnTrackSurface2_x.append(outerNodes_x[n2 * elementsCountAround])
nodesOnTrackSurface2_d1.append(outerNodes_d1[n2 * elementsCountAround])
nodesOnTrackSurface2_d2.append(outerNodes_d2[n2 * elementsCountAround])

trackSurfaceUreter2 = TrackSurface(elementsCount1, elementsCount2, nodesOnTrackSurface2_x,
nodesOnTrackSurface2_d1, nodesOnTrackSurface2_d2)
ureter2Position = TrackSurfacePosition(elementsCountAround // 2 - ureterElementPositionAround + (-1 if ureter1Position.xi1 > 0 else 0),
ureterElementPositionDown,
(1 - ureter1Position.xi1) if ureter1Position.xi1 > 0 else ureter1Position.xi1,
ureter1Position.xi2)

if includeUreter:
elementsCount1 = elementsCountAround // 2
elementsCount2 = elementsCountAlongBladder
# Create trackSurface at the outer layer of the bladder for ureter 1
nodesOnTrackSurface_x = []
nodesOnTrackSurface_d1 = []
nodesOnTrackSurface_d2 = []
for n2 in range(elementsCountAlongBladder + 1):
for n1 in range(elementsCountAround // 2 + 1):
nodesOnTrackSurface_x.append(outerNodes_x[n2 * elementsCountAround + n1])
nodesOnTrackSurface_d1.append(outerNodes_d1[n2 * elementsCountAround + n1])
nodesOnTrackSurface_d2.append(outerNodes_d2[n2 * elementsCountAround + n1])
trackSurfaceUreter1 = TrackSurface(elementsCount1, elementsCount2, nodesOnTrackSurface_x,
nodesOnTrackSurface_d1, nodesOnTrackSurface_d2)

ureter1Position = trackSurfaceUreter1.createPositionProportion(ureterPositionAround, ureterPositionDown)
ureterElementPositionAround = ureter1Position.e1
ureterElementPositionDown = ureter1Position.e2
elementToDeleteStartIdx1 = elementsCountThroughWall * elementsCountAround * (ureterElementPositionDown - (0 if ureter1Position.xi2 > 0.5 else 1)) \
+ ureterElementPositionAround + (1 if ureter1Position.xi1 > 0.5 else 0)

elementIndex = elementToDeleteStartIdx1 - elementsCountAround * ureterElementPositionDown
if ureterElementPositionAround > (elementsCountAround / 4):
elementsCountVentral1 = (elementsCountAround // 4)
else:
elementsCountVentral1 = elementIndex - 1

# Create trackSurface at the outer layer of the bladder for ureter 2
nodesOnTrackSurface2_x = []
nodesOnTrackSurface2_d1 = []
nodesOnTrackSurface2_d2 = []
for n2 in range(elementsCountAlongBladder + 1):
for n1 in range(elementsCountAround // 2, elementsCountAround):
nodesOnTrackSurface2_x.append(outerNodes_x[n2 * elementsCountAround + n1])
nodesOnTrackSurface2_d1.append(outerNodes_d1[n2 * elementsCountAround + n1])
nodesOnTrackSurface2_d2.append(outerNodes_d2[n2 * elementsCountAround + n1])
nodesOnTrackSurface2_x.append(outerNodes_x[n2 * elementsCountAround])
nodesOnTrackSurface2_d1.append(outerNodes_d1[n2 * elementsCountAround])
nodesOnTrackSurface2_d2.append(outerNodes_d2[n2 * elementsCountAround])

trackSurfaceUreter2 = TrackSurface(elementsCount1, elementsCount2, nodesOnTrackSurface2_x,
nodesOnTrackSurface2_d1, nodesOnTrackSurface2_d2)
ureter2Position = TrackSurfacePosition(elementsCountAround // 2 - ureterElementPositionAround + (-1 if ureter1Position.xi1 > 0 else 0),
ureterElementPositionDown,
(1 - ureter1Position.xi1) if ureter1Position.xi1 > 0 else ureter1Position.xi1,
ureter1Position.xi2)
else:
elementsCountVentral1 = elementsCountAround // 4

Expand Down Expand Up @@ -812,14 +813,49 @@ def generateBaseMesh(cls, region, options):
d2Final, nextNodeIdentifier, nextElementIdentifier, elementsCountUreterRadial,
ureterMeshGroup, bladderMeshGroup)

# Apex annotation point
nodeIdentifier = nextNodeIdentifier
idx = 1
element1 = mesh.findElementByIdentifier(idx)
markerPoint = markerPoints.createNode(nodeIdentifier, markerTemplateInternal)
cache.setNode(markerPoint)
markerName.assignString(cache, 'Apex of urinary bladder')
markerLocation.assignMeshLocation(cache, element1, [0.0, 0.0, 1.0])
# Define markers for apex, ureter and urethra junctions with bladder
apexGroup = findOrCreateAnnotationGroupForTerm(annotationGroups, region, get_bladder_term("apex of urinary bladder"))
leftUreterGroup = findOrCreateAnnotationGroupForTerm(annotationGroups, region, get_bladder_term("left ureter junction with bladder"))
rightUreterGroup = findOrCreateAnnotationGroupForTerm(annotationGroups, region, get_bladder_term("right ureter junction with bladder"))
dorsalUrethraGroup = findOrCreateAnnotationGroupForTerm(annotationGroups, region, get_bladder_term("urethra junction with bladder dorsal"))
ventralUrethraGroup = findOrCreateAnnotationGroupForTerm(annotationGroups, region, get_bladder_term("urethra junction with bladder ventral"))

idx1 = 1
xi1 = [0.0, 0.0, 0.0]
markerList = []
markerList.append({"group": apexGroup, "elementId": idx1, "xi": xi1})
if includeUreter:
idx2 = elementsCountAlong * elementsCountAround + elementsCountAroundUreter
xi2 = [0.0, 1.0, 0.0]
markerList.append({"group": leftUreterGroup, "elementId": idx2, "xi": xi2})
idx3 = elementsCountAlong * elementsCountAround + 2 * elementsCountAroundUreter
xi3 = [0.0, 1.0, 0.0]
markerList.append({"group": rightUreterGroup, "elementId": idx3, "xi": xi3})
else:
idx2 = ureterElementPositionDown * elementsCountAround * elementsCountThroughWall + ureterElementPositionAround + 1
xi2 = [ureter1Position.xi1, ureter1Position.xi2, 0.0]
markerList.append({"group": leftUreterGroup, "elementId": idx2, "xi": xi2})
idx3 = ureterElementPositionDown * elementsCountAround * elementsCountThroughWall + elementsCountAround - ureterElementPositionAround
xi3 = [1 - ureter1Position.xi1, ureter1Position.xi2, 0.0]
markerList.append({"group": rightUreterGroup, "elementId": idx3, "xi": xi3})
idx4 = (elementsCountAlongBladder - 1) * elementsCountAround * elementsCountThroughWall + elementsCountAround // 2
xi4 = [1.0, 1.0, 0.0]
markerList.append({"group": dorsalUrethraGroup, "elementId": idx4, "xi": xi4})
idx5 = (elementsCountAlongBladder - 1) * elementsCountAround * elementsCountThroughWall + 1
xi5 = [0.0, 1.0, 0.0]
markerList.append({"group": ventralUrethraGroup, "elementId": idx5, "xi": xi5})

nodeIdentifier = nextNodeIdentifier + elementsCountAroundUreter * 4 * 2 + elementsCountAroundUreter * 2 * 2 * elementsCountUreterRadial
bladderNodesetGroup = bladderGroup.getNodesetGroup(nodes)
for marker in markerList:
annotationGroup = marker["group"]
markerPoint = markerPoints.createNode(nodeIdentifier, markerTemplateInternal)
cache.setNode(markerPoint)
markerLocation.assignMeshLocation(cache, mesh.findElementByIdentifier(marker["elementId"]), marker["xi"])
markerName.assignString(cache, annotationGroup.getName())
annotationGroup.getNodesetGroup(nodes).addNode(markerPoint)
bladderNodesetGroup.addNode(markerPoint)
nodeIdentifier += 1

fm.endChange()
return annotationGroups
Expand Down