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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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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()
Expand Down
139 changes: 97 additions & 42 deletions src/scaffoldmaker/meshtypes/meshtype_3d_bladderurethra1.py
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Original file line number Diff line number Diff line change
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 @@ -813,14 +814,68 @@ def generateBaseMesh(cls, region, options):
ureterMeshGroup, bladderMeshGroup)

# Apex annotation point
nodeIdentifier = nextNodeIdentifier
nodeIdentifier = nextNodeIdentifier + elementsCountAroundUreter * 4 * 2 + elementsCountAroundUreter * 2 * 2 * elementsCountUreterRadial
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])

# Markers for ureters
if includeUreter:
# Left ureter
nodeIdentifier += 1
idx1 = elementsCountAlong * elementsCountAround + elementsCountAroundUreter
element1 = mesh.findElementByIdentifier(idx1)
markerUreter1Point = markerPoints.createNode(nodeIdentifier, markerTemplateInternal)
cache.setNode(markerUreter1Point)
markerName.assignString(cache, 'ureter junction of bladder trigone')
markerLocation.assignMeshLocation(cache, element1, [0.0, 1.0, 1.0])
# Right ureter
nodeIdentifier += 1
idx2 = elementsCountAlong * elementsCountAround + 2 * elementsCountAroundUreter
element2 = mesh.findElementByIdentifier(idx2)
markerUreter2Point = markerPoints.createNode(nodeIdentifier, markerTemplateInternal)
cache.setNode(markerUreter2Point)
markerName.assignString(cache, 'ureter junction of bladder trigone')
markerLocation.assignMeshLocation(cache, element2, [0.0, 1.0, 1.0])
else:
# Left ureter
nodeIdentifier += 1
idx1 = ureterElementPositionDown * elementsCountAround + ureterElementPositionAround + 1
element1 = mesh.findElementByIdentifier(idx1)
markerUreter1Point = markerPoints.createNode(nodeIdentifier, markerTemplateInternal)
cache.setNode(markerUreter1Point)
markerName.assignString(cache, 'ureter junction of bladder trigone')
markerLocation.assignMeshLocation(cache, element1, [ureter1Position.xi1, ureter1Position.xi2, 1.0])
# Right ureter
nodeIdentifier += 1
idx2 = ureterElementPositionDown * elementsCountAround + elementsCountAround - ureterElementPositionAround
element2 = mesh.findElementByIdentifier(idx2)
markerUreter2Point = markerPoints.createNode(nodeIdentifier, markerTemplateInternal)
cache.setNode(markerUreter2Point)
markerName.assignString(cache, 'ureter junction of bladder trigone')
markerLocation.assignMeshLocation(cache, element2, [1-ureter1Position.xi1, ureter1Position.xi2, 1.0])
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I don't like having 4 sets of code to make equivalent points. Prone to maintenance problems.
Can you propose a way to store the points in a structure, e.g. a dict { "name" : "ureter...", "element_id" : idx1, "xi" : [ x, y, z ] }. Then make the 2 points in common code below. I like to see minimum code in special case clauses.
Need to qualify names with left/right.
Do you mean 'ureter junction with bladder trigone'? Is it necessary to specify trigone?


# Markers for urethra
# Dorsal
nodeIdentifier += 1
idx1 = (elementsCountAlongBladder - 1) * elementsCountAround + elementsCountAround // 2
element1 = mesh.findElementByIdentifier(idx1)
markerUreter1Point = markerPoints.createNode(nodeIdentifier, markerTemplateInternal)
cache.setNode(markerUreter1Point)
markerName.assignString(cache, 'urethra junction with bladder dorsal')
markerLocation.assignMeshLocation(cache, element1, [1.0, 1.0, 1.0])
# Ventral
nodeIdentifier += 1
idx1 = (elementsCountAlongBladder - 1) * elementsCountAround + 1
element1 = mesh.findElementByIdentifier(idx1)
markerUreter1Point = markerPoints.createNode(nodeIdentifier, markerTemplateInternal)
cache.setNode(markerUreter1Point)
markerName.assignString(cache, 'urethra junction with bladder ventral')
markerLocation.assignMeshLocation(cache, element1, [0.0, 1.0, 1.0])

fm.endChange()
return annotationGroups

Expand Down