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Multiple annotation groups #80

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merged 3 commits into from
Jul 22, 2020
Merged

Multiple annotation groups #80

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4190dcd
Allow multiple annotation groups for each element groups around, alon…
mlin865 Jul 20, 2020
e8203fa
Update unit tests due to changes in getCubicHermiteArcLength
mlin865 Jul 20, 2020
0788694
Look up groups using object instead of name
mlin865 Jul 21, 2020
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22 changes: 9 additions & 13 deletions src/scaffoldmaker/meshtypes/meshtype_3d_cecum1.py
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Original file line number Diff line number Diff line change
Expand Up @@ -368,19 +368,17 @@ def generateBaseMesh(cls, region, options):

# Create annotation
cecumGroup = AnnotationGroup(region, get_colon_term("caecum"))
annotationGroups = [cecumGroup]

annotationArrayAlong = []
annotationGroupsAlong = []
for i in range(elementsCountAlong):
annotationArrayAlong.append(['caecum'])
annotationGroupsAlong.append([cecumGroup])

annotationArrayThroughWall = []
annotationGroupsThroughWall = []
for i in range(elementsCountThroughWall):
annotationArrayThroughWall.append([''])
annotationGroupsThroughWall.append([ ])

for nSegment in range(segmentCount):
# Make regular segments
xInner, d1Inner, d2Inner, transitElementList, segmentAxis, annotationGroupsAround, annotationArrayAround \
xInner, d1Inner, d2Inner, transitElementList, segmentAxis, annotationGroupsAround \
= colonSegmentTubeMeshInnerPoints.getColonSegmentTubeMeshInnerPoints(nSegment)

# Replace first half of first segment with apex and sample along apex and second half of segment
Expand Down Expand Up @@ -428,7 +426,6 @@ def generateBaseMesh(cls, region, options):
zRefList, innerRadiusAlongCecum, closedProximalEnd)

# Create coordinates and derivatives
annotationGroups += annotationGroupsAround
wallThicknessList = [wallThickness] * (elementsCountAlong + 1)

xList, d1List, d2List, d3List, curvatureList = tubemesh.getCoordinatesFromInner(xWarpedList, d1WarpedList,
Expand Down Expand Up @@ -470,24 +467,23 @@ def generateBaseMesh(cls, region, options):
# Create nodes and elements
if tcThickness > 0:
tubeTCWidthList = colonSegmentTubeMeshInnerPoints.getTubeTCWidthList()
xCecum, d1Cecum, d2Cecum, d3Cecum, annotationGroups, annotationArrayAround = getTeniaColi(
xCecum, d1Cecum, d2Cecum, d3Cecum, annotationGroupsAround = getTeniaColi(
region, xCecum, d1Cecum, d2Cecum, d3Cecum, curvatureList, tcCount, elementsCountAroundTC,
elementsCountAroundHaustrum, elementsCountAlong, elementsCountThroughWall,
tubeTCWidthList, tcThickness, sxRefList, annotationGroups, annotationArrayAround,
closedProximalEnd)
tubeTCWidthList, tcThickness, sxRefList, annotationGroupsAround, closedProximalEnd)

nextNodeIdentifier, nextElementIdentifier, annotationGroups = createNodesAndElementsTeniaColi(
region, xCecum, d1Cecum, d2Cecum, d3Cecum, xFlat, d1Flat, d2Flat, xTexture, d1Texture, d2Texture,
elementsCountAroundTC, elementsCountAroundHaustrum, elementsCountAlong, elementsCountThroughWall,
tcCount, annotationGroups, annotationArrayAround, annotationArrayAlong, annotationArrayThroughWall,
tcCount, annotationGroupsAround, annotationGroupsAlong, annotationGroupsThroughWall,
firstNodeIdentifier, firstElementIdentifier, useCubicHermiteThroughWall, useCrossDerivatives,
closedProximalEnd)

else:
nextNodeIdentifier, nextElementIdentifier, annotationGroups = tubemesh.createNodesAndElements(
region, xCecum, d1Cecum, d2Cecum, d3Cecum, xFlat, d1Flat, d2Flat, xTexture, d1Texture, d2Texture,
elementsCountAround, elementsCountAlong, elementsCountThroughWall,
annotationGroups, annotationArrayAround, annotationArrayAlong, annotationArrayThroughWall,
annotationGroupsAround, annotationGroupsAlong, annotationGroupsThroughWall,
firstNodeIdentifier, firstElementIdentifier, useCubicHermiteThroughWall, useCrossDerivatives,
closedProximalEnd)

Expand Down
44 changes: 18 additions & 26 deletions src/scaffoldmaker/meshtypes/meshtype_3d_colon1.py
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Original file line number Diff line number Diff line change
Expand Up @@ -441,47 +441,41 @@ def generateBaseMesh(cls, region, options):
elementsAlongInDistal = elementsCountAlong - elementsAlongInProximal - elementsAlongInTransverse
elementsCountAlongGroups = [elementsAlongInProximal, elementsAlongInTransverse, elementsAlongInDistal]

annotationGroups = []
colonGroup = AnnotationGroup(region, get_colon_term("colon"))
annotationGroupsAlong = [colonGroup]

if tcCount == 1:
proximalGroup = AnnotationGroup(region, get_colon_term("proximal colon"))
transverseGroup = AnnotationGroup(region, get_colon_term("transverse colon"))
distalGroup = AnnotationGroup(region, get_colon_term("distal colon"))
annotationGroupsAlong += [proximalGroup, transverseGroup, distalGroup]
annotationGroupNamesAlong = [['colon', 'proximal colon'],
['colon', 'transverse colon'],
['colon', 'distal colon']]
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annotationGroupAlong = [[colonGroup, proximalGroup],
[colonGroup, transverseGroup],
[colonGroup, distalGroup]]

elif tcCount == 2:
spiralGroup = AnnotationGroup(region, get_colon_term("spiral colon"))
transverseGroup = AnnotationGroup(region, get_colon_term("transverse colon"))
distalGroup = AnnotationGroup(region, get_colon_term("distal colon"))
annotationGroupsAlong += [spiralGroup, transverseGroup, distalGroup]
annotationGroupNamesAlong = [['colon', 'spiral colon'],
['colon', 'transverse colon'],
['colon', 'distal colon']]
annotationGroupAlong = [[colonGroup, spiralGroup],
[colonGroup, transverseGroup],
[colonGroup, distalGroup]]

elif tcCount == 3:
ascendingGroup = AnnotationGroup(region, get_colon_term("ascending colon"))
transverseGroup = AnnotationGroup(region, get_colon_term("transverse colon"))
descendingGroup = AnnotationGroup(region, get_colon_term("descending colon"))
annotationGroupsAlong += [ascendingGroup, transverseGroup, descendingGroup]
annotationGroupNamesAlong = [['colon', 'ascending colon'],
['colon', 'transverse colon'],
['colon', 'descending colon']]
annotationGroupAlong = [[colonGroup, ascendingGroup],
[colonGroup, transverseGroup],
[colonGroup, descendingGroup]]

annotationGroups += annotationGroupsAlong
annotationArrayAlong = []
annotationGroupsAlong = []
for i in range(len(elementsCountAlongGroups)):
elementsCount = elementsCountAlongGroups[i]
for n in range(elementsCount):
annotationArrayAlong.append(annotationGroupNamesAlong[i])
annotationGroupsAlong.append(annotationGroupAlong[i])

annotationArrayThroughWall = []
annotationGroupsThroughWall = []
for i in range(elementsCountThroughWall):
annotationArrayThroughWall.append([''])
annotationGroupsThroughWall.append([ ])

xExtrude = []
d1Extrude = []
Expand All @@ -499,7 +493,7 @@ def generateBaseMesh(cls, region, options):

for nSegment in range(segmentCount):
# Create inner points
xInner, d1Inner, d2Inner, transitElementList, segmentAxis, annotationGroupsAround, annotationArrayAround\
xInner, d1Inner, d2Inner, transitElementList, segmentAxis, annotationGroupsAround \
= colonSegmentTubeMeshInnerPoints.getColonSegmentTubeMeshInnerPoints(nSegment)

# Project reference point for warping onto central path
Expand All @@ -525,8 +519,6 @@ def generateBaseMesh(cls, region, options):

contractedWallThicknessList = colonSegmentTubeMeshInnerPoints.getContractedWallThicknessList()

annotationGroups += annotationGroupsAround

# Create coordinates and derivatives
xList, d1List, d2List, d3List, curvatureList = tubemesh.getCoordinatesFromInner(xExtrude, d1Extrude,
d2Extrude, d3UnitExtrude, contractedWallThicknessList,
Expand All @@ -538,10 +530,10 @@ def generateBaseMesh(cls, region, options):

if tcThickness > 0:
tubeTCWidthList = colonSegmentTubeMeshInnerPoints.getTubeTCWidthList()
xList, d1List, d2List, d3List, annotationGroups, annotationArrayAround = getTeniaColi(
xList, d1List, d2List, d3List, annotationArrayAround = getTeniaColi(
region, xList, d1List, d2List, d3List, curvatureList, tcCount, elementsCountAroundTC,
elementsCountAroundHaustrum, elementsCountAlong, elementsCountThroughWall,
tubeTCWidthList, tcThickness, sxRefExtrudeList, annotationGroups, annotationArrayAround,
tubeTCWidthList, tcThickness, sxRefExtrudeList, annotationGroupsAround,
closedProximalEnd)

# Create flat and texture coordinates
Expand All @@ -554,7 +546,7 @@ def generateBaseMesh(cls, region, options):
nextNodeIdentifier, nextElementIdentifier, annotationGroups = createNodesAndElementsTeniaColi(
region, xList, d1List, d2List, d3List, xFlat, d1Flat, d2Flat, xTexture, d1Texture, d2Texture,
elementsCountAroundTC, elementsCountAroundHaustrum, elementsCountAlong, elementsCountThroughWall,
tcCount, annotationGroups, annotationArrayAround, annotationArrayAlong, annotationArrayThroughWall,
tcCount, annotationGroupsAround, annotationGroupsAlong, annotationGroupsThroughWall,
firstNodeIdentifier, firstElementIdentifier, useCubicHermiteThroughWall, useCrossDerivatives,
closedProximalEnd)

Expand All @@ -568,7 +560,7 @@ def generateBaseMesh(cls, region, options):
nextNodeIdentifier, nextElementIdentifier, annotationGroups = tubemesh.createNodesAndElements(
region, xList, d1List, d2List, d3List, xFlat, d1Flat, d2Flat, xTexture, d1Texture, d2Texture,
elementsCountAround, elementsCountAlong, elementsCountThroughWall,
annotationGroups, annotationArrayAround, annotationArrayAlong, annotationArrayThroughWall,
annotationGroupsAround, annotationGroupsAlong, annotationGroupsThroughWall,
firstNodeIdentifier, firstElementIdentifier, useCubicHermiteThroughWall, useCrossDerivatives,
closedProximalEnd)

Expand Down
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