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Merge pull request #55 from mlin865/pigColon
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Pig colon
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@rchristie
rchristie authored Jul 6, 2019
2 parents 212caff + 5ae192d commit 82d8e93
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Showing 2 changed files with 229 additions and 117 deletions.
66 changes: 63 additions & 3 deletions scaffoldmaker/meshtypes/meshtype_3d_colon1.py
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Original file line number Diff line number Diff line change
Expand Up @@ -80,6 +80,59 @@ class MeshType_3d_colon1(Scaffold_base):
[ [ 0.1, -1.0, -0.7 ], [ -0.3, -0.7, 0.4 ], [ 0.0, 0.0, 0.5 ], [ 0.0, 0.0, 0.05 ] ],
[ [ -0.4, -2.3, -0.1 ], [ -0.4, -0.6, 0.3 ], [ 0.0, 0.0, 0.5 ], [ 0.0, 0.0, 0.05 ] ] ] )
} ),
'Pig 1' : ScaffoldPackage(MeshType_1d_path1, {
'scaffoldSettings' : {
'Coordinate dimensions' : 3,
'Length' : 1.0,
'Number of elements' : 43
},
'meshEdits' : zinc_utils.exnodeStringFromNodeValues(
[ Node.VALUE_LABEL_VALUE, Node.VALUE_LABEL_D_DS1, Node.VALUE_LABEL_D_DS2, Node.VALUE_LABEL_D2_DS1DS2 ], [
[ [ 8.1, 2.4, 5.1 ], [ -1.5, 0.6, -3.4 ], [ 0.0, 0.0, 0.5 ], [ 0.0, 0.0, 0.05 ] ],
[ [ 6.2, 3.0, 1.8 ], [ -3.0, 0.6, -2.3 ], [ 0.0, 0.0, 0.5 ], [ 0.0, 0.0, 0.05 ] ],
[ [ 2.2, 3.6, 0.5 ], [ -5.5, 1.0, -0.6 ], [ 0.0, 0.0, 0.5 ], [ 0.0, 0.0, 0.05 ] ],
[ [ -2.0, 3.5, 0.8 ], [ -3.6, -2.1, 0.4 ], [ 0.0, 0.0, 0.5 ], [ 0.0, 0.0, 0.05 ] ],
[ [ -4.0, 0.0, 1.3 ], [ 0.0, -4.2, 0.4 ], [ 0.0, 0.0, 0.5 ], [ 0.0, 0.0, 0.05 ] ],
[ [ -2.0, -3.5, 1.7 ], [ 3.6, -2.1, 0.4 ], [ 0.0, 0.0, 0.5 ], [ 0.0, 0.0, 0.05 ] ],
[ [ 2.0, -3.5, 2.1 ], [ 3.6, 2.1, 0.4 ], [ 0.0, 0.0, 0.5 ], [ 0.0, 0.0, 0.05 ] ],
[ [ 4.0, 0.0, 2.5 ], [ 0.0, 4.2, 0.4 ], [ 0.0, 0.0, 0.5 ], [ 0.0, 0.0, 0.05 ] ],
[ [ 2.3, 3.9, 3.1 ], [ -4.1, 2.4, 0.4 ], [ 0.0, 0.0, 0.5 ], [ 0.0, 0.0, 0.05 ] ],
[ [ -2.2, 3.9, 3.5 ], [ -4.1, -2.4, 0.4 ], [ 0.0, 0.0, 0.5 ], [ 0.0, 0.0, 0.05 ] ],
[ [ -4.5, 0.0, 3.9 ], [ 0.0, -4.7, 0.4 ], [ 0.0, 0.0, 0.5 ], [ 0.0, 0.0, 0.05 ] ],
[ [ -2.2, -3.9, 4.4 ], [ 4.1, -2.4, 0.4 ], [ 0.0, 0.0, 0.5 ], [ 0.0, 0.0, 0.05 ] ],
[ [ 2.3, -3.9, 4.8 ], [ 4.1, 2.4, 0.4 ], [ 0.0, 0.0, 0.5 ], [ 0.0, 0.0, 0.05 ] ],
[ [ 4.5, 0.0, 5.1 ], [ 0.3, 3.6, 0.6 ], [ 0.0, 0.0, 0.5 ], [ 0.0, 0.0, 0.05 ] ],
[ [ 2.8, 4.8, 5.5 ], [ -5.1, 2.8, 0.4 ], [ 0.0, 0.0, 0.5 ], [ 0.0, 0.0, 0.05 ] ],
[ [ -2.7, 4.8, 6.5 ], [ -5.0, -2.9, 0.4 ], [ 0.0, 0.0, 0.5 ], [ 0.0, 0.0, 0.05 ] ],
[ [ -5.5, 0.0, 6.3 ], [ 0.0, -5.8, 0.4 ], [ 0.0, 0.0, 0.5 ], [ 0.0, 0.0, 0.05 ] ],
[ [ -2.8, -4.8, 6.7 ], [ 5.0, -2.9, 0.4 ], [ 0.0, 0.0, 0.5 ], [ 0.0, 0.0, 0.05 ] ],
[ [ 2.7, -4.8, 7.1 ], [ 5.0, 2.9, 0.4 ], [ 0.0, 0.0, 0.5 ], [ 0.0, 0.0, 0.05 ] ],
[ [ 5.5, 0.0, 7.5 ], [ 0.0, 5.8, 0.4 ], [ 0.0, 0.0, 0.5 ], [ 0.0, 0.0, 0.05 ] ],
[ [ 3.0, 4.2, 8.2 ], [ -2.5, 1.4, 0.6 ], [ 0.0, 0.0, 0.5 ], [ 0.0, 0.0, 0.05 ] ],
[ [ -1.3, 4.9, 8.8 ], [ -5.0, -1.3, 0.0 ], [ 0.0, 0.0, 0.5 ], [ 0.0, 0.0, 0.05 ] ],
[ [ -4.7, 1.5, 8.8 ], [ -1.4, -5.1, 0.4 ], [ 0.0, 0.0, 0.5 ], [ 0.0, 0.0, 0.05 ] ],
[ [ -3.9, -2.5, 9.5 ], [ 4.4, -0.8, 0.8 ], [ 0.0, 0.0, 0.5 ], [ 0.0, 0.0, 0.05 ] ],
[ [ -1.8, 0.3, 10.0 ], [ 0.0, 3.6, 0.9 ], [ 0.0, 0.0, 0.5 ], [ 0.0, 0.0, 0.05 ] ],
[ [ -0.4, 3.4, 10.5 ], [ 4.1, 2.7, 0.4 ], [ 0.0, 0.0, 0.5 ], [ 0.0, 0.0, 0.05 ] ],
[ [ 3.1, 3.0, 10.3 ], [ 2.2, -1.4, -0.2 ], [ 0.0, 0.0, 0.5 ], [ 0.0, 0.0, 0.05 ] ],
[ [ 4.4, -0.1, 9.6 ], [ -0.6, -4.6, -1.0 ], [ 0.0, 0.0, 0.5 ], [ 0.0, 0.0, 0.05 ] ],
[ [ 2.0, -3.1, 8.5 ], [ -2.7, -1.4, -0.6 ], [ 0.0, 0.0, 0.5 ], [ 0.0, 0.0, 0.05 ] ],
[ [ -1.6, -3.6, 7.6 ], [ -2.8, 1.5, -0.6 ], [ 0.0, 0.0, 0.5 ], [ 0.0, 0.0, 0.05 ] ],
[ [ -3.9, -0.5, 7.0 ], [ -0.2, 3.5, -0.2 ], [ 0.0, 0.0, 0.5 ], [ 0.0, 0.0, 0.05 ] ],
[ [ -2.5, 2.6, 7.0 ], [ 1.8, 1.7, -0.2 ], [ 0.0, 0.0, 0.5 ], [ 0.0, 0.0, 0.05 ] ],
[ [ 1.4, 3.8, 6.8 ], [ 5.3, -1.9, -0.8 ], [ 0.0, 0.0, 0.5 ], [ 0.0, 0.0, 0.05 ] ],
[ [ 3.6, 1.1, 6.5 ], [ 0.2, -2.4, -0.3 ], [ 0.0, 0.0, 0.5 ], [ 0.0, 0.0, 0.05 ] ],
[ [ 1.9, -2.8, 6.2 ], [ -4.1, -3.7, -0.8 ], [ 0.0, 0.0, 0.5 ], [ 0.0, 0.0, 0.05 ] ],
[ [ -1.7, -3.5, 5.7 ], [ -2.0, 1.0, -0.4 ], [ 0.0, 0.0, 0.5 ], [ 0.0, 0.0, 0.05 ] ],
[ [ -3.7, -0.2, 5.1 ], [ 0.2, 4.4, -0.8 ], [ 0.0, 0.0, 0.5 ], [ 0.0, 0.0, 0.05 ] ],
[ [ -1.9, 3.2, 4.6 ], [ 2.3, 1.1, -0.6 ], [ 0.0, 0.0, 0.5 ], [ 0.0, 0.0, 0.05 ] ],
[ [ 1.3, 3.6, 4.4 ], [ 3.7, -1.5, -0.3 ], [ 0.0, 0.0, 0.5 ], [ 0.0, 0.0, 0.05 ] ],
[ [ 3.3, 0.9, 4.0 ], [ -0.4, -2.4, -0.3 ], [ 0.0, 0.0, 0.5 ], [ 0.0, 0.0, 0.05 ] ],
[ [ 2.0, -1.9, 3.6 ], [ -2.7, -1.5, -0.2 ], [ 0.0, 0.0, 0.5 ], [ 0.0, 0.0, 0.05 ] ],
[ [ -1.2, -2.7, 3.1 ], [ -3.0, 0.8, -0.4 ], [ 0.0, 0.0, 0.5 ], [ 0.0, 0.0, 0.05 ] ],
[ [ -1.9, 1.5, 2.2 ], [ 5.5, 4.5, -1.9 ], [ 0.0, 0.0, 0.5 ], [ 0.0, 0.0, 0.05 ] ],
[ [ 14.3, -5.9, -3.0 ], [ 5.2, -4.1, -0.3 ], [ 0.0, 0.0, 0.5 ], [ 0.0, 0.0, 0.05 ] ] ] )
} ),
'Test Line' : ScaffoldPackage(MeshType_1d_path1, {
'scaffoldSettings' : {
'Coordinate dimensions' : 3,
Expand All @@ -103,18 +156,23 @@ def getParameterSetNames():
'Default',
'Human 1',
'Human 2',
'Mouse 1']
'Mouse 1',
'Pig 1']

@classmethod
def getDefaultOptions(cls, parameterSetName='Default'):
if 'Human 2' in parameterSetName:
centralPathOption = cls.centralPathDefaultScaffoldPackages['Human 2']
elif 'Mouse' in parameterSetName:
centralPathOption = cls.centralPathDefaultScaffoldPackages['Mouse 1']
elif 'Pig' in parameterSetName:
centralPathOption = cls.centralPathDefaultScaffoldPackages['Pig 1']
else:
centralPathOption = cls.centralPathDefaultScaffoldPackages['Human 1']
if 'Mouse' in parameterSetName:
segmentProfileOption = ScaffoldPackage(MeshType_3d_colonsegmentsimplemesentery1, defaultParameterSetName = 'Mouse 1')
elif 'Pig' in parameterSetName:
segmentProfileOption = ScaffoldPackage(MeshType_3d_colonsegmentteniacoli1, defaultParameterSetName = 'Pig 1')
else:
segmentProfileOption = ScaffoldPackage(MeshType_3d_colonsegmentteniacoli1, defaultParameterSetName = 'Human 1')
options = {
Expand All @@ -126,6 +184,8 @@ def getDefaultOptions(cls, parameterSetName='Default'):
'Refine number of elements along' : 1,
'Refine number of elements through wall' : 1
}
if 'Pig' in parameterSetName:
options['Number of segments'] = 120
return options

@staticmethod
Expand Down Expand Up @@ -211,14 +271,14 @@ def generateBaseMesh(region, options):
else: # segmentScaffoldType == MeshType_3d_colonsegmentteniacoli1:
elementsCountAroundTC = segmentSettings['Number of elements around tenia coli']
elementsCountAroundHaustrum = segmentSettings['Number of elements around haustrum']
elementsCountAround = (elementsCountAroundTC + elementsCountAroundHaustrum)*3
cornerInnerRadiusFactor = segmentSettings['Corner inner radius factor']
haustrumInnerRadiusFactor = segmentSettings['Haustrum inner radius factor']
segmentLengthEndDerivativeFactor = segmentSettings['Segment length end derivative factor']
segmentLengthMidDerivativeFactor = segmentSettings['Segment length mid derivative factor']
tcCount = segmentSettings['Number of tenia coli']
tcWidth = segmentSettings['Tenia coli width']
tcThickness = segmentSettings['Tenia coli thickness']
elementsCountAround = (elementsCountAroundTC + elementsCountAroundHaustrum)*tcCount

elementsCountAlongSegment = segmentSettings['Number of elements along segment']
elementsCountThroughWall = segmentSettings['Number of elements through wall']
Expand Down Expand Up @@ -263,7 +323,7 @@ def generateBaseMesh(region, options):
annotationGroupsTC, nextNodeIdentifier, nextElementIdentifier = getTeniaColi(region, nextNodeIdentifier, nextElementIdentifier,
useCrossDerivatives, useCubicHermiteThroughWall, xList, d1List, d2List, d3List, elementsCountAroundTC, elementsCountAroundHaustrum,
elementsCountAlong, elementsCountThroughWall, wallThickness, tcWidth, tcThickness, sx, curvatureAlong, factorList, uList,
arcLengthOuterMidLength, length)
arcLengthOuterMidLength, length, tcCount)

annotationGroups += annotationGroupsTC

Expand Down
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