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Update the brainstem branch due to previous mapclient update #176

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Feb 8, 2022
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Update the brainstem branch due to previous mapclient update #176

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103 changes: 102 additions & 1 deletion src/scaffoldmaker/meshtypes/meshtype_3d_brainstem.py
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Original file line number Diff line number Diff line change
Expand Up @@ -247,6 +247,97 @@ class MeshType_3d_brainstem1(Scaffold_base):
'name': get_brainstem_term('midbrain')[0],
'ontId': get_brainstem_term('midbrain')[1]
}]
}),
'Pig 1': ScaffoldPackage(MeshType_1d_path1, {
'scaffoldSettings': {
'Coordinate dimensions': 3,
'D2 derivatives': True,
'D3 derivatives': True,
'Length': 1.0,
'Number of elements': 6
},
'meshEdits': exnodeStringFromNodeValues( # dimensional.
[Node.VALUE_LABEL_VALUE, Node.VALUE_LABEL_D_DS1, Node.VALUE_LABEL_D_DS2, Node.VALUE_LABEL_D2_DS1DS2,
Node.VALUE_LABEL_D_DS3, Node.VALUE_LABEL_D2_DS1DS3], [
([[0.0, 25.6, -29.3], [0.0, -5.4, 3.5], [4.8, 0.0, 0.0], [-0.7, 0.0, 0.0], [0.0, 1.8, 2.9],
[0.0, 1.1, 1.4]]),
([[0.0, 19.5, -25.3], [0.0, -6.7, 4.8], [5.7, 0.0, 0.0], [2.5, 0.0, 0.0], [0.0, 2.8, 4.0],
[0.0, 0.8, 0.7]]),
([[0.0, 12.2, -19.9], [0.0, -6.7, 5.4], [10.1, 0.0, 0.0], [3.0, 0.0, 0.0], [0.0, 3.3, 4.2],
[0.0, 1.5, 0.5]]),
([[0.0, 6.0, -14.5], [0.0, -5.5, 6.3], [12.9, -0.2, -0.2], [0.7, 0.0, 0.0], [0.1, 5.7, 4.9],
[0.0, 2.0, -0.6]]),
([[0.0, 1.5, -7.4], [0.0, -2.8, 7.0], [11.4, 0.0, 0.0], [-0.3, 0.2, 0.0], [0.0, 7.4, 3.0],
[-0.2, 2.4, -1.2]]),
([[0.0, 0.1, -1.0], [0.0, -1.5, 6.9], [11.2, 0.3, 0.1], [-0.5, 0.1, 0.1], [-0.3, 11.3, 2.5],
[-0.1, 1.5, -0.2]]),
([[0.0, -1.5, 6.6], [0.0, -2.0, 7.4], [10.3, 0.2, 0.0], [-1.3, -0.2, -0.0], [-0.2, 9.4, 2.5],
[0.2, -2.3, 0.9]])
]),
'userAnnotationGroups': [
{
'_AnnotationGroup': True,
'dimension': 1,
'identifierRanges': '1-2',
'name': get_brainstem_term('medulla oblongata')[0],
'ontId': get_brainstem_term('medulla oblongata')[1]
},
{
'_AnnotationGroup': True,
'dimension': 1,
'identifierRanges': '3-4',
'name': get_brainstem_term('pons')[0],
'ontId': get_brainstem_term('pons')[1]
},
{
'_AnnotationGroup': True,
'dimension': 1,
'identifierRanges': '5-6',
'name': get_brainstem_term('midbrain')[0],
'ontId': get_brainstem_term('midbrain')[1]
}]
}),
'Sheep 1': ScaffoldPackage(MeshType_1d_path1, {
'scaffoldSettings': {
'Coordinate dimensions': 3,
'D2 derivatives': True,
'D3 derivatives': True,
'Length': 1.0,
'Number of elements': 6
},
'meshEdits': exnodeStringFromNodeValues( # dimensional.
[Node.VALUE_LABEL_VALUE, Node.VALUE_LABEL_D_DS1, Node.VALUE_LABEL_D_DS2, Node.VALUE_LABEL_D2_DS1DS2,
Node.VALUE_LABEL_D_DS3, Node.VALUE_LABEL_D2_DS1DS3], [
([ [ 0.0, 21.3,-33.2], [ 0.0,-7.5, 6.0], [ 4.8, 0.0, 0.0], [ 4.8,-0.0,-0.0], [ 0.0, 2.8, 3.5], [ 0.0, 3.2, 1.3] ] ),
([ [ 0.0, 14.5,-26.7], [ 0.0,-6.1, 7.2], [ 8.5,-0.0,-0.0], [ 2.6, 0.0, 0.0], [ 0.0, 4.9, 4.1], [-0.0, 1.1, 0.1] ] ),
([ [ 0.0, 9.2,-19.0], [ 0.0,-5.2, 7.2], [ 10.1, 0.0, 0.0], [ 1.1,-0.1,-0.0], [ 0.0, 5.0, 3.6], [ 0.1, 0.4,-0.6] ] ),
([ [ 0.0, 4.0,-12.2], [ 0.0,-3.5, 7.0], [ 10.8,-0.2,-0.1], [-0.4, 0.2, 0.0], [ 0.1, 5.7, 2.9], [-0.1, 0.8,-1.4] ] ),
([ [ 0.0, 2.1, -5.5], [ 0.0,-1.2, 7.6], [ 9.4, 0.3, 0.1], [ 0.1, 0.2, 0.1], [-0.2, 6.6, 1.0], [-0.2, 2.2,-0.3] ] ),
([ [ 0.0, 1.9, 2.9], [ 0.0,-2.1, 8.8], [ 11.2, 0.2, 0.1], [ 3.3,-0.1,-0.0], [-0.2, 10.4, 2.5], [ 0.1, 0.3, 2.0] ] ),
([ [ 0.0, -2.3, 11.4], [ 0.0,-6.2, 8.1], [ 16.2, 0.1, 0.0], [ 6.7,-0.2,-0.0], [-0.0, 6.7, 5.1], [ 0.3,-7.7, 3.2] ] )
]),
'userAnnotationGroups': [
{
'_AnnotationGroup': True,
'dimension': 1,
'identifierRanges': '1-2',
'name': get_brainstem_term('medulla oblongata')[0],
'ontId': get_brainstem_term('medulla oblongata')[1]
},
{
'_AnnotationGroup': True,
'dimension': 1,
'identifierRanges': '3-4',
'name': get_brainstem_term('pons')[0],
'ontId': get_brainstem_term('pons')[1]
},
{
'_AnnotationGroup': True,
'dimension': 1,
'identifierRanges': '5-6',
'name': get_brainstem_term('midbrain')[0],
'ontId': get_brainstem_term('midbrain')[1]
}]
})
}

Expand All @@ -261,7 +352,9 @@ def getParameterSetNames():
'Cat 1',
'Human 1',
'Mouse 1',
'Rat 1']
'Rat 1',
'Pig 1',
'Sheep 1']

@classmethod
def getDefaultOptions(cls, parameterSetName='Default'):
Expand All @@ -280,6 +373,12 @@ def getDefaultOptions(cls, parameterSetName='Default'):
if 'Rat 1' in parameterSetName:
centralPathOption = cls.centralPathDefaultScaffoldPackages['Rat 1']

if 'Pig 1' in parameterSetName:
centralPathOption = cls.centralPathDefaultScaffoldPackages['Pig 1']

if 'Sheep 1' in parameterSetName:
centralPathOption = cls.centralPathDefaultScaffoldPackages['Sheep 1']

options = {
'Base parameter set': parameterSetName,
'Central path': copy.deepcopy(centralPathOption),
Expand Down Expand Up @@ -367,6 +466,8 @@ def generateBaseMesh(cls, region, options):
isHuman = 'Human 1' in parameterSetName
isMouse = 'Mouse 1' in parameterSetName
isRat = 'Rat 1' in parameterSetName
isPig = 'Pig 1' in parameterSetName
isSheep = 'Sheep 1' in parameterSetName

centralPath = options['Central path']
brainstemPath = cls.centralPathDefaultScaffoldPackages['Brainstem 1']
Expand Down