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Mouse brainstem #149

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merged 2 commits into from
Jul 12, 2021
Merged

Mouse brainstem #149

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f005290
Created mouse brainstem
arti-sukasem Jun 24, 2021
1f3f4e8
fitted mouse parameters
arti-sukasem Jul 2, 2021
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47 changes: 47 additions & 0 deletions src/scaffoldmaker/meshtypes/meshtype_3d_brainstem.py
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Original file line number Diff line number Diff line change
Expand Up @@ -158,6 +158,48 @@ class MeshType_3d_brainstem1(Scaffold_base):
'ontId': get_brainstem_term('midbrain')[1]
}]
}),
'Mouse 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, 1.5,-3.4], [0.0,-0.1,1.1], [1.4,0.0,0.0], [-0.1,0.0,0.0], [0.0,1.0, 0.1], [0.0, 0.1, 0.9] ] ),
([ [0.0, 1.0,-2.3], [0.0,-0.8,1.0], [1.3,0.0,0.0], [ 0.0,0.0,0.0], [0.0,0.8, 0.7], [0.0, 0.0, 0.6] ] ),
([ [0.0,-0.1,-1.6], [0.0,-1.2,0.8], [1.5,0.0,0.0], [ 0.4,0.0,0.0], [0.0,0.7, 1.0], [0.0, 0.1, 0.1] ] ),
([ [0.0,-1.2,-0.7], [0.0,-0.7,1.2], [2.0,0.0,0.0], [ 0.2,0.0,0.0], [0.0,1.2, 0.7], [0.0, 0.1,-0.1] ] ),
([ [0.0,-1.5, 0.5], [0.0, 0.1,1.4], [2.0,0.0,0.0], [-0.1,0.0,0.0], [0.0,1.4,-0.1], [0.0, 0.1,-0.1] ] ),
([ [0.0,-1.1, 1.9], [0.0,-0.3,1.4], [1.6,0.0,0.0], [-0.1,0.0,0.0], [0.0,1.5, 0.3], [0.0,-0.3, 0.3] ] ),
([ [0.0,-2.1, 3.1], [0.0,-1.3,0.8], [2.0,0.0,0.0], [ 0.8,0.0,0.0], [0.0,0.7, 1.2], [0.0,-0.8, 0.7] ] )
]),
'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]
}]
}),
'Rat 1': ScaffoldPackage(MeshType_1d_path1, {
'scaffoldSettings': {
'Coordinate dimensions': 3,
Expand Down Expand Up @@ -212,6 +254,7 @@ def getParameterSetNames():
'Default',
'Cat 1',
'Human 1',
'Mouse 1',
'Rat 1']

@classmethod
Expand All @@ -225,6 +268,9 @@ def getDefaultOptions(cls, parameterSetName='Default'):
if 'Human 1' in parameterSetName:
centralPathOption = cls.centralPathDefaultScaffoldPackages['Human 1']

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

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

Expand Down Expand Up @@ -313,6 +359,7 @@ def generateBaseMesh(cls, region, options):
parameterSetName = options['Base parameter set']
isCat = 'Cat 1' in parameterSetName
isHuman = 'Human 1' in parameterSetName
isMouse = 'Mouse 1' in parameterSetName
isRat = 'Rat 1' in parameterSetName

centralPath = options['Central path']
Expand Down