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Add parameter sets for mouse and pig bladder #153

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merged 10 commits into from
Aug 22, 2021
Merged

Add parameter sets for mouse and pig bladder #153

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06062fe
Add parameter sets for mouse and pig bladder
keeran97 Jul 16, 2021
7ffcc21
changed line 159 to >1e-12 to account for cases that have values very…
keeran97 Aug 4, 2021
784a92a
made all x-values in central path 0 for all bladders; decreased numbe…
keeran97 Aug 4, 2021
13b9b7a
resized the cat bladder appropriately; alphabetised the species throu…
keeran97 Aug 4, 2021
3fda92a
resized pig bladder
keeran97 Aug 5, 2021
a7d796e
slightly resized human bladder
keeran97 Aug 5, 2021
93cf400
reverted changes to current published bladders
keeran97 Aug 15, 2021
19021f6
resized mouse and pig bladder (all species 1 unit sized)
keeran97 Aug 15, 2021
6c8a2ca
reduced number of elements along bladder (for pig and mouse) and resi…
keeran97 Aug 16, 2021
f271f41
added a tolerance for cross product and ensured vector sd2 is normalised
keeran97 Aug 17, 2021
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207 changes: 181 additions & 26 deletions src/scaffoldmaker/meshtypes/meshtype_3d_bladderurethra1.py
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Expand Up @@ -46,11 +46,45 @@ class MeshType_3d_bladderurethra1(Scaffold_base):
[[0.0, 0.0, 15.0], [0.0, 0.0, 15.0], [0.0, 0.5, 0.0], [0.0, 0.0, -0.5]],
[[0.0, 0.0, 30.0], [0.0, 0.0, 15.0], [0.0, 0.5, 0.0], [0.0, 0.0, -0.5]],
[[0.0, 0.0, 45.0], [0.0, 0.0, 15.0], [0.0, 0.5, 0.0], [0.0, 0.0, -0.5]],
[[0.13, 0.1, 60.45], [0.4, 1.1, 13.5], [0.0, 0.5, 0.0], [0.0, 0.0, -0.5]],
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All central paths here have small components in the x direction which make them asymmetric - these components should be zero i.e. curves only in y-z plane.
Can you please make sure that mouse, pig have zero components for all x components of VALUE, D_DS1, D_DS2 then in meshgenerator smooth derivatives, make sides normal and smooth side cross derivatives then list parameters with appropriate precision (say 4-5 sig figs for largest value) then re-paste in here. Ideally all the other species should also be fixed... to discuss.
[Another comment is that this is the only organ that doesn't give the models an absolute scale in mm for each species; they are all about the same size; I'm not asking you to change this yet, just a comment for now.]

[[0.42, 1.42, 75.2], [0.3, 1.4, 13.2], [0.0, 0.5, 0.0], [0.0, 0.0, -0.5]],
[[0.85, 3.05, 89.94], [-0.2, 1.8, 15.4], [0.0, 0.5, 0.0], [0.0, 0.0, -0.5]],
[[0.26, 5.98, 107.94], [-0.6, 4.5, 16.8], [0.0, 0.5, 0.0], [0.0, 0.0, -0.5]],
[[-0.66, 12.47, 127.07], [0.35, 6.67, 14.8], [0.0, 0.5, 0.0], [0.0, 0.0, -0.5]]]),
[[0.0, 0.1, 60.45], [0.4, 1.1, 13.5], [0.0, 0.5, 0.0], [0.0, 0.0, -0.5]],
[[0.0, 1.42, 75.2], [0.3, 1.4, 13.2], [0.0, 0.5, 0.0], [0.0, 0.0, -0.5]],
[[0.0, 3.05, 89.94], [-0.2, 1.8, 15.4], [0.0, 0.5, 0.0], [0.0, 0.0, -0.5]],
[[0.0, 5.98, 107.94], [-0.6, 4.5, 16.8], [0.0, 0.5, 0.0], [0.0, 0.0, -0.5]],
[[0.0, 12.47, 127.07], [0.35, 6.67, 14.8], [0.0, 0.5, 0.0], [0.0, 0.0, -0.5]]]),
'userAnnotationGroups': [
{
'_AnnotationGroup': True,
'dimension': 1,
'identifierRanges': '1-5',
'name': get_bladder_term('urinary bladder')[0],
'ontId': get_bladder_term('urinary bladder')[1]
},
{
'_AnnotationGroup': True,
'dimension': 1,
'identifierRanges': '6-8',
'name': get_bladder_term('urethra')[0],
'ontId': get_bladder_term('urethra')[1]
}]
}),
'Human 1': ScaffoldPackage(MeshType_1d_path1, {
'scaffoldSettings': {
'Coordinate dimensions': 3,
'D2 derivatives': True,
'Length': 1.0,
'Number of elements': 8
},
'meshEdits': exnodeStringFromNodeValues(
[Node.VALUE_LABEL_VALUE, Node.VALUE_LABEL_D_DS1, Node.VALUE_LABEL_D_DS2, Node.VALUE_LABEL_D2_DS1DS2], [
[[0.0, 0.0, 0.0], [0.0, 0.0, 20.0], [0.0, 0.5, 0.0], [0.0, 0.0, -0.5]],
[[0.0, 0.0, 20.0], [0.0, 0.0, 20.0], [0.0, 0.5, 0.0], [0.0, 0.0, -0.5]],
[[0.0, 0.0, 40.0], [0.0, 0.0, 20], [0.0, 0.5, 0.0], [0.0, 0.0, -0.5]],
[[0.0, 0.0, 60.0], [0.0, 0.0, 20], [0.0, 0.5, 0.0], [0.0, 0.0, -0.5]],
[[0.0, 0.0, 80.0], [-0.4, 0.3, 17.7], [0.0, 0.5, 0.0], [0.0, 0.0, -0.5]],
[[0.0, -2.1, 100.6], [-1.0, -1.9, 17.2], [0.0, 0.5, 0.0], [0.0, 0.0, -0.5]],
[[0.0, -3.8, 120.3], [-1.4, -0.6, 18.8], [0.0, 0.5, 0.0], [0.0, 0.0, -0.5]],
[[0.0, -3.6, 140.5], [-0.1, 2.0, 18.4], [0.0, 0.5, 0.0], [0.0, 0.0, -0.5]],
[[0.0, 0.0, 160.0], [0.9, 4.0, 15.5], [0.0, 0.5, 0.0], [0.0, 0.0, -0.5]]]),
'userAnnotationGroups': [
{
'_AnnotationGroup': True,
Expand All @@ -66,8 +100,8 @@ class MeshType_3d_bladderurethra1(Scaffold_base):
'name': get_bladder_term('urethra')[0],
'ontId': get_bladder_term('urethra')[1]
}]
}),
'Rat 1': ScaffoldPackage(MeshType_1d_path1, {
}),
'Mouse 1': ScaffoldPackage(MeshType_1d_path1, {
'scaffoldSettings': {
'Coordinate dimensions': 3,
'D2 derivatives': True,
Expand All @@ -81,10 +115,10 @@ class MeshType_3d_bladderurethra1(Scaffold_base):
[[0.0, 0.0, 20.0], [0.0, 0.0, 10], [0.0, 0.5, 0.0], [0.0, 0.0, -0.5]],
[[0.0, 0.0, 30.0], [0.0, 0.0, 10], [0.0, 0.5, 0.0], [0.0, 0.0, -0.5]],
[[0.0, 0.0, 40.0], [-0.4, 0.3, 7.7], [0.0, 0.5, 0.0], [0.0, 0.0, -0.5]],
[[-0.5, -2.1, 49.6], [-1.0, -1.9, 7.2], [0.0, 0.5, 0.0], [0.0, 0.0, -0.5]],
[[-0.9, -3.8, 59.3], [-1.4, -0.6, 8.8], [0.0, 0.5, 0.0], [0.0, 0.0, -0.5]],
[[-1.3, -3.6, 71.5], [-0.1, 2.0, 8.4], [0.0, 0.5, 0.0], [0.0, 0.0, -0.5]],
[[0.0, 0.0, 80.0], [0.9, 4.0, 5.5], [0.0, 0.5, 0.0], [0.0, 0.0, -0.5]]]),
[[0.0, -2.1, 45.0], [-1.0, -1.9, 7.2], [0.0, 0.5, 0.0], [0.0, 0.0, -0.5]],
[[0.0, -3.8, 50.0], [-1.4, -0.6, 8.8], [0.0, 0.5, 0.0], [0.0, 0.0, -0.5]],
[[0.0, -3.6, 55.0], [-0.1, 2.0, 8.4], [0.0, 0.5, 0.0], [0.0, 0.0, -0.5]],
[[0.0, 0.0, 60.0], [0.9, 4.0, 5.5], [0.0, 0.5, 0.0], [0.0, 0.0, -0.5]]]),
'userAnnotationGroups': [
{
'_AnnotationGroup': True,
Expand All @@ -100,8 +134,8 @@ class MeshType_3d_bladderurethra1(Scaffold_base):
'name': get_bladder_term('urethra')[0],
'ontId': get_bladder_term('urethra')[1]
}]
}),
'Human 1': ScaffoldPackage(MeshType_1d_path1, {
}),
'Pig 1': ScaffoldPackage(MeshType_1d_path1, {
'scaffoldSettings': {
'Coordinate dimensions': 3,
'D2 derivatives': True,
Expand All @@ -110,15 +144,49 @@ class MeshType_3d_bladderurethra1(Scaffold_base):
},
'meshEdits': exnodeStringFromNodeValues(
[Node.VALUE_LABEL_VALUE, Node.VALUE_LABEL_D_DS1, Node.VALUE_LABEL_D_DS2, Node.VALUE_LABEL_D2_DS1DS2], [
[[0.0, 0.0, 0.0], [0.0, 0.0, 20.0], [0.0, 0.5, 0.0], [0.0, 0.0, -0.5]],
[[0.0, 0.0, 20.0], [0.0, 0.0, 20.0], [0.0, 0.5, 0.0], [0.0, 0.0, -0.5]],
[[0.0, 0.0, 40.0], [0.0, 0.0, 20], [0.0, 0.5, 0.0], [0.0, 0.0, -0.5]],
[[0.0, 0.0, 60.0], [0.0, 0.0, 20], [0.0, 0.5, 0.0], [0.0, 0.0, -0.5]],
[[0.0, 0.0, 80.0], [-0.4, 0.3, 17.7], [0.0, 0.5, 0.0], [0.0, 0.0, -0.5]],
[[-0.5, -2.1, 100.6], [-1.0, -1.9, 17.2], [0.0, 0.5, 0.0], [0.0, 0.0, -0.5]],
[[-0.9, -3.8, 120.3], [-1.4, -0.6, 18.8], [0.0, 0.5, 0.0], [0.0, 0.0, -0.5]],
[[-1.3, -3.6, 140.5], [-0.1, 2.0, 18.4], [0.0, 0.5, 0.0], [0.0, 0.0, -0.5]],
[[0.0, 0.0, 160.0], [0.9, 4.0, 15.5], [0.0, 0.5, 0.0], [0.0, 0.0, -0.5]]]),
[[0.0, 0.0, 0.0], [0.0, 0.0, 23.3], [0.0, 0.5, 0.0], [0.0, 0.0, 0.0]],
[[0.0, 0.0, 25.0], [0.0, 0.0, 21.3], [0.0, 0.5, 0.0], [0.0, 0.0, 0.0]],
[[0.0, 0.0, 40.0], [0.0, 0.0, 20.4], [0.0, 0.5, 0.0], [0.0, 0.0, 0.0]],
[[0.0, 0.0, 65.0], [0.4, 1.0, 24.5], [0.0, 0.5, 0.1], [0.0, -0.0, -0.0]],
[[0.0, 2.4, 90.0], [0.5, 4.2, 23.0], [0.0, 0.5, -0.2], [-0.0, -0.0, -0.1]],
[[0.0, 9.2, 110.0], [0.1, 5.6, 15.4], [-0.0, 0.5, -0.2], [-0.0, 0.0, 0.0]],
[[0.0, 15.3, 125.0], [0.2, 5.3, 12.0], [-0.0, 0.5, -0.2], [0.0, 0.0, -0.1]],
[[0.0, 21.2, 140.0], [0.1, 7.7, 11.9], [0.0, 0.4, -0.3], [0.0, -0.1, -0.1]],
[[0.0, 30.0, 150.0], [2.6, 18.4, 12.5], [-0.0, 0.3, -0.4], [-0.0, -0.2, -0.2]]]),
'userAnnotationGroups': [
{
'_AnnotationGroup': True,
'dimension': 1,
'identifierRanges': '1-4',
'name': get_bladder_term('urinary bladder')[0],
'ontId': get_bladder_term('urinary bladder')[1]
},
{
'_AnnotationGroup': True,
'dimension': 1,
'identifierRanges': '5-8',
'name': get_bladder_term('urethra')[0],
'ontId': get_bladder_term('urethra')[1]
}]
}),
'Rat 1': ScaffoldPackage(MeshType_1d_path1, {
'scaffoldSettings': {
'Coordinate dimensions': 3,
'D2 derivatives': True,
'Length': 1.0,
'Number of elements': 8
},
'meshEdits': exnodeStringFromNodeValues(
[Node.VALUE_LABEL_VALUE, Node.VALUE_LABEL_D_DS1, Node.VALUE_LABEL_D_DS2, Node.VALUE_LABEL_D2_DS1DS2], [
[[0.0, 0.0, 0.0], [0.0, 0.0, 10.0], [0.0, 0.5, 0.0], [0.0, 0.0, -0.5]],
[[0.0, 0.0, 10.0], [0.0, 0.0, 10.0], [0.0, 0.5, 0.0], [0.0, 0.0, -0.5]],
[[0.0, 0.0, 20.0], [0.0, 0.0, 10], [0.0, 0.5, 0.0], [0.0, 0.0, -0.5]],
[[0.0, 0.0, 30.0], [0.0, 0.0, 10], [0.0, 0.5, 0.0], [0.0, 0.0, -0.5]],
[[0.0, 0.0, 40.0], [-0.4, 0.3, 7.7], [0.0, 0.5, 0.0], [0.0, 0.0, -0.5]],
[[0.0, -2.1, 49.6], [-1.0, -1.9, 7.2], [0.0, 0.5, 0.0], [0.0, 0.0, -0.5]],
[[0.0, -3.8, 59.3], [-1.4, -0.6, 8.8], [0.0, 0.5, 0.0], [0.0, 0.0, -0.5]],
[[0.0, -3.6, 71.5], [-0.1, 2.0, 8.4], [0.0, 0.5, 0.0], [0.0, 0.0, -0.5]],
[[0.0, 0.0, 80.0], [0.9, 4.0, 5.5], [0.0, 0.5, 0.0], [0.0, 0.0, -0.5]]]),
'userAnnotationGroups': [
{
'_AnnotationGroup': True,
Expand All @@ -134,8 +202,8 @@ class MeshType_3d_bladderurethra1(Scaffold_base):
'name': get_bladder_term('urethra')[0],
'ontId': get_bladder_term('urethra')[1]
}]
})
}
})
}
ostiumDefaultScaffoldPackages = {
'Ureter Cat 1': ScaffoldPackage(MeshType_3d_ostium1, {
'scaffoldSettings': {
Expand Down Expand Up @@ -188,6 +256,58 @@ class MeshType_3d_bladderurethra1(Scaffold_base):
'Refine number of elements through wall': 1
},
}),
'Ureter Mouse 1': ScaffoldPackage(MeshType_3d_ostium1, {
'scaffoldSettings': {
'Number of vessels': 1,
'Number of elements across common': 2,
'Number of elements around ostium': 8, # implemented for 8
'Number of elements along': 1,
'Unit scale': 1.0,
'Outlet': False,
'Ostium diameter': 1.0,
'Ostium length': 0.25,
'Ostium wall thickness': 0.02,
'Use linear through ostium wall': True,
'Vessel end length factor': 2.0,
'Vessel inner diameter': 0.3,
'Vessel wall thickness': 0.1,
'Vessel angle 1 degrees': 0.0,
'Vessel angle 1 spread degrees': 0.0,
'Vessel angle 2 degrees': 0.0,
'Use linear through vessel wall': True,
'Use cross derivatives': False,
'Refine': False,
'Refine number of elements around': 4,
'Refine number of elements along': 4,
'Refine number of elements through wall': 1
},
}),
'Ureter Pig 1': ScaffoldPackage(MeshType_3d_ostium1, {
'scaffoldSettings': {
'Number of vessels': 1,
'Number of elements across common': 2,
'Number of elements around ostium': 8, # implemented for 8
'Number of elements along': 1,
'Unit scale': 1.0,
'Outlet': False,
'Ostium diameter': 2.3,
'Ostium length': 0.35,
'Ostium wall thickness': 0.3,
'Use linear through ostium wall': True,
'Vessel end length factor': 2.0,
'Vessel inner diameter': 1.3,
'Vessel wall thickness': 0.2,
'Vessel angle 1 degrees': 0.0,
'Vessel angle 1 spread degrees': 0.0,
'Vessel angle 2 degrees': 0.0,
'Use linear through vessel wall': True,
'Use cross derivatives': False,
'Refine': False,
'Refine number of elements around': 4,
'Refine number of elements along': 4,
'Refine number of elements through wall': 1
},
}),
'Ureter Human 1': ScaffoldPackage(MeshType_3d_ostium1, {
'scaffoldSettings': {
'Number of vessels': 1,
Expand Down Expand Up @@ -225,19 +345,30 @@ def getParameterSetNames():
return [
'Default',
'Cat 1',
'Rat 1',
'Human 1']
'Human 1',
'Mouse 1',
'Pig 1',
'Rat 1'
]

@classmethod
def getDefaultOptions(cls, parameterSetName='Default'):
if 'Rat 1' in parameterSetName:
centralPathOption_LUT = cls.centralPathDefaultScaffoldPackages_LUT['Rat 1']
if 'Mouse 1' in parameterSetName:
centralPathOption_LUT = cls.centralPathDefaultScaffoldPackages_LUT['Mouse 1']
if 'Pig 1' in parameterSetName:
centralPathOption_LUT = cls.centralPathDefaultScaffoldPackages_LUT['Pig 1']
elif 'Human 1' in parameterSetName:
centralPathOption_LUT = cls.centralPathDefaultScaffoldPackages_LUT['Human 1']
else:
centralPathOption_LUT = cls.centralPathDefaultScaffoldPackages_LUT['Cat 1']
if 'Rat 1' in parameterSetName:
ureterOption = cls.ostiumDefaultScaffoldPackages['Ureter Rat 1']
if 'Mouse 1' in parameterSetName:
ureterOption = cls.ostiumDefaultScaffoldPackages['Ureter Mouse 1']
if 'Pig 1' in parameterSetName:
ureterOption = cls.ostiumDefaultScaffoldPackages['Ureter Pig 1']
elif 'Human 1' in parameterSetName:
ureterOption = cls.ostiumDefaultScaffoldPackages['Ureter Human 1']
else:
Expand Down Expand Up @@ -281,6 +412,30 @@ def getDefaultOptions(cls, parameterSetName='Default'):
options['Urethra diameter 1'] = 0.75
options['Urethra diameter 2'] = 0.65
options['Urethra wall thickness'] = 0.25
if 'Mouse' in parameterSetName:
options['Major diameter'] = 30.0
options['Minor diameter'] = 30.0
options['Wall thickness'] = 0.2
options['Neck diameter 1'] = 5.0
options['Neck diameter 2'] = 7.0
options['Neck angle degrees'] = 25
options['Ureter position around'] = 0.67 # should be on the dorsal part (> 0.5)
options['Ureter position down'] = 0.83
options['Urethra diameter 1'] = 2.0
options['Urethra diameter 2'] = 2.0
options['Urethra wall thickness'] = 0.25
if 'Pig' in parameterSetName:
options['Major diameter'] = 30.0
options['Minor diameter'] = 30.0
options['Wall thickness'] = 0.3
options['Neck diameter 1'] = 8.0
options['Neck diameter 2'] = 7.5
options['Neck angle degrees'] = 25
options['Ureter position around'] = 0.67 # should be on the dorsal part (> 0.5)
options['Ureter position down'] = 0.83
options['Urethra diameter 1'] = 2.0
options['Urethra diameter 2'] = 2.0
options['Urethra wall thickness'] = 0.25
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Mouse, pig have followed cat in being quite inflated, rat is half inflated, human perhaps a little more. Need to consistently choose a state, probably partly inflated so regular shaped, not over inflated so strained, not under-inflated so wrinkled up, to be the generic reference state. Do a bit of research and propose what you think is the best state.

if 'Human' in parameterSetName:
options['Number of elements along bladder'] = 8
options['Number of elements around'] = 12
Expand Down