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Human uterus #244

Merged
merged 20 commits into from
Apr 11, 2024
+1,569 −187
Merged

Human uterus #244

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262e0ff
Update uterus1 and fix typo
mlin865 Mar 15, 2024
cb4db1f
Allow use of inner coordinates to define network layout scaffold
mlin865 Mar 17, 2024
f4c8e2e
Add uterus2 which uses bifurcation utils functions
mlin865 Mar 18, 2024
675d995
Add unit test for uterus scaffold
mlin865 Mar 18, 2024
a0bf0d1
Fixes issue #245
mlin865 Mar 19, 2024
129db7a
Add serosa/lumen groups to body and vagina for mouse uterus
mlin865 Mar 24, 2024
8125cfe
Add serosa/lumen groups to human uterus
mlin865 Mar 24, 2024
b40e0b1
Edit network layout for human uterus to work with more elements around
mlin865 Mar 24, 2024
27768c2
Update mouse network layout to remove dip
mlin865 Mar 25, 2024
a88b9f3
Update round ligament terms
mlin865 Mar 25, 2024
00dc5eb
Update annotations to left and right uterine tubes
mlin865 Mar 26, 2024
ef2392a
Rename editCoordinates to editCoordinatesField and use targetCoordinates
mlin865 Mar 27, 2024
4a8bfb6
Rearrange nodes and segments from in to out
mlin865 Mar 28, 2024
6d30e9e
Update unit test and marker positions
mlin865 Mar 28, 2024
bed183f
Merge remote-tracking branch 'abi/main' into humanUterus
mlin865 Mar 28, 2024
03f3244
Update input argument for meshEdit in bone meshtype
mlin865 Apr 2, 2024
452509b
blend shared derivatives across network junctions
rchristie Apr 11, 2024
23328c7
Merge pull request #2 from rchristie/blend_derivatives
mlin865 Apr 11, 2024
842c943
Insert edits from blend_derivatives and update test for uterus
mlin865 Apr 11, 2024
015b3b9
Merge remote-tracking branch 'abi/main' into humanUterus
mlin865 Apr 11, 2024
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64 changes: 42 additions & 22 deletions src/scaffoldmaker/annotation/uterus_terms.py
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -4,33 +4,53 @@

# convention: preferred name, preferred id, followed by any other ids and alternative names
uterus_terms = [
("uterus", "UBERON:0000995"),
("serosa of uterus", "UBERON:0001297"),
("body of uterus", "UBERON:0009853"),
("cervix of uterus", "ILX:0745917 "),
("uterine cervix", "UBERON:0000002"),
("uterine wall", "UBERON:0000459"),
("uterine horn", "UBERON:000224"),
("uterine lumen", "UBERON:0013769"),
("body of uterus", "UBERON:0009853", "FMA:17739", "ILX:0730129"),
("broad ligament of uterus", "UBERON:0012332", "FMA:16516", "ILX:0733266"),
("dorsal cervix junction with vagina", "None"),
("dorsal top left horn", "None"),
("dorsal top right horn", "None"),
("external cervical os", "UBERON:0013760", "FMA:76836", "ILX:0736534"),
("fundus", "None"),
("internal cervical os", "UBERON:0013759", "FMA:17747", "ILX:0729495"),
("junction of left round ligament with uterus", "None"),
("junction of right round ligament with uterus", "None"),
("left broad ligament of uterus", "None"),
("left transverse cervical ligament", "None"),
("left uterine horn", "UBERON:0009020"),
("right uterine horn", "UBERON:0009022"),
("serosa of uerine cervix", "None"),
("lumen of uerine cervix", "None"),
("serosa of right horn", "None"),
("lumen of right horn", "None"),
("serosa of left horn", "None"),
("left uterine tube", "UBERON:0001303", "FMA:18484", "ILX:0734218"),
("lumen of body of uterus", "None"),
("lumen of fallopian tube", "None"),
("lumen of left horn", "None"),
("serosa of uterus", "None"),
("lumen of left uterine tube", "None"),
("lumen of right horn", "None"),
("lumen of right uterine tube", "None"),
("lumen of uterine cervix", "None"),
("lumen of uterus", "None"),
("fundus", "None"),
("lumen of vagina", "None"),
("myometrium", "UBERON:0001296", "FMA:17743", " ILX:0735601"),
("pubocervical ligament (TA98)", "ILX:0743760"),
("right broad ligament of uterus", "None"),
("right transverse cervical ligament", "None"),
("right uterine horn", "UBERON:0009022"),
("right uterine tube", "UBERON:0001302", "FMA:18483", "ILX:0724908"),
("serosa of body of uterus", "None"),
("serosa of left uterine tube", "None"),
("serosa of left horn", "None"),
("serosa of right horn", "None"),
("serosa of right uterine tube", "None"),
("serosa of uterine cervix", "None"),
("serosa of uterus", "UBERON:0001297"),
("serosa of vagina", "None"),
("uterine cervix", "UBERON:0000002","FMA:17740", "ILX:0724162"),
("uterine horn", "UBERON:000224"),
("uterine lumen", "UBERON:0013769"),
("uterine wall", "UBERON:0000459", "FMA:17560", "ILX:0735839"),
("uterus", "UBERON:0000995", "FMA:17558", "ILX:0726002"),
("vagina", "UBERON:0000996", "FMA:19949", "ILX:0736016"),
("vagina orifice", "UBERON:0012317", "FMA:19984", "ILX:0729556"),
("ventral cervix junction with vagina", "None"),
("dorsal cervix junction with vagina", "None"),
("dorsal top right horn", "None"),
("ventral top right horn", "None"),
("dorsal top left horn", "None"),
("ventral top left horn", "None"),
("vagina", "None")
]
("ventral top right horn", "None")]

def get_uterus_term(name: str):
"""
Expand Down
30 changes: 18 additions & 12 deletions src/scaffoldmaker/meshtypes/meshtype_3d_bladder1.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -39,9 +39,10 @@ class MeshType_3d_bladder1(Scaffold_base):
'Number of elements': 7
},
'meshEdits': exnode_string_from_nodeset_field_parameters(
['coordinates'],
[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],
[
[[
(1, [[1.98482, -0.23213, 0.00000], [-0.27986, 0.04637, 0.00000], [-0.03267, -0.19717, 0.00000],
[-0.02887, -0.18604, 0.00000], [0.00000, 0.00000, 0.31783], [0.00000, 0.00000, 0.22083]]),
(2, [[1.69774, -0.18588, 0.00000], [-0.29430, 0.04613, 0.00000], [-0.05231, -0.33376, 0.00000],
Expand All @@ -58,7 +59,7 @@ class MeshType_3d_bladder1(Scaffold_base):
[0.00715, 0.05112, 0.00000], [0.00000, 0.00000, 0.09658], [0.00000, 0.00000, -0.04254]]),
(8, [[0.00000, 0.00000, 0.00000], [-0.23137, 0.00000, 0.00000], [-0.00000, -0.05191, 0.00000],
[0.00294, 0.00527, 0.00000], [0.00000, 0.00000, 0.07300], [0.00000, 0.00000, -0.00462]])
]),
]]),
'userAnnotationGroups': [
{
'_AnnotationGroup': True,
Expand All @@ -84,9 +85,10 @@ class MeshType_3d_bladder1(Scaffold_base):
'Number of elements': 7
},
'meshEdits': exnode_string_from_nodeset_field_parameters(
['coordinates'],
[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],
[
[[
(1, [[2.00000, 0.00000, 0.00000], [-0.29240, 0.00000, 0.00000], [0.00000, -0.27079, 0.00000],
[0.00000, -0.26496, 0.00000], [0.00000, 0.00000, 0.53835], [0.00000, 0.00000, 0.14344]]),
(2, [[1.70113, 0.00000, 0.00000], [-0.30534, 0.00000, 0.00000], [0.00000, -0.46797, 0.00000],
Expand All @@ -103,7 +105,7 @@ class MeshType_3d_bladder1(Scaffold_base):
[0.00000, 0.07176, -0.00000], [0.00000, 0.00000, 0.21298], [0.00000, -0.00000, -0.13616]]),
(8, [[0.00000, 0.00000, 0.00000], [-0.24418, 0.00000, 0.00000], [0.00000, -0.11153, 0.00000],
[0.00000, 0.04545, -0.00000], [0.00000, 0.00000, 0.09572], [0.00000, -0.00000, -0.09837]])
]),
]]),
'userAnnotationGroups': [
{
'_AnnotationGroup': True,
Expand All @@ -129,9 +131,10 @@ class MeshType_3d_bladder1(Scaffold_base):
'Number of elements': 7
},
'meshEdits': exnode_string_from_nodeset_field_parameters(
['coordinates'],
[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],
[
[[
(1, [[1.94475, -0.28705, 0.00000], [-0.34493, 0.16731, 0.00000], [-0.08535, -0.17595, 0.00000],
[-0.04402, -0.10886, 0.00000], [0.00000, 0.00000, 0.18665], [0.00000, 0.00000, 0.24107]]),
(2, [[1.61917, -0.14378, 0.00000], [-0.30588, 0.11906, 0.00000], [-0.10871, -0.27931, 0.00000],
Expand All @@ -148,7 +151,7 @@ class MeshType_3d_bladder1(Scaffold_base):
[-0.00525, 0.07201, 0.00000], [0.00000, 0.00000, 0.12027], [0.00000, 0.00000, -0.08509]]),
(8, [[0.00000, 0.00000, 0.00000], [-0.27223, 0.00000, 0.00000], [-0.00000, -0.04285, 0.00000],
[-0.00982, 0.01186, 0.00000], [0.00000, 0.00000, 0.05222], [0.00000, 0.00000, -0.05101]])
]),
]]),
'userAnnotationGroups': [
{
'_AnnotationGroup': True,
Expand All @@ -174,9 +177,10 @@ class MeshType_3d_bladder1(Scaffold_base):
'Number of elements': 7
},
'meshEdits': exnode_string_from_nodeset_field_parameters(
['coordinates'],
[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],
[
[[
(1, [[1.88718, 0.56852, 0.00000], [-0.20674, -0.15833, 0.00000], [0.09002, -0.11754, 0.00000],
[0.13867, -0.25647, 0.00000], [0.00000, 0.00000, 0.11203], [0.00000, 0.00000, 0.47891]]),
(2, [[1.66209, 0.42003, 0.00000], [-0.24279, -0.13815, 0.00000], [0.18168, -0.31927, 0.00000],
Expand All @@ -193,7 +197,7 @@ class MeshType_3d_bladder1(Scaffold_base):
[-0.02501, 0.12449, 0.00000], [0.00000, 0.00000, 0.18610], [0.00000, 0.00000, -0.14240]]),
(8, [[0.00000, 0.00000, 0.00000], [-0.27970, -0.00000, 0.00000], [0.00000, -0.04485, 0.00000],
[-0.00345, 0.06647, 0.00000], [0.00000, 0.00000, 0.05111], [0.00000, 0.00000, -0.12759]])
]),
]]),
'userAnnotationGroups': [
{
'_AnnotationGroup': True,
Expand All @@ -219,9 +223,10 @@ class MeshType_3d_bladder1(Scaffold_base):
'Number of elements': 7
},
'meshEdits': exnode_string_from_nodeset_field_parameters(
['coordinates'],
[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],
[
[[
(1, [[1.98605, -0.21791, 0.00000], [-0.20755, 0.03159, 0.00000], [-0.00760, -0.04989, 0.00000],
[-0.02445, -0.15319, 0.00000], [0.00000, 0.00000, 0.12825], [0.00000, 0.00000, 0.29326]]),
(2, [[1.75787, -0.18270, 0.00000], [-0.24882, 0.03881, 0.00000], [-0.02816, -0.18050, 0.00000],
Expand All @@ -238,7 +243,7 @@ class MeshType_3d_bladder1(Scaffold_base):
[0.00931, 0.08494, 0.00000], [0.00000, 0.00000, 0.19799], [0.00000, 0.00000, -0.12929]]),
(8, [[0.00000, 0.00000, 0.00000], [-0.29834, 0.00000, 0.00000], [0.00000, -0.04096, 0.00000],
[0.00133, 0.04434, 0.00000], [0.00000, 0.00000, 0.08550], [0.00000, 0.00000, -0.09569]])
]),
]]),
'userAnnotationGroups': [
{
'_AnnotationGroup': True,
Expand All @@ -264,9 +269,10 @@ class MeshType_3d_bladder1(Scaffold_base):
'Number of elements': 10
},
'meshEdits': exnode_string_from_nodeset_field_parameters(
['coordinates'],
[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],
[
[[
(1, [[2.00000, 0.00000, 0.00000], [-0.04772, 0.00000, 0.00000], [0.00000, -0.21530, 0.00000],
[0.00000, 0.04601, 0.00000], [0.00000, 0.00000, 0.21530], [0.00000, 0.00000, -0.04601]]),
(2, [[1.90255, 0.00000, 0.00000], [-0.14718, 0.00000, 0.00000], [0.00000, -0.21530, 0.00000],
Expand All @@ -289,7 +295,7 @@ class MeshType_3d_bladder1(Scaffold_base):
[0.00000, 0.11291, 0.00000], [0.00000, 0.00000, 0.21534], [0.00000, 0.00000, -0.11291]]),
(11, [[0.00000, 0.00000, 0.00000], [-0.04779, 0.00000, 0.00000], [0.00000, -0.11534, 0.00000],
[0.00000, 0.08709, 0.00000], [0.00000, 0.00000, 0.11534], [0.00000, 0.00000, -0.08709]])
]),
]]),
'userAnnotationGroups': [
{
'_AnnotationGroup': True,
Expand Down
25 changes: 15 additions & 10 deletions src/scaffoldmaker/meshtypes/meshtype_3d_bladderurethra1.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -45,7 +45,8 @@ class MeshType_3d_bladderurethra1(Scaffold_base):
'Number of elements': 8
},
'meshEdits': exnode_string_from_nodeset_field_parameters(
[Node.VALUE_LABEL_VALUE, Node.VALUE_LABEL_D_DS1, Node.VALUE_LABEL_D_DS2, Node.VALUE_LABEL_D2_DS1DS2], [
['coordinates'],
[Node.VALUE_LABEL_VALUE, Node.VALUE_LABEL_D_DS1, Node.VALUE_LABEL_D_DS2, Node.VALUE_LABEL_D2_DS1DS2], [[
(1, [[0.0000, 0.0000, 0.0000], [0.0000, 0.0000, 15.000], [0.0000, 0.5000, 0.00000], [0.0000, 0.0000, -0.5000]]),
(2, [[0.0000, 0.0000, 15.000], [0.0000, 0.0000, 15.000], [0.0000, 0.5000, 0.00000], [0.0000, 0.0000, -0.5000]]),
(3, [[0.0000, 0.0000, 30.000], [0.0000, 0.0000, 15.000], [0.0000, 0.5000, 0.00000], [0.0000, 0.0000, -0.5000]]),
Expand All @@ -55,7 +56,7 @@ class MeshType_3d_bladderurethra1(Scaffold_base):
(7, [[0.0000, 3.0500, 89.940], [0.0000, 1.8000, 15.400], [0.0000, 0.5000, 0.00000], [0.0000, 0.0000, -0.5000]]),
(8, [[0.0000, 5.9800, 107.94], [0.0000, 4.5000, 16.800], [0.0000, 0.5000, 0.00000], [0.0000, 0.0000, -0.5000]]),
(9, [[0.0000, 12.470, 127.07], [0.0000, 6.6700, 14.800], [0.0000, 0.5000, 0.00000], [0.0000, 0.0000, -0.5000]])
]),
]]),
'userAnnotationGroups': [
{
'_AnnotationGroup': True,
Expand All @@ -80,7 +81,8 @@ class MeshType_3d_bladderurethra1(Scaffold_base):
'Number of elements': 8
},
'meshEdits': exnode_string_from_nodeset_field_parameters(
[Node.VALUE_LABEL_VALUE, Node.VALUE_LABEL_D_DS1, Node.VALUE_LABEL_D_DS2, Node.VALUE_LABEL_D2_DS1DS2], [
['coordinates'],
[Node.VALUE_LABEL_VALUE, Node.VALUE_LABEL_D_DS1, Node.VALUE_LABEL_D_DS2, Node.VALUE_LABEL_D2_DS1DS2], [[
(1, [[0.0000, 0.0000, 0.0000], [0.0000, 0.0000, 20.000], [0.0000, 0.5000, 0.0000], [0.0000, 0.0000, -0.5000]]),
(2, [[0.0000, 0.0000, 20.000], [0.0000, 0.0000, 20.000], [0.0000, 0.5000, 0.0000], [0.0000, 0.0000, -0.5000]]),
(3, [[0.0000, 0.0000, 40.000], [0.0000, 0.0000, 20.000], [0.0000, 0.5000, 0.0000], [0.0000, 0.0000, -0.5000]]),
Expand All @@ -90,7 +92,7 @@ class MeshType_3d_bladderurethra1(Scaffold_base):
(7, [[0.0000, -3.8000, 120.30], [0.0000, -0.6000, 18.800], [0.0000, 0.5000, 0.0000], [0.0000, 0.0000, -0.5000]]),
(8, [[0.0000, -3.6000, 140.50], [0.0000, 2.0000, 18.400], [0.0000, 0.5000, 0.0000], [0.0000, 0.0000, -0.5000]]),
(9, [[0.0000, 0.0000, 160.00], [0.0000, 4.0000, 15.500], [0.0000, 0.5000, 0.0000], [0.0000, 0.0000, -0.5000]])
]),
]]),
'userAnnotationGroups': [
{
'_AnnotationGroup': True,
Expand All @@ -115,7 +117,8 @@ class MeshType_3d_bladderurethra1(Scaffold_base):
'Number of elements': 8
},
'meshEdits': exnode_string_from_nodeset_field_parameters(
[Node.VALUE_LABEL_VALUE, Node.VALUE_LABEL_D_DS1, Node.VALUE_LABEL_D_DS2, Node.VALUE_LABEL_D2_DS1DS2], [
['coordinates'],
[Node.VALUE_LABEL_VALUE, Node.VALUE_LABEL_D_DS1, Node.VALUE_LABEL_D_DS2, Node.VALUE_LABEL_D2_DS1DS2], [[
(1, [[0.000, 0.0000, 0.0000], [0.0000, 0.2107, 19.185], [0.0000, 0.5000, 0.0006], [0.0000, -0.0002, -0.0098]]),
(2, [[0.000, 0.1095, 17.595], [0.0000, 0.0083, 16.005], [0.0000, 0.4999, -0.0074], [0.0000, -0.0000, -0.0062]]),
(3, [[0.000, 0.0347, 32.009], [0.0000, 0.0042, 13.831], [0.0000, 0.4999, -0.0122], [0.0000, 0.0001, 0.0027]]),
Expand All @@ -125,7 +128,7 @@ class MeshType_3d_bladderurethra1(Scaffold_base):
(7, [[0.000, -0.6320, 86.026], [0.0000, -0.5928, 14.006], [0.0000, 0.4997, 0.0193], [0.0000, -0.0027, -0.1007]]),
(8, [[0.000, -1.1544, 99.742], [0.0000, 0.7147, 16.377], [0.0000, 0.4961, -0.0620], [0.0000, -0.0226, -0.1114]]),
(9, [[0.000, 1.2247, 118.63], [0.0000, 4.0316, 21.331], [0.0000, 0.4719, -0.1653], [0.0000, -0.0498, -0.0958]])
]),
]]),
'userAnnotationGroups': [
{
'_AnnotationGroup': True,
Expand All @@ -150,7 +153,8 @@ class MeshType_3d_bladderurethra1(Scaffold_base):
'Number of elements': 8
},
'meshEdits': exnode_string_from_nodeset_field_parameters(
[Node.VALUE_LABEL_VALUE, Node.VALUE_LABEL_D_DS1, Node.VALUE_LABEL_D_DS2, Node.VALUE_LABEL_D2_DS1DS2], [
['coordinates'],
[Node.VALUE_LABEL_VALUE, Node.VALUE_LABEL_D_DS1, Node.VALUE_LABEL_D_DS2, Node.VALUE_LABEL_D2_DS1DS2], [[
(1, [[0.0000, 0.0000, 0.0000], [0.0000, 0.3967, 17.118], [0.0000, 0.4999, -0.0116], [0.0000, 0.0002, 0.0084]]),
(2, [[0.0000, 0.2526, 16.482], [0.0000, 0.1084, 15.844], [0.0000, 0.5000, -0.0034], [0.0000, 0.0001, 0.0073]]),
(3, [[0.0000, 0.2277, 31.687], [0.0000, -0.1005, 16.250], [0.0000, 0.5000, 0.0031], [0.0000, 0.0180, 0.0030]]),
Expand All @@ -160,7 +164,7 @@ class MeshType_3d_bladderurethra1(Scaffold_base):
(7, [[0.0000, -1.3669, 104.42], [0.0000, 0.5462, 17.118], [0.0000, 0.4994, -0.0233], [0.0000, -0.0266, -0.1269]]),
(8, [[0.0000, -0.1150, 119.12], [0.0000, 2.7663, 14.068], [0.0000, 0.4902, -0.0980], [0.0000, -0.0116, -0.0490]]),
(9, [[0.0000, 4.0321, 132.37], [0.0000, 5.4802, 12.315], [0.0000, 0.4691, -0.1728], [0.0000, 0.0080, 0.0382]])
]),
]]),
'userAnnotationGroups': [
{
'_AnnotationGroup': True,
Expand All @@ -185,7 +189,8 @@ class MeshType_3d_bladderurethra1(Scaffold_base):
'Number of elements': 8
},
'meshEdits': exnode_string_from_nodeset_field_parameters(
[Node.VALUE_LABEL_VALUE, Node.VALUE_LABEL_D_DS1, Node.VALUE_LABEL_D_DS2, Node.VALUE_LABEL_D2_DS1DS2], [
['coordinates'],
[Node.VALUE_LABEL_VALUE, Node.VALUE_LABEL_D_DS1, Node.VALUE_LABEL_D_DS2, Node.VALUE_LABEL_D2_DS1DS2], [[
(1, [[0.000, 0.0000, 0.0000], [0.0000, -0.0219, 18.928], [0.0000, 0.5000, 0.0006], [0.0000, 0.0001, -0.0062]]),
(2, [[0.000, 0.1095, 17.595], [0.0000, 0.2409, 16.260], [0.0000, 0.4999, -0.0074], [0.0000, -0.0000, -0.0051]]),
(3, [[0.000, 0.4589, 32.519], [0.0000, 0.3415, 14.001], [0.0000, 0.4999, -0.0122], [0.0000, -0.0000, 0.0018]]),
Expand All @@ -195,7 +200,7 @@ class MeshType_3d_bladderurethra1(Scaffold_base):
(7, [[0.000, -1.6517, 86.875], [0.0000, -0.5654, 14.673], [0.0000, 0.5000, 0.0047], [0.0000, -0.0038, -0.1421]]),
(8, [[0.000, -1.3262, 102.46], [0.0000, 1.8796, 15.041], [0.0000, 0.4872, -0.1123], [0.0000, -0.0646, -0.1586]]),
(9, [[0.000, 1.9903, 116.76], [0.0000, 4.7166, 13.462], [0.0000, 0.4510, -0.2159], [0.0000, -0.1378, -0.1893]])
]),
]]),
'userAnnotationGroups': [
{
'_AnnotationGroup': True,
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5 changes: 3 additions & 2 deletions src/scaffoldmaker/meshtypes/meshtype_3d_bone1.py
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Original file line number Diff line number Diff line change
Expand Up @@ -39,13 +39,14 @@ class MeshType_3d_bone1 (Scaffold_base):
'Number of elements': 3
},
'meshEdits': exnode_string_from_nodeset_field_parameters(
['coordinates'],
[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], [
Node.VALUE_LABEL_D_DS3, Node.VALUE_LABEL_D2_DS1DS3], [[
(1, [[0.0, 0.0, 0.0], [0.0, 0.0, 1.0], [1.0, 0.0, 0.0], [0.0, 0.0, 0.0], [0.0, 1.0, 0.0], [0.0, 0.0, 0.0]]),
(2, [[0.0, 0.0, 1.0], [0.0, 0.0, 1.0], [1.0, 0.0, 0.0], [0.0, 0.0, 0.0], [0.0, 1.0, 0.0], [0.0, 0.0, 0.0]]),
(3, [[0.0, 0.0, 2.0], [0.0, 0.0, 1.0], [1.0, 0.0, 0.0], [0.0, 0.0, 0.0], [0.0, 1.0, 0.0], [0.0, 0.0, 0.0]]),
(4, [[0.0, 0.0, 3.0], [0.0, 0.0, 1.0], [1.0, 0.0, 0.0], [0.0, 0.0, 0.0], [0.0, 1.0, 0.0], [0.0, 0.0, 0.0]])
])
]])
})
}

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