- Author:
- Mabelle Lin <mlin865@aucklanduni.ac.nz>
- Date:
- 2022-09-05 15:35:06+12:00
- Desc:
- Make scaffold reusable in PMR
- Permanent Source URI:
- https://models.cellml.org/workspace/832/rawfile/9f3e0c0f6cbc601f1880ee40d379d5189d5294dc/OrganScaffold-settings.json
{
"scaffold_settings": {
"deleteElementRanges": "",
"displayAxes": true,
"displayElementAxes": false,
"displayElementNumbers": false,
"displayLines": true,
"displayLinesExterior": false,
"displayMarkerPoints": false,
"displayModelRadius": false,
"displayNodeDerivativeLabels": [
"D1",
"D2",
"D3"
],
"displayNodeDerivatives": 0,
"displayNodeNumbers": false,
"displayNodePoints": false,
"displaySurfaces": true,
"displaySurfacesExterior": true,
"displaySurfacesTranslucent": true,
"displaySurfacesWireframe": false,
"modelCoordinatesField": "coordinates",
"scaffoldPackage": {
"_ScaffoldPackage": true,
"rotation": [
0.0,
0.0,
0.0
],
"scaffoldSettings": {
"Central path": {
"_ScaffoldPackage": true,
"meshEdits": "EX Version: 3\nRegion: /\n!#nodeset nodes\nDefine node template: node1\nShape. Dimension=0\n#Fields=1\n1) coordinates, coordinate, rectangular cartesian, real, #Components=3\n x. #Values=6 (value,d/ds1,d/ds2,d2/ds1ds2,d/ds3,d2/ds1ds3)\n y. #Values=6 (value,d/ds1,d/ds2,d2/ds1ds2,d/ds3,d2/ds1ds3)\n z. #Values=6 (value,d/ds1,d/ds2,d2/ds1ds2,d/ds3,d2/ds1ds3)\nNode template: node1\nNode: 1\n 7.309999999999999e+01 -2.070000000000000e+01 1.850000000000000e+01 1.860000000000000e+01 0.000000000000000e+00 0.000000000000000e+00\n 5.020000000000000e+01 -4.190000000000000e+01 -1.090000000000000e+01 -8.199999999999999e+00 0.000000000000000e+00 0.000000000000000e+00\n 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 2.780000000000000e+01 8.600000000000000e+00\nNode: 2\n 5.610000000000000e+01 -1.330000000000000e+01 3.100000000000000e+01 4.600000000000000e+00 0.000000000000000e+00 0.000000000000000e+00\n 1.710000000000000e+01 -2.430000000000000e+01 -1.650000000000000e+01 -4.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00\n 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 3.330000000000000e+01 2.400000000000000e+00\nNode: 3\n 4.700000000000000e+01 -1.190000000000000e+01 3.020000000000000e+01 -4.300000000000000e+00 0.000000000000000e+00 0.000000000000000e+00\n 1.400000000000000e+00 -1.820000000000000e+01 -1.970000000000000e+01 -4.500000000000000e+00 0.000000000000000e+00 0.000000000000000e+00\n 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 3.370000000000000e+01 -7.000000000000000e-01\nNode: 4\n 3.200000000000000e+01 -1.950000000000000e+01 2.070000000000000e+01 -1.370000000000000e+01 0.000000000000000e+00 0.000000000000000e+00\n -1.890000000000000e+01 -1.440000000000000e+01 -2.640000000000000e+01 -4.900000000000000e+00 0.000000000000000e+00 0.000000000000000e+00\n 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 3.160000000000000e+01 -3.700000000000000e+00\nNode: 5\n 1.070000000000000e+01 -2.430000000000000e+01 3.100000000000000e+00 -1.670000000000000e+01 0.000000000000000e+00 0.000000000000000e+00\n -2.630000000000000e+01 1.900000000000000e+00 -2.970000000000000e+01 4.800000000000000e+00 0.000000000000000e+00 0.000000000000000e+00\n 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 2.650000000000000e+01 -8.800000000000001e+00\nNode: 6\n -1.130000000000000e+01 -1.440000000000000e+01 -1.270000000000000e+01 -4.100000000000000e+00 0.000000000000000e+00 0.000000000000000e+00\n -1.440000000000000e+01 1.960000000000000e+01 -1.590000000000000e+01 1.350000000000000e+01 0.000000000000000e+00 0.000000000000000e+00\n 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 1.350000000000000e+01 -7.800000000000000e+00\nNode: 7\n -1.580000000000000e+01 -8.300000000000001e+00 -6.100000000000000e+00 2.800000000000000e+00 0.000000000000000e+00 0.000000000000000e+00\n 7.800000000000000e+00 1.830000000000000e+01 -4.800000000000000e+00 4.400000000000000e+00 0.000000000000000e+00 0.000000000000000e+00\n 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 7.200000000000000e+00 -1.700000000000000e+00\nNode: 8\n -2.620000000000000e+01 -1.180000000000000e+01 -4.400000000000000e+00 -2.600000000000000e+00 0.000000000000000e+00 0.000000000000000e+00\n 2.140000000000000e+01 8.400000000000000e+00 -6.000000000000000e+00 -8.800000000000001e+00 0.000000000000000e+00 0.000000000000000e+00\n 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 8.000000000000000e+00 5.000000000000000e-01\nGroup name: meshEdits\n!#nodeset nodes\nNode group:\n1..8\n",
"rotation": [
0.0,
0.0,
0.0
],
"scaffoldSettings": {
"Coordinate dimensions": 3,
"D2 derivatives": true,
"D3 derivatives": true,
"Length": 1.0,
"Number of elements": 7
},
"scaffoldTypeName": "1D Path 1",
"scale": [
1.0,
1.0,
1.0
],
"translation": [
0.0,
0.0,
0.0
],
"userAnnotationGroups": [
{
"_AnnotationGroup": true,
"dimension": 1,
"identifierRanges": "1",
"name": "fundus of stomach",
"ontId": "UBERON:0001160"
},
{
"_AnnotationGroup": true,
"dimension": 1,
"identifierRanges": "2-4",
"name": "body of stomach",
"ontId": "UBERON:0001161"
},
{
"_AnnotationGroup": true,
"dimension": 1,
"identifierRanges": "5",
"name": "pyloric antrum",
"ontId": "UBERON:0001165"
},
{
"_AnnotationGroup": true,
"dimension": 1,
"identifierRanges": "6",
"name": "pyloric canal",
"ontId": "UBERON:0008858"
},
{
"_AnnotationGroup": true,
"dimension": 1,
"identifierRanges": "7",
"name": "duodenum",
"ontId": "UBERON:0002114"
}
]
},
"Circular muscle layer relative thickness": 0.33,
"Gastro-esophagal junction": {
"_ScaffoldPackage": true,
"rotation": [
0.0,
0.0,
0.0
],
"scaffoldSettings": {
"Number of elements across common": 2,
"Number of elements along": 2,
"Number of elements around ostium": 8,
"Number of elements through wall": 4,
"Number of vessels": 1,
"Ostium diameter": 20.0,
"Ostium inter-vessel distance": 0.0,
"Ostium inter-vessel height": 0.0,
"Ostium length": 10.0,
"Ostium wall relative thicknesses": [
0.47,
0.1,
0.33,
0.1
],
"Ostium wall thickness": 5.0,
"Outlet": false,
"Refine": false,
"Refine number of elements along": 4,
"Refine number of elements around": 4,
"Refine number of elements through wall": 1,
"Unit scale": 1.0,
"Use cross derivatives": false,
"Use linear through ostium wall": true,
"Use linear through vessel wall": true,
"Vessel angle 1 degrees": 0.0,
"Vessel angle 1 spread degrees": 0.0,
"Vessel angle 2 degrees": 0.0,
"Vessel end length factor": 1.0,
"Vessel inner diameter": 3.0,
"Vessel wall relative thicknesses": [
0.47,
0.1,
0.33,
0.1
],
"Vessel wall thickness": 3.0
},
"scaffoldTypeName": "3D Ostium 1",
"scale": [
1.0,
1.0,
1.0
],
"translation": [
0.0,
0.0,
0.0
]
},
"Limiting ridge": false,
"Longitudinal muscle layer relative thickness": 0.1,
"Mucosa relative thickness": 0.47,
"Number of elements around duodenum": 16,
"Number of elements between cardia and duodenum": 7,
"Number of elements between fundus apex and cardia": 3,
"Number of elements through wall": 4,
"Refine": false,
"Refine number of elements surface": 4,
"Refine number of elements through wall": 1,
"Submucosa relative thickness": 0.1,
"Use linear through wall": true,
"Wall thickness": 5.0
},
"scaffoldTypeName": "3D Stomach 1",
"scale": [
1.0,
1.0,
1.0
],
"translation": [
0.0,
0.0,
0.0
]
}
},
"segmentation_data_settings": {
"displayDataContours": true,
"displayDataMarkerNames": true,
"displayDataMarkerPoints": true,
"displayDataPoints": false,
"displayDataRadius": false
}
}
