- Author:
- Mabelle Lin <mlin865@aucklanduni.ac.nz>
- Date:
- 2022-09-05 15:32:21+12:00
- Desc:
- Make scaffold reusable in PMR
- Permanent Source URI:
- https://models.cellml.org/workspace/6c6/rawfile/d9da0dd200c739f2eee390ad9e8a8dd4ae8d1e10/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 1.400000000000000e+00 7.000000000000000e-01 3.200000000000000e+00 -1.300000000000000e+00 0.000000000000000e+00 0.000000000000000e+00\n 2.300000000000000e+00 -2.300000000000000e+00 -6.000000000000000e-01 -5.000000000000000e-01 0.000000000000000e+00 0.000000000000000e+00\n 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 2.600000000000000e+00 9.000000000000000e-01\nNode: 2\n 1.330000000000000e+00 -1.000000000000000e+00 2.000000000000000e+00 -1.100000000000000e+00 0.000000000000000e+00 0.000000000000000e+00\n 1.000000000000000e-01 -2.000000000000000e+00 -1.500000000000000e+00 -1.300000000000000e+00 0.000000000000000e+00 0.000000000000000e+00\n 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 3.100000000000000e+00 1.000000000000000e-01\nNode: 3\n 2.900000000000000e-02 -2.000000000000000e+00 1.000000000000000e+00 -1.300000000000000e+00 0.000000000000000e+00 0.000000000000000e+00\n -1.400000000000000e+00 -9.000000000000000e-01 -2.200000000000000e+00 -8.000000000000000e-01 0.000000000000000e+00 0.000000000000000e+00\n 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 3.000000000000000e+00 -2.000000000000000e-01\nNode: 4\n -2.000000000000000e+00 -2.300000000000000e+00 -3.000000000000000e-01 -1.400000000000000e+00 0.000000000000000e+00 0.000000000000000e+00\n -1.800000000000000e+00 3.000000000000000e-01 -2.900000000000000e+00 2.000000000000000e-01 0.000000000000000e+00 0.000000000000000e+00\n 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 2.800000000000000e+00 -1.000000000000000e-01\nNode: 5\n -4.300000000000000e+00 -1.500000000000000e+00 -1.700000000000000e+00 -8.000000000000000e-01 2.700000000000000e-02 0.000000000000000e+00\n -8.000000000000000e-01 1.400000000000000e+00 -2.100000000000000e+00 1.100000000000000e+00 0.000000000000000e+00 0.000000000000000e+00\n 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 2.567000000000000e+00 -1.000000000000000e-01\nNode: 6\n -5.000000000000000e+00 -2.000000000000000e-01 -1.621000000000000e+00 2.000000000000000e-01 2.000000000000000e-03 0.000000000000000e+00\n 7.000000000000000e-01 1.400000000000000e+00 -1.179000000000000e+00 1.100000000000000e+00 0.000000000000000e+00 0.000000000000000e+00\n 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 2.202000000000000e+00 -7.000000000000000e-01\nNode: 7\n -4.958000000000000e+00 1.000000000000000e-01 -1.208000000000000e+00 6.000000000000000e-01 0.000000000000000e+00 0.000000000000000e+00\n 1.892000000000000e+00 1.000000000000000e+00 -3.900000000000000e-01 3.000000000000000e-01 0.000000000000000e+00 0.000000000000000e+00\n 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 1.400000000000000e+00 -7.000000000000000e-01\nNode: 8\n -4.729000000000000e+00 0.000000000000000e+00 -7.000000000000000e-01 1.000000000000000e-01 0.000000000000000e+00 0.000000000000000e+00\n 2.806000000000000e+00 9.000000000000000e-01 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00\n 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 9.000000000000000e-01 -2.000000000000000e-01\nNode: 9\n -4.800000000000000e+00 -1.000000000000000e-01 -7.300000000000000e-01 -7.000000000000000e-01 0.000000000000000e+00 0.000000000000000e+00\n 3.700000000000000e+00 9.000000000000000e-01 -1.600000000000000e-02 -4.000000000000000e-01 0.000000000000000e+00 0.000000000000000e+00\n 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 8.000000000000000e-01 6.000000000000000e-01\nGroup name: meshEdits\n!#nodeset nodes\nNode group:\n1..9\n",
"rotation": [
0.0,
0.0,
0.0
],
"scaffoldSettings": {
"Coordinate dimensions": 3,
"D2 derivatives": true,
"D3 derivatives": true,
"Length": 1.0,
"Number of elements": 8
},
"scaffoldTypeName": "1D Path 1",
"scale": [
1.0,
1.0,
1.0
],
"translation": [
0.0,
0.0,
0.0
],
"userAnnotationGroups": [
{
"_AnnotationGroup": true,
"dimension": 1,
"identifierRanges": "1-3",
"name": "fundus of stomach",
"ontId": "UBERON:0001160"
},
{
"_AnnotationGroup": true,
"dimension": 1,
"identifierRanges": "4-5",
"name": "body of stomach",
"ontId": "UBERON:0001161"
},
{
"_AnnotationGroup": true,
"dimension": 1,
"identifierRanges": "6",
"name": "pyloric antrum",
"ontId": "UBERON:0001165"
},
{
"_AnnotationGroup": true,
"dimension": 1,
"identifierRanges": "7",
"name": "pyloric canal",
"ontId": "UBERON:0008858"
},
{
"_AnnotationGroup": true,
"dimension": 1,
"identifierRanges": "8",
"name": "duodenum",
"ontId": "UBERON:0002114"
}
]
},
"Circular muscle layer relative thickness": 0.15,
"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": 1.5,
"Ostium inter-vessel distance": 0.0,
"Ostium inter-vessel height": 0.0,
"Ostium length": 1.5,
"Ostium wall relative thicknesses": [
0.75,
0.05,
0.15,
0.05
],
"Ostium wall thickness": 0.35,
"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": 0.5,
"Vessel wall relative thicknesses": [
0.75,
0.05,
0.15,
0.05
],
"Vessel wall thickness": 0.2
},
"scaffoldTypeName": "3D Ostium 1",
"scale": [
1.0,
1.0,
1.0
],
"translation": [
0.0,
0.0,
0.0
]
},
"Limiting ridge": true,
"Longitudinal muscle layer relative thickness": 0.05,
"Mucosa relative thickness": 0.75,
"Number of elements around duodenum": 16,
"Number of elements between cardia and duodenum": 5,
"Number of elements between fundus apex and cardia": 5,
"Number of elements through wall": 4,
"Refine": false,
"Refine number of elements surface": 4,
"Refine number of elements through wall": 1,
"Submucosa relative thickness": 0.05,
"Use linear through wall": true,
"Wall thickness": 0.35
},
"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
}
}
