Location: Generic rat stomach scaffold @ a574d9ad83d0 / OrganScaffold-settings.json

Author:
Mabelle Lin <mlin865@aucklanduni.ac.nz>
Date:
2022-09-05 15:37:42+12:00
Desc:
Make scaffold reusable in PMR
Permanent Source URI:
https://models.cellml.org/workspace/615/rawfile/a574d9ad83d0e2e6bfc6772b4a30ec8c47973d11/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  1.202000000000000e+01 -1.150000000000000e-01  6.618000000000000e+00  4.273000000000000e+00  0.000000000000000e+00  0.000000000000000e+00\n  6.890000000000000e+00 -5.868000000000000e+00 -1.300000000000000e-01 -4.479000000000000e+00  0.000000000000000e+00  0.000000000000000e+00\n  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  7.400000000000000e+00  1.387000000000000e+00\nNode: 2\n  1.045300000000000e+01 -3.014000000000000e+00  8.472000000000000e+00 -5.649999999999999e-01  0.000000000000000e+00  0.000000000000000e+00\n  1.000000000000000e+00 -5.681000000000000e+00 -4.495000000000000e+00 -4.250000000000000e+00  0.000000000000000e+00  0.000000000000000e+00\n  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  8.500000000000000e+00  8.129999999999999e-01\nNode: 3\n  6.100000000000000e+00 -6.119000000000000e+00  5.267000000000000e+00 -4.498000000000000e+00  0.000000000000000e+00  0.000000000000000e+00\n -4.000000000000000e+00 -3.739000000000000e+00 -8.619999999999999e+00 -3.019000000000000e+00  0.000000000000000e+00  0.000000000000000e+00\n  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  9.000000000000000e+00  1.720000000000000e-01\nNode: 4\n -1.200000000000000e+00 -7.509000000000000e+00 -7.000000000000000e-01 -6.147000000000000e+00  0.000000000000000e+00  0.000000000000000e+00\n -5.800000000000000e+00  5.010000000000000e-01 -1.038100000000000e+01  3.290000000000000e-01  0.000000000000000e+00  0.000000000000000e+00\n  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  8.800000000000001e+00 -4.540000000000000e-01\nNode: 5\n -8.198000000000000e+00 -5.873000000000000e+00 -6.570000000000000e+00 -3.357000000000000e+00  0.000000000000000e+00  0.000000000000000e+00\n -2.498000000000000e+00  5.549000000000000e+00 -7.456000000000000e+00  4.494000000000000e+00  0.000000000000000e+00  0.000000000000000e+00\n  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  8.100000000000000e+00 -1.342000000000000e+00\nNode: 6\n -1.129000000000000e+01 -7.770000000000000e-01 -5.607000000000000e+00  1.679000000000000e+00  0.000000000000000e+00  0.000000000000000e+00\n  4.896000000000000e+00  6.708000000000000e+00 -2.449000000000000e+00  4.032000000000000e+00  0.000000000000000e+00  0.000000000000000e+00\n  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  6.200000000000000e+00 -2.652000000000000e+00\nNode: 7\n -1.063100000000000e+01  3.440000000000000e-01 -3.677000000000000e+00  2.178000000000000e+00  0.000000000000000e+00  0.000000000000000e+00\n  9.289000000000000e+00  3.828000000000000e+00  4.800000000000000e-02  3.430000000000000e-01  0.000000000000000e+00  0.000000000000000e+00\n  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  2.800000000000000e+00 -8.190000000000000e-01\nNode: 8\n -1.070000000000000e+01 -3.500000000000000e-01 -2.570000000000000e+00  1.600000000000000e-01  0.000000000000000e+00  0.000000000000000e+00\n  1.220000000000000e+01  2.774000000000000e+00 -3.670000000000000e-01 -6.050000000000000e-01  0.000000000000000e+00  0.000000000000000e+00\n  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  2.687000000000000e+00  2.590000000000000e-01\nNode: 9\n -1.130000000000000e+01 -8.440000000000000e-01 -3.131000000000000e+00 -1.282000000000000e+00  0.000000000000000e+00  0.000000000000000e+00\n  1.480000000000000e+01  2.407000000000000e+00 -1.116000000000000e+00 -8.930000000000000e-01  0.000000000000000e+00  0.000000000000000e+00\n  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  3.400000000000000e+00 -2.590000000000000e-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": 0.18,
                "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": 5.0,
                        "Ostium inter-vessel distance": 0.0,
                        "Ostium inter-vessel height": 0.0,
                        "Ostium length": 5.0,
                        "Ostium wall relative thicknesses": [
                            0.65,
                            0.12,
                            0.18,
                            0.05
                        ],
                        "Ostium wall thickness": 0.5,
                        "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": 2.0,
                        "Vessel wall relative thicknesses": [
                            0.65,
                            0.12,
                            0.18,
                            0.05
                        ],
                        "Vessel wall thickness": 0.3
                    },
                    "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": 0.65,
                "Number of elements around duodenum": 16,
                "Number of elements between cardia and duodenum": 6,
                "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": 0.12,
                "Use linear through wall": true,
                "Wall thickness": 0.5
            },
            "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
    }
}