Location: Generic human stomach scaffold @ cc71de553b5e / OrganScaffold-settings.json

Author:
Mabelle Lin <mlin865@aucklanduni.ac.nz>
Date:
2022-09-05 15:26:43+12:00
Desc:
Making scaffold resusable in PMR
Permanent Source URI:
https://models.fieldml.org/workspace/663/rawfile/cc71de553b5ebaa29af0d3e4f7355a6ff5c1625c/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  7.080000000000000e+01 -1.700000000000000e+01  3.930000000000000e+01 -3.700000000000000e+00  0.000000000000000e+00  0.000000000000000e+00\n  7.230000000000000e+01 -4.790000000000000e+01 -1.390000000000000e+01 -5.900000000000000e+00  0.000000000000000e+00  0.000000000000000e+00\n  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  3.870000000000000e+01  4.500000000000000e+00\nNode: 2\n  5.110000000000000e+01 -2.230000000000000e+01  3.220000000000000e+01 -1.060000000000000e+01  0.000000000000000e+00  0.000000000000000e+00\n  3.070000000000000e+01 -3.490000000000000e+01 -2.050000000000000e+01 -7.200000000000000e+00  0.000000000000000e+00  0.000000000000000e+00\n  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  4.140000000000000e+01  9.000000000000000e-01\nNode: 3\n  2.780000000000000e+01 -2.770000000000000e+01  1.870000000000000e+01 -1.510000000000000e+01  0.000000000000000e+00  0.000000000000000e+00\n  2.700000000000000e+00 -1.840000000000000e+01 -2.820000000000000e+01 -2.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00\n  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  4.090000000000000e+01 -5.000000000000000e+00\nNode: 4\n -3.000000000000000e-01 -2.800000000000000e+01  2.300000000000000e+00 -1.290000000000000e+01  0.000000000000000e+00  0.000000000000000e+00\n -5.800000000000000e+00 -2.600000000000000e+00 -2.560000000000000e+01  4.600000000000000e+00  0.000000000000000e+00  0.000000000000000e+00\n  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  3.230000000000000e+01 -9.400000000000000e+00\nNode: 5\n -2.650000000000000e+01 -2.060000000000000e+01 -7.500000000000000e+00 -6.400000000000000e+00  0.000000000000000e+00  0.000000000000000e+00\n -2.900000000000000e+00  8.000000000000000e+00 -1.920000000000000e+01  8.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00\n  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  2.210000000000000e+01 -6.800000000000000e+00\nNode: 6\n -4.060000000000000e+01 -1.100000000000000e+01 -1.160000000000000e+01 -4.000000000000000e-01  0.000000000000000e+00  0.000000000000000e+00\n  7.400000000000000e+00  1.250000000000000e+01 -1.020000000000000e+01  7.800000000000000e+00  0.000000000000000e+00  0.000000000000000e+00\n  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  1.760000000000000e+01 -5.900000000000000e+00\nNode: 7\n -4.810000000000000e+01 -6.400000000000000e+00 -8.600000000000000e+00  4.000000000000000e-01  0.000000000000000e+00  0.000000000000000e+00\n  2.100000000000000e+01  1.570000000000000e+01 -3.500000000000000e+00  4.400000000000000e+00  0.000000000000000e+00  0.000000000000000e+00\n  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  1.050000000000000e+01 -3.100000000000000e+00\nNode: 8\n -5.290000000000000e+01 -3.200000000000000e+00 -1.110000000000000e+01 -5.500000000000000e+00  0.000000000000000e+00  0.000000000000000e+00\n  3.860000000000000e+01  1.930000000000000e+01 -1.900000000000000e+00 -1.100000000000000e+00  0.000000000000000e+00  0.000000000000000e+00\n  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  1.200000000000000e+01  6.100000000000000e+00\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": "2-3",
                            "name": "body of stomach",
                            "ontId": "UBERON:0001161"
                        },
                        {
                            "_AnnotationGroup": true,
                            "dimension": 1,
                            "identifierRanges": "4-5",
                            "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": 0.25,
                "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": 25.0,
                        "Ostium inter-vessel distance": 0.0,
                        "Ostium inter-vessel height": 0.0,
                        "Ostium length": 15.0,
                        "Ostium wall relative thicknesses": [
                            0.55,
                            0.15,
                            0.25,
                            0.05
                        ],
                        "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": 5.0,
                        "Vessel wall relative thicknesses": [
                            0.55,
                            0.15,
                            0.25,
                            0.05
                        ],
                        "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": 0.05,
                "Mucosa relative thickness": 0.55,
                "Number of elements around duodenum": 16,
                "Number of elements between cardia and duodenum": 6,
                "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": 0.15,
                "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
    }
}