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descriptor.json
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descriptor.json
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{
"name": "Cytomine_VALIS_test_app",
"description": "Cytomine App for VALIS that can register multiple images, and map annotations between them",
"container-image": {
"image": "mamodeiuliege/s_cytomine_valis_test_app",
"type": "singularity"
},
"schema-version": "cytomine-0.1",
"command-line": "CYTOMINE_HOST CYTOMINE_PUBLIC_KEY CYTOMINE_PRIVATE_KEY CYTOMINE_ID_PROJECT CYTOMINE_ID_SOFTWARE ALL_IMAGES IMAGE_CROP REFERENCE_IMAGE IMAGE_ORDERING ALIGN_TOWARD_REFERENCE REGISTRATION_TYPE COMPOSE_NON_RIGID ANNOTATION_TO_MAP IMAGES_TO_WARP CYTOMINE_UPLOAD_HOST MAP_ANNOTATIONS_TO_WARPED_IMAGES MAX_PROC_SIZE MICRO_MAX_PROC_SIZE",
"inputs": [
{
"id": "cytomine_host",
"name": "Cytomine host",
"set-by-server": true,
"optional": false,
"type": "String",
"value-key": "@ID",
"command-line-flag": "--@id"
},
{
"id": "cytomine_public_key",
"name": "Cytomine public key",
"set-by-server": true,
"optional": false,
"type": "String",
"value-key": "@ID",
"command-line-flag": "--@id"
},
{
"id": "cytomine_private_key",
"name": "Cytomine private key",
"set-by-server": true,
"optional": false,
"type": "String",
"value-key": "@ID",
"command-line-flag": "--@id"
},
{
"id": "cytomine_id_project",
"name": "Cytomine project ID",
"set-by-server": true,
"optional": false,
"type": "Number",
"value-key": "@ID",
"command-line-flag": "--@id"
},
{
"id": "cytomine_id_software",
"name": "Cytomine software ID",
"set-by-server": true,
"optional": false,
"type": "Number",
"value-key": "@ID",
"command-line-flag": "--@id"
},
{
"id": "all_images",
"name": "All Images",
"description": "All Images that will be registered to or toward the reference image (may or may not include the reference image)",
"type": "ListDomain",
"uri": "/api/project/$currentProject$/imageinstance.json",
"uri-print-attribute": "instanceFilename",
"uri-sort-attribute": "instanceFilename",
"optional": false,
"value-key": "@ID",
"command-line-flag": "--@id"
},
{
"id": "image_crop",
"name": "Cropping modes for all images [see info]",
"description": "How to define the registration domain relative to all images. One of: 'reference' (defines the reference image as the domain), 'overlap' (means the common area only), 'all' (means the smallest area to include all images).",
"type": "String",
"optional": false,
"value-key": "@ID",
"value-choices": [
"reference",
"overlap",
"all"
],
"default-value": "all",
"command-line-flag": "--@id"
},
{
"id": "reference_image",
"name": "Reference Image",
"description": "Reference Image. Taken from ALL_IMAGES if not given",
"type": "Domain",
"uri": "/api/project/$currentProject$/imageinstance.json",
"uri-print-attribute": "instanceFilename",
"uri-sort-attribute": "instanceFilename",
"optional": true,
"value-key": "@ID",
"command-line-flag": "--@id"
},
{
"id": "image_ordering",
"name": "Image ordering [see info]",
"description": "How to order the images before doing the registration (useful for 3D registration). One of: 'auto' (default, meaning that the order doesn't matter), 'name' (to be ordered by filename), 'created' (to be ordered by addition date to Cytomine)",
"type": "String",
"optional": true,
"value-choices": [
"auto",
"name",
"created"
],
"default-value": "auto",
"value-key": "@ID",
"command-line-flag": "--@id"
},
{
"id": "align_toward_reference",
"name": "Align Toward Reference",
"description": "Align images toward the reference, rather that directly to the reference. Meaningless if fewer than 3 images, see VALIS documentation for more info.",
"type": "Boolean",
"optional": true,
"default-value": false,
"value-key": "@ID",
"command-line-flag": "--@id"
},
{
"id": "registration_type",
"name": "Registration Type [see info]",
"description": "The type of registration performed by VALIS. One of 'rigid' (using affine transformations on lower resolution versions), 'non-rigid' (using non-rigid deformations on lower resolution version), 'micro' (using non-rigid deformations on higher resolution, tunable using MICRO_REG_MAX_DIM_PX).",
"type": "String",
"optional": true,
"value-choices": [
"rigid",
"non-rigid",
"micro"
],
"default-value": "non-rigid",
"value-key": "@ID",
"command-line-flag": "--@id"
},
{
"id": "compose_non_rigid",
"name": "Compose using non rigid deformation",
"description": "See VALIS documentation for more info",
"type": "Boolean",
"optional": true,
"default-value": false,
"value-key": "@ID",
"command-line-flag": "--@id"
},
{
"id": "annotation_to_map",
"name": "Annotations to map",
"description": "Annotations that should be mapped to the reference image after registration",
"type": "ListDomain",
"uri": "/api/annotation.json?project=$currentProject$",
"uri-print-attribute": "id",
"uri-sort-attribute": "id",
"optional": true,
"default-value": "",
"value-key": "@ID",
"command-line-flag": "--@id"
},
{
"id": "images_to_warp",
"name": "Images to deform and upload",
"description": "All Images that should be deformed to match the reference and uploaded to the same project. Must also specify CYTOMINE_UPLOAD_HOST if there are images to deform and upload.",
"type": "ListDomain",
"uri": "/api/project/$currentProject$/imageinstance.json",
"uri-print-attribute": "instanceFilename",
"uri-sort-attribute": "instanceFilename",
"optional": true,
"default-value": "",
"value-key": "@ID",
"command-line-flag": "--@id"
},
{
"id": "cytomine_upload_host",
"name": "Cytomine upload host",
"description": "Cytomine upload host where the images should be uploaded to. Mandatory if there are images to deform and upload.",
"type": "String",
"optional": true,
"default-value": "",
"value-key": "@ID",
"command-line-flag": "--@id"
},
{
"id": "map_annotations_to_warped_images",
"name": "Map annotations to warped images",
"description": "In addition to the reference image, also map annotation to the deformed and uploaded images",
"type": "Boolean",
"optional": true,
"default-value": true,
"value-key": "@ID",
"command-line-flag": "--@id"
},
{
"id": "max_proc_size",
"name": "Maximum processing image size",
"description": "Maximum dimension (in pixel) for any image on which image processing and feature extraction takes place. If None, Valis's default (850) is used",
"type": "Number",
"integer": true,
"optional": true,
"default-value": 1000,
"value-key": "@ID",
"command-line-flag": "--@id"
},
{
"id": "micro_max_proc_size",
"name": "Maximum processing image size (micro)",
"description": "Maximum dimension (in pixel) for any image on which image processing and feature extraction takes place for the micro registration. It is an error to specify this value if REGISTRATION_TYPE is not 'micro'. If None, Valis's default (3000) is used",
"type": "Number",
"integer": true,
"optional": true,
"default-value": 3000,
"value-key": "@ID",
"command-line-flag": "--@id"
}
]
}