descriptor.json

{
  "name": "Segment-CV-AdaptThres-Sample",
  "description": "Detect samples in images using an adaptive threshold.",
  "schema-version": "cytomine-0.1",
  "container-image": {
    "image": "cytomine/s_segment-cv-adaptthres-sample",
    "index": "docker://",
    "type": "singularity"
    },
  "command-line": "python run.py [CYTOMINE_HOST] [CYTOMINE_PUBLIC_KEY] [CYTOMINE_PRIVATE_KEY] [CYTOMINE_ID_PROJECT] [CYTOMINE_ID_SOFTWARE] [LOG_LEVEL] [CYTOMINE_ID_IMAGES] [CYTOMINE_ID_PREDICTED_TERM] [MAX_IMAGE_SIZE] [THRESHOLD_CONSTANT] [THRESHOLD_BLOCKSIZE] [ERODE_ITERATIONS] [DILATE_ITERATIONS] [IMAGE_AREA_PERC_THRESHOLD]",
  "inputs": [
    {
      "id": "cytomine_host",
      "value-key": "[@ID]",
      "command-line-flag": "--@id",
      "name": "Cytomine host",
      "set-by-server": true,
      "optional": false,
      "type": "String"
    },
    {
      "id": "cytomine_public_key",
      "value-key": "[@ID]",
      "command-line-flag": "--@id",
      "name": "Cytomine public key",
      "set-by-server": true,
      "optional": false,
      "type": "String"
    },
    {
      "id": "cytomine_private_key",
      "value-key": "[@ID]",
      "command-line-flag": "--@id",
      "name": "Cytomine private key",
      "set-by-server": true,
      "optional": false,
      "type": "String"
    },
    {
      "id": "cytomine_id_project",
      "value-key": "[@ID]",
      "command-line-flag": "--@id",
      "name": "Cytomine project ID",
      "set-by-server": true,
      "optional": false,
      "type": "Number"
    },
    {
      "id": "cytomine_id_software",
      "value-key": "[@ID]",
      "command-line-flag": "--@id",
      "name": "Cytomine software ID",
      "set-by-server": true,
      "optional": false,
      "type": "Number"
    },
    {
      "id": "cytomine_id_images",
      "value-key": "[@ID]",
      "command-line-flag": "--@id",
      "name": "Cytomine image identifiers",
      "description": "The identifiers of the images to process. If not specified all images of the project will be processed.",
      "set-by-server": false,
      "optional": true,
      "type": "ListDomain",
      "uri": "/api/project/$currentProject$/imageinstance.json",
      "uri-print-attribute": "instanceFilename"
    },
    {
      "id": "cytomine_id_predicted_term",
      "value-key": "[@ID]",
      "command-line-flag": "--@id",
      "name": "Term to predict",
      "description": "The term that will be associated to detected samples",
      "optional": false,
      "type": "Domain",
      "uri": "/api/ontology/$currentOntology$/term.json",
      "uri-print-attribute": "name",
      "uri-sort-attribute": "name"
    },
    {
      "id": "max_image_size",
      "value-key": "[@ID]",
      "command-line-flag": "--@id",
      "name": "Maximum image size",
      "description": "Image is resized during the detection if the real image is larger.",
      "optional": false,
      "type": "Number",
      "integer": true,
      "default-value": "2048"
    },
    {
      "id": "threshold_blocksize",
      "value-key": "[@ID]",
      "command-line-flag": "--@id",
      "name": "Threshold block size",
      "description": "Size of a pixel neighborhood that is used to calculate a threshold value for the pixel",
      "optional": false,
      "type": "Number",
      "default-value": "951"
    },
    {
      "id": "threshold_constant",
      "value-key": "[@ID]",
      "command-line-flag": "--@id",
      "name": "Threshold constant",
      "description": "Constant C used in the computation of threshold value T(x,y) which is the weighted sum of the blockSize * blockSize neighborhood of (x,y) - C",
      "optional": false,
      "type": "Number",
      "default-value": "5"
    },
    {
      "id": "erode_iterations",
      "value-key": "[@ID]",
      "command-line-flag": "--@id",
      "name": "Number of erosions",
      "optional": false,
      "type": "Number",
      "integer": true,
      "default-value": "3"
    },
    {
      "id": "dilate_iterations",
      "value-key": "[@ID]",
      "command-line-flag": "--@id",
      "name": "Number of dilations",
      "optional": false,
      "type": "Number",
      "integer": true,
      "default-value": "3"
    },
    {
      "id": "image_area_perc_threshold",
      "value-key": "[@ID]",
      "command-line-flag": "--@id",
      "name": "Image Area Percentile Threshold",
      "description": "The detected component with an area less than the image area multipled by this percentile value will not be kept",
      "optional": false,
      "type": "Number",
      "integer": true,
      "minimum": 0,
      "maximum": 100,
      "default-value": "5"
    },
    {
      "id": "log_level",
      "value-key": "[@ID]",
      "command-line-flag": "--@id",
      "default": "INFO",
      "name": "Logging verbosity",
      "description": "The level is given by a value among 'DEBUG', 'INFO', 'WARNING', 'ERROR', 'CRITICAL'",
      "set-by-server": false,
      "optional": true,
      "type": "String"
    }
  ]
}