descriptor.json

{
  "command-line": "python run.py CYTOMINE_HOST CYTOMINE_PUBLIC_KEY CYTOMINE_PRIVATE_KEY CYTOMINE_ID_PROJECT CYTOMINE_ID_SOFTWARE CYTOMINE_ID_IMAGES CYTOMINE_ID_ROI_TERM CYTOMINE_REVIEWED_ROI CYTOMINE_ZOOM_LEVEL CYTOMINE_TILE_SIZE CYTOMINE_TILE_OVERLAP CYTOMINE_ROI_ANNOTATIONS N_JOBS UNION_ENABLED MIN_ANNOTATION_AREA MAX_ANNOTATION_AREA TILE_FILTER_MIN_STDDEV TILE_FILTER_MAX_MEAN CYTOMINE_ID_JOB PYXIT_PREDICTION_STEP CYTOMINE_ID_PREDICT_TERM",
  "inputs": [
    {
      "name": "Cytomine host",
      "description": "Cytomine server hostname",
      "set-by-server": true,
      "value-key": "@ID",
      "optional": false,
      "id": "cytomine_host",
      "type": "String",
      "command-line-flag": "--@id"
    },
    {
      "name": "Cytomine public key",
      "description": "Cytomine public key",
      "set-by-server": true,
      "value-key": "@ID",
      "optional": false,
      "id": "cytomine_public_key",
      "type": "String",
      "command-line-flag": "--@id"
    },
    {
      "name": "Cytomine private key",
      "description": "Cytomine private key",
      "set-by-server": true,
      "value-key": "@ID",
      "optional": false,
      "id": "cytomine_private_key",
      "type": "String",
      "command-line-flag": "--@id"
    },
    {
      "name": "Cytomine project id",
      "description": "Cytomine project id",
      "set-by-server": true,
      "value-key": "@ID",
      "optional": false,
      "id": "cytomine_id_project",
      "type": "Number",
      "command-line-flag": "--@id"
    },
    {
      "name": "Cytomine software id",
      "description": "Cytomine software id",
      "set-by-server": true,
      "value-key": "@ID",
      "optional": false,
      "id": "cytomine_id_software",
      "type": "Number",
      "command-line-flag": "--@id"
    },
    {
      "name": "Cytomine image identifiers",
      "description": "The identifiers of the images to process. If not specified all image of the project will be processed.",
      "set-by-server": false,
      "value-key": "@ID",
      "optional": true,
      "id": "cytomine_id_images",
      "type": "ListDomain",
      "uri": "/api/project/$currentProject$/imageinstance.json",
      "uri-print-attribute": "instanceFilename",
      "command-line-flag": "--@id"
    },
    {
      "name": "Cytomine roi term identifier",
      "description": "If specified only process ROIs from annotation having the given term id.",
      "set-by-server": false,
      "value-key": "@ID",
      "optional": true,
      "id": "cytomine_id_roi_term",
      "type": "Domain",
      "uri": "/api/project/$currentProject$/term.json",
      "uri-print-attribute": "name",
      "command-line-flag": "--@id"
    },
    {
      "name": "Cytomine reviewed annotations",
      "description": "Use only reviewed annotations if true, otherwise use basic annotations (not reviewed). Only used if a roi term identifier is provided.",
      "set-by-server": false,
      "value-key": "@ID",
      "optional": true,
      "default-value": false,
      "id": "cytomine_reviewed_roi",
      "type": "Boolean",
      "command-line-flag": "--@id"
    },
    {
      "name": "Region of interest annotations",
      "description": "Identifier of annotations containing the ROIs to process (cytomine_id_images, cytomine_id_roi_term and cytomine_reviewed_roi are ignored when ROIs are provided).",
      "set-by-server": false,
      "value-key": "@ID",
      "optional": true,
      "id": "cytomine_roi_annotations",
      "type": "ListDomain",
      "command-line-flag": "--@id"
    },
    {
      "name": "Cytomine predict term identifier",
      "description": "Identifier of a term to associate with the annotations of the segmented elements if the trained model was trained in binary. If the parameter is not provided, the uploaded annotations will not be associated a term. In case of multiclass training (i.e. not binary), this parameter is ignored.",
      "set-by-server": false,
      "value-key": "@ID",
      "optional": true,
      "id": "cytomine_id_predict_term",
      "type": "Domain",
      "uri": "/api/project/$currentProject$/term.json",
      "uri-print-attribute": "name",
      "command-line-flag": "--@id"
    },
    {
      "name": "Zoom level",
      "description": "The zoom level to apply when fetching the tiles (0 for maximum resolution). If zoom_level > 0, tile size and overlap should be respectively set to 256 and 0 (IIP protocol).",
      "set-by-server": false,
      "value-key": "@ID",
      "default-value": 0,
      "optional": true,
      "id": "cytomine_zoom_level",
      "type": "Number",
      "command-line-flag": "--@id"
    },
    {
      "name": "Tile size",
      "description": "The size of the square tiles in pixels. Each processed image will be splitted into a set of tiles that will be processed independently. If union is enabled, the polygons found on each tiles will be merged when necessary.",
      "set-by-server": false,
      "value-key": "@ID",
      "default-value": 512,
      "optional": true,
      "id": "cytomine_tile_size",
      "type": "Number",
      "command-line-flag": "--@id"
    },
    {
      "name": "Tile overlap",
      "description": "The overlap between tiles to extract (suggested: equal to the pyxit window target dimensions)",
      "set-by-server": false,
      "value-key": "@ID",
      "default-value": 24,
      "optional": true,
      "id": "cytomine_tile_overlap",
      "type": "Number",
      "command-line-flag": "--@id"
    },
    {
      "default-value": 1,
      "name": "Number of jobs",
      "description": "Number of jobs for training",
      "set-by-server": false,
      "value-key": "@ID",
      "optional": true,
      "id": "n_jobs",
      "type": "Number",
      "command-line-flag": "--@id"
    },
    {
      "name": "Union enabled",
      "description": "Whether or not to perform union of detected polygons over tiles.",
      "set-by-server": false,
      "value-key": "@ID",
      "default-value": true,
      "optional": true,
      "id": "union_enabled",
      "type": "Boolean",
      "command-line-flag": "--@id"
    },
    {
      "name": "Min annotations area",
      "description": "Minimum area for annotations. Annotations of which the area is smaller are not uploaded to the server (disabled by default).",
      "set-by-server": false,
      "value-key": "@ID",
      "default-value": 0,
      "optional": true,
      "id": "min_annotation_area",
      "type": "Number",
      "command-line-flag": "--@id"
    },
    {
      "name": "Max annotations area",
      "description": "Maximum area for annotations. Annotations of which the area is larger are not uploaded to the server (-1 for disabling the filter, disabled by default).",
      "set-by-server": false,
      "value-key": "@ID",
      "default-value": -1,
      "optional": true,
      "id": "max_annotation_area",
      "type": "Number",
      "command-line-flag": "--@id"
    },
    {
      "name": "Minimum standard deviation for tile filtering",
      "description": "Minimum standard devation to consider for empty tiles filtering (see tile_filter_enabled for more information).",
      "set-by-server": false,
      "value-key": "@ID",
      "default-value": 0,
      "optional": true,
      "id": "tile_filter_min_stddev",
      "type": "Number",
      "command-line-flag": "--@id"
    },
    {
      "name": "Maximum mean for tile filtering",
      "description": "Maximum mean to consider for empty tiles filtering (see tile_filter_enabled for more information).",
      "set-by-server": false,
      "value-key": "@ID",
      "default-value": 255,
      "optional": true,
      "id": "tile_filter_max_mean",
      "type": "Number",
      "command-line-flag": "--@id"
    },
    {
      "name": "Training job identifier",
      "description": "Identifier of the training job. The job should have the trained model attached (as a \"model.joblib\" attached file) and the properties \u0027binary\u0027, \u0027classes\u0027.",
      "set-by-server": false,
      "value-key": "@ID",
      "optional": false,
      "id": "cytomine_id_job",
      "type": "Domain",
      "uri": "/api/job.json?project=$currentProject$",
      "uri-sort-attribute": "softwareName",
      "uri-print-attribute": "softwareName",
      "command-line-flag": "--@id"
    },
    {
      "name": "Prediction step",
      "description": "Number of pixel to skip for each prediction. By default all pixels get a prediction (value 1)",
      "set-by-server": false,
      "value-key": "@ID",
      "default-value": 1,
      "optional": true,
      "id": "pyxit_prediction_step",
      "type": "Number",
      "command-line-flag": "--@id"
    }
  ],
  "name": "Segment-ML-MultiOutputET-Pred-BI",
  "description": "Segmentation based on extra trees",
  "schema-version": "cytomine-0.1",
  "container-image": {
    "image": "cytomineuliege/s_segment-ml-multioutputet-pred-bi",
    "type": "singularity"
  }
}