descriptor.json

{
  "command-line": "python run.py CYTOMINE_HOST CYTOMINE_PUBLIC_KEY CYTOMINE_PRIVATE_KEY CYTOMINE_ID_PROJECT CYTOMINE_ID_SOFTWARE CYTOMINE_ID_USERS CYTOMINE_ID_IMAGES CYTOMINE_ID_TERMS CYTOMINE_ID_POSITIVE_TERMS CYTOMINE_REVIEWED CYTOMINE_ZOOM_LEVEL CYTOMINE_BINARY PYXIT_TARGET_WIDTH PYXIT_TARGET_HEIGHT N_JOBS PYXIT_TRANSPOSE PYXIT_N_SUBWINDOWS PYXIT_INTERPOLATION PYXIT_FIXED_SIZE PYXIT_COLORSPACE PYXIT_MIN_SIZE PYXIT_MAX_SIZE FOREST_N_ESTIMATORS FOREST_MIN_SAMPLES_SPLIT FOREST_MAX_FEATURES SVM_C SEED SVM",
  "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"
    },
    {
      "default-value": "",
      "name": "Cytomine users ids",
      "description": "(Annotations filtering) Identifiers of users of which the annotations should be selected for training.",
      "set-by-server": false,
      "value-key": "@ID",
      "optional": true,
      "id": "cytomine_id_users",
      "type": "ListDomain",
      "uri": "/api/project/$currentProject$/user.json",
      "uri-print-attribute": "username",
      "command-line-flag": "--@id"
    },
    {
      "default-value": "",
      "name": "Cytomine images ids",
      "description": "(Annotations filtering) Identifiers of images of which the annotations should be selected for training.",
      "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"
    },
    {
      "default-value": "",
      "name": "Cytomine terms ids",
      "description": "(Annotations filtering) Identifiers of terms of which the annotations should be selected for training.",
      "set-by-server": false,
      "value-key": "@ID",
      "optional": true,
      "id": "cytomine_id_terms",
      "type": "ListDomain",
      "uri": "/api/project/$currentProject$/term.json",
      "uri-print-attribute": "name",
      "command-line-flag": "--@id"
    },
    {
      "default-value": "",
      "name": "Cytomine positive terms ids",
      "description": "When provided, binary segmentation is enabled. A subset of the terms of the cytomine_id_terms that should be considered as foreground during the segmentation.",
      "set-by-server": false,
      "value-key": "@ID",
      "optional": true,
      "id": "cytomine_id_positive_terms",
      "type": "ListDomain",
      "uri": "/api/project/$currentProject$/term.json",
      "uri-print-attribute": "name",
      "command-line-flag": "--@id"
    },
    {
      "default-value": 0,
      "name": "Cytomine reviewed",
      "description": "(Annotations filtering) \u00270\u0027 for using regular annotations. \u00271\u0027 for also including reviewed annotations. \u00272\u0027 for using only reviewed annotations.",
      "set-by-server": false,
      "value-key": "@ID",
      "optional": true,
      "id": "cytomine_reviewed",
      "type": "Number",
      "command-line-flag": "--@id"
    },
    {
      "default-value": 0,
      "name": "Cytomine zoom level",
      "description": "The zoom level for reading the slides (0 for max zoom, 1 or more for smaller magnification)",
      "set-by-server": false,
      "value-key": "@ID",
      "optional": true,
      "id": "cytomine_zoom_level",
      "type": "Number",
      "command-line-flag": "--@id"
    },
    {
      "default-value": 24,
      "name": "Pyxit Target Width",
      "description": "pyxit_target_width",
      "set-by-server": false,
      "value-key": "@ID",
      "optional": true,
      "id": "pyxit_target_width",
      "type": "Number",
      "command-line-flag": "--@id"
    },
    {
      "default-value": 24,
      "name": "Pyxit Target Height",
      "description": "pyxit_target_height",
      "set-by-server": false,
      "value-key": "@ID",
      "optional": true,
      "id": "pyxit_target_height",
      "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"
    },
    {
      "default-value": true,
      "name": "Pyxit Transpose",
      "description": "pyxit_transpose",
      "set-by-server": false,
      "value-key": "@ID",
      "optional": true,
      "id": "pyxit_transpose",
      "type": "Boolean",
      "command-line-flag": "--@id"
    },
    {
      "default-value": 100,
      "name": "Pyxit N Subwindows",
      "description": "pyxit_n_subwindows",
      "set-by-server": false,
      "value-key": "@ID",
      "optional": true,
      "id": "pyxit_n_subwindows",
      "type": "Number",
      "command-line-flag": "--@id"
    },
    {
      "default-value": 1,
      "name": "Pyxit Interpolation",
      "description": "pyxit_interpolation",
      "set-by-server": false,
      "value-key": "@ID",
      "optional": true,
      "id": "pyxit_interpolation",
      "type": "Number",
      "command-line-flag": "--@id"
    },
    {
      "default-value": true,
      "name": "Pyxit Fixed Size",
      "description": "pyxit_fixed_size",
      "set-by-server": false,
      "value-key": "@ID",
      "optional": true,
      "id": "pyxit_fixed_size",
      "type": "Boolean",
      "command-line-flag": "--@id"
    },
    {
      "default-value": 2,
      "name": "Pyxit Colorspace",
      "description": "pyxit_colorspace",
      "set-by-server": false,
      "value-key": "@ID",
      "optional": true,
      "id": "pyxit_colorspace",
      "type": "Number",
      "command-line-flag": "--@id"
    },
        {
      "default-value": 0.1,
      "name": "Pyxit Min Size",
      "description": "pyxit_min_size",
      "set-by-server": false,
      "value-key": "@ID",
      "optional": true,
      "id": "pyxit_min_size",
      "type": "Number",
      "command-line-flag": "--@id"
    },
    {
      "default-value": 1,
      "name": "Pyxit Max Size",
      "description": "pyxit_max_size",
      "set-by-server": false,
      "value-key": "@ID",
      "optional": true,
      "id": "pyxit_max_size",
      "type": "Number",
      "command-line-flag": "--@id"
    },
    {
      "default-value": 10,
      "name": "Forest N Estimators",
      "description": "forest_n_estimators",
      "set-by-server": false,
      "value-key": "@ID",
      "optional": true,
      "id": "forest_n_estimators",
      "type": "Number",
      "command-line-flag": "--@id"
    },
    {
      "default-value": 2,
      "name": "Forest Min Samples Split",
      "description": "forest_min_samples_split",
      "set-by-server": false,
      "value-key": "@ID",
      "optional": true,
      "id": "forest_min_samples_split",
      "type": "Number",
      "command-line-flag": "--@id"
    },
    {
      "default-value": 28,
      "name": "Forest Max Features",
      "description": "forest_max_features",
      "set-by-server": false,
      "value-key": "@ID",
      "optional": true,
      "id": "forest_max_features",
      "type": "Number",
      "command-line-flag": "--@id"
    },
    {
      "default-value": 42,
      "name": "Random seed",
      "description": "The random generator integer seed",
      "set-by-server": false,
      "value-key": "@ID",
      "optional": true,
      "id": "seed",
      "type": "Number",
      "command-line-flag": "--@id"
    }
  ],
  "name": "Segment-ML-MultiOutputET-Train",
  "description": "Image segmentation algorithm based on extremely randomized trees",
  "schema-version": "cytomine-0.1",
  "container-image": {
    "image": "cytomineuliege/s_segment-ml-multioutputet-train",
    "type": "singularity"
  }
}