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_REVIEWED CYTOMINE_BINARY CYTOMINE_POSITIVE_TERMS CYTOMINE_DOWNLOAD_ALPHA CYTOMINE_ZOOM_LEVEL N_JOBS SVM_C SEED SVM PYXIT_TRANSPOSE PYXIT_TARGET_WIDTH PYXIT_TARGET_HEIGHT PYXIT_N_SUBWINDOWS PYXIT_MIN_SIZE PYXIT_MAX_SIZE PYXIT_INTERPOLATION PYXIT_FIXED_SIZE PYXIT_COLORSPACE FOREST_N_ESTIMATORS FOREST_MIN_SAMPLES_SPLIT FOREST_MAX_FEATURES ",
  "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": false,
      "id": "cytomine_id_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) '0' for using regular annotations. '1' for also including reviewed annotations. '2' 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": false,
      "name": "Binary classification",
      "description": "Whether (true) or not (false) to treat the problem as a binary classification or not. If true cytomine_positive_terms should contain the list of terms considered as positive. Otherwise, there will be as many classes as terms.",
      "set-by-server": false,
      "value-key": "@ID",
      "optional": true,
      "id": "cytomine_binary",
      "type": "Boolean",
      "command-line-flag": "--@id"
    },
    {
      "default-value": "",
      "name": "Positive terms",
      "description": "If cytomine_binary is true, contains the ids of the terms that represent the positive class.",
      "set-by-server": false,
      "value-key": "@ID",
      "optional": true,
      "id": "cytomine_positive_terms",
      "type": "ListDomain",
      "uri": "/api/project/$currentProject$/term.json",
      "uri-print-attribute": "name",
      "command-line-flag": "--@id"
    },
    {
      "default-value": false,
      "name": "Download alpha channel",
      "description": "Whether (true) or not (false) to download the alpha channel with the crops",
      "set-by-server": false,
      "value-key": "@ID",
      "optional": true,
      "id": "cytomine_download_alpha",
      "type": "Boolean",
      "command-line-flag": "--@id"
    },
    {
      "default-value": 1,
      "name": "Zoom level",
      "description": "Zoom level at which the crops should be downloaded",
      "set-by-server": false,
      "value-key": "@ID",
      "optional": true,
      "id": "cytomine_zoom_level",
      "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": 1,
      "name": "Svm C",
      "description": "svm_c",
      "set-by-server": false,
      "value-key": "@ID",
      "optional": true,
      "id": "svm_c",
      "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"
    },
    {
      "default-value": "false",
      "name": "Svm",
      "description": "svm",
      "set-by-server": false,
      "value-key": "@ID",
      "optional": true,
      "id": "svm",
      "type": "Boolean",
      "command-line-flag": "--@id"
    },
    {
      "default-value": "false",
      "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": 16,
      "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": 16,
      "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": 10,
      "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": 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": 2,
      "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": "false",
      "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": 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": 1,
      "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"
    }
  ],
  "name": "Classify-ML-RandomSubwET-Train",
  "description": "A Cytomine software for classifying crops with Random subwindows and ExtraTrees (training). All images are downloaded to the \u0027/data\u0027 folder.",
  "schema-version": "cytomine-0.1",
  "container-image": {
    "image": "cytomine/s_classify-ml-randomsubwet-train",
    "type": "singularity"
  }
}