Command Line Interface#

The RedBrick CLI offers a simple interface to quickly import and export your images & annotations, and perform other high-level actions.

[1;34musage: [0m[1;35mredbrick[0m [[32m-h[0m] [[32m-v[0m] [[36m--completion [33m{bash,zsh,tcsh}[0m] [32m{config,init,clone,info,export,upload,report} ...[0m

Named Arguments#

-v, --version

show program’s version number and exit

--completion

Possible choices: bash, zsh, tcsh

print shell completion script

Commands#

command: Possible choices: config, init, clone, info, export, upload, report

Sub-commands#

config#

Setup the credentials for your CLI.

[1;34m[0m[1;35mredbrick config[0m [[32m-h[0m] [[36m--org [33mORG[0m] [[36m--key [33mKEY[0m] [[36m--url [33mURL[0m] [[36m--profile [33mPROFILE[0m] [[36m--force[0m] [32m{list,set,add,remove,clear,verify} ...[0m

Positional Arguments#

sub_command: Possible choices: list, set, add, remove, clear, verify

Named Arguments#

--org, -o

Org ID

--key, -k

API Key

--url, -u

Endpoint URL, should default to https://api.redbrickai.com.

--profile, -p

Profile name

--force, -f

Force create new credentials

Default: False

Sub-commands#

list#

List all credential profiles

[1;34m[0m[1;35mredbrick config list[0m [[32m-h[0m]

set#

Set your default credentials profile

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Positional Arguments#

profile: Profile name

add#

Add a new profile

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Named Arguments#

--org, -o: Org ID
--key, -k: Add your API Key.
--url, -u: Endpoint URL, should default to https://api.redbrickai.com.
--profile, -p: Define a name for your authentication profile.

remove#

Remove a profile

[1;34m[0m[1;35mredbrick config remove[0m [[32m-h[0m] [32m[profile][0m

Positional Arguments#

profile: Profile name

clear#

Clear all credentials

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verify#

Verify a profile

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Positional Arguments#

profile: Profile name

init#

Create a new project. We recommend creating a new directory and naming it after your project, initializing your project within the new directory.

$ mkdir new-project
$ cd new-project
$ redbrick init

[1;34m[0m[1;35mredbrick init[0m [[32m-h[0m] [[36m--name [33mNAME[0m] [[36m--taxonomy [33mTAXONOMY[0m] [[36m--reviews [33mREVIEWS[0m] [[36m--workspace [33mWORKSPACE[0m] [[36m--sibling-tasks [33mSIBLING_TASKS[0m] [32m[path][0m

Positional Arguments#

path

Local path of the empty project directory

Default: “.”

Named Arguments#

--name, -n: Project name
--taxonomy, -t: Taxonomy name
--reviews, -r: Number of review stages
--workspace, -w: The workspace that you want to add this project to
--sibling-tasks: Number of tasks created for each uploaded datapoint

clone#

The project will be cloned to a local directory named after your project name.

[1;34m[0m[1;35mredbrick clone[0m [[32m-h[0m] [32m[project][0m [32m[path][0m

Positional Arguments#

project: Project ID or Name
path: Local path of the empty project directory

info#

Get a project’s information

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Positional Arguments#

path

Path of project (Default: current directory)

Default: “.”

Named Arguments#

--get, -g

Possible choices: labelstorage

Get a project’s setting information

--set, -s

Possible choices: labelstorage

Set a project setting

export#

Export data for a project

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                [[36m--dicom-seg[0m] [[36m--mhd[0m] [[36m--clear-cache[0m] [[36m--concurrency [33mCONCURRENCY[0m] [[36m--stage [33mSTAGE[0m] [[36m--destination [33mDESTINATION[0m]
                [32m[type][0m

Positional Arguments#

type

Export type: (latest [default], groundtruth, )

Default: “latest”

Named Arguments#

--with-files

Export with files (e.g. images/video frames)

Default: False

--dicom-to-nifti

Convert DICOM images to NIfTI. Applicable when --with-files is set.

Default: False

--old-format

Whether to export tasks in old format. (Default: False)

Default: False

--without-masks

Exports only tasks JSON without downloading any segmentation masks. Note: This is not recommended for tasks with overlapping labels.

Default: False

--semantic

Whether to export all segmentations as semantic_mask. This will create one segmentation file per class. If this is set to True and a task has multiple instances per class, then attributes belonging to each instance will not be exported.

Default: False

--binary-mask

Whether to export all segmentations as binary masks. This will create one segmentation file per instance.

Default: False

--single-mask

Whether to export all segmentations in a single file. Binary mask will be considered if both binary_mask and single_mask are set.

Default: False

--no-consensus

Whether to export tasks without consensus info. If None, will default to export with consensus info, if it is enabled for the given project.

Default: False

--png

Export labels as PNG masks

Default: False

--rt-struct

Export labels as DICOM RT-Struct. (Only for DICOM images)

Default: False

--dicom-seg

Export labels as DICOM SEG. (Only for DICOM images)

Default: False

--mhd

Export segmentation masks in MHD format.

Default: False

--clear-cache

Clear local cache

Default: False

--concurrency, -c

Concurrency value (Default: 10)

Default: 10

--stage, -s

Export tasks that are currently in the given stage. Applicable only with redbrick export and redbrick export latest

--destination, -d

Destination directory (Default: current directory)

Default: “.”

upload#

Upload files to a project

[1;34m[0m[1;35mredbrick upload[0m [[32m-h[0m] [[36m--as-frames[0m] [[36m--type [33m[{DICOM3D,NIFTI3D,NRRD3D,IMAGE2D,VIDEO,VIDEOFRAMES}][0m] [[36m--as-study[0m] [[36m--json[0m] [[36m--segment-map [33mSEGMENT_MAP[0m] [[36m--storage [33mSTORAGE[0m]
                [[36m--label-storage [33mLABEL_STORAGE[0m] [[36m--ground-truth[0m] [[36m--label-validate[0m] [[36m--prune-segmentations[0m] [[36m--rt-struct[0m] [[36m--dicom-seg[0m] [[36m--mhd[0m] [[36m--clear-cache[0m]
                [[36m--concurrency [33mCONCURRENCY[0m]
                [32mdirectory[0m

Positional Arguments#

directory: The directory containing files to upload to the project

Named Arguments#

--as-frames

Upload video from image frames

Default: False

--type, -t

Possible choices: DICOM3D, NIFTI3D, NRRD3D, IMAGE2D, VIDEO, VIDEOFRAMES

Import file type [’DICOM3D’, ‘NIFTI3D’, ‘NRRD3D’, ‘IMAGE2D’, ‘VIDEO’, ‘VIDEOFRAMES’]

Please refer to our documentation, to understand the required folder structure and supported file types.

Default: “DICOM3D”

--as-study

Group files by study

Default: False

--json

Upload json files with list of task objects

Default: False

--segment-map, -m

Segmentation mapping file path

--storage, -s

Storage method: (redbrick [default], public, )

Default: “redbrick”

--label-storage

Label Storage method: (same as items storage --storage [default], redbrick, public, )

--ground-truth

Upload tasks directly to ground truth.

Default: False

--label-validate

Validate NIfTI label instances and segmentMap. By default, the uploaded NIfTI files are not validated during upload, which can result in invalid files being uploaded. Using this argument validates the files before upload, but may increase the upload time.

Default: False

--prune-segmentations

Prune segmentations that are not part of the series.

Default: False

--rt-struct

Upload segmentations from DICOM RT-Struct files.

Default: False

--dicom-seg

Upload segmentations from DICOM SEG files.

Default: False

--mhd

Upload segmentations from MHD files.

Default: False

--clear-cache

Clear local cache

Default: False

--concurrency, -c

Concurrency value (Default: 10)

Default: 10

report#

Generate an audit report for a project. Exports a JSON file containing all actions & events associated with every task, including:

Who annotated the task
Who uploaded the data
Who reviewed the task
and more.

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Positional Arguments#

type

Export type: (all [default], groundtruth)

Default: “all”

Named Arguments#

--concurrency, -c

Concurrency value (Default: 10)

Default: 10