Command-line tools

To see if the Datamint command-line tools were installed correctly, run:

datamint-config --help

You should see this in the first line:

usage: datamint-config [-h] [--api-key API_KEY] [--default-url DEFAULT_URL] [-i]
(...)

There are two command-line tools available:

• datamint-config: To configure the Datamint API key and URL.

• datamint-upload: To upload DICOM/mp4/png/jpeg files to the Datamint server.

Configuring the Datamint settings

The datamint-config command-line tool is useful for configuring the Datamint API key and URL, consequently avoiding the need to manually pass them as arguments or environment variables to the other commands later.

To manage Datamint configurations, just run

datamint-config

It starts an interactive prompt, guiding you through the configuration process.

To set the API key without the interactive prompt, use the command-line option --api-key:

datamint-config --api-key YOUR_API_KEY

Uploading DICOMs/resources to Datamint server

To upload DICOM files to the Datamint server, use the datamint-upload command. For example, to upload all the DICOM files in the /path/to/dicom_files directory, run:

datamint-upload --path /path/to/dicom_files/

By default, the DICOM files are anonymized before uploading. If you want to retain the personal identifiable information (PII) in the DICOM files, use the --retain-pii flag:

datamint-upload --path /path/to/dicom_files/ --retain-pii

To upload all DICOMs in a directory and also in its subdirectories, you can use the recursive option -r flag:

datamint-upload --path /path/to/dicom_files/ -r

In Datamint, you can use channels to organize your DICOMs/resources. In that case, use the --channel flag:

datamint-upload --path /path/to/video.mp4 --channel "CT scans"

To upload resources, associating them with a tag, run:

datamint-upload --path /path/to/dicom_files --tag "my_tag"

You can specify multiple tags by repeating the --tag flag:

datamint-upload --path /path/to/dicom_files --tag "tag1" --tag "tag2"

You can bypass the inbox/review and directly publish your resources with the --publish flag:

datamint-upload --path /path/to/resource_file --publish

Example using include and exclude extensions options:

To upload only DICOM files, run:

datamint-upload --path /root_dir --include-extensions dcm

To upload all files except the .txt and .csv files, run:

datamint-upload --path /root_dir --exclude-extensions txt,csv

Uploading segmentations along with the resources

To upload segmentations along with the resources, you can use

datamint-upload --path data/OAI_CARE/dicoms/ -r --segmentation_path data/OAI_CARE/segmentations/ --publish

, where both “data/OAI_CARE/dicoms/” and “data/OAI_CARE/segmentations/” must obey the same folder structure. Both folders and files can have arbritary names, but if you want to provide the segmentation label names, the segmentation file names must contain the segmentation name and you must provide a yaml file like this one:

segmentation_names: ["Bones", "BoneHead", "BML"]
class_names: {
    1: "Femur",
    2: "Tibia",
    4: "FC",
    8: "TC",
    16: "PAT"
}

, where the segmentation_names are the names being that a segmentation files (for instance, BoneHead is in ‘Case14_9587749__TSE_BoneHead_2.nii.gz’) and the class_names is mapping the pixel values to the class names. class_names is optional, so you can provide only the segmentation_names if you don’t want to map the pixel values. You can provide the segmentation names file with the –segmentation_names flag:

datamint-upload --path data/OAI_CARE/dicoms/ -r --segmentation_path data/OAI_CARE/segmentations/ --segmentation_names segmentation_names.yaml --publish

To check if the segmentations were uploaded correctly, you can see some information after running your command line:

(...)
Number of images with an associated segmentation: 4 (100%)
Number of segmentations with associated name: 4 (100%)
Do you want to proceed with the upload? (y/n):

All available options

See all available options by running datamint-upload --help:

-h, --help

show this help message and exit

--path FILE

Path to the resource file(s) or a directory

-r [RECURSIVE], –recursive [RECURSIVE]

Recurse folders looking for dicoms. If a number is passed, recurse that number of levels.

--exclude EXCLUDE

Exclude folders that match the specified pattern. Example: “*_not_to_upload” will exclude folders ending with “_not_to_upload

--name CHANNEL, --channel CHANNEL

Channel name (arbritary) to upload the resources to. Useful for organizing the resources in the platform.

--retain-pii

Do not anonymize DICOMs

--retain-attribute RETAIN_ATTRIBUTE

Retain the value of a single attribute code specified as hexidecimal integers. Example: (0x0008, 0x0050) or just (0008, 0050)

--tag TAG

A tag name to be applied to all files

--publish

Publish the uploaded resources, giving them the status “published” instead of “inbox”

--mungfilename MUNGFILENAME

Change the filename in the upload parameters. If set to “all”, the filename becomes the folder names joined together with “_”. If one or more integers are passed (comma-separated), append that depth of folder name to the filename.

--include-extensions INCLUDE_EXTENSIONS

File extensions to be considered for uploading. Default: all file extensions. Example: --include-extensions dcm jpg png

--exclude-extensions EXCLUDE_EXTENSIONS

File extensions to be excluded from uploading. Default: none. Example: --exclude-extensions txt csv

--segmentation_path FILE

Path to the segmentation file(s) or a directory

--segmentation_names FILE

Path to a yaml file containing the segmentation names. The file may contain two keys: “segmentation_names” and “class_names”.

--yes

Automatically answer yes to all prompts

--version

show program’s version number and exit