Docker Wrappers

Overview

The PACSIFIER package includes convenient Docker wrapper scripts that allow users to run CLI commands via Docker without needing to remember complex docker run command syntax. These wrappers handle volume mounting and Docker configuration automatically.

Available Wrapper Scripts

The following Docker wrapper scripts are available:

  • docker_pacsifier: Docker wrapper for the main pacsifier command

  • docker_get_pseudonyms: Docker wrapper for pacsifier-get-pseudonyms

  • docker_add_karnak_tags: Docker wrapper for pacsifier-add-karnak-tags

  • docker_anonymize_dicoms: Docker wrapper for pacsifier-anonymize

  • docker_extract_carestream_report: Docker wrapper for pacsifier-extract-carestream-report

  • docker_move_dumps: Docker wrapper for pacsifier-move-csv

  • docker_create_dicomdir: Docker wrapper for pacsifier-create-dicomdir

Configuration

Docker Image Selection

By default, the wrapper scripts use the pacsifier:latest Docker image. You can override this in two ways:

  1. Set the PACSIFIER_DOCKER_IMAGE environment variable:

export PACSIFIER_DOCKER_IMAGE=pacsifier:1.0.0

  1. Use the --image flag with each command:

docker_pacsifier --image pacsifier:1.0.0 -c config.json -i -q query.csv -d /output --save

Usage Examples

docker_pacsifier

Run the main PACSIFIER command:

docker_pacsifier -c config.json -i -s -q query.csv -d /output

Resume an interrupted extraction:

docker_pacsifier -c config.json -q query.csv -d /output --save --resume

docker_get_pseudonyms

Get pseudonyms for DICOM data:

docker_get_pseudonyms --mode de-id -c config.json -q query.csv -a ProjectName -d /output

docker_add_karnak_tags

Add Karnak tags to DICOM files:

docker_add_karnak_tags -d /path/to/input -n /path/to/new_ids.json -a AlbumName

docker_anonymize_dicoms

Anonymize DICOM files:

docker_anonymize_dicoms -d /path/to/input -o /path/to/output -i -p -a

docker_extract_carestream_report

Extract Carestream reports:

docker_extract_carestream_report -d /path/to/data

docker_move_dumps

Move CSV dump files:

docker_move_dumps -d /path/to/dicom -o /path/to/info

docker_create_dicomdir

Create a DICOMDIR file:

docker_create_dicomdir -d /path/to/input -o /path/to/output

How It Works

Volume Mounting

The wrapper scripts automatically handle Docker volume mounting. When you provide file or directory paths as arguments, the scripts:

  1. Convert the paths to absolute paths

  2. Mount them as Docker volumes at standardized container paths

  3. Pass the container paths to the PACSIFIER CLI commands

For example, when you run:

docker_pacsifier -c /home/user/config.json -q /home/user/query.csv -d /home/user/output --save

The wrapper script:

  1. Mounts /home/user/config.json as /config.json in the container

  2. Mounts /home/user/query.csv as /query.csv in the container

  3. Mounts /home/user/output as /output in the container

  4. Runs pacsifier -c /config.json -q /query.csv -d /output --save inside the container

Network Configuration

By default, the wrapper scripts use --net=host to allow the containerized PACSIFIER to communicate with PACS servers on the host network.

Troubleshooting

Docker Not Found

If you see an error message stating “Docker not found”, ensure that:

  1. Docker is installed on your system

  2. Docker is in your system PATH

  3. You have the necessary permissions to run Docker commands

Image Not Found

If the Docker image is not found, you may need to:

  1. Build the PACSIFIER Docker image first

  2. Specify the correct image name using the --image flag or PACSIFIER_DOCKER_IMAGE environment variable

See Also