pl-dicom_unpack
is a ChRIS
ds plugin which takes in a single "multi-frame" DICOM as input file and unpacks it into a
series of individual dicom files.
This plugin is a simple app to unpack a "multi-frame" dicom into a list of individual dicom slices.
pl-dicom_unpack
is a ChRIS plugin, meaning it can
run from either within ChRIS or the command-line.
To get started with local command-line usage, use Apptainer
(a.k.a. Singularity) to run pl-dicom_unpack
as a container:
apptainer exec docker://fnndsc/pl-dicom_unpack dicom_unpack [--args values...] input/ output/
To print its available options, run:
apptainer exec docker://fnndsc/pl-dicom_unpack dicom_unpack --help
dicom_unpack
requires two positional arguments: a directory containing
input data, and a directory where to create output data.
First, create the input directory and move input data into it.
mkdir incoming/ outgoing/
mv some.dat other.dat incoming/
apptainer exec docker://fnndsc/pl-dicom_unpack:latest dicom_unpack [--args] incoming/ outgoing/
Instructions for developers.
Build a local container image:
docker build -t localhost/fnndsc/pl-dicom_unpack .
Mount the source code dicom_unpack.py
into a container to try out changes without rebuild.
docker run --rm -it --userns=host -u $(id -u):$(id -g) \
-v $PWD/dicom_unpack.py:/usr/local/lib/python3.11/site-packages/dicom_unpack.py:ro \
-v $PWD/in:/incoming:ro -v $PWD/out:/outgoing:rw -w /outgoing \
localhost/fnndsc/pl-dicom_unpack dicom_unpack /incoming /outgoing
Run unit tests using pytest
.
It's recommended to rebuild the image to ensure that sources are up-to-date.
Use the option --build-arg extras_require=dev
to install extra dependencies for testing.
docker build -t localhost/fnndsc/pl-dicom_unpack:dev --build-arg extras_require=dev .
docker run --rm -it localhost/fnndsc/pl-dicom_unpack:dev pytest
Steps for release can be automated by Github Actions. This section is about how to do those steps manually.
Increase the version number in setup.py
and commit this file.
Build and push an image tagged by the version. For example, for version 1.2.3
:
docker build -t docker.io/fnndsc/pl-dicom_unpack:1.2.3 .
docker push docker.io/fnndsc/pl-dicom_unpack:1.2.3
Run chris_plugin_info
to produce a JSON description of this plugin, which can be uploaded to ChRIS.
docker run --rm docker.io/fnndsc/pl-dicom_unpack:1.2.3 chris_plugin_info -d docker.io/fnndsc/pl-dicom_unpack:1.2.3 > chris_plugin_info.json
Intructions on how to upload the plugin to ChRIS can be found here: https://chrisproject.org/docs/tutorials/upload_plugin