MALPEM Brain Segmentation

pl-malpem is a ChRIS ds plugin which takes in ... as input files and creates ... as output files.

Abstract

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Installation

pl-malpem is a ChRIS plugin, meaning it can run from either within ChRIS or the command-line.

Local Usage

To get started with local command-line usage, use Apptainer (a.k.a. Singularity) to run pl-malpem as a container:

apptainer exec docker://fnndsc/pl-malpem malpem_cpl [--args values...] input/ output/

To print its available options, run:

apptainer exec docker://fnndsc/pl-malpem malpem_cpl --help

Examples

malpem_cpl 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-malpem:latest malpem_cpl [--args] incoming/ outgoing/

Development

Instructions for developers.

Building

Build a local container image:

docker build -t localhost/fnndsc/pl-malpem .

Running

Mount the source code malpem_cpl.py into a container to try out changes without rebuild.

docker run --rm -it --userns=host -u $(id -u):$(id -g) \
    -v $PWD/malpem_cpl.py:/usr/local/lib/python3.11/site-packages/malpem_cpl.py:ro \
    -v $PWD/in:/incoming:ro -v $PWD/out:/outgoing:rw -w /outgoing \
    localhost/fnndsc/pl-malpem malpem_cpl /incoming /outgoing

Testing

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-malpem:dev --build-arg extras_require=dev .
docker run --rm -it localhost/fnndsc/pl-malpem:dev pytest

Release

Steps for release can be automated by Github Actions. This section is about how to do those steps manually.

Increase Version Number

Increase the version number in setup.py and commit this file.

Push Container Image

Build and push an image tagged by the version. For example, for version 1.2.3:

docker build -t docker.io/fnndsc/pl-malpem:1.2.3 .
docker push docker.io/fnndsc/pl-malpem:1.2.3

Get JSON Representation

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-malpem:1.2.3 chris_plugin_info -d docker.io/fnndsc/pl-malpem: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