Skip to content

Latest commit

 

History

History
114 lines (75 loc) · 3.79 KB

README.md

File metadata and controls

114 lines (75 loc) · 3.79 KB
Raw

Leg-Length Discrepency - Dynamic Compute Flow

Version MIT License ci

pl-dylld is a ChRIS ds plugin which connects to a parent node containing DICOM images and then dynamically creates a responsive compute flow (including joins). In its output directory, pl-dylld generates various logging/tracking data.

The documentation for entire LLD workflow along with step by step data flow in each of the compute nodes can be found here https://github.com/FNNDSC/CHRIS_docs/blob/master/workflows/LLD.md

Abstract

Automatically calculating the lengths of human legs from XRay images can substantially improve radiological diagnosis time.

Installation

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

Get it from chrisstore.co

Local Usage

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

singularity exec docker://fnndsc/pl-dylld dylld [--args values...] input/ output/

To print its available options, run:

singularity exec docker://fnndsc/pl-dylld dylld --help

Examples

dylld 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/
singularity exec docker://fnndsc/pl-dylld:latest dylld [--args] incoming/ outgoing/

Development

Instructions for developers.

Building

Build a local container image:

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

Running

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

docker run --rm -it --userns=host  \
    -v $PWD/dylld.py:/usr/local/lib/python3.11/site-packages/dylld.py:ro \
    -v $PWD/control:/usr/local/lib/python3.11/site-packages/control:ro \
    -v $PWD/logic:/usr/local/lib/python3.11/site-packages/logic:ro \
    -v $PWD/state:/usr/local/lib/python3.11/site-packages/state:ro \
    -v $PWD/in:/incoming:ro -v $PWD/out:/outgoing:rw -w /outgoing \
    localhost/fnndsc/pl-dylld dylld /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-dylld:dev --build-arg extras_require=dev .
docker run --rm -it localhost/fnndsc/pl-dylld: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-dylld:1.2.3 .
docker push docker.io/fnndsc/pl-dylld:1.2.3

Get JSON Representation

Run chris_plugin_info to produce a JSON description of this plugin, which can be uploaded to a ChRIS Store.

docker run --rm localhost/fnndsc/pl-dylld:dev chris_plugin_info > chris_plugin_info.json