pl-lld_chxr is a ChRIS
ds plugin which takes in LLD (leg length discrepancy) analysis results (e.g. JSON files) and produces filtered summaries and annotated images as output.
This plugin processes outputs from an LLD analysis pipeline and allows:
- Filtering based on measurement differences (limb, tibia, femur)
- Tag-based filtering and parsing
- Selection of input files via glob patterns
- Annotating output images with customizable text overlays
| Argument | Type | Default | Description |
|---|---|---|---|
-f, --fileFilter |
string | json |
Input file filter glob (e.g., json, *.json) |
| Argument | Type | Default | Description |
|---|---|---|---|
-m, --measurementsUnit |
string | '' |
Accepted unit for length measurements |
-d, --limbDifference |
float | inf |
Maximum allowed difference between limbs |
-b, --tibiaDifference |
float | inf |
Maximum allowed tibia difference |
-r, --femurDifference |
float | inf |
Maximum allowed femur difference |
| Argument | Type | Default | Description |
|---|---|---|---|
-s, --splitToken |
string | '' |
Token used to split input tags |
-k, --splitKeyValue |
string | '' |
Character used to split key-value pairs |
-t, --tagInfo |
string | '' |
Accepted tags and their values |
| Argument | Type | Default | Description |
|---|---|---|---|
--outputImageExtension |
string | jpg |
Output image file format |
-q, --addTextPos |
string | top |
Text position on image (top or bottom) |
--addText |
string | '' |
Text to overlay on output image |
--addTextSize |
float | 5.0 |
Font size of overlay text |
--addTextColor |
string | white |
Text color |
--addLineSpace |
float | 0.5 |
Line spacing (smaller = tighter) |
| Argument | Description |
|---|---|
-V, --version |
Print plugin version and exit |
pl-lld_chxr 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-lld_chxr as a container:
apptainer exec docker://fnndsc/pl-lld_chxr lld_chxr [--args values...] input/ output/To print its available options, run:
apptainer exec docker://fnndsc/pl-lld_chxr lld_chxr --helplld_chxr 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-lld_chxr:latest lld_chxr [--args] incoming/ outgoing/Instructions for developers.
Build a local container image:
docker build -t localhost/fnndsc/pl-lld_chxr .Mount the source code lld_chxr.py into a container to try out changes without rebuild.
docker run --rm -it --userns=host -u $(id -u):$(id -g) \
-v $PWD/lld_chxr.py:/usr/local/lib/python3.12/site-packages/lld_chxr.py:ro \
-v $PWD/in:/incoming:ro -v $PWD/out:/outgoing:rw -w /outgoing \
localhost/fnndsc/pl-lld_chxr lld_chxr /incoming /outgoingRun 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-lld_chxr:dev --build-arg extras_require=dev .
docker run --rm -it localhost/fnndsc/pl-lld_chxr:dev pytestSteps 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-lld_chxr:1.2.3 .
docker push docker.io/fnndsc/pl-lld_chxr: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-lld_chxr:1.2.3 chris_plugin_info -d docker.io/fnndsc/pl-lld_chxr:1.2.3 > chris_plugin_info.jsonIntructions on how to upload the plugin to ChRIS can be found here: https://chrisproject.org/docs/tutorials/upload_plugin