fnndsc/pl-dicom_info repository overview

⁠Report on DICOM Tag Information

pl-dicom_info is a ChRIS⁠ ds plugin which which accepts as input a filesystem tree containing nested DICOM files, and generates various reports on each nested directory of DICOM images. Output reports are saved in a concordant location in the output directory.

⁠Abstract

This page briefly describes a ChRIS plugin that is built around pfdicom_tagExtract⁠ and exposes all of its functionality. Please refer to the referenced link for detailed information about the usage flags. Note that this is largely a rewrite of the pl-pfdicom_tagExtract⁠ plugin using the chris_plugin_template⁠ to allow for the new design pattern of "percolating" arg_parsers up from ancestor apps.

⁠Installation

pl-dicom_info 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-dicom_info as a container:

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

To print its available options, run:

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

⁠Examples

You can run dicom_info with a --man flag to get in-line help (including some examples):

singularity exec --cleanenv docker://fnndsc/pl-dicom_info dicom_info --man in out   

Note that being a ChRIS DS plugin, dicom_info requires two positional arguments: a directory containing input data, and a directory where to create output data. The order of these positional arguments in largely irrelevant. We suggest positioning them either at the very front or very end of the CLI.

In this example, assume that you have a directory called in that contains DICOM data. This data can be nested into any arbitrary tree.

singularity exec --cleanenv docker://fnndsc/pl-dicom_info dicom_info in out \
            --fileFilter dcm                                                \
            --outputFileStem '%_md5|6_PatientID-%PatientAge'                \
            --imageFile 'm:%_md5|6_PatientID-%PatientAge.jpg'               \
            --outputFileType raw,json,html,dict,col,csv                     \
            --imageScale 3:none                                             \
            --useIndexhtml                                                  \
            --outputFileType raw,json,html,dict,col,csv

Here, the script will create a summary report in the --outputFileType formats, as well as an upscaled image with no interpolation of the "middle" image (if a series has multiple images). Moreover, the name of the files will start with an md5_sum of DICOM PatientID tag (using the first 6 chars), followed by the PatientAge tag value.

⁠Development

Instructions for developers.

⁠Building

Build a local container image:

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

⁠Running

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

docker run --rm -it --userns=host -u $(id -u):$(id -g) \
    -v $PWD/dicom_info.py:/usr/local/lib/python3.10/site-packages/dicom_info.py:ro \
    -v $PWD/in:/incoming:ro -v $PWD/out:/outgoing:rw -w /outgoing \
    localhost/fnndsc/pl-dicom_info dicom_info /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-dicom_info:dev --build-arg extras_require=dev .
docker run --rm -it localhost/fnndsc/pl-dicom_info: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-dicom_info:1.2.3 .
docker push docker.io/fnndsc/pl-dicom_info: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-dicom_info:dev chris_plugin_info > chris_plugin_info.json