PDF to Image

pl-pdf2img is a ChRIS ds plugin which takes in pdfs as input files and creates jpgs or pngs as output files.

Abstract

Radiological databases, or PACS (Picture Archive and Communication Systems), can typically only store image files in DICOM format. Occasionally text data, often in the form of a report, needs to be added to a Study/Series in a PACS. The canonical way to effect this, is to create a PDF version of the report, convert that to an image, DICOMize this image, and push to a PACS. This ChRIS DS plugin can be used for part of that workflow.

Installation

pl-pdf2img 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-pdf2img as a container:

apptainer exec docker://fnndsc/pl-pdf2img pdf2img [--args values...] input/ output/

To print its available options, run:

apptainer exec docker://fnndsc/pl-pdf2img pdf2img --help

Examples

pdf2img 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-pdf2img:latest pdf2img [--args] incoming/ outgoing/

Development

Instructions for developers.

Building

Build a local container image:

docker build -t localhost/fnndsc/pl-pdf2img .

Running

Mount the source code pdf2img.py into a container to try out changes without rebuild.

docker run --rm -it --userns=host -u $(id -u):$(id -g) \
    -v $PWD/pdf2img.py:/usr/local/lib/python3.11/site-packages/pdf2img.py:ro \
    -v $PWD/in:/incoming:ro -v $PWD/out:/outgoing:rw -w /outgoing \
    localhost/fnndsc/pl-pdf2img pdf2img /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-pdf2img:dev --build-arg extras_require=dev .
docker run --rm -it localhost/fnndsc/pl-pdf2img: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-pdf2img:1.2.3 .
docker push docker.io/fnndsc/pl-pdf2img: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-pdf2img:1.2.3 chris_plugin_info -d docker.io/fnndsc/pl-pdf2img: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