pl-image_textRemove

pl-image_textRemove is a ChRIS ds plugin which takes in image files as input files and removes any burned text on those images

Abstract

Currently, the plugin pl-image_textRemove can take ultra sound images as input and remove specific text, i.e. Patient Name, MRN, and DoB burned on the images. We are working on making this plugin more generic where we can remove specific/all texts from an input image by passing a choice of CLI commands. Under the hood, this plugin uses keras_ocr libraries to recognize text from an image file, and opencv-python to mask and inpaint resultant o/p files.

Installation

pl-image_textRemove 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-image_textRemove as a container:

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

To print its available options, run:

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

Examples

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

Development

Instructions for developers.

Building

Build a local container image:

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

Running

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

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