SeriesMaker-AIDE

View repo · Report Bug · Request Feature

Overview

SeriesMaker-AIDE is a simple AIDE app for testing DICOM end-to-end connectivity with clinical information systems such as PACS or scanner software.

SeriesMaker-AIDE performs the following:

1. Ingests a DICOM Series
2. Duplicates the DICOM Series
3. Edits some basic DICOM metadata
   1. SeriesNumber
   2. InstanceNumber
4. Randomly shuffles PixelData to differentiate edited DICOM Series from original datasets in the Study
5. Outputs the edited DICOM Series

The purpose of SeriesMaker-AIDE is to create a new dummy DICOM Series which can be output to the originating DICOM Study. This is useful for testing and verifying AIDE export destinations.

Developer Instructions

1. Download

git clone https://github.com/GSTT-CSC/SeriesMaker-AIDE.git

2. Setup virtual env

cd SeriesMaker-AIDE

python -m venv venv
source venv/bin/activate

pip install --upgrade pip setuptools wheel
pip install -r app/requirements.txt

3. Create input and output directories

mkdir input output

Run source code with MONAI Deploy

1. Ensure Python venv running
2. Copy DICOM .dcm files to input/ directory

monai-deploy exec app -i input/ -o -output/

# alternatively:
python app -i input/ -o output/

Build and run as MONAI Application Package (MAP)

1. Ensure Python venv running
2. Ensure Docker running
3. Copy DICOM .dcm files to input/ directory

# Package MAP
monai-deploy package app --tag ghcr.io/gstt-csc/seriesmaker-aide/map:0.1.1 -r app/requirements.txt -l DEBUG

# Test MAP with MONAI Deploy
monai-deploy run ghcr.io/gstt-csc/seriesmaker-aide/map:0.1.1 input/ output/

# Push MAP to GHCR
docker push ghcr.io/gstt-csc/seriesmaker-aide/map:0.1.1

Optional

Enter Docker container for testing

docker run --gpus all -it --rm -v /SeriesMaker-AIDE/input:/var/monai/input/ --entrypoint /bin/bash ghcr.io/gstt-csc/seriesmaker-aide/map:0.1.1

Run on specified GPU if machine has >1 available

CUDA_VISIBLE_DEVICES=2 monai-deploy run ghcr.io/gstt-csc/seriesmaker-aide/map:0.1.1 input/ output/