DICOM Check

A tool to index DICOM data and perform some checks for data completeness.

This tool is under development and is intended for experimentation use only.

Usage

Install Requirements

You can pip install the requirements.txt file to install all dependencies:

pip install -r requirements.txt

Test data

Pull some test data for experimentation (HNSCC from The Cancer Imaging Archive):

python test.py

Preprocess

Indexes DICOM data in a directory and produces a report with DICOM series found.

python preprocess.py -t templates/generic-rt.json -r pdf testdata/HNSCC/HNSCC-01-0176

For all options use the command line interface help:

python preprocess.py --help

Match

Maches DICOM series to a template provided.

python match.py -t templates/generic-rt.json -r pdf testdata/HNSCC/HNSCC-01-0176

For all options use the command line interface help:

python match.py --help

Check

Peforms checks defined in template against series data.

python check.py -t templates/generic-rt.json -r pdf testdata/HNSCC/HNSCC-01-0176

For all options use the command line interface help:

python check.py --help

Run on all sub-directories

Run all steps on each sub-directory of a directory:

python run.py -t templates/generic-rt.json -r pdf testdata/HNSCC

Check the testdata/HNSCC/check_results.csv for a summary of all checks performed.