DICOM conversion

For some reason some DICOMs are encoded with some propietary format...

First need to encode these:

find . -name '*.dcm'  | xargs -n1 -P8 -I{} bash -c 'f={}; gdcmconv --raw -F $f ${f/.dcm/_raw.dcm}'

After converting to normal DICOMs we can finally decode to PNG:

find . -name '*_raw.dcm'  | xargs -n1 -P8 -I{} bash -c 'f={}; dcmj2pnm $f | convert - ${f/_raw.dcm/.png}'

Finally we have a lot of PNGs decoded from the dicom files. :)

Steps

Setup a virtual env:

python3 -m venv venv
source venv/bin/activate
pip install -r requirements.txt

1. Run process_data_dir.py
2. Run process_annotations.py
3. Run create_coco.py
4. Run visualize.py # to visualize