Dummy DICOM

Creates a "dummy" dicom with fake PHI pixel burn in and then demonstrate removing it.

Intention

clean.py demonstrates pixel censoring by modifying the image to include a solid rectangle over sensitive burnt in data using the python package deid. When and how censoring is preformed is configured by deid-py.cfg.

Config

Within deid-py.cfg, contains matches a dicom header (here any file assuming UID always includes a . character). and coordinates specifies a rectangle to censor ( 0,0 is the top left corner). For more see deid's dicom pixels documentation

contains SOPInstanceUID .
  coordinates 0,0,512,110

Flywheel

deid-py.cfg is manually translated to deid.yaml for use with deid-export. As of 20250402, this is either an incomplete translation or otherwise not interpreted correctly by the flywheel gear -- no pixel censoring is preformed.

Reproduce

See Makefile.

• Use uv sync to create .venv/. (Created with uv init)
• uv run fake.py creates fake_phi.dcm

TODO:

make -B nii/fake_phi.nii.gz shows fake dicom problems

DICOM appears corrupt: first group:element should be 0x0002:0x0000 '/home/foranw/src/work/dummyDICOM/fake_phi.dcm'
Warning: Instance number (0020,0013) not found: /home/foranw/src/work/dummyDICOM/fake_phi.dcm
Warning: PatientOrient (0018,5100) not specified (issue 642).
Warning: Unable to determine manufacturer (0008,0070), so conversion is not tuned for vendor.

maybe contributing to deid failing?

./01_test_deid.bash

WARNING dicom: not recognized to be in valid format, skipping.

Notes

quick image from dicom

uv tool install git+https://github.com/WillForan/med2image

med2image  --convertOnlySingleDICOM -s m \
   -o scrubbed/fake_phi.jpg \
   -i scrubbed/fake_phi.dcm

git clone https://gitlab.com/flywheel-io/scientific-solutions/gears/deid-export