Concepts

Pipeline order

ingest ──> de-identify ──> QC ──> convert

The order is deliberate:

1. Ingest — discover DICOM, group by SeriesInstanceUID, sort slices along the acquisition normal (robust to oblique scans), and apply rescale slope/intercept so CT data is in Hounsfield units.
2. De-identify — remove/blank PHI in memory before anything is written, so no artefact on disk carries direct identifiers. Source files are never modified.
3. QC — validate geometry and slice spacing and compute intensity statistics, so problems surface while the original DICOM is still available to investigate.
4. Convert — write a geometry-preserving NIfTI/NRRD that loads into Slicer or ITK-SNAP in correct anatomical space.

Headless core, thin GUI

dicom-forge is the headless core. The companion slicer-forge extension is the GUI that calls into it from inside 3D Slicer. This mirrors how Slicer itself is built (ITK/VTK do the work; the GUI is a shell) and means the heavy logic is unit tested in CI without needing Slicer installed.

Optional native dependencies

Ingestion, de-identification, and QC need only pydicom + numpy. Conversion needs SimpleITK/pynrrd/nibabel, which are installed via the convert extra. Calling a conversion function without the extra raises a clear MissingDependencyError.

De-identification levels

Level	Removes direct identifiers	Blanks dates/devices	Blanks everything off the safe-list
basic	✅	❌	❌
moderate	✅	✅	❌
strict	✅	✅	✅

PatientID is replaced with a deterministic, salted SHA-256 pseudonym, so the same patient maps to the same id within a project but cannot be reversed.