Commit a3a54b3
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Add HTJ2K DICOM support and upgrade to pydicom 3.0
Key Changes:
- Upgrade to pydicom 3.0.0 for HTJ2K support
- Replace pydicom-seg with highdicom (pydicom-seg unmaintained)
- Add NvDicomReader for GPU-accelerated DICOM decoding with nvidia-nvimgcodec
NvDicomReader Features:
- HTJ2K transfer syntax support (1.2.840.10008.1.2.4.201/202/203)
- Batch decoding optimization for HTJ2K series
- Proper spatial slice ordering and affine matrix calculation
- Configurable layouts (NumPy D,H,W or ITK W,H,D)
- Fallback to pydicom/SimpleITK when nvimgcodec unavailable
DICOM SEG Improvements:
- Migrate to highdicom for DICOM SEG creation
- Memory-efficient processing with stop_before_pixels
- Support up to 65,535 segments (uint16)
- Preserve ITK/dcmqi fallback path
Optional Dependencies:
- nvidia-nvimgcodec and dcmqi are now optional
- Runtime checks with clear installation instructions
Testing:
- Comprehensive NvDicomReader tests (HTJ2K decoding, consistency, metadata)
- DICOM ↔ NIfTI conversion tests for original and HTJ2K files
- Automatic HTJ2K test data generation
Signed-off-by: Joaquin Anton Guirao <janton@nvidia.com>1 parent 068fc81 commit a3a54b3
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lines changed- monailabel
- datastore/utils
- endpoints
- transform
- sample-apps/radiology/lib
- infers
- trainers
- tests
- unit
- datastore
- transform
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