[Draft] Add HTJ2K DICOM support #1863
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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 <[email protected]>
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Signed-off-by: Joaquin Anton Guirao <[email protected]>
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SachidanandAlle
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Oct 18, 2025
|
Looks good to me.. however better if all E2E is tested and verified for existing use cases to make sure new changes does break. Thank you for trying to improve monai label. |
Signed-off-by: Joaquin Anton Guirao <[email protected]>
…ch processing for large directories Signed-off-by: Joaquin Anton Guirao <[email protected]>
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Add HTJ2K DICOM support and upgrade to pydicom 3.0
Key Changes:
NvDicomReader Features:
DICOM SEG Improvements:
Optional Dependencies:
Testing: