Refactor the preprocessing and segmentation pipeline to handle AP orientation
variations and improve anatomical boundary detection.
Key changes include:
- Implement automated AP orientation detection in `process_single_image`
to handle prone scans by flipping CT and labels when necessary.
- Enhance `segment_spinous_process` using a gap-based approach to identify
the spinal canal, providing more stable thresholds for spinous process
and vertebral body segmentation.
- Improve optimization search space by using the vertebral body (VBODY)
projection for x/z bounding box calculation instead of the whole bone.
- Refactor `render_bone_figure` to unify 2D/3D visualization and support
detailed anatomical coloring (VBODY, spinous process).
- Update `cl_score_torch_xfr` with more robust penalty handling for
out-of-bone and null-voxel regions.
- Add `retry_robust` utility to handle transient NFS file system errors.
- Update `xfr_preprocess.py` to include anatomical segmentation coloring
in rotated level visualizations.
Introduces a new scoring component for vertebral body (VBODY) rewards
to improve optimization accuracy. The update includes:
- Added `vbody_tensor` to `OptimizationContext` and scoring functions
to reward screw placement within the vertebral body.
- Enhanced `segment_spinous_process` with diagnostic capabilities to
detect spinous process absence (e.g., post-laminectomy).
- Improved `resample_img` to prevent physical boundary clipping and
handle interpolation more robustly for CT and label data.
- Implemented a metadata cache using TinyDB in the preprocessing
pipeline to skip low-resolution or insufficient scans efficiently.
- Added robust error handling for NFS-based file operations and
directory creation.
- Added new visualization tools for bone figures and level plotting.
refactor(imaging): improve segmentation and resampling precision
- Refactored `seg_bone` to support original resolution binary masks and
Signed Maurer Distance Maps (SMD) for more accurate boundary handling.
- Updated `resample_img` to use `ceil` for output size calculation to
ensure full physical coverage.
- Optimized `process_single_image` to utilize metadata for skipping
processing of invalid or low-quality scans.
