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.
Refactor the optimization pipeline to eliminate module-level global variables,
improving thread safety and modularity. Introduced `OptimizationContext`
to explicitly manage shared state during cylinder evaluation.
Key changes:
- core: Replace global variables with `OptimizationContext` dataclass in
`objective.py`.
- core: Implement `refine_lateral_longer` in `optimizer.py` for deterministic
local refinement of screw placement.
- core: Update scoring logic in `scoring.py` to use higher penalties for
out-of-bone voxels.
- imaging: Add advanced symmetry detection including `best_symmetry_plane`
and `best_symmetry_axis_angle` in `orientation.py`.
- visualization: Enhance 3D plotting in `res_plot_3d.py` with volume
absorption rendering (Beer-Lambert law) for an X-ray-like appearance.
- xfr_debug: Implement a custom `_Tee` logger to support multi-process
logging with volume and level-specific tags.
- chore: Update `.gitignore` to include local logs and kilo directories.
Refactor the cylinder parameter selection and optimization process to
improve accuracy and robustness.
- Implement `snap_to_discrete_values_xfr` using a KDTree for efficient
mapping of continuous diameter and length values to a predefined
set of discrete points.
- Update `objective_function_xfr` to use the new snapping mechanism
and introduce a weighted loss component for diameter and length.
- Adjust PSO optimization bounds and search ranges in `run_pso_torch_xfr`
to better align with image dimensions and anatomical constraints.
- Refine scoring logic in `cl_score_torch_xfr` with updated penalty
weights for overlaps and out-of-bone voxels.
- Update `config/constant.py` with new allowed diameter and length
ranges.
- Improve `imaging/preprocessing.py` by making `PROGRESS_FILE` a
parameter to allow per-output-directory progress tracking.
- Update `xfr_debug.py` with improved error handling and directory
paths for batch processing.
