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.
