CMC classification consensus

[vergep]

CMC classification consensus.
Based on Procrustes rotation and translation to find consensus parameters

[cfs-data]

Approved with suggestions

[github-actions]

Diff Coverage

Diff: origin/main..HEAD, staged and unstaged changes

• packages/scratch-core/src/conversion/surface_comparison/cmc_classification_median.py (100%)
• packages/scratch-core/src/conversion/surface_comparison/cmc_consensus/criterion.py (100%)
• packages/scratch-core/src/conversion/surface_comparison/cmc_consensus/models.py (100%)
• packages/scratch-core/src/conversion/surface_comparison/cmc_consensus/pipeline.py (81.1%): Missing lines 102,120,194-195,198,203,211,215-216,219
• packages/scratch-core/src/conversion/surface_comparison/cmc_consensus/procrustes.py (95.5%): Missing lines 111-112
• packages/scratch-core/src/conversion/surface_comparison/pipeline.py (100%)

Summary

• Total: 155 lines
• Missing: 12 lines
• Coverage: 92%

packages/scratch-core/src/conversion/surface_comparison/cmc_consensus/pipeline.py

   98             max_abs_angle_distance,
   99         )
  100 
  101         if 2 < len(current_ids) < n_cells:
! 102             _refine(
  103                 current_ids,
  104                 criterion_current,
  105                 cells,
  106                 max_distance,

---

  116 
  117         if len(best_ids) == n_cells:
  118             return best_ids  # outer loop short-circuit
  119 
! 120     return best_ids
  121 
  122 
  123 def _update_congruent_cells(cells: list[Cell], congruent_ids: list[int]) -> None:
  124     """update cell.is_congruent property

---

  190     :param max_distance: maximum distance threshold (meters)
  191     :param max_abs_angle_distance: maximum absolute angle threshold (degrees)
  192     """
  193 
! 194     while True:
! 195         cell_distances, cell_angle_distances = _get_cell_angle_and_position_distances(
  196             current_ids, cells
  197         )
! 198         candidate_ids = np.where(
  199             (cell_distances <= max_distance)
  200             & (cell_angle_distances <= max_abs_angle_distance)
  201         )[0].tolist()
  202 
! 203         criterion_candidate = calculate_criterion(
  204             cell_distances[candidate_ids],
  205             cell_angle_distances[candidate_ids],
  206             max_distance,
  207             max_abs_angle_distance,

---

  207             max_abs_angle_distance,
  208         )
  209 
  210         # Accept if strictly more inlier, or same count with lower criterion
! 211         if len(candidate_ids) > len(current_ids) or (
  212             len(candidate_ids) == len(current_ids)
  213             and criterion_candidate < criterion_current
  214         ):
! 215             criterion_current = criterion_candidate
! 216             current_ids = candidate_ids
  217         else:
  218             # we have our local optimum and return, also for len(candidate_ids) == len(current_ids) and criterion did not improve
! 219             return

---

packages/scratch-core/src/conversion/surface_comparison/cmc_consensus/procrustes.py

  107     )  # (2, 2)
  108 
  109     # If det == -1 we have an unintended reflection; correct it by changing sign of last column of left_singular_vectors.
  110     if np.linalg.det(rotation_matrix) == -1:
! 111         left_singular_vectors[:, -1] *= -1
! 112         rotation_matrix = left_singular_vectors @ right_singular_vectors_transposed
  113 
  114     # Rotation angle: atan2(sin/cos)
  115     (cos, sin) = tuple(rotation_matrix[0])
  116     consensus_rotation_rad = float(np.arctan2(sin, cos))  # -pi <= angle <= pi

---

[github-actions]

Package	Line Rate	Branch Rate	Health
.	96%	92%	✔
computations	94%	67%	✔
container_models	99%	100%	✔
conversion	96%	89%	✔
conversion.export	99%	93%	✔
conversion.filter	97%	89%	✔
conversion.leveling	100%	100%	✔
conversion.leveling.solver	100%	75%	✔
conversion.plots	99%	88%	✔
conversion.preprocess_impression	99%	91%	✔
conversion.preprocess_striation	90%	62%	✔
conversion.profile_correlator	96%	82%	✔
conversion.surface_comparison	99%	89%	✔
conversion.surface_comparison.cell_registration	100%	90%	✔
conversion.surface_comparison.cmc_consensus	91%	65%	✔
extractors	97%	75%	✔
mutations	100%	100%	✔
parsers	97%	50%	✔
parsers.patches	89%	60%	✔
preprocessors	100%	100%	✔
processors	100%	83%	✔
renders	99%	50%	✔
utils	71%	100%	➖
Summary	98% (3383 / 3465)	86% (353 / 412)	✔

Minimum allowed line rate is 50%

[laurensWe]

Thanks for all the changes :)