CMC: Resample marks when anisotropic

packages/scratch-core/src/conversion/exceptions.py

@@ -1,15 +1,3 @@
-class ImageNotIsotropicError(Exception):
-    """Raised when an image is not isotropic."""
-
-    def __init__(self, scale_x: float | int, scale_y: float | int):
-        super().__init__(scale_x, scale_y)
-        self.scale_x = scale_x
-        self.scale_y = scale_y
-
-    def __str__(self) -> str:
-        return f"Image is not isotropic: scale_x={self.scale_x}, while scale_y={self.scale_y}."
-
-
 class NoValidGridCellsError(Exception):
     """Raised when no valid grid cells are generated."""
 

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

@@ -31,7 +31,7 @@
     ProcessedMark,
 )
 from conversion.surface_comparison.utils import (
-    assert_image_is_isotropic,
+    make_image_isotropic,
     resolve_nan_fill_value,
 )
 
@@ -46,6 +46,7 @@ def compare_surfaces(
 
     Executes the pipeline:
 
+    0. **Square up** — either image is resampled to isotropic if the tilt correction left its axes on different scales.
     1. **Resample** — the comparison image is resampled to the pixel size of the reference image.
     2. **Generate grid** — a centered rectangular grid of cells is placed over the reference image.
     3. **Build the full-resolution stage** — the scale-aligned comparison image and reference templates, padded.
@@ -65,14 +66,12 @@ def compare_surfaces(
         search configuration, and CMC classification thresholds.
     :returns: A ComparisonResult containing per-cell registration results, the consensus rotation and
         translation, and CMC counts.
-    :raises ValueError: If the image's pixel grid is not isotropic.
     """
-    reference_image = reference_mark.filtered_mark.scan_image
-    comparison_image_original = comparison_mark.filtered_mark.scan_image
-
-    # Everything below uses scale_x for both axes, so anisotropy would go unnoticed.
-    assert_image_is_isotropic(reference_image)
-    assert_image_is_isotropic(comparison_image_original)
+    # Everything below uses scale_x for both axes, so anisotropy left by the tilt correction must be removed first.
+    reference_image = make_image_isotropic(reference_mark.filtered_mark.scan_image)
+    comparison_image_original = make_image_isotropic(
+        comparison_mark.filtered_mark.scan_image
+    )
 
     # Step 1: Resample comparison to reference scale (for the fine stage)
     logger.debug("starting resample")

packages/scratch-core/src/conversion/surface_comparison/utils.py

@@ -5,13 +5,13 @@
 
 from container_models.base import FloatArray1D, FloatArray2D, Points2D
 from container_models.scan_image import ScanImage
-from conversion.exceptions import ImageNotIsotropicError
+from conversion.resample import resample_scan_image_nan_aware
 from conversion.surface_comparison.models import Cell, ComparisonParams
 
-# Tolerances for np.isclose() when comparing pixel scales (e.g. isotropy check, matching scales between images).
-# Tilt correction divides each axis by its own cos(tilt), so 5e-3 accepts a tilt difference up to ~5.7 degrees.
+# Tolerances for np.isclose() when comparing pixel scales (isotropy check, matching scales between images).
+# atol stays 0.0 to keep the check relative; at 1e-3 the axes drift apart by ~1 pixel per 1000 pixels.
 SCALE_COMPARISON_ATOL = 0.0
-SCALE_COMPARISON_RTOL = 5e-3
+SCALE_COMPARISON_RTOL = 1e-3
 
 
 def convert_meters_to_pixels(
@@ -101,16 +101,29 @@ def _cells_correlation_to_grid(cells: Sequence[Cell]) -> FloatArray2D:
     return cell_correlations
 
 
-def assert_image_is_isotropic(scan_image: ScanImage) -> None:
-    if not np.isclose(
+def make_image_isotropic(scan_image: ScanImage) -> ScanImage:
+    """
+    Put *scan_image* on a square pixel grid, which the rest of the CMC pipeline assumes.
+
+    Images are resampled to isotropic when parsed, but the tilt correction divides each axis by its own
+    cos(tilt) and so reintroduces a small anisotropy. Differences below SCALE_COMPARISON_RTOL are left alone.
+
+    :param scan_image: Image to resample to isotropic resolution
+    :returns: The image itself when already isotropic, otherwise a copy resampled onto scale_x
+    """
+    if np.isclose(
         scan_image.scale_x,
         scan_image.scale_y,
         atol=SCALE_COMPARISON_ATOL,
         rtol=SCALE_COMPARISON_RTOL,
     ):
-        raise ImageNotIsotropicError(
-            scale_x=scan_image.scale_x, scale_y=scan_image.scale_y
-        )
+        return scan_image
+    logger.debug(
+        "Resampling to isotropic: scale_x={:.4g}, scale_y={:.4g}",
+        scan_image.scale_x,
+        scan_image.scale_y,
+    )
+    return resample_scan_image_nan_aware(scan_image, scan_image.scale_x)
 
 
 def resolve_nan_fill_value(

src/processors/router.py

@@ -1,7 +1,7 @@
 from http import HTTPStatus
 
 from conversion.data_formats import MarkImpressionType
-from conversion.exceptions import ImageNotIsotropicError, NoValidGridCellsError
+from conversion.exceptions import NoValidGridCellsError
 from conversion.export.mark import load_mark_from_path, save_mark
 from conversion.export.profile import load_profile_from_path
 from conversion.surface_comparison.models import ProcessedMark
@@ -103,7 +103,7 @@ async def calculate_score_impression(impression_params: CalculateScoreImpression
             comparison_mark=mark_comp_processed,
             params=impression_params.comparison_params,
         )
-    except (NoValidGridCellsError, ImageNotIsotropicError) as exception:
+    except NoValidGridCellsError as exception:
         message = str(exception)
         logger.error(message)
         raise HTTPException(HTTPStatus.UNPROCESSABLE_ENTITY, message)

tests/processors/test_router.py

@@ -287,22 +287,6 @@ def load_side_effect(*args, **kwargs):
         assert response.status_code == HTTPStatus.UNPROCESSABLE_ENTITY
         assert "expected a MarkImpressionType" in response.json()["detail"]
 
-    def test_image_not_isotropic_returns_422(self, client: TestClient, json_data: dict) -> None:
-        """422 is returned when the mark image has different scale_x and scale_y."""
-        anisotropic_mark = Mark(
-            scan_image=ScanImage(data=np.array([[0.0]]), scale_x=1e-6, scale_y=2e-6),
-            mark_type=MarkImpressionType.BREECH_FACE_IMPRESSION,
-        )
-
-        def load_side_effect(*args, **kwargs):
-            return anisotropic_mark
-
-        with patch("processors.router.load_mark_from_path", side_effect=load_side_effect):
-            response = client.post("/processor/" + ProcessorEndpoint.CALCULATE_SCORE_IMPRESSION, json=json_data)
-
-        assert response.status_code == HTTPStatus.UNPROCESSABLE_ENTITY
-        assert "not isotropic" in response.json()["detail"]
-
     def test_no_valid_grid_cells_returns_422(self, client: TestClient, json_data: dict) -> None:
         """422 is returned when the mark image is all-NaN so no grid cells can be generated."""
         all_nan_mark = Mark(