[Draft] Revert overrides

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

@@ -4,30 +4,54 @@
 (e.g., breech face impressions) through leveling, filtering, and resampling steps.
 """
 
-from dataclasses import asdict
+from pydantic import BaseModel
 
 from container_models.base import DepthData
 from conversion.data_formats import Mark
 from conversion.filter import (
-    apply_gaussian_filter_mark,
     apply_filter_pipeline,
+    apply_gaussian_filter_mark,
 )
 from conversion.leveling import SurfaceTerms, level_map
 from conversion.mask import crop_to_mask
 from conversion.preprocess_impression.center import compute_center_local
-from conversion.preprocess_impression.parameters import PreprocessingImpressionParams
 from conversion.preprocess_impression.resample import (
-    resample,
     needs_resampling,
+    resample,
 )
 from conversion.preprocess_impression.tilt import apply_tilt_correction
-from conversion.preprocess_impression.utils import update_mark_data, Point2D
+from conversion.preprocess_impression.utils import Point2D, update_mark_data
 from conversion.resample import get_scaling_factors, resample_array_2d
 
 
+class ImpressionParams(BaseModel):
+    pixel_size: float | None = None
+    adjust_pixel_spacing: bool = True
+    level_offset: bool = True
+    level_tilt: bool = True
+    level_2nd: bool = True
+    interp_method: str = "cubic"
+    highpass_cutoff: float | None = 250.0e-6
+    lowpass_cutoff: float | None = 5.0e-6
+    highpass_regression_order: int = 2
+    lowpass_regression_order: int = 0
+
+    @property
+    def surface_terms(self) -> SurfaceTerms:
+        """Convert leveling flags to SurfaceTerms."""
+        terms = SurfaceTerms.NONE
+        if self.level_offset:
+            terms |= SurfaceTerms.OFFSET
+        if self.level_tilt:
+            terms |= SurfaceTerms.TILT_X | SurfaceTerms.TILT_Y
+        if self.level_2nd:
+            terms |= SurfaceTerms.ASTIG_45 | SurfaceTerms.DEFOCUS | SurfaceTerms.ASTIG_0
+        return terms
+
+
 def preprocess_impression_mark(
     mark: Mark,
-    params: PreprocessingImpressionParams,
+    params: ImpressionParams,
 ) -> tuple[Mark, Mark]:
     """
     Preprocess trimmed impression image data.
@@ -101,7 +125,7 @@ def preprocess_impression_mark(
     )
 
     # Build output metadata
-    mark.meta_data.update(**asdict(params))
+    mark.meta_data.update(**params.model_dump())
 
     return mark_filtered, mark_leveled_final
 

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

@@ -6,26 +6,34 @@
 - Fine rotation to align striations horizontally and profile extraction
 """
 
-from dataclasses import asdict
-
 import numpy as np
+from pydantic import BaseModel
 
 from container_models.base import FloatArray2D
 from container_models.scan_image import ScanImage
 from conversion.data_formats import Mark
 from conversion.filter import (
-    cutoff_to_gaussian_sigma,
     apply_striation_preserving_filter_1d,
+    cutoff_to_gaussian_sigma,
 )
-from conversion.preprocess_striation import PreprocessingStriationParams
 from conversion.preprocess_striation.alignment import fine_align_bullet_marks
 from conversion.preprocess_striation.shear import propagate_nan
 from conversion.profile_correlator import Profile
 
 
+class StriationParams(BaseModel):
+    highpass_cutoff: float = 2e-3
+    lowpass_cutoff: float = 2.5e-4
+    cut_borders_after_smoothing: bool = True
+    use_mean: bool = True
+    angle_accuracy: float = 0.1
+    max_iter: int = 25
+    subsampling_factor: int = 1
+
+
 def preprocess_striation_mark(
     mark: Mark,
-    params: PreprocessingStriationParams,
+    params: StriationParams,
 ) -> tuple[Mark, Profile]:
     """
     Complete the preprocessing pipeline for striated marks.
@@ -89,7 +97,7 @@ def preprocess_striation_mark(
     # Build meta_data with mask and total_angle
     aligned_meta_data = {
         **mark.meta_data,
-        **asdict(params),
+        **params.model_dump(),
         "total_angle": total_angle,
     }
 

packages/scratch-core/tests/conversion/preprocess_striation/test_preprocess_data.py

@@ -2,27 +2,29 @@
 Tests for preprocess_striation.py and related filter functions.
 """
 
+from math import ceil
+
 import numpy as np
 import pytest
-from math import ceil
 from scipy.constants import micro
 
 from container_models.scan_image import ScanImage
 from conversion.data_formats import MarkType
-from ..helper_functions import make_mark
 from conversion.filter import (
     apply_striation_preserving_filter_1d,
     cutoff_to_gaussian_sigma,
 )
 from conversion.filter.gaussian import _apply_nan_weighted_gaussian_1d
 from conversion.preprocess_striation import (
-    PreprocessingStriationParams,
     apply_shape_noise_removal,
     fine_align_bullet_marks,
     preprocess_striation_mark,
 )
-from conversion.preprocess_striation.shear import shear_data_by_shifting_profiles
 from conversion.preprocess_striation.alignment import _detect_striation_angle
+from conversion.preprocess_striation.pipeline import StriationParams
+from conversion.preprocess_striation.shear import shear_data_by_shifting_profiles
+
+from ..helper_functions import make_mark
 
 
 def test_cutoff_to_gaussian_sigma():
@@ -336,7 +338,7 @@ def test_preprocess_striation_mark():
         scale_y=micro,
         mark_type=MarkType.BULLET_LEA_STRIATION,
     )
-    params = PreprocessingStriationParams(
+    params = StriationParams(
         highpass_cutoff=2e-3,
         lowpass_cutoff=2.5e-4,
         cut_borders_after_smoothing=False,

packages/scratch-core/tests/conversion/preprocess_striation/test_striation_matlab.py

@@ -12,18 +12,18 @@
 
 from container_models.base import DepthData
 from conversion.data_formats import MarkType
-from ..helper_functions import make_mark
 from conversion.preprocess_striation import (
-    PreprocessingStriationParams,
     preprocess_striation_mark,
 )
+from conversion.preprocess_striation.pipeline import StriationParams
+
 from ..helper_functions import (
     _compute_correlation,
-    _crop_to_common_shape,
     _compute_difference_stats,
+    _crop_to_common_shape,
+    make_mark,
 )
 
-
 MARK_TYPE_MAPPING = {
     "bullet lea striation": MarkType.BULLET_LEA_STRIATION,
     "bullet gea striation": MarkType.BULLET_GEA_STRIATION,
@@ -166,7 +166,7 @@ def run_python_preprocessing(
     test_case: MatlabTestCase,
 ) -> tuple[np.ndarray, np.ndarray | None, float | None]:
     """Run Python preprocess_striation_mark and return the results."""
-    params = PreprocessingStriationParams(
+    params = StriationParams(
         highpass_cutoff=test_case.cutoff_hi * micro,
         lowpass_cutoff=test_case.cutoff_lo * micro,
         use_mean=test_case.use_mean,

packages/scratch-core/tests/conversion/test_impression.py

@@ -15,8 +15,8 @@
     _points_are_collinear,
     compute_center_local,
 )
-from conversion.preprocess_impression.parameters import PreprocessingImpressionParams
 from conversion.preprocess_impression.preprocess_impression import (
+    ImpressionParams,
     preprocess_impression_mark,
 )
 from conversion.preprocess_impression.resample import needs_resampling
@@ -422,7 +422,7 @@ def test_basic_pipeline_runs(self):
             scale_y=micro,
             mark_type=MarkType.FIRING_PIN_IMPRESSION,
         )
-        params = PreprocessingImpressionParams(
+        params = ImpressionParams(
             pixel_size=2 * micro,
             adjust_pixel_spacing=False,
             level_offset=True,
@@ -446,7 +446,7 @@ def test_output_has_correct_scale(self):
             mark_type=MarkType.FIRING_PIN_IMPRESSION,
         )
         target_size = 2 * micro
-        params = PreprocessingImpressionParams(
+        params = ImpressionParams(
             pixel_size=target_size,
             adjust_pixel_spacing=False,
         )
@@ -468,7 +468,7 @@ def test_output_is_smaller_after_downsampling(self):
             scale_y=micro,
             mark_type=MarkType.FIRING_PIN_IMPRESSION,
         )
-        params = PreprocessingImpressionParams(
+        params = ImpressionParams(
             pixel_size=2 * micro,  # 2x downsampling
             adjust_pixel_spacing=False,
         )
@@ -491,7 +491,7 @@ def test_filtered_and_leveled_differ(self):
             scale_y=micro,
             mark_type=MarkType.FIRING_PIN_IMPRESSION,
         )
-        params = PreprocessingImpressionParams(
+        params = ImpressionParams(
             adjust_pixel_spacing=False,
             highpass_cutoff=50 * micro,  # Apply high-pass to create difference
         )
@@ -514,7 +514,7 @@ def test_breech_face_uses_circle_center(self):
             scale_y=micro,
             mark_type=MarkType.BREECH_FACE_IMPRESSION,
         )
-        params = PreprocessingImpressionParams(
+        params = ImpressionParams(
             pixel_size=micro,  # No resampling
             adjust_pixel_spacing=False,
         )
@@ -535,7 +535,7 @@ def test_no_resampling_when_pixel_size_matches(self):
             scale_y=micro,
             mark_type=MarkType.FIRING_PIN_IMPRESSION,
         )
-        params = PreprocessingImpressionParams(
+        params = ImpressionParams(
             pixel_size=micro,  # Same as input
             adjust_pixel_spacing=False,
         )
@@ -555,7 +555,7 @@ def test_is_resampled_flag_set_on_resampling(self):
             scale_y=micro,
             mark_type=MarkType.FIRING_PIN_IMPRESSION,
         )
-        params = PreprocessingImpressionParams(
+        params = ImpressionParams(
             pixel_size=2 * micro,  # Different from input
             adjust_pixel_spacing=False,
         )
@@ -575,7 +575,7 @@ def test_without_lowpass_filter(self):
             scale_y=micro,
             mark_type=MarkType.FIRING_PIN_IMPRESSION,
         )
-        params = PreprocessingImpressionParams(
+        params = ImpressionParams(
             pixel_size=2 * micro,
             adjust_pixel_spacing=False,
             lowpass_cutoff=None,
@@ -596,7 +596,7 @@ def test_without_highpass_filter(self):
             scale_y=micro,
             mark_type=MarkType.FIRING_PIN_IMPRESSION,
         )
-        params = PreprocessingImpressionParams(
+        params = ImpressionParams(
             pixel_size=2 * micro,
             adjust_pixel_spacing=False,
             highpass_cutoff=None,
@@ -617,7 +617,7 @@ def test_without_any_filters(self):
             scale_y=micro,
             mark_type=MarkType.FIRING_PIN_IMPRESSION,
         )
-        params = PreprocessingImpressionParams(
+        params = ImpressionParams(
             pixel_size=2 * micro,
             adjust_pixel_spacing=False,
             lowpass_cutoff=None,
@@ -639,7 +639,7 @@ def test_with_tilt_adjustment(self):
             scale_y=micro,
             mark_type=MarkType.FIRING_PIN_IMPRESSION,
         )
-        params = PreprocessingImpressionParams(
+        params = ImpressionParams(
             pixel_size=2 * micro,
             adjust_pixel_spacing=True,
         )
@@ -659,7 +659,7 @@ def test_with_second_order_leveling(self):
             scale_y=micro,
             mark_type=MarkType.FIRING_PIN_IMPRESSION,
         )
-        params = PreprocessingImpressionParams(
+        params = ImpressionParams(
             pixel_size=2 * micro,
             adjust_pixel_spacing=False,
             level_offset=True,
@@ -682,7 +682,7 @@ def test_output_data_is_finite_where_valid(self):
             scale_y=micro,
             mark_type=MarkType.FIRING_PIN_IMPRESSION,
         )
-        params = PreprocessingImpressionParams(
+        params = ImpressionParams(
             pixel_size=2 * micro,
             adjust_pixel_spacing=False,
         )
@@ -715,7 +715,7 @@ def test_leveled_preserves_form(self):
             scale_y=micro,
             mark_type=MarkType.FIRING_PIN_IMPRESSION,
         )
-        params = PreprocessingImpressionParams(
+        params = ImpressionParams(
             pixel_size=micro,
             adjust_pixel_spacing=False,
             level_offset=True,

packages/scratch-core/tests/conversion/test_impression_matlab.py

@@ -11,15 +11,16 @@
 
 from container_models.base import FloatArray2D
 from conversion.data_formats import MarkType
-from .helper_functions import make_mark
 from conversion.preprocess_impression.preprocess_impression import (
+    ImpressionParams,
     preprocess_impression_mark,
 )
-from conversion.preprocess_impression.parameters import PreprocessingImpressionParams
+
 from .helper_functions import (
     _compute_correlation,
-    _crop_to_common_shape,
     _compute_difference_stats,
+    _crop_to_common_shape,
+    make_mark,
 )
 
 
@@ -32,7 +33,7 @@ class MatlabTestCase:
     input_data: FloatArray2D
     pixel_spacing: tuple[float, float]
     # Processing options
-    params: PreprocessingImpressionParams
+    params: ImpressionParams
     use_circle_center: bool
     # Expected output
     output_data: FloatArray2D
@@ -89,7 +90,7 @@ def from_directory(cls, case_dir: Path) -> "MatlabTestCase":
                 lowpass_cutoff = cutoff_val
                 lowpass_order = int(f.get("n_order", 0))
 
-        params = PreprocessingImpressionParams(
+        params = ImpressionParams(
             adjust_pixel_spacing=meta.get("adjust_pixel_spacing", False),
             level_offset=level_offset,
             level_tilt=level_tilt,

packages/scratch-core/tests/conversion/test_preprocess_data_matlab_comparison.py

@@ -11,17 +11,18 @@
 import pytest
 from scipy.constants import micro
 
-from container_models.base import DepthData, BinaryMask, StriationProfile
+from container_models.base import BinaryMask, DepthData, StriationProfile
 from conversion.data_formats import MarkType
-from .helper_functions import make_mark
 from conversion.preprocess_striation import (
-    PreprocessingStriationParams,
     preprocess_striation_mark,
 )
+from conversion.preprocess_striation.pipeline import StriationParams
+
 from .helper_functions import (
     _compute_correlation,
-    _crop_to_common_shape,
     _compute_difference_stats,
+    _crop_to_common_shape,
+    make_mark,
 )
 
 
@@ -170,7 +171,7 @@ def run_python_preprocessing(
         mark_type=mark_type,
     )
 
-    params = PreprocessingStriationParams(
+    params = StriationParams(
         highpass_cutoff=test_case.cutoff_hi * micro,
         lowpass_cutoff=test_case.cutoff_lo * micro,
         use_mean=test_case.use_mean,