Implement the python implementation of PreprocessData (Step 2 and Step 3)

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

@@ -51,7 +51,7 @@ def _determine_bounding_box(mask: MaskArray) -> tuple[slice, slice]:
 
     y_min, x_min = np.min(non_zero_coords, axis=1)
     y_max, x_max = np.max(non_zero_coords, axis=1)
-    return slice(x_min, x_max + 1), slice(y_min, y_max + 1)
+    return slice(y_min, y_max + 1), slice(x_min, x_max + 1)
 
 
 def mask_and_crop_2d_array(

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

@@ -9,13 +9,13 @@
 from container_models.base import ScanMap2DArray
 from container_models.scan_image import ScanImage
 from conversion.data_formats import 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.filter import (
+from conversion.filter import (
     apply_gaussian_filter_to_mark,
     apply_filtering_pipeline,
 )
+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,

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

@@ -0,0 +1,25 @@
+from dataclasses import dataclass
+
+
+@dataclass
+class PreprocessingStriationParams:
+    """Processing parameters for striation preprocessing.
+
+    :param cutoff_hi: Cutoff wavelength for shape removal in meters (highpass filter).
+    :param cutoff_lo: Cutoff wavelength for noise removal in meters (lowpass filter).
+    :param cut_borders_after_smoothing: If True, crop filter edge artifacts.
+    :param use_mean: If True, use mean for profile extraction; if False, use median.
+    :param angle_accuracy: Target angle accuracy in degrees for fine alignment.
+    :param max_iter: Maximum iterations for fine alignment.
+    :param extra_sub_samp: Additional subsampling factor for gradient detection.
+    :param shape_noise_removal: If True, apply shape and noise removal filters.
+    """
+
+    cutoff_hi: float = 2000e-6
+    cutoff_lo: float = 250e-6
+    cut_borders_after_smoothing: bool = True
+    use_mean: bool = True
+    angle_accuracy: float = 0.1
+    max_iter: int = 25
+    extra_sub_samp: int = 1
+    shape_noise_removal: bool = True