Add filter needles

[Raytesnel]

Adds Filters:
- FilterNeedles
- FilterMedian
These two are used in rotation.py
I shuffeled the order a bit around to extract some logic like if No bounding_box is given then we dont need to rotate, but only crop and mask. by reordening i could extract that piece in put it in the controller.py. so we don't call a rotate function without the need for rotation. tests that were only cropping and masking not rotating are deleted. because we already coverd those tests and extrected that usecase.

things i like to fix but didnt (yet).
i would like to extract CropToMask from the rotate_crop_and_mask_image_by_crop so we could have a pure Rotation function. and create the pipeline without hiding buisness logic.
stuff like making the margin bigger when rotation would be ideal to put it in the controller and not inside the execution.

[github-actions]

Diff Coverage

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

• packages/scratch-core/src/computations/spatial.py (81.8%): Missing lines 23,25
• packages/scratch-core/src/conversion/rotate.py (100%)
• packages/scratch-core/src/mutations/filter.py (100%)
• packages/scratch-core/src/mutations/spatial.py (100%)
• packages/scratch-core/src/parsers/loaders.py (100%)
• src/preprocessors/controller.py (50.0%): Missing lines 33-36

Summary

• Total: 99 lines
• Missing: 6 lines
• Coverage: 93%

packages/scratch-core/src/computations/spatial.py

Lines 19-28

  19     x_min = max(0, x_coords.min() + margin)
  20     x_max = min(mask.shape[1], x_coords.max() - margin + 1)
  21 
  22     if x_min >= x_max:
! 23         raise ValueError("Slice results in x_min >= x_max. Margin may be too large.")
  24     if y_min >= y_max:
! 25         raise ValueError("Slice results in y_min >= y_max. Margin may be too large.")
  26 
  27     return slice(y_min, y_max), slice(x_min, x_max)

---

src/preprocessors/controller.py

Lines 29-40

  29     scan_image: ScanImage, mark_type: MarkType, mask: BinaryMask, bounding_box: BoundingBox | None
  30 ) -> Mark:
  31     """Parse a scan file and extract a mark by rotating, cropping, masking, and resampling."""
  32     if bounding_box is None:
! 33         logger.info("Masking and Cropping scan image")
! 34         scan_image_masked = Mask(mask=mask)(scan_image).unwrap()
! 35         scan_image_cleaned = FilterNeedles()(scan_image_masked).unwrap()
! 36         rotated_image = CropToMask(mask=mask)(scan_image_cleaned).unwrap()
  37     else:
  38         logger.info("Rotating Masking and Cropping scan image")
  39         rotated_image = rotate_crop_and_mask_image_by_crop(scan_image=scan_image, mask=mask, bounding_box=bounding_box)
  40     logger.info("Transforming scan image to mark")

---

[github-actions]

Package	Line Rate	Branch Rate	Health
.	96%	88%	✔
comparators	100%	100%	✔
computations	85%	50%	✔
container_models	99%	100%	✔
conversion	95%	78%	✔
conversion.export	100%	100%	✔
conversion.filter	97%	89%	✔
conversion.leveling	100%	100%	✔
conversion.leveling.solver	100%	75%	✔
conversion.plots	98%	88%	✔
conversion.preprocess_impression	99%	91%	✔
conversion.preprocess_striation	89%	58%	✔
conversion.profile_correlator	96%	82%	✔
conversion.surface_comparison	96%	88%	✔
conversion.surface_comparison.cell_registration	100%	100%	✔
extractors	99%	75%	✔
mutations	100%	100%	✔
parsers	98%	80%	✔
parsers.patches	89%	60%	✔
preprocessors	97%	85%	✔
processors	99%	100%	✔
renders	98%	67%	✔
utils	92%	75%	✔
Summary	97% (3325 / 3421)	84% (358 / 426)	✔

Minimum allowed line rate is 50%