Merge branch '797-improve-type-hints-and-docstring-for-calculate_regi…

…stration_image_based' into tmp-remove-anyof-from-pydantic-v2-schema

CHANGELOG.md

@@ -5,9 +5,13 @@
 * Tasks:
  * Fix issue with masked ROI & relabeling in Cellpose task (\#785).
  * Fix issue with masking ROI label types in masked_loading_wrapper for Cellpose task (\#785).
+ * Fix issue with masking ROI label types in `masked_loading_wrapper` for Cellpose task (\#785).
+ * Enable workaround to support yx images in Cellpose task (\#789).
+ * Fix error handling in `calculate_registration_image_based` (\#799).
+ * Fix minor issues with call-signature and type hints in `calculate_registration_image_based` (\#799).
+
 * Development:
  * Switch all core models to pydantic v2 (\#790).
- * Enable workaround to support yx images in Cellpose task (\#789).
 
 # 1.1.0
 
@@ -23,7 +27,7 @@
  * Rename `task.cellpose_transforms` into `tasks.cellpose_utils` (\#738).
  * Fix wrong repeated overlap checks for bounding-boxes in Cellpose task (\#778).
  * Fix minor MIP issues related to plate metadata and expecting acquisition metadata in all NGFF plates(\#781).
- * Add chi2_shift option to Calculate Registration (image-based) task(\#741).
+ * Add `chi2_shift` option to Calculate Registration (image-based) task(\#741).
 * Development:
  * Switch to transitional pydantic.v1 imports, changes pydantic requirement to `==1.10.16` or `>=2.6.3` (\#760).
  * Support JSON-Schema generation for `Enum` task arguments (\#749).

fractal_tasks_core/__FRACTAL_MANIFEST__.json

@@ -1076,7 +1076,7 @@
  },
  "RegistrationMethod": {
  "title": "RegistrationMethod",
- "description": "An enumeration.",
+ "description": "RegistrationMethod Enum class",
  "enum": [
  "phase_cross_correlation",
  "chi2_shift"

fractal_tasks_core/tasks/calculate_registration_image_based.py

@@ -48,6 +48,16 @@
 
 
 class RegistrationMethod(Enum):
+ """
+ RegistrationMethod Enum class
+
+ Attributes:
+ PHASE_CROSS_CORRELATION: phase cross correlation based on scikit-image
+ (works with 2D & 3D images).
+ CHI2_SHIFT: chi2 shift based on image-registration library
+ (only works with 2D images).
+ """
+
  PHASE_CROSS_CORRELATION = "phase_cross_correlation"
  CHI2_SHIFT = "chi2_shift"
 
@@ -66,7 +76,7 @@ def calculate_registration_image_based(
  init_args: InitArgsRegistration,
  # Core parameters
  wavelength_id: str,
- method: RegistrationMethod = "phase_cross_correlation",
+ method: RegistrationMethod = RegistrationMethod.PHASE_CROSS_CORRELATION,
  roi_table: str = "FOV_ROI_table",
  level: int = 2,
 ) -> None:
@@ -137,11 +147,11 @@ def calculate_registration_image_based(
  # Check if data is 3D (as not all registration methods work in 3D)
  # TODO: Abstract this check into a higher-level Zarr loading class
  if is_3D(data_reference_zyx):
- if method == "chi2_shift":
+ if method == RegistrationMethod(RegistrationMethod.CHI2_SHIFT):
  raise ValueError(
- "The `chi2_shift` registration method has not been "
- "implemented for 3D images and the input image had a shape of "
- f"{data_reference_zyx.shape}."
+ f"The `{RegistrationMethod.CHI2_SHIFT}` registration method "
+ "has not been implemented for 3D images and the input image "
+ f"had a shape of {data_reference_zyx.shape}."
  )
 
  # Read ROIs