Run poetry run pre-commit run --all-files

fractal_tasks_core/tasks/_registration_utils.py

@@ -238,7 +238,6 @@ def apply_registration_to_single_ROI_table(
     return roi_table
 
 
-
 def chi2_shift_out(img_ref, img_cycle_x):
     """
     Helper function to get the output of chi2_shift into the same format as
@@ -252,17 +251,16 @@ def chi2_shift_out(img_ref, img_cycle_x):
     Returns:
         list: list of tuple of shift in y and x direction.
     """
-    x, y, a, b = chi2_shift(np.squeeze(img_ref),
-                            np.squeeze(img_cycle_x))
+    x, y, a, b = chi2_shift(np.squeeze(img_ref), np.squeeze(img_cycle_x))
 
-    '''
+    """
     running into issues when using direct float output for fractal.
-    When rounding to integer and using integer dtype, it typically works 
+    When rounding to integer and using integer dtype, it typically works
     but for some reasons fails when run over a whole 384 well plate (but
     the well where it fails works fine when run alone). The original verison
-    works fine however. Trying to round to integer, but still use float64 
+    works fine however. Trying to round to integer, but still use float64
     dtype like original version.
-    '''
-    shifts = np.array([-int(np.round(y)), -int(np.round(x))], dtype='float64')
+    """
+    shifts = np.array([-int(np.round(y)), -int(np.round(x))], dtype="float64")
 
-    return [shifts]
+    return [shifts]

fractal_tasks_core/tasks/calculate_registration_image_based.py

@@ -36,8 +36,10 @@
 from fractal_tasks_core.tables import write_table
 from fractal_tasks_core.tasks._registration_utils import (
     calculate_physical_shifts,
+)
+from fractal_tasks_core.tasks._registration_utils import chi2_shift_out
+from fractal_tasks_core.tasks._registration_utils import (
     get_ROI_table_with_translation,
-    chi2_shift_out,
 )
 from fractal_tasks_core.tasks.io_models import InitArgsRegistration
 
@@ -59,7 +61,7 @@ def calculate_registration_image_based(
     init_args: InitArgsRegistration,
     # Core parameters
     wavelength_id: str,
-    method: Literal[tuple([key for key,value in REG_METHODS.items()])],
+    method: Literal[tuple([key for key, value in REG_METHODS.items()])],
     roi_table: str = "FOV_ROI_table",
     level: int = 2,
 ) -> None:

tests/tasks/test_registration.py

@@ -198,8 +198,8 @@ def patched_segment_ROI(
 
     return mask.astype(label_dtype)
 
-@pytest.mark.parametrize("method", ["phase_cross_correlation",
-                                    "chi2_shift"])
+
+@pytest.mark.parametrize("method", ["phase_cross_correlation", "chi2_shift"])
 def test_multiplexing_registration(
     zenodo_images_multiplex_shifted: list[str],
     tmp_path,