Remove one final invocation logger dep from autofocus

src/openflexure_microscope_server/things/autofocus.py

@@ -484,28 +484,26 @@ class AutofocusThing(lt.Thing):
         images_dir: str,
         autofocus_dz: int,
         save_resolution: tuple[int, int],
-        logger: lt.deps.InvocationLogger,
     ) -> StackParams:
         """Set up the parameters used for all stacks in a scan.
 
         :param images_dir: the folder to save all images
         :param autofocus_dz: the range to autofocus over if a stack fails
         :param save_resolution: The resolution to save the captures to disk with
-        :param logger: A logger passed from the calling Thing
 
         :returns: A StackParams object with the required parameters.
         """
         # Coerce min_images_to_test parameter
         min_images_to_test = self.stack_min_images_to_test
         if min_images_to_test < MIN_TEST_IMAGE_COUNT:
-            logger.warning(
+            self.logger.warning(
                 f"Cannot test only {min_images_to_test} image(s) as this will fail. "
                 "Setting min images to test to lowest possible value of"
                 f"{MIN_TEST_IMAGE_COUNT}."
             )
             min_images_to_test = MIN_TEST_IMAGE_COUNT
         elif min_images_to_test > MAX_TEST_IMAGE_COUNT:
-            logger.warning(
+            self.logger.warning(
                 f"Testing {min_images_to_test} images will cause defocus. "
                 "Setting min images to test to highest possible value of "
                 f"{MAX_TEST_IMAGE_COUNT}."
@@ -513,7 +511,7 @@ class AutofocusThing(lt.Thing):
             min_images_to_test = MAX_TEST_IMAGE_COUNT
         elif min_images_to_test % 2 == 0:
             min_images_to_test += 1
-            logger.warning(
+            self.logger.warning(
                 "Minimum number of images to test should be odd, setting to "
                 f"{min_images_to_test}."
             )
@@ -524,19 +522,19 @@ class AutofocusThing(lt.Thing):
         # min_images_to_save
         images_to_save = self.stack_images_to_save
         if images_to_save <= 0:
-            logger.warning(
+            self.logger.warning(
                 "At least 1 images must be saved. Setting images to save to 1."
             )
             images_to_save = 1
         elif images_to_save > min_images_to_test:
-            logger.warning(
+            self.logger.warning(
                 f"Cannot save {images_to_save} images as this above the minimum "
                 f"number to test. Setting images to save to {MAX_TEST_IMAGE_COUNT}."
             )
             images_to_save = min_images_to_test
         elif images_to_save % 2 == 0:
             images_to_save += 1
-            logger.warning(
+            self.logger.warning(
                 f"Images to save should be odd, setting to {images_to_save}."
             )
         # Set the Thing property to the coerced value

src/openflexure_microscope_server/things/smart_scan.py

@@ -378,7 +378,6 @@ class SmartScanThing(lt.Thing):
                 images_dir=self._ongoing_scan.images_dir,
                 autofocus_dz=self.autofocus_dz,
                 save_resolution=self._scan_data.save_resolution,
-                logger=self._scan_logger,
             )
             self._preview_stitcher = stitching.PreviewStitcher(
                 self._ongoing_scan.images_dir,

tests/test_stack.py

@@ -26,7 +26,6 @@ from openflexure_microscope_server.things.autofocus import (
     _get_peak_turning_point,
 )
 
-LOGGER = logging.getLogger("mock-invocation_logger")
 RANDOM_GENERATOR = np.random.default_rng()
 
 
@@ -274,10 +273,7 @@ def test_create_stack(autofocus_thing, caplog):
     initial_images_to_save = autofocus_thing.stack_images_to_save
     with caplog.at_level(logging.INFO):
         stack_params = autofocus_thing.create_stack_params(
-            autofocus_dz=2000,
-            images_dir="/this/is/fake",
-            save_resolution=(1640, 1232),
-            logger=LOGGER,
+            autofocus_dz=2000, images_dir="/this/is/fake", save_resolution=(1640, 1232)
         )
 
     assert len(caplog.records) == 0
@@ -304,10 +300,7 @@ def test_coercing_stack_test_ims(
 
     with caplog.at_level(logging.WARNING):
         stack_params = autofocus_thing.create_stack_params(
-            autofocus_dz=2000,
-            images_dir="/this/is/fake",
-            save_resolution=(1640, 1232),
-            logger=LOGGER,
+            autofocus_dz=2000, images_dir="/this/is/fake", save_resolution=(1640, 1232)
         )
 
     assert len(caplog.records) == 1
@@ -335,10 +328,7 @@ def test_coercing_stack_save_ims(
 
     with caplog.at_level(logging.WARNING):
         stack_params = autofocus_thing.create_stack_params(
-            autofocus_dz=2000,
-            images_dir="/this/is/fake",
-            save_resolution=(1640, 1232),
-            logger=LOGGER,
+            autofocus_dz=2000, images_dir="/this/is/fake", save_resolution=(1640, 1232)
         )
 
     assert len(caplog.records) == 1
@@ -353,10 +343,7 @@ def test_coercing_stack_save_ims(
 def test_run_smart_stack(pass_on, autofocus_thing, mocker):
     """Test Running smart stack with the stack passing on different attempts."""
     stack_params = autofocus_thing.create_stack_params(
-        autofocus_dz=2000,
-        images_dir="/this/is/fake",
-        save_resolution=(1640, 1232),
-        logger=LOGGER,
+        autofocus_dz=2000, images_dir="/this/is/fake", save_resolution=(1640, 1232)
     )
     assert stack_params.max_attempts == 3
 
@@ -417,10 +404,7 @@ def setup_and_run_z_stack(check_returns, check_turning_points, autofocus_thing,
         results). If it a tuple (or anything else), it is set as a return value.
     """
     stack_params = autofocus_thing.create_stack_params(
-        autofocus_dz=2000,
-        images_dir="/this/is/fake",
-        save_resolution=(1640, 1232),
-        logger=LOGGER,
+        autofocus_dz=2000, images_dir="/this/is/fake", save_resolution=(1640, 1232)
     )
     stack_params.settling_time = 0  # Don't settle or tests take forever.