Use backlash compensation in smart scan and autofocus

src/openflexure_microscope_server/things/autofocus.py

@@ -22,7 +22,7 @@ import labthings_fastapi as lt
 from labthings_fastapi.types.numpy import NDArray
 
 from .camera import BaseCamera, CaptureParams
-from .stage import BaseStage
+from .stage import BacklashCompensation, BaseStage
 
 LOGGER = logging.getLogger(__name__)
 MIN_TEST_IMAGE_COUNT = 3
@@ -458,14 +458,17 @@ class AutofocusThing(lt.Thing):
         up to 10 times.
         """
         attempt = 0
-        backlash = 200
 
         with JPEGSharpnessMonitor(self._stage, self._cam) as sharpness_monitor:
             while attempt < 10:
                 attempt += 1
                 if start == "centre":
-                    self._stage.move_relative(x=0, y=0, z=-int(backlash + dz / 2))
+                    self._stage.move_relative(
-                    self._stage.move_relative(x=0, y=0, z=backlash)
+                        x=0,
+                        y=0,
+                        z=-int(dz / 2),
+                        backlash_compensation=BacklashCompensation.Z_ONLY,
+                    )
 
                 # Always start centrally for future runs
                 start = "centre"
@@ -480,8 +483,10 @@ class AutofocusThing(lt.Thing):
                 target_max = np.max(heights) - dz / 5
 
                 # move to the peak
-                self._stage.move_absolute(z=peak_height - backlash)
+                self._stage.move_absolute(
-                self._stage.move_absolute(z=peak_height)
+                    z=peak_height,
+                    backlash_compensation=BacklashCompensation.Z_ONLY,
+                )
 
                 if target_min < peak_height < target_max:
                     # If it is within the target range then return
@@ -622,12 +627,10 @@ class AutofocusThing(lt.Thing):
         # Better to start too low and take too many images than too high and need to refocus
         self._stage.move_relative(
             z=-int(
-                stack_parameters.steps_undershoot
+                stack_parameters.steps_undershoot + stack_parameters.stack_z_range / 2
-                + stack_parameters.backlash_correction
+            ),
-                + stack_parameters.stack_z_range / 2
+            backlash_compensation=BacklashCompensation.Z_ONLY,
-            )
         )
-        self._stage.move_relative(z=stack_parameters.backlash_correction)
 
         captures: list[CaptureInfo] = []
         # Always check for focus using the the last `min_images_to_test` in the

src/openflexure_microscope_server/things/smart_scan.py

@@ -37,7 +37,7 @@ from openflexure_microscope_server.utilities import coerce_thing_selector
 # Things
 from .camera import BaseCamera
 from .scan_workflows import ScanWorkflow
-from .stage import BaseStage
+from .stage import BacklashCompensation, BaseStage
 
 T = TypeVar("T")
 P = ParamSpec("P")
@@ -311,6 +311,7 @@ class SmartScanThing(lt.Thing):
             x=next_point[0],
             y=next_point[1],
             z=z_estimate,
+            backlash_compensation=BacklashCompensation.XY_ONLY,
         )
 
         return (next_point[0], next_point[1], z_estimate)

src/openflexure_microscope_server/things/stage/__init__.py

@@ -142,7 +142,9 @@ class BaseStage(lt.Thing):
         """Current position of the stage."""
         return self._apply_axis_direction(self._hardware_position)
 
-    backlash_steps: dict[str, int] = lt.setting(default={"x": 200, "y": 200, "z": 200})
+    backlash_steps: dict[str, int] = lt.setting(
+        default={"x": 200, "y": 200, "z": 200}, readonly=True
+    )
     """The number of steps to elimate backlash. The sign sets the direction.
 
     A positive number sets the direction of the second move in a backlash correction.

tests/unit_tests/test_autofocus.py

@@ -60,6 +60,8 @@ def test_looping_autofocus(start_z, max_loc, centre, attempts_expected, passes,
 
     def adjust_pos(**kwargs: int) -> None:
         """Move relative should update position. So make a side effect for the mock."""
+        # Remove backlash compensation from the dict if it exists.
+        kwargs.pop("backlash_compensation", None)
         for axis, value in kwargs.items():
             autofocus_thing._stage.position[axis] += value