Create aquisition routines for scan workflows, remove background detector from base ScanWorkflow class

src/openflexure_microscope_server/things/scan_workflows.py

@@ -7,7 +7,6 @@ from openflexure_microscope_server.scan_planners import ScanPlanner, SmartSpiral
 from openflexure_microscope_server.stitching import STITCHING_RESOLUTION
 from openflexure_microscope_server.things.autofocus import AutofocusThing
 from openflexure_microscope_server.things.background_detect import (
-    BackgroundDetectAlgorithm,
     ChannelDeviationLUV,
 )
 from openflexure_microscope_server.things.camera_stage_mapping import CameraStageMapper
@@ -20,14 +19,10 @@ class ScanWorkflow(lt.Thing):
     scan planning, aquisition routine.
     """
 
-    # All workdlows must have at least one background detector and a set class for scan
+    # All workdlows must have a set class for scan planning
-    # planning
-    _background_detector: Optional[
-        BackgroundDetectAlgorithm | Mapping[str, BackgroundDetectAlgorithm]
-    ] = lt.thing_slot()
     _planner_cls: type[ScanPlanner]
 
-    # All workdlows set a save resolution
+    # All workflows set a save resolution
     save_resolution: tuple[int, int] = lt.setting(default=(1640, 1232))
     """A tuple of the image resolution to capture."""
 
@@ -56,15 +51,26 @@ class ScanWorkflow(lt.Thing):
             is returned if it is not possible to stitch the scan.
         """
         raise NotImplementedError(
-            "Each specific ScanWorkflow must implement a `all_settings`. "
+            "Each specific ScanWorkflow must implement a `all_settings`. method."
-            "method."
         )
 
-    def pre_scan_routine(self) -> None:
+    def pre_scan_routine(self, settings: dict) -> None:
         raise NotImplementedError(
             "Each specific ScanWorkflow must implement a pre-scan routine."
         )
 
+    def new_scan_planner(self, settings: dict, position: Mapping[str, int]) -> None:
+        raise NotImplementedError(
+            "Each specific ScanWorkflow must implement a ``new_scan_planner`` method."
+        )
+
+    def aquisition_routine(
+        self, settings: dict, xyz_pos: tuple[int, int, int]
+    ) -> tuple[bool, Optional[int]]:
+        raise NotImplementedError(
+            "Each specific ScanWorkflow must implement an aquisition routine"
+        )
+
 
 class HistoScanWorkflow(ScanWorkflow):
     # Thing Slots
@@ -184,5 +190,53 @@ class HistoScanWorkflow(ScanWorkflow):
         # If not use the other stage axes
         return x_move_stage["y"], y_move_stage["x"]
 
-    def pre_scan_routine(self) -> None:
+    def pre_scan_routine(self, settings: dict) -> None:
-        self._autofocus.looping_autofocus(dz=self.autofocus_dz, start="centre")
+        self._autofocus.looping_autofocus(dz=settings["autofocus_dz"], start="centre")
+
+    def new_scan_planner(self, settings: dict, position: Mapping[str, int]) -> None:
+        # The initial plan for the scan should be a single x,y position. All future
+        # moves will be planned around this point. In future, route planner could
+        # have multiple starting positions, each of which will be visited before the
+        # scan can end.
+        planner_settings = {
+            "dx": settings["dx"],
+            "dy": settings["dy"],
+            "max_dist": settings["max_dist"],
+        }
+        return self._planner_cls(
+            initial_position=(position["x"], position["y"]),
+            planner_settings=planner_settings,
+        )
+
+    def aquisition_routine(
+        self, settings: dict, xyz_pos: tuple[int, int, int]
+    ) -> tuple[bool, Optional[int]]:
+        """Perform aquisition routine. This is run at each scan location.
+
+        :return: A tuple of whether an image was taken, and the z-position for focus.
+            If failed to find focus, returns for the focus z-position.
+        """
+        # If skipping background, take an image to check if current field of view is background
+        if settings["skip_background"]:
+            capture_image, bg_message = self._cam.image_is_sample()
+
+        if not capture_image:
+            msg = f"Skipping {xyz_pos} as it is {bg_message}."
+            self.logger.info(msg)
+            return False, None
+
+        save_on_failure = settings["skip_background"]
+
+        focused, focused_height = self._autofocus.run_smart_stack(
+            stack_parameters=self.stack_params,
+            save_on_failure=save_on_failure,
+        )
+        # An image was captured if we are focussed or we are not skipping background.
+        imaged = focused or save_on_failure
+
+        # run_smart_stage always returns a focus height for the sharpest image even
+        # if it failed to find a good focus. Set to None if not focussed.
+        if not focused:
+            focused_height = None
+
+        return imaged, focused_height

src/openflexure_microscope_server/things/smart_scan.py

@@ -22,19 +22,18 @@ from typing import (
     TypeVar,
 )
 
-import numpy as np
 from fastapi import HTTPException
 from fastapi.responses import FileResponse
 from pydantic import BaseModel
 
 import labthings_fastapi as lt
 
-from openflexure_microscope_server import scan_directories, scan_planners, stitching
+from openflexure_microscope_server import scan_directories, stitching
 
 # Things
 from .autofocus import AutofocusThing, StackParams
 from .camera import BaseCamera
-from .camera_stage_mapping import CameraStageMapper, CSMUncalibratedError
+from .camera_stage_mapping import CameraStageMapper
 from .scan_workflows import HistoScanWorkflow, ScanWorkflow
 from .stage import BaseStage
 
@@ -284,6 +283,9 @@ class SmartScanThing(lt.Thing):
     @_scan_running
     def _manage_stitching_threads(self) -> None:
         """Manage the stitching threads, starting them if needed and not already running."""
+        if self.scan_data.stitching_settings is None:
+            # This scan can't stitch.
+            return
         # Assume 4 images means at least one offset in x and y, making the stitching
         # well constrained.
         if self.scan_data.image_count > 3 and not self.preview_stitcher.running:
@@ -354,18 +356,9 @@ class SmartScanThing(lt.Thing):
         This loop runs during a scan, until no more scan x,y positions
         are remaining.
         """
-        # The initial plan for the scan should be a single x,y position. All future
+        workflow_settings = self.scan_data.workflow_settings
-        # moves will be planned around this point. In future, route planner could
+        route_planner = workflow.new_scan_planner(
-        # have multiple starting positions, each of which will be visited before the
+            workflow_settings, self._stage.position
-        # scan can end.
-        planner_settings = {
-            "dx": self.scan_data.dx,
-            "dy": self.scan_data.dy,
-            "max_dist": self.scan_data.max_dist,
-        }
-        route_planner = scan_planners.SmartSpiral(
-            initial_position=(self._stage.position["x"], self._stage.position["y"]),
-            planner_settings=planner_settings,
         )
 
         # The loop tests if the scan should continue, moves to the next position,
@@ -383,43 +376,30 @@ class SmartScanThing(lt.Thing):
                 new_pos_xyz[1],
                 self._stage.position["z"],
             )
-
+            imaged, focus_height = workflow.aquisition_routine(
-            capture_image = True
+                workflow_settings, current_pos_xyz
-            # If skipping background, take an image to check if current field of view is background
-            if self.scan_data.skip_background:
-                capture_image, bg_message = self._cam.image_is_sample()
-
-            if not capture_image:
-                route_planner.mark_location_visited(
-                    new_pos_xyz, imaged=False, focused=False
-                )
-                msg = f"Skipping {new_pos_xyz} as it is {bg_message}."
-                self.logger.info(msg)
-                continue
-
-            focused, focused_height = self._autofocus.run_smart_stack(
-                stack_parameters=self.stack_params,
-                save_on_failure=not self.scan_data.skip_background,
             )
 
-            current_pos_xyz = (new_pos_xyz[0], new_pos_xyz[1], focused_height)
+            if focus_height is None:
-
+                focused = False
-            # An image was captured if we are focussed or we are not skipping background.
+            else:
-            imaged = focused or not self.scan_data.skip_background
+                current_pos_xyz = (new_pos_xyz[0], new_pos_xyz[1], focus_height)
 
             route_planner.mark_location_visited(
                 current_pos_xyz, imaged=imaged, focused=focused
             )
 
-            # increment capture counter as thread has completed
+            if imaged:
-            self.scan_data.image_count += 1
+                # increment capture counter as thread has completed
-            # Add it to the incremental zip
+                self.scan_data.image_count += 1
-            self.ongoing_scan.zip_files()
+                # Add it to the incremental zip
+                self.ongoing_scan.zip_files()
 
     @_scan_running
     def _return_to_starting_position(self) -> None:
         """Return to the initial scan position, if set."""
         self.logger.info("Returning to starting position.")
+
         if self._scan_data is not None:
             self._stage.move_absolute(
                 **self.scan_data.starting_position, block_cancellation=True