Convert Stage to a Protocol

The Stage is now implemented as a runtime-checkable Protocol.

Part of this led to the realisation that we can't create a DirectThingClient
based on a Protocol, only on a concrete Thing. While it might be
a good idea to address that in LabThings in due course, for now
we work around it by creating both a Protocol and a stub class. The stub class implements the protocol, and
can be used to declare a dependency.

src/openflexure_microscope_server/things/auto_recentre_stage.py

@@ -4,11 +4,10 @@ import logging
 from labthings_fastapi.thing import Thing
 from labthings_fastapi.dependencies.thing import direct_thing_client_dependency
 from labthings_fastapi.decorators import thing_action
-from .stage import Stage
+from .stage import StageDependency as StageDep
 from openflexure_microscope_server.things.autofocus import AutofocusThing
 from openflexure_microscope_server.things.camera_stage_mapping import CameraStageMapper
 
-StageDep = direct_thing_client_dependency(Stage, "/stage/")
 CSMDep = direct_thing_client_dependency(CameraStageMapper, "/camera_stage_mapping/")
 AutofocusDep = direct_thing_client_dependency(AutofocusThing, "/autofocus/")
 

src/openflexure_microscope_server/things/autofocus.py

@@ -21,11 +21,10 @@ from labthings_fastapi.decorators import thing_action
 from labthings_fastapi.types.numpy import NDArray
 from .camera import RawCameraDependency as Camera
 from .camera import CameraDependency as WrappedCamera
-from .stage import Stage as StageThing
+from .stage import StageDependency as Stage
 import numpy as np
 from pydantic import BaseModel
 
-Stage = direct_thing_client_dependency(StageThing, "/stage/")
 
 ### Autofocus utilities
 

src/openflexure_microscope_server/things/camera/simulation.py

@@ -25,7 +25,7 @@ from labthings_fastapi.types.numpy import NDArray
 from labthings_fastapi.server import ThingServer
 
 from . import BaseCamera, JPEGBlob
-from ..stage import Stage
+from ..stage import StageProtocol as Stage
 
 
 class SimulatedCamera(BaseCamera):

src/openflexure_microscope_server/things/camera_stage_mapping.py

@@ -21,17 +21,13 @@ from camera_stage_mapping.camera_stage_calibration_1d import (
     calibrate_backlash_1d,
     image_to_stage_displacement_from_1d,
 )
-from camera_stage_mapping.camera_stage_tracker import Tracker
-from .camera import CameraDependency as Camera
-from .stage import Stage as StageThing
-
-from labthings_fastapi.dependencies.thing import direct_thing_client_dependency
 from labthings_fastapi.dependencies.invocation import InvocationCancelledError, InvocationLogger
 from labthings_fastapi.types.numpy import NDArray, denumpify, DenumpifyingDict
 from labthings_fastapi.decorators import thing_action, thing_property
 from labthings_fastapi.thing import Thing
-
+from camera_stage_mapping.camera_stage_tracker import Tracker
-Stage = direct_thing_client_dependency(StageThing, "/stage/")
+from .camera import CameraDependency as Camera
+from .stage import StageDependency as Stage
 
 CoordinateType = Tuple[float, float, float]
 XYCoordinateType = Tuple[float, float]

src/openflexure_microscope_server/things/smart_scan.py

@@ -29,13 +29,12 @@ from labthings_fastapi.dependencies.invocation import CancelHook, InvocationLogg
 from labthings_fastapi.decorators import thing_action, thing_property, fastapi_endpoint
 from labthings_fastapi.outputs.blob import blob_type
 from .camera import CameraDependency as CamDep
-from .stage import Stage
+from .stage import StageDependency as StageDep
 from openflexure_microscope_server.things.autofocus import AutofocusThing
 from openflexure_microscope_server.things.camera_stage_mapping import CameraStageMapper
 from openflexure_microscope_server.things.auto_recentre_stage import RecentringThing
 
 
-StageDep = direct_thing_client_dependency(Stage, "/stage/")
 CSMDep = direct_thing_client_dependency(CameraStageMapper, "/camera_stage_mapping/")
 AutofocusDep = direct_thing_client_dependency(AutofocusThing, "/autofocus/")
 RecentreStage = direct_thing_client_dependency(RecentringThing, "/auto_recentre_stage/")

src/openflexure_microscope_server/things/stage/__init__.py

@@ -1,16 +1,63 @@
 from __future__ import annotations
+from typing import Any, Protocol, TypeAlias, runtime_checkable
 from labthings_fastapi.descriptors.property import PropertyDescriptor
 from labthings_fastapi.thing import Thing
 from labthings_fastapi.decorators import thing_action, thing_property
 from labthings_fastapi.dependencies.invocation import CancelHook
+from labthings_fastapi.dependencies.thing import direct_thing_client_dependency
 from collections.abc import Sequence, Mapping
 
+@runtime_checkable
+class StageProtocol(Protocol):
+    """A protocol for the OpenFlexure translation stage
+    """
+    _axis_names: Sequence[str]
 
-class Stage(Thing):
+    @property
-    """A dummy stage for testing purposes
+    def axis_names(self) -> Sequence[str]:
+        """The names of the stage's axes, in order."""
+        ...
+
+    @property
+    def position(self) -> Mapping[str, int]:
+        """Current position of the stage"""
+        ...
+
+    @property
+    def moving() -> bool:
+        "Whether the stage is in motion"
+        ...
+
+    @property
+    def thing_state(self) -> Mapping[str, Any]:
+        """Summary metadata describing the current state of the stage"""
+        ...
     
-    This stage should work similarly to a Sangaboard stage, but without any
+    def move_relative(self, cancel: CancelHook, block_cancellation: bool=False, **kwargs: Mapping[str, int]):
-    hardware attached.
+        """Make a relative move. Keyword arguments should be axis names."""
+        ...
+
+    def move_absolute(self, cancel: CancelHook, block_cancellation: bool=False, **kwargs: Mapping[str, int]):
+        """Make an absolute move. Keyword arguments should be axis names."""
+        ...
+        
+    def set_zero_position(self):
+        """Make the current position zero in all axes
+        
+        This action does not move the stage, but resets the position to zero.
+        It is intended for use after manually or automatically recentring the
+        stage.
+        """
+        ...
+
+
+class BaseStage(Thing):
+    """A base stage class for OpenFlexure translation stages
+    
+    This can't be used directly but should reduce boilerplate code when
+    implementing new stages. A minimal working stage must implement
+    `move_relative` and `move_absolute` actions, which update the
+    `position` property on completion, and provide `set_zero_position`.
     """
     _axis_names = ("x", "y", "z")
 
@@ -41,17 +88,26 @@ class Stage(Thing):
         return {
             "position": self.position
         }
-    
+
+
+class StageStub(BaseStage):
+    """A Stub Thing for the OpenFlexure translation stage
+
+    As of LabThings-FastAPI 0.0.7, we can't make a thing client dependency
+    based on a protocol, because the protocol is not a Thing, and its
+    methods/properties are not decorated as Affordances. This stub class
+    is a workaround for that limitation, and should not be used directly.
+    """
     @thing_action
     def move_relative(self, cancel: CancelHook, block_cancellation: bool=False, **kwargs: Mapping[str, int]):
         """Make a relative move. Keyword arguments should be axis names."""
-        raise NotImplementedError("Subclasses should implement this method")
+        raise NotImplementedError("StageStub should not be used directly")
 
     @thing_action
     def move_absolute(self, cancel: CancelHook, block_cancellation: bool=False, **kwargs: Mapping[str, int]):
         """Make an absolute move. Keyword arguments should be axis names."""
-        raise NotImplementedError("Subclasses should implement this method")
+        raise NotImplementedError("StageStub should not be used directly")
-        
+
     @thing_action
     def set_zero_position(self):
         """Make the current position zero in all axes
@@ -60,4 +116,7 @@ class Stage(Thing):
         It is intended for use after manually or automatically recentring the
         stage.
         """
-        raise NotImplementedError("Subclasses should implement this method")
+        raise NotImplementedError("StageStub should not be used directly")
+
+
+StageDependency: TypeAlias = direct_thing_client_dependency(StageStub, "/stage/")

src/openflexure_microscope_server/things/stage/dummy.py

@@ -4,10 +4,10 @@ from labthings_fastapi.dependencies.invocation import CancelHook, InvocationCanc
 from collections.abc import Mapping
 import time
 
-from . import Stage
+from . import BaseStage
 
 
-class DummyStage(Stage):
+class DummyStage(BaseStage):
     """A dummy stage for testing purposes
     
     This stage should work similarly to a Sangaboard stage, but without any