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Merge branch 'start-to-remove-deps' into 'v3'

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Start to remove deps

See merge request openflexure/openflexure-microscope-server!451
This commit is contained in:
Julian Stirling 2025-12-16 16:23:28 +00:00
commit b5fdc0778d
8 changed files with 31 additions and 140 deletions
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73
src/openflexure_microscope_server/things/camera/__init__.py
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@ -10,7 +10,6 @@ from __future__ import annotations
import io
import json
import logging
import os
import tempfile
import time
@ -34,8 +33,6 @@ from openflexure_microscope_server.background_detect import (
)
from openflexure_microscope_server.ui import ActionButton, PropertyControl
LOGGER = logging.getLogger(__name__)
class JPEGBlob(lt.blob.Blob):
"""A class representing a JPEG image as a LabThings FastAPI Blob."""
@ -282,8 +279,6 @@ class BaseCamera(lt.Thing):
@lt.action
def capture_jpeg(
self,
metadata_getter: lt.deps.GetThingStates,
logger: lt.deps.InvocationLogger,
stream_name: str = "main",
wait: Optional[float] = None,
) -> JPEGBlob:
@ -292,9 +287,6 @@ class BaseCamera(lt.Thing):
This will use the internal capture image functionally of capture_image of
the specific camera being used.
:param metadata_getter: LabThings GetThingStates dependency, automatically
injected.
:param logger: LabThings InvocationLogger dependency, automatically injected.
:param stream_name: A stream name supported by this camera.
:param wait: (Optional, float) Set a timeout in seconds. If None it will
use the default for the underlying camera.
@ -305,13 +297,12 @@ class BaseCamera(lt.Thing):
img = self.capture_image(stream_name, wait)
capture_metadata = self._capture_metadata(metadata_getter())
capture_metadata = self._capture_metadata()
self._save_capture(
jpeg_path=jpeg_path,
image=img,
metadata=capture_metadata,
logger=logger,
)
return JPEGBlob.from_temporary_directory(directory, fname)
@ -390,70 +381,43 @@ class BaseCamera(lt.Thing):
def capture_and_save(
self,
jpeg_path: str,
logger: lt.deps.InvocationLogger,
metadata_getter: lt.deps.GetThingStates,
save_resolution: Optional[Tuple[int, int]] = None,
) -> None:
"""Capture an image and save it to disk.
:param jpeg_path: The path to save the file to
:param logger: This should be injected automatically by Labthings FastAPI
when calling the action
:param metadata_getter: This should be injected automatically by Labthings
FastAPI when calling the action
:param save_resolution: can be set to resize the image before saving. By
default this is None meaning that the image is saved at original resolution.
"""
image, capture_metadata = self._robust_image_capture(
metadata_getter,
logger=logger,
)
image, capture_metadata = self._robust_image_capture()
self._save_capture(
jpeg_path,
image,
capture_metadata,
logger,
save_resolution,
)
self._save_capture(jpeg_path, image, capture_metadata, save_resolution)
@lt.action
def capture_to_memory(
self,
logger: lt.deps.InvocationLogger,
metadata_getter: lt.deps.GetThingStates,
buffer_max: int = 1,
) -> int:
def capture_to_memory(self, buffer_max: int = 1) -> int:
"""Capture an image to memory. This can be saved later with ``save_from_memory``.
Note that only one image is held in memory so this will overwrite any image
in memory.
:param logger: This should be injected automatically by Labthings FastAPI
when calling the action
:param metadata_getter: This should be injected automatically by Labthings
FastAPI when calling the action
:param buffer_max: The maximum number of images that should be in the buffer
once this images is added. Default is 1.
:returns: the buffer id of the image captured
"""
image, metadata = self._robust_image_capture(metadata_getter, logger)
image, metadata = self._robust_image_capture()
return self._memory_buffer.add_image(image, metadata, buffer_max=buffer_max)
@lt.action
def save_from_memory(
self,
jpeg_path: str,
logger: lt.deps.InvocationLogger,
save_resolution: Optional[Tuple[int, int]] = None,
buffer_id: Optional[int] = None,
) -> None:
"""Save an image that has been captured to memory.
:param jpeg_path: The path to save the file to
:param logger: This should be injected automatically by Labthings FastAPI
when calling the action
:param save_resolution: can be set to resize the image before saving. By
default this is None meaning that the image is saved at original
resolution.
@ -466,7 +430,6 @@ class BaseCamera(lt.Thing):
jpeg_path=jpeg_path,
image=image,
metadata=metadata,
logger=logger,
save_resolution=save_resolution,
)
@ -475,11 +438,7 @@ class BaseCamera(lt.Thing):
"""Clear all images in memory."""
self._memory_buffer.clear()
def _robust_image_capture(
self,
metadata_getter: lt.deps.GetThingStates,
logger: lt.deps.InvocationLogger,
) -> Tuple[Image, Mapping[str, Any]]:
def _robust_image_capture(self) -> Tuple[Image, Mapping[str, Any]]:
"""Capture an image in memory and return it with metadata.
This robust capturing method attempts to capture the image five times
@ -491,22 +450,19 @@ class BaseCamera(lt.Thing):
"""
for capture_attempts in range(5):
try:
metadata = metadata_getter()
capture_metadata = self._capture_metadata(metadata)
capture_metadata = self._capture_metadata()
image = self.capture_image(stream_name="main", wait=5)
return image, capture_metadata
except TimeoutError:
logger.warning(
self.logger.warning(
f"Attempt {capture_attempts + 1} to capture image timed out. Do you have enough RAM?"
)
raise CaptureError("An error occurred while capturing after 5 attempts")
def _capture_metadata(
self,
metadata: Mapping[str, Any],
) -> dict:
def _capture_metadata(self) -> dict:
"""Return the metadata for a capture, from the thing states, time and known names."""
metadata = self._thing_server_interface.get_thing_states()
current_time = datetime.now()
return {
"capture_time": current_time.timestamp(),
@ -566,12 +522,11 @@ class BaseCamera(lt.Thing):
jpeg_path: str,
image: Image,
metadata: dict,
logger: lt.deps.InvocationLogger,
save_resolution: Optional[Tuple[int, int]] = None,
) -> None:
"""Save the captured image and metadata to disk.
A warning (via InvocationLogger) is raised if metadata is failed to be added
A warning is logged if metadata cannot be added.
:raises IOError: if the file cannot be saved
@ -593,7 +548,7 @@ class BaseCamera(lt.Thing):
except Exception:
# We need to capture any exception as there are many reasons metadata
# might not be added. We warn rather than log the error.
logger.exception(f"Failed to add metadata to {jpeg_path}")
self.logger.exception(f"Failed to add metadata to {jpeg_path}")
except Exception as e:
raise IOError(f"An error occurred while saving {jpeg_path}") from e
@ -639,7 +594,7 @@ class BaseCamera(lt.Thing):
def detector_name(self, name: str) -> None:
"""Validate and set detector_name."""
if name not in self.background_detectors:
LOGGER.warning(f"{name} is not a valid background detector name.")
self.logger.warning(f"{name} is not a valid background detector name.")
self._detector_name = name
@property
@ -697,7 +652,7 @@ class BaseCamera(lt.Thing):
obj.settings = instance_data["settings"]
obj.background_data = instance_data["background_data"]
else:
LOGGER.warning(
self.logger.warning(
f"No background detector named {name}, settings will be discarded."
)

30
src/openflexure_microscope_server/things/stage/__init__.py
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@ -133,24 +133,15 @@ class BaseStage(lt.Thing):
self.axis_inverted = direction
@lt.action
def move_relative(
self,
cancel: lt.deps.CancelHook,
block_cancellation: bool = False,
**kwargs: int,
) -> None:
def move_relative(self, block_cancellation: bool = False, **kwargs: int) -> None:
"""Make a relative move. Keyword arguments should be axis names."""
self._hardware_move_relative(
cancel=cancel,
block_cancellation=block_cancellation,
**self._apply_axis_direction(kwargs),
)
def _hardware_move_relative(
self,
cancel: lt.deps.CancelHook,
block_cancellation: bool = False,
**kwargs: int,
self, block_cancellation: bool = False, **kwargs: int
) -> Never:
"""Make a relative move in the coordinate system used by the physical hardware.
@ -161,22 +152,15 @@ class BaseStage(lt.Thing):
)
@lt.action
def move_absolute(
self,
cancel: lt.deps.CancelHook,
block_cancellation: bool = False,
**kwargs: int,
) -> None:
def move_absolute(self, block_cancellation: bool = False, **kwargs: int) -> None:
"""Make an absolute move. Keyword arguments should be axis names."""
self._hardware_move_absolute(
cancel=cancel,
block_cancellation=block_cancellation,
**self._apply_axis_direction(kwargs),
)
def _hardware_move_absolute(
self,
cancel: lt.deps.CancelHook,
block_cancellation: bool = False,
**kwargs: int,
) -> Never:
@ -212,20 +196,16 @@ class BaseStage(lt.Thing):
return (position_dict["x"], position_dict["y"], position_dict["z"])
@lt.action
def move_to_xyz_position(
self, cancel: lt.deps.CancelHook, xyz_pos: tuple[int, int, int]
) -> None:
def move_to_xyz_position(self, xyz_pos: tuple[int, int, int]) -> None:
"""Move to the location specified by an (x, y, z) tuple.
:param cancel: A cancel hook for cancelling the move. This dependency should be
injected automatically by LabThings-FastAPI
:param xyz_pos: The (x, y, z) position to move to.
:raises KeyError: if this stage does not have axes named "x", "y", and "z".
This method provides the interface expected by the camera_stage_mapping.
"""
self.move_absolute(cancel=cancel, x=xyz_pos[0], y=xyz_pos[1], z=xyz_pos[2])
self.move_absolute(x=xyz_pos[0], y=xyz_pos[1], z=xyz_pos[2])
StageDependency = lt.deps.direct_thing_client_dependency(BaseStage, "stage")

6
src/openflexure_microscope_server/things/stage/dummy.py
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@ -55,7 +55,6 @@ class DummyStage(BaseStage):
def _hardware_move_relative(
self,
cancel: lt.deps.CancelHook,
block_cancellation: bool = False,
**kwargs: int,
) -> None:
@ -71,7 +70,7 @@ class DummyStage(BaseStage):
if block_cancellation:
time.sleep(dt)
else:
cancel.sleep(dt)
lt.cancellable_sleep(dt)
fraction_complete = (time.time() - start_time) / (dt * max_displacement)
self.instantaneous_position = {
ax: self._hardware_position[ax] + int(fraction_complete * disp)
@ -93,7 +92,6 @@ class DummyStage(BaseStage):
def _hardware_move_absolute(
self,
cancel: lt.deps.CancelHook,
block_cancellation: bool = False,
**kwargs: int,
) -> None:
@ -104,7 +102,7 @@ class DummyStage(BaseStage):
if axis in self.axis_names
}
self._hardware_move_relative(
cancel, block_cancellation=block_cancellation, **displacement
block_cancellation=block_cancellation, **displacement
)
@lt.action

13
src/openflexure_microscope_server/things/stage/sangaboard.py
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@ -2,7 +2,6 @@
from __future__ import annotations
import logging
import threading
import time
from collections.abc import Mapping
@ -18,8 +17,6 @@ import sangaboard
from . import BaseStage
LOGGER = logging.getLogger(__name__)
REQUIRED_VERSION = semver.Version.parse("1.0.0")
RECOMMENDED_VERSION = semver.Version.parse("1.0.4")
@ -117,14 +114,13 @@ class SangaboardThing(BaseStage):
# Warn if version is below recommended
if version < RECOMMENDED_VERSION:
LOGGER.warning(
self.logger.warning(
f"Sangaboard firmware version {version} is below the recommended "
f"{RECOMMENDED_VERSION}."
)
def _hardware_move_relative(
self,
cancel: lt.deps.CancelHook,
block_cancellation: bool = False,
**kwargs: int,
) -> None:
@ -138,7 +134,7 @@ class SangaboardThing(BaseStage):
sb.query("notify_on_stop")
else:
while sb.query("moving?") == "true":
cancel.sleep(0.1)
lt.cancellable_sleep(0.1)
except lt.exceptions.InvocationCancelledError as e:
# If the move has been cancelled, stop it but don't handle the exception.
# We need the exception to propagate in order to stop any calling tasks,
@ -151,7 +147,6 @@ class SangaboardThing(BaseStage):
def _hardware_move_absolute(
self,
cancel: lt.deps.CancelHook,
block_cancellation: bool = False,
**kwargs: int,
) -> None:
@ -164,7 +159,7 @@ class SangaboardThing(BaseStage):
if axis in self.axis_names
}
self._hardware_move_relative(
cancel, block_cancellation=block_cancellation, **displacement
block_cancellation=block_cancellation, **displacement
)
@lt.action
@ -203,7 +198,7 @@ class SangaboardThing(BaseStage):
# cannot be used.
intended_brightness = float(return_value[7:])
on_brightness = 0.32
LOGGER.warning(
self.logger.warning(
"Brightness control is not yet implemented. Desired brightness: "
f"{intended_brightness}. Set brightness: {on_brightness}"
)

4
src/openflexure_microscope_server/things/system.py
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@ -121,9 +121,9 @@ class OpenFlexureSystem(lt.Thing):
return CommandOutput(output=out, error=err)
@lt.action
def get_things_state(self, metadata_getter: lt.deps.GetThingStates) -> Mapping:
def get_things_state(self) -> Mapping:
"""Metadata summarising the current state of all Things in the server."""
return metadata_getter()
return self._thing_server_interface.get_thing_states()
@property
def thing_state(self) -> Mapping[str, Any]:

19
tests/mock_things/mock_cancel.py
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@ -1,19 +0,0 @@
"""Create a fake CancelHook used instead of a dependency, it cannot be used to cancel!
Certain actions require a CancelHook to be supplied if called directly. The only method
we use from the LabThings CancelHook is ``sleep()``. The CanceHook ``sleep()`` works
exactly like ``time.sleep()`` except with raise an ``InvocationCancelledError`` if the
server receives a cancellation request.
This is just an object with a sleep method.
"""
import time
class MockCancel:
"""A class to use when directly calling an action with CancelHook dependency."""
def sleep(self, time_in_seconds: float) -> None:
"""Sleep for the input number of seconds."""
time.sleep(time_in_seconds)

26
tests/test_stage.py
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@ -18,8 +18,6 @@ from openflexure_microscope_server.things.stage import (
)
from openflexure_microscope_server.things.stage.dummy import DummyStage
from .mock_things.mock_cancel import MockCancel
# Keep the size and number of moves fairly small or the tests can take forever
point3d = st.tuples(
st.integers(min_value=-100, max_value=100),
@ -60,12 +58,7 @@ def test_override_base_movement():
class BadStage1(BaseStage):
@lt.action
def move_relative(
self,
cancel: lt.deps.CancelHook,
block_cancellation: bool = False,
**kwargs: int,
):
def move_relative(self, block_cancellation: bool = False, **kwargs: int):
pass
with pytest.raises(RedefinedBaseMovementError):
@ -73,12 +66,7 @@ def test_override_base_movement():
class BadStage2(BaseStage):
@lt.action
def move_absolute(
self,
cancel: lt.deps.CancelHook,
block_cancellation: bool = False,
**kwargs: int,
):
def move_absolute(self, block_cancellation: bool = False, **kwargs: int):
pass
with pytest.raises(RedefinedBaseMovementError):
@ -200,7 +188,6 @@ def _test_move_relative(dummy_stage, axis_inverted, path):
:param axis_inverted: Is used to set the inversion.
:param path: The 3d path to move over, generated by hypothesis.
"""
cancel = MockCancel()
dummy_stage.axis_inverted = axis_inverted
# Explicitly do axes calculation here to check logic in main code.
x_dir = -1 if axis_inverted["x"] else 1
@ -209,9 +196,7 @@ def _test_move_relative(dummy_stage, axis_inverted, path):
position = list(dummy_stage.position.values())
for movement in path:
dummy_stage.move_relative(
cancel=cancel, x=movement[0], y=movement[1], z=movement[2]
)
dummy_stage.move_relative(x=movement[0], y=movement[1], z=movement[2])
position = [pos + move for pos, move in zip(position, movement, strict=True)]
stage_pos = dummy_stage.get_xyz_position()
hw_pos = dummy_stage._hardware_position
@ -257,7 +242,6 @@ def _test_move_absolute(dummy_stage, axis_inverted, path):
:param axis_inverted: Is used to set the inversion.
:param path: The 3d path to move over, generated by hypothesis.
"""
cancel = MockCancel()
dummy_stage.axis_inverted = axis_inverted
# Explicitly do axes calculation here to check logic in main code.
x_dir = -1 if axis_inverted["x"] else 1
@ -265,9 +249,7 @@ def _test_move_absolute(dummy_stage, axis_inverted, path):
z_dir = -1 if axis_inverted["z"] else 1
position = list(dummy_stage.position.values())
for move_to in path:
dummy_stage.move_absolute(
cancel=cancel, x=move_to[0], y=move_to[1], z=move_to[2]
)
dummy_stage.move_absolute(x=move_to[0], y=move_to[1], z=move_to[2])
position = move_to
stage_pos = dummy_stage.get_xyz_position()
hw_pos = dummy_stage._hardware_position