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Clean up from suggestions

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This commit is contained in:
jaknapper 2026-05-08 17:39:49 +01:00
parent cab960fe2c
commit bea7447f26
1 changed files with 57 additions and 17 deletions
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74
src/openflexure_microscope_server/things/autofocus.py
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@ -34,10 +34,7 @@ class NotStreamingError(RuntimeError):
"""No images captured from stream. The camera is almost certainly not streaming."""
class SharpnessMethod(enum.Enum):
"""The possible SharpnessMethods for autofocus."""
class SharpnessMethod(enum.Enum):
class SharpnessMethod(enum.IntFlag):
"""The possible SharpnessMethods for autofocus.
Use powers of two for the methods so they can be selected bitwise. This allows choosing what to record
@ -268,13 +265,20 @@ class JPEGSharpnessMonitor:
stage: BaseStage,
camera: BaseCamera,
method: SharpnessMethod = SharpnessMethod.JPEG,
record: Optional[int] = None,
record: Optional[SharpnessMethod] = None,
) -> None:
"""Initialise a new JPEGSharpnessMonitor. The args are injected automatically.
:param stage: A direct_thing_client dependency for the the microscope stage.
:param camera: A raw_thing_client depeendency for the camera. This is a raw
dependency as the underlying class needs to be
dependency as required by the underlying class.
:param method: The sharpness metric used when evaluating autofocus.
:param record: Bitmask of sharpness metrics to record while monitoring.
If ``None``, only the metric specified by ``method`` is recorded.
:raises ValueError: If ``method`` is not included in ``record``.
:raises ValueError: If ``SharpnessMethod.FOCUS_FOM`` is requested but
the camera does not support FocusFoM measurements.
"""
self.camera = camera
self.stage = stage
@ -295,7 +299,12 @@ class JPEGSharpnessMonitor:
@property
def stage_positions(self) -> Sequence[Mapping[str, int]]:
"""The positions recorded for the stage."""
"""The positions recorded for the stage.
:raises ValueError: If stage position recording is not enabled.
"""
if not self._stage_positions:
raise ValueError("Stage positions have not been recorded yet.")
return self._stage_positions
@property
@ -310,12 +319,22 @@ class JPEGSharpnessMonitor:
@property
def jpeg_sizes(self) -> Sequence[int]:
"""The recorded JPEG frame sizes used as a sharpness metric."""
"""The recorded JPEG frame sizes used as a sharpness metric.
:raises ValueError: If JPEG sharpness recording is not enabled.
"""
if not self.record & SharpnessMethod.JPEG:
raise ValueError("JPEG sizes are not being recorded.")
return self._jpeg_sizes
@property
def focus_foms(self) -> Sequence[float]:
"""The recorded FocusFoM values."""
"""The recorded FocusFoM values.
:raises ValueError: If FocusFoM recording is not enabled.
"""
if not self.record & SharpnessMethod.FOCUS_FOM:
raise ValueError("FocusFoM values are not being recorded.")
return self._focus_foms
running = False
@ -464,18 +483,28 @@ class AutofocusThing(lt.Thing):
dz: int = 2000,
start: Literal["centre", "base"] = "centre",
sharpness_metric: SharpnessMethod = SharpnessMethod.JPEG,
record: Optional[Int]
record: Optional[SharpnessMethod] = None
) -> SharpnessDataArrays:
"""Sweep the stage up and down, then move to the sharpest point.
This method will will move down by dz/2, sweep up by dz, and then evaluate
the position where the image was sharpest. We'll then move back down, and
finally up to the sharpest point.
This method will move down by dz/2, sweep up by dz, and then evaluate
the position where the image was sharpest. We'll then move back down,
and finally up to the sharpest point.
sharpness_metric is either JPEG file size (JPEG) or inbuilt figure of metric (FOCUS_FOM).
:param dz: Total z-range (in steps) used for the autofocus sweep.
:param start: Starting position of the sweep. "centre" begins at -dz/2,
while "base" begins from the current position.
:param sharpness_metric: Sharpness metric used for evaluation. Either
JPEG file size (JPEG) or inbuilt figure of metric (FOCUS_FOM).
:param record: Optional bitmask of sharpness metrics to record during
acquisition. If None, defaults to recording only the selected
sharpness_metric.
:returns: SharpnessDataArrays containing all recorded sharpness and
stage position data for the sweep.
"""
with JPEGSharpnessMonitor(
self._stage, self._cam, sharpness_metric
self._stage, self._cam, sharpness_metric, record=record,
) as sharpness_monitor:
# Move to (-dz / 2)
if start == "centre":
@ -525,6 +554,7 @@ class AutofocusThing(lt.Thing):
dz: int = 2000,
start: Literal["centre", "base"] = "centre",
sharpness_metric: SharpnessMethod = SharpnessMethod.JPEG,
record: Optional[SharpnessMethod] = None,
) -> tuple[list[float], list[float]]:
"""Repeatedly autofocus the stage until it looks focused.
@ -533,12 +563,22 @@ class AutofocusThing(lt.Thing):
is close to focus, but not quite within ``dz/2``. It will attempt to autofocus
up to 10 times.
sharpness_metric is either JPEG file size (JPEG) or inbuilt figure of metric (FOCUS_FOM).
:param dz: Total z-range (in steps) used for the autofocus sweep.
:param start: Starting position of the sweep. "centre" begins at -dz/2,
while "base" begins from the current position.
:param sharpness_metric: Sharpness metric used for evaluation. Either
JPEG file size (JPEG) or inbuilt figure of metric (FOCUS_FOM).
:param record: Optional bitmask of sharpness metrics to record during
acquisition. If None, defaults to recording only the selected
sharpness_metric.
:returns: SharpnessDataArrays containing all recorded sharpness and
stage position data for the sweep.
"""
attempt = 0
with JPEGSharpnessMonitor(
self._stage, self._cam, sharpness_metric
self._stage, self._cam, sharpness_metric, record=record,
) as sharpness_monitor:
while attempt < 10:
attempt += 1