rahix/openflexure-microscope-server
1
0
Fork 0
Code Issues Pull requests Projects Releases Packages Wiki Activity Actions

Allow users to specify method for autofocus

Browse source
This commit is contained in:
jaknapper 2026-05-07 19:45:24 +01:00
parent 881970ce34
commit 664bb00c12
1 changed files with 26 additions and 6 deletions
Download patch file Download diff file Expand all files Collapse all files

32
src/openflexure_microscope_server/things/autofocus.py
View file

@ -380,6 +380,14 @@ class JPEGSharpnessMonitor:
sharpnesses = np.array(self.jpeg_sizes)
elif self.method == SharpnessMethod.FOCUS_FOM:
sharpnesses = np.array(self.focus_foms)
# If no valid FocusFoM values were recorded, fall back to JPEG size
if np.all(np.isnan(self.focus_foms)):
LOGGER.warning(
"Sharpness method FOCUS_FOM selected, but no FocusFoM values "
"were recorded. Falling back to JPEG sharpness."
)
sharpnesses = np.array(self.jpeg_sizes)
else:
raise ValueError(f"Unknown sharpness method: {self.method}")
stage_times: np.ndarray = np.array(self.stage_times)[istart:istop]
@ -449,14 +457,19 @@ class AutofocusThing(lt.Thing):
self,
dz: int = 2000,
start: Literal["centre", "base"] = "centre",
sharpness_metric: SharpnessMethod = SharpnessMethod.JPEG,
) -> 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.
sharpness_metric is either JPEG file size (JPEG) or inbuilt figure of metric (FOCUS_FOM).
"""
with JPEGSharpnessMonitor(self._stage, self._cam) as sharpness_monitor:
with JPEGSharpnessMonitor(
self._stage, self._cam, sharpness_metric
) as sharpness_monitor:
# Move to (-dz / 2)
if start == "centre":
sharpness_monitor.focus_rel(-dz // 2)
@ -483,7 +496,7 @@ class AutofocusThing(lt.Thing):
"""Make a move (or a series of moves) and monitor sharpness.
This method will will make a series of relative moves in z, and
return the sharpness (JPEG size) vs time, along with timestamps
return the sharpness (JPEG size and FOM) vs time, along with timestamps
for the moves. This can be used to calibrate autofocus.
Each move is relative to the last one, i.e. we will finish at
@ -504,6 +517,7 @@ class AutofocusThing(lt.Thing):
self,
dz: int = 2000,
start: Literal["centre", "base"] = "centre",
sharpness_metric: SharpnessMethod = SharpnessMethod.JPEG,
) -> tuple[list[float], list[float]]:
"""Repeatedly autofocus the stage until it looks focused.
@ -511,10 +525,14 @@ class AutofocusThing(lt.Thing):
in the middle 3/5 of its range. Such logic can be helpful if the microscope
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).
"""
attempt = 0
with JPEGSharpnessMonitor(self._stage, self._cam) as sharpness_monitor:
with JPEGSharpnessMonitor(
self._stage, self._cam, sharpness_metric
) as sharpness_monitor:
while attempt < 10:
attempt += 1
if start == "centre":
@ -531,9 +549,11 @@ class AutofocusThing(lt.Thing):
focus_data_index, _ = sharpness_monitor.focus_rel(
dz, block_cancellation=True
)
_times, heights, sizes = sharpness_monitor.move_data(focus_data_index)
_times, heights, sharpnesses = sharpness_monitor.move_data(
focus_data_index
)
peak_height = heights[np.argmax(sizes)]
peak_height = heights[np.argmax(sharpnesses)]
target_min = np.min(heights) + dz / 5
target_max = np.max(heights) - dz / 5
@ -545,7 +565,7 @@ class AutofocusThing(lt.Thing):
if target_min < peak_height < target_max:
# If it is within the target range then return
return heights.tolist(), sizes.tolist()
return heights.tolist(), sharpnesses.tolist()
raise NoFocusFoundError(
"Looping autofocus couldn't converge on a focus location."
)