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Give sharpness monitor a descriptive name, not m

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jaknapper 2025-04-25 12:29:11 +01:00
parent bf6437b42c
commit f50580cdd0
1 changed files with 18 additions and 18 deletions
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36
src/openflexure_microscope_server/things/autofocus.py
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@ -147,14 +147,14 @@ class SharpnessDataArrays(BaseModel):
class AutofocusThing(Thing):
"""The Thing concerned with combinations of z axis movements and the camera.
Actions here involve moving a stage in z, and using the camera to either
capture images (generally, z-stacking) and measuring the sharpness of the
field of view to assess focus (autofocus and testing the success of a z-stack)"""
@thing_action
def fast_autofocus(
self,
m: SharpnessMonitorDep,
sharpness_monitor: SharpnessMonitorDep,
dz: int = 2000,
start: str = "centre",
) -> SharpnessDataArrays:
@ -164,27 +164,27 @@ class AutofocusThing(Thing):
the position where the image was sharpest. We'll then move back down, and
finally up to the sharpest point.
"""
with m.run():
with sharpness_monitor.run():
# Move to (-dz / 2)
if start == "centre":
m.focus_rel(-dz / 2)
sharpness_monitor.focus_rel(-dz / 2)
# Move to dz while monitoring sharpness
# i: Sharpness monitor index for this move
# z: Final z position after move
i, z = m.focus_rel(dz, block_cancellation=True)
i, z = sharpness_monitor.focus_rel(dz, block_cancellation=True)
# Get the z position with highest sharpness from the previous move (index i)
fz: int = m.sharpest_z_on_move(i)
fz: int = sharpness_monitor.sharpest_z_on_move(i)
# Move all the way to the start so it's consistent
i, z = m.focus_rel(-dz)
i, z = sharpness_monitor.focus_rel(-dz)
# Move to the target position fz (relative move of (fz - z))
m.focus_rel(fz - z)
sharpness_monitor.focus_rel(fz - z)
# Return all focus data
return m.data_dict()
return sharpness_monitor.data_dict()
@thing_action
def z_move_and_measure_sharpness(
self,
m: SharpnessMonitorDep,
sharpness_monitor: SharpnessMonitorDep,
dz: Sequence[int],
wait: float = 0,
) -> SharpnessDataArrays:
@ -200,16 +200,16 @@ class AutofocusThing(Thing):
If `wait` is specified, we will wait for that many seconds
between moves.
"""
with m.run():
with sharpness_monitor.run():
for i, current_dz in enumerate(dz):
if i > 0 and wait > 0:
time.sleep(wait)
m.focus_rel(current_dz)
return m.data_dict()
sharpness_monitor.focus_rel(current_dz)
return sharpness_monitor.data_dict()
@thing_action
def looping_autofocus(
self, stage: Stage, m: SharpnessMonitorDep, dz=2000, start="centre"
self, stage: Stage, sharpness_monitor: SharpnessMonitorDep, dz=2000, start="centre"
):
"""Repeatedly autofocus the stage until it looks focused.
@ -222,14 +222,14 @@ class AutofocusThing(Thing):
attempts = 0
backlash = 200
with m.run():
with sharpness_monitor.run():
while repeat and attempts < 10:
if start == "centre":
stage.move_relative(x=0, y=0, z=-(backlash + dz / 2))
stage.move_relative(x=0, y=0, z=backlash)
i, z = m.focus_rel(dz, block_cancellation=True)
_, heights, sizes = m.move_data(i)
i, z = sharpness_monitor.focus_rel(dz, block_cancellation=True)
_, heights, sizes = sharpness_monitor.move_data(i)
peak_height = heights[np.argmax(sizes)]
height_min = np.min(heights)
@ -301,7 +301,7 @@ class AutofocusThing(Thing):
"""Run a z stack, saving all images to stack_dir and copying the
central image to stack_dir"""
stack_dz = self.stack_dz
images_to_capture = self.images_to_capture
images_to_capture = self.stack_images_to_capture
stack_z_range = stack_dz * (images_to_capture - 1)
stage.move_relative(z=-stack_z_range / 2)