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Don't use PM for O3 autofocus #205

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Merged
merged 2 commits into from
Oct 23, 2025
Merged

Don't use PM for O3 autofocus #205

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c1a77e7
debug - don't use PM for O3 autofocus
ieivanov Sep 10, 2025
1f69966
add deprecation note
ieivanov Oct 23, 2025
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13 changes: 8 additions & 5 deletions mantis/acquisition/acq_engine.py
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Original file line number Diff line number Diff line change
Expand Up @@ -939,8 +939,11 @@ def check_acq_finished(axes, dataset):
else:
logger.error('O3 autofocus is taking longer than expected - aborting.')
microscope_operations.abort_acquisition_sequence(self.ls_acq.mmc, camera)
acq.await_completion() # Cleanup
logger.debug('Would have waited for acquisition to complete')
# acq.await_completion() # Cleanup
logger.debug('Closing dataset')
acq.get_dataset().close() # Close dataset
logger.debug('Acquisition aborted')
else:
z_stack = microscope_operations.acquire_defocus_stack(
mmc, z_stage, z_range, backlash_correction_distance=KIM101_BACKLASH
Expand Down Expand Up @@ -979,8 +982,8 @@ def refocus_ls_path(
o3_position = float(self.ls_acq.mmc.get_property(o3_z_stage, 'Position'))
logger.debug(f'Starting O3 position: {o3_position} um')

o3_z_start = -3.3
o3_z_end = 3.3
o3_z_start = -5.0
o3_z_end = 5.0
o3_z_step = 0.3
if scan_left:
logger.info('O3 refocus will scan further to the left')
Expand Down Expand Up @@ -1016,7 +1019,7 @@ def refocus_ls_path(
data = self.acquire_ls_defocus_stack(
z_range=o3_range_abs,
galvo_range=galvo_range_abs,
use_pycromanager=True,
use_pycromanager=False,
)

# Abort if the acquisition failed
Expand Down Expand Up @@ -1426,7 +1429,7 @@ def await_cz_acq_completion(self):
time.sleep(wait_time)

def abort_stalled_acquisition(self):
buffer_time = 5
buffer_time = 10
lf_acq_aborted = False
ls_acq_aborted = False

Expand Down
13 changes: 9 additions & 4 deletions mantis/acquisition/microscope_operations.py
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Original file line number Diff line number Diff line change
Expand Up @@ -337,6 +337,7 @@ def acquire_defocus_stack(
backlash_correction_distance: int = 0,
):
"""Snap image at every z position and put image in a Micro-manager datastore
Note: KinesisPiezoMotor stage is deprecated

Parameters
----------
Expand All @@ -361,19 +362,20 @@ def acquire_defocus_stack(

"""
data = []
relative_z_steps = np.hstack((z_range[0], np.diff(z_range)))
# relative_z_steps = np.hstack((z_range[0], np.diff(z_range)))

# get z0 and define move_z callable for the given stage
if isinstance(z_stage, str):
# this is a MM stage
move_z = partial(mmc.set_relative_position, z_stage) # test if this works
move_z = partial(mmc.set_position, z_stage) # test if this works
elif isinstance(z_stage, KinesisPiezoMotor):
# this is a pylablib stage
move_z = partial(set_relative_kim101_position, z_stage)
else:
raise RuntimeError(f'Unknown z stage: {z_stage}')

for z_ind, rel_z in enumerate(relative_z_steps):
move_z(z_range[0]); time.sleep(0.3)
for z_ind, rel_z in enumerate(z_range):
# set z position
move_z(rel_z)

Expand All @@ -400,7 +402,7 @@ def acquire_defocus_stack(
datastore.put_image(image)

# reset z stage
move_z(-relative_z_steps.sum() + backlash_correction_distance)
# move_z(-relative_z_steps.sum() + backlash_correction_distance)

return np.asarray(data)

Expand Down Expand Up @@ -553,8 +555,11 @@ def abort_acquisition_sequence(
"""

for stage in sequenced_stages:
logger.debug(f'Stopping sequence on stage {stage}')
mmc.stop_stage_sequence(stage)
logger.debug('Stopping camera sequence acquisition')
mmc.stop_sequence_acquisition(camera)
logger.debug('Clearing circular buffer')
mmc.clear_circular_buffer()


Expand Down
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