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Abort stalled o3 autofocus #203

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Merged
merged 2 commits into from
Sep 4, 2025
Merged

Abort stalled o3 autofocus #203

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b06631d
abort stalled O3 autofocus
ieivanov Aug 21, 2025
2f509df
add note on hardcoded value
ieivanov Sep 4, 2025
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74 changes: 55 additions & 19 deletions mantis/acquisition/acq_engine.py
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Original file line number Diff line number Diff line change
Expand Up @@ -793,7 +793,7 @@ def acquire_ls_defocus_stack(
z_range: Iterable,
galvo_range: Iterable,
use_pycromanager: bool = False,
) -> np.array:
) -> np.ndarray:
"""Acquire defocus stacks at different galvo positions and return image data

Parameters
Expand All @@ -812,7 +812,7 @@ def acquire_ls_defocus_stack(

Returns
-------
data : np.array
data : np.ndarray

"""
data = []
Expand Down Expand Up @@ -853,25 +853,56 @@ def acquire_ls_defocus_stack(
# acquire stacks at different galvo positions
for p_idx, p in enumerate(galvo_range):
# set galvo position
mmc.set_position(galvo, p0 + p)
microscope_operations.set_z_position(mmc, galvo, p0 + p)

# acquire defocus stack
if use_pycromanager:
mmc.set_position(z_stage, z_range[0]) # prep o3 stage
with Acquisition(
tempdir.name, f'ls_refocus_p{p_idx}', port=LS_ZMQ_PORT, show_display=False
) as acq:
acq.acquire(
multi_d_acquisition_events(
z_start=z_range[0],
z_end=z_range[-1],
z_step=z_range[1] - z_range[0],
),
)
ds = acq.get_dataset()
data.append(np.asarray(ds.as_array()))
ds.close()
mmc.set_position(z_stage, z_range[len(z_range) // 2]) # reset o3 stage
global acq_finished
acq_finished = False
acq_fps = 20 # TODO: hardcoded for now
camera = 'Prime BSI Express'
num_slices = len(z_range)
acq_duration = num_slices / acq_fps + 5 # Extra buffer time

def check_acq_finished(axes, dataset):
global acq_finished
if axes['z'] == num_slices - 1:
acq_finished = True

microscope_operations.set_z_position(mmc, z_stage, z_range[0])

logger.debug('Starting pycromanager O3 autofocus acquisition')
events = multi_d_acquisition_events(
z_start=z_range[0],
z_end=z_range[-1],
z_step=z_range[1] - z_range[0],
)
acq = Acquisition(
tempdir.name,
f'ls_refocus_p{p_idx}',
port=LS_ZMQ_PORT,
image_saved_fn=check_acq_finished,
show_display=False,
)
acq.acquire(events)
acq.mark_finished()
start_time = time.time()
while not acq_finished and time.time() - start_time < acq_duration:
time.sleep(0.2)
if acq_finished:
acq.await_completion()
logger.debug('Pycromanager acquisition finished. Fetching data')
ds = acq.get_dataset()
data.append(np.asarray(ds.as_array()))
logger.debug('Data retrieved. Closing dataset')
ds.close()
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
acq.get_dataset().close() # Close dataset

microscope_operations.set_z_position(mmc, z_stage, z_range[len(z_range) // 2])
else:
z_stack = microscope_operations.acquire_defocus_stack(
mmc, z_stage, z_range, backlash_correction_distance=KIM101_BACKLASH
Expand All @@ -888,7 +919,7 @@ def acquire_ls_defocus_stack(
)

# Reset galvo
mmc.set_position(galvo, p0)
microscope_operations.set_z_position(mmc, galvo, p0)

# Reset shutter
microscope_operations.reset_shutter(mmc, auto_shutter_state, shutter_state)
Expand Down Expand Up @@ -943,6 +974,11 @@ def refocus_ls_path(
use_pycromanager=True,
)

# Abort if the acquisition failed
if not data.size > 0:
logger.error('No data was acquired during O3 autofocus - aborting.')
return success, scan_left, scan_right

# Save acquired stacks in logs
timestamp = datetime.now().strftime("%Y%m%dT%H%M%S")
tifffile.imwrite(
Expand Down
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