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Merge branch 'remove_autofocus_test' into 'v3'

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Remove autofocus test

See merge request openflexure/openflexure-microscope-server!255
This commit is contained in:
Joe Knapper 2025-05-08 17:02:03 +00:00
commit 97beb9147b
2 changed files with 10 additions and 78 deletions
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16
src/openflexure_microscope_server/things/autofocus.py
View file

@ -253,22 +253,6 @@ class AutofocusThing(Thing):
stage.move_absolute(z=peak_height)
return heights.tolist(), sizes.tolist()
@thing_action
def verify_focus_sharpness(
self, sweep_sizes: list, camera: WrappedCamera, threshold: float = 0.95
):
"""Take the sharpness curve of the autofocus, and the size of the current frame
to see if the autofocus completed successfully. Returns True if current sharpness
is within "leniency" number of frames from the peak of the autofocus"""
current_sharpness = camera.grab_jpeg_size(stream_name="lores")
peak = np.max(sweep_sizes)
base = np.min(sweep_sizes)
cutoff = threshold * (peak - base)
return current_sharpness >= base + cutoff
@thing_property
def stack_images_to_capture(self) -> int:
"""The number of images to capture and save in a stack

72
src/openflexure_microscope_server/things/smart_scan.py
View file

@ -43,30 +43,6 @@ BackgroundDep = direct_thing_client_dependency(
IMAGE_REGEX = re.compile(r"-?[0-9]+_-?[0-9]+\.jpeg$")
def unpack_autofocus(scan_data):
"""Extract z, sharpness data from a move_and_measure call
Data will start at `start_index`, i.e. `start_index` points are dropped
from the beginning of the array.
"""
jpeg_times = scan_data["jpeg_times"]
jpeg_sizes = scan_data["jpeg_sizes"]
jpeg_sizes_mb = [x / 10**3 for x in jpeg_sizes]
stage_times = scan_data["stage_times"]
stage_positions = scan_data["stage_positions"]
stage_height = [pos[2] for pos in stage_positions]
jpeg_heights = np.interp(jpeg_times, stage_times, stage_height)
def turningpoints(lst):
dx = np.diff(lst)
return dx[1:] * dx[:-1] < 0
turning = np.where(turningpoints(jpeg_heights))[0] + 1
return jpeg_heights[turning[0] : turning[1]], jpeg_sizes_mb[turning[0] : turning[1]]
class NotEnoughFreeSpaceError(IOError):
pass
@ -603,8 +579,16 @@ class SmartScanThing(Thing):
focused = False
if self._scan_data["autofocus_on"]:
focused, focused_z = self._try_autofocus(new_pos_xyz)
current_pos_xyz = (new_pos_xyz[0], new_pos_xyz[1], focused_z)
self._autofocus.looping_autofocus(
dz=self._scan_data["autofocus_dz"], start="centre"
)
current_pos_xyz = (
new_pos_xyz[0],
new_pos_xyz[1],
self._stage.position["z"],
)
# Without a test for autofocus success, assume it worked
focused = True
route_planner.mark_location_visited(
current_pos_xyz, imaged=True, focused=focused
@ -628,42 +612,6 @@ class SmartScanThing(Thing):
scan_name=self._ongoing_scan_name,
)
@_scan_running
def _try_autofocus(
self,
this_xyz: tuple[int, int, int],
) -> bool:
"""
Try to perform autofocus and return boolean for if successful
Args:
this_xyz is the current x,y,z position.
Return True, focused_height on successful autofocus.
Return False, initial_height if failed after 3 tries - the position will be the initial estimate
"""
attempts = 0
max_attempts = 3
dz = self._scan_data["autofocus_dz"]
while attempts < max_attempts:
attempts += 1
_, jpeg_sizes = self._autofocus.looping_autofocus(dz=dz, start="centre")
time.sleep(0.2)
autofocus_sharp_enough = self._autofocus.verify_focus_sharpness(
sweep_sizes=jpeg_sizes, camera=CamDep, threshold=0.92
)
# If sharp enough, break and return success, otherwise go to start and try again
if autofocus_sharp_enough:
return True, self._stage.position["z"]
else:
self._stage.move_absolute(z=this_xyz[2])
self._scan_logger.warning("Could not autofocus after 3 attempts.")
return False, self._stage.position["z"]
@_scan_running
def _return_to_starting_position(self):
self._scan_logger.info("Returning to starting position.")