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Fixed focused path tracking, move to estimated focus before autofocus

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This commit is contained in:
jaknapper 2025-04-22 14:33:27 +01:00
parent 7cb1a3980e
commit 3bcc71304e
1 changed files with 13 additions and 7 deletions
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20
src/openflexure_microscope_server/things/smart_scan.py
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@ -363,7 +363,7 @@ class SmartScanThing(Thing):
self._stage.move_absolute(
x=next_point[0],
y=next_point[1],
z=z_estimate - self._scan_data["autofocus_dz"] / 2,
z=z_estimate,
)
return (next_point[0], next_point[1], z_estimate)
@ -553,6 +553,11 @@ class SmartScanThing(Thing):
next_pos_xy, z_est = route_planner.get_next_location_and_z_estimate()
new_pos_xyz = self._move_to_next_point(next_pos_xy, z_est)
current_pos_xyz = (
new_pos_xyz[0],
new_pos_xyz[1],
self._stage.position["z"],
)
capture_image = True
# If skipping background, take an image to check if it is background
@ -571,10 +576,11 @@ class SmartScanThing(Thing):
focused = False
if self._scan_data["autofocus_on"]:
focused = self._try_autofocus(new_pos_xyz)
focused, focused_z = self._try_autofocus(new_pos_xyz)
current_pos_xyz = (new_pos_xyz[0], new_pos_xyz[1], focused_z)
route_planner.mark_location_visited(
new_pos_xyz, imaged=True, focused=focused
current_pos_xyz, imaged=True, focused=focused
)
# wait for the previous capture to be saved, i.e. don't leave more than one image saving in the background
@ -606,8 +612,8 @@ class SmartScanThing(Thing):
Args:
this_xyz is the current x,y,z position.
Return True on successful autofocus.
Return False if failed after 3 tries - the position will be the initial estimate
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
@ -624,13 +630,13 @@ class SmartScanThing(Thing):
# If sharp enough, break and return success, otherwise go to start and try again
if autofocus_sharp_enough:
return True
return True, self._stage.position["z"]
else:
z = this_xyz[2] - dz / 2 if attempts < max_attempts else this_xyz[2]
self._stage.move_absolute(z=z)
self._scan_logger.warning("Could not autofocus after 3 attempts.")
return False
return False, self._stage.position["z"]
@_scan_running
def _wait_for_capture_thread(self) -> None: