rahix/openflexure-microscope-server
1
0
Fork 0
Code Issues Pull requests Projects Releases Packages Wiki Activity Actions

Remove focus_change_acceptable test, autofocus from centre

Browse source
This commit is contained in:
jaknapper 2025-04-17 17:20:40 +01:00
parent 5d8a1073b2
commit 7cb1a3980e
1 changed files with 2 additions and 31 deletions
Download patch file Download diff file Expand all files Collapse all files

33
src/openflexure_microscope_server/things/smart_scan.py
View file

@ -66,30 +66,6 @@ def unpack_autofocus(scan_data):
return jpeg_heights[turning[0] : turning[1]], jpeg_sizes_mb[turning[0] : turning[1]] return jpeg_heights[turning[0] : turning[1]], jpeg_sizes_mb[turning[0] : turning[1]]
def focus_change_acceptable(prev_pos, prev_z, new_pos, new_z, fractional_limit):
"""Return true if the change in z-position is small enough.
A large change in z-position in an indication of focus failure.
fractional_limit is the largest ratio of change in z to change in xy that's allowed
"""
prev_xy = np.asarray(prev_pos, dtype="float64")
new_xy = np.asarray(new_pos, dtype="float64")
dist = np.sqrt(np.sum(((new_xy - prev_xy) / 10**4) ** 2, dtype="float64"))
focus_change = abs(new_z - prev_z) / 10**4
if dist == 0:
print(f"Not moved between {prev_pos} and {new_pos}")
movement_ratio = 0
else:
movement_ratio = np.divide(focus_change, dist, dtype="float64")
if movement_ratio > fractional_limit:
return False
return True
class NotEnoughFreeSpaceError(IOError): class NotEnoughFreeSpaceError(IOError):
pass pass
@ -595,8 +571,7 @@ class SmartScanThing(Thing):
focused = False focused = False
if self._scan_data["autofocus_on"]: if self._scan_data["autofocus_on"]:
closest_xyz = route_planner.closest_focus_site(new_pos_xyz[:2]) focused = self._try_autofocus(new_pos_xyz)
focused = self._try_autofocus(new_pos_xyz, closest_xyz)
route_planner.mark_location_visited( route_planner.mark_location_visited(
new_pos_xyz, imaged=True, focused=focused new_pos_xyz, imaged=True, focused=focused
@ -624,15 +599,12 @@ class SmartScanThing(Thing):
def _try_autofocus( def _try_autofocus(
self, self,
this_xyz: tuple[int, int, int], this_xyz: tuple[int, int, int],
closest_xyz: Optional[tuple[int, int, int]],
) -> bool: ) -> bool:
""" """
Try to perform autofocus and return boolean for if successful Try to perform autofocus and return boolean for if successful
Args: Args:
this_xyz is the current x,y,z position. this_xyz is the current x,y,z position.
closest_xyz is the (x, y, z) coordinates of the closest position, this is None
if no previous images have been taken or in focus
Return True on successful autofocus. Return True on successful autofocus.
Return False if failed after 3 tries - the position will be the initial estimate Return False if failed after 3 tries - the position will be the initial estimate
@ -644,8 +616,7 @@ class SmartScanThing(Thing):
while attempts < max_attempts: while attempts < max_attempts:
attempts += 1 attempts += 1
_, jpeg_sizes = self._autofocus.looping_autofocus(dz=dz, start="base") _, jpeg_sizes = self._autofocus.looping_autofocus(dz=dz, start="centre")
current_height = self._stage.position["z"]
time.sleep(0.2) time.sleep(0.2)
autofocus_sharp_enough = self._autofocus.verify_focus_sharpness( autofocus_sharp_enough = self._autofocus.verify_focus_sharpness(
sweep_sizes=jpeg_sizes, camera=CamDep, threshold=0.92 sweep_sizes=jpeg_sizes, camera=CamDep, threshold=0.92