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Maximum lateral range and minimum autofocus range

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This commit is contained in:
jaknapper 2024-01-11 20:38:47 +00:00
parent e611840aca
commit c4e02d9087
1 changed files with 40 additions and 33 deletions
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73
src/openflexure_microscope_server/things/smart_scan.py
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@ -384,6 +384,11 @@ class SmartScanThing(Thing):
# Before anything else, check that we've got a background set
# It's annoying to have to wait to find out!
max_dist = self.max_range
if self.autofocus_dz == 0:
logger.info(f'Running scan without autofocus')
elif self.autofocus_dz <= 200:
logger.warning(f'Your dz range is {self.autofocus_dz} steps, which is too short to attempt to focus. Running without autofocus')
if self.skip_background:
d = background_detect.background_distributions
@ -489,40 +494,42 @@ class SmartScanThing(Thing):
path.append(pos)
attempts = 0
while True:
recentre.looping_autofocus(dz=self.autofocus_dz)
current_height = stage.position["z"]
if self.autofocus_dz > 200:
while True:
recentre.looping_autofocus(dz=self.autofocus_dz)
current_height = stage.position["z"]
# if there have been successful autofocuses in this scan, find the closest one in x-y
# test if the change in z between them exceeds a ratio (indicating a failed autofocus)
if len(focused_path) > 0:
nearest_focused_site = focused_path[closest(loc, focused_path)]
result = limit_focus_change(
nearest_focused_site[0:2],
nearest_focused_site[-1],
loc[0:2],
current_height,
0.3,
# if there have been successful autofocuses in this scan, find the closest one in x-y
# test if the change in z between them exceeds a ratio (indicating a failed autofocus)
if len(focused_path) > 0:
nearest_focused_site = focused_path[closest(loc, focused_path)]
result = limit_focus_change(
nearest_focused_site[0:2],
nearest_focused_site[-1],
loc[0:2],
current_height,
0.3,
)
# if there haven't been any previous autofocuses, we have to assume this one worked
else:
result = "accept"
# if the autofocus worked, add the current position to the list of successful locations
if result == "accept":
loc = list(stage.position.values())
focused_path.append(loc)
break
if attempts >= 3:
logger.warning("Could not autofocus after 5 attempts.")
break
# if the autofocus was rejected, we return to the height of the closest successful autofocus. not perfect, but better than wandering out of focus
logger.info(
"The focus has shifted further than we expect: retrying."
)
# if there haven't been any previous autofocuses, we have to assume this one worked
else:
result = "accept"
# if the autofocus worked, add the current position to the list of successful locations
if result == "accept":
loc = list(stage.position.values())
focused_path.append(loc)
break
if attempts >= 3:
logger.warning("Could not autofocus after 5 attempts.")
break
# if the autofocus was rejected, we return to the height of the closest successful autofocus. not perfect, but better than wandering out of focus
logger.info(
"The focus has shifted further than we expect: retrying."
)
stage.move_absolute(z=int(focused_path[z_index][2]))
attempts += 1
stage.move_absolute(z=int(focused_path[z_index][2]))
attempts += 1
name = f"image_{loc[0]}_{loc[1]}.jpg"
# img = Image.open(cam.capture_jpeg(resolution="full").open())
@ -607,7 +614,7 @@ class SmartScanThing(Thing):
@thing_property
def max_range(self) -> int:
"""The maximum distance from the centre of the scan before we break"""
return self.thing_settings.get("max_range", 400000)
return self.thing_settings.get("max_range", 70000)
@max_range.setter
def max_range(self, value: int) -> None: