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

Test the success of refocusing

Browse source
This commit is contained in:
Joe Knapper 2024-02-13 15:24:42 +00:00
parent f2d85cb891
commit f1c315783c
2 changed files with 50 additions and 17 deletions
Download patch file Download diff file Expand all files Collapse all files

42
src/openflexure_microscope_server/things/smart_scan.py
View file

@ -640,24 +640,29 @@ class SmartScanThing(Thing):
attempts = 0
if self.autofocus_dz > 200:
while True:
autofocus.looping_autofocus(dz=self.autofocus_dz, start = 'base')
jpeg_zs, jpeg_sizes = autofocus.looping_autofocus(dz=self.autofocus_dz, start = 'base')
current_height = stage.position["z"]
autofocus_success = autofocus.verify_focus_sharpness(sweep_sizes = jpeg_sizes, camera = CamDep, leniency = 1)
logger.info(f"We just tested the focus! Result was {autofocus_success}")
# 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 autofocus_success:
# 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
# if there haven't been any previous autofocuses, we have to assume this one worked
else:
result = "accept"
else:
result = "accept"
result = "reject"
# if the autofocus worked, add the current position to the list of successful locations
if result == "accept":
@ -762,6 +767,15 @@ class SmartScanThing(Thing):
def max_range(self, value: int) -> None:
self.thing_settings["max_range"] = value
@thing_property
def stitch_tiff(self) -> bool:
"""The maximum distance from the centre of the scan before we break"""
return self.thing_settings.get("stitch_tiff", False)
@stitch_tiff.setter
def stitch_tiff(self, value: bool) -> None:
self.thing_settings["stitch_tiff"] = value
@thing_property
def skip_background(self) -> bool:
"""Whether to detect and skip empty fields of view