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

A stack that tests whether the sharpest image is towards the middle

Browse source
This commit is contained in:
jaknapper 2025-05-21 14:03:22 +01:00
parent 67e8b19603
commit 3e164102f6
3 changed files with 100 additions and 39 deletions
Download patch file Download diff file Expand all files Collapse all files

36
src/openflexure_microscope_server/things/smart_scan.py
View file

@ -620,6 +620,8 @@ class SmartScanThing(Thing):
self._manage_stitching_threads()
next_pos_xy, z_est = route_planner.get_next_location_and_z_estimate()
self._scan_logger.info(z_est)
self._scan_logger.info(self._stage.position["z"])
new_pos_xyz = self._move_to_next_point(next_pos_xy, z_est)
current_pos_xyz = (
new_pos_xyz[0],
@ -642,32 +644,18 @@ class SmartScanThing(Thing):
self._scan_logger.info(msg)
continue
focused = False
if self._scan_data["autofocus_on"]:
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
focused_height = self._autofocus.run_z_stack(
images_dir=self._ongoing_scan_images_dir,
)
current_pos_xyz = (
new_pos_xyz[0],
new_pos_xyz[1],
focused_height,
)
route_planner.mark_location_visited(
current_pos_xyz, imaged=True, focused=focused
)
site_folder = os.path.join(
self._ongoing_scan_images_dir,
"stacks",
f"{new_pos_xyz[0]}_{new_pos_xyz[1]}",
)
os.makedirs(site_folder, exist_ok=True)
self._autofocus.run_z_stack(
images_dir=self._ongoing_scan_images_dir,
stack_dir=site_folder,
current_pos_xyz, imaged=True, focused=True
)
# increment capure counter as thread has completed