rahix/openflexure-microscope-server
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Fixing a number of issues from the merge and refactor.

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This commit is contained in:
Julian Stirling 2025-06-26 18:29:12 +01:00
parent 61dd5e4958
commit 6a87805b47
3 changed files with 13 additions and 38 deletions
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13
src/openflexure_microscope_server/things/smart_scan.py
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@ -656,6 +656,7 @@ class SmartScanThing(Thing):
focused_height = self._autofocus.run_smart_stack(
images_dir=self._ongoing_scan_images_dir,
autofocus_dz=self._scan_data["autofocus_dz"],
capture_resolution=self._scan_data["capture_resolution"],
)
current_pos_xyz = (
@ -668,18 +669,6 @@ class SmartScanThing(Thing):
current_pos_xyz, imaged=True, focused=True
)
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,
capture_resolution=self._scan_data["capture_resolution"],
)
# increment capure counter as thread has completed
self._scan_images_taken += 1
# Add it to the incremental zip