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Start smart stack parameters in scan workflow

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This commit is contained in:
Julian Stirling 2026-01-15 16:04:24 +00:00
parent 54ed78c832
commit adab5bae24
4 changed files with 191 additions and 140 deletions
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15
src/openflexure_microscope_server/things/smart_scan.py
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@ -253,7 +253,14 @@ class SmartScanThing(lt.Thing):
# Record starting position so it can be returned to at end of scan.
starting_position = self._stage.position
workflow_settings, stitching_settings = workflow.all_settings()
images_dir = self.ongoing_scan.images_dir
# Type narrowing
if images_dir is None:
raise RuntimeError("Couldn't run scan, images directory was not created.")
workflow_settings, stitching_settings = workflow.all_settings(
images_dir=images_dir
)
# If stitching settings is None then this workflow doesn't support stitching.
auto_stitch = self.stitch_automatically and stitching_settings is not None
@ -305,15 +312,11 @@ class SmartScanThing(lt.Thing):
workflow.pre_scan_routine(self._scan_data)
self.ongoing_scan.save_scan_data(self._scan_data)
images_dir = self.ongoing_scan.images_dir
# Type narrowing
if images_dir is None:
raise RuntimeError(
"Couldn't run scan, images directory was not created."
)
self._stack_params = self._autofocus.create_stack_params(
images_dir=images_dir,
autofocus_dz=self.scan_data.autofocus_dz,
save_resolution=self.scan_data.save_resolution,
)
self._preview_stitcher = stitching.PreviewStitcher(
images_dir,
overlap=self.scan_data.overlap,