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Complete testing of HistoScanWorkflow

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This commit is contained in:
Julian Stirling 2026-01-16 18:16:50 +00:00
parent 1bc6b9e0c4
commit b22fcf4b88
2 changed files with 153 additions and 6 deletions
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18
src/openflexure_microscope_server/things/scan_workflows.py
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@ -422,20 +422,22 @@ class HistoScanWorkflow(ScanWorkflow[HistoScanSettingsModel]):
:return: A tuple of whether an image was taken, and the z-position for focus.
If failed to find focus, returns for the focus z-position.
"""
# If skipping background, take an image to check if current field of view is background
if settings.skip_background:
# If skipping background, take an image to check if current field of view
# is background
image_array = self._cam.grab_as_array(stream_name="lores")
capture_image, bg_message = self._background_detector.image_is_sample(
image_array
)
del image_array
if not capture_image:
msg = f"Skipping {xyz_pos} as it is {bg_message}."
self.logger.info(msg)
return False, None
if not capture_image:
# Return early if the image is background.
msg = f"Skipping {xyz_pos} as it is {bg_message}."
self.logger.info(msg)
return False, None
save_on_failure = settings.skip_background
save_on_failure = not settings.skip_background
focus_height: Optional[int]
focused, focus_height = self._autofocus.run_smart_stack(
@ -445,6 +447,10 @@ class HistoScanWorkflow(ScanWorkflow[HistoScanSettingsModel]):
# An image was captured if we are focussed or we are not skipping background.
imaged = focused or save_on_failure
if not imaged:
msg = f"Stack failed at {xyz_pos} treating as background."
self.logger.info(msg)
# run_smart_stage always returns a focus height for the sharpest image even
# if it failed to find a good focus. Set to None if not focussed.
if not focused: