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Apply suggestions from code review of branch More-workflow-layers

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Co-authored-by: Joe Knapper <joe.knapper@glasgow.ac.uk>
This commit is contained in:
Julian Stirling 2026-02-11 10:46:40 +00:00
parent af5c8f01da
commit 5d5bae7f79
1 changed files with 7 additions and 7 deletions
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14
src/openflexure_microscope_server/things/scan_workflows.py
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@ -123,7 +123,7 @@ class ScanWorkflow(Generic[SettingModelType], lt.Thing):
) -> tuple[bool, Optional[int]]: ) -> tuple[bool, Optional[int]]:
"""Overload to set the acquisition routine that happens at each scan site. """Overload to set the acquisition routine that happens at each scan site.
:param settings: The settings for this scan as a HistoScanSettingsModel :param settings: The settings for this scan, which should be a SettingModelType
:param xyz_pos: The current position as a tuple or 3 ints. :param xyz_pos: The current position as a tuple or 3 ints.
:return: A tuple of whether an image was taken, and the z-position for focus. :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 failed to find focus, returns for the focus z-position.
@ -139,9 +139,9 @@ class ScanWorkflow(Generic[SettingModelType], lt.Thing):
images_dir: str, images_dir: str,
save_resolution: tuple[int, int], save_resolution: tuple[int, int],
) -> tuple[bool, Optional[int]]: ) -> tuple[bool, Optional[int]]:
"""Atuofocus and then capture, this can be used as an acquisition routine. """Autofocus and then capture, this can be used as an acquisition routine.
:param dz: The dz for autofoucs. :param dz: The dz for autofocus.
:param images_dir: The path to the directory for saving images.. :param images_dir: The path to the directory for saving images..
:param save_resolution: The resolution to save images at. :param save_resolution: The resolution to save images at.
@ -168,11 +168,11 @@ class ScanWorkflow(Generic[SettingModelType], lt.Thing):
class RectGridWorkflow(ScanWorkflow[SettingModelType], Generic[SettingModelType]): class RectGridWorkflow(ScanWorkflow[SettingModelType], Generic[SettingModelType]):
"""A generic workflow for any scan that captures images on a rectilinear grid.""" """A generic workflow for any scan that captures images on a rectilinear grid."""
# Thing Slots # Redefine _csm Thing Slot, as CSM is required for any RectGridWorkflow
_csm: CameraStageMapper = lt.thing_slot() _csm: CameraStageMapper = lt.thing_slot()
overlap: float = lt.setting(default=0.45, ge=0.1, le=0.7) overlap: float = lt.setting(default=0.45, ge=0.1, le=0.7)
"""The fraction that adjacent images should overlap in x or y. """The fraction that adjacent images should overlap in x and y.
This must be between 0.1 and 0.7. This must be between 0.1 and 0.7.
""" """
@ -206,7 +206,7 @@ class RectGridWorkflow(ScanWorkflow[SettingModelType], Generic[SettingModelType]
""" """
csm_image_res = self._csm.image_resolution csm_image_res = self._csm.image_resolution
if csm_image_res is None: if csm_image_res is None:
raise RuntimeError("CSM not set. Scan shouldn't have progresses this far.") raise RuntimeError("CSM not set. Scan shouldn't have progressed this far.")
# Calculate displacements in image coordinates # Calculate displacements in image coordinates
dx_img = csm_image_res[1] * (1 - overlap) dx_img = csm_image_res[1] * (1 - overlap)
@ -641,7 +641,7 @@ class RegularGridWorkflow(RectGridWorkflow[RegularGridSettingsModel]):
) -> tuple[bool, Optional[int]]: ) -> tuple[bool, Optional[int]]:
"""Autofocus and capture. """Autofocus and capture.
:param settings: The settings for this scan as a HistoScanSettingsModel :param settings: The settings for this scan as a RegularGridSettingsModel
:param xyz_pos: The current position as a tuple or 3 ints. :param xyz_pos: The current position as a tuple or 3 ints.
:return: A tuple of whether an image was taken, and the z-position for focus. :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 failed to find focus, returns for the focus z-position.