RectangleWorkflow as a baseclass
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jaknapper
parent
6294cde471
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f1845c3039
3 changed files with 59 additions and 200 deletions
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@ -485,9 +485,6 @@ class HistoScanWorkflow(ScanWorkflow[HistoScanSettingsModel]):
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"""A list of PropertyControl objects to create the settings in the scan tab."""
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return [
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property_control_for(self, "overlap", label="Image Overlap (0.1-0.7)"),
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property_control_for(
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self, "skip_background", label="Detect and Skip Empty Fields "
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),
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property_control_for(
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self, "stack_images_to_save", label="Images in Stack to Save"
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),
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@ -499,11 +496,14 @@ class HistoScanWorkflow(ScanWorkflow[HistoScanSettingsModel]):
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property_control_for(self, "stack_dz", label="Stack dz (steps)"),
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property_control_for(self, "autofocus_dz", label="Autofocus Range (steps)"),
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property_control_for(self, "max_range", label="Maximum Distance (steps)"),
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property_control_for(
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self, "skip_background", label="Detect and Skip Empty Fields "
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),
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]
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class SnakeSettingsModel(BaseModel):
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"""The settings for a scan with the SnakeWorkflow.
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class RectangleSettingsModel(BaseModel):
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"""The settings for a scan with a regular grid of dx and dy for x_count, y_count steps.
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This includes settings calculated when starting. This will be held by smart scan
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during a scan and serialised to disk.
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@ -519,49 +519,39 @@ class SnakeSettingsModel(BaseModel):
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save_resolution: tuple[int, int]
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class SnakeWorkflow(ScanWorkflow[SnakeSettingsModel]):
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"""A workflow optimised for snaking around samples.
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TypeSettings = TypeVar("TypeSettings", bound=RectangleSettingsModel)
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This workflow generates a list of coordinates in a rectangle, and snakes
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around them from the top left (assuming positive dx and dy).
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"""
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display_name: str = lt.property(default="Snake Scan", readonly=True)
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ui_blurb: str = lt.property(
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default=(
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"This scan workflow is optimised for scanning over a rectangle. It "
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"snakes down and right from the starting point, over a defined grid."
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),
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readonly=True,
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)
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class SnakeSettingsModel(RectangleSettingsModel):
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"""Settings for Snake scan."""
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_settings_model = SnakeSettingsModel
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_planner_cls: type[ScanPlanner] = SnakeScan
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pass
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class RasterSettingsModel(RectangleSettingsModel):
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"""Settings for Raster scan."""
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pass
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class RectangleWorkflow(ScanWorkflow[TypeSettings], Generic[TypeSettings]):
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"""Abstract workflow for rectangular scans."""
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# Settings and planner must be set by subclass
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_settings_model: type[TypeSettings]
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_planner_cls: type[ScanPlanner]
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# Thing Slots
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_cam: BaseCamera = lt.thing_slot()
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_csm: CameraStageMapper = lt.thing_slot()
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_autofocus: AutofocusThing = lt.thing_slot()
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_stage: BaseStage = lt.thing_slot()
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# Scan settings
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# Shared scan settings
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autofocus_dz: int = lt.setting(default=1000, ge=200, le=2000)
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"""The z distance to perform an autofocus in steps.
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Must be greater than or equal to 200, and less than or equal to 2000.
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"""
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overlap: float = lt.setting(default=0.45, ge=0.1, le=0.7)
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"""The fraction that adjacent images should overlap in x or y.
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This must be between 0.1 and 0.7.
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"""
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x_count: int = lt.setting(default=3)
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y_count: int = lt.setting(default=2)
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# The noqa statement is because scan_name is unused but is needed for equivalence
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# with other workflows that may want to validate the scan name.
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def check_before_start(self, scan_name: str) -> None: # noqa: ARG002
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"""Before starting a scan, check that camera-stage-mapping is set.
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@ -576,9 +566,7 @@ class SnakeWorkflow(ScanWorkflow[SnakeSettingsModel]):
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"""Whether this scanworkflow is ready to start."""
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return not self._csm.calibration_required
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def all_settings(
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self, images_dir: str
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) -> tuple[SnakeSettingsModel, StitchingSettings]:
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def all_settings(self, images_dir: str) -> tuple[TypeSettings, StitchingSettings]:
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"""Return the workflow and stitching settings.
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:param images_dir: The directory that images are to be written to.
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@ -609,25 +597,21 @@ class SnakeWorkflow(ScanWorkflow[SnakeSettingsModel]):
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return scan_settings, stitching_settings
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def pre_scan_routine(self, settings: SnakeSettingsModel) -> None:
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"""Autofocus before starting the scan.
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def pre_scan_routine(self, settings: TypeSettings) -> None:
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"""Perform these steps before starting the scan.
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:param settings: The settings for this scan as a SnakeSettingsModel
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In this case, only autofocus.
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"""
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self._autofocus.looping_autofocus(dz=settings.autofocus_dz, start="centre")
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def new_scan_planner(
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self, settings: SnakeSettingsModel, position: Mapping[str, int]
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self, settings: TypeSettings, position: Mapping[str, int]
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) -> ScanPlanner:
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"""Return a new scan planner object.
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:param settings: The settings for this scan as a SnakeSettingsModel
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:param position: The starting position as a mapping of axes names to int.
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"""
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# The initial plan for the scan should be a single x,y position. All future
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# moves will be planned around this point. In future, route planner could
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# have multiple starting positions, each of which will be visited before the
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# scan can end.
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planner_settings = {
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"dx": settings.dx,
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"dy": settings.dy,
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@ -640,13 +624,14 @@ class SnakeWorkflow(ScanWorkflow[SnakeSettingsModel]):
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)
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def acquisition_routine(
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self, settings: SnakeSettingsModel, xyz_pos: tuple[int, int, int]
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self, settings: TypeSettings, xyz_pos: tuple[int, int, int]
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) -> tuple[bool, Optional[int]]:
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"""Perform acquisition routine. This is run at each scan location.
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:param settings: The settings for this scan as a SnakeSettingsModel
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:param settings: The settings for this scan as the correct setting model
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:param xyz_pos: The current position as a tuple or 3 ints.
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:return: A tuple of whether an image was taken, and the z-position for focus.
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In this method, image is always taken, so first return is True.
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If failed to find focus, returns for the focus z-position.
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"""
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self._autofocus.fast_autofocus(dz=settings.autofocus_dz)
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@ -657,8 +642,7 @@ class SnakeWorkflow(ScanWorkflow[SnakeSettingsModel]):
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save_resolution=settings.save_resolution,
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)
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imaged = True
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return imaged, focus_height
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return True, focus_height
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@lt.property
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def settings_ui(self) -> list[PropertyControl]:
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@ -671,23 +655,26 @@ class SnakeWorkflow(ScanWorkflow[SnakeSettingsModel]):
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]
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class RasterSettingsModel(BaseModel):
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"""The settings for a scan with the Raster Workflow.
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class SnakeWorkflow(RectangleWorkflow[SnakeSettingsModel]):
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"""A workflow optimised for snaking around samples.
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This is identical to the SnakeSettings, but is subclassed for clarity.
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This workflow generates a list of coordinates in a rectangle, and snakes
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around them from the top left (assuming positive dx and dy).
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"""
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overlap: float
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dx: int
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dy: int
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x_count: int
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y_count: int
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images_dir: str
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autofocus_dz: int
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save_resolution: tuple[int, int]
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display_name: str = lt.property(default="Snake Scan", readonly=True)
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ui_blurb: str = lt.property(
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default=(
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"This scan workflow is optimised for scanning over a rectangle. It "
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"snakes down and right from the starting point, over a defined grid."
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),
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readonly=True,
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)
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_settings_model = SnakeSettingsModel
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_planner_cls = SnakeScan
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class RasterWorkflow(ScanWorkflow[RasterSettingsModel]):
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class RasterWorkflow(RectangleWorkflow[RasterSettingsModel]):
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"""A workflow optimised for snaking around samples.
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This workflow generates a list of coordinates in a rectangle, and always
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@ -705,136 +692,4 @@ class RasterWorkflow(ScanWorkflow[RasterSettingsModel]):
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)
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_settings_model = RasterSettingsModel
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_planner_cls: type[ScanPlanner] = RasterScan
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# Thing Slots
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_cam: BaseCamera = lt.thing_slot()
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_csm: CameraStageMapper = lt.thing_slot()
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_autofocus: AutofocusThing = lt.thing_slot()
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_stage: BaseStage = lt.thing_slot()
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# Scan settings
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autofocus_dz: int = lt.setting(default=1000, ge=200, le=2000)
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"""The z distance to perform an autofocus in steps.
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Must be greater than or equal to 200, and less than or equal to 2000.
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"""
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overlap: float = lt.setting(default=0.45, ge=0.1, le=0.7)
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"""The fraction that adjacent images should overlap in x or y.
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This must be between 0.1 and 0.7.
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"""
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x_count: int = lt.setting(default=3)
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y_count: int = lt.setting(default=2)
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# The noqa statement is because scan_name is unused but is needed for equivalence
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# with other workflows that may want to validate the scan name.
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def check_before_start(self, scan_name: str) -> None: # noqa: ARG002
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"""Before starting a scan, check that camera-stage-mapping is set.
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Raise error if:
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- camera stage mapping is not set
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"""
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if self._csm.calibration_required:
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raise RuntimeError("Camera Stage Mapping is not calibrated.")
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@lt.property
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def ready(self) -> bool:
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"""Whether this scanworkflow is ready to start."""
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return not self._csm.calibration_required
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def all_settings(
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self, images_dir: str
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) -> tuple[RasterSettingsModel, StitchingSettings]:
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"""Return the workflow and stitching settings.
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:param images_dir: The directory that images are to be written to.
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:return: A tuple containing the settings model for this workflow and the
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settings model for stitching.
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"""
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stitching_settings = StitchingSettings(
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overlap=self.overlap,
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correlation_resize=STITCHING_RESOLUTION[0] / self.save_resolution[0],
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)
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dx, dy = self._calc_displacement_from_overlap(self.overlap)
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self.logger.info(
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f"Based on an overlap of {self.overlap}, the stage will make steps of "
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f"{dx}, {dy}"
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)
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scan_settings = self._settings_model(
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overlap=self.overlap,
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dx=dx,
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dy=dy,
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x_count=self.x_count,
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y_count=self.y_count,
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images_dir=images_dir,
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autofocus_dz=self.autofocus_dz,
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save_resolution=self.save_resolution,
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)
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return scan_settings, stitching_settings
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def pre_scan_routine(self, settings: RasterSettingsModel) -> None:
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"""Autofocus before starting the scan.
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:param settings: The settings for this scan as a SnakeSettingsModel
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"""
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self._autofocus.looping_autofocus(dz=settings.autofocus_dz, start="centre")
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def new_scan_planner(
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self, settings: RasterSettingsModel, position: Mapping[str, int]
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) -> ScanPlanner:
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"""Return a new scan planner object.
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:param settings: The settings for this scan as a SnakeSettingsModel
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:param position: The starting position as a mapping of axes names to int.
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"""
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# The initial plan for the scan should be a single x,y position. All future
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# moves will be planned around this point. In future, route planner could
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# have multiple starting positions, each of which will be visited before the
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# scan can end.
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planner_settings = {
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"dx": settings.dx,
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"dy": settings.dy,
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"x_count": settings.x_count,
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"y_count": settings.y_count,
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}
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return self._planner_cls(
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initial_position=(position["x"], position["y"]),
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planner_settings=planner_settings,
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)
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def acquisition_routine(
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self, settings: RasterSettingsModel, xyz_pos: tuple[int, int, int]
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) -> tuple[bool, Optional[int]]:
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"""Perform acquisition routine. This is run at each scan location.
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:param settings: The settings for this scan as a RasterSettingsModel
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:param xyz_pos: The current position as a tuple or 3 ints.
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:return: A tuple of whether an image was taken, and the z-position for focus.
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If failed to find focus, returns for the focus z-position.
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"""
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self._autofocus.fast_autofocus(dz=settings.autofocus_dz)
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focus_height = self._stage.get_xyz_position()[2]
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filename = f"img_{xyz_pos[0]}_{xyz_pos[1]}_{focus_height}.jpeg"
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self._cam.capture_and_save(
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jpeg_path=os.path.join(settings.images_dir, filename),
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save_resolution=settings.save_resolution,
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)
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imaged = True
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return imaged, focus_height
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@lt.property
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def settings_ui(self) -> list[PropertyControl]:
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"""A list of PropertyControl objects to create the settings in the scan tab."""
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return [
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property_control_for(self, "overlap", label="Image Overlap (0.1-0.7)"),
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property_control_for(self, "x_count", label="Number of columns"),
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property_control_for(self, "y_count", label="Number of rows"),
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property_control_for(self, "autofocus_dz", label="Autofocus Range (steps)"),
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]
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_planner_cls = RasterScan
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