Further layering of the classes for scan workflows
This commit is contained in:
Julian Stirling
parent
1f01717a1b
commit
15798d9b7d
1 changed files with 110 additions and 126 deletions
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@ -68,6 +68,9 @@ class ScanWorkflow(Generic[SettingModelType], lt.Thing):
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# CSM may not be set, and isn't required for a workflow. Allow for it to exist or be None
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_csm: Optional[CameraStageMapper] = lt.thing_slot()
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_cam: BaseCamera = lt.thing_slot()
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_stage: BaseStage = lt.thing_slot()
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_autofocus: AutofocusThing = lt.thing_slot()
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def check_before_start(self, scan_name: str) -> None:
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"""Check before the scan starts. Throw an error if the scan shouldn't start.
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@ -117,11 +120,42 @@ class ScanWorkflow(Generic[SettingModelType], lt.Thing):
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def acquisition_routine(
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self, settings: SettingModelType, xyz_pos: tuple[int, int, int]
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) -> tuple[bool, Optional[int]]:
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"""Overload to set the acquisition routine that happens at each scan site."""
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"""Overload to set the acquisition routine that happens at each scan site.
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:param settings: The settings for this scan as a HistoScanSettingsModel
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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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raise NotImplementedError(
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"Each specific ScanWorkflow must implement an acquisition routine"
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)
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def _autofocus_and_capture(
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self,
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xyz_pos: tuple[int, int, int],
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dz: int,
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images_dir: str,
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save_resolution: tuple[int, int],
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) -> tuple[bool, Optional[int]]:
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"""Atuofocus and then capture, this can be used as an acquisition routine.
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:param dz: The dz for autofoucs.
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:param images_dir: The path to the directory for saving images..
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:param save_resolution: The resolution to save images at.
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:return: A tuple ready to pass out of acquisition routine.
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"""
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self._autofocus.fast_autofocus(dz=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(images_dir, filename),
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save_resolution=save_resolution,
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)
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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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"""A list of PropertyControl objects to create the settings in the scan tab."""
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@ -129,13 +163,35 @@ class ScanWorkflow(Generic[SettingModelType], lt.Thing):
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"Each scan workflow must implement a settings_ui method."
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)
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def _require_csm(self) -> CameraStageMapper:
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"""Give each model the option to require CSM. Return it if present."""
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if self._csm is None:
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raise RuntimeError(
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"CameraStageMapping not set, and is required for this workflow."
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)
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return self._csm
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class RectGridWorkflow(ScanWorkflow[SettingModelType], Generic[SettingModelType]):
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"""A generic workflow for any scan that captures images on a rectilinear grid."""
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# Thing Slots
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_csm: CameraStageMapper = lt.thing_slot()
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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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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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# 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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def _calc_displacement_from_overlap(self, overlap: float) -> tuple[int, int]:
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"""Use camera stage mapping to calculate x and y displacement from given overlap.
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@ -147,9 +203,7 @@ class ScanWorkflow(Generic[SettingModelType], lt.Thing):
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:raises RuntimeError: If there is no camera stage mapper Thing available or if CMS isn't calibrated.
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"""
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csm = self._require_csm()
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csm_image_res = csm.image_resolution
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csm_image_res = self._csm.image_resolution
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if csm_image_res is None:
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raise RuntimeError("CSM not set. Scan shouldn't have progresses this far.")
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@ -157,16 +211,33 @@ class ScanWorkflow(Generic[SettingModelType], lt.Thing):
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dx_img = csm_image_res[1] * (1 - overlap)
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dy_img = csm_image_res[0] * (1 - overlap)
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x_move_stage = csm.convert_image_to_stage_coordinates(x=dx_img, y=0)
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y_move_stage = csm.convert_image_to_stage_coordinates(x=0, y=dy_img)
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x_move_stage = self._csm.convert_image_to_stage_coordinates(x=dx_img, y=0)
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y_move_stage = self._csm.convert_image_to_stage_coordinates(x=0, y=dy_img)
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# Assume no rotation or skew and take only the aligned axis of vector.
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# Coerce to positive integer, but correct if x and y are flipped
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if abs(x_move_stage["x"]) > abs(x_move_stage["y"]):
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return x_move_stage["x"], y_move_stage["y"]
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# If not use the other stage axes. Note "dx" will be the movement in camera y.
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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"{y_move_stage['x']}, {x_move_stage['y']}"
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)
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return y_move_stage["x"], x_move_stage["y"]
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def _get_stitching_settings_model(self) -> StitchingSettings:
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"""Return a stitching settings model based on current settings."""
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return 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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@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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class HistoScanSettingsModel(BaseModel):
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"""The settings for a scan with the HistoScanWorkflow.
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@ -176,14 +247,14 @@ class HistoScanSettingsModel(BaseModel):
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"""
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overlap: float
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max_dist: int
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dx: int
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dy: int
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max_dist: int
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skip_background: bool
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smart_stack_params: SmartStackParams
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class HistoScanWorkflow(ScanWorkflow[HistoScanSettingsModel]):
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class HistoScanWorkflow(RectGridWorkflow[HistoScanSettingsModel]):
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"""A workflow optimised for scanning Histopathology samples.
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This workflow automatically plans its own path around a sample spiralling out from
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@ -201,12 +272,9 @@ class HistoScanWorkflow(ScanWorkflow[HistoScanSettingsModel]):
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)
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_settings_model = HistoScanSettingsModel
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_planner_cls: type[ScanPlanner] = SmartSpiral
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_planner_cls = SmartSpiral
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# Thing Slots
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_background_detector: ChannelDeviationLUV = lt.thing_slot()
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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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# Scan settings
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@ -216,21 +284,9 @@ class HistoScanWorkflow(ScanWorkflow[HistoScanSettingsModel]):
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This uses the settings from the ``BackgroundDetectThing``.
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"""
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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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max_range: int = lt.setting(default=45000)
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"""The maximum distance in steps from the centre of the scan."""
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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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# Stacking settings
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stack_images_to_save: int = lt.setting(default=1)
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@ -305,16 +361,8 @@ class HistoScanWorkflow(ScanWorkflow[HistoScanSettingsModel]):
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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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stitching_settings = self._get_stitching_settings_model()
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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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smart_stack_params = self.create_smart_stack_params(
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images_dir=images_dir,
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@ -502,7 +550,7 @@ class HistoScanWorkflow(ScanWorkflow[HistoScanSettingsModel]):
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]
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class RectangleSettingsModel(BaseModel):
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class RegularGridSettingsModel(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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@ -519,86 +567,28 @@ class RectangleSettingsModel(BaseModel):
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save_resolution: tuple[int, int]
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TypeSettings = TypeVar("TypeSettings", bound=RectangleSettingsModel)
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class SnakeSettingsModel(RectangleSettingsModel):
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"""Settings for Snake scan."""
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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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# 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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class RegularGridWorkflow(RectGridWorkflow[RegularGridSettingsModel]):
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"""A base workflow for any workflow that uses a regular rectangular grid."""
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x_count: int = lt.setting(default=3, ge=1)
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"""The number of columns in the scan."""
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y_count: int = lt.setting(default=2, ge=1)
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"""The number of columns and rows in the scan.
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Must be at least 1.
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"""
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"""The number of rows in the scan."""
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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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_settings_model = RegularGridSettingsModel
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_planner_cls: type[SnakeScan] | type[RasterScan]
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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(self, images_dir: str) -> tuple[TypeSettings, StitchingSettings]:
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def all_settings(
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self, images_dir: str
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) -> tuple[RegularGridSettingsModel, Optional[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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stitching_settings = self._get_stitching_settings_model()
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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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@ -613,7 +603,7 @@ class RectangleWorkflow(ScanWorkflow[TypeSettings], Generic[TypeSettings]):
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return scan_settings, stitching_settings
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def pre_scan_routine(self, settings: TypeSettings) -> None:
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def pre_scan_routine(self, settings: RegularGridSettingsModel) -> None:
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"""Perform these steps before starting the scan.
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In this case, only autofocus.
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@ -623,7 +613,7 @@ class RectangleWorkflow(ScanWorkflow[TypeSettings], Generic[TypeSettings]):
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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: TypeSettings, position: Mapping[str, int]
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self, settings: RegularGridSettingsModel, position: Mapping[str, int]
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) -> ScanPlanner:
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"""Return a new scan planner object.
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@ -642,26 +632,22 @@ class RectangleWorkflow(ScanWorkflow[TypeSettings], Generic[TypeSettings]):
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)
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def acquisition_routine(
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self, settings: TypeSettings, xyz_pos: tuple[int, int, int]
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self, settings: RegularGridSettingsModel, 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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"""Autofocus and capture.
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:param settings: The settings for this scan as the correct setting model
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:param settings: The settings for this scan as a HistoScanSettingsModel
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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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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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return self._autofocus_and_capture(
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xyz_pos=xyz_pos,
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dz=settings.autofocus_dz,
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images_dir=settings.images_dir,
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save_resolution=settings.save_resolution,
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)
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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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"""A list of PropertyControl objects to create the settings in the scan tab."""
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@ -673,7 +659,7 @@ class RectangleWorkflow(ScanWorkflow[TypeSettings], Generic[TypeSettings]):
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]
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class SnakeWorkflow(RectangleWorkflow[SnakeSettingsModel]):
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class SnakeWorkflow(RegularGridWorkflow):
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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 snakes
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@ -688,11 +674,10 @@ class SnakeWorkflow(RectangleWorkflow[SnakeSettingsModel]):
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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(RectangleWorkflow[RasterSettingsModel]):
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class RasterWorkflow(RegularGridWorkflow):
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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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@ -709,5 +694,4 @@ class RasterWorkflow(RectangleWorkflow[RasterSettingsModel]):
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readonly=True,
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)
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_settings_model = RasterSettingsModel
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_planner_cls = RasterScan
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