704 lines
26 KiB
Python
704 lines
26 KiB
Python
"""Scan workflows set different ways that smart scan can behave.
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This module contains the base ``ScanWorkflow`` class that all workflows should subclass,
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as well as specific workflows.
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"""
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from __future__ import annotations
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import os
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from typing import (
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Generic,
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Literal,
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Mapping,
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Optional,
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TypeVar,
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)
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from pydantic import BaseModel
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import labthings_fastapi as lt
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from openflexure_microscope_server.scan_planners import (
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RegularGridPlanner,
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ScanPlanner,
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SmartSpiral,
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)
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from openflexure_microscope_server.stitching import (
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STITCHING_RESOLUTION,
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StitchingSettings,
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)
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from openflexure_microscope_server.things.autofocus import (
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MAX_TEST_IMAGE_COUNT,
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MIN_TEST_IMAGE_COUNT,
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AutofocusThing,
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SmartStackParams,
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)
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from openflexure_microscope_server.things.background_detect import (
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ChannelDeviationLUV,
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)
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from openflexure_microscope_server.things.camera import BaseCamera
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from openflexure_microscope_server.things.camera_stage_mapping import CameraStageMapper
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from openflexure_microscope_server.things.stage import BaseStage
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from openflexure_microscope_server.ui import PropertyControl, property_control_for
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SettingModelType = TypeVar("SettingModelType", bound=BaseModel)
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class ScanWorkflow(Generic[SettingModelType], lt.Thing):
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"""A base class for all Scanworkflows.
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Scan workflows set the behaviour of a scan, including the background detection,
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scan planning, acquisition routine.
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"""
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display_name: str = lt.property(default="Base Workflow", readonly=True)
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ui_blurb: str = lt.property(
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default="If you see this message, something is wrong.", readonly=True
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)
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_settings_model: type[SettingModelType]
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# All workflows must have a set class for scan planning
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_planner_cls: type[ScanPlanner]
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# All workflows set a save resolution
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save_resolution: tuple[int, int] = lt.setting(default=(1640, 1232))
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"""A tuple of the image resolution to capture."""
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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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# Camera, stage and autofocus are all required by any scan workflow
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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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The scan_name is passed to this function to enable workflows to validate the
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scan name if needed.
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"""
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raise NotImplementedError(
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"Each specific ScanWorkflow must implement a check_before_start."
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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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raise NotImplementedError(
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"Each specific ScanWorkflow must implement a ready property."
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)
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def all_settings(
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self, images_dir: str
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) -> tuple[SettingModelType, Optional[StitchingSettings]]:
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"""Return the scan settings and the stitching settings.
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- The specific settings for this scan workflow are returned as a Base Model of
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the type set when defining the class.
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- Stitiching settings are returned either as a StitchingSettings object or None
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is returned if it is not possible to stitch the scan.
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"""
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raise NotImplementedError(
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"Each specific ScanWorkflow must implement a `all_settings`. method."
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)
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def pre_scan_routine(self, settings: SettingModelType) -> None:
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"""Overload to set the routine that happens before each scan."""
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raise NotImplementedError(
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"Each specific ScanWorkflow must implement a pre-scan routine."
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)
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def new_scan_planner(
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self, settings: SettingModelType, position: Mapping[str, int]
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) -> ScanPlanner:
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"""Return the a new scan planner object for a scan."""
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raise NotImplementedError(
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"Each specific ScanWorkflow must implement a ``new_scan_planner`` method."
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)
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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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:param settings: The settings for this scan, which should be a SettingModelType
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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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"""Autofocus and then capture, this can be used as an acquisition routine.
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:param dz: The dz for autofocus.
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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. In this method,
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image is always taken, so first return is True.
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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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raise NotImplementedError(
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"Each scan workflow must implement a settings_ui method."
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)
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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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# Redefine _csm Thing Slot, as CSM is required for any RectGridWorkflow
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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 and 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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:param overlap: The desired overlap as a fraction of the image. i.e. 0.5 means
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that each image should overlap its nearest neighbour by 50%.
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:returns: (dx, dy) - the x and y displacements in steps
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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_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 progressed this far.")
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# Calculate displacements in image coordinates
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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 = 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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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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"""
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overlap: float
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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(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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the centre position, scanning only where it detects sample.
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"""
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display_name: str = lt.property(default="Histo 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 H&E stained biopsies. It "
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"spirals out from the starting location, scanning only where it detects "
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"sample. It also works well for many other flat, well-featured samples."
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),
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readonly=True,
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)
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_settings_model = HistoScanSettingsModel
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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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# Scan settings
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skip_background: bool = lt.setting(default=True)
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"""Whether to detect and skip empty fields of view.
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This uses the settings from the ``BackgroundDetectThing``.
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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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# Stacking settings
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stack_images_to_save: int = lt.setting(default=1)
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"""The number of images to save in a stack.
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Defaults to 1 unless you need to see either side of focus
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"""
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stack_min_images_to_test: int = lt.setting(default=9)
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"""The minimum number of images to capture in a stack.
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This many images are captures and tested for focus, if the focus is not central
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enough more images may be captured. After new images are captured, this value sets
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the number of images used for checking if focus is achieved.
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Defaults to 9 which balances reliability and speed.
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"""
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stack_dz: int = lt.setting(default=50)
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"""Distance in steps between images in a z-stack.
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Suggested values:
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* 50 for 60-100x
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* 100 for 40x
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* 200 for 20x
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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 background and camera-stage-mapping are set.
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Raise error if:
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- background is to be skipped but is not set
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- camera stage mapping is not set
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Raise warning if not using background detect that scan will go on until max steps reached
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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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if self.skip_background:
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if not self._background_detector.ready:
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raise RuntimeError(
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"Background is not set: you need to calibrate background detection."
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)
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else:
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self.logger.warning(
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"This scan will run in a spiral from the starting point "
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f"until you cancel it, or until it has moved by {self.max_range} steps "
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"in every direction. Make sure you watch it run to stop it leaving "
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"the area of interest, or (worse) leading the microscope's range "
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"of motion."
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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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if self._csm.calibration_required:
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return False
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if not self.skip_background:
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return True
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return self._background_detector.ready
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def all_settings(
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self, images_dir: str
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) -> tuple[HistoScanSettingsModel, 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 = self._get_stitching_settings_model()
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dx, dy = self._calc_displacement_from_overlap(self.overlap)
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smart_stack_params = self.create_smart_stack_params(
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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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scan_settings = HistoScanSettingsModel(
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overlap=self.overlap,
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max_dist=self.max_range,
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dx=dx,
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dy=dy,
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skip_background=self.skip_background,
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smart_stack_params=smart_stack_params,
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)
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return scan_settings, stitching_settings
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def create_smart_stack_params(
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self,
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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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) -> SmartStackParams:
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"""Set up the parameters used for all stacks in a scan.
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:param images_dir: the folder to save all images
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:param autofocus_dz: the range to autofocus over if a stack fails
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:param save_resolution: The resolution to save the captures to disk with
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:returns: A StackSmartParams object with the required parameters.
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"""
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# Coerce min_images_to_test parameter
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min_images_to_test = self.stack_min_images_to_test
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if min_images_to_test < MIN_TEST_IMAGE_COUNT:
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self.logger.warning(
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f"Cannot test only {min_images_to_test} image(s) as this will fail. "
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"Setting min images to test to lowest possible value of"
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f"{MIN_TEST_IMAGE_COUNT}."
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)
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min_images_to_test = MIN_TEST_IMAGE_COUNT
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elif min_images_to_test > MAX_TEST_IMAGE_COUNT:
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self.logger.warning(
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f"Testing {min_images_to_test} images will cause defocus. "
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"Setting min images to test to highest possible value of "
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f"{MAX_TEST_IMAGE_COUNT}."
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)
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min_images_to_test = MAX_TEST_IMAGE_COUNT
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elif min_images_to_test % 2 == 0:
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min_images_to_test += 1
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self.logger.warning(
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"Minimum number of images to test should be odd, setting to "
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f"{min_images_to_test}."
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)
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# Set the Thing property to the coerced value
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self.stack_min_images_to_test = min_images_to_test
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# Coerce the images to save parameter to be positive, odd, and less than
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# min_images_to_save
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images_to_save = self.stack_images_to_save
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if images_to_save <= 0:
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self.logger.warning(
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"At least 1 images must be saved. Setting images to save to 1."
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)
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images_to_save = 1
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elif images_to_save > min_images_to_test:
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self.logger.warning(
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f"Cannot save {images_to_save} images as this above the minimum "
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f"number to test. Setting images to save to {MAX_TEST_IMAGE_COUNT}."
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)
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images_to_save = min_images_to_test
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elif images_to_save % 2 == 0:
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images_to_save += 1
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self.logger.warning(
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f"Images to save should be odd, setting to {images_to_save}."
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)
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# Set the Thing property to the coerced value
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self.stack_images_to_save = images_to_save
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return SmartStackParams(
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stack_dz=self.stack_dz,
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images_to_save=self.stack_images_to_save,
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min_images_to_test=self.stack_min_images_to_test,
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autofocus_dz=autofocus_dz,
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images_dir=images_dir,
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save_resolution=save_resolution,
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)
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def pre_scan_routine(self, settings: HistoScanSettingsModel) -> None:
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"""Autofocus before starting the scan.
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:param settings: The settings for this scan as a HistoScanSettingsModel
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"""
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self._autofocus.looping_autofocus(
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dz=settings.smart_stack_params.autofocus_dz, start="centre"
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)
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def new_scan_planner(
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self, settings: HistoScanSettingsModel, 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 HistoScanSettingsModel
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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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"max_dist": settings.max_dist,
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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: HistoScanSettingsModel, 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 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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if settings.skip_background:
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# If skipping background, take an image to check if current field of view
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# is background
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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:
|
|
# 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 = not settings.skip_background
|
|
|
|
focus_height: Optional[int]
|
|
focused, focus_height = self._autofocus.run_smart_stack(
|
|
stack_parameters=settings.smart_stack_params,
|
|
save_on_failure=save_on_failure,
|
|
)
|
|
# 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:
|
|
focus_height = None
|
|
|
|
return imaged, focus_height
|
|
|
|
@lt.property
|
|
def settings_ui(self) -> list[PropertyControl]:
|
|
"""A list of PropertyControl objects to create the settings in the scan tab."""
|
|
return [
|
|
property_control_for(self, "overlap", label="Image Overlap (0.1-0.7)"),
|
|
property_control_for(
|
|
self, "stack_images_to_save", label="Images in Stack to Save"
|
|
),
|
|
property_control_for(
|
|
self,
|
|
"stack_min_images_to_test",
|
|
label="Minimum number of images to test for focus",
|
|
),
|
|
property_control_for(self, "stack_dz", label="Stack dz (steps)"),
|
|
property_control_for(self, "autofocus_dz", label="Autofocus Range (steps)"),
|
|
property_control_for(self, "max_range", label="Maximum Distance (steps)"),
|
|
property_control_for(
|
|
self, "skip_background", label="Detect and Skip Empty Fields "
|
|
),
|
|
]
|
|
|
|
|
|
class RegularGridSettingsModel(BaseModel):
|
|
"""The settings for a scan with a regular grid of dx and dy for x_count, y_count steps.
|
|
|
|
This includes settings calculated when starting. This will be held by smart scan
|
|
during a scan and serialised to disk.
|
|
"""
|
|
|
|
overlap: float
|
|
dx: int
|
|
dy: int
|
|
x_count: int
|
|
y_count: int
|
|
style: Literal["snake", "raster"]
|
|
images_dir: str
|
|
autofocus_dz: int
|
|
save_resolution: tuple[int, int]
|
|
|
|
|
|
class RegularGridWorkflow(RectGridWorkflow[RegularGridSettingsModel]):
|
|
"""A base workflow for any workflow that uses a regular rectangular grid."""
|
|
|
|
x_count: int = lt.setting(default=3, ge=1)
|
|
"""The number of columns in the scan."""
|
|
y_count: int = lt.setting(default=2, ge=1)
|
|
"""The number of rows in the scan."""
|
|
|
|
_settings_model = RegularGridSettingsModel
|
|
_planner_cls = RegularGridPlanner
|
|
_grid_style: Literal["snake", "raster"]
|
|
|
|
def all_settings(
|
|
self, images_dir: str
|
|
) -> tuple[RegularGridSettingsModel, Optional[StitchingSettings]]:
|
|
"""Return the workflow and stitching settings.
|
|
|
|
:param images_dir: The directory that images are to be written to.
|
|
:return: A tuple containing the settings model for this workflow and the
|
|
settings model for stitching.
|
|
"""
|
|
stitching_settings = self._get_stitching_settings_model()
|
|
dx, dy = self._calc_displacement_from_overlap(self.overlap)
|
|
|
|
scan_settings = self._settings_model(
|
|
overlap=self.overlap,
|
|
dx=dx,
|
|
dy=dy,
|
|
x_count=self.x_count,
|
|
y_count=self.y_count,
|
|
style=self._grid_style,
|
|
images_dir=images_dir,
|
|
autofocus_dz=self.autofocus_dz,
|
|
save_resolution=self.save_resolution,
|
|
)
|
|
|
|
return scan_settings, stitching_settings
|
|
|
|
def pre_scan_routine(self, settings: RegularGridSettingsModel) -> None:
|
|
"""Perform these steps before starting the scan.
|
|
|
|
In this case, only autofocus.
|
|
|
|
:param settings: The settings for this scan as as the relevant SettingsModel type.
|
|
"""
|
|
self._autofocus.looping_autofocus(dz=settings.autofocus_dz, start="centre")
|
|
|
|
def new_scan_planner(
|
|
self, settings: RegularGridSettingsModel, position: Mapping[str, int]
|
|
) -> ScanPlanner:
|
|
"""Return a new scan planner object.
|
|
|
|
:param settings: The settings for this scan as a SnakeSettingsModel
|
|
:param position: The starting position as a mapping of axes names to int.
|
|
"""
|
|
planner_settings = {
|
|
"dx": settings.dx,
|
|
"dy": settings.dy,
|
|
"x_count": settings.x_count,
|
|
"y_count": settings.y_count,
|
|
"style": settings.style,
|
|
}
|
|
return self._planner_cls(
|
|
initial_position=(position["x"], position["y"]),
|
|
planner_settings=planner_settings,
|
|
)
|
|
|
|
def acquisition_routine(
|
|
self, settings: RegularGridSettingsModel, xyz_pos: tuple[int, int, int]
|
|
) -> tuple[bool, Optional[int]]:
|
|
"""Autofocus and capture.
|
|
|
|
:param settings: The settings for this scan as a RegularGridSettingsModel
|
|
: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.
|
|
If failed to find focus, returns for the focus z-position.
|
|
"""
|
|
return self._autofocus_and_capture(
|
|
xyz_pos=xyz_pos,
|
|
dz=settings.autofocus_dz,
|
|
images_dir=settings.images_dir,
|
|
save_resolution=settings.save_resolution,
|
|
)
|
|
|
|
@lt.property
|
|
def settings_ui(self) -> list[PropertyControl]:
|
|
"""A list of PropertyControl objects to create the settings in the scan tab."""
|
|
return [
|
|
property_control_for(self, "overlap", label="Image Overlap (0.1-0.7)"),
|
|
property_control_for(self, "x_count", label="Number of columns"),
|
|
property_control_for(self, "y_count", label="Number of rows"),
|
|
property_control_for(self, "autofocus_dz", label="Autofocus Range (steps)"),
|
|
]
|
|
|
|
|
|
class SnakeWorkflow(RegularGridWorkflow):
|
|
"""A workflow optimised for snaking around samples.
|
|
|
|
This workflow generates a list of coordinates in a rectangle, and snakes
|
|
around them from the top left (assuming positive dx and dy).
|
|
"""
|
|
|
|
display_name: str = lt.property(default="Snake Scan", readonly=True)
|
|
ui_blurb: str = lt.property(
|
|
default=(
|
|
"This scan workflow is optimised for scanning over a rectangle. It "
|
|
"snakes down and right from the starting point, over a defined grid."
|
|
),
|
|
readonly=True,
|
|
)
|
|
_grid_style = "snake"
|
|
|
|
|
|
class RasterWorkflow(RegularGridWorkflow):
|
|
"""A workflow optimised for snaking around samples.
|
|
|
|
This workflow generates a list of coordinates in a rectangle, and always
|
|
moves right across a row, then moves down a row while moving to the starting
|
|
column (assuming positive dx and dy).
|
|
"""
|
|
|
|
display_name: str = lt.property(default="Raster Scan", readonly=True)
|
|
ui_blurb: str = lt.property(
|
|
default=(
|
|
"This scan workflow is optimised for performing a raster scan over a rectangle. It "
|
|
"always moves down and right from the starting point, over a defined grid."
|
|
),
|
|
readonly=True,
|
|
)
|
|
|
|
_grid_style = "raster"
|