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4 changed files with 111 additions and 191 deletions
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@ -21,7 +21,7 @@ from pydantic import BaseModel, computed_field, field_validator, model_validator
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import labthings_fastapi as lt
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from labthings_fastapi.types.numpy import NDArray
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from .camera import BaseCamera, CaptureParams, validate_capture_params
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from .camera import BaseCamera, CaptureParams
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from .stage import BaseStage
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LOGGER = logging.getLogger(__name__)
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@ -75,6 +75,22 @@ class StackParams(BaseModel):
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origin: StackOrigin = StackOrigin.START
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"""Where the stack is positioned relative to the current z position."""
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@field_validator("images_to_save")
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@classmethod
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def validate_images_to_save(cls, value: int) -> int:
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"""Validate that the number of images to save is greater than zero."""
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if value <= 0:
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raise ValueError(f"Invalid number of images to save: {value}. Must be > 0.")
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return value
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@field_validator("settling_time")
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@classmethod
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def validate_settling_time(cls, value: float) -> float:
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"""Validate that settling time is zero or positive."""
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if value < 0:
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raise ValueError(f"Invalid settling time: {value}. Must be positive or 0.")
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return value
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class SmartStackParams(StackParams):
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"""A class for holding smart stack parameters, and returning computed ones."""
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@ -765,10 +781,6 @@ class AutofocusThing(lt.Thing):
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- Final z position
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- List of z positions captured
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"""
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# Validate parameters and raise Exception if unsuitable
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validate_stack_params(stack_parameters=stack_parameters)
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validate_capture_params(capture_parameters=capture_parameters)
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captures: list[CaptureInfo] = []
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z_positions: list[int] = []
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@ -869,24 +881,3 @@ def _count_turning_points(sharpnesses: np.ndarray) -> int:
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d_sharpnesses = d_sharpnesses[prominent]
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# count the sign changes
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return int(np.sum(d_sharpnesses[1:] * d_sharpnesses[:-1] < 0))
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def validate_stack_params(stack_parameters: StackParams) -> None:
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"""Validate stack parameters for a z-stack acquisition.
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Ensures that the parameters allow a physical stack, without negative or zero
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values where they would cause crashes.
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:param stack_parameters: StackParams object containing stacking settings.
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:raises ValueError: If any stack_parameters are found to be unusable.
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"""
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if stack_parameters.images_to_save <= 0:
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raise ValueError(
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f"Invalid number of images to save: {stack_parameters.images_to_save}. Must be > 0."
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)
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if stack_parameters.settling_time < 0:
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raise ValueError(
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f"Invalid settling time: {stack_parameters.settling_time}. Must be positive or 0."
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)
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@ -20,7 +20,7 @@ from typing import Any, Literal, Mapping, Optional, Self, Tuple
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import numpy as np
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import piexif
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from PIL import Image
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from pydantic import BaseModel
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from pydantic import BaseModel, field_validator
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import labthings_fastapi as lt
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from labthings_fastapi.types.numpy import NDArray
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@ -54,37 +54,28 @@ class CaptureParams(BaseModel):
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images_dir: str
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save_resolution: tuple[int, int]
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@field_validator("save_resolution")
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@classmethod
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def validate_save_resolution(cls, value: Tuple[int, int]) -> Tuple[int, int]:
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"""Validate that save_resolution is a tuple with exactly two positive integers."""
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if not isinstance(value, tuple):
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raise TypeError("Save resolution should be a tuple")
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if len(value) != 2 or any(not isinstance(x, int) or x <= 0 for x in value):
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raise ValueError(
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f"Invalid save_resolution: {value}. "
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"Must be a tuple of two positive integers."
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)
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return value
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def validate_capture_params(capture_parameters: CaptureParams) -> None:
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"""Validate capture parameters for a capture.
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Ensures that the save resolution is a tuple of two positive integers
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and that the images directory is a non-empty string.
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:param capture_parameters: CaptureParams object containing acquisition settings.
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:raises ValueError: If `save_resolution` is not a tuple of two positive integers,
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or if `images_dir` is not a non-empty string.
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"""
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if (
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not isinstance(capture_parameters.save_resolution, tuple)
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or len(capture_parameters.save_resolution) != 2
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or not all(
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isinstance(x, int) and x > 0 for x in capture_parameters.save_resolution
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)
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):
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raise ValueError(
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f"Invalid save_resolution: {capture_parameters.save_resolution}. Must "
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"be a tuple of two positive integers."
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)
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if (
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not isinstance(capture_parameters.images_dir, str)
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or not capture_parameters.images_dir
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):
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raise ValueError(
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f"Invalid images_dir: {capture_parameters.images_dir}. Must be a non-empty string."
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)
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@field_validator("images_dir")
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@classmethod
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def validate_images_dir(cls, value: str) -> str:
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"""Validate that images_dir is a non-empty string."""
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if not isinstance(value, str) or not value:
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raise ValueError(
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f"Invalid images_dir: {value}. Must be a non-empty string."
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)
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return value
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class NoImageInMemoryError(RuntimeError):
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@ -240,10 +240,14 @@ class RectGridWorkflow(ScanWorkflow[SettingModelType], Generic[SettingModelType]
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correlation_resize=STITCHING_RESOLUTION[0] / self.save_resolution[0],
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)
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def _build_scan_settings(self, base_kwargs: dict) -> SettingModelType:
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"""Construct the _settings_model."""
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return self._settings_model(**base_kwargs)
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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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"""Return scan settings and the 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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@ -252,19 +256,17 @@ class RectGridWorkflow(ScanWorkflow[SettingModelType], Generic[SettingModelType]
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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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capture_params = CaptureParams(
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images_dir=images_dir, save_resolution=self.save_resolution
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)
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base_kwargs = {
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"overlap": self.overlap,
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"dx": dx,
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"dy": dy,
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"capture_params": CaptureParams(
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images_dir=images_dir, save_resolution=self.save_resolution
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),
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"autofocus_params": AutofocusParams(dz=self.autofocus_dz),
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}
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autofocus_params = AutofocusParams(dz=self.autofocus_dz)
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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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capture_params=capture_params,
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autofocus_params=autofocus_params,
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)
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scan_settings = self._build_scan_settings(base_kwargs)
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return scan_settings, stitching_settings
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@ -389,38 +391,14 @@ class HistoScanWorkflow(RectGridWorkflow[HistoScanSettingsModel]):
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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 settings 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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capture_params = CaptureParams(
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images_dir=images_dir,
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save_resolution=self.save_resolution,
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)
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autofocus_params = AutofocusParams(dz=self.autofocus_dz)
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smart_stack_params = self.create_smart_stack_params()
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scan_settings = HistoScanSettingsModel(
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overlap=self.overlap,
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def _build_scan_settings(self, base_kwargs: dict) -> HistoScanSettingsModel:
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return HistoScanSettingsModel(
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**base_kwargs,
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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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capture_params=capture_params,
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autofocus_params=autofocus_params,
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smart_stack_params=smart_stack_params,
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smart_stack_params=self.create_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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) -> SmartStackParams:
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@ -615,38 +593,14 @@ class RegularGridWorkflow(RectGridWorkflow[RegularGridSettingsModel]):
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_planner_cls = RegularGridPlanner
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_grid_style: Literal["snake", "raster"]
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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 = self._get_stitching_settings_model()
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dx, dy = self._calc_displacement_from_overlap(self.overlap)
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capture_params = CaptureParams(
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images_dir=images_dir,
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save_resolution=self.save_resolution,
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)
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autofocus_params = AutofocusParams(dz=self.autofocus_dz)
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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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def _build_scan_settings(self, base_kwargs: dict) -> RegularGridSettingsModel:
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return RegularGridSettingsModel(
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**base_kwargs,
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x_count=self.x_count,
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y_count=self.y_count,
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style=self._grid_style,
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capture_params=capture_params,
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autofocus_params=autofocus_params,
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)
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return scan_settings, stitching_settings
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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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