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Joe Knapper 2026-02-25 13:19:38 +00:00 • committed by Julian Stirling
parent 43fa793698
commit 63338f8ea0
4 changed files with 111 additions and 191 deletions
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90
src/openflexure_microscope_server/things/scan_workflows.py
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@ -240,10 +240,14 @@ class RectGridWorkflow(ScanWorkflow[SettingModelType], Generic[SettingModelType]
correlation_resize=STITCHING_RESOLUTION[0] / self.save_resolution[0],
)
def _build_scan_settings(self, base_kwargs: dict) -> SettingModelType:
"""Construct the _settings_model."""
return self._settings_model(**base_kwargs)
def all_settings(
self, images_dir: str
) -> tuple[SettingModelType, Optional[StitchingSettings]]:
"""Return the scan settings and the stitching settings.
"""Return scan settings and the 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
@ -252,19 +256,17 @@ class RectGridWorkflow(ScanWorkflow[SettingModelType], Generic[SettingModelType]
stitching_settings = self._get_stitching_settings_model()
dx, dy = self._calc_displacement_from_overlap(self.overlap)
capture_params = CaptureParams(
images_dir=images_dir, save_resolution=self.save_resolution
)
base_kwargs = {
"overlap": self.overlap,
"dx": dx,
"dy": dy,
"capture_params": CaptureParams(
images_dir=images_dir, save_resolution=self.save_resolution
),
"autofocus_params": AutofocusParams(dz=self.autofocus_dz),
}
autofocus_params = AutofocusParams(dz=self.autofocus_dz)
scan_settings = self._settings_model(
overlap=self.overlap,
dx=dx,
dy=dy,
capture_params=capture_params,
autofocus_params=autofocus_params,
)
scan_settings = self._build_scan_settings(base_kwargs)
return scan_settings, stitching_settings
@ -389,38 +391,14 @@ class HistoScanWorkflow(RectGridWorkflow[HistoScanSettingsModel]):
return True
return self._background_detector.ready
def all_settings(
self, images_dir: str
) -> tuple[HistoScanSettingsModel, StitchingSettings]:
"""Return the workflow settings 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)
capture_params = CaptureParams(
images_dir=images_dir,
save_resolution=self.save_resolution,
)
autofocus_params = AutofocusParams(dz=self.autofocus_dz)
smart_stack_params = self.create_smart_stack_params()
scan_settings = HistoScanSettingsModel(
overlap=self.overlap,
def _build_scan_settings(self, base_kwargs: dict) -> HistoScanSettingsModel:
return HistoScanSettingsModel(
**base_kwargs,
max_dist=self.max_range,
dx=dx,
dy=dy,
skip_background=self.skip_background,
capture_params=capture_params,
autofocus_params=autofocus_params,
smart_stack_params=smart_stack_params,
smart_stack_params=self.create_smart_stack_params(),
)
return scan_settings, stitching_settings
def create_smart_stack_params(
self,
) -> SmartStackParams:
@ -615,38 +593,14 @@ class RegularGridWorkflow(RectGridWorkflow[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)
capture_params = CaptureParams(
images_dir=images_dir,
save_resolution=self.save_resolution,
)
autofocus_params = AutofocusParams(dz=self.autofocus_dz)
scan_settings = self._settings_model(
overlap=self.overlap,
dx=dx,
dy=dy,
def _build_scan_settings(self, base_kwargs: dict) -> RegularGridSettingsModel:
return RegularGridSettingsModel(
**base_kwargs,
x_count=self.x_count,
y_count=self.y_count,
style=self._grid_style,
capture_params=capture_params,
autofocus_params=autofocus_params,
)
return scan_settings, stitching_settings
def pre_scan_routine(self, settings: RegularGridSettingsModel) -> None:
"""Perform these steps before starting the scan.