openflexure_microscope_server.things.scan_workflows.RegularGridWorkflow

class documentation

class RegularGridWorkflow(RectGridWorkflow[RegGridSettingModelType], SmartStackMixin, Generic[RegGridSettingModelType]): (source)

Known subclasses: openflexure_microscope_server.things.scan_workflows.RasterWorkflow, openflexure_microscope_server.things.scan_workflows.SnakeWorkflow

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A base workflow for any workflow that uses a regular rectangular grid.

Method acquisition_routine Autofocus and capture.
Method new_scan_planner Return a new scan planner object.
Method pre_scan_routine Perform these steps before starting the scan.
Method settings_ui Return the UI for the workflow's settings in the scan tab.
Class Variable x_count The number of columns in the scan.
Class Variable y_count The number of rows in the scan.
Method _build_scan_settings Construct the SettingModel for all_settings.
Class Variable _grid_style Undocumented
Class Variable _settings_model Undocumented

Inherited from RectGridWorkflow:

Method all_settings Return scan settings and the stitching settings.
Method check_before_start Before starting a scan, check that camera-stage-mapping is set.
Class Variable autofocus_dz The z distance to perform an autofocus in steps.
Class Variable overlap The fraction that adjacent images should overlap in x and y.
Property ready Whether this scanworkflow is ready to start.
Method _calc_displacement_from_overlap Use camera stage mapping to calculate x and y displacement from given overlap.
Method _get_stitching_settings_model Return a stitching settings model based on current settings.
Class Variable _csm Undocumented

Inherited from ScanWorkflow (via RectGridWorkflow):

Class Variable display_name Undocumented
Class Variable save_resolution A tuple of the image resolution to capture.
Class Variable ui_blurb Undocumented
Method _autofocus_and_capture Autofocus and then capture, this can be used as an acquisition routine.
Class Variable _autofocus Undocumented
Class Variable _cam Undocumented
Class Variable _planner_cls Undocumented
Class Variable _stage Undocumented

Inherited from SmartStackMixin (via RectGridWorkflow, ScanWorkflow):

Method create_smart_stack_params Set up the parameters used for all smart stacks in a scan.
Method smart_stack_property_controls Return smart stack property controls for the UI.
Class Variable stack_dz Distance in steps between images in a z-stack.
Instance Variable stack_images_to_save The number of images to save in a stack.
Instance Variable stack_min_images_to_test The minimum number of images to capture in a stack.
Property as_workflow Return self as a ScanWorkflow.
Method _perform_smart_stack Perform acquisition a smart stack.
def acquisition_routine(self, settings: RegGridSettingModelType, xyz_pos: tuple[int, int, int]) -> tuple[bool, int | None]: (source)
overrides openflexure_microscope_server.things.scan_workflows.ScanWorkflow.acquisition_routine

Autofocus and capture.

Parameters
settings:RegGridSettingModelTypeThe settings for this scan as the relevant SettingsModel type.
xyz_pos:tuple[int, int, int]The current position as a tuple or 3 ints.
Returns
tuple[bool, int | None]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.
def new_scan_planner(self, settings: RegGridSettingModelType, position: Mapping[str, int]) -> ScanPlanner: (source)
overrides openflexure_microscope_server.things.scan_workflows.ScanWorkflow.new_scan_planner

Return a new scan planner object.

Parameters
settings:RegGridSettingModelTypeThe settings for this scan as the relevant SettingsModel type.
position:Mapping[str, int]The starting position as a mapping of axes names to int.
Returns
ScanPlannerUndocumented
def pre_scan_routine(self, settings: RegGridSettingModelType): (source)
overrides openflexure_microscope_server.things.scan_workflows.ScanWorkflow.pre_scan_routine

Perform these steps before starting the scan.

In this case, only autofocus.

Parameters
settings:RegGridSettingModelTypeThe settings for this scan as as the relevant SettingsModel type.
@lt.endpoint('get', 'settings_ui', responses=UI_ELEMENT_RESPONSE)
def settings_ui(self) -> UIElementList: (source)
overrides openflexure_microscope_server.things.scan_workflows.ScanWorkflow.settings_ui

Return the UI for the workflow's settings in the scan tab.

x_count: int = (source)

The number of columns in the scan.

y_count: int = (source)

The number of rows in the scan.

def _build_scan_settings(self, base_kwargs: dict) -> RegGridSettingModelType: (source)
overrides openflexure_microscope_server.things.scan_workflows.RectGridWorkflow._build_scan_settings

Construct the SettingModel for all_settings.

_grid_style: Literal['snake', 'raster'] = (source)
overridden in openflexure_microscope_server.things.scan_workflows.RasterWorkflow, openflexure_microscope_server.things.scan_workflows.SnakeWorkflow

Undocumented

_settings_model: type[RegGridSettingModelType] = (source)
overrides openflexure_microscope_server.things.scan_workflows.ScanWorkflow._settings_model

Undocumented