openflexure_microscope_server.things.scan_workflows.RegularGridWorkflow

class documentation

class RegularGridWorkflow(RectGridWorkflow[RegularGridSettingsModel]): (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	`all_settings`	Return the workflow and stitching settings.
Method	`new_scan_planner`	Return a new scan planner object.
Method	`pre_scan_routine`	Perform these steps before starting the scan.
Class Variable	`x_count`	The number of columns in the scan.
Class Variable	`y_count`	The number of rows in the scan.
Property	`settings_ui`	A list of PropertyControl objects to create the settings in the scan tab.
Class Variable	`_grid_style`	Undocumented

Inherited from RectGridWorkflow:

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	`_settings_model`	Undocumented
Class Variable	`_stage`	Undocumented

def acquisition_routine(self, settings: RegularGridSettingsModel, 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:`RegularGridSettingsModel`	The settings for this scan as a RegularGridSettingsModel
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 all_settings(self, images_dir: str) -> tuple[RegularGridSettingsModel, StitchingSettings | None]: (source) ¶

overrides openflexure_microscope_server.things.scan_workflows.ScanWorkflow.all_settings

Return the workflow and stitching settings.

Parameters
images_dir:`str`	The directory that images are to be written to.

Returns
`tuple[RegularGridSettingsModel, StitchingSettings \| None]`	A tuple containing the settings model for this workflow and the settings model for stitching.

def new_scan_planner(self, settings: RegularGridSettingsModel, 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:`RegularGridSettingsModel`	The settings for this scan as a SnakeSettingsModel
position:`Mapping[str, int]`	The starting position as a mapping of axes names to int.

Returns
`ScanPlanner`	Undocumented

def pre_scan_routine(self, settings: RegularGridSettingsModel): (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:`RegularGridSettingsModel`	The settings for this scan as as the relevant SettingsModel type.

x_count: int = (source) ¶

The number of columns in the scan.

y_count: int = (source) ¶

The number of rows in the scan.

@lt.property

settings_ui: list[PropertyControl] = (source) ¶

overrides openflexure_microscope_server.things.scan_workflows.ScanWorkflow.settings_ui

A list of PropertyControl objects to create the settings in the scan tab.

_grid_style: Literal['snake', 'raster'] = (source) ¶

overridden in openflexure_microscope_server.things.scan_workflows.RasterWorkflow, openflexure_microscope_server.things.scan_workflows.SnakeWorkflow

Undocumented