openflexure_microscope_server.things.scan_workflows.CChipWorkflow

class documentation

class CChipWorkflow(RectGridWorkflow[CChipScanSettingsModel]): (source)

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A workflow optimised for scanning the well of a CChip.

This workflow generates a list of coordinates in a rectangle, and snakes around them from the top left (assuming positive dx and dy), stacking the grid and above.

Method acquisition_routine Autofocus and capture a z-stack starting at the focused position.
Method create_stack_params Set up the parameters used for all stacks in a scan.
Method new_scan_planner Return a new scan planner object.
Method pre_scan_routine No autofocus, a looping autofocus on a CChip could corrupt the entire scan.
Class Variable display_name Undocumented
Class Variable overlap The fraction that adjacent images should overlap in x and y.
Class Variable stack_dz Distance in steps between images in a z-stack.
Class Variable stack_images_to_save The number of images to save in a stack.
Class Variable ui_blurb Undocumented
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.
Method _build_scan_settings Construct the SettingModel for all_settings.
Class Variable _grid_style 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.
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 save_resolution A tuple of the image resolution to capture.
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: CChipScanSettingsModel, xyz_pos: tuple[int, int, int]) -> tuple[bool, int | None]: (source)
overrides openflexure_microscope_server.things.scan_workflows.ScanWorkflow.acquisition_routine

Autofocus and capture a z-stack starting at the focused position.

The routine performs a fast autofocus using the provided dz. The focused z-height becomes the starting position for the stack and is also the height of the first captured image.

A stack of self.stack_images_to_save images is then acquired. Each subsequent image is captured after moving the stage upward by self.stack_dz steps in z.

Parameters
settings:CChipScanSettingsModelThe settings for this scan as a CChipSettingsModel
xyz_pos:tuple[int, int, int]The (x, y, z) position associated with this acquisition.
Returns
tuple[bool, int | None](True, focus_height) where focus_height is the autofocus z-position and the height of the first image in the stack.
def create_stack_params(self) -> StackParams: (source)

Set up the parameters used for all stacks in a scan.

Returns
StackParamsA StackSmartParams object with the required parameters.
def new_scan_planner(self, settings: CChipScanSettingsModel, 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:CChipScanSettingsModelThe 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: CChipScanSettingsModel): (source)
overrides openflexure_microscope_server.things.scan_workflows.ScanWorkflow.pre_scan_routine

No autofocus, a looping autofocus on a CChip could corrupt the entire scan.

display_name: str = (source)
overrides openflexure_microscope_server.things.scan_workflows.ScanWorkflow.display_name

Undocumented

overlap: float = (source)
overrides openflexure_microscope_server.things.scan_workflows.RectGridWorkflow.overlap

The fraction that adjacent images should overlap in x and y.

This must be between 0.1 and 0.7.

stack_dz: int = (source)

Distance in steps between images in a z-stack.

stack_images_to_save: int = (source)

The number of images to save in a stack.

Defaults to 1 unless you need to see either side of focus

ui_blurb: str = (source)
overrides openflexure_microscope_server.things.scan_workflows.ScanWorkflow.ui_blurb

Undocumented

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.

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

Construct the SettingModel for all_settings.

_grid_style: Literal['snake'] = (source)

Undocumented