navigate.controller.sub_controllers.autofocus.AutofocusPopupController

class navigate.controller.sub_controllers.autofocus.AutofocusPopupController(view: AutofocusPopup, parent_controller: Controller)

Bases: GUIController

Class creates the popup to configure autofocus parameters.

__init__(view: AutofocusPopup, parent_controller: Controller) → None

Parameters:

• view (AutofocusPopup) – The view of the autofocus popup.

• parent_controller (navigate.controller.controller.Controller) – The parent controller of the autofocus popup.

Methods

__init__(view, parent_controller)	param view: The view of the autofocus popup.
close_popup(*_)	Close the popup window
display_autofocus_progress(data)	Queue the latest autofocus measurements for a Tk-thread update.
display_plot(data_and_flags)	Display autofocus data, handling segmentation, plot mode, and redraw.
execute(command, *args)	This function is called when a command is passed from a child process.
handle_autofocus_complete(payload)	Handle autofocus completion metadata for defocus calibration.
initialize()	This function is called when the controller is initialized
populate_experiment_values()	Refresh current hardware choices and display saved autofocus settings.
refresh_bounds_validation()	Refresh advisory scan bounds feedback from current stage state.
register_event_listener(event_name, ...)	Register event listener in the parent_controller
set_acquisition_state(state)	Update the acquisition lifecycle state and popup actions.
set_autofocus_state(is_active)	Update autofocus activity and popup actions.
set_experiment_values()	Sets values of widgets based on experiment setting
show_autofocus_setting(*_)	Show Autofocus Parameters
show_verbose_info(*info)	Prints verbose information to the console
showup()	Refresh current microscope choices and show the popup window.
start_autofocus()	Start autofocus only if the selected hardware target is still current.
stop_acquisition()	Stop the active acquisition through the main controller.
update_device_ref(*_)	Refresh eligible devices and references without editing stored settings.
update_experiment_values(*args)	Collects all the values of widgets
update_setting_dict(parameter)	Show Autofocus Parameters

Attributes

CALIBRATION_ACTIONS
custom_events	Custom events for this controller
defocus_calibration_reference	Return popup-independent defocus calibration reference state.
widgets	The autofocus setting dictionary.
microscope_name	The microscope name.
setting_dict	The autofocus setting dictionary.
autofocus_fig	The autofocus figure.
autofocus_coarse	The autofocus coarse plot.
coarse_plot	The autofocus coarse plot.

close_popup(*_: tuple[str]) → None

Close the popup window

Parameters:

_ (tuple[str]) – The event arguments.

display_autofocus_progress(data) → None

Queue the latest autofocus measurements for a Tk-thread update.

display_plot(data_and_flags: tuple[numpy.ndarray, bool, bool]) → None

Display autofocus data, handling segmentation, plot mode, and redraw.

This method unpacks and normalizes incoming data, splits it into coarse and fine segments according to the current autofocus settings, renders scatter and/or line plots on the coarse axes, optionally clears previous data, marks the detected maximum(s), and schedules a non-blocking canvas redraw.

Parameters:

data_and_flags (tuple[np.ndarray, bool, bool]) – Tuple of (data, line_plot, clear_data). data contains sample rows with stage positions in column 0 and signal values in column 1. line_plot overlays a continuous red line when true, and clear_data clears the axes and draws peak indicators when true.

Raises:

ValueError – May be raised if data is empty or has fewer than two columns (propagated from internal processing or from _plot_maxima).

execute(command, *args)

This function is called when a command is passed from a child process.

Parameters:

• command (str) – command name

• args (tuple) – command arguments

handle_autofocus_complete(payload: dict) → None

Handle autofocus completion metadata for defocus calibration.

initialize()

This function is called when the controller is initialized

This function initializes GUI based on configuration setting parameter: configuration_controller set range value for entry or spinbox widgets; add values to combobox get other necessary information for configuration.yml

populate_experiment_values() → None

Refresh current hardware choices and display saved autofocus settings.

Inactive settings remain stored but are not offered as acquisition targets. Preserve a valid selection within the same microscope.

refresh_bounds_validation() → list[str]

Refresh advisory scan bounds feedback from current stage state.

Returns:

Immediately knowable bounds diagnostics.

Return type:

list[str]

register_event_listener(event_name, event_handler)

Register event listener in the parent_controller

Parameters:

• event_name (str) – event name

• event_handler (function) – event handler

set_acquisition_state(state: str) → None

Update the acquisition lifecycle state and popup actions.

set_autofocus_state(is_active: bool) → None

Update autofocus activity and popup actions.

set_experiment_values()

Sets values of widgets based on experiment setting

setting_dict is a dictionary

show_autofocus_setting(*_: tuple[str]) → None

Show Autofocus Parameters

Parameters:

_ (tuple[str]) – The event arguments.

show_verbose_info(*info)

Prints verbose information to the console

Parameters:

info (tuple) – information to be printed

showup() → None

Refresh current microscope choices and show the popup window.

start_autofocus() → None

Start autofocus only if the selected hardware target is still current.

Unavailable targets produce a user-facing error before any acquisition state or calibration values are changed.

stop_acquisition() → None

Stop the active acquisition through the main controller.

update_device_ref(*_: tuple[str]) → None

Refresh eligible devices and references without editing stored settings.

Parameters:

_ (tuple[str]) – The event arguments.

update_experiment_values(*args)

Collects all the values of widgets

setting_dict is a reference of experiment dictionary update the dictionary directly

update_setting_dict(parameter: str) → callable

Show Autofocus Parameters

Parameters:

parameter (str) – The parameter to be updated.

Returns:

The function to update the parameter

Return type:

callable

autofocus_coarse

The autofocus coarse plot.

Type:

object

autofocus_fig

The autofocus figure.

Type:

object

coarse_plot

The autofocus coarse plot.

Type:

object

property custom_events: dict[str, callable]

Custom events for this controller

Returns:

The custom events for this controller.

Return type:

dict[str, callable]

property defocus_calibration_reference: Optional[dict]

Return popup-independent defocus calibration reference state.

microscope_name

The microscope name.

Type:

str

parent_controller

parent controller

Type:

Controller

setting_dict

The autofocus setting dictionary.

Type:

dict

view

GUI view

Type:

tkinter.Tk

widgets

The autofocus setting dictionary.

Type:

dict