navigate.controller.controller.Controller

class navigate.controller.controller.Controller(root: tkinter.Tk, splash_screen: tkinter.Toplevel, configuration_path: str | os.PathLike[str], experiment_path: str | os.PathLike[str], waveform_constants_path: str | os.PathLike[str], rest_api_path: str | os.PathLike[str], waveform_templates_path: str | os.PathLike[str], gui_configuration_path: str | os.PathLike[str], multi_positions_path: str | os.PathLike[str], log_queue: mp.Queue | None, args: Any)

Bases: object

Navigate Controller

__init__(root: tkinter.Tk, splash_screen: tkinter.Toplevel, configuration_path: str | os.PathLike[str], experiment_path: str | os.PathLike[str], waveform_constants_path: str | os.PathLike[str], rest_api_path: str | os.PathLike[str], waveform_templates_path: str | os.PathLike[str], gui_configuration_path: str | os.PathLike[str], multi_positions_path: str | os.PathLike[str], log_queue: mp.Queue | None, args: Any) → None

Initialize the Navigate Controller.

Parameters:

root (tkinter.Tk) – Tk root window.
splash_screen (tkinter.Toplevel) – Splash window shown before the main window is initialized.
configuration_path (str | os.PathLike[str]) – Path to the global configuration YAML file.
experiment_path (str | os.PathLike[str]) – Path to the experiment YAML file.
waveform_constants_path (str | os.PathLike[str]) – Path to the waveform constants YAML file.
rest_api_path (str | os.PathLike[str]) – Path to the REST API configuration YAML file.
waveform_templates_path (str | os.PathLike[str]) – Path to the waveform templates YAML file.
gui_configuration_path (str | os.PathLike[str]) – Path to the GUI configuration YAML file.
multi_positions_path (str | os.PathLike[str]) – Path to the multi-position YAML file.
log_queue (multiprocessing.Queue | None) – Queue used for cross-process logging.
args (Any) – Command-line arguments used for runtime options.

Return type:

None

Methods

`__init__`(root, splash_screen, ...)	Initialize the Navigate Controller.
`add_acquisition_mode`(name, acquisition_obj)	Add and Acquisition Mode.
`capture_image`(command, mode, *args)	Trigger the model to capture images.
`change_microscope`(microscope_name[, zoom])	Change the microscope configuration.
`destroy_virtual_microscope`(microscope_name)	Destroy virtual microscopes.
`enable_resize`()	Enable window resize handling.
`execute`(command, *args)	Handle controller commands from sub-controllers and UI callbacks.
`initialize_cam_view`()	Populate view and maximum intensity projection tabs.
`launch_additional_microscopes`()	Launch and wire up auxiliary microscope display windows.
`move_stage`(pos_dict)	Trigger the model to move the stage.
`populate_experiment_setting`([file_name, ...])	Load experiment file and populate model.experiment and configure view.
`prepare_acquire_data`()	Prepare the acquisition data.
`query_select_microscope`(microscope_name)	Query a specific microscope for its current stage positions.
`register_event_listener`(event_name, ...)	Register an event listener.
`register_event_listeners`(events)	Register multiple event listeners.
`resize`(event)	Resize the GUI.
`set_mode_of_sub`(mode)	Communicates imaging mode to sub-controllers.
`sloppy_stop`()	Keep trying to stop the model until successful.
`stop_stage`()	Stop the stage.
`update_acquire_control`()	Bind Acquire Bar controls to the current stage control handlers.
`update_buffer`()	Update the shared image buffer for the active camera geometry.
`update_event`()	Update the View/Controller based on events from the Model.
`update_experiment_setting`()	Update experiment settings from GUI state.
`update_frame_rate`(frame_rate)	Update the frame rate display in the GUI.
`update_stage_controller_silent`(ret_pos_dict)	Send updates to the stage GUI
`update_stage_limits`(microscope_name)	Update stage limits on the device side
`use_asi_model`()	Check if the model uses ASI hardware.

Attributes

`root`	Tk.tk GUI instance.
`resize_ready_flag`	Flag to indicate if the GUI is ready for resizing.
`splash_screen`	Tk.tk GUI instance.
`configuration_path`	Path to the configuration yaml file.
`experiment_path`	Path to the experiment yaml file.
`waveform_constants_path`	Path to the waveform constants yaml file.
`rest_api_path`	Path to the REST API yaml file.
`waveform_templates_path`	Path to the waveform templates yaml file.
`gui_configuration_path`	Path to the GUI configuration yaml file.
`args`	Non-default command line input arguments for
`threads_pool`	Thread pool for the controller.
`event_queue`	Queue for retrieving events ('event_name', value) from model
`manager`	A shared memory manager
`configuration`	Configuration dictionary
`show_img_pipe`	Pipe for sending images from model to view.
`default_experiment_file`	Path to the default experiment yaml file.
`configuration_controller`	Configuration Controller object.
`view`	View object in MVC architecture.
`event_listeners`	Event listeners for the controller.
`acquire_bar_controller`	Acquire Bar Sub-Controller.
`channels_tab_controller`	Channels Tab Sub-Controller.
`multiposition_tab_controller`	Multi-Position Tab Sub-Controller.
`camera_view_controller`	Camera View Tab Sub-Controller.
`mip_setting_controller`	MIP Settings Tab Sub-Controller.
`camera_setting_controller`	Camera Settings Tab Sub-Controller.
`stage_controller`	Stage Sub-Controller.
`waveform_tab_controller`	Waveform Display Sub-Controller.
`keystroke_controller`	Keystroke Sub-Controller.
`menu_controller`	Menu Sub-Controller.
`plugin_acquisition_modes`	acquisition modes from plugins
`plugin_controller`	Plugin Sub-Controller
`img_width`	Number of x_pixels from microscope configuration file.
`img_height`	Number of y_pixels from microscope configuration file.
`data_buffer`	Pre-allocated shared memory array.
`additional_microscopes`	Additional microscopes.
`additional_microscopes_configs`	Additional microscope configurations.
`stop_acquisition_flag`	Flag for stopping acquisition.
`current_image_id`	current image id in the buffer
`resize_event_id`	ID for the resize event.Only works on Windows OS.

add_acquisition_mode(name: str, acquisition_obj: Callable[[str], Any]) → None

Add and Acquisition Mode.

Parameters:

name (str) – Name of the acquisition mode.
acquisition_obj (Callable[[str], Any]) – Factory or class that produces an acquisition mode object.

Return type:

None

capture_image(command: str, mode: str, *args: Any) → None

Trigger the model to capture images.

Parameters:

command (str) – Capture command passed to the model (for example "acquire").
mode (str) – Acquisition mode (for example "continuous" or "single").
*args (Any) – Command-specific positional arguments.

Return type:

None

change_microscope(microscope_name: str, zoom: str | None = None) → None

Change the microscope configuration.

Parameters:

microscope_name (str) – Name of the microscope to switch to.
zoom (str | None, optional) – Zoom value to set for the microscope. If None, keep current zoom.

Return type:

None

destroy_virtual_microscope(microscope_name: str, destroy_window: bool = True) → None

Destroy virtual microscopes.

Parameters:

microscope_name (str) – The microscope name
destroy_window (bool) – The flag to dismiss window.

Return type:

None

enable_resize() → None

Enable window resize handling.

Return type:: None

execute(command: str, *args: Any) → Any

Handle controller commands from sub-controllers and UI callbacks.

The controller configuration is synchronized with model state and commands are dispatched to worker threads or executed locally based on command type.

Parameters:

command (str) – Command name routed to controller/model operations.
*args (Any) – Command-specific positional arguments.

Returns:

Command-dependent return value. Most commands return None; some, such as "get_stage_position", return structured data.

Return type:

Any

initialize_cam_view() → None

Populate view and maximum intensity projection tabs.

Communicates with the camera view controller and mip setting controller to set the minimum and maximum counts, as well as the default channel settings.

Return type:: None

launch_additional_microscopes() → None

Launch and wire up auxiliary microscope display windows.

Return type:: None

move_stage(pos_dict: dict[str, Any]) → None

Trigger the model to move the stage.

Parameters:: pos_dict (dict[str, Any]) – Dictionary of axis positions
Return type:: None

populate_experiment_setting(file_name: str | os.PathLike[str] | None = None, in_initialize: bool = False) → None

Load experiment file and populate model.experiment and configure view.

Confirms that the experiment file exists. Sends the experiment file to the model and the controller. Populates the GUI with these settings.

Parameters:

file_name (str | os.PathLike[str] | None, optional) – Path to a non-default experiment YAML file to load.
in_initialize (bool, optional) – True when called during controller initialization to skip reloading experiment YAML from disk.

Return type:

None

prepare_acquire_data() → bool

Prepare the acquisition data.

Updates model.experiment. Sets sub-controller’s mode to ‘live’ when ‘continuous is selected, or ‘stop’.

Returns:: True if all settings are valid, False otherwise.
Return type:: bool

query_select_microscope(microscope_name: str) → None

Query a specific microscope for its current stage positions.

Parameters:: microscope_name (str) – Microscope name to query from the model.
Return type:: None

register_event_listener(event_name: str, event_handler: Callable[[Any], None]) → None

Register an event listener.

Parameters:

event_name (str) – Name of the event.
event_handler (Callable[[Any], None]) – The function to handle the event.

Return type:

None

register_event_listeners(events: dict[str, Callable[[Any], NoneType]]) → None

Register multiple event listeners.

Parameters:: events (dict[str, Callable[[Any], None]]) – Dictionary of event names and handlers.
Return type:: None

resize(event: Event) → None

Resize the GUI.

Parameters:: event (tkinter.Event) – Tk <Configure> event emitted during window size changes.
Return type:: None

set_mode_of_sub(mode: str) → None

Communicates imaging mode to sub-controllers.

Parameters:: mode (str) – Imaging mode such as "live" or "stop".
Return type:: None

sloppy_stop() → None

Keep trying to stop the model until successful.

TODO: Delete this function!!!

This is set up to get around the conflict between self.threads_pool.createThread(‘model’, target) commands and the need to stop as abruptly as possible when the user hits stop. Here we leverage ObjectInSubprocess’ refusal to let us access the model from two threads to our advantage, and just try repeatedly until we get a command in front of the next command in the model threads_pool resource. We should instead pause the model thread pool and interject our stop command, or clear the queue in threads_pool.

Return type:: None

stop_stage() → None

Stop the stage.

Grab the stopped position from the stage and update the GUI control values accordingly.

Return type:: None

update_acquire_control() → None

Bind Acquire Bar controls to the current stage control handlers.

Return type:: None

update_buffer() → None

Update the shared image buffer for the active camera geometry.

Return type:: None

update_event() → None

Update the View/Controller based on events from the Model.

This method runs on the Tk thread and drains all pending model events.

Return type:: None

update_experiment_setting() → str

Update experiment settings from GUI state.

Collect settings from sub-controllers, validate values, and synchronize configuration data used by model commands.

Returns:: Concatenated warning message if validation fails, otherwise an empty string.
Return type:: str

update_frame_rate(frame_rate: float) → None

Update the frame rate display in the GUI.

Updates the frame rate in the camera settings tab and the acquire bar controller. This method receives the accurate frame rate calculated from the model’s run_data_process method.

Parameters:: frame_rate (float) – The frame rate in frames per second (Hz).
Return type:: None

update_stage_controller_silent(ret_pos_dict: dict[str, Any]) → None

Send updates to the stage GUI

Parameters:: ret_pos_dict (dict[str, Any]) – Dictionary of axis positions
Return type:: None

update_stage_limits(microscope_name: str) → None

Update stage limits on the device side

Parameters:: microscope_name (str) – Microscope name.
Return type:: None

use_asi_model() → bool

Check if the model uses ASI hardware.

Returns:: True if the model uses ASI hardware, False if it uses NI hardware.
Return type:: bool
Raises:: ValueError – If the DAQ type is unknown.

acquire_bar_controller

Acquire Bar Sub-Controller.

Type:: AcquireBarController

additional_microscopes

Additional microscopes.

Type:: dict

additional_microscopes_configs

Additional microscope configurations.

Type:: dict

args

Non-default command line input arguments for

Type:: iterable

camera_setting_controller

Camera Settings Tab Sub-Controller.

Type:: CameraSettingController

camera_view_controller

Camera View Tab Sub-Controller.

Type:: CameraViewController

channels_tab_controller

Channels Tab Sub-Controller.

Type:: ChannelsTabController

configuration

Configuration dictionary

Type:: dict

configuration_controller

Configuration Controller object.

Type:: ConfigurationController

configuration_path

Path to the configuration yaml file.

Type:: string

current_image_id

current image id in the buffer

Type:: int

data_buffer

Pre-allocated shared memory array.

Type:: SharedNDArray

default_experiment_file

Path to the default experiment yaml file.

Type:: string

event_listeners

Event listeners for the controller.

Type:: dict

event_queue

Queue for retrieving events (‘event_name’, value) from model

Type:: mp.Queue

experiment_path

Path to the experiment yaml file.

Type:: string

gui_configuration_path

Path to the GUI configuration yaml file.

Type:: string

img_height

Number of y_pixels from microscope configuration file.

Type:: int

img_width

Number of x_pixels from microscope configuration file.

Type:: int

keystroke_controller

Keystroke Sub-Controller.

Type:: KeystrokeController

manager

A shared memory manager

Type:: Manager

menu_controller

Menu Sub-Controller.

Type:: MenuController

mip_setting_controller

MIP Settings Tab Sub-Controller.

Type:: MIPSettingController

multiposition_tab_controller

Multi-Position Tab Sub-Controller.

Type:: MultiPositionController

plugin_acquisition_modes

acquisition modes from plugins

Type:: dict

plugin_controller

Plugin Sub-Controller

Type:: PluginsController

resize_event_id

ID for the resize event.Only works on Windows OS.

Type:: int

resize_ready_flag

Flag to indicate if the GUI is ready for resizing.

Type:: bool

rest_api_path

Path to the REST API yaml file.

Type:: string

root

Tk.tk GUI instance.

Type:: Tk top-level widget

show_img_pipe

Pipe for sending images from model to view.

Type:: mp.Pipe

splash_screen

Tk.tk GUI instance.

Type:: Tk top-level widget

stage_controller

Stage Sub-Controller.

Type:: StageController

stop_acquisition_flag

Flag for stopping acquisition.

Type:: bool

threads_pool

Thread pool for the controller.

Type:: Object

view

View object in MVC architecture.

Type:: View

waveform_constants_path

Path to the waveform constants yaml file.

Type:: string

waveform_tab_controller

Waveform Display Sub-Controller.

Type:: WaveformTabController

waveform_templates_path

Path to the waveform templates yaml file.

Type:: string