app

class ClearMapApp(experiment_controller, bus, gui_controller)

Bases: ClearMapAppBase

The Main class of the GUI. This class focuses on the real business logic of the application. This represents the main window which has instances of the different tabs derived from GenericTab , which correspond to different steps of the program.

add_asset()

amend_ui()

Setup the loggers and all the post instantiation fixes to the UI

assert_src_folder_set()

conf_load_error_msg(conf_name)

Display an error message on missing config file

Parameters:

conf_name (str) – The name of the config to load (without params and extension)

display_about()

get_tab_widget(tab_title)

Get the tab widget by its title

Parameters:

tab_title (str) – The title of the tab to get

Returns

GenericTab

The tab matching the title

handle_tab_click(index: int)

load_sample() → bool

Load the sample configuration.

If the sample path does not exist, prompt the user to clone an existing config, load a default config, or cancel. If the sample path exists, ensure a sample ID is set. The return value tells the caller whether they need to call boot_open().

Returns

bool

• True: Existing experiment; caller must call boot_open().

• False: Either new experiment already bootstrapped & opened, or user canceled (src_folder is cleared).

manage_assets()

patch_warnings_color()

prompt_experiment_folder()

Prompt the user for the main experiment data folder and set it

reload_prefs()

reset()

reset_loggers()

select_tab(tab_name: str) → QWidget | None

set_tabs(tabs: Iterable[GenericTab])

Sets the tabs received from the GuiController

set_tabs_progress_watchers(nested=False)

Set the progress_watcher of all the tab managers

Parameters:

nested (bool) – Whether to set the progress watcher of the tab managers to a nested progress watcher

setup_loggers(src_folder)

setup_menus()

show_workspace_info()

trigger_workspace_reset()

Delete workspace.yml and reload the experiment.

property sample_manager

property src_folder: str

class ClearMapAppBase

Bases: QMainWindow, Ui_ClearMapGui

The interface for the ClearMapGui class

It deals with the basics of logic of the main window, the plotting progress bars and performance monitors and appearance. Anything more application related is coded in the child class.

static create_missing_file_msg(f_type: str, f_path: Path | str, default_path: Path | str) → tuple[str, str]

clear_plots()

Remove all plots currently displayed in the DataViewer area of the interface The underlying widgets are also scheduled for garbage collection

compute_default_font_size()

Gets the most represented font size in the program. This is the default font size

Returns

int

The default font size

file_exists(f_path: Path) → bool

find_child_by_name(child_name: str, child_type: type[QWidget], parent: QWidget | None = None) → QWidget | None

Find children in the window or any other widget

Parameters:

• child_name (str) – The name of the widget we are looking for

• child_type – The type of widget to search

• parent (QWidget) – The parent widget to start from. If none given, will use the main window.

Returns

QWidget

The child widget matching the name and type

fix_btns_stylesheet()

fix_sizes()

fix_styles()

The meta function calling all the style functions

fix_tooltips_stylesheet()

fix_widgets_backgrounds()

graph_by_name(name: str) → QWidget

Search self.graphs for name

Parameters:

name (str) – The objectName of the graph widget we are looking for

handle_step_name_change(step_name: str)

Handle a change of the name of the current computation step by registering the new step and updating the progress dialog

Parameters:

step_name (str) – The new step name

handle_sub_step_change(step_name: str)

Handle a change of the name of the current computation sub step by updating the progress dialog and logging the new substep

Parameters:

step_name (str) – The new step name

log_progress(msg: str)

make_progress_dialog(title: str = 'Processing', n_steps: int = 1, maximum: int = 100, abort: Callable | None = None, parent: QWidget | None = None)

Create a single or nested (2 nested bars) progress dialog. The dialog is initialised with the parameters below and linked to self.progress_watcher to drive updates of the titles and progress bar.

Parameters:

• title (str) – The title of the dialog

• n_steps (int) – The number of steps of the main step for nested dialogs

• maximum (int) – The maximum value of the progress bar (or the second bar for nested dialogs)

• abort (function) – The function to trigger when the abort button is clicked

• parent (QWidget) – The parent widget to the dialog

monkey_patch()

patch_tool_boxes()

Sets all toolboxes to the first item on startup regardless of the last closed state o f the ui file in QtCreator

popup(msg: str, base_msg: str = 'Missing configuration file', print_warning: bool = True) → QMessageBox

Display a warning popup message which the user has to dismiss by clicking OK Optionally, a warning is also printed to the logs

Parameters:

• msg (str) – The more detailed text to display

• base_msg (str) – The quick description of the problem

• print_warning (bool) – Whether to also print msg to logs

Returns

QMessageBox

The popup message box

print_error_msg(msg: str | Exception)

Print a message in red in the statusbar

Parameters:

msg (str) – The message to be printed

print_status_msg(msg: str)

Print a message in green in the statusbar

Parameters:

msg (str) – The message to be printed

print_warning_msg(msg: str)

Print a message in yellow in the statusbar

Parameters:

msg (str) – The message to be printed

set_font()

set_font_size(target_font_size=8)

Set the font sizes of the widgets based on target_font_size. All fonts will be shifted based on that size. This should preserve the size relationships of the fonts in the program. It is assumed that the program uses 4 font sizes: - small - regular - big - and huge

This will shift font sizes so that the supplied size corresponds to the new regular size.

Parameters:

target_font_size (int) – The main font size

set_tabs_progress_watchers(nested: bool = False)

setup_icons()

Patch the icons of the program

setup_monitoring_bars()

Create the performance monitoring bars in the status bar

setup_plots(dvs: list[DataViewer], graph_names: list[str] | None = None)

Set the plots provided as argument in the DataViewer area of the UI in a grid format. The items in the list have to be derived from QWidget

Parameters:

• dvs (List[DataViewer]) – The list of DataViewer (or any other QWidget derived object) to add to the display grid

• graph_names (None or List[str]) – Optional The names attached to the graphs for later reference

signal_process_finished(msg: str = 'Idle, waiting for input')

Handles the end of the current computation with a message to be printed and logged. It will also notify and close the progress dialog window if there is one

Parameters:

msg (str) – The message to display

update_cpu_bars(cpu_percent: int, thread_percent: int, ram_percent: int)

Update the performance monitoring bars in the status bar

Parameters:

• cpu_percent (int) – The CPU usage percent to display

• thread_percent (int) – The percent usage of the main ClearMap thread to display

• ram_percent (int) – The RAM usage percent to display

update_gpu_bars(gpu_percent: int, v_ram_percent: int)

Update the performance monitoring bars in the status bar

Parameters:

• gpu_percent (int) – The GPU usage percent to display

• v_ram_percent (int) – The Graphics RAM usage percent to display

wrap_in_thread(func: Callable, *args, **kwargs)

Wraps the function in a thread to ensure that the GUI remains responsive In general all processing done in the GUI should go through this method

Parameters:

• func (function) – The function to wrap

• args – The arguments to the function func

• kwargs – The keyword arguments to forward to func

Returns

The result of the execution of the function func

class GuiController(bus: EventBus, experiment, tab_registry: TabRegistry, group_controller: AnalysisGroupController)

Bases: BusSubscriberMixin

The controller of the GUI. It is responsible for building the main window, installing the tabs and handling events from the EventBus. It interacts with the ExperimentController to manage the business logic of the application.

begin_hydration()

end_hydration()

set_mode(mode: AppMode)

start(app_: ClearMapApp, centered: bool = True)

property hydrating: bool

True when either the controller or the experiment is mid-hydration.

property tabs: Iterable[Any]

build_business_objects(bus: EventBus)

entry_point()

main(app_, splash_)

overlay_splash_message(msg: str) → None