pydetecdiv.app.gui

Main widgets to use with persistent windows

class pydetecdiv.app.gui.FileMenu(parent: MainWindow, *args, **kwargs)

Bases: QMenu

The main window File menu

class pydetecdiv.app.gui.DataMenu(parent: MainWindow, *args, **kwargs)

Bases: QMenu

The main window File menu

class pydetecdiv.app.gui.PluginMenu(parent: MainWindow, *args, **kwargs)

Bases: QMenu

Plugin menus

class pydetecdiv.app.gui.MainToolBar(parent: MainWindow, name: str = 'Main toolbar', **kwargs)

Bases: QToolBar

The main toolbar of the main window

class pydetecdiv.app.gui.MainStatusBar

Bases: QStatusBar

The status bar of the main window

show_memory_usage() → None

Show memory usage in status bar

class pydetecdiv.app.gui.Quit(parent: MainWindow | MainToolBar)

Bases: QAction

Quit action, interrupting the application

class pydetecdiv.app.gui.Help(parent: MainWindow | MainToolBar)

Bases: QAction

Action requesting global help

show_info() → None

Shows information about the application (version, authors, licence)

pydetecdiv.app.gui.Windows

Classes for persistent windows of the GUI

class pydetecdiv.app.gui.Windows.MainWindow

Bases: QMainWindow

The principal window

closeEvent(_: QCloseEvent) → None

Response to close event signal. Settings are saved in order to save the current window geometry and state.

add_tabbed_window(title: str) → TabbedWindow

Add a new Tabbed Mdi subwindow to visualize related information and analyses

Parameters:

title – the title for the tabbed viewer window

Returns:

the new tabbed viewer widget

subwindow_activation(subwindow: QMdiArea) → None

When a tabbed viewer is activated (its focus is set), then the Image resource selector should be fed with the corresponding image resource information(FOV name, stage dataset, channel)

Parameters:

subwindow – the activated sub-window

property active_subwindow: QMdiArea | None

A property returning the currently active subwindow in the MDI area

Returns:

the currently active tabbed window in the MDI area

class pydetecdiv.app.gui.Windows.ImageResourceChooser(parent: MainWindow)

Bases: QDockWidget

A dockable widget with a form for choosing an image resource to display in a new tabbed viewer. The image resource is determined by the FOV name, the dataset (stage) and a channel

set_choice(p_name: str) → None

Set the available values for FOVs, datasets and channels given a project name

Parameters:

p_name – the project name

accept() → None

When the OK button is clicked, then open a new TabbedViewer window and display the selected Image resource

class pydetecdiv.app.gui.Windows.DrawingToolsPalette(parent: MainWindow)

Bases: QDockWidget

A dockable window with tools for drawing ROIs and other items.

unset_tools() → None

Unset all available tools

current_tool() → QToolButton | None

Return the currently checked tool

Returns:

the currently checked tool

set_item_width(width: int)

Sets the width of the currently selected item, using the spinbox in drawing tools

Parameters:

width – the desired width

set_item_height(height: int)

Sets the height of the currently selected item, using the spinbox in drawing tools

Parameters:

height – the desired height

class pydetecdiv.app.gui.Windows.Cursor(parent: DrawingToolsPalette)

Bases: QToolButton

QToolButton to activate the tool for selecting and dragging items in the view

select_tool() → None

Select the Cursor tool

class pydetecdiv.app.gui.Windows.DrawRect(parent: DrawingToolsPalette)

Bases: QToolButton

A QToolButton to activate the tool for drawing a ROI

select_tool() → None

Select the DrawRect tool

class pydetecdiv.app.gui.Windows.DuplicateItem(parent: DrawingToolsPalette)

Bases: QToolButton

A QToolButton to activate the tool for duplicating a ROI

select_tool() → None

Select the DuplicateItem tool

class pydetecdiv.app.gui.Windows.DrawPoint(parent: DrawingToolsPalette)

Bases: QToolButton

A QToolButton to activate the tool for duplicating a ROI

select_tool() → None

Select the DuplicateItem tool

class pydetecdiv.app.gui.Windows.AnalysisToolsTree(parent: MainWindow)

Bases: QDockWidget

A dockable window with tools for image analysis.

pydetecdiv.app.gui.ActionsSettings

Handling actions to edit and manage settings

class pydetecdiv.app.gui.ActionsSettings.SettingsDialog

Bases: QDialog

A dialog window to edit application settings

toggle_buttons() → None

Enable or disable OK and Apply buttons depending upon the validity of input text

select_workspace() → None

Method opening a Directory chooser to select the workspace directory

select_appdata_path() → None

Method opening a Directory chooser to select the toolbox directory

select_toolbox_path() → None

Method opening a Directory chooser to select the toolbox directory

clicked(button: QPushButton)

Slot responding to a click on one of the buttons in the button box.

Parameters:

button – the clicked button

apply()

Save the contents of the settings editor into the settings file when the OK button has been clicked

reset()

Reset the contents of the settings editor to the values currently in the settings file

class pydetecdiv.app.gui.ActionsSettings.Settings(parent: QWidget)

Bases: QAction

Action to open a session editor window

pydetecdiv.app.gui.ActionsProject

Handling actions to open, create and interact with projects

class pydetecdiv.app.gui.ActionsProject.ProjectAction(value)

An Enum class of the various actions applicable to projects (New, Open, Delete)

class pydetecdiv.app.gui.ActionsProject.ProjectDialog(list_projects: list[str], project_action: ProjectAction = ProjectAction.Open)

A generic dialog window to create or open a project

static project_name_validator() → QRegularExpressionValidator

Name validator to filter invalid character in project name

Returns:

the validator

project_name_changed() → None

Slot checking whether the project name input is empty or not and enabling or disabling Ok button accordingly

get_project_name() → str

Method returning the chosen project name, either from QLineEdit (new project) or QComboBox (open project)

Returns:

the project name

accept() → None

Action triggered by clicking on the accept button in the button box. It is either create a new project if the project name does not exist yet or open an existing project otherwise. This method also checks whether the project name is empty.

open_create_project(project_name: str) → None

Open a project called project_name, create a new project if it does not exist, and set the Window title accordingly before closing the project connexion.

Parameters:

project_name – the name of the project to open/create

delete_project(project_name: str) → None

Delete project called project_name,

Parameters:

project_name – the name of the project to delete

class pydetecdiv.app.gui.ActionsProject.NewProject(parent: QWidget)

Action to open a for project creation

static create_project() → None

Opens dialog window to create a new project

class pydetecdiv.app.gui.ActionsProject.OpenProject(parent: QWidget)

Action to open a project chooser window

open_project() → None

Opens dialog window to open a project

class pydetecdiv.app.gui.ActionsProject.DeleteProject(parent: QWidget)

Action to open a project chooser window

pydetecdiv.app.gui.ActionsData

Handling actions to open, create and interact with projects

class pydetecdiv.app.gui.ActionsData.FileListView(parent: QWidget)

Bases: QListView

A class extending QListView to display source for image data. Defines a context menu to clear or toggle selection, remove selected sources, clear list

contextMenuEvent(e: QContextMenuEvent) → None

Definition of a context menu to clear or toggle selection of sources in list model, remove selected sources from the list model, clear the source list model

Parameters:

e – mouse event providing the position of the context menu

unselect() → None

Clear selection model

toggle() → None

Toggle selection model, selected sources are deselected and unselected ones are selected

remove_items() → None

Delete selected sources

clear_list() → None

Clear the source list

class pydetecdiv.app.gui.ActionsData.ImportMetaDataDialog

Bases: QDialog

A dialog window to choose sources for metadata files to import images and create Image resources

add_files() → None

Open a file chooser dialog box and add selected files to the source model

add_dir() → None

Open a directory chooser dialog box and add selected directory to the source model

add_path(path: str) → None

Add the input path to the source model

Parameters:

path – the metadata file path

accept() → None

Launches import of data in response to Ok button

import_data() → None

Import files whose list is defined by the sources in self.list_model

class pydetecdiv.app.gui.ActionsData.ImportDataDialog

Bases: QDialog

A dialog window to choose sources for image data files to import into the project raw dataset

add_files() → None

Open a file chooser dialog box and add selected files to the source model

add_dir() → None

Open a directory chooser dialog box and add selected directory to the source model

add_path(path: str) → None

Add the input path to the source model

Parameters:

path – the Data path

get_destinations() → list[str]

Get the list of subdirectories in the destination raw dataset directory

Returns:

list of subdirectories in the destination raw dataset directory

file_list() → list[str]

Expands all source specification to return a list of files to import

Returns:

file name list

accept() → None

Import files whose list is defined by the sources in self.list_model

import_data() → None

Import image data from source specified in list_model into project raw dataset and triggers a progress signal with the number of files that have been copied so far

count_imported_files(destination: str, n_start: int) → int

Count imported files in destination directory to assess progress

Parameters:

• destination – destination directory which files are imported into

• n_start – the number of files already in the destination directory before import

Returns:

the number of imported files

cancel_import(initial_files: set[str], n_files0: int, project: Project, processes: list[Popen]) → None

Manage cancellation of import. Terminate all copy processes before launching deletion of files that were already copied. Then cancel persistence operations on Data objects, and eventually stop the host thread.

Parameters:

• initial_files – the set of files before import was started

• n_files0 – the initial number of files

• project – the current Project

• processes – import processes that are running and should be cancelled

source_list_is_not_empty() → None

Checks the source list is not empty, enables OK button if not

static sub_directory_name_validator() → QRegularExpressionValidator

Name validator to filter invalid character in directory name

Returns:

the validator

class pydetecdiv.app.gui.ActionsData.ImportData(parent: QWidget)

Bases: QAction

Action to import raw data images into a project

class pydetecdiv.app.gui.ActionsData.ImportMetaData(parent: QWidget)

Bases: QAction

Action to import raw data images into a project

class pydetecdiv.app.gui.ActionsData.AddPathDialog(parent_window: QWidget)

Bases: QDialog

A dialog window to select a path pointing to files or directories to import

accept() → None

Accept the path input text and add it to the source list

path_specification_changed() → None

Checks the path input text actually exists and enables Apply and OK buttons accordingly

class pydetecdiv.app.gui.ActionsData.CreateFOV(parent: QWidget)

Bases: QAction

Action to import raw data images into a project

enable(raw_data_count: int)

Enable or disable this action in the Data menu whether there are raw data or not.

Parameters:

raw_data_count – the number of files in raw dataset

class pydetecdiv.app.gui.ActionsData.ComputeDriftDialog(title: str = None)

Bases: Dialog

A dialog window to run drift correction computations for a selection of FOVs

update_fov_list(project_name: str) → dict[str, FOV]

Return the list of FOVs in the project as a dictionary mapping actual FOV objects to their names

Parameters:

project_name – the name of the project

Returns:

a dictionary of FOVs in project

accept() → None

Launch the drift computation and the associated waiting dialog

compute_drift(Z: int = 0, C: int = 0) → None

Compute the drift for the given Z and C as references

Parameters:

• Z – the reference z-layer

• C – the reference channel

class pydetecdiv.app.gui.ActionsData.ComputeDrift(parent: QWidget)

Bases: QAction

Action to compute drift correction

enable(project_name: str) → None

Enable or disable this action in the Data menu whether there are raw data or not.

Parameters:

project_name – the name of the project

open_dialog() → None

Open the Compute-drift dialog window

class pydetecdiv.app.gui.ActionsData.ApplyDrift(parent: QWidget)

Bases: QAction

Action to set or unset drift correction

enable(project_name: str)

Enable or disable this action in the Data menu whether there are raw data or not.

Parameters:

project_name – the name of the project

pydetecdiv.app.gui.RawData2FOV

Dialog window handling the definition of patterns for FOV creation from raw data file names

class pydetecdiv.app.gui.RawData2FOV.RawData2FOV

Bases: QDialog, Ui_RawData2FOV

A class extending the QDialog and the Ui_RawData2FOV classes. Ui_RawData2FOV was created using QTDesigner

reset() → None

Reset the form with default patterns and colours

get_regex() → dict[str, str]

Build the complete regular expression from the individual patterns

Returns:

the regular expression string

change_sample_style() → None

Change the colours of file name samples showing the pattern matches.

static find_matches(urls: list[str], regexes: dict[str, str]) → dict[str, list[Match]]

Find a list of matches with the defined regular expressions

Parameters:

• urls

• regexes – the list of regular expressions to match

Returns:

a list of matches

static get_match_spans(matches: dict[str, list[Match]], group: int) → dict[str, list[tuple[int, int]]]

Get the list of group positions for matches

Parameters:

• matches – the list of matches

• group – the group index to retrieve the spans for

Returns:

a dictionary of spans for the patterns (FOV, C, T, Z)

static get_match_span(match, group: int = 2) → tuple[int, int] | None

Get the span of a given group in a match

Parameters:

• match – the match

• group – the group index

Returns:

the group match span

colourize_matches(matches: dict[str, list[Match]]) → None

Find matches in file name samples and colourize them accordingly. Non-matching pattern check boxes’ background is set to orange. Conflicting patterns (having overlapping matches) are shown in red.

Parameters:

matches – the list of matches to colourize

static overlap(start1: int | None, end1: int | None, start2: int | None, end2: int | None) → bool

Checks whether positions overlap

Parameters:

• start1 – start of first span

• end1 – end of first span

• start2 – start of second span

• end2 – end of second span

Returns:

True if spans overlap, False otherwise

colourize_labels(pattern: str, colour: QColor) → None

Colourize the file name samples matching the pattern with the specified colour

Parameters:

• pattern – the pattern

• colour – the colour

clear_colours() → None

Clear colours to avoid overlapping style sheets

choose_colour(object_name: str) → None

Choose colour for a given pattern specified by its object name

Parameters:

object_name – the object name

show_chosen_colours() → None

Show the chosen colour in the little square box on the right and the border of the pattern.

button_clicked(button: QPushButton)

React to clicked button

Parameters:

button – the button that was clicked

create_fov_annotate(regex: str) → None

The actual FOV creation and data annotation method

Parameters:

regex – the regular expression to use for data annotation