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cellects.gui.cellects

cellects.gui.cellects

Main window for Cellects application managing stacked workflow steps.

This module implements a user-assisted image analysis workflow using a QStackedWidget to navigate between configuration and analysis phases. It provides windows for data setup, image/video processing, output requirements, and advanced parameters. Automatic algorithm suggestions are offered at each step while allowing full user customization. Uses SaveAllVarsThread in background operations to maintain UI responsiveness.

Main Components CellectsMainWidget : Central stacked widget managing workflow navigation

Notes Uses QThread for background operations to maintain UI responsiveness.

CellectsMainWidget

Bases: QStackedWidget

Main widget: this is the main window of the Cellects application.

Source code in src/cellects/gui/cellects.py 
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class CellectsMainWidget(QtWidgets.QStackedWidget):
    """ Main widget: this is the main window of the Cellects application. """

    def __init__(self):
        """

        Initializes the Cellects application window and sets up initial state.

        Sets the title, dimensions, and default values for various attributes
        required to manage the GUI's state and display settings.
        Initializes a ProgramOrganizer object and loads its variable dictionary.

        Attributes
        ----------
        pre_processing_done : bool
            Indicates whether pre-processing has been completed.
        last_is_first : bool
            Tracks if the last operation was the first in sequence.
        last_tab : str
            The most recently accessed tab name (default: "data_specifications").
        screen_height : int
            Height of the monitor in pixels.
        screen_width : int
            Width of the monitor in pixels.
        im_max_width : int
            Maximum width allowed for displayed images (default: 570).
        im_max_height : int
            Maximum height allowed for displayed images (default: 266).
        image_window_width_diff : int
            Difference in width between image window and max image size.
        image_window_height_diff : int
            Difference in height between image window and max image size.
        image_to_display : ndarray
            Placeholder for the image to be displayed (initialized as zeros).
        i : int
            Counter or index used in the application.
        po : ProgramOrganizer
            Instance managing the organization and variables of the program.
        """
        super().__init__()

        self.setWindowTitle('Cellects')
        self.thread_dict = {}
        self.thread_dict['PrecompileNJIT'] = PrecompileNJITThread()
        self.thread_dict['PrecompileNJIT'].start()
        self.pre_processing_done: bool = False
        self.last_is_first: bool = True
        self.last_tab: str = "data_specifications"
        self.pre_processing_done: bool = False
        self.screen_height = get_monitors()[0].height
        self.screen_width = get_monitors()[0].width
        self.im_max_width = 570
        self.im_max_height = 266
        self.image_window_width_diff = 1380 - 570
        self.image_window_height_diff = 750 - 266
        self.image_to_display = np.zeros((self.im_max_height, self.im_max_width, 3), np.uint8)
        self.i = 1
        self.po = ProgramOrganizer()
        self.po.load_variable_dict()
        self.resize(1380, 750)

    def instantiate_cellects(self):
        """
        Initiates the Cellects application by setting up the main window and starting various threads.

        Extended Description
        ---------------------
        This method is responsible for initializing the Cellects application. It sets up the main window, creates necessary widgets, and starts the required threads for background operations.

        Other Parameters
        ----------------
        night_mode : bool, optional
            Indicates whether the application should run in night mode. This parameter is managed by another part of
            the code and should not be set directly.
        """
        logging.info("Instantiate Cellects")
        self.firstwindow = FirstWindow(
            self,
            night_mode=self.po.all['night_mode'])
        self.insertWidget(0, self.firstwindow)

        self.instantiate_widgets()

        self.thread_dict['SaveAllVars'] = SaveAllVarsThread(self)
        self.change_widget(0)
        self.center()

    def instantiate_widgets(self, several_folder_included: bool=True):
        """
        Instantiate various windows for the application's GUI.

        This function configures the main GUI windows for image and video analysis,
        output requirements, and advanced parameters.

        Parameters
        ----------
        several_folder_included: bool, optional
            A flag to determine whether the `IfSeveralFoldersWindow` should be instantiated. Default is `True`.
        """
        logging.info("Other widgets are instantiating")
        if several_folder_included:
            self.ifseveralfolderswindow = IfSeveralFoldersWindow(self, night_mode=self.po.all['night_mode'])
            self.insertWidget(1, self.ifseveralfolderswindow)
        self.imageanalysiswindow = ImageAnalysisWindow(self, night_mode=self.po.all['night_mode'])
        self.insertWidget(2, self.imageanalysiswindow)

        self.videoanalysiswindow = VideoAnalysisWindow(self, night_mode=self.po.all['night_mode'])
        self.insertWidget(3, self.videoanalysiswindow)

        self.requiredoutputwindow = RequiredOutput(self, night_mode=self.po.all['night_mode'])
        self.insertWidget(4, self.requiredoutputwindow)

        self.advancedparameterswindow = AdvancedParameters(self, night_mode=self.po.all['night_mode'])
        self.insertWidget(5, self.advancedparameterswindow)


    def update_widget(self, idx: int, widget_to_call):
        """ Update widget at its position (idx) in the stack """
        self.insertWidget(idx, widget_to_call)

    def change_widget(self, idx: int):
        """ Display a widget using its position (idx) in the stack """
        self.setCurrentIndex(idx)  # Index that new widget
        self.updateGeometry()
        self.currentWidget().setVisible(True)
        if idx == 3 or idx == 5:
            self.currentWidget().display_conditionally_visible_widgets()

    def center(self):
        """
        Centers the window on the screen.

        Moves the window to the center of the available screen geometry.
        Allows users to always see the application's windows in a consistent
        position, regardless of screen resolution or window size.
        """
        qr = self.frameGeometry()
        # cp = QtWidgets.QDesktopWidget().availableGeometry().center()  # PyQt 5
        cp = QtGui.QGuiApplication.primaryScreen().availableGeometry().center()  # Pyside 6
        qr.moveCenter(cp)
        self.move(qr.topLeft())

    def closeEvent(self, event):
        """
        Close the application window and handle cleanup.

        Parameters
        ----------
        event : QCloseEvent
            The close event that triggered this function.

        Notes
        -----
        This function does not return any value and is intended for event
        handling purposes only.
        """
        reply = QtWidgets.QMessageBox.question(
            self,
            'Closing Cellects',
            'Are you sure you want to exit?',
            QtWidgets.QMessageBox.Yes | QtWidgets.QMessageBox.No,
            QtWidgets.QMessageBox.No)

        if reply == QtWidgets.QMessageBox.Yes:
            logging.info("Interrupting all threads.")
            if self.count() >= 6:
                windows = [self.thread_dict.items(), self.imageanalysiswindow.thread_dict.items(),
                           self.ifseveralfolderswindow.thread_dict.items(),
                           self.videoanalysiswindow.thread_dict.items(), self.firstwindow.thread_dict.items()]
                for window in windows:
                    for thread_name, thread in window:
                        thread.requestInterruption()
                        thread.wait(15000)
            logging.info("Closing main window.")
            event.accept()
        else:
            event.ignore()

__init__()

Initializes the Cellects application window and sets up initial state.

Sets the title, dimensions, and default values for various attributes required to manage the GUI's state and display settings. Initializes a ProgramOrganizer object and loads its variable dictionary.

Attributes:

Name Type Description
pre_processing_done bool

Indicates whether pre-processing has been completed.
last_is_first bool

Tracks if the last operation was the first in sequence.
last_tab str

The most recently accessed tab name (default: "data_specifications").
screen_height int

Height of the monitor in pixels.
screen_width int

Width of the monitor in pixels.
im_max_width int

Maximum width allowed for displayed images (default: 570).
im_max_height int

Maximum height allowed for displayed images (default: 266).
image_window_width_diff int

Difference in width between image window and max image size.
image_window_height_diff int

Difference in height between image window and max image size.
image_to_display ndarray

Placeholder for the image to be displayed (initialized as zeros).
i int

Counter or index used in the application.
po ProgramOrganizer

Instance managing the organization and variables of the program.
Source code in src/cellects/gui/cellects.py 
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def __init__(self):
    """

    Initializes the Cellects application window and sets up initial state.

    Sets the title, dimensions, and default values for various attributes
    required to manage the GUI's state and display settings.
    Initializes a ProgramOrganizer object and loads its variable dictionary.

    Attributes
    ----------
    pre_processing_done : bool
        Indicates whether pre-processing has been completed.
    last_is_first : bool
        Tracks if the last operation was the first in sequence.
    last_tab : str
        The most recently accessed tab name (default: "data_specifications").
    screen_height : int
        Height of the monitor in pixels.
    screen_width : int
        Width of the monitor in pixels.
    im_max_width : int
        Maximum width allowed for displayed images (default: 570).
    im_max_height : int
        Maximum height allowed for displayed images (default: 266).
    image_window_width_diff : int
        Difference in width between image window and max image size.
    image_window_height_diff : int
        Difference in height between image window and max image size.
    image_to_display : ndarray
        Placeholder for the image to be displayed (initialized as zeros).
    i : int
        Counter or index used in the application.
    po : ProgramOrganizer
        Instance managing the organization and variables of the program.
    """
    super().__init__()

    self.setWindowTitle('Cellects')
    self.thread_dict = {}
    self.thread_dict['PrecompileNJIT'] = PrecompileNJITThread()
    self.thread_dict['PrecompileNJIT'].start()
    self.pre_processing_done: bool = False
    self.last_is_first: bool = True
    self.last_tab: str = "data_specifications"
    self.pre_processing_done: bool = False
    self.screen_height = get_monitors()[0].height
    self.screen_width = get_monitors()[0].width
    self.im_max_width = 570
    self.im_max_height = 266
    self.image_window_width_diff = 1380 - 570
    self.image_window_height_diff = 750 - 266
    self.image_to_display = np.zeros((self.im_max_height, self.im_max_width, 3), np.uint8)
    self.i = 1
    self.po = ProgramOrganizer()
    self.po.load_variable_dict()
    self.resize(1380, 750)

center()

Centers the window on the screen.

Moves the window to the center of the available screen geometry. Allows users to always see the application's windows in a consistent position, regardless of screen resolution or window size.

Source code in src/cellects/gui/cellects.py 
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def center(self):
    """
    Centers the window on the screen.

    Moves the window to the center of the available screen geometry.
    Allows users to always see the application's windows in a consistent
    position, regardless of screen resolution or window size.
    """
    qr = self.frameGeometry()
    # cp = QtWidgets.QDesktopWidget().availableGeometry().center()  # PyQt 5
    cp = QtGui.QGuiApplication.primaryScreen().availableGeometry().center()  # Pyside 6
    qr.moveCenter(cp)
    self.move(qr.topLeft())

change_widget(idx)

Display a widget using its position (idx) in the stack

Source code in src/cellects/gui/cellects.py 
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def change_widget(self, idx: int):
    """ Display a widget using its position (idx) in the stack """
    self.setCurrentIndex(idx)  # Index that new widget
    self.updateGeometry()
    self.currentWidget().setVisible(True)
    if idx == 3 or idx == 5:
        self.currentWidget().display_conditionally_visible_widgets()

closeEvent(event)

Close the application window and handle cleanup.

Parameters:

Name Type Description Default
event QCloseEvent

The close event that triggered this function.

 required
Notes

This function does not return any value and is intended for event handling purposes only.

Source code in src/cellects/gui/cellects.py 
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def closeEvent(self, event):
    """
    Close the application window and handle cleanup.

    Parameters
    ----------
    event : QCloseEvent
        The close event that triggered this function.

    Notes
    -----
    This function does not return any value and is intended for event
    handling purposes only.
    """
    reply = QtWidgets.QMessageBox.question(
        self,
        'Closing Cellects',
        'Are you sure you want to exit?',
        QtWidgets.QMessageBox.Yes | QtWidgets.QMessageBox.No,
        QtWidgets.QMessageBox.No)

    if reply == QtWidgets.QMessageBox.Yes:
        logging.info("Interrupting all threads.")
        if self.count() >= 6:
            windows = [self.thread_dict.items(), self.imageanalysiswindow.thread_dict.items(),
                       self.ifseveralfolderswindow.thread_dict.items(),
                       self.videoanalysiswindow.thread_dict.items(), self.firstwindow.thread_dict.items()]
            for window in windows:
                for thread_name, thread in window:
                    thread.requestInterruption()
                    thread.wait(15000)
        logging.info("Closing main window.")
        event.accept()
    else:
        event.ignore()

instantiate_cellects()

Initiates the Cellects application by setting up the main window and starting various threads.

Extended Description

This method is responsible for initializing the Cellects application. It sets up the main window, creates necessary widgets, and starts the required threads for background operations.

Other Parameters:

Name Type Description
night_mode bool

Indicates whether the application should run in night mode. This parameter is managed by another part of the code and should not be set directly.
Source code in src/cellects/gui/cellects.py 
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def instantiate_cellects(self):
    """
    Initiates the Cellects application by setting up the main window and starting various threads.

    Extended Description
    ---------------------
    This method is responsible for initializing the Cellects application. It sets up the main window, creates necessary widgets, and starts the required threads for background operations.

    Other Parameters
    ----------------
    night_mode : bool, optional
        Indicates whether the application should run in night mode. This parameter is managed by another part of
        the code and should not be set directly.
    """
    logging.info("Instantiate Cellects")
    self.firstwindow = FirstWindow(
        self,
        night_mode=self.po.all['night_mode'])
    self.insertWidget(0, self.firstwindow)

    self.instantiate_widgets()

    self.thread_dict['SaveAllVars'] = SaveAllVarsThread(self)
    self.change_widget(0)
    self.center()

instantiate_widgets(several_folder_included=True)

Instantiate various windows for the application's GUI.

This function configures the main GUI windows for image and video analysis, output requirements, and advanced parameters.

Parameters:

Name Type Description Default
several_folder_included bool

A flag to determine whether the IfSeveralFoldersWindow should be instantiated. Default is True.

 True
Source code in src/cellects/gui/cellects.py 
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def instantiate_widgets(self, several_folder_included: bool=True):
    """
    Instantiate various windows for the application's GUI.

    This function configures the main GUI windows for image and video analysis,
    output requirements, and advanced parameters.

    Parameters
    ----------
    several_folder_included: bool, optional
        A flag to determine whether the `IfSeveralFoldersWindow` should be instantiated. Default is `True`.
    """
    logging.info("Other widgets are instantiating")
    if several_folder_included:
        self.ifseveralfolderswindow = IfSeveralFoldersWindow(self, night_mode=self.po.all['night_mode'])
        self.insertWidget(1, self.ifseveralfolderswindow)
    self.imageanalysiswindow = ImageAnalysisWindow(self, night_mode=self.po.all['night_mode'])
    self.insertWidget(2, self.imageanalysiswindow)

    self.videoanalysiswindow = VideoAnalysisWindow(self, night_mode=self.po.all['night_mode'])
    self.insertWidget(3, self.videoanalysiswindow)

    self.requiredoutputwindow = RequiredOutput(self, night_mode=self.po.all['night_mode'])
    self.insertWidget(4, self.requiredoutputwindow)

    self.advancedparameterswindow = AdvancedParameters(self, night_mode=self.po.all['night_mode'])
    self.insertWidget(5, self.advancedparameterswindow)

update_widget(idx, widget_to_call)

Update widget at its position (idx) in the stack

Source code in src/cellects/gui/cellects.py 
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def update_widget(self, idx: int, widget_to_call):
    """ Update widget at its position (idx) in the stack """
    self.insertWidget(idx, widget_to_call)