Code#

Module : mainwindow#

This module contains the main window of the application.

The code uses PySide6 to create the GUI. Each widget and layout in the code are structured using a with blocks structure to ensure clean code and proper memory management.

class mainwindow.Window#

Window Class

This class represents the main application window for STEM EDX ML. It manages the user interface, signals, and interactions with the objects and graphs.

Attributes#

keystr: A default key identifier for object selection.
objectsObjectsManager: Manages the objects within the application. (Objects designed STEM-EDX data or results from decomposition algorithms).
signalsdict: A dictionary storing different signal instances for UI updates.
graphslist: A list storing references to currently added graphs. (Graphs designed the plots from decomposition results).
selected_objectobject: Keeps track of the currently selected object in the tree view.

Methods#

__onLoadFileClicked():: Opens a file dialog to load a .pts file and adds it to the object manager.
__onAddGraphClicked():: Handles the addition of graphs based on selected objects in the tree widget.
__onSelectObjectChanged():: Updates the displayed image based on the selected object and colourscale.
__onPCAClicked():: Applies the PCA algorithm on selected objects and displays progress.
__onNMFClicked():: Applies the NMF algorithm on selected objects and displays progress.
__onImageTitleChanged(title):: Updates the image title based on user input.

class SignalManager#

Signal Manager Class

s : Signal - A signal that transmits three object parameters.

Module : stem#

This module contains the functions to manage STEM-EDX data. It includes functions to load data, apply decomposition algorithms (PCA, NMF), and visualize results.

class stem.Decomposition(data, method='svd', n_components=3, normalize_poissonian_noise=True, parent_object=None)#

next_component()#

save_plot(path)#

Save the plot of factors and loadings to a specified file path.

Parameters#

pathstr: The file path where the plot will be saved.

Notes#

This function creates a figure with two subplots: one for the factors and one for the loadings. The factors plot displays the intensity as a function of energy (in keV), and the loadings plot displays the loadings data as an image. The figure is saved as a transparent image file at the specified path.

class stem.STEM_EDX_DATA(path, data=None, name='STEM_EDX_Object', signal_type='EDS_TEM', rebin_energy=1)#

apply_NMF(n_components=3)#

Apply Non-negative Matrix Factorisation (NMF) to the data. This method applies NMF to the data stored in the instance. It checks if the NMF has already been applied with the same parameters and skips the computation if so. If the NMF is successful, it stores the result in self.sub_items.

Returns#

str: ‘Success’ if NMF is applied successfully, ‘Failed’ otherwise.

apply_PCA()#

Apply Principal Component Analysis (PCA) to the data. This method applies PCA using Singular Value Decomposition (SVD) with a specified number of components and an option to normalise Poissonian noise. If the decomposition has already been applied, it will not be re-applied.

Returns#

str: ‘Success’ if PCA was successfully applied, ‘Failed’ otherwise.

rebin(factor=(2, 2, 1))#

Rebin the data

Parameters#

factortuple, optional: Rebin (x, y, Energy) axes, by default (2, 2, 1)

Module : utils#

This module contains utility functions used in the application. In particular, PySide6 widgets were updated to be more suitable for mainwindow code structure.

class utils.CustomToolbar(canvas, parent=None)#

A custom toolbar for a matplotlib canvas, removing unwanted buttons and adding a spin box for selecting components.

Parameters#

canvasFigureCanvas: The matplotlib canvas to which this toolbar is attached.
parentQWidget, optional: The parent widget of this toolbar (default is None).

Methods#

handle_component(value): Handles the change in selected component and updates the display.

handle_component(value)#

Handles the selection of a component and updates the current widget.

Parameters#

valueAny: The value representing the selected component.

class utils.ObjectsManager(parent)#

A manager for handling objects with unique names.

Attributes#

objectsdict: A dictionary storing objects with their names as keys.
idint: An identifier for the number of objects added.

Methods#

__getitem__(key): Retrieves an object by its name.
add_object(obj): Adds a new object to the manager.

add_object(obj)#

Adds an object to the collection.

Parameters#

objobject: The object to be added. It must have a ‘name’ attribute.

Returns#

object: The added object.

Raises#

ValueError: If an object with the same name already exists in the collection.

class utils.Worker(objects, selected_objects, action, n_components=3)#

A QThread subclass that performs actions on selected objects and emits progress signals.

Parameters#

objectsdict: A dictionary of objects on which actions will be performed.
selected_objectslist: A list of object names to be processed.
actionstr: The action to be performed on the selected objects. Supported actions are ‘PCA’ and ‘NMF’.

Attributes#

progressSignal: Signal emitted to indicate progress as an integer percentage.
errorslist: A list of object names for which the action failed.

Methods#

run(): Executes the specified action on the selected objects and emits progress signals.

run()#

Executes the specified action (‘PCA’ or ‘NMF’) on selected objects and updates the progress.

The function iterates over the selected objects and applies the specified action (‘PCA’ or ‘NMF’) to each object.
Progress is emitted as a percentage after processing each object.
If the action fails for any object, the object’s name is appended to the errors list.

utils.show_message(title, message, type='error')#

Displays a message box with a specified title, message, and type.

Parameters#

titlestr: The title of the message box.
messagestr: The content of the message to be displayed.
typestr, optional: The type of the message box, either ‘error’ or ‘information’. Modifies the icon displayed. Default is ‘error’.

Returns#

None

class utils.x_GraphTabWidget(key, parent, parent_object, child_object)#

A custom QWidget for displaying graph tabs with factors and loadings plots.

Parameters#

keystr: A unique identifier for the widget.
parentQWidget: The parent widget.
parent_objectobject: An object containing the data and settings for the plots.
child_objectobject: An object containing the selected component and its data.

Attributes#

keystr: A unique identifier for the widget.
parentQWidget: The parent widget.
parent_objectobject: An object containing the data and settings for the plots.
child_objectobject: An object containing the selected component and its data.
layoutQVBoxLayout: The layout manager for the widget.
xlist: The x-axis values for the factors plot.
figFigure: The matplotlib figure object.
factors_plotAxes: The axes for the factors plot.
loadings_plotAxes: The axes for the loadings plot.
canvasFigureCanvas: The canvas for rendering the matplotlib figure.
toolbarCustomToolbar: The custom toolbar for the canvas.

Methods#

update(): Updates the plots with the current data.

update()#: Updates the plots for factors and loadings based on the selected component. This method clears the current plots and updates them with the data from the selected component of the child object. It sets the x-axis limits, labels, titles, and grid for the factors plot, and sets the title for the loadings plot. It also adjusts the layout and redraws the canvas.

class utils.x_QComboBox(parent, name, objects, signals, signal='', tooltip='', label='')#

A custom QComboBox widget with additional functionality for handling signals and updating items dynamically.

Parameters#

parentQWidget: The parent widget.
namestr: The name of the combobox.
objectsobject: An object containing the items to be added to the combobox.
signalsdict: A dictionary of signals for the combobox.
signalstr, optional: The signal key for updating the combobox (default is ‘’).
tooltipstr, optional: The tooltip text for the combobox (default is ‘’).
labelstr, optional: The label text to be displayed next to the combobox (default is ‘’).

Attributes#

parentQWidget: The parent widget.
namestr: The name of the combobox.
keystr: A unique key for the combobox.
objectsobject: An object containing the items to be added to the combobox.
signalsdict: A dictionary of signals for the combobox.
signalpyqtSignal: The signal for updating the combobox.
layoutQHBoxLayout: The layout containing the combobox and optional label.
comboboxQComboBox: The combobox widget.

Methods#

update(items): Updates the items in the combobox while preserving the current index.

update(items)#

Updates the items in the combobox while preserving the current index.

Parameters#

itemslist of str: A list of new items to be added to the combobox.

class utils.x_QHBoxLayout(parent, name)#

A custom QHBoxLayout class that supports context management and automatic key generation.

Parameters#

parentQWidget or QLayout: The parent widget or layout.
namestr: The name to be appended to the parent’s key or used as the key.

Attributes#

parentQWidget or QLayout: The parent widget or layout.
keystr: The generated key based on the parent’s key and the provided name.

Methods#

__enter__(): Sets the layout for the parent widget or adds the layout to the parent layout.
__exit__(*args): Placeholder for context management exit.

class utils.x_QImage_Label(parent, signals, signal='', coord_label=None, title_input=None)#

A custom QLabel widget for displaying and interacting with images.

Parameters#

parentQWidget: The parent widget.
signalsdict: A dictionary of signals for communication.
signalstr, optional: The signal key for updating the combobox (default is ‘’).
coord_labelQLabel, optional: A label for displaying coordinates (default is None).
title_inputQLineEdit, optional: An input for the title (default is None).

Attributes#

parentQWidget: The parent widget.
layoutQHBoxLayout: The layout for the widget.
coord_labelQLabel: A label for displaying coordinates.
title_inputQLineEdit: An input for the title.
titlestr: The title of the image.
pixmapQPixmap: The pixmap of the image.
imagendarray: The image data.
pixmap_offsettuple: The offset of the pixmap.
pixel_sizeint: The size of each pixel.
min_img_xfloat: The minimum x-coordinate of the image.
min_img_yfloat: The minimum y-coordinate of the image.
max_img_xfloat: The maximum x-coordinate of the image.
max_img_yfloat: The maximum y-coordinate of the image.
signalsdict: A dictionary of signals for communication.
signalpyqtSignal: The signal for updating the image.

Methods#

update(image, colorscale=’Greyscale’): Updates the displayed image with the given colourscale.
set_pixmap_params(image, offset, pixel_size, min_img_x, min_img_y, max_img_x, max_img_y): Sets the parameters for the pixmap.
mousePressEvent(event): Handles mouse press events.
mouseMoveEvent(event): Handles mouse move events.
enterEvent(event): Handles the cursor when entering the widget.
leaveEvent(event): Handles the cursor when leaving the widget.

enterEvent(event)#: Handles the event when the cursor enters the specific area.

leaveEvent(event)#: Handles the event when the cursor leaves the specific area.

mouseMoveEvent(event: QMouseEvent)#

Handle the mouse move event to update the coordinate label with the current mouse position and corresponding image value.

Parameters#

eventQMouseEvent: The mouse event containing the current position of the mouse cursor.

set_pixmap_params(image, offset, pixel_size, min_img_x, min_img_y, max_img_x, max_img_y)#

Set parameters for the pixmap.

Parameters#

imageQImage: The image to be used for the pixmap.
offsetQPoint: The offset position of the pixmap.
pixel_sizeint: The size of each pixel in the pixmap.
min_img_xint: The minimum x-coordinate of the image.
min_img_yint: The minimum y-coordinate of the image.
max_img_xint: The maximum x-coordinate of the image.
max_img_yint: The maximum y-coordinate of the image.

update(image, colorscale='Greyscale')#

Update the display with a new image and apply a colourscale.

Parameters#

imagenumpy.ndarray or str: The image to be displayed. If a string is provided, the function returns without updating.
colorscalestr, optional: The colourscale to be applied to the image. Default is ‘Greyscale’.

class utils.x_QLabel(parent, label='', alignment=AlignmentFlag.AlignLeft)#

A custom QLabel wrapper class.

Parameters#

parentQWidget: The parent widget to which this label belongs.
labelstr, optional: The text to be displayed on the label (default is an empty string).
alignmentQt.Alignment, optional: The alignment of the label text (default is Qt.AlignLeft).

Attributes#

parentQWidget: The parent widget.
labelQLabel: The QLabel instance with the specified text and alignment.

Methods#

__init__(parent, label=’’, alignment=Qt.AlignLeft): Initialises the x_QLabel instance and adds it to the parent’s layout.

class utils.x_QLineEdit(parent, name, tooltip='', label='', placeholder='', default='')#

A custom QLineEdit widget with additional features.

Parameters#

parentQWidget: The parent widget.
namestr: The name of the QLineEdit widget.
tooltipstr, optional: The tooltip text for the QLineEdit widget (default is ‘’).
labelstr, optional: The label text to be displayed alongside the QLineEdit widget (default is ‘’).
placeholderstr, optional: The placeholder text for the QLineEdit widget (default is ‘’).
defaultstr, optional: The default text for the QLineEdit widget (default is ‘’).

Attributes#

parentQWidget: The parent widget.
namestr: The name of the QLineEdit widget.
keystr: A unique key generated by combining the parent’s key and the name.
layoutQHBoxLayout: The layout containing the QLineEdit and optional QLabel.
line_editQLineEdit: The QLineEdit widget.

class utils.x_QPushButton(parent, name, objects, tooltip='', label='')#

A custom QPushButton class that integrates with a parent layout and allows for additional configuration such as tooltips and labels.

Parameters#

parentQWidget: The parent widget to which this button belongs.
namestr: The name of the button.
objectslist: A list of objects associated with this button.
tooltipstr, optional: The tooltip text for the button (default is an empty string).
labelstr, optional: The label text to be displayed alongside the button (default is an empty string).

Attributes#

parentQWidget: The parent widget.
namestr: The name of the button.
keystr: A unique key generated by combining the parent’s key and the button’s name.
objectslist: A list of objects associated with this button.
layoutQHBoxLayout: The horizontal box layout that contains the button and its label.
buttonQPushButton: The QPushButton instance created by this class.

class utils.x_QSeparator(window, parent, orientation='H')#

A custom QFrame separator widget. Parameters ———- window : QWidget

The parent window for the separator.

parentQBoxLayout: The layout to which the separator will be added.
orientationstr, optional: The orientation of the separator, either ‘H’ for horizontal or ‘V’ for vertical. Default is ‘H’.

Methods#

__init__(window, parent, orientation=’H’): Initializes the separator with the given orientation and adds it to the parent layout.

class utils.x_QTab(parent, name)#

A custom QWidget class for creating a tab with a specific name and parent.

Parameters#

parentQWidget: The parent widget to which this tab belongs.
namestr: The name of the tab.

Attributes#

namestr: The name of the tab.
parentQWidget: The parent widget to which this tab belongs.
keystr: A unique key for the tab, derived from the parent’s key and the tab’s name.
layoutQVBoxLayout: The layout manager for the tab, aligned to the top.

Methods#

__enter__(): Adds the tab to the parent widget.
__exit__(*args): Placeholder for context manager exit, does nothing.

class utils.x_QTabWidget(parent, name, movable=False, closable=False)#

A custom QTabWidget with additional functionality.

Parameters#

parentQWidget: The parent widget.
namestr: The name of the tab widget.
movablebool, optional: If True, tabs can be moved by the user (default is False).
closablebool, optional: If True, tabs can be closed by the user (default is False).

Attributes#

namestr: The name of the tab widget.
parentQWidget: The parent widget.
keystr: A unique key for the tab widget, combining the parent’s key and name.

Methods#

__enter__(): Adds the widget to the parent when used in a context manager.
__exit__(*args): Placeholder for context manager exit, does nothing.

class utils.x_QTreeWidget(parent, name, objects, signals, window, columns=1, headers=['Column'])#

A custom QTreeWidget class for managing and displaying hierarchical data.

Parameters#

parentQWidget: The parent widget.
namestr: The name of the tree widget.
objectsobject: The object containing the data to be displayed.
signalsdict: A dictionary of signals for communication.
windowQMainWindow: The main window, used for displaying message boxes.
columnsint, optional: The number of columns in the tree widget (default is 1).
headerslist of str, optional: The headers for the columns (default is [‘Column’]).

Methods#

__enter__(): Enter the runtime context related to this object.
__exit__(*args): Exit the runtime context related to this object.
update(): Update the tree widget with the current data.
__context_menu(position): Display a context menu at the given position.

update()#: Update the tree widget with the current objects and their sub-items. Clears the existing tree and repopulates it with the objects and their respective sub-items. Each item is made checkable and enabled. Emits a signal after updating the tree.

class utils.x_QVBoxLayout(parent, name, ratio=1)#

A custom QVBoxLayout class that supports context management and layout ratio.

Parameters#

parentQWidget or QLayout: The parent widget or layout to which this layout will be added.
namestr: A unique name for this layout, used to generate a key.
ratioint, optional: The ratio for adding this layout to its parent, by default 1.

Attributes#

parentQWidget or QLayout: The parent widget or layout.
ratioint: The ratio for adding this layout to its parent.
keystr: A unique key generated from the parent’s key and the provided name.

Methods#

__enter__(): Sets the layout for the parent widget or adds it to the parent layout.
__exit__(*args): Placeholder for context management exit, does nothing.

Module : colorscales#

This module contains the color scales used in the application. The color scales are used to represent the datacube in the top right layout.

colorscales.Greyscale(N)#

colorscales.Hot(N)#

colorscales.Inferno(N)#

colorscales.Jet(N)#

colorscales.Plasma(N)#

colorscales.Viridis(N)#

Table of Contents

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Module : mainwindow#

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Module : stem#

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Module : utils#

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Module : colorscales#