Module Widefield-Imaging-Acquisition.gui.scout

Classes

class App

QWidget(parent: QWidget = None, flags: Union[Qt.WindowFlags, Qt.WindowType] = Qt.WindowFlags())

Initialize the application

Expand source code

class App(QWidget):
    def __init__(self):
        """Initialize the application"""
        super().__init__()
        self.cwd = os.path.dirname(os.path.dirname(__file__))
        self.roi_extent = None
        self.image_index = 0
        self.previous_index = 0
        self.files_to_read = True
        self.live_preview_light_index = 0

        self.initUI()

    def closeEvent(self, *args, **kwargs):
        """Stop all processes when closing the application"""
        self.files_to_read = False

    def initUI(self):
        """Initialize the user interface"""
        self.setWindowTitle("Brain Scout")
        self.setGeometry(10, 10, 640, 480)
        self.grid_layout = QGridLayout()
        self.grid_layout.setAlignment(Qt.AlignLeft)
        self.grid_layout.setAlignment(Qt.AlignTop)
        # self.grid_layout.setContentsMargins(0, 0, 0, 0)
        self.setLayout(self.grid_layout)

        self.settings_window = QVBoxLayout()
        self.settings_window.setAlignment(Qt.AlignLeft)
        self.settings_window.setAlignment(Qt.AlignTop)
        self.grid_layout.addLayout(self.settings_window, 0, 0)

        self.settings_window2 = QVBoxLayout()
        self.settings_window2.setAlignment(Qt.AlignLeft)
        self.settings_window2.setAlignment(Qt.AlignTop)
        self.grid_layout.addLayout(self.settings_window2, 0, 1)

        # ----
        self.directory_window = QHBoxLayout()
        self.directory_window.setAlignment(Qt.AlignLeft)
        self.directory_window.setAlignment(Qt.AlignTop)
        self.choose_directory_button = QPushButton("Select Directory")
        self.choose_directory_button.setIcon(
            QIcon(os.path.join(self.cwd, "gui", "icons", "folder-plus.png"))
        )
        self.choose_directory_button.clicked.connect(self.choose_directory)
        self.directory_window.addWidget(self.choose_directory_button)
        self.directory_cell = QLineEdit("")
        self.directory_cell.setReadOnly(True)
        self.directory_window.addWidget(self.directory_cell)

        self.settings_window.addLayout(self.directory_window)

        # ----
        self.light_channel_layout = QHBoxLayout()
        self.preview_light_label = QLabel("Light Channel Preview")
        self.light_channel_layout.addWidget(self.preview_light_label)
        self.preview_light_combo = QComboBox()
        self.preview_light_combo.setEnabled(False)
        self.preview_light_combo.currentIndexChanged.connect(
            self.change_preview_light_channel
        )
        self.light_channel_layout.addWidget(self.preview_light_combo)
        self.settings_window.addLayout(self.light_channel_layout)

        # self.import_window = QHBoxLayout()
        # self.import_progress = QLabel("0% Imported")
        # self.import_window.addWidget(self.import_progress)
        # self.settings_window.addLayout(self.import_window)

        # --

        # -------------

        self.index_window = QVBoxLayout()
        self.current_index_window = QHBoxLayout()
        self.current_index_label = QLabel("Current Index:")
        self.current_index_window.addWidget(self.current_index_label)
        self.current_index = QLineEdit("0")
        self.current_index.textChanged.connect(self.adjust_index)
        self.current_index_window.addWidget(self.current_index)
        self.index_window.addLayout(self.current_index_window)
        self.start_index_window = QHBoxLayout()
        self.start_index_label = QLabel("Start Index:")
        self.start_index_window.addWidget(self.start_index_label)
        self.start_index = QLineEdit("0")
        self.start_index_window.addWidget(self.start_index)
        self.index_window.addLayout(self.start_index_window)
        self.end_index_window = QHBoxLayout()
        self.end_index_label = QLabel("End Index:")
        self.end_index_window.addWidget(self.end_index_label)
        self.end_index = QLineEdit("0")
        self.end_index_window.addWidget(self.end_index)
        self.index_window.addLayout(self.end_index_window)
        self.settings_window2.addLayout(self.index_window)
        # self.settings_window.addStretch()

        self.make_time_course_button = QPushButton("Generate Time Course")
        self.make_time_course_button.setIcon(
            QIcon(os.path.join(self.cwd, "gui", "icons", "chart-line.png"))
        )
        self.make_time_course_button.clicked.connect(self.make_time_course)
        self.make_time_course_layout = QHBoxLayout()
        self.make_time_course_layout.setAlignment(Qt.AlignLeft)
        self.make_time_course_layout.setAlignment(Qt.AlignTop)
        self.make_time_course_layout.addWidget(self.make_time_course_button)
        self.make_time_course_container = QWidget()
        self.make_time_course_container.setLayout(self.make_time_course_layout)
        self.grid_layout.addWidget(self.make_time_course_container, 2, 1)

        # -------
        self.slider_layout = QHBoxLayout()
        self.slider_layout.setAlignment(Qt.AlignLeft)
        self.slider_layout.setAlignment(Qt.AlignTop)
        # self.slider_layout.setContentsMargins(0, 0, 0, 0)
        self.slider_layout.addWidget(QLabel("Start"))

        self.time_slider = QSlider(Qt.Horizontal, self)
        self.time_slider.setRange(0, 0)
        self.time_slider.setValue(0)
        self.time_slider.valueChanged.connect(self.adjust_time)
        self.slider_layout.addWidget(self.time_slider)
        self.slider_layout.addWidget(QLabel("End"))

        self.settings_window.addLayout(self.slider_layout)

        # -------------
        # self.graphics_layout =QHBoxLayout()

        # self.graphics_layout.addWidget(self.image_view)

        self.time_course = PlotWindow(subplots=False)
        self.time_course.plot([1, 2, 3], [1, 2, 3], root=False)
        self.grid_layout.addWidget(self.time_course, 1, 1)
        # self.grid_layout.addLayout(self.graphics_layout, 1, 0)

        # -------------
        self.show()

    def initialize_roi(self):
        self.roi_buttons = QStackedLayout()
        self.roi_buttons.setAlignment(Qt.AlignLeft)
        self.roi_buttons.setAlignment(Qt.AlignTop)
        # self.roi_buttons.setContentsMargins(0, 0, 0, 0)
        self.roi_layout1 = QHBoxLayout()
        self.roi_layout1.setAlignment(Qt.AlignLeft)
        self.roi_layout1.setAlignment(Qt.AlignTop)
        # self.roi_layout1.setContentsMargins(0, 0, 0, 0)
        self.reset_roi_button = QPushButton("Reset ROI")
        self.reset_roi_button.setIcon(
            QIcon(os.path.join(self.cwd, "gui", "icons", "zoom-out-area.png"))
        )
        self.reset_roi_button.setEnabled(False)
        self.reset_roi_button.clicked.connect(self.reset_roi)
        self.roi_layout1.addWidget(self.reset_roi_button)

        self.set_roi_button = QPushButton("Set ROI")
        self.set_roi_button.setIcon(
            QIcon(os.path.join(self.cwd, "gui", "icons", "zoom-in-area.png"))
        )
        self.set_roi_button.clicked.connect(self.set_roi)
        self.roi_layout1.addWidget(self.set_roi_button)

        self.roi_layout1_container = QWidget()
        self.roi_layout1_container.setLayout(self.roi_layout1)

        self.roi_layout2 = QHBoxLayout()
        self.roi_layout2.setAlignment(Qt.AlignLeft)
        self.roi_layout2.setAlignment(Qt.AlignTop)
        # self.roi_layout2.setContentsMargins(0, 0, 0, 0)
        self.cancel_roi_button = QPushButton("Cancel")
        self.cancel_roi_button.setIcon(
            QIcon(os.path.join(self.cwd, "gui", "icons", "zoom-cancel.png"))
        )
        self.cancel_roi_button.clicked.connect(self.cancel_roi)
        self.roi_layout2.addWidget(self.cancel_roi_button)

        self.save_roi_button = QPushButton("Save ROI")
        self.save_roi_button.setIcon(
            QIcon(os.path.join(self.cwd, "gui", "icons", "zoom-check.png"))
        )
        self.save_roi_button.clicked.connect(self.save_roi)
        self.roi_layout2.addWidget(self.save_roi_button)
        self.roi_layout2_container = QWidget()
        self.roi_layout2_container.setLayout(self.roi_layout2)

        self.roi_buttons.addWidget(self.roi_layout1_container)
        self.roi_buttons.addWidget(self.roi_layout2_container)

        self.grid_layout.addLayout(self.roi_buttons, 2, 0)

    def change_preview_light_channel(self):
        """Change the light channel for the live preview"""
        self.live_preview_light_index = self.preview_light_combo.currentIndex()
        self.adjust_time()

    def actualize_lights(self):
        """Update the lights list in the combo box"""
        self.preview_light_combo.clear()
        if len(self.dictionary["Lights"]) == 0:
            self.preview_light_combo.setEnabled(False)
        else:
            self.preview_light_combo.setEnabled(True)
        for light in self.dictionary["Lights"]:
            self.preview_light_combo.addItem(light)
        self.preview_light_combo.setCurrentIndex(0)

    def choose_directory(self):
        """Choose the directory where to save the files"""
        self.directory = str(QFileDialog.getExistingDirectory(self, "Select Directory"))
        self.directory_cell.setText(self.directory)
        self.frames = []
        potential_dic = os.listdir(self.directory)
        for file in potential_dic:
            if ".json" in file:
                self.dictionary = get_dictionary(os.path.join(self.directory, file))
        self.dimensions = self.dictionary["Dimensions"]
        self.initialize_plot()
        self.initialize_roi()
        self.open_import_thread()

    def initialize_plot(self):
        try:
            self.image_view
        except Exception:
            self.image_view = PlotWindow()
            self.grid_layout.addWidget(self.image_view, 1, 0)
        self.plot_image = plt.imshow(
            np.zeros((self.dimensions[1], self.dimensions[0])),
            cmap="binary_r",
            vmin=0,
            vmax=4096,
            origin="lower",
        )
        self.plot_image.axes.get_xaxis().set_visible(False)
        self.plot_image.axes.axes.get_yaxis().set_visible(False)

    def open_import_thread(self):
        """Open the thread that will import the frames"""
        self.import_thread = Thread(target=self.import_frames)
        self.import_thread.start()

    def import_frames(self):
        try:
            self.frames = []
            self.time_slider.setEnabled(False)
            potential_data = os.listdir(os.path.join(self.directory, "data"))
            for file in potential_data:
                if ".npy" in file:
                    self.concatenate_frames(file)
            self.frame_number = self.frames.shape[0]
            self.split_frames = separate_images(self.dictionary["Lights"], self.frames)
            self.end_index.setText(f"{self.frame_number-1}")
            self.time_slider.setRange(0, self.frame_number - 1)
            self.time_slider.setEnabled(True)
            self.actualize_lights()
        except Exception as err:
            print(err)
            pass

    def concatenate_frames(self, file):
        """Concatenate the frames in the directory"""
        if len(self.frames) == 0:
            self.frames = np.load(os.path.join(self.directory, "data", file))
        else:
            self.frames = np.concatenate(
                (self.frames, np.load(os.path.join(self.directory, "data", file)))
            )

    def set_roi(self):
        """Set the ROI"""
        self.roi_buttons.setCurrentIndex(1)
        self.cancel_roi_button.setEnabled(True)
        self.save_roi_button.setEnabled(False)

        def onselect_function(eclick, erelease):
            """Save the ROI dimensions as attributes"""
            self.roi_extent = self.rect_selector.extents
            self.save_roi_button.setEnabled(True)

        self.rect_selector = RectangleSelector(
            self.plot_image.axes,
            onselect_function,
            drawtype="box",
            useblit=True,
            button=[1, 3],
            minspanx=5,
            minspany=5,
            spancoords="pixels",
            interactive=True,
        )

    def reset_roi(self):
        """Reset the ROI"""
        plt.figure(self.image_view.figure.number)
        plt.ion()
        plt.xlim(0, self.dimensions[0])
        plt.ylim(0, self.dimensions[1])
        self.roi_extent = None
        self.reset_roi_button.setEnabled(False)
        self.set_roi_button.setEnabled(True)
        self.reset_roi_button.setEnabled(False)

    def cancel_roi(self):
        """Cancel the ROI selection"""
        # self.activate_buttons(buttons=self.enabled_buttons)
        self.roi_buttons.setCurrentIndex(0)
        self.rect_selector.clear()
        self.rect_selector = None

    def save_roi(self):
        """Save the ROI"""
        # self.activate_buttons(buttons=self.enabled_buttons)
        self.roi_buttons.setCurrentIndex(0)
        plt.figure(self.image_view.figure.number)
        plt.ion()
        plt.xlim(self.roi_extent[0], self.roi_extent[1])
        plt.ylim(self.roi_extent[2], self.roi_extent[3])
        self.rect_selector.clear()
        self.rect_selector = None
        self.reset_roi_button.setEnabled(True)
        self.set_roi_button.setEnabled(True)

    def adjust_index(self):
        """Adjust the index"""
        try:
            self.time_slider.setValue(int(self.current_index.text()))
        except Exception:
            pass

    def adjust_time(self):
        plt.ion()
        try:
            self.image_index = self.time_slider.value()
            self.current_index.setText(str(self.image_index))
            self.open_live_preview_thread()
        except Exception as err:
            print(err)
            pass

    def open_live_preview_thread(self):
        """Open the thread that will show the live preview"""
        self.live_preview_thread = Thread(target=self.live_preview)
        self.live_preview_thread.start()

    def live_preview(self):
        self.plot_image.set(
            array=self.split_frames[self.live_preview_light_index][
                self.image_index // len(self.dictionary["Lights"])
            ]
        )

    def make_time_course(self):
        try:
            if self.roi_extent:
                print(
                    shrink_array(
                        self.split_frames[self.live_preview_light_index],
                        self.roi_extent,
                    )
                )
                y_values = get_timecourse(
                    shrink_array(
                        self.split_frames[self.live_preview_light_index],
                        self.roi_extent,
                    ),
                    int(self.start_index.text()) // len(self.dictionary["Lights"]),
                    int(self.end_index.text()) // len(self.dictionary["Lights"]),
                )
            else:
                y_values = get_timecourse(
                    self.split_frames[self.live_preview_light_index],
                    int(self.start_index.text()) // len(self.dictionary["Lights"]),
                    int(self.end_index.text()) // len(self.dictionary["Lights"]),
                )
            plt.figure(self.time_course.figure.number)
            plt.ion()
            plt.clf()
            plt.plot(y_values)
        except Exception as err:
            print(err)
            pass

    def activate_buttons(self, buttons):
        """Activate the buttons in a list"""
        for button in buttons:
            button.setEnabled(True)

    def deactivate_buttons(self, buttons):
        """Deactivate the buttons in a list"""
        for button in buttons:
            button.setDisabled(True)

Ancestors

• PyQt5.QtWidgets.QWidget
• PyQt5.QtCore.QObject
• sip.wrapper
• PyQt5.QtGui.QPaintDevice
• sip.simplewrapper

Methods

def activate_buttons(self, buttons)

Activate the buttons in a list

Expand source code

def activate_buttons(self, buttons):
    """Activate the buttons in a list"""
    for button in buttons:
        button.setEnabled(True)

def actualize_lights(self)

Update the lights list in the combo box

Expand source code

def actualize_lights(self):
    """Update the lights list in the combo box"""
    self.preview_light_combo.clear()
    if len(self.dictionary["Lights"]) == 0:
        self.preview_light_combo.setEnabled(False)
    else:
        self.preview_light_combo.setEnabled(True)
    for light in self.dictionary["Lights"]:
        self.preview_light_combo.addItem(light)
    self.preview_light_combo.setCurrentIndex(0)

def adjust_index(self)

Adjust the index

Expand source code

def adjust_index(self):
    """Adjust the index"""
    try:
        self.time_slider.setValue(int(self.current_index.text()))
    except Exception:
        pass

def adjust_time(self)

Expand source code

def adjust_time(self):
    plt.ion()
    try:
        self.image_index = self.time_slider.value()
        self.current_index.setText(str(self.image_index))
        self.open_live_preview_thread()
    except Exception as err:
        print(err)
        pass

def cancel_roi(self)

Cancel the ROI selection

Expand source code

def cancel_roi(self):
    """Cancel the ROI selection"""
    # self.activate_buttons(buttons=self.enabled_buttons)
    self.roi_buttons.setCurrentIndex(0)
    self.rect_selector.clear()
    self.rect_selector = None

def change_preview_light_channel(self)

Change the light channel for the live preview

Expand source code

def change_preview_light_channel(self):
    """Change the light channel for the live preview"""
    self.live_preview_light_index = self.preview_light_combo.currentIndex()
    self.adjust_time()

def choose_directory(self)

Choose the directory where to save the files

Expand source code

def choose_directory(self):
    """Choose the directory where to save the files"""
    self.directory = str(QFileDialog.getExistingDirectory(self, "Select Directory"))
    self.directory_cell.setText(self.directory)
    self.frames = []
    potential_dic = os.listdir(self.directory)
    for file in potential_dic:
        if ".json" in file:
            self.dictionary = get_dictionary(os.path.join(self.directory, file))
    self.dimensions = self.dictionary["Dimensions"]
    self.initialize_plot()
    self.initialize_roi()
    self.open_import_thread()

def closeEvent(self, *args, **kwargs)

Stop all processes when closing the application

Expand source code

def closeEvent(self, *args, **kwargs):
    """Stop all processes when closing the application"""
    self.files_to_read = False

def concatenate_frames(self, file)

Concatenate the frames in the directory

Expand source code

def concatenate_frames(self, file):
    """Concatenate the frames in the directory"""
    if len(self.frames) == 0:
        self.frames = np.load(os.path.join(self.directory, "data", file))
    else:
        self.frames = np.concatenate(
            (self.frames, np.load(os.path.join(self.directory, "data", file)))
        )

def deactivate_buttons(self, buttons)

Deactivate the buttons in a list

Expand source code

def deactivate_buttons(self, buttons):
    """Deactivate the buttons in a list"""
    for button in buttons:
        button.setDisabled(True)

def import_frames(self)

Expand source code

def import_frames(self):
    try:
        self.frames = []
        self.time_slider.setEnabled(False)
        potential_data = os.listdir(os.path.join(self.directory, "data"))
        for file in potential_data:
            if ".npy" in file:
                self.concatenate_frames(file)
        self.frame_number = self.frames.shape[0]
        self.split_frames = separate_images(self.dictionary["Lights"], self.frames)
        self.end_index.setText(f"{self.frame_number-1}")
        self.time_slider.setRange(0, self.frame_number - 1)
        self.time_slider.setEnabled(True)
        self.actualize_lights()
    except Exception as err:
        print(err)
        pass

def initUI(self)

Initialize the user interface

Expand source code

def initUI(self):
    """Initialize the user interface"""
    self.setWindowTitle("Brain Scout")
    self.setGeometry(10, 10, 640, 480)
    self.grid_layout = QGridLayout()
    self.grid_layout.setAlignment(Qt.AlignLeft)
    self.grid_layout.setAlignment(Qt.AlignTop)
    # self.grid_layout.setContentsMargins(0, 0, 0, 0)
    self.setLayout(self.grid_layout)

    self.settings_window = QVBoxLayout()
    self.settings_window.setAlignment(Qt.AlignLeft)
    self.settings_window.setAlignment(Qt.AlignTop)
    self.grid_layout.addLayout(self.settings_window, 0, 0)

    self.settings_window2 = QVBoxLayout()
    self.settings_window2.setAlignment(Qt.AlignLeft)
    self.settings_window2.setAlignment(Qt.AlignTop)
    self.grid_layout.addLayout(self.settings_window2, 0, 1)

    # ----
    self.directory_window = QHBoxLayout()
    self.directory_window.setAlignment(Qt.AlignLeft)
    self.directory_window.setAlignment(Qt.AlignTop)
    self.choose_directory_button = QPushButton("Select Directory")
    self.choose_directory_button.setIcon(
        QIcon(os.path.join(self.cwd, "gui", "icons", "folder-plus.png"))
    )
    self.choose_directory_button.clicked.connect(self.choose_directory)
    self.directory_window.addWidget(self.choose_directory_button)
    self.directory_cell = QLineEdit("")
    self.directory_cell.setReadOnly(True)
    self.directory_window.addWidget(self.directory_cell)

    self.settings_window.addLayout(self.directory_window)

    # ----
    self.light_channel_layout = QHBoxLayout()
    self.preview_light_label = QLabel("Light Channel Preview")
    self.light_channel_layout.addWidget(self.preview_light_label)
    self.preview_light_combo = QComboBox()
    self.preview_light_combo.setEnabled(False)
    self.preview_light_combo.currentIndexChanged.connect(
        self.change_preview_light_channel
    )
    self.light_channel_layout.addWidget(self.preview_light_combo)
    self.settings_window.addLayout(self.light_channel_layout)

    # self.import_window = QHBoxLayout()
    # self.import_progress = QLabel("0% Imported")
    # self.import_window.addWidget(self.import_progress)
    # self.settings_window.addLayout(self.import_window)

    # --

    # -------------

    self.index_window = QVBoxLayout()
    self.current_index_window = QHBoxLayout()
    self.current_index_label = QLabel("Current Index:")
    self.current_index_window.addWidget(self.current_index_label)
    self.current_index = QLineEdit("0")
    self.current_index.textChanged.connect(self.adjust_index)
    self.current_index_window.addWidget(self.current_index)
    self.index_window.addLayout(self.current_index_window)
    self.start_index_window = QHBoxLayout()
    self.start_index_label = QLabel("Start Index:")
    self.start_index_window.addWidget(self.start_index_label)
    self.start_index = QLineEdit("0")
    self.start_index_window.addWidget(self.start_index)
    self.index_window.addLayout(self.start_index_window)
    self.end_index_window = QHBoxLayout()
    self.end_index_label = QLabel("End Index:")
    self.end_index_window.addWidget(self.end_index_label)
    self.end_index = QLineEdit("0")
    self.end_index_window.addWidget(self.end_index)
    self.index_window.addLayout(self.end_index_window)
    self.settings_window2.addLayout(self.index_window)
    # self.settings_window.addStretch()

    self.make_time_course_button = QPushButton("Generate Time Course")
    self.make_time_course_button.setIcon(
        QIcon(os.path.join(self.cwd, "gui", "icons", "chart-line.png"))
    )
    self.make_time_course_button.clicked.connect(self.make_time_course)
    self.make_time_course_layout = QHBoxLayout()
    self.make_time_course_layout.setAlignment(Qt.AlignLeft)
    self.make_time_course_layout.setAlignment(Qt.AlignTop)
    self.make_time_course_layout.addWidget(self.make_time_course_button)
    self.make_time_course_container = QWidget()
    self.make_time_course_container.setLayout(self.make_time_course_layout)
    self.grid_layout.addWidget(self.make_time_course_container, 2, 1)

    # -------
    self.slider_layout = QHBoxLayout()
    self.slider_layout.setAlignment(Qt.AlignLeft)
    self.slider_layout.setAlignment(Qt.AlignTop)
    # self.slider_layout.setContentsMargins(0, 0, 0, 0)
    self.slider_layout.addWidget(QLabel("Start"))

    self.time_slider = QSlider(Qt.Horizontal, self)
    self.time_slider.setRange(0, 0)
    self.time_slider.setValue(0)
    self.time_slider.valueChanged.connect(self.adjust_time)
    self.slider_layout.addWidget(self.time_slider)
    self.slider_layout.addWidget(QLabel("End"))

    self.settings_window.addLayout(self.slider_layout)

    # -------------
    # self.graphics_layout =QHBoxLayout()

    # self.graphics_layout.addWidget(self.image_view)

    self.time_course = PlotWindow(subplots=False)
    self.time_course.plot([1, 2, 3], [1, 2, 3], root=False)
    self.grid_layout.addWidget(self.time_course, 1, 1)
    # self.grid_layout.addLayout(self.graphics_layout, 1, 0)

    # -------------
    self.show()

def initialize_plot(self)

Expand source code

def initialize_plot(self):
    try:
        self.image_view
    except Exception:
        self.image_view = PlotWindow()
        self.grid_layout.addWidget(self.image_view, 1, 0)
    self.plot_image = plt.imshow(
        np.zeros((self.dimensions[1], self.dimensions[0])),
        cmap="binary_r",
        vmin=0,
        vmax=4096,
        origin="lower",
    )
    self.plot_image.axes.get_xaxis().set_visible(False)
    self.plot_image.axes.axes.get_yaxis().set_visible(False)

def initialize_roi(self)

Expand source code

def initialize_roi(self):
    self.roi_buttons = QStackedLayout()
    self.roi_buttons.setAlignment(Qt.AlignLeft)
    self.roi_buttons.setAlignment(Qt.AlignTop)
    # self.roi_buttons.setContentsMargins(0, 0, 0, 0)
    self.roi_layout1 = QHBoxLayout()
    self.roi_layout1.setAlignment(Qt.AlignLeft)
    self.roi_layout1.setAlignment(Qt.AlignTop)
    # self.roi_layout1.setContentsMargins(0, 0, 0, 0)
    self.reset_roi_button = QPushButton("Reset ROI")
    self.reset_roi_button.setIcon(
        QIcon(os.path.join(self.cwd, "gui", "icons", "zoom-out-area.png"))
    )
    self.reset_roi_button.setEnabled(False)
    self.reset_roi_button.clicked.connect(self.reset_roi)
    self.roi_layout1.addWidget(self.reset_roi_button)

    self.set_roi_button = QPushButton("Set ROI")
    self.set_roi_button.setIcon(
        QIcon(os.path.join(self.cwd, "gui", "icons", "zoom-in-area.png"))
    )
    self.set_roi_button.clicked.connect(self.set_roi)
    self.roi_layout1.addWidget(self.set_roi_button)

    self.roi_layout1_container = QWidget()
    self.roi_layout1_container.setLayout(self.roi_layout1)

    self.roi_layout2 = QHBoxLayout()
    self.roi_layout2.setAlignment(Qt.AlignLeft)
    self.roi_layout2.setAlignment(Qt.AlignTop)
    # self.roi_layout2.setContentsMargins(0, 0, 0, 0)
    self.cancel_roi_button = QPushButton("Cancel")
    self.cancel_roi_button.setIcon(
        QIcon(os.path.join(self.cwd, "gui", "icons", "zoom-cancel.png"))
    )
    self.cancel_roi_button.clicked.connect(self.cancel_roi)
    self.roi_layout2.addWidget(self.cancel_roi_button)

    self.save_roi_button = QPushButton("Save ROI")
    self.save_roi_button.setIcon(
        QIcon(os.path.join(self.cwd, "gui", "icons", "zoom-check.png"))
    )
    self.save_roi_button.clicked.connect(self.save_roi)
    self.roi_layout2.addWidget(self.save_roi_button)
    self.roi_layout2_container = QWidget()
    self.roi_layout2_container.setLayout(self.roi_layout2)

    self.roi_buttons.addWidget(self.roi_layout1_container)
    self.roi_buttons.addWidget(self.roi_layout2_container)

    self.grid_layout.addLayout(self.roi_buttons, 2, 0)

def live_preview(self)

Expand source code

def live_preview(self):
    self.plot_image.set(
        array=self.split_frames[self.live_preview_light_index][
            self.image_index // len(self.dictionary["Lights"])
        ]
    )

def make_time_course(self)

Expand source code

def make_time_course(self):
    try:
        if self.roi_extent:
            print(
                shrink_array(
                    self.split_frames[self.live_preview_light_index],
                    self.roi_extent,
                )
            )
            y_values = get_timecourse(
                shrink_array(
                    self.split_frames[self.live_preview_light_index],
                    self.roi_extent,
                ),
                int(self.start_index.text()) // len(self.dictionary["Lights"]),
                int(self.end_index.text()) // len(self.dictionary["Lights"]),
            )
        else:
            y_values = get_timecourse(
                self.split_frames[self.live_preview_light_index],
                int(self.start_index.text()) // len(self.dictionary["Lights"]),
                int(self.end_index.text()) // len(self.dictionary["Lights"]),
            )
        plt.figure(self.time_course.figure.number)
        plt.ion()
        plt.clf()
        plt.plot(y_values)
    except Exception as err:
        print(err)
        pass

def open_import_thread(self)

Open the thread that will import the frames

Expand source code

def open_import_thread(self):
    """Open the thread that will import the frames"""
    self.import_thread = Thread(target=self.import_frames)
    self.import_thread.start()

def open_live_preview_thread(self)

Open the thread that will show the live preview

Expand source code

def open_live_preview_thread(self):
    """Open the thread that will show the live preview"""
    self.live_preview_thread = Thread(target=self.live_preview)
    self.live_preview_thread.start()

def reset_roi(self)

Reset the ROI

Expand source code

def reset_roi(self):
    """Reset the ROI"""
    plt.figure(self.image_view.figure.number)
    plt.ion()
    plt.xlim(0, self.dimensions[0])
    plt.ylim(0, self.dimensions[1])
    self.roi_extent = None
    self.reset_roi_button.setEnabled(False)
    self.set_roi_button.setEnabled(True)
    self.reset_roi_button.setEnabled(False)

def save_roi(self)

Save the ROI

Expand source code

def save_roi(self):
    """Save the ROI"""
    # self.activate_buttons(buttons=self.enabled_buttons)
    self.roi_buttons.setCurrentIndex(0)
    plt.figure(self.image_view.figure.number)
    plt.ion()
    plt.xlim(self.roi_extent[0], self.roi_extent[1])
    plt.ylim(self.roi_extent[2], self.roi_extent[3])
    self.rect_selector.clear()
    self.rect_selector = None
    self.reset_roi_button.setEnabled(True)
    self.set_roi_button.setEnabled(True)

def set_roi(self)

Set the ROI

Expand source code

def set_roi(self):
    """Set the ROI"""
    self.roi_buttons.setCurrentIndex(1)
    self.cancel_roi_button.setEnabled(True)
    self.save_roi_button.setEnabled(False)

    def onselect_function(eclick, erelease):
        """Save the ROI dimensions as attributes"""
        self.roi_extent = self.rect_selector.extents
        self.save_roi_button.setEnabled(True)

    self.rect_selector = RectangleSelector(
        self.plot_image.axes,
        onselect_function,
        drawtype="box",
        useblit=True,
        button=[1, 3],
        minspanx=5,
        minspany=5,
        spancoords="pixels",
        interactive=True,
    )