cellects 0.1.2__py3-none-any.whl → 0.2.6__py3-none-any.whl

cellects/gui/video_analysis_window.py

@@ -1,12 +1,20 @@
 #!/usr/bin/env python3
-"""
-This is the third main widget of the GUI of Cellects
-It process the video analysis computations by running threads connected to the program_organizer,
-especially, most computation are then processed by the MotionAnalysis class
+"""Third main widget for Cellects GUI enabling video analysis configuration and execution.
+
+This module implements a video tracking interface for analyzing cell movement through configurable parameters like
+ arena selection, segmentation methods, and smoothing thresholds. It provides interactive controls including spinboxes,
+  comboboxes, buttons for detection/post-processing, and an image display area with full-screen support. Threaded
+  operations (VideoReaderThread, OneArenaThread) handle background processing to maintain UI responsiveness.
+
+Main Components
+VideoAnalysisWindow : QWidget subclass implementing the video analysis interface with tab navigation, parameter
+controls, and thread coordination
+
+Notes
+Uses QThread for background operations to maintain UI responsiveness.
 """
 import logging
 import numpy as np
-import cv2
 from PySide6 import QtWidgets, QtCore
 
 from cellects.core.cellects_threads import (
@@ -15,13 +23,54 @@ from cellects.core.cellects_threads import (
 from cellects.gui.custom_widgets import (
     MainTabsType, InsertImage, FullScreenImage, PButton, Spinbox,
     Combobox, Checkbox, FixedText)
+from cellects.gui.ui_strings import FW, VAW
 
 
 class VideoAnalysisWindow(MainTabsType):
     def __init__(self, parent, night_mode):
+        """
+        Initialize the VideoAnalysis window with a parent widget and night mode setting.
+
+        Parameters
+        ----------
+        parent : QWidget
+            The parent widget to which this window will be attached.
+        night_mode : bool
+            A boolean indicating whether the night mode should be enabled.
+
+        Examples
+        --------
+        >>> from PySide6 import QtWidgets
+        >>> from cellects.gui.cellects import CellectsMainWidget
+        >>> from cellects.gui.video_analysis_window import VideoAnalysisWindow
+        >>> import sys
+        >>> app = QtWidgets.QApplication([])
+        >>> parent = CellectsMainWidget()
+        >>> session = VideoAnalysisWindow(parent, False)
+        >>> session.true_init()
+        >>> parent.insertWidget(0, session)
+        >>> parent.show()
+        >>> sys.exit(app.exec())
+        """
         super().__init__(parent, night_mode)
         logging.info("Initialize VideoAnalysisWindow")
         self.setParent(parent)
+        self.true_init()
+
+    def true_init(self):
+        """
+        Initialize the video tracking interface and set up its UI components.
+
+        Extended Description
+        --------------------
+        This method initializes various tabs, threads, and UI elements for the video tracking interface. It sets up
+        event handlers for tab clicks and configures layout components such as labels, buttons, spinboxes, and
+        comboboxes.
+
+        Notes
+        -----
+        This method assumes that the parent widget has a 'po' attribute with specific settings and variables.
+        """
         self.data_tab.set_not_in_use()
         self.image_tab.set_not_usable()
         self.video_tab.set_in_use()
@@ -33,21 +82,10 @@ class VideoAnalysisWindow(MainTabsType):
         self.thread['ChangeOneRepResult'] = ChangeOneRepResultThread(self.parent())
         self.thread['RunAll'] = RunAllThread(self.parent())
         self.previous_arena = 0
-
-        self.layout = QtWidgets.QGridLayout()
-        self.grid_widget = QtWidgets.QWidget()
-
-        # self.title = FixedText('Video tracking', police=30, night_mode=self.parent().po.all['night_mode'])
-        # self.title.setAlignment(QtCore.Qt.AlignHCenter)
         curr_row_main_layout = 0
         ncol = 1
-        # self.layout.addWidget(self.title, curr_row_main_layout, 0, 2, ncol)
-        # curr_row_main_layout += 2
-        self.layout.addItem(self.vertical_space, curr_row_main_layout, 0, 1, ncol)
+        self.Vlayout.addItem(self.vertical_space)#, curr_row_main_layout, 0, 1, ncol)
         curr_row_main_layout += 1
-        #
-        # self.layout.addWidget(self.arena_widget, curr_row_main_layout, 0)
-        # curr_row_main_layout += 1
 
         # Open subtitle
         self.general_step_widget = QtWidgets.QWidget()
@@ -61,7 +99,7 @@ class VideoAnalysisWindow(MainTabsType):
         self.general_step_layout.addWidget(self.general_step_button)
         self.general_step_layout.addItem(self.horizontal_space)
         self.general_step_widget.setLayout(self.general_step_layout)
-        self.layout.addWidget(self.general_step_widget, curr_row_main_layout, 0, 1, ncol)
+        self.Vlayout.addWidget(self.general_step_widget)#, curr_row_main_layout, 0, 1, ncol)
         curr_row_main_layout += 1
 
         # Open central widget
@@ -72,18 +110,12 @@ class VideoAnalysisWindow(MainTabsType):
         self.left_options_widget = QtWidgets.QWidget()
         self.left_options_layout = QtWidgets.QVBoxLayout()
         self.left_options_widget.setSizePolicy(QtWidgets.QSizePolicy.Maximum, QtWidgets.QSizePolicy.Maximum)
-        # self.left_options_widget.setFixedWidth(420)
 
         self.arena_widget = QtWidgets.QWidget()
         self.arena_layout = QtWidgets.QHBoxLayout()
-        self.arena_label = FixedText('Arena to analyze:',
-                                       tip="Among selected folders, choose a arena from the first folder\nThen, click on *Quick (or *Full) detection* to load and analyse one arena\nFinally, click on *Read* to see the resulting analysis\n\nSupplementary information:\nLoading will be faster if videos are already saved as ind_*.npy\n*Post processing* automatically runs *Detection* and *Detection* automatically runs *Load One arena*\nEach being faster than the previous one",
+        self.arena_label = FixedText(VAW["Arena_to_analyze"]["label"] + ':',
+                                       tip=VAW["Arena_to_analyze"]["tips"],
                                        night_mode=self.parent().po.all['night_mode'])
-        # if isinstance(self.parent().po.all['sample_number_per_folder'], int):
-        #     self.parent().po.all['folder_number'] = 1
-        # if self.parent().po.all['folder_number'] > 1:
-        #     sample_size = self.parent().po.all['sample_number_per_folder']
-        # else:
         sample_size = self.parent().po.all['sample_number_per_folder'][0]
         if self.parent().po.all['arena'] > sample_size:
             self.parent().po.all['arena'] = 1
@@ -92,12 +124,9 @@ class VideoAnalysisWindow(MainTabsType):
                                night_mode=self.parent().po.all['night_mode'])
         self.arena.valueChanged.connect(self.arena_changed)
 
-        # self.arena_layout.addItem(self.horizontal_space)
         self.arena_layout.addWidget(self.arena_label)
         self.arena_layout.addWidget(self.arena)
-        # self.arena_layout.addItem(self.horizontal_space)
         self.arena_widget.setLayout(self.arena_layout)
-        # self.arena_layout.setAlignment(QtCore.Qt.AlignHCenter)
         self.left_options_layout.addWidget(self.arena_widget)
 
 
@@ -110,13 +139,12 @@ class VideoAnalysisWindow(MainTabsType):
             self.parent().po.vars['repeat_video_smoothing'] = self.parent().po.vars['iterate_smoothing']
         self.maximal_growth_factor = Spinbox(min=0, max=0.5, val=self.parent().po.vars['maximal_growth_factor'],
                                             decimals=3, night_mode=self.parent().po.all['night_mode'])
-        self.maximal_growth_factor_label = FixedText('Maximal growth factor:',
-                                                    tip="This factor should be tried and increased (resp. decreases)\nif the analysis underestimates (resp. overestimates) the cell size.\nThe maximal growth factor is a proportion of pixels in the image. \nIt tells Cellects how much the cell(s) can possibly move or grow from one image to the next.\nIn other words, this is the upper limit of the proportion of the image\nthat can change from being the background to being covered by the cell(s).",
+        self.maximal_growth_factor_label = FixedText(VAW["Maximal_growth_factor"]["label"] + ':',
+                                                    tip=VAW["Maximal_growth_factor"]["tips"],
                                                     night_mode=self.parent().po.all['night_mode'])
         self.maximal_growth_factor.valueChanged.connect(self.maximal_growth_factor_changed)
         self.growth_per_frame_layout.addWidget(self.maximal_growth_factor_label)
         self.growth_per_frame_layout.addWidget(self.maximal_growth_factor)
-        # self.growth_per_frame_layout.setAlignment(QtCore.Qt.AlignHCenter)
         self.growth_per_frame_widget.setLayout(self.growth_per_frame_layout)
         self.left_options_layout.addWidget(self.growth_per_frame_widget)
 
@@ -124,45 +152,36 @@ class VideoAnalysisWindow(MainTabsType):
         self.iterate_layout = QtWidgets.QHBoxLayout()
         self.repeat_video_smoothing = Spinbox(min=0, max=10, val=self.parent().po.vars['repeat_video_smoothing'],
                                          night_mode=self.parent().po.all['night_mode'])
-        self.repeat_video_smoothing_label = FixedText('Repeat video smoothing:',
-                                                 tip="Increase (with steps of 1) if video noise is the source of detection failure",
+        self.repeat_video_smoothing_label = FixedText(VAW["Temporal_smoothing"]["label"] + ':',
+                                                 tip=VAW["Temporal_smoothing"]["tips"],
                                                  night_mode=self.parent().po.all['night_mode'])
         self.repeat_video_smoothing.valueChanged.connect(self.repeat_video_smoothing_changed)
         self.iterate_layout.addWidget(self.repeat_video_smoothing_label)
         self.iterate_layout.addWidget(self.repeat_video_smoothing)
-        # self.iterate_layout.setAlignment(QtCore.Qt.AlignHCenter)
         self.iterate_widget.setLayout(self.iterate_layout)
         self.left_options_layout.addWidget(self.iterate_widget)
 
 
-        self.select_option_label = FixedText('Segmentation method:',
-                                             tip='Select the option allowing the best cell delimitation.',
+        self.select_option_label = FixedText(VAW["Segmentation_method"]["label"] + ':',
+                                             tip=VAW["Segmentation_method"]["tips"],
                                              night_mode=self.parent().po.all['night_mode'])
         self.select_option = Combobox([], night_mode=self.parent().po.all['night_mode'])
         self.select_option_label.setSizePolicy(QtWidgets.QSizePolicy.Maximum, QtWidgets.QSizePolicy.Maximum)
         self.select_option.setSizePolicy(QtWidgets.QSizePolicy.Maximum, QtWidgets.QSizePolicy.Maximum)
         self.select_option.setFixedWidth(175)
-        # self.select_option_label.setFixedWidth(265)
-        # self.select_option.setFixedWidth(150)
         self.select_option.addItem("1. Frame by frame")
         self.select_option.addItem("2. Dynamical threshold")
         self.select_option.addItem("3. Dynamical slope")
         self.select_option.addItem("4. Threshold and Slope")
         self.select_option.addItem("5. Threshold or Slope")
-        # for option in range(5):
-        #     self.select_option.addItem(f"Option {option + 1}")
         self.select_option.setCurrentIndex(self.parent().po.all['video_option'])
         self.select_option.currentTextChanged.connect(self.option_changed)
-        # self.select_option_label.setVisible(self.parent().po.vars["color_number"] == 2)
-        # self.select_option.setVisible(self.parent().po.vars["color_number"] == 2)
 
         # Open the choose best option row layout
         self.options_row_widget = QtWidgets.QWidget()
         self.options_row_layout = QtWidgets.QHBoxLayout()
-        # self.options_row_layout.addItem(self.horizontal_space)
         self.options_row_layout.addWidget(self.select_option_label)
         self.options_row_layout.addWidget(self.select_option)
-        # self.options_row_layout.addItem(self.horizontal_space)
         self.options_row_layout.setAlignment(QtCore.Qt.AlignHCenter)
         self.options_row_layout.setAlignment(QtCore.Qt.AlignVCenter)
         self.options_row_widget.setLayout(self.options_row_layout)
@@ -184,13 +203,19 @@ class VideoAnalysisWindow(MainTabsType):
         self.right_options_widget = QtWidgets.QWidget()
         self.right_options_layout = QtWidgets.QVBoxLayout()
         self.right_options_widget.setSizePolicy(QtWidgets.QSizePolicy.Maximum, QtWidgets.QSizePolicy.Maximum)
-        # self.right_options_widget.setFixedWidth(420)
 
         self.compute_all_options_label = FixedText('Compute all options',
-                                                   tip='Uncheck to do a Post processing on only one option and earn computation time\nSelecting one of the remaining options will display the result from a Detection',
+                                                   tip=VAW["Segmentation_method"]["tips"],
                                                    night_mode=self.parent().po.all['night_mode'])
         self.compute_all_options_cb = Checkbox(self.parent().po.all['compute_all_options'])
-        self.compute_all_options_cb.setStyleSheet("margin-left:0%; margin-right:0%;")
+        self.compute_all_options_cb.setStyleSheet("QCheckBox::indicator {width: 12px;height: 12px;background-color: transparent;"
+                            "border-radius: 5px;border-style: solid;border-width: 1px;"
+                            "border-color: rgb(100,100,100);}"
+                            "QCheckBox::indicator:checked {background-color: rgb(70,130,180);}"
+                            "QCheckBox:checked, QCheckBox::indicator:checked {border-color: black black white white;}"
+                            "QCheckBox:checked {background-color: transparent;}"
+                            "QCheckBox:margin-left {0%}"
+                            "QCheckBox:margin-right {0%}")
         self.compute_all_options_cb.stateChanged.connect(self.compute_all_options_check)
         self.all_options_row_widget = QtWidgets.QWidget()
         self.all_options_row_layout = QtWidgets.QHBoxLayout()
@@ -201,11 +226,13 @@ class VideoAnalysisWindow(MainTabsType):
         self.all_options_row_widget.setLayout(self.all_options_row_layout)
         self.right_options_layout.addWidget(self.all_options_row_widget)
 
-        self.load_one_arena = PButton('Load One arena', night_mode=self.parent().po.all['night_mode'])
+        self.load_one_arena = PButton(VAW["Load_one_arena"]["label"], tip=VAW["Load_one_arena"]["tips"],
+                                      night_mode=self.parent().po.all['night_mode'])
         self.load_one_arena.clicked.connect(self.load_one_arena_is_clicked)
-        self.detection = PButton('Detection', night_mode=self.parent().po.all['night_mode'])
+        self.detection = PButton(VAW["Detection"]["label"], tip=VAW["Detection"]["tips"],
+                                 night_mode=self.parent().po.all['night_mode'])
         self.detection.clicked.connect(self.detection_is_clicked)
-        self.read = PButton('Read', night_mode=self.parent().po.all['night_mode'])
+        self.read = PButton(VAW["Read"]["label"], tip=VAW["Read"]["tips"], night_mode=self.parent().po.all['night_mode'])
         self.read.clicked.connect(self.read_is_clicked)
         self.read.setVisible(False)
         self.right_options_layout.addWidget(self.load_one_arena, alignment=QtCore.Qt.AlignCenter)
@@ -219,10 +246,7 @@ class VideoAnalysisWindow(MainTabsType):
         self.video_display_layout.addItem(self.horizontal_space)
         # Close central widget
         self.video_display_widget.setLayout(self.video_display_layout)
-        # self.video_display_widget.setSizePolicy(QtWidgets.QSizePolicy.Maximum, QtWidgets.QSizePolicy.Maximum)
-        # self.video_display_widget.setAlignment(QtCore.Qt.AlignHCenter)
-        # self.video_display_widget.setFixedHeight(500)
-        self.layout.addWidget(self.video_display_widget, curr_row_main_layout, 0)
+        self.Vlayout.addWidget(self.video_display_widget)#, curr_row_main_layout, 0)
         curr_row_main_layout += 1
 
         # Open Second step row
@@ -234,15 +258,21 @@ class VideoAnalysisWindow(MainTabsType):
         self.fading_widget = QtWidgets.QWidget()
         self.fading_layout = QtWidgets.QHBoxLayout()
         self.do_fading = Checkbox(self.parent().po.vars['do_fading'])
-        self.do_fading.setStyleSheet("margin-left:0%; margin-right:0%;")
+        self.do_fading.setStyleSheet("QCheckBox::indicator {width: 12px;height: 12px;background-color: transparent;"
+                            "border-radius: 5px;border-style: solid;border-width: 1px;"
+                            "border-color: rgb(100,100,100);}"
+                            "QCheckBox::indicator:checked {background-color: rgb(70,130,180);}"
+                            "QCheckBox:checked, QCheckBox::indicator:checked {border-color: black black white white;}"
+                            "QCheckBox:checked {background-color: transparent;}"
+                            "QCheckBox:margin-left {0%}"
+                            "QCheckBox:margin-right {0%}")
         self.do_fading.stateChanged.connect(self.do_fading_check)
         self.fading = Spinbox(min=- 1, max=1, val=self.parent().po.vars['fading'], decimals=2,
                                night_mode=self.parent().po.all['night_mode'])
-        self.fading_label = FixedText('Fading detection',
-                                       tip="Set a value between -1 and 1\nnear - 1: it will never detect when the cell leaves an area\nnear 1: it may stop detecting cell (because cell will be considered left from any area)",
+        self.fading_label = FixedText(VAW["Fading_detection"]["label"],
+                                       tip=VAW["Fading_detection"]["tips"],
                                        night_mode=self.parent().po.all['night_mode'])
         self.fading.valueChanged.connect(self.fading_changed)
-        # self.fading.setVisible(self.parent().po.vars['do_fading'])
         self.fading_layout.addWidget(self.do_fading)
         self.fading_layout.addWidget(self.fading_label)
         self.fading_layout.addWidget(self.fading)
@@ -250,23 +280,23 @@ class VideoAnalysisWindow(MainTabsType):
         self.fading_widget.setLayout(self.fading_layout)
         self.second_step_layout.addWidget(self.fading_widget)
 
-        self.post_processing = PButton('Post processing', night_mode=self.parent().po.all['night_mode'])
+        self.post_processing = PButton(VAW["Post_processing"]["label"], tip=VAW["Post_processing"]["tips"],
+                                       night_mode=self.parent().po.all['night_mode'])
         self.post_processing.clicked.connect(self.post_processing_is_clicked)
         self.second_step_layout.addWidget(self.post_processing)
-        # self.second_step_layout.addWidget(self.post_processing, alignment=QtCore.Qt.AlignCenter)
 
-        self.save_one_result = PButton('Save One Result', night_mode=self.parent().po.all['night_mode'])
+        self.save_one_result = PButton(VAW["Save_one_result"]["label"], tip=VAW["Save_one_result"]["tips"],
+                                       night_mode=self.parent().po.all['night_mode'])
         self.save_one_result.clicked.connect(self.save_one_result_is_clicked)
         self.second_step_layout.addWidget(self.save_one_result)
-        # self.second_step_layout.addWidget(self.save_one_result, alignment=QtCore.Qt.AlignCenter)
 
         # Close Second step row
         self.second_step_layout.setAlignment(QtCore.Qt.AlignHCenter)
         self.second_step_layout.addItem(self.horizontal_space)
         self.second_step_widget.setLayout(self.second_step_layout)
-        self.layout.addItem(self.vertical_space, curr_row_main_layout, 0, 1, ncol)
+        self.Vlayout.addItem(self.vertical_space)#, curr_row_main_layout, 0, 1, ncol)
         curr_row_main_layout += 1
-        self.layout.addWidget(self.second_step_widget, curr_row_main_layout, 0)
+        self.Vlayout.addWidget(self.second_step_widget)#, curr_row_main_layout, 0)
         curr_row_main_layout += 1
 
         # Open last options row widget
@@ -274,42 +304,27 @@ class VideoAnalysisWindow(MainTabsType):
         self.last_options_layout = QtWidgets.QHBoxLayout()
         self.last_options_layout.addItem(self.horizontal_space)
 
-        # #  advanced mode widget
-        # self.advanced_mode_widget = QtWidgets.QWidget()
-        # self.advanced_mode_layout = QtWidgets.QHBoxLayout()
-        # advanced_mode = self.parent().po.all['expert_mode']
-        # self.advanced_mode_cb = Checkbox(self.parent().po.all['expert_mode'])
-        # self.advanced_mode_cb.setStyleSheet("margin-left:0%; margin-right:0%;")
-        # self.advanced_mode_cb.stateChanged.connect(self.advanced_mode_check)
-        # self.advanced_mode_label = FixedText('Go to step 2 directly', align='l',
-        #                                      tip="Allow the user to try Post processing before having tuned the parameters related to Detection.",
-        #                                      night_mode=self.parent().po.all['night_mode'])
-        # # self.advanced_mode_label.setAlignment(QtCore.Qt.AlignTop)
-        # self.advanced_mode_layout.addWidget(self.advanced_mode_cb)
-        # self.advanced_mode_layout.addWidget(self.advanced_mode_label)
-        # self.advanced_mode_layout.addItem(self.horizontal_space)
-        # self.advanced_mode_layout.setAlignment(QtCore.Qt.AlignHCenter)
-        # self.advanced_mode_widget.setLayout(self.advanced_mode_layout)
-        # self.last_options_layout.addWidget(self.advanced_mode_widget)
-
-        self.advanced_parameters = PButton('Advanced Parameters', night_mode=self.parent().po.all['night_mode'])
+        self.advanced_parameters = PButton(FW["Advanced_parameters"]["label"], tip=FW["Advanced_parameters"]["tips"],
+                                           night_mode=self.parent().po.all['night_mode'])
         self.advanced_parameters.clicked.connect(self.advanced_parameters_is_clicked)
         self.last_options_layout.addWidget(self.advanced_parameters)
 
         #  Required Outputs widget
-        self.required_outputs = PButton('Required Outputs', night_mode=self.parent().po.all['night_mode'])
+        self.required_outputs = PButton(FW["Required_outputs"]["label"], tip=FW["Required_outputs"]["tips"],
+                                        night_mode=self.parent().po.all['night_mode'])
         self.required_outputs.clicked.connect(self.required_outputs_is_clicked)
         self.last_options_layout.addWidget(self.required_outputs)
 
         #  Save all choices widget
-        self.save_all_vars = PButton('Save all choices', night_mode=self.parent().po.all['night_mode'])
+        self.save_all_vars = PButton(VAW["Save_all_choices"]["label"], tip=VAW["Save_all_choices"]["tips"],
+                                     night_mode=self.parent().po.all['night_mode'])
         self.save_all_vars.clicked.connect(self.save_current_settings)
         self.last_options_layout.addWidget(self.save_all_vars)
 
         # Close last options widget
         self.last_options_layout.addItem(self.horizontal_space)
         self.last_options_widget.setLayout(self.last_options_layout)
-        self.layout.addWidget(self.last_options_widget, curr_row_main_layout, 0)
+        self.Vlayout.addWidget(self.last_options_widget)#, curr_row_main_layout, 0)
         curr_row_main_layout += 1
 
         self.message = QtWidgets.QLabel(self)
@@ -320,7 +335,8 @@ class VideoAnalysisWindow(MainTabsType):
         self.previous = PButton('Previous', night_mode=self.parent().po.all['night_mode'])
         self.previous.clicked.connect(self.previous_is_clicked)
 
-        self.run_all = PButton('Run All', night_mode=self.parent().po.all['night_mode'])
+        self.run_all = PButton(VAW["Run_All"]["label"], tip=VAW["Run_All"]["tips"],
+                               night_mode=self.parent().po.all['night_mode'])
         self.run_all.clicked.connect(self.run_all_is_clicked)
 
         # Open last row widget
@@ -332,21 +348,32 @@ class VideoAnalysisWindow(MainTabsType):
         self.last_row_layout.addWidget(self.run_all)
         # Close last row widget
         self.last_row_widget.setLayout(self.last_row_layout)
-        self.layout.addItem(self.vertical_space, curr_row_main_layout, 0, 1, ncol)
-        self.layout.addWidget(self.last_row_widget, curr_row_main_layout, 0)
+        self.Vlayout.addItem(self.vertical_space)#, curr_row_main_layout, 0, 1, ncol)
+        self.Vlayout.addWidget(self.last_row_widget)#, curr_row_main_layout + 1, 0)
 
-        self.grid_widget.setLayout(self.layout)
-        self.Vlayout.addItem(self.vertical_space)
-        self.Vlayout.addWidget(self.grid_widget)
         self.setLayout(self.Vlayout)
-        # self.advanced_mode_check()
 
     def display_conditionally_visible_widgets(self):
+        """
+        Display Conditionally Visible Widgets
+        """
         self.select_option_label.setVisible(self.parent().po.vars["color_number"] == 2)
         self.select_option.setVisible(self.parent().po.vars["color_number"] == 2)
         self.fading.setVisible(self.parent().po.vars['do_fading'])
 
     def step_done_is_clicked(self):
+        """
+        Step the analysis progress when 'Done' button is clicked.
+
+        Increments the current step and updates the UI accordingly based on the
+        new step value. Updates labels, tooltips, and visibility of widgets.
+
+        Notes
+        -----
+        This method is automatically called when the 'Done' button is clicked.
+        It updates the GUI elements to reflect progress in a multi-step
+        analysis process.
+        """
         self.current_step += 1
         if self.current_step == 1:
             self.general_step_label.setText('Step 2: Tune fading and advanced parameters to improve Post processing')
@@ -361,6 +388,9 @@ class VideoAnalysisWindow(MainTabsType):
             self.general_step_button.setVisible(False)
 
     def reset_general_step(self):
+        """
+        Reset the general step counter and update UI labels.
+        """
         self.current_step = 0
         self.general_step_label.setText('Step 1: Tune parameters to improve Detection')
         self.general_step_label.setToolTip('Detection uses only the visible parameters and those\npreviously determined on the first or last image.')
@@ -368,13 +398,29 @@ class VideoAnalysisWindow(MainTabsType):
         self.second_step_widget.setVisible(False)
 
     def full_screen_display(self, event):
+        """
+        Full-screen display of an image.
+
+        This method creates a full-screen image popup and displays it. The
+        full-screen image is initialized with the current image to display,
+        and its size is set to match the screen dimensions.
+        """
         self.popup_img = FullScreenImage(self.parent().image_to_display, self.parent().screen_width, self.parent().screen_height)
         self.popup_img.show()
 
     def option_changed(self):
         """
-        Update the video, save parameters
-        :return:
+        Handles the logic for changing video option settings and logging the appropriate actions.
+
+        This method is responsible for updating various flags and configuration variables
+        based on the selected video option. It also logs informational messages regarding
+        the behavior of the segmentation algorithms being enabled or disabled.
+
+        Notes
+        -----
+        This function updates the parent object's configuration variables and logs messages
+        based on the selected video option. The behavior changes depending on the number of
+        colors detected and the specific video option chosen.
         """
         self.parent().po.all['video_option'] = self.select_option.currentIndex()
         self.parent().po.vars['frame_by_frame_segmentation'] = False
@@ -401,26 +447,17 @@ class VideoAnalysisWindow(MainTabsType):
                 elif self.parent().po.all['video_option'] == 4:
                     logging.info(f"This option will detect cell(s) using the dynamic threshold OR slope algorithms with a maximal growth factor of {self.parent().po.vars['maximal_growth_factor']}")
                     self.parent().po.vars['true_if_use_light_AND_slope_else_OR'] = False
-        # self.parent().po.motion
-
-    # def advanced_mode_check(self):
-    #     advanced_mode = self.advanced_mode_cb.isChecked()
-    #     self.parent().po.all['expert_mode'] = advanced_mode
-    #     self.second_step_widget.setVisible(advanced_mode or self.current_step > 0)
-    #     if advanced_mode:
-    #         if self.current_step == 0:
-    #             self.current_step += 1
-    #             self.general_step_label.setText('Step 2: Tune fading and advanced parameters to improve Post processing')
-    #         self.save_one_result.setVisible(self.current_step == 2)
-
-        # self.maximal_growth_factor.setVisible(advanced_mode)
-        # self.maximal_growth_factor_label.setVisible(advanced_mode)
-        # self.fading.setVisible(advanced_mode)
-        # self.fading_label.setVisible(advanced_mode)
-        # self.repeat_video_smoothing.setVisible(advanced_mode)
-        # self.repeat_video_smoothing_label.setVisible(advanced_mode)
 
     def data_tab_is_clicked(self):
+        """
+        Handles the logic for when the "Data specifications" button is clicked in the interface,
+        leading to the FirstWindow.
+
+        Notes
+        -----
+        This function displays an error message when a thread relative to the current window is running.
+        This function also save the id of the following window for later use.
+        """
         if self.thread['VideoReader'].isRunning() or self.thread['OneArena'].isRunning() or self.thread['ChangeOneRepResult'].isRunning() or self.parent().firstwindow.thread["RunAll"].isRunning():
             self.message.setText("Wait for the analysis to end, or restart Cellects")
         else:
@@ -428,6 +465,15 @@ class VideoAnalysisWindow(MainTabsType):
             self.parent().change_widget(0)  # FirstWidget
 
     def image_tab_is_clicked(self):
+        """
+        Handles the logic for when the "Image analysis" button is clicked in the interface,
+        leading to the image analysis window.
+
+        Notes
+        -----
+        This function displays an error message when a thread relative to the current window is running.
+        This function also save the id of the following window for later use.
+        """
         if self.image_tab.state != "not_usable":
             if self.thread['VideoReader'].isRunning() or self.thread['OneArena'].isRunning() or self.thread[
                 'ChangeOneRepResult'].isRunning() or self.parent().firstwindow.thread["RunAll"].isRunning():
@@ -438,27 +484,59 @@ class VideoAnalysisWindow(MainTabsType):
 
 
     def required_outputs_is_clicked(self):
+        """
+        Sets the required outputs flag and changes the widget to the "Required Output" window.
+        """
         self.parent().last_is_first = False
         self.parent().change_widget(4)  # RequiredOutput
 
     def advanced_parameters_is_clicked(self):
+        """
+        Modifies the interface to display advanced parameters.
+        """
         self.parent().last_is_first = False
         self.parent().widget(5).update_csc_editing_display()
         self.parent().change_widget(5)  # AdvancedParameters
 
     def previous_is_clicked(self):
+        """
+        Transition to the previous tab based on current tab history.
+
+        This method handles the logic for navigating back through the
+        application's tabs when "previous" is clicked. It updates the current
+        tab to the one that was last visited, cycling through the predefined
+        order of tabs.
+
+        Notes
+        -----
+        This function is part of a state-machine-like navigation system that
+        tracks tab history. It assumes the parent widget has methods `last_tab`
+        and `change_widget` for managing the current view.
+        """
         if self.parent().last_tab == "data_specifications":
             self.parent().change_widget(0)  # FirstWidget
         elif self.parent().last_tab == "image_analysis":
             self.parent().change_widget(2)  # ThirdWidget
         self.parent().last_tab = "video_analysis"
-        # self.parent().change_widget(2)  # SecondWidget
 
     def save_all_vars_thread(self):
+        """
+        Start the 'SaveAllVars' thread if it is not already running.
+
+        This method is used to ensure that variable saving operations are performed
+        in a separate thread to avoid blocking the main application.
+        """
         if not self.parent().thread['SaveAllVars'].isRunning():
             self.parent().thread['SaveAllVars'].start()  # SaveAllVarsThreadInThirdWidget
 
     def save_current_settings(self):
+        """
+        Saves the current settings from UI components to persistent storage.
+
+        This method captures the values of various UI components and stores
+        them in a persistent data structure to ensure settings are saved across
+        sessions.
+        """
         self.parent().po.vars['maximal_growth_factor'] = self.maximal_growth_factor.value()
         self.parent().po.vars['repeat_video_smoothing'] = int(np.round(self.repeat_video_smoothing.value()))
         self.parent().po.vars['do_fading'] = self.do_fading.isChecked()
@@ -468,24 +546,40 @@ class VideoAnalysisWindow(MainTabsType):
         self.save_all_vars_thread()
 
     def repeat_video_smoothing_changed(self):
+        """
+        Save the repeat_video_smoothing spinbox value to set how many times the pixel intensity dynamics will be
+        smoothed.
+        """
         self.parent().po.vars['repeat_video_smoothing'] = int(np.round(self.repeat_video_smoothing.value()))
-        # self.save_all_vars_is_clicked()
 
     def do_fading_check(self):
+        """
+        Save the fading checkbox value to allow cases where pixels can be left by the specimen(s).
+        """
         self.parent().po.vars['do_fading'] = self.do_fading.isChecked()
         self.fading.setVisible(self.parent().po.vars['do_fading'])
 
     def fading_changed(self):
+        """
+        Save the fading spinbox value to modify how intensity must decrease to detect a pixel left by the specimen(s).
+        """
         self.parent().po.vars['fading'] = self.fading.value()
-        # self.save_all_vars_is_clicked()
 
     def maximal_growth_factor_changed(self):
+        """
+        Save the maximal_growth_factor spinbox value to modulate the maximal growth between two frames.
+        """
         self.parent().po.vars['maximal_growth_factor'] = self.maximal_growth_factor.value()
-        # self.save_all_vars_is_clicked()
 
     def arena_changed(self):
         """
-            Put motion to None allows the class OneArenaThread to load the selected arena
+        Resets the loaded arena when its video and processing threads are not running.
+
+        Notes
+        -----
+        This function is part of a larger class responsible for managing video and
+        arena processing threads. It should be called when all relevant threads are not
+        running to ensure the arena's state is properly reset.
         """
         if not self.thread['VideoReader'].isRunning() and not self.thread['OneArena'].isRunning() and not self.thread['ChangeOneRepResult'].isRunning():
             self.parent().po.motion = None
@@ -494,31 +588,64 @@ class VideoAnalysisWindow(MainTabsType):
             self.parent().po.all['arena'] = int(np.round(self.arena.value()))
 
     def load_one_arena_is_clicked(self):
+        """
+        Load one arena if clicked.
+
+        Resets the general step, sets `load_quick_full` to 0, and runs the arena in a separate thread.
+        """
         self.reset_general_step()
-        # self.save_all_vars_is_clicked()
         self.parent().po.load_quick_full = 0
         self.run_one_arena_thread()
 
     def compute_all_options_check(self):
+        """
+        Save the compute_all_options checkbox value to process every video segmentation algorithms during the next run.
+        """
         self.parent().po.all['compute_all_options'] = self.compute_all_options_cb.isChecked()
 
     def detection_is_clicked(self):
+        """
+        Trigger detection when a button is clicked.
+
+        This method handles the logic when the user clicks the "detection" button.
+        It resets certain states, sets a flag for quick full processing,
+        and starts a thread to run the detection in one arena.
+
+        Notes
+        -----
+        This method is part of a larger state machine for handling user interactions.
+        It assumes that the parent object has a `po` attribute with a `load_quick_full`
+        flag and a method to run an arena thread.
+        """
         self.reset_general_step()
-        # self.save_all_vars_is_clicked()
         self.parent().po.load_quick_full = 1
         self.run_one_arena_thread()
 
     def post_processing_is_clicked(self):
-        # self.save_all_vars_is_clicked()
+        """
+        Trigger post-processing when a button is clicked.
+
+        Extended Description
+        -------------------
+        This function updates the parent object's load_quick_full attribute,
+        logs a specific variable value, and runs an arena thread.
+        """
         self.parent().po.load_quick_full = 2
         logging.info(self.parent().po.vars['maximal_growth_factor'])
         self.run_one_arena_thread()
 
     def run_one_arena_thread(self):
         """
-            Make sure that the previous thread is not running and start the OneArenaThread
-            According to the button clicked, this class will only load, load and quick segment,
-            or load, quickly segment and fully detect the cell(s) dynamic
+        Run the OneArena thread for processing.
+
+        Executes the OneArena thread to load video, initialize analysis,
+        stop any running instance of the thread, save settings, and connect
+        signals for displaying messages, images, and handling completion events.
+
+        Notes
+        -----
+        Ensures that the previous arena settings are cleared and connects signals
+        to display messages and images during thread execution.
         """
         if self.thread['OneArena']._isRunning:
             self.thread['OneArena'].stop()
@@ -526,20 +653,23 @@ class VideoAnalysisWindow(MainTabsType):
         if self.previous_arena != self.parent().po.all['arena']:
             self.parent().po.motion = None
         self.message.setText("Load the video and initialize analysis, wait...")
-        # if not self.parent().po.first_exp_ready_to_run:
-        #     self.parent().po.use_data_to_run_cellects_quickly = True
         self.thread['OneArena'].start()  # OneArenaThreadInThirdWidget
         self.thread['OneArena'].message_from_thread_starting.connect(self.display_message_from_thread)
         self.thread['OneArena'].when_loading_finished.connect(self.when_loading_thread_finished)
         self.thread['OneArena'].when_detection_finished.connect(self.when_detection_finished)
         self.thread['OneArena'].image_from_thread.connect(self.display_image_during_thread)
 
-    def when_loading_thread_finished(self, save_loaded_video):
+    def when_loading_thread_finished(self, save_loaded_video: bool):
+        """
+        Ends the loading thread process and handles post-loading actions.
+
+        Notes
+        ----------
+        This method assumes that the parent object has a `po` attribute with an
+        'arena' key and a `load_quick_full` attribute. It also assumes that the
+        parent object has a 'thread' dictionary and a message UI component.
+        """
         self.previous_arena = self.parent().po.all['arena']
-        # if not self.parent().po.vars['already_greyscale']:
-        #     self.parent().po.motion.analysis_instance = self.parent().po.motion.visu.copy()
-        # else:
-        #     self.parent().po.motion.analysis_instance = self.parent().po.motion.converted_video.copy()
         if save_loaded_video:
             self.thread['WriteVideo'] = WriteVideoThread(self.parent())
             self.thread['WriteVideo'].start()
@@ -547,13 +677,32 @@ class VideoAnalysisWindow(MainTabsType):
             self.message.setText("Loading done, you can watch the video")
         self.read.setVisible(True)
 
-    def when_detection_finished(self, message):
-        # self.option_changed()
+    def when_detection_finished(self, message: str):
+        """
+        Handles the completion of video detection and updates the UI accordingly.
+
+        When the video detection is finished, this function waits for the
+        VideoReader thread to complete if it's running. It then processes the
+        last frame of the video based on the configured visualization and motion
+        detection settings. Finally, it updates the UI with the processed image
+        and sets appropriate labels' visibility.
+
+        Parameters
+        ----------
+        message : str
+            The message to display upon completion of detection.
+            This could be a status update or any relevant information.
+
+        Notes
+        -----
+        This function assumes that the parent object has attributes `po` and
+        `image_to_display`, and methods like `display_image.update_image`.
+        """
         self.previous_arena = self.parent().po.all['arena']
         if self.thread['VideoReader'].isRunning():  # VideoReaderThreadInThirdWidget
             self.thread['VideoReader'].wait()
         if self.parent().po.load_quick_full > 0:
-            image = self.parent().po.motion.segmentation[-1, ...]
+            image = self.parent().po.motion.segmented[-1, ...]
         if self.parent().po.motion.visu is None:
             image = self.parent().po.motion.converted_video[-1, ...] * (1 - image)
             image = np.round(image).astype(np.uint8)
@@ -563,20 +712,34 @@ class VideoAnalysisWindow(MainTabsType):
             image = self.parent().po.motion.visu[-1, ...] * (1 - image)
         self.parent().image_to_display = image
         self.display_image.update_image(image)
-
         self.message.setText(message)
-
         self.select_option_label.setVisible(self.parent().po.vars["color_number"] == 2)
         self.select_option.setVisible(self.parent().po.vars["color_number"] == 2)
         self.read.setVisible(True)
-        # self.save_one_result.setVisible(True)
 
-    def display_image_during_thread(self, dictionary):
+    def display_image_during_thread(self, dictionary: dict):
+        """
+        Display an image and set a message during a thread operation.
+
+        Parameters
+        ----------
+        dictionary : dict
+            A dictionary containing the 'message' and 'current_image'.
+                The message is a string to display.
+                The current_image is the image data that will be displayed.
+        """
         self.message.setText(dictionary['message'])
         self.parent().image_to_display = dictionary['current_image']
         self.display_image.update_image(dictionary['current_image'])
 
     def save_one_result_is_clicked(self):
+        """
+        Finalize one arena analysis and save the result if conditions are met.
+
+        This function checks various conditions before starting a thread to
+        finalize the analysis and save the result. It ensures that certain
+        threads are not running before proceeding.
+        """
         if self.parent().po.motion is not None:
             if self.parent().po.load_quick_full == 2:
                 if not self.thread['OneArena'].isRunning() and not self.thread['ChangeOneRepResult'].isRunning():
@@ -592,56 +755,71 @@ class VideoAnalysisWindow(MainTabsType):
             self.message.setText("Run Post processing first")
 
     def read_is_clicked(self):
+        """
+        Read a video corresponding to a numbered arena (numbered using natural sorting) in the image
+
+        This function checks if the detection has been run and if the video reader or analysis thread is running.
+        If both threads are idle, it starts the video reading process. Otherwise, it updates the message accordingly.
+        """
         if self.parent().po.motion is not None:
-            if self.parent().po.motion.segmentation is not None:
+            if self.parent().po.motion.segmented is not None:
                 if not self.thread['OneArena'].isRunning() and not self.thread['VideoReader'].isRunning():
                     self.thread['VideoReader'].start()  # VideoReaderThreadInThirdWidget
                     self.thread['VideoReader'].message_from_thread.connect(self.display_image_during_thread)
-                    # if self.parent().po.computed_video_options[self.parent().po.all['video_option']]:
-                    #     self.message.setText("Run detection to visualize analysis")
                 else:
                     self.message.setText("Wait for the analysis to end")
             else:
                 self.message.setText("Run detection first")
         else:
             self.message.setText("Run detection first")
-    #
-    # def video_display(self, dictionary):
-    #     self.drawn_image = dictionary['image']
-    #     self.display_image.update_image(dictionary['image'], self.parent().po.vars['contour_color'])
-    #     self.message.setText(dictionary['message'])
-    #     # self.message.setText(f"Reading done, try to change parameters if necessary")
 
     def run_all_is_clicked(self):
+        """
+        Handle the click event to start the complete analysis.
+
+        This function checks if any threads are running and starts the
+        'RunAll' thread if none of them are active. It also updates
+        various attributes and messages related to the analysis process.
+
+        Notes
+        -----
+        This function will only start the analysis if no other threads
+        are running. It updates several attributes of the parent object.
+        """
         if self.thread['OneArena'].isRunning() or self.thread['ChangeOneRepResult'].isRunning():
             self.message.setText("Wait for the current analysis to end")
         else:
             if self.thread['VideoReader'].isRunning():
                 self.thread['VideoReader'].wait()
-            # self.save_all_vars_is_clicked()
-            # self.save_current_settings()
             if self.parent().firstwindow.thread["RunAll"].isRunning():
                 self.message.setText('Analysis has already begun in the first window.')
             else:
                 if not self.thread['RunAll'].isRunning():
-                    # self.save_all_vars_is_clicked()
                     self.save_current_settings()
                     self.parent().po.motion = None
                     self.parent().po.converted_video = None
                     self.parent().po.converted_video2 = None
                     self.parent().po.visu = None
                     self.message.setText("Complete analysis has started, wait...")
-                    # if not self.parent().po.first_exp_ready_to_run:
-                    #     self.parent().po.use_data_to_run_cellects_quickly = True
                     self.thread['RunAll'].start()  # RunAllThread
                     self.thread['RunAll'].message_from_thread.connect(self.display_message_from_thread)
                     self.thread['RunAll'].image_from_thread.connect(self.display_image_during_thread)
-                    # self.parent().imageanalysiswindow.true_init()
 
-    def display_message_from_thread(self, text_from_thread):
+    def display_message_from_thread(self, text_from_thread: str):
+        """
+        Updates the message displayed in the UI with text from a thread.
+
+        Parameters
+        ----------
+        text_from_thread : str
+            The text to be displayed in the UI message.
+        """
         self.message.setText(text_from_thread)
 
     def closeEvent(self, event):
+        """
+        Handle the close event for a QWidget.
+        """
         event.accept