loader and home docs

nellie_napari/nellie_home.py

@@ -10,7 +10,43 @@
 
 
 class Home(QWidget):
+    """
+    The Home screen for the Nellie application, displayed in the napari viewer.
+    It provides options to start using the application, navigate to the file selection tab, and take screenshots.
+
+    Attributes
+    ----------
+    viewer : napari.viewer.Viewer
+        The napari viewer instance.
+    nellie : object
+        Reference to the main Nellie object containing image processing pipelines and functions.
+    layout : QVBoxLayout
+        The vertical layout to organize the widgets on the home screen.
+    start_button : QPushButton
+        Button to start the application and navigate to the file selection tab.
+    screenshot_button : QPushButton
+        Button to take a screenshot of the current napari viewer canvas.
+
+    Methods
+    -------
+    __init__(napari_viewer, nellie, parent=None)
+        Initializes the home screen with a logo, title, description, and navigation buttons.
+    screenshot(event=None)
+        Takes a screenshot of the napari viewer and saves it to a specified folder.
+    """
     def __init__(self, napari_viewer: 'napari.viewer.Viewer', nellie, parent=None):
+        """
+        Initializes the Home screen with a logo, title, description, and buttons for navigation and screenshot functionality.
+
+        Parameters
+        ----------
+        napari_viewer : napari.viewer.Viewer
+            Reference to the napari viewer instance.
+        nellie : object
+            Reference to the main Nellie object containing image processing pipelines and functions.
+        parent : QWidget, optional
+            Optional parent widget (default is None).
+        """
         super().__init__(parent)
         self.nellie = nellie
         self.viewer = napari_viewer
@@ -72,6 +108,14 @@ def __init__(self, napari_viewer: 'napari.viewer.Viewer', nellie, parent=None):
         self.layout.addWidget(self.screenshot_button, alignment=Qt.AlignCenter)
 
     def screenshot(self, event=None):
+        """
+        Takes a screenshot of the napari viewer and saves it as a PNG file in a specified folder.
+
+        Parameters
+        ----------
+        event : optional
+            An event object, if triggered by a key binding or button click (default is None).
+        """
         if self.nellie.im_info is None:
             show_info("No file selected, cannot take screenshot")
             return

nellie_napari/nellie_loader.py

@@ -10,7 +10,54 @@
 
 
 class NellieLoader(QTabWidget):
+    """
+    The main loader class for managing the different stages of the Nellie pipeline within the napari viewer. This class
+    provides a tabbed interface for file selection, processing, visualization, analysis, and settings management.
+
+    Attributes
+    ----------
+    home : Home
+        The home tab instance, providing an overview of the Nellie pipeline.
+    file_select : NellieFileSelect
+        The file selection tab instance, allowing users to select and validate image files.
+    processor : NellieProcessor
+        The image processing tab instance, where users can process images through the Nellie pipeline.
+    visualizer : NellieVisualizer
+        The visualization tab instance, where processed images can be visualized.
+    analyzer : NellieAnalysis
+        The analysis tab instance, enabling users to analyze processed image data.
+    settings : Settings
+        The settings tab instance, allowing users to configure various settings for the Nellie pipeline.
+    home_tab, file_select_tab, processor_tab, visualizer_tab, analysis_tab, settings_tab : int
+        Integer values representing the index of the respective tabs.
+    im_info : ImInfo or None
+        Contains metadata and information about the selected image file.
+    im_info_list : list of ImInfo or None
+        A list of ImInfo objects when batch processing is enabled (multiple files).
+
+    Methods
+    -------
+    add_tabs()
+        Adds the individual tabs to the widget.
+    reset()
+        Resets the state of the loader, removing and reinitializing all tabs.
+    on_tab_change(index)
+        Slot that is triggered when the user changes the tab.
+    go_process()
+        Initializes and enables the processing and visualization tabs for image processing.
+    """
     def __init__(self, napari_viewer: 'napari.viewer.Viewer', parent=None):
+        """
+        Initializes the NellieLoader class, creating instances of the individual tabs for home, file selection,
+        processing, visualization, analysis, and settings.
+
+        Parameters
+        ----------
+        napari_viewer : napari.viewer.Viewer
+            Reference to the napari viewer instance.
+        parent : QWidget, optional
+            Optional parent widget (default is None).
+        """
         super().__init__(parent)
         self.home = Home(napari_viewer, self)
         self.file_select = NellieFileSelect(napari_viewer, self)
@@ -33,6 +80,11 @@ def __init__(self, napari_viewer: 'napari.viewer.Viewer', parent=None):
         self.im_info_list = None
 
     def add_tabs(self):
+        """
+        Adds the individual tabs for Home, File validation, Process, Visualize, Analyze, and Settings.
+        Initially disables the Process, Visualize, and Analyze tabs until they are needed.
+        """
+        ...
         self.home_tab = self.addTab(self.home, "Home")
         self.file_select_tab = self.addTab(self.file_select, "File validation")
         self.processor_tab = self.addTab(self.processor, "Process")
@@ -45,6 +97,10 @@ def add_tabs(self):
         self.setTabEnabled(self.analysis_tab, False)
 
     def reset(self):
+        """
+        Resets the state of the loader, reinitializing all tabs. This method is typically called when the user
+        wants to start a new session with a fresh file selection and settings.
+        """
         self.setCurrentIndex(self.home_tab)
 
         # needs to be in reverse order
@@ -66,6 +122,15 @@ def reset(self):
         self.im_info_list = None
 
     def on_tab_change(self, index):
+        """
+        Event handler that is triggered when the user changes the active tab. Initializes the Analyze or Visualize
+        tabs if they are selected for the first time, and always initializes the Settings tab.
+
+        Parameters
+        ----------
+        index : int
+            The index of the newly selected tab.
+        """
         if index == self.analysis_tab:  # Check if the Analyze tab is selected
             if not self.analyzer.initialized:
                 show_info("Initializing analysis tab")
@@ -77,6 +142,10 @@ def on_tab_change(self, index):
         self.settings.post_init()
 
     def go_process(self):
+        """
+        Prepares the image(s) for processing and visualization. This method is called after a file has been selected
+        and validated. It enables the Process and Visualize tabs and initializes them.
+        """
         if self.file_select.batch_fileinfo_list is None:
             self.im_info = self.file_select.im_info
         else: