Reviewing PR

A typo was found in the gui sub-controller. All other changes are negligible.

Author: AdvancedImagingUTSW

src/navigate/controller/controller.py

@@ -174,28 +174,24 @@ def __init__(
         logger.info(f"Spec - Waveform Constants Path: {waveform_constants_path}")
         logger.info(f"Spec - Rest API Path: {rest_api_path}")
 
-        # Wire up pipes
         #: mp.Pipe: Pipe for sending images from model to view.
         self.show_img_pipe = self.model.create_pipe("show_img_pipe")
 
-        # save default experiment file
         #: string: Path to the default experiment yaml file.
         self.default_experiment_file = experiment_path
 
-        # waveform setting file
         #: string: Path to the waveform constants yaml file.
         self.waveform_constants_path = waveform_constants_path
 
-        # Configuration Reader
         #: ConfigurationController: Configuration Controller object.
         self.configuration_controller = ConfigurationController(self.configuration)
 
-        # Initialize the View
         #: View: View object in MVC architecture.
         self.view = view(root)
 
-        # Sub Gui Controllers
+        #: dict: Event listeners for the controller.
         self.event_listeners = {}
+
         #: AcquireBarController: Acquire Bar Sub-Controller.
         self.acquire_bar_controller = AcquireBarController(self.view.acqbar, self)
 
@@ -235,7 +231,7 @@ def __init__(
         #: KeystrokeController: Keystroke Sub-Controller.
         self.keystroke_controller = KeystrokeController(self.view, self)
 
-        # Exit
+        # Exit the program when the window is closed
         self.view.root.protocol(
             "WM_DELETE_WINDOW", self.acquire_bar_controller.exit_program
         )
@@ -249,22 +245,19 @@ def __init__(
         # self.microscope = self.configuration['configuration']
         # ['microscopes'].keys()[0]  # Default to the first microscope
 
-        # Initialize the menus
         #: MenuController: Menu Sub-Controller.
         self.menu_controller = MenuController(view=self.view, parent_controller=self)
         self.menu_controller.initialize_menus()
 
         #: dict: acquisition modes from plugins
         self.plugin_acquisition_modes = {}
 
-        # add plugin menus
         #: PluginsController: Plugin Sub-Controller
         self.plugin_controller = PluginsController(
             view=self.view, parent_controller=self
         )
         self.plugin_controller.load_plugins()
 
-        # Create default data buffer
         #: int: Number of x_pixels from microscope configuration file.
         self.img_width = 0
 
@@ -474,8 +467,10 @@ def update_experiment_setting(self):
             "multiposition_count"
         ] = len(positions)
 
-        if self.configuration["experiment"]["MicroscopeState"]["is_multiposition"] \
-            and len(positions) == 0:
+        if (
+            self.configuration["experiment"]["MicroscopeState"]["is_multiposition"]
+            and len(positions) == 0
+        ):
             # Update the view and override the settings.
             self.configuration["experiment"]["MicroscopeState"][
                 "is_multiposition"
@@ -1262,15 +1257,40 @@ def update_event(self):
                     print(f"*** unhandled event: {event}, {value}")
 
     def add_acquisition_mode(self, name, acquisition_obj):
+        """Add and Acquisition Mode.
+
+        Parameters
+        ----------
+        name : string
+            Name of the acquisition mode.
+        acquisition_obj : object
+            Object of the acquisition mode.
+        """
         if name in self.plugin_acquisition_modes:
             print(f"*** plugin acquisition mode {name} exists, can't add another one!")
             return
         self.plugin_acquisition_modes[name] = acquisition_obj(name)
         self.acquire_bar_controller.add_mode(name)
 
     def register_event_listener(self, event_name, event_handler):
+        """Register an event listener.
+
+        Parameters
+        ----------
+        event_name : string
+            Name of the event.
+        event_handler : function
+            Function to handle the event.
+        """
         self.event_listeners[event_name] = event_handler
 
     def register_event_listeners(self, events):
+        """Register multiple event listeners.
+
+        Parameters
+        ----------
+        events : dict
+            Dictionary of event names and handlers.
+        """
         for event_name, event_handler in events.items():
             self.register_event_listener(event_name, event_handler)

src/navigate/controller/sub_controllers/adaptive_optics.py

@@ -443,6 +443,7 @@ def plot_tw_trace(self):
 
     @property
     def custom_events(self):
+        """dict: Custom events for this controller"""
         return {
             "ao_save_report": self.save_report_to_file,
             "mirror_update": self.plot_mirror,

src/navigate/controller/sub_controllers/autofocus.py

@@ -274,6 +274,5 @@ def display_plot(self, data_and_flags):
 
     @property
     def custom_events(self):
-        return {
-            "autofocus": self.display_plot
-        }
+        """dict: Custom events for this controller"""
+        return {"autofocus": self.display_plot}

src/navigate/controller/sub_controllers/camera_settings.py

@@ -582,7 +582,7 @@ def update_camera_device_related_setting(self):
 
     def update_camera_parameters_silent(self, value):
         """Update GUI camera parameters
-        
+
         Parameters
         ----------
         value : tuple
@@ -598,6 +598,5 @@ def update_camera_parameters_silent(self, value):
 
     @property
     def custom_events(self):
-        return {
-            "display_camera_parameters": self.update_camera_parameters_silent
-        }
+        """dict: Custom events for this controller"""
+        return {"display_camera_parameters": self.update_camera_parameters_silent}

src/navigate/controller/sub_controllers/camera_view.py

@@ -1241,6 +1241,5 @@ def try_to_display_image(self, image_id):
 
     @property
     def custom_events(self):
-        return {
-            "ilastik_mask": self.display_mask
-        }
+        """dict: Custom events for this controller"""
+        return {"ilastik_mask": self.display_mask}

src/navigate/controller/sub_controllers/channels_tab.py

@@ -103,9 +103,8 @@ def __init__(self, view, parent_controller=None):
         self.stack_acq_vals["step_size"].trace_add("write", self.update_z_steps)
         self.stack_acq_vals["start_position"].trace_add("write", self.update_z_steps)
         self.stack_acq_vals["end_position"].trace_add("write", self.update_z_steps)
-        self.stack_acq_vals["start_focus"].trace_add(
-            "write", self.update_z_steps
-        )  # TODO: could be remove later
+        # TODO: could be remove later
+        self.stack_acq_vals["start_focus"].trace_add("write", self.update_z_steps)
         self.stack_acq_buttons["set_start"].configure(
             command=self.update_start_position
         )
@@ -850,6 +849,5 @@ def set_exposure_time(self, channel_exposure_time):
 
     @property
     def custom_events(self):
-        return {
-            "exposure_time": self.set_exposure_time
-        }
+        """Custom events for the channels tab."""
+        return {"exposure_time": self.set_exposure_time}

src/navigate/controller/sub_controllers/gui.py

@@ -117,12 +117,20 @@ def show_verbose_info(self, *info):
         logger.info(f"{self.__class__.__name__} : {info}")
 
     def register_event_listener(self, event_name, event_handler):
-        """Register event listner in the parent_controller
+        """Register event listener in the parent_controller
+
+        Parameters
+        ----------
+        event_name : str
+            event name
+        event_handler : function
+            event handler
         """
-        if not hasattr(self.parent_controller, "event_listners"):
-            self.parent_controller.event_listerners = {}
+        if not hasattr(self.parent_controller, "event_listeners"):
+            self.parent_controller.event_listeners = {}
         self.parent_controller.event_listeners[event_name] = event_handler
 
     @property
     def custom_events(self):
+        """Custom events for the controller"""
         return {}

src/navigate/controller/sub_controllers/multiposition.py

@@ -288,6 +288,5 @@ def remove_positions(self, position_flag_list):
 
     @property
     def custom_events(self):
-        return {
-            "remove_positions": self.remove_positions
-        }
+        """Return custom events for the Multi-Position Controller."""
+        return {"remove_positions": self.remove_positions}

src/navigate/controller/sub_controllers/plugins.py

@@ -223,7 +223,9 @@ def build_tab_window(self, plugin_name, frame, controller):
             plugin_frame = frame(self.view.settings)
             self.view.settings.add(plugin_frame, text=plugin_name, sticky=tk.NSEW)
             plugin_controller = controller(plugin_frame, self.parent_controller)
-            self.parent_controller.register_event_listeners(getattr(plugin_controller, "custom_events", {}))
+            self.parent_controller.register_event_listeners(
+                getattr(plugin_controller, "custom_events", {})
+            )
             controller_name = (
                 "__plugin" + "_".join(plugin_name.lower().split()) + "_controller"
             )
@@ -273,7 +275,9 @@ def func(*args, **kwargs):
             plugin_frame.grid(row=0, column=0, sticky=tk.NSEW, padx=10, pady=10)
 
             plugin_controller = controller(plugin_frame, self.parent_controller)
-            self.parent_controller.register_event_listeners(getattr(plugin_controller, "custom_events", {}))
+            self.parent_controller.register_event_listeners(
+                getattr(plugin_controller, "custom_events", {})
+            )
 
             plugin_controller.popup = popup
             popup.deiconify()

src/navigate/controller/sub_controllers/waveform_tab.py

@@ -337,6 +337,5 @@ def set_waveform_template(self, template_name):
 
     @property
     def custom_events(self):
-        return {
-            "waveform": self.update_waveforms
-        }
+        """Custom events for the waveform tab"""
+        return {"waveform": self.update_waveforms}