Fix tests, uniform formatting.

Author: AdvancedImagingUTSW

src/navigate/controller/sub_controllers/__init__.py

@@ -11,9 +11,7 @@
 from .waveform_popup import WaveformPopupController  # noqa
 from .autofocus import AutofocusPopupController  # noqa
 from .features_popup import FeaturePopupController  # noqa
-from .feature_advanced_setting import (
-    FeatureAdvancedSettingController,  # noqa
-)
+from .feature_advanced_setting import FeatureAdvancedSettingController  # noqa
 from .keystrokes import KeystrokeController  # noqa
 from .multiposition import MultiPositionController  # noqa
 from .ilastik import IlastikPopupController  # noqa

src/navigate/controller/sub_controllers/acquire_bar.py

@@ -54,20 +54,21 @@ def __init__(self, view, parent_controller):
         Parameters
         ----------
         view : object
-            Instance of the Acquire Bar View.
-        parent_view : object
-            Instance of the Main View.
+            Instance of the View.
         parent_controller : object
             Instance of the Main Controller.
         """
         super().__init__(view, parent_controller)
 
         #: str: Acquisition image mode.
         self.mode = "live"
+
         #: bool: Whether the image will be saved.
         self.is_save = False
+
         #: bool: Whether the microscope is acquiring.
         self.is_acquiring = False
+
         #: dict: Dictionary of different operating modes.
         self.mode_dict = {
             "Continuous Scan": "live",
@@ -101,10 +102,6 @@ def progress_bar(self, images_received, microscope_state, mode, stop=False):
             Number of images received in the controller.
         stop : bool
             Stop flag to set back to 0.
-
-        Examples
-        --------
-        >>> progress_bar(0, microscope_state, mode)
         """
 
         if images_received == 0:
@@ -230,10 +227,6 @@ def set_mode(self, mode):
         ----------
         mode: str
             Mode could be: 'live', 'z-stack', 'single', 'projection',
-
-        Examples
-        --------
-        >>> set_mode('live')
         """
         # update pull down combobox
         reverse_dict = dict(map(lambda v: (v[1], v[0]), self.mode_dict.items()))
@@ -253,10 +246,6 @@ def get_mode(self):
         -------
         mode : str
             Current imaging mode.
-
-        Examples
-        --------
-        >>> get_mode()
         """
         return self.mode
 
@@ -266,12 +255,7 @@ def add_mode(self, mode):
             self.view.pull_down["values"] = list(self.mode_dict.keys())
 
     def stop_acquire(self):
-        """Stop the acquisition.
-
-        Examples
-        --------
-        >>> stop_acquire()
-        """
+        """Stop the acquisition."""
         self.stop_progress_bar()
         self.view.acquire_btn.configure(text="Acquire")
         self.view.acquire_btn.configure(state="normal")

src/navigate/controller/sub_controllers/camera_map.py

@@ -62,10 +62,13 @@ def __init__(self, view, parent_controller=None):
             Parent controller of this controller.
         """
         super().__init__(view, parent_controller)
+
         #: str: Path to the camera maps directory.
         self.map_path = os.path.join(get_navigate_path(), "camera_maps")
+
         #: np.ndarray: Offset map.
         self.off = None
+
         #: np.ndarray: Variance map.
         self.var = None
 
@@ -79,10 +82,6 @@ def showup(self):
         """Show the popup.
 
         This method is called by the parent controller.
-
-        Example
-        -------
-        >>> self.parent_controller.show_popup("camera_map_setting_popup")
         """
         self.view.showup()
 
@@ -138,13 +137,11 @@ def display_plot(self):
 
         self.view.axs[0].hist(self.off.ravel(), bins=range(0, 2**8))
         self.view.axs[1].hist(self.var.ravel() * 0.47 * 0.47, bins=range(0, 2**8))
-
         self.view.axs[0].set_xlabel("Offset (counts)")
         self.view.axs[0].set_ylabel("Frequency")
         self.view.axs[0].set_yscale("log")
         self.view.axs[1].set_xlabel("Variance (counts$^2$)")
         self.view.axs[1].set_ylabel("Frequency")
         self.view.axs[1].set_yscale("log")
         self.view.fig.tight_layout()
-
         self.view.fig.canvas.draw_idle()

src/navigate/controller/sub_controllers/camera_settings.py

@@ -58,44 +58,59 @@ def __init__(self, view, parent_controller=None):
         """
         super().__init__(view, parent_controller)
 
-        # default values
         #: bool: True if in initialization
         self.in_initialization = True
+
         #: str: Resolution value
         self.resolution_value = "1x"
+
         #: str: Mode value
         self.mode = "stop"
+
         #: str: Solvent type
         self.solvent = "BABB"
 
         # Getting Widgets/Buttons
+
         #: dict: Mode widgets
         self.mode_widgets = view.camera_mode.get_widgets()
+
         #: dict: Framerate widgets
         self.framerate_widgets = view.framerate_info.get_widgets()
+
         #: dict: ROI widgets
         self.roi_widgets = view.camera_roi.get_widgets()
+
         #: dict: ROI buttons
         self.roi_btns = view.camera_roi.get_buttons()
 
         # initialize
+
         #: int: Default pixel size
         self.default_pixel_size = None
+
         #: int: Default width
         #: int: Default height
         self.default_width, self.default_height = None, None
+
         #: int: Trigger type - 1: Internal, 2: External, 3: Synchronous
         self.trigger_source = None
+
         #: int: Trigger active - 1: Edge, 2: Level, 3: Synchronous
         self.trigger_active = None
+
         #: int: Readout speed
         self.readout_speed = None
+
         #: int: Camera width step interval
         self.step_width = 4
+
         #: int: Camera height step interval
         self.step_height = 4
+
         #: int: Camera width minimum
         self.min_width = 4
+
         #: int: Camera height minimum
         self.min_height = 4
         self.initialize()
@@ -187,6 +202,7 @@ def populate_experiment_values(self):
         self.camera_setting_dict = self.parent_controller.configuration["experiment"][
             "CameraParameters"
         ]
+
         #: dict: Microscope state dictionary
         self.microscope_state_dict = self.parent_controller.configuration["experiment"][
             "MicroscopeState"

src/navigate/controller/sub_controllers/channels_settings.py

@@ -98,10 +98,6 @@ def set_mode(self, mode="stop"):
         ----------
         mode : str
             "stop" or "live"
-
-        Examples
-        --------
-        >>> self.set_mode("live")
         """
 
         self.mode = mode
@@ -127,12 +123,7 @@ def set_mode(self, mode="stop"):
                 self.view.defocus_spins[i].config(state=state)
 
     def initialize(self):
-        """Populates the laser and filter wheel options in the View.
-
-        Examples
-        --------
-        >>> self.initialize()
-        """
+        """Populates the laser and filter wheel options in the View."""
         setting_dict = self.configuration_controller.channels_info
         for i in range(self.num):
             self.view.laser_pulldowns[i]["values"] = setting_dict["laser"]
@@ -263,10 +254,6 @@ def channel_callback(self, channel_id, widget_name):
         -------
         success : bool
             Whether the callback function is executed successfully.
-
-        Examples
-        --------
-        >>> self.channel_callback(0, "laser")
         """
 
         channel_vals = self.get_vals_by_channel(channel_id)
@@ -399,10 +386,6 @@ def get_vals_by_channel(self, index):
         -------
         dict
             The values of the channel widgets.
-
-        Examples
-        --------
-        >>> self.get_vals_by_channel(0)
         """
         if index < 0 or index >= self.num:
             return {}
@@ -435,10 +418,6 @@ def get_index(self, dropdown_name, value):
         -------
         int
             The index of the value in the dropdown list.
-
-        Examples
-        --------
-        >>> self.get_index("laser", "488")
         """
         if not value:
             return -1

src/navigate/controller/sub_controllers/features_popup.py

@@ -69,10 +69,13 @@ def __init__(self, view, parent_controller, feature_list_id=0):
             The id of the feature list, by default 0
         """
         super().__init__(view, parent_controller)
+
         #: int: The id of the feature in the feature list.
         self.feature_list_id = feature_list_id
+
         #: list: The list of feature names.
         self.features = []
+
         #: list: The list of feature structure.
         self.feature_structure = []
 

src/navigate/controller/sub_controllers/ilastik.py

@@ -63,14 +63,19 @@ def __init__(self, view, parent_controller, service_url):
             url of the navigate_server for ilastik
         """
         super().__init__(view, parent_controller)
+
         #: str: url of the navigate_server for ilastik
         self.service_url = service_url
+
         #: str: ilastik project file name
         self.project_filename = None
+
         #: bool: show segmentation flag
         self.show_segmentation_flag = False
+
         #: bool: mark position flag
         self.mark_position_flag = False
+
         #: dict: label dictionary
         self.label_dict = None
         self.showup()

src/navigate/controller/sub_controllers/keystrokes.py

@@ -71,14 +71,17 @@ def __init__(self, main_view, parent_controller):
         # Main view
         #: tk.Frame: Main view
         self.main_view = main_view.root
+
         #: tk.Notebook: Main tabs
         self.main_tabs = main_view.settings
 
         # Controllers for all sub frames
         #: CameraViewController: Camera View Controller
         self.camera_controller = parent_controller.camera_view_controller
+
         #: MultipositionTableController: Multiposition Table Controller
         self.multi_controller = parent_controller.multiposition_tab_controller
+
         #: StageController: Stage Controller
         self.stage_controller = parent_controller.stage_controller
 
@@ -133,11 +136,6 @@ def camera_controller_mouse_wheel_enter(self, event):
         ----------
         event : tkinter event
             Mouse wheel event
-
-        Example
-        -------
-        >>> self.camera_view.canvas.bind("<Enter>",
-        >>> self.camera_controller_mouse_wheel_enter)
         """
         self.view.root.unbind("<MouseWheel>")  # get rid of scrollbar mousewheel
         if platform.system() != "Linux":
@@ -159,11 +157,6 @@ def camera_controller_mouse_wheel_leave(self, event):
         ----------
         event : tkinter event
             Mouse wheel event
-
-        Example
-        -------
-        >>> self.camera_view.canvas.bind("<Leave>",
-        >>> self.camera_controller_mouse_wheel_leave)
         """
 
         if platform.system() != "Linux":
@@ -182,10 +175,6 @@ def switch_tab(self, event):
         ----------
         event : tkinter event
             Tab key event
-
-        Example
-        -------
-        >>> self.main_view.bind("<Control-Key-1>", self.switch_tab)
         """
 
         key_val = int(event.keysym)
@@ -199,10 +188,6 @@ def widget_undo(self, event):
         ----------
         event : tkinter event
             Undo key event
-
-        Example
-        -------
-        >>> self.main_view.bind_all('<Control-Key-z>', self.widget_undo)
         """
         if isinstance(event.widget, ValidatedEntry) or isinstance(
             event.widget, ValidatedSpinbox
@@ -216,10 +201,6 @@ def widget_redo(self, event):
         ----------
         event : tkinter event
             Redo key event
-
-        Example
-        -------
-        >>> self.main_view.bind_all('<Control-Key-y>', self.widget_redo)
         """
 
         if isinstance(event.widget, ValidatedEntry) or isinstance(

src/navigate/controller/sub_controllers/microscope_popup.py

@@ -65,16 +65,22 @@ def __init__(self, view, parent_controller, microscope_info):
 
         """
         super().__init__(view, parent_controller)
+
         #: tk.Toplevel-derived: The popup window.
         self.view = MicroscopeSettingPopupWindow(view, microscope_info)
+
         #: dict: A dictionary containing the widgets.
         self.widgets = self.view.get_widgets()
+
         #: dict: A dictionary containing the variables.
         self.variables = self.view.get_variables()
+
         #: dict: A dictionary containing the buttons.
         self.buttons = self.view.get_buttons()
+
         #: dict: A dictionary containing the microscope information.
         self.microscope_info = microscope_info
+
         #: str: The name of the primary microscope.
         self.primary_microscope = None