Rename sub-controllers

Author: AdvancedImagingUTSW

src/navigate/controller/sub_controllers/__init__.py

@@ -2,24 +2,25 @@
 Sub-controllers for navigate.
 """
 
-from .stage_controller import StageController  # noqa
-from .acquire_bar_controller import AcquireBarController  # noqa
-from .channels_tab_controller import ChannelsTabController  # noqa
-from .camera_view_controller import CameraViewController  # noqa
-from .camera_setting_controller import CameraSettingController  # noqa
-from .waveform_tab_controller import WaveformTabController  # noqa
-from .waveform_popup_controller import WaveformPopupController  # noqa
-from .autofocus_popup_controller import AutofocusPopupController  # noqa
-from .features_popup_controller import FeaturePopupController  # noqa
-from .feature_advanced_setting_controller import (
+from .stages import StageController  # noqa
+from .acquire_bar import AcquireBarController  # noqa
+from .channels_tab import ChannelsTabController  # noqa
+from .camera_view import CameraViewController  # noqa
+from .camera_settings import CameraSettingController  # noqa
+from .waveform_tab import WaveformTabController  # noqa
+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 .keystroke_controller import KeystrokeController  # noqa
-from .multi_position_controller import MultiPositionController  # noqa
-from .ilastik_popup_controller import IlastikPopupController  # noqa
-from .camera_map_setting_popup_controller import CameraMapSettingPopupController  # noqa
-from .microscope_popup_controller import MicroscopePopupController  # noqa
-from .adaptiveoptics_popup_controller import AdaptiveOpticsPopupController  # noqa
+from .keystrokes import KeystrokeController  # noqa
+from .multiposition import MultiPositionController  # noqa
+from .ilastik import IlastikPopupController  # noqa
+from .camera_map import CameraMapSettingPopupController  # noqa
+from .microscope_popup import MicroscopePopupController  # noqa
+from .adaptive_optics import AdaptiveOpticsPopupController  # noqa
+
 # from .uninstall_plugin_controller import UninstallPluginController  # noqa
-from .plugins_controller import PluginsController, UninstallPluginController  # noqa
-from .menu_controller import MenuController  # noqa
+from .plugins import PluginsController, UninstallPluginController  # noqa
+from .menus import MenuController  # noqa

src/navigate/controller/sub_controllers/acquire_bar_controller.py renamed to src/navigate/controller/sub_controllers/acquire_bar.py

@@ -37,7 +37,7 @@
 # Third Party Imports
 
 # Local Imports
-from navigate.controller.sub_controllers.gui_controller import GUIController
+from navigate.controller.sub_controllers.gui import GUIController
 from navigate.view.popups.acquire_popup import AcquirePopUp
 
 # Logger Setup
@@ -171,10 +171,7 @@ def progress_bar(self, images_received, microscope_state, mode, stop=False):
                     except ZeroDivisionError:
                         pass
 
-                if (
-                    mode == "z-stack"
-                    or mode == "ConstantVelocityAcquisition"
-                ):
+                if mode == "z-stack" or mode == "ConstantVelocityAcquisition":
                     top_percent_complete = 100 * (
                         images_received / top_anticipated_images
                     )
@@ -223,9 +220,7 @@ def update_progress_label(self, seconds_left):
         hours, remainder = divmod(seconds_left, 3600)
         minutes, seconds = divmod(remainder, 60)
         self.view.total_acquisition_label.config(
-            text=f"{int(hours):02}"
-                 f":{int(minutes):02}"
-                 f":{int(seconds):02}"
+            text=f"{int(hours):02}" f":{int(minutes):02}" f":{int(seconds):02}"
         )
 
     def set_mode(self, mode):

src/navigate/controller/sub_controllers/adaptiveoptics_popup_controller.py renamed to src/navigate/controller/sub_controllers/adaptive_optics.py

@@ -39,7 +39,7 @@
 # from matplotlib.axes import Axes
 
 # Local application imports
-from navigate.controller.sub_controllers.gui_controller import GUIController
+from navigate.controller.sub_controllers.gui import GUIController
 
 # Logger Setup
 p = __name__.split(".")[1]
@@ -318,7 +318,7 @@ def run_tony_wilson(self):
         # set the saving file name before running
         if self.widgets["save_report"]["variable"].get():
             save_dir = self.parent_controller.configuration["experiment"]["Saving"][
-            "save_directory"
+                "save_directory"
             ]
 
             self.report_path = filedialog.asksaveasfilename(
@@ -334,7 +334,7 @@ def save_report_to_file(self, report):
         full_report = {}
 
         for i, page in enumerate(report):
-            full_report[f"iter_{i}"] = page       
+            full_report[f"iter_{i}"] = page
 
         import pandas as pd
 

src/navigate/controller/sub_controllers/autofocus_popup_controller.py renamed to src/navigate/controller/sub_controllers/autofocus.py

@@ -38,7 +38,7 @@
 from tkinter import messagebox
 
 # Local Imports
-from navigate.controller.sub_controllers.gui_controller import GUIController
+from navigate.controller.sub_controllers.gui import GUIController
 from navigate.tools.common_functions import combine_funcs
 
 
@@ -62,13 +62,17 @@ def __init__(self, view, parent_controller):
             The parent controller of the autofocus popup.
         """
         super().__init__(view, parent_controller)
+
         #: dict: The autofocus setting dictionary.
         self.widgets = self.view.get_widgets()
+
         #: object: The autofocus figure.
         self.autofocus_fig = self.view.fig
+
         #: object: The autofocus coarse plot.
         self.autofocus_coarse = self.view.coarse
         self.populate_experiment_values()
+
         #: object: The autofocus coarse plot.
         self.coarse_plot = None
 
@@ -147,7 +151,7 @@ def start_autofocus(self):
                     value = float(setting_dict[f"{k}_range"])
                     if step <= 0 or value < step:
                         warning_message += f"{k} settings are not correct!\n"
-                except:
+                except Exception:
                     warning_message += f"{k} settings are not correct!\n"
         if warning_message:
             messagebox.showerror(

src/navigate/controller/sub_controllers/camera_map_setting_popup_controller.py renamed to src/navigate/controller/sub_controllers/camera_map.py

@@ -39,7 +39,7 @@
 import tifffile
 
 # Local application imports
-from navigate.controller.sub_controllers.gui_controller import GUIController
+from navigate.controller.sub_controllers.gui import GUIController
 from navigate.config import get_navigate_path
 from navigate.model.analysis.camera import compute_scmos_offset_and_variance_map
 

src/navigate/controller/sub_controllers/camera_setting_controller.py renamed to src/navigate/controller/sub_controllers/camera_settings.py

@@ -36,7 +36,7 @@
 # Third Party Imports
 
 # Local Imports
-from navigate.controller.sub_controllers.gui_controller import GUIController
+from navigate.controller.sub_controllers.gui import GUIController
 
 # Logger Setup
 p = __name__.split(".")[1]
@@ -445,7 +445,7 @@ def calculate_physical_dimensions(self):
         try:
             x_pixel = float(self.roi_widgets["Width"].get())
             y_pixel = float(self.roi_widgets["Height"].get())
-        except ValueError as e:
+        except ValueError:
             return
 
         microscope_state_dict = self.parent_controller.configuration["experiment"][
@@ -500,7 +500,7 @@ def update_number_of_pixels(self, *args):
 
         if self.pixel_event_id:
             self.view.after_cancel(self.pixel_event_id)
-        
+
         pixels = self.mode_widgets["Pixels"].get()
         if pixels == "":
             return

src/navigate/controller/sub_controllers/camera_view_controller.py renamed to src/navigate/controller/sub_controllers/camera_view.py

@@ -44,7 +44,7 @@
 import copy
 
 # Local Imports
-from navigate.controller.sub_controllers.gui_controller import GUIController
+from navigate.controller.sub_controllers.gui import GUIController
 from navigate.model.analysis.camera import compute_signal_to_noise
 from navigate.tools.common_functions import VariableWithLock
 

src/navigate/controller/sub_controllers/channel_setting_controller.py renamed to src/navigate/controller/sub_controllers/channels_settings.py

@@ -37,7 +37,7 @@
 # Third party imports
 
 # Local application imports
-from navigate.controller.sub_controllers.gui_controller import GUIController
+from navigate.controller.sub_controllers.gui import GUIController
 
 # Logger Setup
 p = __name__.split(".")[1]

src/navigate/controller/sub_controllers/channels_tab_controller.py renamed to src/navigate/controller/sub_controllers/channels_tab.py

@@ -40,11 +40,11 @@
 import tkinter as tk
 
 # Local Imports
-from navigate.controller.sub_controllers.gui_controller import GUIController
-from navigate.controller.sub_controllers.channel_setting_controller import (
+from navigate.controller.sub_controllers.gui import GUIController
+from navigate.controller.sub_controllers.channels_settings import (
     ChannelSettingController,
 )
-from navigate.controller.sub_controllers.tiling_wizard_controller import (
+from navigate.controller.sub_controllers.tiling import (
     TilingWizardController,
 )
 

src/navigate/controller/sub_controllers/feature_advanced_setting_controller.py renamed to src/navigate/controller/sub_controllers/feature_advanced_setting.py

@@ -40,8 +40,6 @@
 
 # Local application imports
 from navigate.model.features import feature_related_functions
-
-# from navigate.model.features.feature_related_functions import convert_str_to_feature_list
 from navigate.view.popups.feature_list_popup import FeatureAdvancedSettingPopup
 from navigate.tools.file_functions import load_yaml_file, save_yaml_file
 from navigate.tools.common_functions import load_module_from_file
@@ -85,7 +83,7 @@ def refresh_popup_window(self, popup):
 
         Parameters
         ----------
-        popup : navigate.view.popups.feature_list_popup.FeatureAdvancedSettingPopup
+        popup : FeatureAdvancedSettingPopup
             The popup window
         """
         feature_name = popup.feature_name_widget.get()
@@ -190,7 +188,9 @@ def save_parameters(self):
                         if row[1].get() == "None":
                             feature_parameter_config[arg_name][row[0].get()] = None
                         else:
-                            feature_parameter_config[arg_name][row[0].get()] = row[1].get()
+                            feature_parameter_config[arg_name][row[0].get()] = row[
+                                1
+                            ].get()
                     else:
                         unloaded_functions.append(row[0].get())
 
@@ -208,15 +208,13 @@ def save_parameters(self):
         if unloaded_functions:
             if len(unloaded_functions) == 1:
                 alert_message = f"Function {unloaded_functions[0]} isn't loaded!"
-            else: 
-                alert_message = f"Functions {', '.join(unloaded_functions)} are not loaded!"
-            messagebox.showwarning(
-                title="Warning",
-                message=alert_message
-            )
+            else:
+                alert_message = (
+                    f"Functions {', '.join(unloaded_functions)} are not loaded!"
+                )
+            messagebox.showwarning(title="Warning", message=alert_message)
         self.popup.popup.attributes("-topmost", 1)
 
-
     def exit_func(self):
         """Exit the popup window"""
         self.save_parameters()