Merge branch 'develop' into pr/941

Author: AdvancedImagingUTSW

src/navigate/controller/sub_controllers/__init__.py

@@ -2,24 +2,23 @@
 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 (
-    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 .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 .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
@@ -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:
@@ -171,10 +168,7 @@ 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 +217,7 @@ 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):
@@ -235,10 +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()))
@@ -258,10 +246,6 @@ def get_mode(self):
         -------
         mode : str
             Current imaging mode.
-
-        Examples
-        --------
-        >>> get_mode()
         """
         return self.mode
 
@@ -271,12 +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/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
 
@@ -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_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]
@@ -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"
@@ -450,7 +466,7 @@ 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"][
@@ -505,7 +521,7 @@ 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