Merge sides

src/aslm/controller/aslm_configuration_controller.py

@@ -75,9 +75,9 @@ def get_pixels(self, verbose=False):
                 self.configuration.CameraParameters['y_pixels']]
 
     def get_framerate(self, verbose=False):
-        '''
+        """
         # Gets default framerate info from camera
-        '''
+        """
         pass  # TODO Kevin this is where you pull in and then calculate the info from the config file to initializing the framerate widgets
 
     def get_stage_position(self):

src/aslm/controller/aslm_controller.py

@@ -34,9 +34,7 @@
 #  Standard Library Imports
 import tkinter
 import multiprocessing as mp
-import time
 import threading
-from pathlib import Path
 
 # Third Party Imports
 
@@ -62,7 +60,8 @@
 # Local Model Imports
 from aslm.model.aslm_model import Model
 from aslm.model.aslm_model_config import Session as session
-from aslm.model.concurrency.concurrency_tools import ObjectInSubprocess, SharedNDArray
+from aslm.model.concurrency.concurrency_tools import ObjectInSubprocess
+from aslm.tools.common_dict_tools import update_settings_common, update_stage_dict
 
 # debug
 from aslm.controller.aslm_debug import Debug_Module
@@ -71,11 +70,11 @@
 from pathlib import Path
 
 # Logger Setup
-
 import logging
 p = __name__.split(".")[1]
 logger = logging.getLogger(p)
 
+
 class ASLM_controller:
     """ ASLM Controller
 
@@ -140,7 +139,7 @@ def __init__(
 
         # etl setting file
         self.etl_constants_path = etl_constants_path
-        self.etl_setting = session(self.etl_constants_path, self.verbose)
+        self.etl_constants = session(self.etl_constants_path, self.verbose)
 
         # Initialize the View
         self.view = view(root)
@@ -285,10 +284,12 @@ def popup_etl_setting():
             etl_setting_popup = remote_popup(self.view)  # TODO: should we rename etl_setting popup to remote_focus_popup?
             self.etl_controller = Etl_Popup_Controller(etl_setting_popup,
                                                        self,
-                                                       self.verbose,
-                                                       self.etl_setting,
+                                                       self.etl_constants,
                                                        self.etl_constants_path,
-                                                       self.experiment.GalvoParameters)
+                                                       self.configuration,
+                                                       self.experiment.GalvoParameters,
+                                                       self.verbose)
+
             self.etl_controller.set_experiment_values(self.resolution_value.get())
             self.etl_controller.set_mode(self.acquire_bar_controller.mode)
 
@@ -335,7 +336,7 @@ def popup_autofocus_setting():
         meso_res_sub_menu = tkinter.Menu(self.view.menubar.menu_resolution)
         self.view.menubar.menu_resolution.add_cascade(menu=meso_res_sub_menu,label='Mesoscale')
 
-        for res in self.etl_setting.ETLConstants['low'].keys():
+        for res in self.etl_constants.ETLConstants['low'].keys():
             meso_res_sub_menu.add_radiobutton(label=res,
                                               variable=self.resolution_value,
                                               value=res)
@@ -449,7 +450,7 @@ def set_mode_of_sub(self, mode):
             self.etl_controller.set_mode(mode)
         if mode == 'stop':
             # GUI Failsafe
-            self.acquire_bar_controller.view.acquire_btn.configure(text='Acquire')
+            self.acquire_bar_controller.stop_acquire()
 
     def update_camera_view(self):
         r"""Update the real-time parameters in the camera view (channel number, max counts, image, etc.)
@@ -546,6 +547,7 @@ def execute(self, command, *args):
                 'laser_info': self.resolution_info.ETLConstants[self.resolution][self.mag]
                 }
             """
+            update_settings_common(self, args)
             self.threads_pool.createThread('model', lambda: self.model.run_command('update_setting', *args))
 
         elif command == 'autofocus':
@@ -715,9 +717,7 @@ def move_stage(self, pos_dict):
         """
 
         # Update our local stage dictionary
-        for axis, val in pos_dict.items():
-            ax = axis.split('_')[0]
-            self.experiment.StageParameters[ax] = val
+        update_stage_dict(self, pos_dict)
 
         # Pass to model
         self.model.move_stage(pos_dict)

src/aslm/controller/sub_controllers/acquire_bar_controller.py

@@ -44,6 +44,7 @@
 p = __name__.split(".")[1]
 logger = logging.getLogger(p)
 
+
 class Acquire_Bar_Controller(GUI_Controller):
     def __init__(self, view, parent_controller, verbose=False):
         super().__init__(view, parent_controller, verbose)
@@ -153,9 +154,7 @@ def launch_popup_window(self):
             # tell the controller to stop acquire(continuous mode)
             self.parent_controller.execute('stop_acquire')
         else:
-            # if the mode is 'live'
-            if self.mode == 'live':
-                self.view.acquire_btn.configure(text='Stop')
+            self.view.acquire_btn.configure(text='Stop')
             self.parent_controller.execute('acquire')
 
     def update_microscope_mode(self, *args):
@@ -174,8 +173,6 @@ def update_file_type(self, file_type):
         """
         self.saving_settings['file_type'] = file_type.get()
 
-
-
     def launch_acquisition(self, popup_window):
         """
         # Once the popup window has been filled out, we first create the save path using the create_save_path function.
@@ -198,6 +195,9 @@ def launch_acquisition(self, popup_window):
             # Close the window
             popup_window.popup.dismiss(self.verbose)
 
+            # We are now acquiring
+            self.view.acquire_btn.configure(text='Stop')
+
     def exit_program(self):
         self.show_verbose_info("Exiting Program")
         # call the central controller to stop all the threads

src/aslm/controller/sub_controllers/autofocus_popup_controller.py

@@ -90,9 +90,9 @@ def start_autofocus(self):
         self.parent_controller.execute('autofocus')
 
     def display_plot(self, data):
-        '''
+        """
         ### Displays a plot of [focus, entropy] with data from autofocus routine
-        '''
+        """
 
         coarse_range = self.setting_dict['coarse_range']
         coarse_step = self.setting_dict['coarse_step_size']

src/aslm/controller/sub_controllers/camera_setting_controller.py

@@ -78,9 +78,9 @@ def __init__(
             )
 
     def initialize(self, config):
-        '''
+        """
         ## Function that sets widgets based on data given from main controller/config
-        '''
+        """
 
         # Get Default Configuration Values
         self.default_pixel_size = config.configuration.CameraParameters['pixel_size_in_microns']
@@ -206,7 +206,7 @@ def update_experiment_values(self, setting_dict):
         return True
 
     def update_sensor_mode(self, *args):
-        '''
+        """
         Updates text in readout widget based on what sensor mode is selected
         If we are in the Light Sheet mode, then we want the camera
         self.model.CameraParameters['sensor_mode']) == 12
@@ -215,7 +215,7 @@ def update_sensor_mode(self, *args):
         self.model.CameraParameters['sensor_mode']) == 1
 
         Should initialize from the configuration file to the default version
-        '''
+        """
         # Camera Mode
         sensor_value = self.mode_widgets['Sensor'].widget.get()
         if sensor_value == 'Normal':

src/aslm/controller/sub_controllers/camera_view_controller.py

@@ -80,6 +80,7 @@ def __init__(self, view, parent_controller=None, verbose=False):
         #  Stored Images
         self.tk_image = None
         self.image = None
+        self.cross_hair_image = None
         self.saturated_pixels = None
 
         # Widget Defaults
@@ -103,9 +104,9 @@ def __init__(self, view, parent_controller=None, verbose=False):
         self.bit_depth = 8  # bit-depth for PIL presentation.
 
     def initialize(self, name, data):
-        '''
+        """
         # Function that sets widgets based on data given from main controller/config
-        '''
+        """
         # Pallete section (colors, autoscale, min/max counts)
         # keys = ['Frames to Avg', 'Image Max Counts', 'Channel']
         if name == 'minmax':
@@ -180,10 +181,6 @@ def update_max_counts(self):
                 # Update GUI
                 self.image_metrics['Image'].set(np.max(self.temp_array))
 
-                if self.verbose:
-                    print("Rolling Average: ", self.image_count, self.rolling_frames)
-                logger.debug(f"Rolling Average: , {self.image_count}, {self.rolling_frames}")
-
     def downsample_image(self):
         """
         #  Down-sample the data for image display according to the configuration file.
@@ -278,8 +275,7 @@ def add_crosshair(self):
             self.cross_hair_image[height, :] = 1
 
     def apply_LUT(self):
-        """
-        Applies a LUT to the image.
+        r"""Applies a LUT to the image.
         Red is reserved for saturated pixels.
         self.color_values = ['gray', 'gradient', 'rainbow']
         """
@@ -335,15 +331,11 @@ def toggle_min_max_buttons(self):
         if self.autoscale is True:  # Autoscale Enabled
             self.image_palette['Min'].widget['state'] = 'disabled'
             self.image_palette['Max'].widget['state'] = 'disabled'
-            if self.verbose:
-                print("Autoscale Enabled")
             logger.debug("Autoscale Enabled")
 
         elif self.autoscale is False:  # Autoscale Disabled
             self.image_palette['Min'].widget['state'] = 'normal'
             self.image_palette['Max'].widget['state'] = 'normal'
-            if self.verbose:
-                print("Autoscale Disabled")
             logger.debug("Autoscale Disabled")
             self.update_min_max_counts()
 
@@ -357,7 +349,5 @@ def update_min_max_counts(self):
         """
         self.min_counts = self.image_palette['Min'].get()
         self.max_counts = self.image_palette['Max'].get()
-        if self.verbose:
-            print("Min and Max counts scaled to ", self.min_counts, self.max_counts)
         logger.debug(f"Min and Max counts scaled to, {self.min_counts}, {self.max_counts}")
 

src/aslm/controller/sub_controllers/channel_setting_controller.py

@@ -40,9 +40,9 @@
 p = __name__.split(".")[1]
 logger = logging.getLogger(p)
 
-'''
+"""
 TODO Create a dictionary for widgets that holds a list of widgets for each column.Will attempt after formatting.
-'''
+"""
 
 class Channel_Setting_Controller(GUI_Controller):
     def __init__(self, view, parent_controller=None, verbose=False):

src/aslm/controller/sub_controllers/channels_tab_controller.py

@@ -237,11 +237,12 @@ def set_mode(self, mode):
         self.mode = mode
         self.channel_setting_controller.set_mode(mode)
 
-        state = 'normal' if mode == 'stop' else 'disabled'
-        self.view.stack_acq_frame.step_size_spinbox['state'] = state
-        self.view.stack_acq_frame.start_pos_spinbox['state'] = state
-        self.view.stack_acq_frame.end_pos_spinbox['state'] = state
+        state = 'active' if mode == 'stop' else 'disabled'
+        self.stack_acq_widgets['step_size'].state([state])
+        self.stack_acq_widgets['start_position'].state([state])
+        self.stack_acq_widgets['end_position'].state([state])
 
+        state = 'normal' if mode == 'stop' else 'disabled'
         self.view.stack_timepoint_frame.save_check['state'] = state
         self.view.stack_timepoint_frame.stack_pause_spinbox['state'] = state
         self.view.stack_timepoint_frame.exp_time_spinbox['state'] = state