spacr 0.0.2__py3-none-any.whl → 0.0.6__py3-none-any.whl

spacr/gui_mask_app.py

@@ -1,10 +1,10 @@
-import spacr, sys, ctypes, csv, matplotlib
+#import customtkinter as ctk
+
+import sys, ctypes, matplotlib
 import tkinter as tk
 from tkinter import ttk, scrolledtext
-from ttkthemes import ThemedTk
 from matplotlib.figure import Figure
 from matplotlib.backends.backend_tkagg import FigureCanvasTkAgg
-from matplotlib.figure import Figure
 matplotlib.use('Agg')
 from tkinter import filedialog
 from multiprocessing import Process, Queue, Value
@@ -16,12 +16,42 @@ except AttributeError:
     pass
 
 from .logger import log_function_call
-from .gui_utils import ScrollableFrame, StdoutRedirector, safe_literal_eval, clear_canvas, main_thread_update_function, create_dark_mode, set_dark_style, set_default_font, generate_fields, process_stdout_stderr
-from .gui_utils import mask_variables, check_mask_gui_settings, preprocess_generate_masks_wrapper, read_settings_from_csv, update_settings_from_csv #, add_mask_gui_defaults
+from .gui_utils import ScrollableFrame, StdoutRedirector, ToggleSwitch, CustomButton, ToolTip
+from .gui_utils import clear_canvas, main_thread_update_function, set_dark_style, generate_fields, process_stdout_stderr, set_default_font, style_text_boxes
+from .gui_utils import mask_variables, check_mask_gui_settings, preprocess_generate_masks_wrapper, read_settings_from_csv, update_settings_from_csv, create_menu_bar
 
 thread_control = {"run_thread": None, "stop_requested": False}
 
-@log_function_call
+def toggle_test_mode():
+    global vars_dict
+    current_state = vars_dict['test_mode'][2].get()
+    new_state = not current_state
+    vars_dict['test_mode'][2].set(new_state)
+    if new_state:
+        test_mode_button.config(bg="blue")
+    else:
+        test_mode_button.config(bg="gray")
+
+def toggle_advanced_settings():
+    global vars_dict
+
+    timelapse_settings = ['timelapse', 'timelapse_memory', 'timelapse_remove_transient', 'timelapse_mode', 'timelapse_objects', 'timelapse_displacement', 'timelapse_frame_limits', 'fps']
+    misc_settings = ['examples_to_plot', 'all_to_mip', 'pick_slice', 'skip_mode']
+    opperational_settings = ['preprocess', 'masks', 'randomize', 'batch_size', 'custom_regex', 'merge', 'normalize_plots', 'workers', 'plot', 'remove_background', 'lower_quantile']
+
+    advanced_settings = timelapse_settings+misc_settings+opperational_settings
+
+    # Toggle visibility of advanced settings
+    for setting in advanced_settings:
+        label, widget, var = vars_dict[setting]
+        if advanced_var.get() is False:
+            label.grid_remove()  # Hide the label
+            widget.grid_remove()  # Hide the widget
+        else:
+            label.grid()  # Show the label
+            widget.grid()  # Show the widget
+
+#@log_function_call
 def initiate_abort():
     global thread_control
     if thread_control.get("stop_requested") is not None:
@@ -32,25 +62,21 @@ def initiate_abort():
         if thread_control["run_thread"].is_alive():
             thread_control["run_thread"].terminate()
         thread_control["run_thread"] = None
-        
-@log_function_call
+
+#@log_function_call
 def run_mask_gui(q, fig_queue, stop_requested):
     global vars_dict
     process_stdout_stderr(q)
     try:
         settings = check_mask_gui_settings(vars_dict)
-        #settings = add_mask_gui_defaults(settings)
-        #for key in settings:
-        #    value = settings[key]
-        #    print(key, value, type(value))
         preprocess_generate_masks_wrapper(settings, q, fig_queue)
     except Exception as e:
         q.put(f"Error during processing: {e}")
         traceback.print_exc()
     finally:
         stop_requested.value = 1
-    
-@log_function_call
+
+#@log_function_call
 def start_process(q, fig_queue):
     global thread_control
     if thread_control.get("run_thread") is not None:
@@ -60,140 +86,137 @@ def start_process(q, fig_queue):
     thread_control["stop_requested"] = stop_requested
     thread_control["run_thread"] = Process(target=run_mask_gui, args=(q, fig_queue, stop_requested))
     thread_control["run_thread"].start()
-    
+
 def import_settings(scrollable_frame):
     global vars_dict
 
     csv_file_path = filedialog.askopenfilename(filetypes=[("CSV files", "*.csv")])
     csv_settings = read_settings_from_csv(csv_file_path)
     variables = mask_variables()
-    #variables = add_mask_gui_defaults(variables)
     new_settings = update_settings_from_csv(variables, csv_settings)
     vars_dict = generate_fields(new_settings, scrollable_frame)
+
+#@log_function_call
+def initiate_mask_root(parent_frame, width, height):
+    global vars_dict, q, canvas, fig_queue, canvas_widget, thread_control, advanced_var, scrollable_frame
+
+    style = ttk.Style(parent_frame)
+    set_dark_style(style)
+    style_text_boxes(style)
+    set_default_font(parent_frame, font_name="Arial", size=8)
+    parent_frame.configure(bg='black')
+    parent_frame.grid_rowconfigure(0, weight=1)
+    parent_frame.grid_columnconfigure(0, weight=1)
     
-@log_function_call
-def initiate_mask_root(width, height):
-    global root, vars_dict, q, canvas, fig_queue, canvas_widget, thread_control
-        
-    theme = 'breeze'
-    
-    if theme in ['clam']:
-        root = tk.Tk()
-        style = ttk.Style(root)
-        style.theme_use(theme) #plastik, clearlooks, elegance, default was clam #alt, breeze, arc
-        set_dark_style(style)
-    elif theme in ['breeze']:
-        root = ThemedTk(theme="breeze")
-        style = ttk.Style(root)
-        set_dark_style(style)
-        
-    set_default_font(root, font_name="Arial", size=10)
-    #root.state('zoomed')  # For Windows to maximize the window
-    root.attributes('-fullscreen', True)
-    root.geometry(f"{width}x{height}")
-    root.title("SpaCer: generate masks")
     fig_queue = Queue()
-            
+
     def _process_fig_queue():
         global canvas
         try:
             while not fig_queue.empty():
                 clear_canvas(canvas)
                 fig = fig_queue.get_nowait()
-                #set_fig_text_properties(fig, font_size=8)
                 for ax in fig.get_axes():
                     ax.set_xticks([])  # Remove x-axis ticks
                     ax.set_yticks([])  # Remove y-axis ticks
                     ax.xaxis.set_visible(False)  # Hide the x-axis
                     ax.yaxis.set_visible(False)  # Hide the y-axis
-                    #ax.title.set_fontsize(14) 
-                #disable_interactivity(fig)
                 fig.tight_layout()
-                fig.set_facecolor('#333333')
+                fig.set_facecolor('black')
                 canvas.figure = fig
                 fig_width, fig_height = canvas_widget.winfo_width(), canvas_widget.winfo_height()
                 fig.set_size_inches(fig_width / fig.dpi, fig_height / fig.dpi, forward=True)
-                canvas.draw_idle() 
+                canvas.draw_idle()
         except Exception as e:
             traceback.print_exc()
-            #pass
         finally:
             canvas_widget.after(100, _process_fig_queue)
-            
-    # Process queue for console output
+
     def _process_console_queue():
         while not q.empty():
             message = q.get_nowait()
             console_output.insert(tk.END, message)
             console_output.see(tk.END)
         console_output.after(100, _process_console_queue)
-        
-    # Vertical container for settings and console
-    vertical_container = tk.PanedWindow(root, orient=tk.HORIZONTAL) #VERTICAL
-    vertical_container.pack(fill=tk.BOTH, expand=True)
 
-    # Scrollable Frame for user settings
-    scrollable_frame = ScrollableFrame(vertical_container, bg='#333333')
-    vertical_container.add(scrollable_frame, stretch="always")
+    vertical_container = tk.PanedWindow(parent_frame, orient=tk.HORIZONTAL)
+    vertical_container.grid(row=0, column=0, sticky=tk.NSEW)
+    parent_frame.grid_rowconfigure(0, weight=1)
+    parent_frame.grid_columnconfigure(0, weight=1)
 
-    # Setup for user input fields (variables)
+    # Settings Section
+    settings_frame = tk.Frame(vertical_container, bg='black')
+    vertical_container.add(settings_frame, stretch="always")
+    settings_label = ttk.Label(settings_frame, text="Settings", style="Custom.TLabel")
+    settings_label.grid(row=0, column=0, pady=10, padx=10)
+    scrollable_frame = ScrollableFrame(settings_frame, width=600)
+    scrollable_frame.grid(row=1, column=0, sticky="nsew")
+    settings_frame.grid_rowconfigure(1, weight=1)
+    settings_frame.grid_columnconfigure(0, weight=1)
+    
+    # Create advanced settings checkbox
+    advanced_var = tk.BooleanVar(value=False)
+    advanced_Toggle = ToggleSwitch(scrollable_frame.scrollable_frame, text="Advanced Settings", variable=advanced_var, command=toggle_advanced_settings)
+    advanced_Toggle.grid(row=48, column=0, pady=10, padx=10)
     variables = mask_variables()
     vars_dict = generate_fields(variables, scrollable_frame)
+    toggle_advanced_settings()
+    vars_dict['Test mode'] = (None, None, tk.BooleanVar(value=False))
     
-    # Horizontal container for Matplotlib figure and the vertical pane (for settings and console)
-    horizontal_container = tk.PanedWindow(vertical_container, orient=tk.VERTICAL) #HORIZONTAL
-    vertical_container.add(horizontal_container, stretch="always")
+    # Button section
+    test_mode_button = CustomButton(scrollable_frame.scrollable_frame, text="Test Mode", command=toggle_test_mode)
+    test_mode_button.grid(row=47, column=1, pady=10, padx=10)
+    import_btn = CustomButton(scrollable_frame.scrollable_frame, text="Import", command=lambda: import_settings(scrollable_frame))
+    import_btn.grid(row=47, column=0, pady=10, padx=10)
+    run_button = CustomButton(scrollable_frame.scrollable_frame, text="Run", command=lambda: start_process(q, fig_queue))
+    run_button.grid(row=45, column=0, pady=10, padx=10)
+    abort_button = CustomButton(scrollable_frame.scrollable_frame, text="Abort", command=initiate_abort)
+    abort_button.grid(row=45, column=1, pady=10, padx=10)
+    progress_label = ttk.Label(scrollable_frame.scrollable_frame, text="Processing: 0%", background="black", foreground="white") # Create progress field
+    progress_label.grid(row=50, column=0, columnspan=2, sticky="ew", pady=(5, 0), padx=10)
 
-    # Matplotlib figure setup
-    figure = Figure(figsize=(30, 4), dpi=100, facecolor='#333333')
+    # Plot Canvas Section
+    plot_frame = tk.PanedWindow(vertical_container, orient=tk.VERTICAL) # Horizontal container for Matplotlib figure and the vertical pane (for settings and console)
+    vertical_container.add(plot_frame, stretch="always")
+    figure = Figure(figsize=(30, 4), dpi=100, facecolor='black') # Matplotlib figure setup
     plot = figure.add_subplot(111)
     plot.plot([], [])  # This creates an empty plot.
     plot.axis('off')
-
-    # Embedding the Matplotlib figure in the Tkinter window
-    canvas = FigureCanvasTkAgg(figure, master=horizontal_container)
-    canvas.get_tk_widget().configure(cursor='arrow', background='#333333', highlightthickness=0)
-    #canvas.get_tk_widget().configure(cursor='arrow')
+    canvas = FigureCanvasTkAgg(figure, master=plot_frame) # Embedd Matplotlib figure in Tkinter window
+    canvas.get_tk_widget().configure(cursor='arrow', background='black', highlightthickness=0)
     canvas_widget = canvas.get_tk_widget()
-    horizontal_container.add(canvas_widget, stretch="always")
+    plot_frame.add(canvas_widget, stretch="always")
     canvas.draw()
     canvas.figure = figure
 
-    # Console output setup below the settings
-    console_output = scrolledtext.ScrolledText(vertical_container, height=10)
-    vertical_container.add(console_output, stretch="always")
+    # Console Section
+    console_frame = tk.Frame(vertical_container, bg='black')
+    vertical_container.add(console_frame, stretch="always")
+    console_label = ttk.Label(console_frame, text="Console", background="black", foreground="white")
+    console_label.grid(row=0, column=0, pady=10, padx=10)
+    console_output = scrolledtext.ScrolledText(console_frame, height=10, bg='black', fg='white', insertbackground='white')
+    console_output.grid(row=1, column=0, sticky="nsew")
+    console_frame.grid_rowconfigure(1, weight=1)
+    console_frame.grid_columnconfigure(0, weight=1)
 
-    # Queue and redirection setup for updating console output safely
     q = Queue()
     sys.stdout = StdoutRedirector(console_output)
     sys.stderr = StdoutRedirector(console_output)
-    
-    # This is your GUI setup where you create the Run button
-    run_button = ttk.Button(scrollable_frame.scrollable_frame, text="Run",command=lambda: start_process(q, fig_queue))
-    run_button.grid(row=45, column=0, pady=10)
-    
-    abort_button = ttk.Button(scrollable_frame.scrollable_frame, text="Abort", command=initiate_abort)
-    abort_button.grid(row=45, column=1, pady=10)
-    
-    progress_label = ttk.Label(scrollable_frame.scrollable_frame, text="Processing: 0%", background="#333333", foreground="white")
-    progress_label.grid(row=41, column=0, columnspan=2, sticky="ew", pady=(5, 0))
-    
-    # Create the Import Settings button
-    import_btn = tk.Button(root, text="Import Settings", command=lambda: import_settings(scrollable_frame))
-    import_btn.pack(pady=20)
-    
+
     _process_console_queue()
     _process_fig_queue()
-    create_dark_mode(root, style, console_output)
-    
-    root.after(100, lambda: main_thread_update_function(root, q, fig_queue, canvas_widget, progress_label))
     
-    return root, vars_dict
+    parent_frame.after(100, lambda: main_thread_update_function(parent_frame, q, fig_queue, canvas_widget, progress_label))
+
+    return parent_frame, vars_dict
 
 def gui_mask():
-    global vars_dict, root
-    root, vars_dict = initiate_mask_root(1000, 1500)
+    root = tk.Tk()
+    root.geometry("1000x800")
+    root.title("SpaCer: generate masks")
+    initiate_mask_root(root, 1000, 800)
+    create_menu_bar(root)
     root.mainloop()
-    
+
 if __name__ == "__main__":
     gui_mask()

spacr/gui_measure_app.py

@@ -1,13 +1,11 @@
-import sys, traceback, matplotlib, ctypes, csv
+import sys, traceback, matplotlib, ctypes
 import tkinter as tk
 from tkinter import ttk, scrolledtext
 from matplotlib.figure import Figure
 from matplotlib.backends.backend_tkagg import FigureCanvasTkAgg
-import matplotlib.pyplot as plt
 matplotlib.use('Agg')  # Use the non-GUI Agg backend
 from multiprocessing import Process, Queue, Value
-from ttkthemes import ThemedTk
-from tkinter import filedialog, StringVar, BooleanVar, IntVar, DoubleVar, Tk
+from tkinter import filedialog
 
 try:
     ctypes.windll.shcore.SetProcessDpiAwareness(True)
@@ -15,21 +13,48 @@ except AttributeError:
     pass
 
 from .logger import log_function_call
-from .gui_utils import ScrollableFrame, StdoutRedirector, process_stdout_stderr, set_dark_style, set_default_font, generate_fields, create_dark_mode, main_thread_update_function
-from .gui_utils import measure_variables, measure_crop_wrapper, clear_canvas, safe_literal_eval, check_measure_gui_settings, read_settings_from_csv, update_settings_from_csv
+from .gui_utils import ScrollableFrame, StdoutRedirector, CustomButton, ToggleSwitch, ToolTip
+from .gui_utils import process_stdout_stderr, set_dark_style, set_default_font, generate_fields, main_thread_update_function, create_menu_bar
+from .gui_utils import measure_variables, measure_crop_wrapper, clear_canvas, check_measure_gui_settings, read_settings_from_csv, update_settings_from_csv, style_text_boxes
 
 thread_control = {"run_thread": None, "stop_requested": False}
 
-@log_function_call
+def toggle_test_mode():
+    global vars_dict
+    current_state = vars_dict['test_mode'][2].get()
+    new_state = not current_state
+    vars_dict['test_mode'][2].set(new_state)
+    if new_state:
+        test_mode_button.config(bg="blue")
+    else:
+        test_mode_button.config(bg="gray")
+
+def toggle_advanced_settings():
+    global vars_dict
+
+    timelapse_settings = ['timelapse', 'timelapse_objects']
+    misc_settings = ['representative_images', 'plot', 'plot_filtration', 'include_uninfected', 'dialate_pngs', 'dialate_png_ratios']
+    opperational_settings = ['max_workers','experiment','cells','cell_loc','pathogens','pathogen_loc','treatments','treatment_loc','channel_of_interest','compartments','measurement','nr_imgs', 'um_per_pixel']
+    
+    advanced_settings = timelapse_settings+misc_settings+opperational_settings
+
+    # Toggle visibility of advanced settings
+    for setting in advanced_settings:
+        label, widget, var = vars_dict[setting]
+        if advanced_var.get() is False:
+            label.grid_remove()  # Hide the label
+            widget.grid_remove()  # Hide the widget
+        else:
+            label.grid()  # Show the label
+            widget.grid()  # Show the widget
+
+#@log_function_call
 def run_measure_gui(q, fig_queue, stop_requested):
     global vars_dict
     process_stdout_stderr(q)
     try:
         print('hello')
         settings = check_measure_gui_settings(vars_dict)
-        #for key in settings:
-        #    value = settings[key]
-        #    print(key, value, type(value))
         measure_crop_wrapper(settings=settings, q=q, fig_queue=fig_queue)
     except Exception as e:
         q.put(f"Error during processing: {e}")
@@ -37,7 +62,7 @@ def run_measure_gui(q, fig_queue, stop_requested):
     finally:
         stop_requested.value = 1
 
-@log_function_call
+#@log_function_call
 def start_process(q, fig_queue):
     global thread_control
     if thread_control.get("run_thread") is not None:
@@ -48,7 +73,7 @@ def start_process(q, fig_queue):
     thread_control["run_thread"] = Process(target=run_measure_gui, args=(q, fig_queue, stop_requested))
     thread_control["run_thread"].start()
 
-@log_function_call
+#@log_function_call
 def initiate_abort():
     global thread_control
     if thread_control.get("stop_requested") is not None:
@@ -60,7 +85,7 @@ def initiate_abort():
             thread_control["run_thread"].terminate()
         thread_control["run_thread"] = None
 
-@log_function_call
+#@log_function_call
 def import_settings(scrollable_frame):
     global vars_dict
 
@@ -70,29 +95,18 @@ def import_settings(scrollable_frame):
     new_settings = update_settings_from_csv(variables, csv_settings)
     vars_dict = generate_fields(new_settings, scrollable_frame)
 
-@log_function_call
-def initiate_measure_root(width, height):
-    global root, vars_dict, q, canvas, fig_queue, canvas_widget, thread_control, variables
-    
-    theme = 'breeze'
+#@log_function_call
+def initiate_measure_root(parent_frame):#, width, height):
+    global vars_dict, q, canvas, fig_queue, canvas_widget, thread_control, variables, advanced_var, scrollable_frame
     
-    if theme in ['clam']:
-        root = tk.Tk()
-        style = ttk.Style(root)
-        style.theme_use(theme) #plastik, clearlooks, elegance, default was clam #alt, breeze, arc
-        set_dark_style(style)
-
-    elif theme in ['breeze']:
-        root = ThemedTk(theme="breeze")
-        style = ttk.Style(root)
-        set_dark_style(style)
-    
-    set_default_font(root, font_name="Arial", size=10)
-    #root.state('zoomed')  # For Windows to maximize the window
-    root.attributes('-fullscreen', True)
-    root.geometry(f"{width}x{height}")
-    root.configure(bg='#333333')
-    root.title("SpaCer: generate masks")
+    style = ttk.Style(parent_frame)
+    set_dark_style(style)
+    style_text_boxes(style)
+    set_default_font(parent_frame, font_name="Arial", size=8)
+
+    parent_frame.configure(bg='black')
+    parent_frame.grid_rowconfigure(0, weight=1)
+    parent_frame.grid_columnconfigure(0, weight=1)
     fig_queue = Queue()
     
     def _process_fig_queue():
@@ -101,27 +115,22 @@ def initiate_measure_root(width, height):
             while not fig_queue.empty():
                 clear_canvas(canvas)
                 fig = fig_queue.get_nowait()
-                #set_fig_text_properties(fig, font_size=8)
                 for ax in fig.get_axes():
                     ax.set_xticks([])  # Remove x-axis ticks
                     ax.set_yticks([])  # Remove y-axis ticks
                     ax.xaxis.set_visible(False)  # Hide the x-axis
                     ax.yaxis.set_visible(False)  # Hide the y-axis
-                    #ax.title.set_fontsize(14) 
-                #disable_interactivity(fig)
                 fig.tight_layout()
-                fig.set_facecolor('#333333')
+                fig.set_facecolor('black')
                 canvas.figure = fig
                 fig_width, fig_height = canvas_widget.winfo_width(), canvas_widget.winfo_height()
                 fig.set_size_inches(fig_width / fig.dpi, fig_height / fig.dpi, forward=True)
-                canvas.draw_idle() 
+                canvas.draw_idle()
         except Exception as e:
             traceback.print_exc()
-            #pass
         finally:
             canvas_widget.after(100, _process_fig_queue)
-            
-    # Process queue for console output
+
     def _process_console_queue():
         while not q.empty():
             message = q.get_nowait()
@@ -129,71 +138,83 @@ def initiate_measure_root(width, height):
             console_output.see(tk.END)
         console_output.after(100, _process_console_queue)
 
-    # Vertical container for settings and console
-    vertical_container = tk.PanedWindow(root, orient=tk.HORIZONTAL) #VERTICAL
-    vertical_container.pack(fill=tk.BOTH, expand=True)
-
-    # Scrollable Frame for user settings
-    scrollable_frame = ScrollableFrame(vertical_container)
-    vertical_container.add(scrollable_frame, stretch="always")
-
-    # Setup for user input fields (variables)
+    vertical_container = tk.PanedWindow(parent_frame, orient=tk.HORIZONTAL)
+    vertical_container.grid(row=0, column=0, sticky=tk.NSEW)
+    parent_frame.grid_rowconfigure(0, weight=1)
+    parent_frame.grid_columnconfigure(0, weight=1)
+
+    # Settings Section
+    settings_frame = tk.Frame(vertical_container, bg='black')
+    vertical_container.add(settings_frame, stretch="always")
+    settings_label = ttk.Label(settings_frame, text="Settings", background="black", foreground="white")
+    settings_label.grid(row=0, column=0, pady=10, padx=10)
+    scrollable_frame = ScrollableFrame(settings_frame, width=500)
+    scrollable_frame.grid(row=1, column=0, sticky="nsew")
+    settings_frame.grid_rowconfigure(1, weight=1)
+    settings_frame.grid_columnconfigure(0, weight=1)
+    
+    # Create advanced settings checkbox
+    advanced_var = tk.BooleanVar(value=False)
+    advanced_Toggle = ToggleSwitch(scrollable_frame.scrollable_frame, text="Advanced Settings", variable=advanced_var, command=toggle_advanced_settings)
+    advanced_Toggle.grid(row=48, column=0, pady=10, padx=10)
     variables = measure_variables()
     vars_dict = generate_fields(variables, scrollable_frame)
+    toggle_advanced_settings()
+    vars_dict['Test mode'] = (None, None, tk.BooleanVar(value=False))
     
-    # Horizontal container for Matplotlib figure and the vertical pane (for settings and console)
-    horizontal_container = tk.PanedWindow(vertical_container, orient=tk.VERTICAL) #HORIZONTAL
-    vertical_container.add(horizontal_container, stretch="always")
-
-    # Matplotlib figure setup
-    figure = Figure(figsize=(30, 4), dpi=100, facecolor='#333333')
+    # Button section
+    test_mode_button = CustomButton(scrollable_frame.scrollable_frame, text="Test Mode", command=toggle_test_mode)
+    test_mode_button.grid(row=47, column=1, pady=10, padx=10)
+    import_btn = CustomButton(scrollable_frame.scrollable_frame, text="Import Settings", command=lambda: import_settings(scrollable_frame))
+    import_btn.grid(row=47, column=0, pady=20, padx=20)
+    run_button = CustomButton(scrollable_frame.scrollable_frame, text="Run", command=lambda: start_process(q, fig_queue))
+    run_button.grid(row=45, column=0, pady=20, padx=20)
+    abort_button = CustomButton(scrollable_frame.scrollable_frame, text="Abort", command=initiate_abort)
+    abort_button.grid(row=45, column=1, pady=20, padx=20)
+    progress_label = ttk.Label(scrollable_frame.scrollable_frame, text="Processing: 0%", background="black", foreground="white") # Create progress field
+    progress_label.grid(row=50, column=0, columnspan=2, sticky="ew", pady=(5, 0), padx=10)
+
+    # Plot Canvas Section
+    plot_frame = tk.PanedWindow(vertical_container, orient=tk.VERTICAL)
+    vertical_container.add(plot_frame, stretch="always")
+    figure = Figure(figsize=(30, 4), dpi=100, facecolor='black')
     plot = figure.add_subplot(111)
-    plot.plot([], [])  # This creates an empty plot.
+    plot.plot([], [])
     plot.axis('off')
-
-    # Embedding the Matplotlib figure in the Tkinter window
-    canvas = FigureCanvasTkAgg(figure, master=horizontal_container)
-    canvas.get_tk_widget().configure(cursor='arrow', background='#333333', highlightthickness=0)
-    #canvas.get_tk_widget().configure(cursor='arrow')
+    canvas = FigureCanvasTkAgg(figure, master=plot_frame)
+    canvas.get_tk_widget().configure(cursor='arrow', background='black', highlightthickness=0)
     canvas_widget = canvas.get_tk_widget()
-    horizontal_container.add(canvas_widget, stretch="always")
+    plot_frame.add(canvas_widget, stretch="always")
     canvas.draw()
     canvas.figure = figure
 
-    # Console output setup below the settings
-    console_output = scrolledtext.ScrolledText(vertical_container, height=10)
-    vertical_container.add(console_output, stretch="always")
+    # Console Section
+    console_frame = tk.Frame(vertical_container, bg='black')
+    vertical_container.add(console_frame, stretch="always")
+    console_label = ttk.Label(console_frame, text="Console", background="black", foreground="white")
+    console_label.grid(row=0, column=0, pady=10, padx=10)
+    console_output = scrolledtext.ScrolledText(console_frame, height=10, bg='black', fg='white', insertbackground='white')
+    console_output.grid(row=1, column=0, sticky="nsew")
+    console_frame.grid_rowconfigure(1, weight=1)
+    console_frame.grid_columnconfigure(0, weight=1)
 
-    # Queue and redirection setup for updating console output safely
     q = Queue()
     sys.stdout = StdoutRedirector(console_output)
     sys.stderr = StdoutRedirector(console_output)
     
-    # This is your GUI setup where you create the Run button
-    run_button = ttk.Button(scrollable_frame.scrollable_frame, text="Run",command=lambda: start_process(q, fig_queue))
-    run_button.grid(row=40, column=0, pady=10)
-    
-    abort_button = ttk.Button(scrollable_frame.scrollable_frame, text="Abort", command=initiate_abort)
-    abort_button.grid(row=40, column=1, pady=10)
-    
-    progress_label = ttk.Label(scrollable_frame.scrollable_frame, text="Progress: ", background="#333333", foreground="white")
-    progress_label.grid(row=41, column=0, columnspan=2, sticky="ew", pady=(5, 0))
-    
-    # Create the Import Settings button
-    import_btn = tk.Button(root, text="Import Settings", command=lambda: import_settings(scrollable_frame))
-    import_btn.pack(pady=20)
-    
     _process_console_queue()
     _process_fig_queue()
-    create_dark_mode(root, style, console_output)
     
-    #root.after(100, lambda: main_thread_update_function(root, q, fig_queue, canvas_widget, progress_label))
+    parent_frame.after(100, lambda: main_thread_update_function(parent_frame, q, fig_queue, canvas_widget, progress_label))
     
-    return root, vars_dict
+    return parent_frame, vars_dict
 
 def gui_measure():
-    global vars_dict, root
-    root, vars_dict = initiate_measure_root(1000, 1500)
+    root = tk.Tk()
+    root.geometry("1000x800")
+    root.title("SpaCer: generate masks")
+    initiate_measure_root(root, 1000, 800)
+    create_menu_bar(root)
     root.mainloop()
 
 if __name__ == "__main__":