spacr 0.1.1__py3-none-any.whl → 0.1.6__py3-none-any.whl

spacr/gui_utils.py

@@ -1,56 +1,34 @@
-import os, spacr, inspect, traceback, io, sys, ast, ctypes, matplotlib, re, csv, requests
-import matplotlib.pyplot as plt
-matplotlib.use('Agg')
-import numpy as np
+import io, sys, ast, ctypes, re, csv, ast
 import tkinter as tk
-from tkinter import ttk, messagebox
-import tkinter.font as tkFont
-from torchvision import models
-#from ttf_opensans import opensans
+from tkinter import ttk
 
-from tkinter import font as tkFont
-
-
-from .logger import log_function_call
+from . gui_core import initiate_root
+from .gui_elements import spacrLabel, spacrCheckbutton, set_dark_style
 
 try:
     ctypes.windll.shcore.SetProcessDpiAwareness(True)
 except AttributeError:
     pass
 
-class ToolTip:
-    def __init__(self, widget, text):
-        self.widget = widget
-        self.text = text
-        self.tooltip_window = None
-        widget.bind("<Enter>", self.show_tooltip)
-        widget.bind("<Leave>", self.hide_tooltip)
-
-    def show_tooltip(self, event):
-        x = event.x_root + 20
-        y = event.y_root + 10
-        self.tooltip_window = tk.Toplevel(self.widget)
-        self.tooltip_window.wm_overrideredirect(True)
-        self.tooltip_window.wm_geometry(f"+{x}+{y}")
-        label = tk.Label(self.tooltip_window, text=self.text, background="yellow", relief='solid', borderwidth=1)
-        label.pack()
+def set_default_font(root, font_name="Helvetica", size=12):
+    default_font = (font_name, size)
+    root.option_add("*Font", default_font)
+    root.option_add("*TButton.Font", default_font)
+    root.option_add("*TLabel.Font", default_font)
+    root.option_add("*TEntry.Font", default_font)
 
-    def hide_tooltip(self, event):
-        if self.tooltip_window:
-            self.tooltip_window.destroy()
-        self.tooltip_window = None
-
-def load_app(root, app_name, app_func):
-    # Cancel all scheduled after tasks
-    if hasattr(root, 'after_tasks'):
-        for task in root.after_tasks:
-            root.after_cancel(task)
-    root.after_tasks = []
+def proceed_with_app(root, app_name, app_func):
+    from .app_annotate import gui_annotate
+    from .app_make_masks import gui_make_masks
+    from .gui import gui_app
 
     # Clear the current content frame
     if hasattr(root, 'content_frame'):
         for widget in root.content_frame.winfo_children():
-            widget.destroy()
+            try:
+                widget.destroy()
+            except tk.TclError as e:
+                print(f"Error destroying widget: {e}")
     else:
         root.content_frame = tk.Frame(root)
         root.content_frame.grid(row=1, column=0, sticky="nsew")
@@ -58,658 +36,74 @@ def load_app(root, app_name, app_func):
         root.grid_columnconfigure(0, weight=1)
 
     # Initialize the new app in the content frame
-    app_func(root.content_frame)
-
-def create_menu_bar(root):
-    from .gui_mask_app import initiate_mask_root
-    from .gui_measure_app import initiate_measure_root
-    from .annotate_app import initiate_annotation_app_root
-    from .mask_app import initiate_mask_app_root
-    from .gui_classify_app import initiate_classify_root
-
-    gui_apps = {
-        "Mask": initiate_mask_root,
-        "Measure": initiate_measure_root,
-        "Annotate": initiate_annotation_app_root,
-        "Make Masks": initiate_mask_app_root,
-        "Classify": initiate_classify_root
-    }
-
-    def load_app_wrapper(app_name, app_func):
-        load_app(root, app_name, app_func)
-
-    # Create the menu bar
-    menu_bar = tk.Menu(root, bg="#008080", fg="white")
-    # Create a "SpaCr Applications" menu
-    app_menu = tk.Menu(menu_bar, tearoff=0, bg="#008080", fg="white")
-    menu_bar.add_cascade(label="SpaCr Applications", menu=app_menu)
-    # Add options to the "SpaCr Applications" menu
-    for app_name, app_func in gui_apps.items():
-        app_menu.add_command(label=app_name, command=lambda app_name=app_name, app_func=app_func: load_app_wrapper(app_name, app_func))
-    # Add a separator and an exit option
-    app_menu.add_separator()
-    app_menu.add_command(label="Exit", command=root.quit)
-    # Configure the menu for the root window
-    root.config(menu=menu_bar)
-
-class CustomButton(tk.Frame):
-    def __init__(self, parent, text="", command=None, font=None, *args, **kwargs):
-        super().__init__(parent, *args, **kwargs)
-        self.text = text
-        self.command = command
-
-        self.canvas = tk.Canvas(self, width=150, height=50, highlightthickness=0, bg="black")
-        self.canvas.grid(row=0, column=0)
-
-        self.button_bg = self.create_rounded_rectangle(0, 0, 150, 50, radius=20, fill="#800080")
-
-        # Use the passed font or default to Helvetica if not provided
-        self.font_style = font if font else tkFont.Font(family="Helvetica", size=12, weight=tkFont.NORMAL)
-        self.button_text = self.canvas.create_text(75, 25, text=self.text, fill="white", font=self.font_style)
-
-        self.bind("<Enter>", self.on_enter)
-        self.bind("<Leave>", self.on_leave)
-        self.bind("<Button-1>", self.on_click)
-        self.canvas.bind("<Enter>", self.on_enter)
-        self.canvas.bind("<Leave>", self.on_leave)
-        self.canvas.bind("<Button-1>", self.on_click)
-
-    def on_enter(self, event=None):
-        self.canvas.itemconfig(self.button_bg, fill="#993399")
-
-    def on_leave(self, event=None):
-        self.canvas.itemconfig(self.button_bg, fill="#800080")
-
-    def on_click(self, event=None):
-        if self.command:
-            self.command()
-
-    def create_rounded_rectangle(self, x1, y1, x2, y2, radius=20, **kwargs):
-        points = [x1 + radius, y1,
-                  x1 + radius, y1,
-                  x2 - radius, y1,
-                  x2 - radius, y1,
-                  x2, y1,
-                  x2, y1 + radius,
-                  x2, y1 + radius,
-                  x2, y2 - radius,
-                  x2, y2 - radius,
-                  x2, y2,
-                  x2 - radius, y2,
-                  x2 - radius, y2,
-                  x1 + radius, y2,
-                  x1 + radius, y2,
-                  x1, y2,
-                  x1, y2 - radius,
-                  x1, y2 - radius,
-                  x1, y1 + radius,
-                  x1, y1 + radius,
-                  x1, y1]
-
-        return self.canvas.create_polygon(points, **kwargs, smooth=True)
-
-class ToggleSwitch(ttk.Frame):
-    def __init__(self, parent, text="", variable=None, command=None, *args, **kwargs):
-        super().__init__(parent, *args, **kwargs)
-        self.text = text
-        self.variable = variable if variable else tk.BooleanVar()
-        self.command = command
-        
-        self.canvas = tk.Canvas(self, width=40, height=20, highlightthickness=0, bd=0, bg="black")
-        self.canvas.grid(row=0, column=1, padx=(10, 0))
-        
-        # Background rounded rectangle with smaller dimensions and no outline
-        self.switch_bg = self.create_rounded_rectangle(2, 2, 38, 18, radius=9, outline="", fill="#fff")
-
-        # Switch ball with no outline
-        self.switch = self.canvas.create_oval(4, 4, 16, 16, outline="", fill="#800080")  # Purple initially
-        
-        self.label = ttk.Label(self, text=self.text, background="black", foreground="white")
-        self.label.grid(row=0, column=0, padx=(0, 10))
-        
-        self.bind("<Button-1>", self.toggle)
-        self.canvas.bind("<Button-1>", self.toggle)
-        self.label.bind("<Button-1>", self.toggle)
-        
-        self.update_switch()
-
-    def toggle(self, event=None):
-        self.variable.set(not self.variable.get())
-        self.animate_switch()
-        if self.command:
-            self.command()
-
-    def update_switch(self):
-        if self.variable.get():
-            self.canvas.itemconfig(self.switch, fill="#008080")  # Teal
-            self.canvas.coords(self.switch, 24, 4, 36, 16)  # Move switch to the right
-        else:
-            self.canvas.itemconfig(self.switch, fill="#800080")  # Purple
-            self.canvas.coords(self.switch, 4, 4, 16, 16)  # Move switch to the left
-
-    def animate_switch(self):
-        if self.variable.get():
-            start_x, end_x = 4, 24
-            final_color = "#008080"  # Teal
-        else:
-            start_x, end_x = 24, 4
-            final_color = "#800080"  # Purple
-
-        self.animate_movement(start_x, end_x, final_color)
-
-    def animate_movement(self, start_x, end_x, final_color):
-        step = 1 if start_x < end_x else -1
-        for i in range(start_x, end_x, step):
-            self.canvas.coords(self.switch, i, 4, i + 12, 16)
-            self.canvas.update()
-            self.after(10)  # Small delay for smooth animation
-        self.canvas.itemconfig(self.switch, fill=final_color)
-
-    def get(self):
-        return self.variable.get()
-
-    def set(self, value):
-        self.variable.set(value)
-        self.update_switch()
-
-    def create_rounded_rectangle(self, x1, y1, x2, y2, radius=9, **kwargs):  # Smaller radius for smaller switch
-        points = [x1 + radius, y1,
-                  x1 + radius, y1,
-                  x2 - radius, y1,
-                  x2 - radius, y1,
-                  x2, y1,
-                  x2, y1 + radius,
-                  x2, y1 + radius,
-                  x2, y2 - radius,
-                  x2, y2 - radius,
-                  x2, y2,
-                  x2 - radius, y2,
-                  x2 - radius, y2,
-                  x1 + radius, y2,
-                  x1 + radius, y2,
-                  x1, y2,
-                  x1, y2 - radius,
-                  x1, y2 - radius,
-                  x1, y1 + radius,
-                  x1, y1 + radius,
-                  x1, y1]
-
-        return self.canvas.create_polygon(points, **kwargs, smooth=True)
-    
-def set_default_font(root, font_name="Helvetica", size=12):
-    default_font = (font_name, size)
-    root.option_add("*Font", default_font)
-    root.option_add("*TButton.Font", default_font)
-    root.option_add("*TLabel.Font", default_font)
-    root.option_add("*TEntry.Font", default_font)
-
-def check_and_download_font_v1():
-    font_name = "Helvetica"
-    font_dir = "fonts"
-    font_path = os.path.join(font_dir, "OpenSans-Regular.ttf")
-
-    # Check if the font is already available
-    available_fonts = list(tkFont.families())
-    if font_name not in available_fonts:
-        print(f"Font '{font_name}' not found. Downloading...")
-        if not os.path.exists(font_dir):
-            os.makedirs(font_dir)
-
-        if not os.path.exists(font_path):
-            url = "https://github.com/google/fonts/blob/main/apache/opensans/OpenSans-Regular.ttf?raw=true"
-            response = requests.get(url)
-            with open(font_path, "wb") as f:
-                f.write(response.content)
-
-        # Load the font
-        try:
-            tkFont.nametofont("TkDefaultFont").configure(family=font_name, size=10)
-            tkFont.nametofont("TkTextFont").configure(family=font_name, size=10)
-            tkFont.nametofont("TkHeadingFont").configure(family=font_name, size=12)
-        except tk.TclError:
-            tkFont.nametofont("TkDefaultFont").configure(family="Helvetica", size=10)
-            tkFont.nametofont("TkTextFont").configure(family="Helvetica", size=10)
-            tkFont.nametofont("TkHeadingFont").configure(family="Helvetica", size=12)
+    if app_name == "Mask":
+        initiate_root(root.content_frame, 'mask')
+    elif app_name == "Measure":
+        initiate_root(root.content_frame, 'measure')
+    elif app_name == "Classify":
+        initiate_root(root.content_frame, 'classify')
+    elif app_name == "Sequencing":
+        initiate_root(root.content_frame, 'sequencing')
+    elif app_name == "Umap":
+        initiate_root(root.content_frame, 'umap')
+    elif app_name == "Annotate":
+        gui_annotate()
+    elif app_name == "Make Masks":
+        gui_make_masks()
     else:
-        tkFont.nametofont("TkDefaultFont").configure(family=font_name, size=10)
-        tkFont.nametofont("TkTextFont").configure(family=font_name, size=10)
-        tkFont.nametofont("TkHeadingFont").configure(family=font_name, size=12)
-
-def style_text_boxes_v1(style):
-    check_and_download_font()
-    font_style = tkFont.Font(family="Helvetica", size=10)  # Define the Helvetica font
-    style.configure('TEntry', padding='5 5 5 5', borderwidth=1, relief='solid', fieldbackground='#000000', foreground='#ffffff', font=font_style)
-    style.configure('TCombobox', fieldbackground='#000000', background='#000000', foreground='#ffffff', font=font_style)
-    style.configure('Custom.TButton', padding='10 10 10 10', borderwidth=1, relief='solid', background='#008080', foreground='#ffffff', font=font_style)
-    style.map('Custom.TButton',
-              background=[('active', '#66b2b2'), ('disabled', '#004d4d'), ('!disabled', '#008080')],
-              foreground=[('active', '#ffffff'), ('disabled', '#888888')])
-    style.configure('Custom.TLabel', padding='5 5 5 5', borderwidth=1, relief='flat', background='#000000', foreground='#ffffff', font=font_style)
-    style.configure('TCheckbutton', background='#333333', foreground='#ffffff', indicatoron=False, relief='flat', font=font_style)
-    style.map('TCheckbutton', background=[('selected', '#555555'), ('active', '#555555')])
+        raise ValueError(f"Invalid app name: {app_name}")
 
-def check_and_download_font():
-    font_name = "Helvetica"
-    font_dir = "fonts"
-    font_path = os.path.join(font_dir, "OpenSans-Regular.ttf")
-
-    # Check if the font is already available
-    available_fonts = list(tkFont.families())
-    if font_name not in available_fonts:
-        print(f"Font '{font_name}' not found. Downloading...")
-        if not os.path.exists(font_dir):
-            os.makedirs(font_dir)
-
-        if not os.path.exists(font_path):
-            url = "https://github.com/google/fonts/blob/main/apache/opensans/OpenSans-Regular.ttf?raw=true"
-            response = requests.get(url)
-            with open(font_path, "wb") as f:
-                f.write(response.content)
+def load_app(root, app_name, app_func):
+    # Cancel all scheduled after tasks
+    if hasattr(root, 'after_tasks'):
+        for task in root.after_tasks:
+            root.after_cancel(task)
+    root.after_tasks = []
 
-        # Load the font
-        try:
-            tkFont.nametofont("TkDefaultFont").configure(family=font_name, size=10)
-            tkFont.nametofont("TkTextFont").configure(family=font_name, size=10)
-            tkFont.nametofont("TkHeadingFont").configure(family=font_name, size=12)
-        except tk.TclError:
-            tkFont.nametofont("TkDefaultFont").configure(family="Helvetica", size=10)
-            tkFont.nametofont("TkTextFont").configure(family="Helvetica", size=10)
-            tkFont.nametofont("TkHeadingFont").configure(family="Helvetica", size=12)
+    # Exit functionality only for the annotation app
+    if app_name != "Annotate" and hasattr(root, 'current_app_exit_func'):
+        root.next_app_func = proceed_with_app
+        root.next_app_args = (app_name, app_func)  # Ensure correct arguments
+        root.current_app_exit_func()
     else:
-        tkFont.nametofont("TkDefaultFont").configure(family=font_name, size=10)
-        tkFont.nametofont("TkTextFont").configure(family=font_name, size=10)
-        tkFont.nametofont("TkHeadingFont").configure(family=font_name, size=12)
-
-def style_text_boxes(style):
-    check_and_download_font()
-    font_style = tkFont.Font(family="Helvetica", size=10)  # Define the Helvetica font
-    style.configure('TEntry', padding='5 5 5 5', borderwidth=1, relief='solid', fieldbackground='#000000', foreground='#ffffff', font=font_style)
-    style.configure('TCombobox', fieldbackground='#000000', background='#000000', foreground='#ffffff', font=font_style)
-    style.configure('Custom.TButton', padding='10 10 10 10', borderwidth=1, relief='solid', background='#008080', foreground='#ffffff', font=font_style)
-    style.map('Custom.TButton',
-              background=[('active', '#66b2b2'), ('disabled', '#004d4d'), ('!disabled', '#008080')],
-              foreground=[('active', '#ffffff'), ('disabled', '#888888')])
-    style.configure('Custom.TLabel', padding='5 5 5 5', borderwidth=1, relief='flat', background='#000000', foreground='#ffffff', font=font_style)
-    style.configure('TCheckbutton', background='#333333', foreground='#ffffff', indicatoron=False, relief='flat', font=font_style)
-    style.map('TCheckbutton', background=[('selected', '#555555'), ('active', '#555555')])
-
+        proceed_with_app(root, app_name, app_func)
 
-def read_settings_from_csv(csv_file_path):
-    settings = {}
-    with open(csv_file_path, newline='') as csvfile:
-        reader = csv.DictReader(csvfile)
-        for row in reader:
-            key = row['Key']
-            value = row['Value']
-            settings[key] = value
-    return settings
-
-def update_settings_from_csv(variables, csv_settings):
-    new_settings = variables.copy()  # Start with a copy of the original settings
-    for key, value in csv_settings.items():
-        if key in new_settings:
-            # Get the variable type and options from the original settings
-            var_type, options, _ = new_settings[key]
-            # Update the default value with the CSV value, keeping the type and options unchanged
-            new_settings[key] = (var_type, options, value)
-    return new_settings
-
-def safe_literal_eval(value):
+def parse_list(value):
     try:
-        # First, try to evaluate as a literal
-        return ast.literal_eval(value)
-    except (ValueError, SyntaxError):
-        # If it fails, return the value as it is (a string)
-        return value
-
-def disable_interactivity(fig):
-    if hasattr(fig.canvas, 'toolbar'):
-        fig.canvas.toolbar.pack_forget()
-
-    event_handlers = fig.canvas.callbacks.callbacks
-    for event, handlers in list(event_handlers.items()):
-        for handler_id in list(handlers.keys()):
-            fig.canvas.mpl_disconnect(handler_id)
-
-class ScrollableFrame(ttk.Frame):
-    def __init__(self, container, *args, bg='black', **kwargs):
-        super().__init__(container, *args, **kwargs)
-        self.configure(style='TFrame')  # Ensure this uses the styled frame from dark mode
-        
-        canvas = tk.Canvas(self, bg=bg)  # Set canvas background to match dark mode
-        scrollbar = ttk.Scrollbar(self, orient="vertical", command=canvas.yview)
-        
-        self.scrollable_frame = ttk.Frame(canvas, style='TFrame')  # Ensure it uses the styled frame
-        self.scrollable_frame.bind(
-            "<Configure>",
-            lambda e: canvas.configure(scrollregion=canvas.bbox("all"))
-        )
-        
-        canvas.create_window((0, 0), window=self.scrollable_frame, anchor="nw")
-        canvas.configure(yscrollcommand=scrollbar.set)
-        
-        canvas.pack(side="left", fill="both", expand=True)
-        scrollbar.pack(side="right", fill="y")
-
-class StdoutRedirector_v1(object):
-    def __init__(self, text_widget):
-        self.text_widget = text_widget
-
-    def write(self, string):
-        self.text_widget.insert(tk.END, string)
-        self.text_widget.see(tk.END)
-
-    def flush(self):
-        pass
-
-class StdoutRedirector:
-    def __init__(self, text_widget):
-        self.text_widget = text_widget
-
-    def write(self, string):
-        try:
-            if self.text_widget.winfo_exists():
-                self.text_widget.insert(tk.END, string)
-                self.text_widget.see(tk.END)
-        except tk.TclError:
-            pass  # Handle or log the error as needed
-
-    def flush(self):
-        pass
-
-def check_mask_gui_settings(vars_dict):
-    settings = {}
-    for key, var in vars_dict.items():
-        value = var.get()
-        
-        # Handle conversion for specific types if necessary
-        if key in ['channels', 'timelapse_frame_limits']:  # Assuming these should be lists
-            try:
-                # Convert string representation of a list into an actual list
-                settings[key] = eval(value)
-            except:
-                messagebox.showerror("Error", f"Invalid format for {key}. Please enter a valid list.")
-                return
-        elif key in ['nucleus_channel', 'cell_channel', 'pathogen_channel', 'examples_to_plot', 'batch_size', 'timelapse_memory', 'workers', 'fps', 'magnification']:  # Assuming these should be integers
-            try:
-                settings[key] = int(value) if value else None
-            except ValueError:
-                messagebox.showerror("Error", f"Invalid number for {key}.")
-                return
-        elif key in ['nucleus_background', 'cell_background', 'pathogen_background', 'nucleus_Signal_to_noise', 'cell_Signal_to_noise', 'pathogen_Signal_to_noise', 'nucleus_CP_prob', 'cell_CP_prob', 'pathogen_CP_prob', 'lower_quantile']:  # Assuming these should be floats
-            try:
-                settings[key] = float(value) if value else None
-            except ValueError:
-                messagebox.showerror("Error", f"Invalid number for {key}.")
-                return
+        parsed_value = ast.literal_eval(value)
+        if isinstance(parsed_value, list):
+            return parsed_value
         else:
-            settings[key] = value
-    return settings
-
-def check_measure_gui_settings(vars_dict):
-    settings = {}
-    for key, var in vars_dict.items():
-        value = var.get()  # Retrieves the string representation for entries or the actual value for checkboxes and combos.
-
-        try:
-            if key in ['channels', 'png_dims']:
-                settings[key] = [int(chan) for chan in ast.literal_eval(value)] if value else []
-                
-            elif key in ['cell_loc', 'pathogen_loc', 'treatment_loc']:
-                # Convert to a list of lists of strings, ensuring all structures are lists.
-                settings[key] = [list(map(str, sublist)) for sublist in ast.literal_eval(value)] if value else []
-
-            elif key == 'dialate_png_ratios':
-                settings[key] = [float(num) for num in ast.literal_eval(value)] if value else []
-
-            elif key == 'normalize':
-                settings[key] = [int(num) for num in ast.literal_eval(value)] if value else []
-
-            # Directly assign string values for these specific keys
-            elif key in ['normalize_by', 'experiment', 'measurement', 'input_folder']:
-                settings[key] = value
-
-            elif key == 'png_size':
-                settings[key] = [list(map(int, dim)) for dim in ast.literal_eval(value)] if value else []
-            
-            # Ensure these are lists of strings, converting from tuples if necessary
-            elif key in ['timelapse_objects', 'crop_mode', 'cells', 'pathogens', 'treatments']:
-                eval_value = ast.literal_eval(value) if value else []
-                settings[key] = list(map(str, eval_value)) if isinstance(eval_value, (list, tuple)) else [str(eval_value)]
-
-            # Handling for single non-string values (int, float, bool)
-            elif key in ['cell_mask_dim', 'cell_min_size', 'nucleus_mask_dim', 'nucleus_min_size', 'pathogen_mask_dim', 'pathogen_min_size', 'cytoplasm_min_size', 'max_workers', 'channel_of_interest', 'nr_imgs']:
-                settings[key] = int(value) if value else None
-
-            elif key == 'um_per_pixel':
-                settings[key] = float(value) if value else None
-
-            # Handling boolean values based on checkboxes
-            elif key in ['save_png', 'use_bounding_box', 'save_measurements', 'plot', 'plot_filtration', 'include_uninfected', 'dialate_pngs', 'timelapse', 'representative_images']:
-                settings[key] = var.get()
-
-        except SyntaxError as e:
-            print(f"Syntax error processing {key}: {str(e)}")
-            #messagebox.showerror("Error", f"Syntax error processing {key}: {str(e)}")
-            return None
-        except Exception as e:
-            print(f"Error processing {key}: {str(e)}")
-            #messagebox.showerror("Error", f"Error processing {key}: {str(e)}")
-            return None
-
-    return settings
-
-def check_classify_gui_settings(vars_dict):
-    settings = {}
-    for key, var in vars_dict.items():
-        value = var.get()  # This retrieves the string representation for entries or the actual value for checkboxes and combos
-
-        try:
-            if key in ['src', 'measurement']:
-                # Directly assign string values
-                settings[key] = str(value)
-            elif key in ['cell_mask_dim', 'image_size', 'batch_size', 'epochs', 'gradient_accumulation_steps', 'num_workers']:
-                # Convert to integer
-                settings[key] = int(value)
-            elif key in ['val_split', 'learning_rate', 'weight_decay', 'dropout_rate']:
-                # Convert to float
-                settings[key] = float(value)
-            elif key == 'classes':
-                # Evaluate as list
-                settings[key] = ast.literal_eval(value)
-
-            elif key in ['model_type','optimizer_type','schedule','loss_type','train_mode']:
-                settings[key] = value
-
-            elif key in ['gradient_accumulation','normalize','save','plot', 'init_weights','amsgrad','use_checkpoint','intermedeate_save','pin_memory', 'num_workers','verbose']:
-                settings[key] = bool(value)
-
-        except SyntaxError as e:
-            messagebox.showerror("Error", f"Syntax error processing {key}: {str(e)}")
-            return None
-        except Exception as e:
-            messagebox.showerror("Error", f"Error processing {key}: {str(e)}")
-            return None
-
-    return settings
-
-def check_sim_gui_settings(vars_dict):
-    settings = {}
-    for key, var in vars_dict.items():
-        value = var.get()  # This retrieves the string representation for entries or the actual value for checkboxes and combos
-
-        try:
-            if key in ['src', 'name', 'variable']:
-                # Directly assign string values
-                settings[key] = str(value)
-            
-            elif key in ['nr_plates', 'number_of_genes','number_of_active_genes','avg_genes_per_well','avg_cells_per_well','avg_reads_per_gene']:
-                #generate list of integers from list
-                ls = [int(num) for num in ast.literal_eval(value)]
-                if len(ls) == 3 and ls[2] > 0:
-                    list_of_integers = list(range(ls[0], ls[1], ls[2]))
-                    list_of_integers = [num + 1 if num == 0 else num for num in list_of_integers]
-                else:
-                    list_of_integers = [ls[0]]
-                settings[key] = list_of_integers
-                
-            elif key in ['sequencing_error','well_ineq_coeff','gene_ineq_coeff', 'positive_mean']:
-                #generate list of floats from list
-                ls = [float(num) for num in ast.literal_eval(value)]
-                if len(ls) == 3 and ls[2] > 0:
-                    list_of_floats = np.linspace(ls[0], ls[1], ls[2])
-                    list_of_floats.tolist()
-                    list_of_floats = [x if x != 0.0 else x + 0.01 for x in list_of_floats]
-                else:
-                    list_of_floats = [ls[0]]
-                settings[key] = list_of_floats
-
-            elif key in ['plot', 'random_seed']:
-                # Evaluate as bool
-                settings[key] = bool(value)
-                
-            elif key in ['number_of_control_genes', 'replicates', 'max_workers']:
-                # Convert to integer
-                settings[key] = int(value)
-                
-        except SyntaxError as e:
-            messagebox.showerror("Error", f"Syntax error processing {key}: {str(e)}")
-            return None
-        except Exception as e:
-            messagebox.showerror("Error", f"Error processing {key}: {str(e)}")
-            return None
-
-    return settings
-
-def sim_variables():
-    variables = {
-        'name':('entry', None, 'plates_2_4_8'),
-        'variable':('entry', None, 'all'),
-        'src':('entry', None, '/home/olafsson/Desktop/simulations'),
-        'number_of_control_genes':('entry', None, 30),
-        'replicates':('entry', None, 4),
-        'max_workers':('entry', None, 1),
-        'plot':('check', None, True),
-        'random_seed':('check', None, True),
-        'nr_plates': ('entry', None, '[8,8,0]'),# '[2,2,8]'
-        'number_of_genes': ('entry', None, '[100, 100, 0]'), #[1384, 1384, 0]
-        'number_of_active_genes': ('entry', None, '[10,10,0]'),
-        'avg_genes_per_well': ('entry', None, '[2, 10, 2]'),
-        'avg_cells_per_well': ('entry', None, '[100, 100, 0]'),
-        'positive_mean': ('entry', None, '[0.8, 0.8, 0]'),
-        'avg_reads_per_gene': ('entry', None, '[1000,1000, 0]'),
-        'sequencing_error': ('entry', None, '[0.01, 0.01, 0]'),
-        'well_ineq_coeff': ('entry', None, '[0.3,0.3,0]'),
-        'gene_ineq_coeff': ('entry', None, '[0.8,0.8,0]'),
-    }
-    return variables
+            raise ValueError
+    except (ValueError, SyntaxError):
+        raise ValueError("Invalid format for list")
+    
+def create_input_field(frame, label_text, row, var_type='entry', options=None, default_value=None):
+    label_column = 0
+    widget_column = 1
 
-def add_measure_gui_defaults(settings):
-    settings['compartments'] = ['pathogen', 'cytoplasm']
-    return settings
+    # Configure the column widths
+    frame.grid_columnconfigure(label_column, weight=0)  # Allow the label column to expand
+    frame.grid_columnconfigure(widget_column, weight=1)  # Allow the widget column to expand
 
-def measure_variables():
-    variables = {
-        'input_folder':('entry', None, '/mnt/data/CellVoyager/40x/einar/mitotrackerHeLaToxoDsRed_20240224_123156/test_gui/merged'),
-        'channels': ('combo', ['[0,1,2,3]','[0,1,2]','[0,1]','[0]'], '[0,1,2,3]'),
-        'cell_mask_dim':('entry', None, 4),
-        'cell_min_size':('entry', None, 0),
-        'cytoplasm_min_size':('entry', None, 0),
-        'nucleus_mask_dim':('entry', None, 5),
-        'nucleus_min_size':('entry', None, 0),
-        'pathogen_mask_dim':('entry', None, 6),
-        'pathogen_min_size':('entry', None, 0),
-        'save_png':('check', None, True),
-        'crop_mode':('entry', None, '["cell"]'),
-        'use_bounding_box':('check', None, True),
-        'png_size': ('entry', None, '[[224,224]]'), 
-        'normalize':('entry', None, '[2,98]'),
-        'png_dims':('entry', None, '[1,2,3]'),
-        'normalize_by':('combo', ['fov', 'png'], 'png'),
-        'save_measurements':('check', None, True),
-        'representative_images':('check', None, True),
-        'plot':('check', None, True),
-        'plot_filtration':('check', None, True),
-        'include_uninfected':('check', None, True),
-        'dialate_pngs':('check', None, False),
-        'dialate_png_ratios':('entry', None, '[0.2]'),
-        'timelapse':('check', None, False),
-        'timelapse_objects':('combo', ['["cell"]', '["nucleus"]', '["pathogen"]', '["cytoplasm"]'], '["cell"]'),
-        'max_workers':('entry', None, 30),
-        'experiment':('entry', None, 'experiment name'),
-        'cells':('entry', None, ['HeLa']),
-        'cell_loc': ('entry', None, '[["c1","c2"], ["c3","c4"]]'),
-        'pathogens':('entry', None, '["wt","mutant"]'),
-        'pathogen_loc': ('entry', None, '[["c1","c2"], ["c3","c4"]]'),
-        'treatments': ('entry', None, '["cm","lovastatin_20uM"]'),
-        'treatment_loc': ('entry', None, '[["c1","c2"], ["c3","c4"]]'),
-        'channel_of_interest':('entry', None, 3),
-        'compartments':('entry', None, '["pathogen","cytoplasm"]'),
-        'measurement':('entry', None, 'mean_intensity'),
-        'nr_imgs':('entry', None, 32),
-        'um_per_pixel':('entry', None, 0.1)
-    }
-    return variables
+    # Right-align the label text and the label itself
+    label = spacrLabel(frame, text=label_text, background="black", foreground="white", anchor='e', justify='right')
+    label.grid(column=label_column, row=row, sticky=tk.E, padx=(5, 2), pady=5)  # Align label to the right
 
-def classify_variables():
-    
-    def get_torchvision_models():
-        # Fetch all public callable attributes from torchvision.models that are functions
-        model_names = [name for name, obj in inspect.getmembers(models) 
-                    if inspect.isfunction(obj) and not name.startswith("__")]
-        return model_names
-    
-    model_names = get_torchvision_models()
-    variables = {
-        'src':('entry', None, '/mnt/data/CellVoyager/40x/einar/mitotrackerHeLaToxoDsRed_20240224_123156/test_gui/merged'),
-        'cell_mask_dim':('entry', None, 4),
-        'classes':('entry', None, '["nc","pc"]'),
-        'measurement':('entry', None, 'mean_intensity'),
-        'model_type': ('combo', model_names, 'resnet50'),
-        'optimizer_type': ('combo', ['adamw','adam'], 'adamw'),
-        'schedule': ('combo', ['reduce_lr_on_plateau','step_lr'], 'reduce_lr_on_plateau'),
-        'loss_type': ('combo', ['focal_loss', 'binary_cross_entropy_with_logits'], 'focal_loss'),
-        'image_size': ('entry', None, 224),
-        'batch_size': ('entry', None, 12),
-        'epochs': ('entry', None, 2),
-        'val_split': ('entry', None, 0.1),
-        'train_mode': ('combo', ['erm', 'irm'], 'erm'),
-        'learning_rate': ('entry', None, 0.0001),
-        'weight_decay': ('entry', None, 0.00001),
-        'dropout_rate': ('entry', None, 0.1),
-        'gradient_accumulation': ('check', None, True),
-        'gradient_accumulation_steps': ('entry', None, 4),
-        'normalize': ('check', None, True),
-        'save': ('check', None, True), 
-        'plot': ('check', None, True),
-        'init_weights': ('check', None, True),
-        'amsgrad': ('check', None, True),
-        'use_checkpoint': ('check', None, True),
-        'intermedeate_save': ('check', None, True),
-        'pin_memory': ('check', None, True),
-        'num_workers': ('entry', None, 30),
-        'verbose': ('check', None, True),
-    }
-    return variables
-    
-def create_input_field(frame, label_text, row, var_type='entry', options=None, default_value=None):
-    label = ttk.Label(frame, text=label_text, style='Custom.TLabel')  # Apply Custom.TLabel style for labels
-    label.grid(column=0, row=row, sticky=tk.W, padx=5, pady=5)
-    
     if var_type == 'entry':
         var = tk.StringVar(value=default_value)  # Set default value
         entry = ttk.Entry(frame, textvariable=var, style='TEntry')  # Apply TEntry style for entries
-        entry.grid(column=1, row=row, sticky=tk.EW, padx=5)
+        entry.grid(column=widget_column, row=row, sticky=tk.W, padx=(2, 5), pady=5)  # Align widget to the left
         return (label, entry, var)  # Return both the label and the entry, and the variable
     elif var_type == 'check':
         var = tk.BooleanVar(value=default_value)  # Set default value (True/False)
-        check = ToggleSwitch(frame, text=label_text, variable=var)  # Use ToggleSwitch class
-        check.grid(column=1, row=row, sticky=tk.W, padx=5)
+        check = spacrCheckbutton(frame, text="", variable=var, style='TCheckbutton')
+        check.grid(column=widget_column, row=row, sticky=tk.W, padx=(2, 5), pady=5)  # Align widget to the left
         return (label, check, var)  # Return both the label and the checkbutton, and the variable
     elif var_type == 'combo':
         var = tk.StringVar(value=default_value)  # Set default value
         combo = ttk.Combobox(frame, textvariable=var, values=options, style='TCombobox')  # Apply TCombobox style
-        combo.grid(column=1, row=row, sticky=tk.EW, padx=5)
+        combo.grid(column=widget_column, row=row, sticky=tk.W, padx=(2, 5), pady=5)  # Align widget to the left
         if default_value:
             combo.set(default_value)
         return (label, combo, var)  # Return both the label and the combobox, and the variable
@@ -717,227 +111,6 @@ def create_input_field(frame, label_text, row, var_type='entry', options=None, d
         var = None  # Placeholder in case of an undefined var_type
         return (label, None, var)
 
-def mask_variables():
-    variables = {
-        'src': ('entry', None, '/mnt/data/CellVoyager/40x/einar/mitotrackerHeLaToxoDsRed_20240224_123156/test_gui'),
-        'metadata_type': ('combo', ['cellvoyager', 'cq1', 'nikon', 'zeis', 'custom'], 'cellvoyager'),
-        'custom_regex': ('entry', None, None),
-        'experiment': ('entry', None, 'exp'),
-        'channels': ('combo', ['[0,1,2,3]','[0,1,2]','[0,1]','[0]'], '[0,1,2,3]'),
-        'magnification': ('combo', [20, 40, 60,], 40),
-        'nucleus_channel': ('combo', [0,1,2,3, None], 0),
-        'nucleus_background': ('entry', None, 100),
-        'nucleus_Signal_to_noise': ('entry', None, 5),
-        'nucleus_CP_prob': ('entry', None, 0),
-        'cell_channel': ('combo', [0,1,2,3, None], 3),
-        'cell_background': ('entry', None, 100),
-        'cell_Signal_to_noise': ('entry', None, 5),
-        'cell_CP_prob': ('entry', None, 0),
-        'pathogen_channel': ('combo', [0,1,2,3, None], 2),
-        'pathogen_background': ('entry', None, 100),
-        'pathogen_Signal_to_noise': ('entry', None, 3),
-        'pathogen_CP_prob': ('entry', None, 0),
-        'preprocess': ('check', None, True),
-        'masks': ('check', None, True),
-        'examples_to_plot': ('entry', None, 1),
-        'randomize': ('check', None, True),
-        'batch_size': ('entry', None, 50),
-        'timelapse': ('check', None, False),
-        'timelapse_displacement': ('entry', None, None),
-        'timelapse_memory': ('entry', None, 0),
-        'timelapse_frame_limits': ('entry', None, '[0,1000]'),
-        'timelapse_remove_transient': ('check', None, True),
-        'timelapse_mode': ('combo',  ['trackpy', 'btrack'], 'trackpy'),
-        'timelapse_objects': ('combo', ['cell','nucleus','pathogen','cytoplasm', None], None),
-        'fps': ('entry', None, 2),
-        'remove_background': ('check', None, True),
-        'lower_quantile': ('entry', None, 0.01),
-        'merge': ('check', None, False),
-        'normalize_plots': ('check', None, True),
-        'all_to_mip': ('check', None, False),
-        'pick_slice': ('check', None, False),
-        'skip_mode': ('entry', None, None),
-        'save': ('check', None, True),
-        'plot': ('check', None, True),
-        'workers': ('entry', None, 30),
-        'verbose': ('check', None, True),
-    }
-    return variables
-
-def add_mask_gui_defaults(settings):
-    settings['remove_background'] = True
-    settings['fps'] = 2
-    settings['all_to_mip'] = False
-    settings['pick_slice'] = False
-    settings['merge'] = False
-    settings['skip_mode'] = ''
-    settings['verbose'] = False
-    settings['normalize_plots'] = True
-    settings['randomize'] = True
-    settings['preprocess'] = True
-    settings['masks'] = True
-    settings['examples_to_plot'] = 1
-    return settings
-
-def generate_fields(variables, scrollable_frame):
-    vars_dict = {}
-    row = 0
-    tooltips = {
-        "src": "Path to the folder containing the images.",
-        "metadata_type": "Type of metadata to expect in the images. This will determine how the images are processed. If 'custom' is selected, you can provide a custom regex pattern to extract metadata from the image names",
-        "custom_regex": "Custom regex pattern to extract metadata from the image names. This will only be used if 'custom' is selected for 'metadata_type'.",
-        "experiment": "Name of the experiment. This will be used to name the output files.",
-        "channels": "List of channels to use for the analysis. The first channel is 0, the second is 1, and so on. For example, [0,1,2] will use channels 0, 1, and 2.",
-        "magnification": "At what magnification the images were taken. This will be used to determine the size of the objects in the images.",
-        "nucleus_channel": "The channel to use for the nucleus. If None, the nucleus will not be segmented.",
-        "nucleus_background": "The background intensity for the nucleus channel. This will be used to remove background noise.",
-        "nucleus_Signal_to_noise": "The signal-to-noise ratio for the nucleus channel. This will be used to determine the range of intensities to normalize images to for nucleus segmentation.",
-        "nucleus_CP_prob": "The cellpose probability threshold for the nucleus channel. This will be used to segment the nucleus.",
-        "cell_channel": "The channel to use for the cell. If None, the cell will not be segmented.",
-        "cell_background": "The background intensity for the cell channel. This will be used to remove background noise.",
-        "cell_Signal_to_noise": "The signal-to-noise ratio for the cell channel. This will be used to determine the range of intensities to normalize images to for cell segmentation.",
-        "cell_CP_prob": "The cellpose probability threshold for the cell channel. This will be used to segment the cell.",
-        "pathogen_channel": "The channel to use for the pathogen. If None, the pathogen will not be segmented.",
-        "pathogen_background": "The background intensity for the pathogen channel. This will be used to remove background noise.",
-        "pathogen_Signal_to_noise": "The signal-to-noise ratio for the pathogen channel. This will be used to determine the range of intensities to normalize images to for pathogen segmentation.",
-        "pathogen_CP_prob": "The cellpose probability threshold for the pathogen channel. This will be used to segment the pathogen.",
-        "preprocess": "Whether to preprocess the images before segmentation. This includes background removal and normalization. Set to False only if this step has already been done.",
-        "masks": "Whether to generate masks for the segmented objects. If True, masks will be generated for the nucleus, cell, and pathogen.",
-        "examples_to_plot": "The number of images to plot for each segmented object. This will be used to visually inspect the segmentation results and normalization .",
-        "randomize": "Whether to randomize the order of the images before processing. Recommended to avoid bias in the segmentation.",
-        "batch_size": "The batch size to use for processing the images. This will determine how many images are processed at once. Images are normalized and segmented in batches. Lower if application runs out of RAM or VRAM.",
-        "timelapse": "Whether to process the images as a timelapse.",
-        "timelapse_displacement": "The displacement between frames in the timelapse. This will be used to align the frames before processing.",
-        "timelapse_memory": "The number of frames to in tandem objects must be present in to be considered the same object in the timelapse.",
-        "timelapse_frame_limits": "The frame limits to use for the timelapse. This will determine which frames are processed. For example, [5,20] will process frames 5 to 20.",
-        "timelapse_remove_transient": "Whether to remove transient objects in the timelapse. Transient objects are present in fewer than all frames.",
-        "timelapse_mode": "The mode to use for processing the timelapse. 'trackpy' uses the trackpy library for tracking objects, while 'btrack' uses the btrack library.",
-        "timelapse_objects": "The objects to track in the timelapse (cell, nucleus or pathogen). This will determine which objects are tracked over time. If None, all objects will be tracked.",
-        "fps": "Frames per second of the automatically generated timelapse movies.",
-        "remove_background": "Whether to remove background noise from the images. This will help improve the quality of the segmentation.",
-        "lower_quantile": "The lower quantile to use for normalizing the images. This will be used to determine the range of intensities to normalize images to.",
-        "merge_pathogens": "Whether to merge pathogen objects that share more than 75% of their perimiter.",
-        "normalize_plots": "Whether to normalize the plots.",
-        "all_to_mip": "Whether to convert all images to maximum intensity projections before processing.",
-        "pick_slice": "Whether to pick a single slice from the z-stack images. If False, the maximum intensity projection will be used.",
-        "skip_mode": "The mode to use for skipping images. This will determine how to handle images that cannot be processed.",
-        "save": "Whether to save the results to disk.",
-        "plot": "Whether to plot the results.",
-        "workers": "The number of workers to use for processing the images. This will determine how many images are processed in parallel. Increase to speed up processing.",
-        "verbose": "Whether to print verbose output during processing.",
-        "input_folder": "Path to the folder containing the images.",
-        "cell_mask_dim": "The dimension of the array the cell mask is saved in.",
-        "cell_min_size": "The minimum size of cell objects in pixels2.",
-        "cytoplasm_min_size": "The minimum size of cytoplasm objects in pixels2.",
-        "nucleus_mask_dim": "The dimension of the array the nucleus mask is saved in.",
-        "nucleus_min_size": "The minimum size of nucleus objects in pixels2.",
-        "pathogen_mask_dim": "The dimension of the array the pathogen mask is saved in.",
-        "pathogen_min_size": "The minimum size of pathogen objects in pixels2.",
-        "save_png": "Whether to save the segmented objects as PNG images.",
-        "crop_mode": "The mode to use for cropping the images. This will determine which objects are cropped from the images (cell, nucleus, pathogen, cytoplasm).",
-        "use_bounding_box": "Whether to use the bounding box of the objects for cropping. If False, only the object itself will be cropped.",
-        "png_size": "The size of the PNG images to save. This will determine the size of the saved images.",
-        "normalize": "The percentiles to use for normalizing the images. This will be used to determine the range of intensities to normalize images to., if None, no normalization is done.",
-        "png_dims": "The dimensions of the PNG images to save. This will determine the dimensions of the saved images. Maximum of 3 dimensions e.g. [1,2,3].",
-        "normalize_by": "Whether to normalize the images by field of view (fov) or by PNG image (png).",
-        "save_measurements": "Whether to save the measurements to disk.",
-        "representative_images": "Whether to save representative images of the segmented objects (Not working yet).",
-        "plot": "Whether to plot results.",
-        "plot_filtration": "Whether to plot the filtration steps.",
-        "include_uninfected": "Whether to include uninfected cells in the analysis.",
-        "dialate_pngs": "Whether to dialate the PNG images before saving.",
-        "dialate_png_ratios": "The ratios to use for dialating the PNG images. This will determine the amount of dialation applied to the images before cropping.",
-        "timelapse_objects": "The objects to track in the timelapse (cell, nucleus or pathogen). This will determine which objects are tracked over time. If None, all objects will be tracked.",
-        "max_workers": "The number of workers to use for processing the images. This will determine how many images are processed in parallel. Increase to speed up processing.",
-        "cells: ": "The cell types to include in the analysis.",
-        "cell_loc": "The locations of the cell types in the images.",
-        "pathogens": "The pathogen types to include in the analysis.",
-        "pathogen_loc": "The locations of the pathogen types in the images.",
-        "treatments": "The treatments to include in the analysis.",
-        "treatment_loc": "The locations of the treatments in the images.",
-        "channel_of_interest": "The channel of interest to use for the analysis.",
-        "compartments": "The compartments to measure in the images.",
-        "measurement": "The measurement to use for the analysis.",
-        "nr_imgs": "The number of images to plot.",
-        "um_per_pixel": "The micrometers per pixel for the images.",
-    }
-
-    for key, (var_type, options, default_value) in variables.items():
-        label, widget, var = create_input_field(scrollable_frame.scrollable_frame, key, row, var_type, options, default_value)
-        vars_dict[key] = (label, widget, var)  # Store the label, widget, and variable
-        
-        # Add tooltip to the label if it exists in the tooltips dictionary
-        if key in tooltips:
-            ToolTip(label, tooltips[key])
-        
-        row += 1
-    return vars_dict
-
-class TextRedirector(object):
-    def __init__(self, widget, queue):
-        self.widget = widget
-        self.queue = queue
-
-    def write(self, str):
-        self.queue.put(str)
-
-    def flush(self):
-        pass
-
-def create_dark_mode(root, style, console_output):
-    dark_bg = 'black'
-    light_text = 'white'
-    dark_text = 'black'
-    input_bg = '#555555'  # Slightly lighter background for input fields
-    
-    # Configure ttkcompartments('TFrame', background=dark_bg)
-    style.configure('TLabel', background=dark_bg, foreground=light_text)
-    style.configure('TEntry', fieldbackground=input_bg, foreground=dark_text, background=dark_bg)
-    style.configure('TButton', background=dark_bg, foreground=dark_text)
-    style.map('TButton', background=[('active', dark_bg)], foreground=[('active', dark_text)])
-    style.configure('Dark.TCheckbutton', background=dark_bg, foreground=dark_text)
-    style.map('Dark.TCheckbutton', background=[('active', dark_bg)], foreground=[('active', dark_text)])
-    style.configure('TCombobox', fieldbackground=input_bg, foreground=dark_text, background=dark_bg, selectbackground=input_bg, selectforeground=dark_text)
-    style.map('TCombobox', fieldbackground=[('readonly', input_bg)], selectbackground=[('readonly', input_bg)], foreground=[('readonly', dark_text)])
-    
-    if console_output != None:
-        console_output.config(bg=dark_bg, fg=light_text, insertbackground=light_text) #, font=("Helvetica", 12)
-    root.configure(bg=dark_bg)
-    
-def set_dark_style(style):
-    style.configure('TFrame', background='black')
-    style.configure('TLabel', background='black', foreground='white')
-    style.configure('TEntry', background='black', foreground='white')
-    style.configure('TCheckbutton', background='black', foreground='white')
-
-##@log_function_call   
-def main_thread_update_function(root, q, fig_queue, canvas_widget, progress_label):
-    try:
-        ansi_escape_pattern = re.compile(r'\x1B\[[0-?]*[ -/]*[@-~]')
-        while not q.empty():
-            message = q.get_nowait()
-            clean_message = ansi_escape_pattern.sub('', message)
-            if clean_message.startswith("Progress"):
-                progress_label.config(text=clean_message)
-            if clean_message.startswith("\rProgress"):
-                progress_label.config(text=clean_message)
-            elif clean_message.startswith("Successfully"):
-                progress_label.config(text=clean_message)
-            elif clean_message.startswith("Processing"):
-                progress_label.config(text=clean_message)
-            elif clean_message.startswith("scale"):
-                pass
-            elif clean_message.startswith("plot_cropped_arrays"):
-                pass
-            elif clean_message == "" or clean_message == "\r" or clean_message.strip() == "":
-                pass
-            else:
-                print(clean_message)
-    except Exception as e:
-        print(f"Error updating GUI canvas: {e}")
-    finally:
-        root.after(100, lambda: main_thread_update_function(root, q, fig_queue, canvas_widget, progress_label))
-
 def process_stdout_stderr(q):
     """
     Redirect stdout and stderr to the queue q.
@@ -959,137 +132,8 @@ class WriteToQueue(io.TextIOBase):
     def flush(self):
         pass
 
-def clear_canvas(canvas):
-    # Clear each plot (axes) in the figure
-    for ax in canvas.figure.get_axes():
-        ax.clear()
-
-    # Redraw the now empty canvas without changing its size
-    canvas.draw_idle()
-    
-def measure_crop_wrapper(settings, q, fig_queue):
-    """
-    Wraps the measure_crop function to integrate with GUI processes.
-    
-    Parameters:
-    - settings: dict, The settings for the measure_crop function.
-    - q: multiprocessing.Queue, Queue for logging messages to the GUI.
-    - fig_queue: multiprocessing.Queue, Queue for sending figures to the GUI.
-    """
-
-    def my_show():
-        """
-        Replacement for plt.show() that queues figures instead of displaying them.
-        """
-        fig = plt.gcf()
-        fig_queue.put(fig)  # Queue the figure for GUI display
-        plt.close(fig)  # Prevent the figure from being shown by plt.show()
-
-    # Temporarily override plt.show
-    original_show = plt.show
-    plt.show = my_show
-
-    try:
-        print('start')
-        spacr.measure.measure_crop(settings=settings)
-    except Exception as e:
-        errorMessage = f"Error during processing: {e}"
-        q.put(errorMessage)  # Send the error message to the GUI via the queue
-        traceback.print_exc()
-    finally:
-        plt.show = original_show  # Restore the original plt.show function
-        
-#@log_function_call
-def preprocess_generate_masks_wrapper(settings, q, fig_queue):
-    """
-    Wraps the measure_crop function to integrate with GUI processes.
-    
-    Parameters:
-    - settings: dict, The settings for the measure_crop function.
-    - q: multiprocessing.Queue, Queue for logging messages to the GUI.
-    - fig_queue: multiprocessing.Queue, Queue for sending figures to the GUI.
-    """
-
-    def my_show():
-        """
-        Replacement for plt.show() that queues figures instead of displaying them.
-        """
-        fig = plt.gcf()
-        fig_queue.put(fig)  # Queue the figure for GUI display
-        plt.close(fig)  # Prevent the figure from being shown by plt.show()
-
-    # Temporarily override plt.show
-    original_show = plt.show
-    plt.show = my_show
-
-    try:
-        spacr.core.preprocess_generate_masks(settings['src'], settings=settings)
-    except Exception as e:
-        errorMessage = f"Error during processing: {e}"
-        q.put(errorMessage)  # Send the error message to the GUI via the queue
-        traceback.print_exc()
-    finally:
-        plt.show = original_show  # Restore the original plt.show function
-
-def train_test_model_wrapper(settings, q, fig_queue):
-    """
-    Wraps the measure_crop function to integrate with GUI processes.
-    
-    Parameters:
-    - settings: dict, The settings for the measure_crop function.
-    - q: multiprocessing.Queue, Queue for logging messages to the GUI.
-    - fig_queue: multiprocessing.Queue, Queue for sending figures to the GUI.
-    """
-
-    def my_show():
-        """
-        Replacement for plt.show() that queues figures instead of displaying them.
-        """
-        fig = plt.gcf()
-        fig_queue.put(fig)  # Queue the figure for GUI display
-        plt.close(fig)  # Prevent the figure from being shown by plt.show()
-
-    # Temporarily override plt.show
-    original_show = plt.show
-    plt.show = my_show
-
-    try:
-        spacr.core.train_test_model(settings['src'], settings=settings)
-    except Exception as e:
-        errorMessage = f"Error during processing: {e}"
-        q.put(errorMessage)  # Send the error message to the GUI via the queue
-        traceback.print_exc()
-    finally:
-        plt.show = original_show  # Restore the original plt.show function
-        
-        
-def run_multiple_simulations_wrapper(settings, q, fig_queue):
-    """
-    Wraps the run_multiple_simulations function to integrate with GUI processes.
-    
-    Parameters:
-    - settings: dict, The settings for the run_multiple_simulations function.
-    - q: multiprocessing.Queue, Queue for logging messages to the GUI.
-    - fig_queue: multiprocessing.Queue, Queue for sending figures to the GUI.
-    """
-
-    def my_show():
-        """
-        Replacement for plt.show() that queues figures instead of displaying them.
-        """
-        fig = plt.gcf()
-        fig_queue.put(fig)  # Queue the figure for GUI display
-        plt.close(fig)  # Prevent the figure from being shown by plt.show()
-
-    # Temporarily override plt.show
-    original_show = plt.show
-    plt.show = my_show
-
-    try:
-        spacr.sim.run_multiple_simulations(settings=settings)
-    except Exception as e:
-        errorMessage = f"Error during processing: {e}"
-        q.put(errorMessage)  # Send the error message to the GUI via the queue
-        traceback.print_exc()
-    finally:
-        plt.show = original_show  # Restore the original plt.show function
+def cancel_after_tasks(frame):
+    if hasattr(frame, 'after_tasks'):
+        for task in frame.after_tasks:
+            frame.after_cancel(task)
+        frame.after_tasks.clear()