spacr 0.1.63__py3-none-any.whl → 0.1.75__py3-none-any.whl

spacr/app_make_masks.py

@@ -1,925 +1,51 @@
-import os
-import numpy as np
-import tkinter as tk
-import imageio.v2 as imageio
-from collections import deque
-from PIL import Image, ImageTk
-from skimage.draw import polygon, line
-from skimage.transform import resize
-from scipy.ndimage import binary_fill_holes, label
 import tkinter as tk
 from tkinter import ttk
+from .gui import MainApp
 
-from .gui_elements import spacrFrame, spacrButton, set_dark_style, create_menu_bar, set_default_font
-
-class modify_masks:
-
-    def __init__(self, root, folder_path, scale_factor):
-        self.root = root
-        self.folder_path = folder_path
-        self.scale_factor = scale_factor
-        self.image_filenames = sorted([f for f in os.listdir(folder_path) if f.endswith(('.png', '.jpg', '.jpeg', '.tif', '.tiff'))])
-        self.masks_folder = os.path.join(folder_path, 'masks')
-        self.current_image_index = 0
-        self.initialize_flags()
-        self.canvas_width = self.root.winfo_screenheight() -100
-        self.canvas_height = self.root.winfo_screenheight() -100
-        self.root.configure(bg='black')
-        self.setup_navigation_toolbar()
-        self.setup_mode_toolbar()
-        self.setup_function_toolbar()
-        self.setup_zoom_toolbar()
-        self.setup_canvas()
-        self.load_first_image()
-    
-    ####################################################################################################
-    # Helper functions#
-    ####################################################################################################
-    
-    def update_display(self):
-        if self.zoom_active:
-            self.display_zoomed_image()
-        else:
-            self.display_image()
-    
-    def update_original_mask_from_zoom(self):
-        y0, y1, x0, x1 = self.zoom_y0, self.zoom_y1, self.zoom_x0, self.zoom_x1
-        zoomed_mask_resized = resize(self.zoom_mask, (y1 - y0, x1 - x0), order=0, preserve_range=True).astype(np.uint8)
-        self.mask[y0:y1, x0:x1] = zoomed_mask_resized
-        
-    def update_original_mask(self, zoomed_mask, x0, x1, y0, y1):
-        actual_mask_region = self.mask[y0:y1, x0:x1]
-        target_shape = actual_mask_region.shape
-        resized_mask = resize(zoomed_mask, target_shape, order=0, preserve_range=True).astype(np.uint8)
-        if resized_mask.shape != actual_mask_region.shape:
-            raise ValueError(f"Shape mismatch: resized_mask {resized_mask.shape}, actual_mask_region {actual_mask_region.shape}")
-        self.mask[y0:y1, x0:x1] = np.maximum(actual_mask_region, resized_mask)
-        self.mask = self.mask.copy()
-        self.mask[y0:y1, x0:x1] = np.maximum(self.mask[y0:y1, x0:x1], resized_mask)
-        self.mask = self.mask.copy()
-
-    def get_scaling_factors(self, img_width, img_height, canvas_width, canvas_height):
-        x_scale = img_width / canvas_width
-        y_scale = img_height / canvas_height
-        return x_scale, y_scale
-    
-    def canvas_to_image(self, x_canvas, y_canvas):
-        x_scale, y_scale = self.get_scaling_factors(
-            self.image.shape[1], self.image.shape[0],
-            self.canvas_width, self.canvas_height
-        )
-        x_image = int(x_canvas * x_scale)
-        y_image = int(y_canvas * y_scale)
-        return x_image, y_image
-
-    def apply_zoom_on_enter(self, event):
-        if self.zoom_active and self.zoom_rectangle_start is not None:
-            self.set_zoom_rectangle_end(event)
-        
-    def normalize_image(self, image, lower_quantile, upper_quantile):
-        lower_bound = np.percentile(image, lower_quantile)
-        upper_bound = np.percentile(image, upper_quantile)
-        normalized = np.clip(image, lower_bound, upper_bound)
-        normalized = (normalized - lower_bound) / (upper_bound - lower_bound)
-        max_value = np.iinfo(image.dtype).max
-        normalized = (normalized * max_value).astype(image.dtype)
-        return normalized
-    
-    def resize_arrays(self, img, mask):
-        original_dtype = img.dtype
-        scaled_height = int(img.shape[0] * self.scale_factor)
-        scaled_width = int(img.shape[1] * self.scale_factor)
-        scaled_img = resize(img, (scaled_height, scaled_width), anti_aliasing=True, preserve_range=True)
-        scaled_mask = resize(mask, (scaled_height, scaled_width), order=0, anti_aliasing=False, preserve_range=True)
-        stretched_img = resize(scaled_img, (self.canvas_height, self.canvas_width), anti_aliasing=True, preserve_range=True)
-        stretched_mask = resize(scaled_mask, (self.canvas_height, self.canvas_width), order=0, anti_aliasing=False, preserve_range=True)
-        return stretched_img.astype(original_dtype), stretched_mask.astype(original_dtype)
-    
-    ####################################################################################################
-    #Initiate canvas elements#
-    ####################################################################################################
-    
-    def load_first_image(self):
-        self.image, self.mask = self.load_image_and_mask(self.current_image_index)
-        self.original_size = self.image.shape
-        self.image, self.mask = self.resize_arrays(self.image, self.mask)
-        self.display_image()
-
-    def setup_canvas(self):
-        self.canvas = tk.Canvas(self.root, width=self.canvas_width, height=self.canvas_height, bg='black')
-        self.canvas.pack()
-        self.canvas.bind("<Motion>", self.update_mouse_info)
-
-    def initialize_flags(self):
-        self.zoom_rectangle_start = None
-        self.zoom_rectangle_end = None
-        self.zoom_rectangle_id = None
-        self.zoom_x0 = None
-        self.zoom_y0 = None
-        self.zoom_x1 = None
-        self.zoom_y1 = None
-        self.zoom_mask = None
-        self.zoom_image = None
-        self.zoom_image_orig = None
-        self.zoom_scale = 1
-        self.drawing = False
-        self.zoom_active = False
-        self.magic_wand_active = False
-        self.brush_active = False
-        self.dividing_line_active = False
-        self.dividing_line_coords = []
-        self.current_dividing_line = None
-        self.lower_quantile = tk.StringVar(value="1.0")
-        self.upper_quantile = tk.StringVar(value="99.9")
-        self.magic_wand_tolerance = tk.StringVar(value="1000")
-
-    def update_mouse_info(self, event):
-        x, y = event.x, event.y
-        intensity = "N/A"
-        mask_value = "N/A"
-        pixel_count = "N/A"  
-        if self.zoom_active:
-            if 0 <= x < self.canvas_width and 0 <= y < self.canvas_height:
-                intensity = self.zoom_image_orig[y, x] if self.zoom_image_orig is not None else "N/A"
-                mask_value = self.zoom_mask[y, x] if self.zoom_mask is not None else "N/A"
-        else:
-            if 0 <= x < self.image.shape[1] and 0 <= y < self.image.shape[0]:
-                intensity = self.image[y, x]
-                mask_value = self.mask[y, x]
-        if mask_value != "N/A" and mask_value != 0:
-            pixel_count = np.sum(self.mask == mask_value)
-        self.intensity_label.config(text=f"Intensity: {intensity}")
-        self.mask_value_label.config(text=f"Mask: {mask_value}, Area: {pixel_count}")
-        self.mask_value_label.config(text=f"Mask: {mask_value}")
-        if mask_value != "N/A" and mask_value != 0:
-            self.pixel_count_label.config(text=f"Area: {pixel_count}")
-        else:
-            self.pixel_count_label.config(text="Area: N/A")
-    
-    def setup_navigation_toolbar(self):
-        navigation_toolbar = tk.Frame(self.root, bg='black')
-        navigation_toolbar.pack(side='top', fill='x')
-        prev_btn = tk.Button(navigation_toolbar, text="Previous", command=self.previous_image, bg='black', fg='white')
-        prev_btn.pack(side='left')
-        next_btn = tk.Button(navigation_toolbar, text="Next", command=self.next_image, bg='black', fg='white')
-        next_btn.pack(side='left')
-        save_btn = tk.Button(navigation_toolbar, text="Save", command=self.save_mask, bg='black', fg='white')
-        save_btn.pack(side='left')
-        self.intensity_label = tk.Label(navigation_toolbar, text="Image: N/A", bg='black', fg='white')
-        self.intensity_label.pack(side='right')
-        self.mask_value_label = tk.Label(navigation_toolbar, text="Mask: N/A", bg='black', fg='white')
-        self.mask_value_label.pack(side='right')
-        self.pixel_count_label = tk.Label(navigation_toolbar, text="Area: N/A", bg='black', fg='white')
-        self.pixel_count_label.pack(side='right')
-
-    def setup_mode_toolbar(self):
-        self.mode_toolbar = tk.Frame(self.root, bg='black')
-        self.mode_toolbar.pack(side='top', fill='x')
-        self.draw_btn = tk.Button(self.mode_toolbar, text="Draw", command=self.toggle_draw_mode, bg='black', fg='white')
-        self.draw_btn.pack(side='left')
-        self.magic_wand_btn = tk.Button(self.mode_toolbar, text="Magic Wand", command=self.toggle_magic_wand_mode, bg='black', fg='white')
-        self.magic_wand_btn.pack(side='left')
-        tk.Label(self.mode_toolbar, text="Tolerance:", bg='black', fg='white').pack(side='left')
-        self.tolerance_entry = tk.Entry(self.mode_toolbar, textvariable=self.magic_wand_tolerance, bg='black', fg='white')
-        self.tolerance_entry.pack(side='left')
-        tk.Label(self.mode_toolbar, text="Max Pixels:", bg='black', fg='white').pack(side='left')
-        self.max_pixels_entry = tk.Entry(self.mode_toolbar, bg='black', fg='white')
-        self.max_pixels_entry.insert(0, "1000")
-        self.max_pixels_entry.pack(side='left')
-        self.erase_btn = tk.Button(self.mode_toolbar, text="Erase", command=self.toggle_erase_mode, bg='black', fg='white')
-        self.erase_btn.pack(side='left')
-        self.brush_btn = tk.Button(self.mode_toolbar, text="Brush", command=self.toggle_brush_mode, bg='black', fg='white')
-        self.brush_btn.pack(side='left')
-        self.brush_size_entry = tk.Entry(self.mode_toolbar, bg='black', fg='white')
-        self.brush_size_entry.insert(0, "10")
-        self.brush_size_entry.pack(side='left')
-        tk.Label(self.mode_toolbar, text="Brush Size:", bg='black', fg='white').pack(side='left')
-        self.dividing_line_btn = tk.Button(self.mode_toolbar, text="Dividing Line", command=self.toggle_dividing_line_mode, bg='black', fg='white')
-        self.dividing_line_btn.pack(side='left')
-
-    def setup_function_toolbar(self):
-        self.function_toolbar = tk.Frame(self.root, bg='black')
-        self.function_toolbar.pack(side='top', fill='x')
-        self.fill_btn = tk.Button(self.function_toolbar, text="Fill", command=self.fill_objects, bg='black', fg='white')
-        self.fill_btn.pack(side='left')
-        self.relabel_btn = tk.Button(self.function_toolbar, text="Relabel", command=self.relabel_objects, bg='black', fg='white')
-        self.relabel_btn.pack(side='left')
-        self.clear_btn = tk.Button(self.function_toolbar, text="Clear", command=self.clear_objects, bg='black', fg='white')
-        self.clear_btn.pack(side='left')
-        self.invert_btn = tk.Button(self.function_toolbar, text="Invert", command=self.invert_mask, bg='black', fg='white')
-        self.invert_btn.pack(side='left')
-        remove_small_btn = tk.Button(self.function_toolbar, text="Remove Small", command=self.remove_small_objects, bg='black', fg='white')
-        remove_small_btn.pack(side='left')
-        tk.Label(self.function_toolbar, text="Min Area:", bg='black', fg='white').pack(side='left')
-        self.min_area_entry = tk.Entry(self.function_toolbar, bg='black', fg='white')
-        self.min_area_entry.insert(0, "100")  # Default minimum area
-        self.min_area_entry.pack(side='left')
-
-    def setup_zoom_toolbar(self):
-        self.zoom_toolbar = tk.Frame(self.root, bg='black')
-        self.zoom_toolbar.pack(side='top', fill='x')
-        self.zoom_btn = tk.Button(self.zoom_toolbar, text="Zoom", command=self.toggle_zoom_mode, bg='black', fg='white')
-        self.zoom_btn.pack(side='left')
-        self.normalize_btn = tk.Button(self.zoom_toolbar, text="Apply Normalization", command=self.apply_normalization, bg='black', fg='white')
-        self.normalize_btn.pack(side='left')
-        tk.Label(self.zoom_toolbar, text="Lower Percentile:", bg='black', fg='white').pack(side='left')
-        self.lower_entry = tk.Entry(self.zoom_toolbar, textvariable=self.lower_quantile, bg='black', fg='white')
-        self.lower_entry.pack(side='left')
-        
-        tk.Label(self.zoom_toolbar, text="Upper Percentile:", bg='black', fg='white').pack(side='left')
-        self.upper_entry = tk.Entry(self.zoom_toolbar, textvariable=self.upper_quantile, bg='black', fg='white')
-        self.upper_entry.pack(side='left')
-
-        
-    def load_image_and_mask(self, index):
-        image_path = os.path.join(self.folder_path, self.image_filenames[index])
-        image = imageio.imread(image_path)        
-        mask_path = os.path.join(self.masks_folder, self.image_filenames[index])
-        if os.path.exists(mask_path):
-            print(f'loading mask:{mask_path} for image: {image_path}')
-            mask = imageio.imread(mask_path)
-            if mask.dtype != np.uint8:
-                mask = (mask / np.max(mask) * 255).astype(np.uint8)
-        else:
-            mask = np.zeros(image.shape[:2], dtype=np.uint8)
-            print(f'loaded new mask for image: {image_path}')
-        return image, mask
-    
-    ####################################################################################################
-    # Image Display functions#
-    ####################################################################################################
-    def display_image(self):
-        if self.zoom_rectangle_id is not None:
-            self.canvas.delete(self.zoom_rectangle_id)
-            self.zoom_rectangle_id = None
-        lower_quantile = float(self.lower_quantile.get()) if self.lower_quantile.get() else 1.0
-        upper_quantile = float(self.upper_quantile.get()) if self.upper_quantile.get() else 99.9
-        normalized = self.normalize_image(self.image, lower_quantile, upper_quantile)
-        combined = self.overlay_mask_on_image(normalized, self.mask)
-        self.tk_image = ImageTk.PhotoImage(image=Image.fromarray(combined))
-        self.canvas.create_image(0, 0, anchor='nw', image=self.tk_image)
-
-    def display_zoomed_image(self):
-        if self.zoom_rectangle_start and self.zoom_rectangle_end:
-            # Convert canvas coordinates to image coordinates
-            x0, y0 = self.canvas_to_image(*self.zoom_rectangle_start)
-            x1, y1 = self.canvas_to_image(*self.zoom_rectangle_end)
-            x0, x1 = min(x0, x1), max(x0, x1)
-            y0, y1 = min(y0, y1), max(y0, y1)
-            self.zoom_x0 = x0
-            self.zoom_y0 = y0
-            self.zoom_x1 = x1
-            self.zoom_y1 = y1
-            # Normalize the entire image
-            lower_quantile = float(self.lower_quantile.get()) if self.lower_quantile.get() else 1.0
-            upper_quantile = float(self.upper_quantile.get()) if self.upper_quantile.get() else 99.9
-            normalized_image = self.normalize_image(self.image, lower_quantile, upper_quantile)
-            # Extract the zoomed portion of the normalized image and mask
-            self.zoom_image = normalized_image[y0:y1, x0:x1]
-            self.zoom_image_orig = self.image[y0:y1, x0:x1]
-            self.zoom_mask = self.mask[y0:y1, x0:x1]
-            original_mask_area = self.mask.shape[0] * self.mask.shape[1]
-            zoom_mask_area = self.zoom_mask.shape[0] * self.zoom_mask.shape[1]
-            if original_mask_area > 0:
-                self.zoom_scale = original_mask_area/zoom_mask_area
-            # Resize the zoomed image and mask to fit the canvas
-            canvas_height = self.canvas.winfo_height()
-            canvas_width = self.canvas.winfo_width()
-            
-            if self.zoom_image.size > 0 and canvas_height > 0 and canvas_width > 0:
-                self.zoom_image = resize(self.zoom_image, (canvas_height, canvas_width), preserve_range=True).astype(self.zoom_image.dtype)
-                self.zoom_image_orig = resize(self.zoom_image_orig, (canvas_height, canvas_width), preserve_range=True).astype(self.zoom_image_orig.dtype)
-                #self.zoom_mask = resize(self.zoom_mask, (canvas_height, canvas_width), preserve_range=True).astype(np.uint8)
-                self.zoom_mask = resize(self.zoom_mask, (canvas_height, canvas_width), order=0, preserve_range=True).astype(np.uint8)
-                combined = self.overlay_mask_on_image(self.zoom_image, self.zoom_mask)
-                self.tk_image = ImageTk.PhotoImage(image=Image.fromarray(combined))
-                self.canvas.create_image(0, 0, anchor='nw', image=self.tk_image)
-
-    def overlay_mask_on_image(self, image, mask, alpha=0.5):
-        if len(image.shape) == 2:
-            image = np.stack((image,) * 3, axis=-1)
-        mask = mask.astype(np.int32)
-        max_label = np.max(mask)
-        np.random.seed(0)
-        colors = np.random.randint(0, 255, size=(max_label + 1, 3), dtype=np.uint8)
-        colors[0] = [0, 0, 0]  # background color
-        colored_mask = colors[mask]
-        image_8bit = (image / 256).astype(np.uint8)
-        # Blend the mask and the image with transparency
-        combined_image = np.where(mask[..., None] > 0, 
-                                  np.clip(image_8bit * (1 - alpha) + colored_mask * alpha, 0, 255), 
-                                  image_8bit)
-        # Convert the final image back to uint8
-        combined_image = combined_image.astype(np.uint8)
-        return combined_image
-    
-    ####################################################################################################
-    # Navigation functions#
-    ####################################################################################################
-    
-    def previous_image(self):
-        if self.current_image_index > 0:
-            self.current_image_index -= 1
-            self.initialize_flags()            
-            self.image, self.mask = self.load_image_and_mask(self.current_image_index)
-            self.original_size = self.image.shape
-            self.image, self.mask = self.resize_arrays(self.image, self.mask)
-            self.display_image()
-
-    def next_image(self):
-        if self.current_image_index < len(self.image_filenames) - 1:
-            self.current_image_index += 1
-            self.initialize_flags()            
-            self.image, self.mask = self.load_image_and_mask(self.current_image_index)
-            self.original_size = self.image.shape
-            self.image, self.mask = self.resize_arrays(self.image, self.mask)
-            self.display_image()
-            
-    def save_mask(self):
-        if self.current_image_index < len(self.image_filenames):
-            original_size = self.original_size
-            if self.mask.shape != original_size:
-                resized_mask = resize(self.mask, original_size, order=0, preserve_range=True).astype(np.uint16)
-            else:
-                resized_mask = self.mask
-            resized_mask, _ = label(resized_mask > 0)
-            save_folder = os.path.join(self.folder_path, 'masks')
-            if not os.path.exists(save_folder):
-                os.makedirs(save_folder)
-            image_filename = os.path.splitext(self.image_filenames[self.current_image_index])[0] + '.tif'
-            save_path = os.path.join(save_folder, image_filename)
-
-            print(f"Saving mask to: {save_path}")  # Debug print
-            imageio.imwrite(save_path, resized_mask)
-
-    ####################################################################################################
-    # Zoom Functions #
-    ####################################################################################################
-    def set_zoom_rectangle_start(self, event):
-        if self.zoom_active:
-            self.zoom_rectangle_start = (event.x, event.y)
-    
-    def set_zoom_rectangle_end(self, event):
-        if self.zoom_active:
-            self.zoom_rectangle_end = (event.x, event.y)
-            if self.zoom_rectangle_id is not None:
-                self.canvas.delete(self.zoom_rectangle_id)
-                self.zoom_rectangle_id = None
-            self.display_zoomed_image()  
-            self.canvas.unbind("<Motion>")  
-            self.canvas.unbind("<Button-1>")
-            self.canvas.unbind("<Button-3>")  
-            self.canvas.bind("<Motion>", self.update_mouse_info)
-            
-    def update_zoom_box(self, event):
-        if self.zoom_active and self.zoom_rectangle_start is not None:
-            if self.zoom_rectangle_id is not None:
-                self.canvas.delete(self.zoom_rectangle_id)
-            # Assuming event.x and event.y are already in image coordinates
-            self.zoom_rectangle_end = (event.x, event.y)
-            x0, y0 = self.zoom_rectangle_start
-            x1, y1 = self.zoom_rectangle_end
-            self.zoom_rectangle_id = self.canvas.create_rectangle(x0, y0, x1, y1, outline="red", width=2)
-    
-    ####################################################################################################
-    # Mode activation#
-    ####################################################################################################
-    
-    def toggle_zoom_mode(self):
-        if not self.zoom_active:
-            self.brush_btn.config(text="Brush")
-            self.canvas.unbind("<B1-Motion>")
-            self.canvas.unbind("<B3-Motion>")
-            self.canvas.unbind("<ButtonRelease-1>")
-            self.canvas.unbind("<ButtonRelease-3>")
-            self.zoom_active = True
-            self.drawing = False
-            self.magic_wand_active = False
-            self.erase_active = False
-            self.brush_active = False
-            self.dividing_line_active = False
-            self.draw_btn.config(text="Draw")
-            self.erase_btn.config(text="Erase")
-            self.magic_wand_btn.config(text="Magic Wand")
-            self.zoom_btn.config(text="Zoom ON")
-            self.dividing_line_btn.config(text="Dividing Line")
-            self.canvas.unbind("<Button-1>")
-            self.canvas.unbind("<Button-3>")
-            self.canvas.unbind("<Motion>")
-            self.canvas.bind("<Button-1>", self.set_zoom_rectangle_start)
-            self.canvas.bind("<Button-3>", self.set_zoom_rectangle_end)
-            self.canvas.bind("<Motion>", self.update_zoom_box)
-        else:
-            self.zoom_active = False
-            self.zoom_btn.config(text="Zoom")
-            self.canvas.unbind("<Button-1>")
-            self.canvas.unbind("<Button-3>")
-            self.canvas.unbind("<Motion>")
-            self.zoom_rectangle_start = self.zoom_rectangle_end = None
-            self.zoom_rectangle_id = None
-            self.display_image()
-            self.canvas.bind("<Motion>", self.update_mouse_info)
-            self.zoom_rectangle_start = None
-            self.zoom_rectangle_end = None
-            self.zoom_rectangle_id = None
-            self.zoom_x0 = None
-            self.zoom_y0 = None
-            self.zoom_x1 = None
-            self.zoom_y1 = None
-            self.zoom_mask = None
-            self.zoom_image = None
-            self.zoom_image_orig = None
-
-    def toggle_brush_mode(self):
-        self.brush_active = not self.brush_active
-        if self.brush_active:
-            self.drawing = False
-            self.magic_wand_active = False
-            self.erase_active = False
-            self.brush_btn.config(text="Brush ON")
-            self.draw_btn.config(text="Draw")
-            self.erase_btn.config(text="Erase")
-            self.magic_wand_btn.config(text="Magic Wand")
-            self.canvas.unbind("<Button-1>")
-            self.canvas.unbind("<Button-3>")
-            self.canvas.unbind("<Motion>")
-            self.canvas.bind("<B1-Motion>", self.apply_brush)  # Left click and drag to apply brush
-            self.canvas.bind("<B3-Motion>", self.erase_brush)  # Right click and drag to erase with brush
-            self.canvas.bind("<ButtonRelease-1>", self.apply_brush_release)  # Left button release
-            self.canvas.bind("<ButtonRelease-3>", self.erase_brush_release)  # Right button release
-        else:
-            self.brush_active = False
-            self.brush_btn.config(text="Brush")
-            self.canvas.unbind("<B1-Motion>")
-            self.canvas.unbind("<B3-Motion>")
-            self.canvas.unbind("<ButtonRelease-1>")
-            self.canvas.unbind("<ButtonRelease-3>")
-
-    def image_to_canvas(self, x_image, y_image):
-        x_scale, y_scale = self.get_scaling_factors(
-            self.image.shape[1], self.image.shape[0],
-            self.canvas_width, self.canvas_height
-        )
-        x_canvas = int(x_image / x_scale)
-        y_canvas = int(y_image / y_scale)
-        return x_canvas, y_canvas
-
-    def toggle_dividing_line_mode(self):
-        self.dividing_line_active = not self.dividing_line_active
-        if self.dividing_line_active:
-            self.drawing = False
-            self.magic_wand_active = False
-            self.erase_active = False
-            self.brush_active = False
-            self.draw_btn.config(text="Draw")
-            self.erase_btn.config(text="Erase")
-            self.magic_wand_btn.config(text="Magic Wand")
-            self.brush_btn.config(text="Brush")
-            self.dividing_line_btn.config(text="Dividing Line ON")
-            self.canvas.unbind("<Button-1>")
-            self.canvas.unbind("<ButtonRelease-1>")
-            self.canvas.unbind("<Motion>")
-            self.canvas.bind("<Button-1>", self.start_dividing_line)
-            self.canvas.bind("<ButtonRelease-1>", self.finish_dividing_line)
-            self.canvas.bind("<Motion>", self.update_dividing_line_preview)
-        else:
-            print("Dividing Line Mode: OFF")
-            self.dividing_line_active = False
-            self.dividing_line_btn.config(text="Dividing Line")
-            self.canvas.unbind("<Button-1>")
-            self.canvas.unbind("<ButtonRelease-1>")
-            self.canvas.unbind("<Motion>")
-            self.display_image()
-
-    def start_dividing_line(self, event):
-        if self.dividing_line_active:
-            self.dividing_line_coords = [(event.x, event.y)]
-            self.current_dividing_line = self.canvas.create_line(event.x, event.y, event.x, event.y, fill="red", width=2)
-
-    def finish_dividing_line(self, event):
-        if self.dividing_line_active:
-            self.dividing_line_coords.append((event.x, event.y))
-            if self.zoom_active:
-                self.dividing_line_coords = [self.canvas_to_image(x, y) for x, y in self.dividing_line_coords]
-            self.apply_dividing_line()
-            self.canvas.delete(self.current_dividing_line)
-            self.current_dividing_line = None
-
-    def update_dividing_line_preview(self, event):
-        if self.dividing_line_active and self.dividing_line_coords:
-            x, y = event.x, event.y
-            if self.zoom_active:
-                x, y = self.canvas_to_image(x, y)
-            self.dividing_line_coords.append((x, y))
-            canvas_coords = [(self.image_to_canvas(*pt) if self.zoom_active else pt) for pt in self.dividing_line_coords]
-            flat_canvas_coords = [coord for pt in canvas_coords for coord in pt]
-            self.canvas.coords(self.current_dividing_line, *flat_canvas_coords)
-
-    def apply_dividing_line(self):
-        if self.dividing_line_coords:
-            coords = self.dividing_line_coords
-            if self.zoom_active:
-                coords = [self.canvas_to_image(x, y) for x, y in coords]
-
-            rr, cc = [], []
-            for (x0, y0), (x1, y1) in zip(coords[:-1], coords[1:]):
-                line_rr, line_cc = line(y0, x0, y1, x1)
-                rr.extend(line_rr)
-                cc.extend(line_cc)
-            rr, cc = np.array(rr), np.array(cc)
-
-            mask_copy = self.mask.copy()
-
-            if self.zoom_active:
-                # Update the zoomed mask
-                self.zoom_mask[rr, cc] = 0
-                # Reflect changes to the original mask
-                y0, y1, x0, x1 = self.zoom_y0, self.zoom_y1, self.zoom_x0, self.zoom_x1
-                zoomed_mask_resized_back = resize(self.zoom_mask, (y1 - y0, x1 - x0), order=0, preserve_range=True).astype(np.uint8)
-                self.mask[y0:y1, x0:x1] = zoomed_mask_resized_back
-            else:
-                # Directly update the original mask
-                mask_copy[rr, cc] = 0
-                self.mask = mask_copy
-
-            labeled_mask, num_labels = label(self.mask > 0)
-            self.mask = labeled_mask
-            self.update_display()
-
-            self.dividing_line_coords = []
-            self.canvas.unbind("<Button-1>")
-            self.canvas.unbind("<ButtonRelease-1>")
-            self.canvas.unbind("<Motion>")
-            self.dividing_line_active = False
-            self.dividing_line_btn.config(text="Dividing Line")
-
-    def toggle_draw_mode(self):
-        self.drawing = not self.drawing
-        if self.drawing:
-            self.brush_btn.config(text="Brush")
-            self.canvas.unbind("<B1-Motion>")
-            self.canvas.unbind("<B3-Motion>")
-            self.canvas.unbind("<ButtonRelease-1>")
-            self.canvas.unbind("<ButtonRelease-3>")
-            self.magic_wand_active = False
-            self.erase_active = False
-            self.brush_active = False
-            self.draw_btn.config(text="Draw ON")
-            self.magic_wand_btn.config(text="Magic Wand")
-            self.erase_btn.config(text="Erase")
-            self.draw_coordinates = []
-            self.canvas.unbind("<Button-1>")
-            self.canvas.unbind("<Motion>")
-            self.canvas.bind("<B1-Motion>", self.draw)
-            self.canvas.bind("<ButtonRelease-1>", self.finish_drawing)
-        else:
-            self.drawing = False
-            self.draw_btn.config(text="Draw")
-            self.canvas.unbind("<B1-Motion>")
-            self.canvas.unbind("<ButtonRelease-1>")
-            
-    def toggle_magic_wand_mode(self):
-        self.magic_wand_active = not self.magic_wand_active
-        if self.magic_wand_active:
-            self.brush_btn.config(text="Brush")
-            self.canvas.unbind("<B1-Motion>")
-            self.canvas.unbind("<B3-Motion>")
-            self.canvas.unbind("<ButtonRelease-1>")
-            self.canvas.unbind("<ButtonRelease-3>")
-            self.drawing = False
-            self.erase_active = False
-            self.brush_active = False
-            self.draw_btn.config(text="Draw")
-            self.erase_btn.config(text="Erase")
-            self.magic_wand_btn.config(text="Magic Wand ON")
-            self.canvas.bind("<Button-1>", self.use_magic_wand)
-            self.canvas.bind("<Button-3>", self.use_magic_wand)
-        else:
-            self.magic_wand_btn.config(text="Magic Wand")
-            self.canvas.unbind("<Button-1>")
-            self.canvas.unbind("<Button-3>")
-            
-    def toggle_erase_mode(self):
-        self.erase_active = not self.erase_active
-        if self.erase_active:
-            self.brush_btn.config(text="Brush")
-            self.canvas.unbind("<B1-Motion>")
-            self.canvas.unbind("<B3-Motion>")
-            self.canvas.unbind("<ButtonRelease-1>")
-            self.canvas.unbind("<ButtonRelease-3>")
-            self.erase_btn.config(text="Erase ON")
-            self.canvas.bind("<Button-1>", self.erase_object)
-            self.drawing = False
-            self.magic_wand_active = False
-            self.brush_active = False
-            self.draw_btn.config(text="Draw")
-            self.magic_wand_btn.config(text="Magic Wand")
-        else:
-            self.erase_active = False
-            self.erase_btn.config(text="Erase")
-            self.canvas.unbind("<Button-1>")
+def initiate_make_mask_app(parent_frame):
+    from .gui_elements import modify_masks
+    # Set up the settings window
+    settings_window = tk.Toplevel(parent_frame)
+    settings_window.title("Make Masks Settings")
+    settings_window.configure(bg='black')  # Set the background color to black
     
-    ####################################################################################################
-    # Mode functions#
-    ####################################################################################################
+    # Use the existing function to create the settings UI
+    settings_frame = tk.Frame(settings_window, bg='black')  # Set the background color to black
+    settings_frame.pack(fill=tk.BOTH, expand=True)
     
-    def apply_brush_release(self, event):
-        if hasattr(self, 'brush_path'):
-            for x, y, brush_size in self.brush_path:
-                img_x, img_y = (x, y) if self.zoom_active else self.canvas_to_image(x, y)
-                x0 = max(img_x - brush_size // 2, 0)
-                y0 = max(img_y - brush_size // 2, 0)
-                x1 = min(img_x + brush_size // 2, self.zoom_mask.shape[1] if self.zoom_active else self.mask.shape[1])
-                y1 = min(img_y + brush_size // 2, self.zoom_mask.shape[0] if self.zoom_active else self.mask.shape[0])
-                if self.zoom_active:
-                    self.zoom_mask[y0:y1, x0:x1] = 255
-                    self.update_original_mask_from_zoom()
-                else:
-                    self.mask[y0:y1, x0:x1] = 255
-            del self.brush_path
-            self.canvas.delete("temp_line")
-            self.update_display()
-
-    def erase_brush_release(self, event):
-        if hasattr(self, 'erase_path'):
-            for x, y, brush_size in self.erase_path:
-                img_x, img_y = (x, y) if self.zoom_active else self.canvas_to_image(x, y)
-                x0 = max(img_x - brush_size // 2, 0)
-                y0 = max(img_y - brush_size // 2, 0)
-                x1 = min(img_x + brush_size // 2, self.zoom_mask.shape[1] if self.zoom_active else self.mask.shape[1])
-                y1 = min(img_y + brush_size // 2, self.zoom_mask.shape[0] if self.zoom_active else self.mask.shape[0])
-                if self.zoom_active:
-                    self.zoom_mask[y0:y1, x0:x1] = 0                    
-                    self.update_original_mask_from_zoom()
-                else:
-                    self.mask[y0:y1, x0:x1] = 0
-            del self.erase_path
-            self.canvas.delete("temp_line")
-            self.update_display()
-        
-    def apply_brush(self, event):
-        brush_size = int(self.brush_size_entry.get())
-        x, y = event.x, event.y
-        if not hasattr(self, 'brush_path'):
-            self.brush_path = []
-            self.last_brush_coord = (x, y)
-        if self.last_brush_coord:
-            last_x, last_y = self.last_brush_coord
-            rr, cc = line(last_y, last_x, y, x)
-            for ry, rx in zip(rr, cc):
-                self.brush_path.append((rx, ry, brush_size))
-
-        self.canvas.create_line(self.last_brush_coord[0], self.last_brush_coord[1], x, y, width=brush_size, fill="blue", tag="temp_line")
-        self.last_brush_coord = (x, y)
-
-    def erase_brush(self, event):
-        brush_size = int(self.brush_size_entry.get())
-        x, y = event.x, event.y
-        if not hasattr(self, 'erase_path'):
-            self.erase_path = []
-            self.last_erase_coord = (x, y)
-        if self.last_erase_coord:
-            last_x, last_y = self.last_erase_coord
-            rr, cc = line(last_y, last_x, y, x)
-            for ry, rx in zip(rr, cc):
-                self.erase_path.append((rx, ry, brush_size))
-
-        self.canvas.create_line(self.last_erase_coord[0], self.last_erase_coord[1], x, y, width=brush_size, fill="white", tag="temp_line")
-        self.last_erase_coord = (x, y)
-
-    def erase_object(self, event):
-        x, y = event.x, event.y
-        if self.zoom_active:
-            canvas_x, canvas_y = x, y
-            zoomed_x = int(canvas_x * (self.zoom_image.shape[1] / self.canvas_width))
-            zoomed_y = int(canvas_y * (self.zoom_image.shape[0] / self.canvas_height))
-            orig_x = int(zoomed_x * ((self.zoom_x1 - self.zoom_x0) / self.canvas_width) + self.zoom_x0)
-            orig_y = int(zoomed_y * ((self.zoom_y1 - self.zoom_y0) / self.canvas_height) + self.zoom_y0)
-            if orig_x < 0 or orig_y < 0 or orig_x >= self.image.shape[1] or orig_y >= self.image.shape[0]:
-                print("Point is out of bounds in the original image.")
-                return
-        else:
-            orig_x, orig_y = x, y
-        label_to_remove = self.mask[orig_y, orig_x]
-        if label_to_remove > 0:
-            self.mask[self.mask == label_to_remove] = 0
-        self.update_display()
-            
-    def use_magic_wand(self, event):
-        x, y = event.x, event.y
-        tolerance = int(self.magic_wand_tolerance.get())
-        maximum = int(self.max_pixels_entry.get())
-        action = 'add' if event.num == 1 else 'erase'
-        if self.zoom_active:
-            self.magic_wand_zoomed((x, y), tolerance, action)
-        else:
-            self.magic_wand_normal((x, y), tolerance, action)
-    
-    def apply_magic_wand(self, image, mask, seed_point, tolerance, maximum, action='add'):
-        x, y = seed_point
-        initial_value = image[y, x].astype(np.float32)
-        visited = np.zeros_like(image, dtype=bool)
-        queue = deque([(x, y)])
-        added_pixels = 0
-
-        while queue and added_pixels < maximum:
-            cx, cy = queue.popleft()
-            if visited[cy, cx]:
-                continue
-            visited[cy, cx] = True
-            current_value = image[cy, cx].astype(np.float32)
-
-            if np.linalg.norm(abs(current_value - initial_value)) <= tolerance:
-                if mask[cy, cx] == 0:
-                    added_pixels += 1
-                mask[cy, cx] = 255 if action == 'add' else 0
-
-                if added_pixels >= maximum:
-                    break
-
-                for dx, dy in [(-1, 0), (1, 0), (0, -1), (0, 1)]:
-                    nx, ny = cx + dx, cy + dy
-                    if 0 <= nx < image.shape[1] and 0 <= ny < image.shape[0] and not visited[ny, nx]:
-                        queue.append((nx, ny))
-        return mask
-
-    def magic_wand_normal(self, seed_point, tolerance, action):
-        try:
-            maximum = int(self.max_pixels_entry.get())
-        except ValueError:
-            print("Invalid maximum value; using default of 1000")
-            maximum = 1000 
-        self.mask = self.apply_magic_wand(self.image, self.mask, seed_point, tolerance, maximum, action)
-        self.display_image()
-        
-    def magic_wand_zoomed(self, seed_point, tolerance, action):
-        if self.zoom_image_orig is None or self.zoom_mask is None:
-            print("Zoomed image or mask not initialized")
-            return
-        try:
-            maximum = int(self.max_pixels_entry.get())
-            maximum = maximum * self.zoom_scale
-        except ValueError:
-            print("Invalid maximum value; using default of 1000")
-            maximum = 1000
-            
-        canvas_x, canvas_y = seed_point
-        if canvas_x < 0 or canvas_y < 0 or canvas_x >= self.zoom_image_orig.shape[1] or canvas_y >= self.zoom_image_orig.shape[0]:
-            print("Selected point is out of bounds in the zoomed image.")
-            return
-        
-        self.zoom_mask = self.apply_magic_wand(self.zoom_image_orig, self.zoom_mask, (canvas_x, canvas_y), tolerance, maximum, action)
-        y0, y1, x0, x1 = self.zoom_y0, self.zoom_y1, self.zoom_x0, self.zoom_x1
-        zoomed_mask_resized_back = resize(self.zoom_mask, (y1 - y0, x1 - x0), order=0, preserve_range=True).astype(np.uint8)
-        if action == 'erase':
-            self.mask[y0:y1, x0:x1] = np.where(zoomed_mask_resized_back == 0, 0, self.mask[y0:y1, x0:x1])
-        else:
-            self.mask[y0:y1, x0:x1] = np.where(zoomed_mask_resized_back > 0, zoomed_mask_resized_back, self.mask[y0:y1, x0:x1])
-        self.update_display()
-                
-    def draw(self, event):
-        if self.drawing:
-            x, y = event.x, event.y
-            if self.draw_coordinates:
-                last_x, last_y = self.draw_coordinates[-1]
-                self.current_line = self.canvas.create_line(last_x, last_y, x, y, fill="yellow", width=3)
-            self.draw_coordinates.append((x, y))
-            
-    def draw_on_zoomed_mask(self, draw_coordinates):
-        canvas_height = self.canvas.winfo_height()
-        canvas_width = self.canvas.winfo_width()
-        zoomed_mask = np.zeros((canvas_height, canvas_width), dtype=np.uint8)
-        rr, cc = polygon(np.array(draw_coordinates)[:, 1], np.array(draw_coordinates)[:, 0], shape=zoomed_mask.shape)
-        zoomed_mask[rr, cc] = 255
-        return zoomed_mask
-            
-    def finish_drawing(self, event):
-        if len(self.draw_coordinates) > 2:
-            self.draw_coordinates.append(self.draw_coordinates[0])
-            if self.zoom_active:
-                x0, x1, y0, y1 = self.zoom_x0, self.zoom_x1, self.zoom_y0, self.zoom_y1
-                zoomed_mask = self.draw_on_zoomed_mask(self.draw_coordinates)
-                self.update_original_mask(zoomed_mask, x0, x1, y0, y1)
-            else:
-                rr, cc = polygon(np.array(self.draw_coordinates)[:, 1], np.array(self.draw_coordinates)[:, 0], shape=self.mask.shape)
-                self.mask[rr, cc] = np.maximum(self.mask[rr, cc], 255)
-                self.mask = self.mask.copy()
-            self.canvas.delete(self.current_line)
-            self.draw_coordinates.clear()
-        self.update_display()
-            
-    def finish_drawing_if_active(self, event):
-        if self.drawing and len(self.draw_coordinates) > 2:
-            self.finish_drawing(event)
-
-    ####################################################################################################
-    # Single function butons#
-    ####################################################################################################
-            
-    def apply_normalization(self):
-        self.lower_quantile.set(self.lower_entry.get())
-        self.upper_quantile.set(self.upper_entry.get())
-        self.update_display()
-
-    def fill_objects(self):
-        binary_mask = self.mask > 0
-        filled_mask = binary_fill_holes(binary_mask)
-        self.mask = filled_mask.astype(np.uint8) * 255
-        labeled_mask, _ = label(filled_mask)
-        self.mask = labeled_mask
-        self.update_display()
-
-    def relabel_objects(self):
-        mask = self.mask
-        labeled_mask, num_labels = label(mask > 0)
-        self.mask = labeled_mask
-        self.update_display()
-        
-    def clear_objects(self):
-        self.mask = np.zeros_like(self.mask)
-        self.update_display()
-
-    def invert_mask(self):
-        self.mask = np.where(self.mask > 0, 0, 1)
-        self.relabel_objects()
-        self.update_display()
-        
-    def remove_small_objects(self):
-        try:
-            min_area = int(self.min_area_entry.get())
-        except ValueError:
-            print("Invalid minimum area value; using default of 100")
-            min_area = 100
-
-        labeled_mask, num_labels = label(self.mask > 0)
-        for i in range(1, num_labels + 1):  # Skip background
-            if np.sum(labeled_mask == i) < min_area:
-                self.mask[labeled_mask == i] = 0  # Remove small objects
-        self.update_display()
-
-##@log_function_call
-def initiate_mask_app_root(parent_frame):
-    style = ttk.Style(parent_frame)
-    set_dark_style(style)
-    set_default_font(parent_frame, font_name="Arial", size=8)
-    
-    container = tk.PanedWindow(parent_frame, orient=tk.HORIZONTAL)
-    container.pack(fill=tk.BOTH, expand=True)
-
-    scrollable_frame = spacrFrame(container, bg='black')
-    container.add(scrollable_frame, stretch="always")
-
-    # Setup input fields
     vars_dict = {
-        'folder_path': ttk.Entry(scrollable_frame.scrollable_frame),
-        'scale_factor': ttk.Entry(scrollable_frame.scrollable_frame)
+        'folder_path': ttk.Entry(settings_frame),
+        'scale_factor': ttk.Entry(settings_frame)
     }
 
     # Arrange input fields and labels
     row = 0
     for name, entry in vars_dict.items():
-        ttk.Label(scrollable_frame.scrollable_frame, text=f"{name.replace('_', ' ').capitalize()}:").grid(row=row, column=0)
+        ttk.Label(settings_frame, text=f"{name.replace('_', ' ').capitalize()}:",
+                  background="black", foreground="white").grid(row=row, column=0)
         entry.grid(row=row, column=1)
         row += 1
 
     # Function to be called when "Run" button is clicked
-    def run_app():
+    def start_make_mask_app():
         folder_path = vars_dict['folder_path'].get()
-        scale_factor = float(vars_dict['scale_factor'].get())
-        
-        # Clear previous content instead of destroying the root
-        for widget in parent_frame.winfo_children():
-            widget.destroy()
-        
-        # Start the modify_masks application in the same root window
-        app_instance = modify_masks(parent_frame, folder_path, scale_factor)
-        
-    run_button = spacrButton(scrollable_frame.scrollable_frame, text="Run", command=run_app)
-    run_button.grid(row=row, column=0, columnspan=2, pady=10, padx=10)
+        try:
+            scale_factor = float(vars_dict['scale_factor'].get())
+        except ValueError:
+            scale_factor = None  # Handle invalid input gracefully
 
-    return parent_frame
+        # Convert empty strings to None
+        folder_path = folder_path if folder_path != '' else None
 
-def gui_make_masks():
-    root = tk.Tk()
-    width = root.winfo_screenwidth()
-    height = root.winfo_screenheight()
-    root.geometry(f"{width}x{height}")
-    root.title("Mask Application")
+        settings_window.destroy()
+        modify_masks(parent_frame, folder_path, scale_factor)
     
-    # Clear previous content if any
-    if hasattr(root, 'content_frame'):
-        for widget in root.content_frame.winfo_children():
-            widget.destroy()
-        root.content_frame.grid_forget()
-    else:
-        root.content_frame = tk.Frame(root)
-        root.content_frame.grid(row=1, column=0, sticky="nsew")
-        root.grid_rowconfigure(1, weight=1)
-        root.grid_columnconfigure(0, weight=1)
-    
-    initiate_mask_app_root(root.content_frame)
-    create_menu_bar(root)
-    root.mainloop()
+    run_button = tk.Button(settings_window, text="Start Make Masks", command=start_make_mask_app, bg='black', fg='white')
+    run_button.pack(pady=10)
+
+def start_make_mask_app():
+    app = MainApp(default_app="Make Masks")
+    app.mainloop()
 
 if __name__ == "__main__":
-    gui_make_masks()
+    start_make_mask_app()