spacr 0.1.55__py3-none-any.whl → 0.1.61__py3-none-any.whl

spacr/__init__.py

@@ -14,6 +14,10 @@ from . import timelapse
 from . import deep_spacr
 from . import app_annotate
 from . import gui_utils
+from . import gui_elements
+from . import gui_core
+from . import gui_run
+from . import gui_wrappers
 from . import app_make_masks
 from . import app_mask
 from . import app_measure
@@ -37,7 +41,6 @@ __all__ = [
     "app_annotate",
     "gui_utils",
     "app_make_masks",
-    "app_make_masks_v2",
     "app_mask",
     "app_measure",
     "app_classify",

spacr/app_annotate.py

@@ -13,7 +13,7 @@ from IPython.display import display, HTML
 from tkinter import font as tkFont
 from tkinter import TclError
 
-from .gui_utils import spacrFrame, spacrButton, set_dark_style, create_menu_bar, set_default_font
+from .gui_elements import spacrFrame, spacrButton, set_dark_style, create_menu_bar, set_default_font
 
 class ImageApp:
     def __init__(self, root, db_path, src, image_type=None, channels=None, grid_rows=None, grid_cols=None, image_size=(200, 200), annotation_column='annotate', normalize=False, percentiles=(1,99), measurement=None, threshold=None):

spacr/app_make_masks.py

@@ -9,11 +9,8 @@ from skimage.transform import resize
 from scipy.ndimage import binary_fill_holes, label
 import tkinter as tk
 from tkinter import ttk
-from ttkthemes import ThemedTk
 
-from .logger import log_function_call
-
-from .gui_utils import spacrFrame, spacrButton, set_dark_style, create_menu_bar, set_default_font
+from .gui_elements import spacrFrame, spacrButton, set_dark_style, create_menu_bar, set_default_font
 
 class modify_masks:
 

spacr/core.py

@@ -1668,7 +1668,7 @@ def preprocess_generate_masks(src, settings={}):
 
     from .io import preprocess_img_data, _load_and_concatenate_arrays
     from .plot import plot_merged, plot_arrays
-    from .utils import _pivot_counts_table, check_mask_folder, adjust_cell_masks, _merge_cells_based_on_parasite_overlap, process_masks
+    from .utils import _pivot_counts_table, check_mask_folder, adjust_cell_masks
     from .settings import set_default_settings_preprocess_generate_masks, set_default_plot_merge_settings
     
     settings = set_default_settings_preprocess_generate_masks(src, settings)

spacr/gui.py

@@ -1,10 +1,10 @@
 import tkinter as tk
 from tkinter import ttk
 from PIL import Image, ImageTk
-import os
-import requests
+import os, requests
 from multiprocessing import set_start_method
-from .gui_utils import set_dark_style, create_menu_bar, initiate_root, spacrButton
+from .gui_elements import spacrButton, create_menu_bar, set_dark_style
+from .gui_core import initiate_root
 from .app_annotate import initiate_annotation_app_root
 from .app_make_masks import initiate_mask_app_root
 

spacr/gui_core.py

@@ -0,0 +1,608 @@
+import os, traceback, ctypes, matplotlib, requests, csv, re
+matplotlib.use('Agg')
+import tkinter as tk
+from tkinter import ttk
+import tkinter.font as tkFont
+from tkinter import filedialog
+from tkinter import font as tkFont
+from multiprocessing import Process, Value, Queue, Manager, set_start_method
+from tkinter import ttk, scrolledtext
+from matplotlib.figure import Figure
+from matplotlib.backends.backend_tkagg import FigureCanvasTkAgg
+import time
+import requests
+from huggingface_hub import list_repo_files
+
+from .settings import set_default_train_test_model, get_measure_crop_settings, set_default_settings_preprocess_generate_masks, get_analyze_reads_default_settings, set_default_umap_image_settings
+from .gui_elements import create_menu_bar, spacrButton, spacrLabel, spacrFrame, spacrCheckbutton, spacrDropdownMenu ,set_dark_style, set_default_font
+from . gui_run import run_mask_gui, run_measure_gui, run_classify_gui, run_sequencing_gui, run_umap_gui
+
+try:
+    ctypes.windll.shcore.SetProcessDpiAwareness(True)
+except AttributeError:
+    pass
+
+# Define global variables
+q = None
+console_output = None
+parent_frame = None
+vars_dict = None
+canvas = None
+canvas_widget = None
+scrollable_frame = None
+progress_label = None
+fig_queue = None
+
+thread_control = {"run_thread": None, "stop_requested": False}
+
+def initiate_abort():
+    global thread_control
+    if thread_control.get("stop_requested") is not None:
+        if isinstance(thread_control["stop_requested"], Value):
+            thread_control["stop_requested"].value = 1
+
+    if thread_control.get("run_thread") is not None:
+        thread_control["run_thread"].join(timeout=5)
+        if thread_control["run_thread"].is_alive():
+            thread_control["run_thread"].terminate()
+        thread_control["run_thread"] = None
+
+def start_process(q, fig_queue, settings_type='mask'):
+    global thread_control, vars_dict
+    from .settings import check_settings
+
+    settings = check_settings(vars_dict)
+    if thread_control.get("run_thread") is not None:
+        initiate_abort()
+    stop_requested = Value('i', 0)  # multiprocessing shared value for inter-process communication
+    thread_control["stop_requested"] = stop_requested
+    if settings_type == 'mask':
+        thread_control["run_thread"] = Process(target=run_mask_gui, args=(settings, q, fig_queue, stop_requested))
+    elif settings_type == 'measure':
+        thread_control["run_thread"] = Process(target=run_measure_gui, args=(settings, q, fig_queue, stop_requested))
+    elif settings_type == 'classify':
+        thread_control["run_thread"] = Process(target=run_classify_gui, args=(settings, q, fig_queue, stop_requested))
+    elif settings_type == 'sequencing':
+        thread_control["run_thread"] = Process(target=run_sequencing_gui, args=(settings, q, fig_queue, stop_requested))
+    elif settings_type == 'umap':
+        thread_control["run_thread"] = Process(target=run_umap_gui, args=(settings, q, fig_queue, stop_requested))
+    thread_control["run_thread"].start()
+
+def import_settings(settings_type='mask'):
+
+    global vars_dict, scrollable_frame
+    from .settings import generate_fields
+
+    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
+
+    csv_file_path = filedialog.askopenfilename(filetypes=[("CSV files", "*.csv")])
+
+    if not csv_file_path:  # If no file is selected, return early
+        return
+    
+    csv_settings = read_settings_from_csv(csv_file_path)
+    if settings_type == 'mask':
+        settings = set_default_settings_preprocess_generate_masks(src='path', settings={})
+    elif settings_type == 'measure':
+        settings = get_measure_crop_settings(settings={})
+    elif settings_type == 'classify':
+        settings = set_default_train_test_model(settings={})
+    elif settings_type == 'sequencing':
+        settings = get_analyze_reads_default_settings(settings={})
+    elif settings_type == 'umap':
+        settings = set_default_umap_image_settings(settings={})
+    else:
+        raise ValueError(f"Invalid settings type: {settings_type}")
+    
+    variables = convert_settings_dict_for_gui(settings)
+    new_settings = update_settings_from_csv(variables, csv_settings)
+    vars_dict = generate_fields(new_settings, scrollable_frame)
+
+def convert_settings_dict_for_gui(settings):
+    variables = {}
+    special_cases = {
+        'metadata_type': ('combo', ['cellvoyager', 'cq1', 'nikon', 'zeis', 'custom'], 'cellvoyager'),
+        'channels': ('combo', ['[0,1,2,3]', '[0,1,2]', '[0,1]', '[0]'], '[0,1,2,3]'),
+        'cell_mask_dim': ('combo', ['0', '1', '2', '3', '4', '5', '6', '7', '8', None], None),
+        'nucleus_mask_dim': ('combo', ['0', '1', '2', '3', '4', '5', '6', '7', '8', None], None),
+        'pathogen_mask_dim': ('combo', ['0', '1', '2', '3', '4', '5', '6', '7', '8', None], None),
+        #'crop_mode': ('combo', ['cell', 'nucleus', 'pathogen', '[cell, nucleus, pathogen]', '[cell,nucleus, pathogen]'], ['cell']),
+        'magnification': ('combo', [20, 40, 60], 20),
+        'nucleus_channel': ('combo', [0, 1, 2, 3, None], None),
+        'cell_channel': ('combo', [0, 1, 2, 3, None], None),
+        'pathogen_channel': ('combo', [0, 1, 2, 3, None], None),
+        'timelapse_mode': ('combo', ['trackpy', 'btrack'], 'trackpy'),
+        'timelapse_objects': ('combo', ['cell', 'nucleus', 'pathogen', 'cytoplasm', None], None),
+        'model_type': ('combo', ['resnet50', 'other_model'], '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'),
+        'normalize_by': ('combo', ['fov', 'png'], 'png'),
+    }
+
+    for key, value in settings.items():
+        if key in special_cases:
+            variables[key] = special_cases[key]
+        elif isinstance(value, bool):
+            variables[key] = ('check', None, value)
+        elif isinstance(value, int) or isinstance(value, float):
+            variables[key] = ('entry', None, value)
+        elif isinstance(value, str):
+            variables[key] = ('entry', None, value)
+        elif value is None:
+            variables[key] = ('entry', None, value)
+        elif isinstance(value, list):
+            variables[key] = ('entry', None, str(value))
+        else:
+            variables[key] = ('entry', None, str(value))
+    return variables
+
+def setup_settings_panel(vertical_container, settings_type='mask', frame_height=500, frame_width=1000):
+    global vars_dict, scrollable_frame
+    from .settings import set_default_settings_preprocess_generate_masks, get_measure_crop_settings, set_default_train_test_model, get_analyze_reads_default_settings, set_default_umap_image_settings, generate_fields
+
+    settings_frame = tk.Frame(vertical_container, bg='black', height=frame_height, width=frame_width)
+    vertical_container.add(settings_frame, stretch="always")
+    settings_label = spacrLabel(settings_frame, text="Settings", background="black", foreground="white", anchor='center', justify='center', align="center")
+    settings_label.grid(row=0, column=0, pady=10, padx=10)
+    scrollable_frame = spacrFrame(settings_frame, bg='black', width=frame_width)
+    scrollable_frame.grid(row=1, column=0, sticky="nsew")
+    settings_frame.grid_rowconfigure(1, weight=1)
+    settings_frame.grid_columnconfigure(0, weight=1)
+
+    if settings_type == 'mask':
+        settings = set_default_settings_preprocess_generate_masks(src='path', settings={})
+    elif settings_type == 'measure':
+        settings = get_measure_crop_settings(settings={})
+    elif settings_type == 'classify':
+        settings = set_default_train_test_model(settings={})
+    elif settings_type == 'sequencing':
+        settings = get_analyze_reads_default_settings(settings={})
+    elif settings_type == 'umap':
+        settings = set_default_umap_image_settings(settings={})
+    else:
+        raise ValueError(f"Invalid settings type: {settings_type}")
+
+    variables = convert_settings_dict_for_gui(settings)
+    vars_dict = generate_fields(variables, scrollable_frame)
+    print("Settings panel setup complete")
+    return scrollable_frame, vars_dict
+
+def setup_plot_section(vertical_container):
+    global canvas, canvas_widget
+    plot_frame = tk.PanedWindow(vertical_container, orient=tk.VERTICAL)
+    vertical_container.add(plot_frame, stretch="always")
+    figure = Figure(figsize=(30, 4), dpi=100, facecolor='black')
+    plot = figure.add_subplot(111)
+    plot.plot([], [])  # This creates an empty plot.
+    plot.axis('off')
+    canvas = FigureCanvasTkAgg(figure, master=plot_frame)
+    canvas.get_tk_widget().configure(cursor='arrow', background='black', highlightthickness=0)
+    canvas_widget = canvas.get_tk_widget()
+    plot_frame.add(canvas_widget, stretch="always")
+    canvas.draw()
+    canvas.figure = figure
+    return canvas, canvas_widget
+
+def setup_console(vertical_container):
+    global console_output
+    print("Setting up console frame")
+    console_frame = tk.Frame(vertical_container, bg='black')
+    vertical_container.add(console_frame, stretch="always")
+    console_label = spacrLabel(console_frame, text="Console", background="black", foreground="white", anchor='center', justify='center', align="center")
+    console_label.grid(row=0, column=0, pady=10, padx=10)
+    console_output = scrolledtext.ScrolledText(console_frame, height=10, bg='black', fg='white', insertbackground='white')
+    console_output.grid(row=1, column=0, sticky="nsew")
+    console_frame.grid_rowconfigure(1, weight=1)
+    console_frame.grid_columnconfigure(0, weight=1)
+    print("Console setup complete")
+    return console_output
+
+def setup_progress_frame(vertical_container):
+    global progress_output
+    progress_frame = tk.Frame(vertical_container, bg='black')
+    vertical_container.add(progress_frame, stretch="always")
+    label_frame = tk.Frame(progress_frame, bg='black')
+    label_frame.grid(row=0, column=0, sticky="ew", pady=(5, 0), padx=10)
+    progress_label = spacrLabel(label_frame, text="Processing: 0%", background="black", foreground="white", font=('Helvetica', 12), anchor='w', justify='left', align="left")
+    progress_label.grid(row=0, column=0, sticky="w")
+    progress_output = scrolledtext.ScrolledText(progress_frame, height=10, bg='black', fg='white', insertbackground='white')
+    progress_output.grid(row=1, column=0, sticky="nsew")
+    progress_frame.grid_rowconfigure(1, weight=1)
+    progress_frame.grid_columnconfigure(0, weight=1)
+    print("Progress frame setup complete")
+    return progress_output
+
+def download_hug_dataset():
+    global vars_dict, q
+    dataset_repo_id = "einarolafsson/toxo_mito"
+    settings_repo_id = "einarolafsson/spacr_settings"
+    dataset_subfolder = "plate1"
+    local_dir = os.path.join(os.path.expanduser("~"), "datasets")  # Set to the home directory
+
+    # Download the dataset
+    try:
+        dataset_path = download_dataset(dataset_repo_id, dataset_subfolder, local_dir)
+        if 'src' in vars_dict:
+            vars_dict['src'][2].set(dataset_path)
+            q.put(f"Set source path to: {vars_dict['src'][2].get()}\n")
+        q.put(f"Dataset downloaded to: {dataset_path}\n")
+    except Exception as e:
+        q.put(f"Failed to download dataset: {e}\n")
+
+    # Download the settings files
+    try:
+        settings_path = download_dataset(settings_repo_id, "", local_dir)
+        q.put(f"Settings downloaded to: {settings_path}\n")
+    except Exception as e:
+        q.put(f"Failed to download settings: {e}\n")
+
+def download_dataset(repo_id, subfolder, local_dir=None, retries=5, delay=5):
+    global q
+    """
+    Downloads a dataset or settings files from Hugging Face and returns the local path.
+
+    Args:
+        repo_id (str): The repository ID (e.g., 'einarolafsson/toxo_mito' or 'einarolafsson/spacr_settings').
+        subfolder (str): The subfolder path within the repository (e.g., 'plate1' or the settings subfolder).
+        local_dir (str): The local directory where the files will be saved. Defaults to the user's home directory.
+        retries (int): Number of retry attempts in case of failure.
+        delay (int): Delay in seconds between retries.
+
+    Returns:
+        str: The local path to the downloaded files.
+    """
+    if local_dir is None:
+        local_dir = os.path.join(os.path.expanduser("~"), "datasets")
+
+    local_subfolder_dir = os.path.join(local_dir, subfolder if subfolder else "settings")
+    if not os.path.exists(local_subfolder_dir):
+        os.makedirs(local_subfolder_dir)
+    elif len(os.listdir(local_subfolder_dir)) > 0:
+        q.put(f"Files already downloaded to: {local_subfolder_dir}")
+        return local_subfolder_dir
+
+    attempt = 0
+    while attempt < retries:
+        try:
+            files = list_repo_files(repo_id, repo_type="dataset")
+            subfolder_files = [file for file in files if file.startswith(subfolder) or (subfolder == "" and file.endswith('.csv'))]
+
+            for file_name in subfolder_files:
+                for download_attempt in range(retries):
+                    try:
+                        url = f"https://huggingface.co/datasets/{repo_id}/resolve/main/{file_name}?download=true"
+                        response = requests.get(url, stream=True)
+                        response.raise_for_status()
+
+                        local_file_path = os.path.join(local_subfolder_dir, os.path.basename(file_name))
+                        with open(local_file_path, 'wb') as file:
+                            for chunk in response.iter_content(chunk_size=8192):
+                                file.write(chunk)
+                        q.put(f"Downloaded file: {file_name}")
+                        break
+                    except (requests.HTTPError, requests.Timeout) as e:
+                        q.put(f"Error downloading {file_name}: {e}. Retrying in {delay} seconds...")
+                        time.sleep(delay)
+                else:
+                    raise Exception(f"Failed to download {file_name} after multiple attempts.")
+
+            return local_subfolder_dir
+
+        except (requests.HTTPError, requests.Timeout) as e:
+            q.put(f"Error downloading files: {e}. Retrying in {delay} seconds...")
+            attempt += 1
+            time.sleep(delay)
+
+    raise Exception("Failed to download files after multiple attempts.")
+
+
+def setup_button_section(horizontal_container, settings_type='mask', settings_row=5, run=True, abort=True, download=True, import_btn=True):
+    global button_frame, run_button, abort_button, download_dataset_button, import_button, q, fig_queue, vars_dict
+
+    button_frame = tk.Frame(horizontal_container, bg='black')
+    horizontal_container.add(button_frame, stretch="always", sticky="nsew")
+    button_frame.grid_rowconfigure(0, weight=0)
+    button_frame.grid_rowconfigure(1, weight=1)
+    button_frame.grid_columnconfigure(0, weight=1)
+
+    categories_label = spacrLabel(button_frame, text="Categories", background="black", foreground="white", font=('Helvetica', 12), anchor='center', justify='center', align="center")  # Increase font size
+    categories_label.grid(row=0, column=0, pady=10, padx=10)
+
+    button_scrollable_frame = spacrFrame(button_frame, bg='black')
+    button_scrollable_frame.grid(row=1, column=0, sticky="nsew")
+
+    btn_col = 0
+    btn_row = 1
+    
+    if run:
+        run_button = spacrButton(button_scrollable_frame.scrollable_frame, text="Run", command=lambda: start_process(q, fig_queue, settings_type), font=('Helvetica', 12))
+        run_button.grid(row=btn_row, column=btn_col, pady=5, padx=5, sticky='ew')
+        btn_row += 1
+
+    if abort and settings_type in ['mask', 'measure', 'classify', 'sequencing', 'umap']:
+        abort_button = spacrButton(button_scrollable_frame.scrollable_frame, text="Abort", command=initiate_abort, font=('Helvetica', 12))
+        abort_button.grid(row=btn_row, column=btn_col, pady=5, padx=5, sticky='ew')
+        btn_row += 1
+
+    if download and settings_type in ['mask']:
+        download_dataset_button = spacrButton(button_scrollable_frame.scrollable_frame, text="Download", command=download_hug_dataset, font=('Helvetica', 12))
+        download_dataset_button.grid(row=btn_row, column=btn_col, pady=5, padx=5, sticky='ew')
+        btn_row += 1
+
+    if import_btn:
+        import_button = spacrButton(button_scrollable_frame.scrollable_frame, text="Import", command=lambda: import_settings(settings_type), font=('Helvetica', 12))
+        import_button.grid(row=btn_row, column=btn_col, pady=5, padx=5, sticky='ew')
+
+    # Call toggle_settings after vars_dict is initialized
+    if vars_dict is not None:
+        toggle_settings(button_scrollable_frame)
+    return button_scrollable_frame
+
+def toggle_settings_v1(button_scrollable_frame):
+    global vars_dict
+    from .settings import categories
+
+    if vars_dict is None:
+        raise ValueError("vars_dict is not initialized.")
+
+    def toggle_category(settings, var):
+        for setting in settings:
+            if setting in vars_dict:
+                label, widget, _ = vars_dict[setting]
+                if var.get() == 0:
+                    label.grid_remove()
+                    widget.grid_remove()
+                else:
+                    label.grid()
+                    widget.grid()
+
+    row = 1
+    col = 3 
+    category_idx = 0
+
+    for category, settings in categories.items():
+        if any(setting in vars_dict for setting in settings):
+            category_var = tk.IntVar(value=0)
+            vars_dict[category] = (None, None, category_var)
+            toggle = spacrCheckbutton(
+                button_scrollable_frame.scrollable_frame, 
+                text=category, 
+                variable=category_var, 
+                command=lambda cat=settings, var=category_var: toggle_category(cat, var)
+            )
+            # Directly set the style
+            style = ttk.Style()
+            font_style = tkFont.Font(family="Helvetica", size=12, weight="bold")
+            style.configure('Spacr.TCheckbutton', font=font_style, background='black', foreground='#ffffff', indicatoron=False, relief='flat')
+            style.map('Spacr.TCheckbutton', background=[('selected', 'black'), ('active', 'black')], foreground=[('selected', '#ffffff'), ('active', '#ffffff')])
+            toggle.configure(style='Spacr.TCheckbutton')
+            toggle.grid(row=row, column=col, sticky="w", pady=2, padx=2)
+            #row += 1
+            col += 1
+            category_idx += 1
+
+            if category_idx % 4 == 0:  
+                row += 1
+                col = 2
+
+    for settings in categories.values():
+        for setting in settings:
+            if setting in vars_dict:
+                label, widget, _ = vars_dict[setting]
+                label.grid_remove()
+                widget.grid_remove()
+
+
+def toggle_settings(button_scrollable_frame):
+    global vars_dict
+    from .settings import categories
+
+    if vars_dict is None:
+        raise ValueError("vars_dict is not initialized.")
+
+    active_categories = set()
+
+    def toggle_category(settings):
+        for setting in settings:
+            if setting in vars_dict:
+                label, widget, _ = vars_dict[setting]
+                if widget.grid_info():
+                    label.grid_remove()
+                    widget.grid_remove()
+                else:
+                    label.grid()
+                    widget.grid()
+
+    def on_category_select(selected_category):
+        if selected_category == "Select Category":
+            return
+        #print(f"Selected category: {selected_category}")
+        if selected_category in categories:
+            toggle_category(categories[selected_category])
+            if selected_category in active_categories:
+                active_categories.remove(selected_category)
+            else:
+                active_categories.add(selected_category)
+        category_dropdown.update_styles(active_categories)
+        category_var.set("Select Category")  # Reset dropdown text to "Select Category"
+
+    category_var = tk.StringVar()
+    non_empty_categories = [category for category, settings in categories.items() if any(setting in vars_dict for setting in settings)]
+    category_dropdown = spacrDropdownMenu(button_scrollable_frame.scrollable_frame, category_var, non_empty_categories, command=on_category_select)
+    category_dropdown.grid(row=1, column=3, sticky="ew", pady=2, padx=2)
+
+    for category, settings in categories.items():
+        if any(setting in vars_dict for setting in settings):
+            vars_dict[category] = (None, None, tk.IntVar(value=0))
+            # Initially hide all settings
+            for setting in settings:
+                if setting in vars_dict:
+                    label, widget, _ = vars_dict[setting]
+                    label.grid_remove()
+                    widget.grid_remove()
+
+def process_fig_queue():
+    global canvas, fig_queue, canvas_widget, parent_frame
+
+    def clear_canvas(canvas):
+        for ax in canvas.figure.get_axes():
+            ax.clear()
+        canvas.draw_idle()
+
+    try:
+        while not fig_queue.empty():
+            clear_canvas(canvas)
+            fig = fig_queue.get_nowait()
+            for ax in fig.get_axes():
+                ax.set_xticks([])  # Remove x-axis ticks
+                ax.set_yticks([])  # Remove y-axis ticks
+                ax.xaxis.set_visible(False)  # Hide the x-axis
+                ax.yaxis.set_visible(False)  # Hide the y-axis
+            fig.tight_layout()
+            fig.set_facecolor('black')
+            canvas.figure = fig
+            fig_width, fig_height = canvas_widget.winfo_width(), canvas_widget.winfo_height()
+            fig.set_size_inches(fig_width / fig.dpi, fig_height / fig.dpi, forward=True)
+            canvas.draw_idle()
+    except Exception as e:
+        traceback.print_exc()
+    finally:
+        after_id = canvas_widget.after(100, process_fig_queue)
+        parent_frame.after_tasks.append(after_id)
+
+def process_console_queue():
+    global q, console_output, parent_frame
+    while not q.empty():
+        message = q.get_nowait()
+        console_output.insert(tk.END, message)
+        console_output.see(tk.END)
+    after_id = console_output.after(100, process_console_queue)
+    parent_frame.after_tasks.append(after_id)
+
+def set_globals(q_var, console_output_var, parent_frame_var, vars_dict_var, canvas_var, canvas_widget_var, scrollable_frame_var, progress_label_var, fig_queue_var):
+    global q, console_output, parent_frame, vars_dict, canvas, canvas_widget, scrollable_frame, progress_label, fig_queue
+    q = q_var
+    console_output = console_output_var
+    parent_frame = parent_frame_var
+    vars_dict = vars_dict_var
+    canvas = canvas_var
+    canvas_widget = canvas_widget_var
+    scrollable_frame = scrollable_frame_var
+    progress_label = progress_label_var
+    fig_queue = fig_queue_var
+
+def setup_frame(parent_frame):
+    style = ttk.Style(parent_frame)
+    set_dark_style(style)
+    set_default_font(parent_frame, font_name="Helvetica", size=8)
+    parent_frame.configure(bg='black')
+    parent_frame.grid_rowconfigure(0, weight=1)
+    parent_frame.grid_columnconfigure(0, weight=1)
+    vertical_container = tk.PanedWindow(parent_frame, orient=tk.VERTICAL, bg='black')
+    vertical_container.grid(row=0, column=0, sticky=tk.NSEW)
+    horizontal_container = tk.PanedWindow(vertical_container, orient=tk.HORIZONTAL, bg='black')
+    vertical_container.add(horizontal_container, stretch="always")
+    horizontal_container.grid_columnconfigure(0, weight=1)
+    horizontal_container.grid_columnconfigure(1, weight=1)
+    settings_frame = tk.Frame(horizontal_container, bg='black')
+    settings_frame.grid_rowconfigure(0, weight=0)
+    settings_frame.grid_rowconfigure(1, weight=1)
+    settings_frame.grid_columnconfigure(0, weight=1)
+    horizontal_container.add(settings_frame, stretch="always", sticky="nsew")
+    return parent_frame, vertical_container, horizontal_container
+
+def initiate_root(parent, settings_type='mask'):
+
+    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))
+
+    global q, fig_queue, parent_frame, scrollable_frame, button_frame, vars_dict, canvas, canvas_widget, progress_label, button_scrollable_frame
+    print("Initializing root with settings_type:", settings_type)
+    parent_frame = parent
+
+    if not hasattr(parent_frame, 'after_tasks'):
+        parent_frame.after_tasks = []
+
+    for widget in parent_frame.winfo_children():
+        if widget.winfo_exists():
+            try:
+                widget.destroy()
+            except tk.TclError as e:
+                print(f"Error destroying widget: {e}")
+
+    q = Queue()
+    fig_queue = Queue()
+    parent_frame, vertical_container, horizontal_container = setup_frame(parent_frame)
+    scrollable_frame, vars_dict = setup_settings_panel(horizontal_container, settings_type)  # Adjust height and width as needed
+    button_scrollable_frame = setup_button_section(horizontal_container, settings_type)
+    canvas, canvas_widget = setup_plot_section(vertical_container)
+    console_output = setup_console(vertical_container)
+
+    if settings_type in ['mask', 'measure', 'classify', 'sequencing']:
+        progress_output = setup_progress_frame(vertical_container)
+    else:
+        progress_output = None
+
+    set_globals(q, console_output, parent_frame, vars_dict, canvas, canvas_widget, scrollable_frame, progress_label, fig_queue)
+    process_console_queue()
+    process_fig_queue()
+    after_id = parent_frame.after(100, lambda: main_thread_update_function(parent_frame, q, fig_queue, canvas_widget, progress_label))
+    parent_frame.after_tasks.append(after_id)
+    print("Root initialization complete")
+    return parent_frame, vars_dict
+
+def start_gui_app(settings_type='mask'):
+    global q, fig_queue, parent_frame, scrollable_frame, vars_dict, canvas, canvas_widget, progress_label
+    root = tk.Tk()
+    width = root.winfo_screenwidth()
+    height = root.winfo_screenheight()
+    root.geometry(f"{width}x{height}")
+    root.title(f"SpaCr: {settings_type.capitalize()}")
+    root.content_frame = tk.Frame(root)
+    print("Starting GUI app with settings_type:", settings_type)
+    initiate_root(root.content_frame, settings_type)
+    create_menu_bar(root)
+    root.mainloop()