# Source code for spacr.app_annotate

    import tkinter as tk
    from tkinter import ttk
    from .gui import MainApp
    from .gui_elements import set_dark_style, spacrButton

    def convert_to_number(value):
        try:
            return int(value)
        except ValueError:
            try:
                return float(value)
            except ValueError:
                raise ValueError(f"Unable to convert '{value}' to an integer or float.")

    def initiate_annotation_app(parent_frame):
        from .gui_utils import generate_annotate_fields, annotate_app, convert_to_number
        # Set up the settings window
        settings_window = tk.Toplevel(parent_frame)
        settings_window.title("Annotation Settings")
        style_out = set_dark_style(ttk.Style())
        settings_window.configure(bg=style_out['bg_color'])
        settings_frame = tk.Frame(settings_window, bg=style_out['bg_color'])
        settings_frame.pack(fill=tk.BOTH, expand=True)
        vars_dict = generate_annotate_fields(settings_frame)

        def start_annotation_app():
            settings = {key: data['entry'].get() for key, data in vars_dict.items()}
            settings['channels'] = settings['channels'].split(',')
            settings['img_size'] = list(map(int, settings['img_size'].split(',')))  # Convert string to list of integers
            settings['percentiles'] = list(map(convert_to_number, settings['percentiles'].split(','))) if settings['percentiles'] else [2, 98]
            settings['normalize'] = True
            #settings['normalize'] = settings['normalize'].lower() == 'true'
            settings['normalize_channels'] = settings['normalize_channels'].split(',')
            settings['outline'] = settings['outline'].split(',') if settings['outline'] else None
            settings['outline_threshold_factor'] = float(settings['outline_threshold_factor']) if settings['outline_threshold_factor'] else 1.0
            settings['outline_sigma'] = float(settings['outline_threshold_factor']) if settings['outline_threshold_factor'] else 1.0

            try:
                settings['measurement'] = settings['measurement'].split(',') if settings['measurement'] else None
                settings['threshold'] = None if settings['threshold'].lower() == 'none' else int(settings['threshold'])
            except:
                settings['measurement']  = None
                settings['threshold'] = None

            settings['db'] = settings.get('db', 'default.db')

            # Convert empty strings to None
            for key, value in settings.items():
                if isinstance(value, list):
                    settings[key] = [v if v != '' else None for v in value]
                elif value == '':
                    settings[key] = None

            settings_window.destroy()
            annotate_app(parent_frame, settings)

        start_button = spacrButton(settings_window, text="annotate", command=start_annotation_app, show_text=False)
        start_button.pack(pady=10)

    def start_annotate_app():
        app = MainApp(default_app="Annotate")
        app.mainloop()

    if __name__ == "__main__":
        start_annotate_app()