spacr 0.1.0__py3-none-any.whl → 0.1.1__py3-none-any.whl

spacr/gui.py

@@ -59,10 +59,10 @@ class MainApp(tk.Tk):
 
         # Load the logo image
         if not self.load_logo(logo_frame):
-            tk.Label(logo_frame, text="Logo not found", bg="black", fg="white", font=('Arial', 24, tkFont.NORMAL)).pack(padx=10, pady=10)
+            tk.Label(logo_frame, text="Logo not found", bg="black", fg="white", font=('Helvetica', 24, tkFont.NORMAL)).pack(padx=10, pady=10)
 
         # Add SpaCr text below the logo with padding for sharper text
-        tk.Label(logo_frame, text="SpaCr", bg="black", fg="#008080", font=('Arial', 24, tkFont.NORMAL)).pack(padx=10, pady=10)
+        tk.Label(logo_frame, text="SpaCr", bg="black", fg="#008080", font=('Helvetica', 24, tkFont.NORMAL)).pack(padx=10, pady=10)
 
         # Create a frame for the buttons and descriptions
         buttons_frame = tk.Frame(self.content_frame, bg="black")
@@ -72,10 +72,10 @@ class MainApp(tk.Tk):
             app_func, app_desc = app_data
 
             # Create custom button with text
-            button = CustomButton(buttons_frame, text=app_name, command=lambda app_name=app_name: self.load_app(app_name))
+            button = CustomButton(buttons_frame, text=app_name, command=lambda app_name=app_name: self.load_app(app_name), font=('Helvetica', 12))
             button.grid(row=i, column=0, pady=10, padx=10, sticky="w")
 
-            description_label = tk.Label(buttons_frame, text=app_desc, bg="black", fg="white", wraplength=800, justify="left", font=('Arial', 10, tkFont.NORMAL))
+            description_label = tk.Label(buttons_frame, text=app_desc, bg="black", fg="white", wraplength=800, justify="left", font=('Helvetica', 10, tkFont.NORMAL))
             description_label.grid(row=i, column=1, pady=10, padx=10, sticky="w")
 
         # Ensure buttons have a fixed width
@@ -131,7 +131,7 @@ class MainApp(tk.Tk):
 
         app_frame = tk.Frame(self.content_frame, bg="black")
         app_frame.pack(fill=tk.BOTH, expand=True)
-        selected_app_func(app_frame, self.winfo_width(), self.winfo_height())
+        selected_app_func(app_frame)#, self.winfo_width(), self.winfo_height())
 
     def clear_frame(self, frame):
         for widget in frame.winfo_children():

spacr/gui_2.py

@@ -1,52 +1,93 @@
-import customtkinter as ctk
+import tkinter as tk
+from tkinter import ttk
+from tkinter import font as tkFont
 from PIL import Image, ImageTk
 import os
 import requests
 
-class MainApp(ctk.CTk):
+# Import your GUI apps
+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
+
+from .gui_utils import CustomButton, style_text_boxes
+
+class MainApp(tk.Tk):
     def __init__(self):
         super().__init__()
         self.title("SpaCr GUI Collection")
-        self.geometry("1200x800")
-        ctk.set_appearance_mode("dark")  # Modes: "System" (standard), "Dark", "Light"
-        ctk.set_default_color_theme("dark-blue")  # Themes: "blue" (standard), "green", "dark-blue")
-        
-        # Set scaling factor for high DPI displays; use a floating-point value.
-        self.tk.call('tk', 'scaling', 1.5)
-        
+        self.geometry("1100x1500")
+        self.configure(bg="black")
+        #self.attributes('-fullscreen', True)
+
+        style = ttk.Style()
+        style_text_boxes(style)
+
+        self.gui_apps = {
+            "Mask": (initiate_mask_root, "Generate cellpose masks for cells, nuclei and pathogen images."),
+            "Measure": (initiate_measure_root, "Measure single object intensity and morphological feature. Crop and save single object image"),
+            "Annotate": (initiate_annotation_app_root, "Annotation single object images on a grid. Annotations are saved to database."),
+            "Make Masks": (initiate_mask_app_root, "Adjust pre-existing Cellpose models to your specific dataset for improved performance"),
+            "Classify": (initiate_classify_root, "Train Torch Convolutional Neural Networks (CNNs) or Transformers to classify single object images.")
+        }
+
+        self.selected_app = tk.StringVar()
         self.create_widgets()
 
     def create_widgets(self):
-        self.content_frame = ctk.CTkFrame(self)
-        self.content_frame.pack(fill="both", expand=True, padx=20, pady=20)
+        # Create the menu bar
+        #create_menu_bar(self)
+        # Create a canvas to hold the selected app and other elements
+        self.canvas = tk.Canvas(self, bg="black", highlightthickness=0, width=4000, height=4000)
+        self.canvas.grid(row=0, column=0, sticky="nsew")
+        self.grid_rowconfigure(0, weight=1)
+        self.grid_columnconfigure(0, weight=1)
+        # Create a frame inside the canvas to hold the main content
+        self.content_frame = tk.Frame(self.canvas, bg="black")
+        self.content_frame.pack(fill=tk.BOTH, expand=True)
+        # Create startup screen with buttons for each GUI app
+        self.create_startup_screen()
 
-        logo_frame = ctk.CTkFrame(self.content_frame)
+    def create_startup_screen(self):
+        self.clear_frame(self.content_frame)
+
+        # Create a frame for the logo and description
+        logo_frame = tk.Frame(self.content_frame, bg="black")
         logo_frame.pack(pady=20, expand=True)
 
+        # Load the logo image
         if not self.load_logo(logo_frame):
-            ctk.CTkLabel(logo_frame, text="Logo not found", text_color="white", font=('Helvetica', 24)).pack(padx=10, pady=10)
-
-        ctk.CTkLabel(logo_frame, text="SpaCr", text_color="#00BFFF", font=('Helvetica', 36, "bold")).pack(padx=10, pady=10)
-
-        button = ctk.CTkButton(
-            self.content_frame,
-            text="Mask",
-            command=self.load_mask_app,
-            width=250,
-            height=60,
-            corner_radius=20,
-            fg_color="#1E90FF",
-            hover_color="#4682B4",
-            text_color="white",
-            font=("Helvetica", 18, "bold")
-        )
-        button.pack(pady=20)
+            tk.Label(logo_frame, text="Logo not found", bg="black", fg="white", font=('Helvetica', 24)).pack(padx=10, pady=10)
+
+        # Add SpaCr text below the logo with padding for sharper text
+        tk.Label(logo_frame, text="SpaCr", bg="black", fg="#008080", font=('Helvetica', 24)).pack(padx=10, pady=10)
+
+        # Create a frame for the buttons and descriptions
+        buttons_frame = tk.Frame(self.content_frame, bg="black")
+        buttons_frame.pack(pady=10, expand=True, padx=10)
+
+        for i, (app_name, app_data) in enumerate(self.gui_apps.items()):
+            app_func, app_desc = app_data
+
+            # Create custom button with text
+            button = CustomButton(buttons_frame, text=app_name, command=lambda app_name=app_name: self.load_app(app_name, app_func), font=('Helvetica', 12))
+            button.grid(row=i, column=0, pady=10, padx=10, sticky="w")
+
+            description_label = tk.Label(buttons_frame, text=app_desc, bg="black", fg="white", wraplength=800, justify="left", font=('Helvetica', 12))
+            description_label.grid(row=i, column=1, pady=10, padx=10, sticky="w")
+
+        # Ensure buttons have a fixed width
+        buttons_frame.grid_columnconfigure(0, minsize=150)
+        # Ensure descriptions expand as needed
+        buttons_frame.grid_columnconfigure(1, weight=1)
 
     def load_logo(self, frame):
         def download_image(url, save_path):
             try:
                 response = requests.get(url, stream=True)
-                response.raise_for_status()
+                response.raise_for_status()  # Raise an HTTPError for bad responses
                 with open(save_path, 'wb') as f:
                     for chunk in response.iter_content(chunk_size=8192):
                         f.write(chunk)
@@ -57,34 +98,63 @@ class MainApp(ctk.CTk):
 
         try:
             img_path = os.path.join(os.path.dirname(__file__), 'logo_spacr.png')
+            print(f"Trying to load logo from {img_path}")
             logo_image = Image.open(img_path)
         except (FileNotFoundError, Image.UnidentifiedImageError):
+            print(f"File {img_path} not found or is not a valid image. Attempting to download from GitHub.")
             if download_image('https://raw.githubusercontent.com/EinarOlafsson/spacr/main/spacr/logo_spacr.png', img_path):
                 try:
+                    print(f"Downloaded file size: {os.path.getsize(img_path)} bytes")
                     logo_image = Image.open(img_path)
                 except Image.UnidentifiedImageError as e:
+                    print(f"Downloaded file is not a valid image: {e}")
                     return False
             else:
                 return False
         except Exception as e:
+            print(f"An error occurred while loading the logo: {e}")
             return False
-
         try:
-            logo_image = logo_image.resize((200, 200), Image.Resampling.LANCZOS)
+            logo_image = logo_image.resize((800, 800), Image.Resampling.LANCZOS)
             logo_photo = ImageTk.PhotoImage(logo_image)
-            logo_label = ctk.CTkLabel(frame, image=logo_photo)
+            logo_label = tk.Label(frame, image=logo_photo, bg="black")
             logo_label.image = logo_photo  # Keep a reference to avoid garbage collection
             logo_label.pack()
             return True
         except Exception as e:
+            print(f"An error occurred while processing the logo image: {e}")
             return False
 
-    def load_mask_app(self):
-        print("Mask app loaded.")  # Placeholder for mask app loading function
+    def load_app_v1(self, app_name):
+        selected_app_func, _ = self.gui_apps[app_name]
+        self.clear_frame(self.content_frame)
+
+        app_frame = tk.Frame(self.content_frame, bg="black")
+        app_frame.pack(fill=tk.BOTH, expand=True)
+        selected_app_func(app_frame)
+
+    def load_app(root, app_name, app_func):
+        if hasattr(root, 'current_app_id'):
+            root.after_cancel(root.current_app_id)
+        root.current_app_id = None
+
+        # Clear the current content frame
+        for widget in root.content_frame.winfo_children():
+            widget.destroy()
+
+        # Initialize the selected app
+        app_frame = tk.Frame(root.content_frame, bg="black")
+        app_frame.pack(fill=tk.BOTH, expand=True)
+        app_func(app_frame)
+
+    def clear_frame(self, frame):
+        for widget in frame.winfo_children():
+            widget.destroy()
+
 
 def gui_app():
     app = MainApp()
     app.mainloop()
 
 if __name__ == "__main__":
-    gui_app()
+    gui_app()

spacr/gui_classify_app.py

@@ -69,13 +69,13 @@ def import_settings(scrollable_frame):
     vars_dict = generate_fields(new_settings, scrollable_frame)
 
 #@log_function_call
-def initiate_classify_root(parent_frame):#, width, height):
+def initiate_classify_root(parent_frame):
     global vars_dict, q, canvas, fig_queue, canvas_widget, thread_control
     
     style = ttk.Style(parent_frame)
     set_dark_style(style)
     style_text_boxes(style)
-    set_default_font(parent_frame, font_name="Arial", size=8)
+    set_default_font(parent_frame, font_name="Helvetica", size=8)
 
     parent_frame.configure(bg='#333333')
     parent_frame.grid_rowconfigure(0, weight=1)
@@ -179,7 +179,7 @@ def gui_classify():
     root = tk.Tk()
     root.geometry("1000x800")
     root.title("SpaCer: generate masks")
-    initiate_classify_root(root, 1000, 800)
+    initiate_classify_root(root),
     create_menu_bar(root)
     root.mainloop()
 

spacr/gui_mask_app.py

@@ -97,19 +97,23 @@ def import_settings(scrollable_frame):
     vars_dict = generate_fields(new_settings, scrollable_frame)
 
 #@log_function_call
-def initiate_mask_root(parent_frame, width, height):
+def initiate_mask_root(parent_frame):
     global vars_dict, q, canvas, fig_queue, canvas_widget, thread_control, advanced_var, scrollable_frame
 
     style = ttk.Style(parent_frame)
     set_dark_style(style)
     style_text_boxes(style)
-    set_default_font(parent_frame, font_name="Arial", size=8)
+    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)
     
     fig_queue = Queue()
 
+    # Initialize after_tasks if not already done
+    if not hasattr(parent_frame, 'after_tasks'):
+        parent_frame.after_tasks = []
+
     def _process_fig_queue():
         global canvas
         try:
@@ -130,14 +134,20 @@ def initiate_mask_root(parent_frame, width, height):
         except Exception as e:
             traceback.print_exc()
         finally:
-            canvas_widget.after(100, _process_fig_queue)
+            after_id = canvas_widget.after(100, _process_fig_queue)
+            parent_frame.after_tasks.append(after_id)
 
     def _process_console_queue():
         while not q.empty():
             message = q.get_nowait()
             console_output.insert(tk.END, message)
             console_output.see(tk.END)
-        console_output.after(100, _process_console_queue)
+        after_id = console_output.after(100, _process_console_queue)
+        parent_frame.after_tasks.append(after_id)
+
+    # Clear previous content if any
+    for widget in parent_frame.winfo_children():
+        widget.destroy()
 
     vertical_container = tk.PanedWindow(parent_frame, orient=tk.HORIZONTAL)
     vertical_container.grid(row=0, column=0, sticky=tk.NSEW)
@@ -172,17 +182,17 @@ def initiate_mask_root(parent_frame, width, height):
     run_button.grid(row=45, column=0, pady=10, padx=10)
     abort_button = CustomButton(scrollable_frame.scrollable_frame, text="Abort", command=initiate_abort)
     abort_button.grid(row=45, column=1, pady=10, padx=10)
-    progress_label = ttk.Label(scrollable_frame.scrollable_frame, text="Processing: 0%", background="black", foreground="white") # Create progress field
+    progress_label = ttk.Label(scrollable_frame.scrollable_frame, text="Processing: 0%", background="black", foreground="white")
     progress_label.grid(row=50, column=0, columnspan=2, sticky="ew", pady=(5, 0), padx=10)
 
     # Plot Canvas Section
-    plot_frame = tk.PanedWindow(vertical_container, orient=tk.VERTICAL) # Horizontal container for Matplotlib figure and the vertical pane (for settings and console)
+    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') # Matplotlib figure setup
+    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) # Embedd Matplotlib figure in Tkinter window
+    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")
@@ -206,15 +216,28 @@ def initiate_mask_root(parent_frame, width, height):
     _process_console_queue()
     _process_fig_queue()
     
-    parent_frame.after(100, lambda: main_thread_update_function(parent_frame, q, fig_queue, canvas_widget, progress_label))
+    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)
 
     return parent_frame, vars_dict
 
 def gui_mask():
     root = tk.Tk()
     root.geometry("1000x800")
-    root.title("SpaCer: generate masks")
-    initiate_mask_root(root, 1000, 800)
+    root.title("SpaCr: generate masks")
+    
+    # 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_root(root.content_frame)
     create_menu_bar(root)
     root.mainloop()
 

spacr/gui_measure_app.py

@@ -86,29 +86,24 @@ def initiate_abort():
         thread_control["run_thread"] = None
 
 #@log_function_call
-def import_settings(scrollable_frame):
-    global vars_dict
-
-    csv_file_path = filedialog.askopenfilename(filetypes=[("CSV files", "*.csv")])
-    csv_settings = read_settings_from_csv(csv_file_path)
-    variables = measure_variables()
-    new_settings = update_settings_from_csv(variables, csv_settings)
-    vars_dict = generate_fields(new_settings, scrollable_frame)
-
-#@log_function_call
-def initiate_measure_root(parent_frame):#, width, height):
+def initiate_measure_root(parent_frame):
     global vars_dict, q, canvas, fig_queue, canvas_widget, thread_control, variables, advanced_var, scrollable_frame
     
     style = ttk.Style(parent_frame)
     set_dark_style(style)
     style_text_boxes(style)
-    set_default_font(parent_frame, font_name="Arial", size=8)
+    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)
+
     fig_queue = Queue()
     
+    # Initialize after_tasks if not already done
+    if not hasattr(parent_frame, 'after_tasks'):
+        parent_frame.after_tasks = []
+
     def _process_fig_queue():
         global canvas
         try:
@@ -129,14 +124,20 @@ def initiate_measure_root(parent_frame):#, width, height):
         except Exception as e:
             traceback.print_exc()
         finally:
-            canvas_widget.after(100, _process_fig_queue)
+            after_id = canvas_widget.after(100, _process_fig_queue)
+            parent_frame.after_tasks.append(after_id)
 
     def _process_console_queue():
         while not q.empty():
             message = q.get_nowait()
             console_output.insert(tk.END, message)
             console_output.see(tk.END)
-        console_output.after(100, _process_console_queue)
+        after_id = console_output.after(100, _process_console_queue)
+        parent_frame.after_tasks.append(after_id)
+
+    # Clear previous content if any
+    for widget in parent_frame.winfo_children():
+        widget.destroy()
 
     vertical_container = tk.PanedWindow(parent_frame, orient=tk.HORIZONTAL)
     vertical_container.grid(row=0, column=0, sticky=tk.NSEW)
@@ -205,15 +206,29 @@ def initiate_measure_root(parent_frame):#, width, height):
     _process_console_queue()
     _process_fig_queue()
     
-    parent_frame.after(100, lambda: main_thread_update_function(parent_frame, q, fig_queue, canvas_widget, progress_label))
+    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)
     
     return parent_frame, vars_dict
 
+
 def gui_measure():
     root = tk.Tk()
     root.geometry("1000x800")
-    root.title("SpaCer: generate masks")
-    initiate_measure_root(root, 1000, 800)
+    root.title("SpaCr: measure objects")
+    
+    # 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_measure_root(root.content_frame)
     create_menu_bar(root)
     root.mainloop()
 

spacr/gui_utils.py

@@ -40,21 +40,27 @@ class ToolTip:
             self.tooltip_window.destroy()
         self.tooltip_window = None
 
-
 def load_app(root, app_name, app_func):
-    # Destroy the current window
-    root.destroy()
-    # Create a new window for the app
-    app_window = tk.Tk()
-    app_window.title(f"SpaCr - {app_name}")
-    app_window.geometry("1200x800")
-    #app_window.attributes('-fullscreen', True)
-    app_window.configure(bg="black")
-    create_menu_bar(app_window)  # Add menu to the new window
-    app_func(app_window, app_window.winfo_width(), app_window.winfo_height())
+    # Cancel all scheduled after tasks
+    if hasattr(root, 'after_tasks'):
+        for task in root.after_tasks:
+            root.after_cancel(task)
+    root.after_tasks = []
+
+    # Clear the current content frame
+    if hasattr(root, 'content_frame'):
+        for widget in root.content_frame.winfo_children():
+            widget.destroy()
+    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)
 
-def create_menu_bar(root):
+    # 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
@@ -68,6 +74,10 @@ def create_menu_bar(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
@@ -75,7 +85,7 @@ def create_menu_bar(root):
     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(root, app_name, app_func))
+        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)
@@ -83,7 +93,7 @@ def create_menu_bar(root):
     root.config(menu=menu_bar)
 
 class CustomButton(tk.Frame):
-    def __init__(self, parent, text="", command=None, *args, **kwargs):
+    def __init__(self, parent, text="", command=None, font=None, *args, **kwargs):
         super().__init__(parent, *args, **kwargs)
         self.text = text
         self.command = command
@@ -93,8 +103,8 @@ class CustomButton(tk.Frame):
 
         self.button_bg = self.create_rounded_rectangle(0, 0, 150, 50, radius=20, fill="#800080")
 
-        # Create a Tkinter font object using OpenSans
-        self.font_style = tkFont.Font(family="Arial", size=12, weight=tkFont.NORMAL)
+        # 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)
@@ -137,7 +147,7 @@ class CustomButton(tk.Frame):
                   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)
@@ -226,15 +236,60 @@ class ToggleSwitch(ttk.Frame):
 
         return self.canvas.create_polygon(points, **kwargs, smooth=True)
     
-def set_default_font(root, font_name="Arial", size=12):
+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)
+    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')])
+
 def check_and_download_font():
-    font_name = "Arial"
+    font_name = "Helvetica"
     font_dir = "fonts"
     font_path = os.path.join(font_dir, "OpenSans-Regular.ttf")
 
@@ -257,9 +312,9 @@ def check_and_download_font():
             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="Arial", size=10)
-            tkFont.nametofont("TkTextFont").configure(family="Arial", size=10)
-            tkFont.nametofont("TkHeadingFont").configure(family="Arial", size=12)
+            tkFont.nametofont("TkDefaultFont").configure(family="Helvetica", size=10)
+            tkFont.nametofont("TkTextFont").configure(family="Helvetica", size=10)
+            tkFont.nametofont("TkHeadingFont").configure(family="Helvetica", size=12)
     else:
         tkFont.nametofont("TkDefaultFont").configure(family=font_name, size=10)
         tkFont.nametofont("TkTextFont").configure(family=font_name, size=10)
@@ -267,7 +322,7 @@ def check_and_download_font():
 
 def style_text_boxes(style):
     check_and_download_font()
-    font_style = tkFont.Font(family="Arial", size=10)  # Define the Arial 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)
@@ -279,7 +334,6 @@ def style_text_boxes(style):
     style.map('TCheckbutton', background=[('selected', '#555555'), ('active', '#555555')])
 
 
-
 def read_settings_from_csv(csv_file_path):
     settings = {}
     with open(csv_file_path, newline='') as csvfile:
@@ -337,7 +391,7 @@ class ScrollableFrame(ttk.Frame):
         canvas.pack(side="left", fill="both", expand=True)
         scrollbar.pack(side="right", fill="y")
 
-class StdoutRedirector(object):
+class StdoutRedirector_v1(object):
     def __init__(self, text_widget):
         self.text_widget = text_widget
 
@@ -348,6 +402,21 @@ class StdoutRedirector(object):
     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():
@@ -804,8 +873,6 @@ def generate_fields(variables, scrollable_frame):
         row += 1
     return vars_dict
 
-
-    
 class TextRedirector(object):
     def __init__(self, widget, queue):
         self.widget = widget
@@ -834,7 +901,7 @@ def create_dark_mode(root, style, console_output):
     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=("Arial", 12)
+        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):
@@ -1025,4 +1092,4 @@ def run_multiple_simulations_wrapper(settings, q, fig_queue):
         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   
+        plt.show = original_show  # Restore the original plt.show function

{spacr-0.1.0.dist-info → spacr-0.1.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: spacr
-Version: 0.1.0
+Version: 0.1.1
 Summary: Spatial phenotype analysis of crisp screens (SpaCr)
 Home-page: https://github.com/EinarOlafsson/spacr
 Author: Einar Birnir Olafsson

{spacr-0.1.0.dist-info → spacr-0.1.1.dist-info}/RECORD

@@ -10,13 +10,13 @@ spacr/deep_spacr.py,sha256=N0o7ILD2p1FTfU4DFxnpjs00xjLhwib-ev0XGqA6muU,37035
 spacr/foldseek.py,sha256=YIP1d4Ci6CeA9jSyiv-HTDbNmAmcSM9Y_DaOs7wYzLY,33546
 spacr/get_alfafold_structures.py,sha256=ehx_MQgb12k3hFecP6cYVlm5TLO8iWjgevy8ESyS3cw,3544
 spacr/graph_learning.py,sha256=1tR-ZxvXE3dBz1Saw7BeVFcrsUFu9OlUZeZVifih9eo,13070
-spacr/gui.py,sha256=zu-i8ezLJ03jNRACK7CRgNhkM8g8-pJFwZ-OSDFzsPg,6498
-spacr/gui_2.py,sha256=FPlmvGm1VIood_YBnG44IafgjjaVfagybTnjVEOs5Ig,3299
-spacr/gui_classify_app.py,sha256=LY33wott1mR7AFYwBI9ZQZYY16lBB-wuaY4pL_poaQ0,7884
-spacr/gui_mask_app.py,sha256=WKkAH0jv-SnfaZdJ8MkC7mkUIVSSrNE8lUfH3QBvUak,9747
-spacr/gui_measure_app.py,sha256=5vjjds5NFaOcE8XeuWDug9k-NI4jbTrwp54sJ7DNaNI,9625
+spacr/gui.py,sha256=ugBksLGOHdtOLlEuRyyc59TrkYKu3rDf8JxEgiBSVao,6536
+spacr/gui_2.py,sha256=ZAI5quQYbhQJ40vK0NCqU_UMSPLkpfeQpomBWUSM0fc,6946
+spacr/gui_classify_app.py,sha256=W_epjHsM3P9JfYDWFre694r9suXR_oEtBLvs6WAE_po,7860
+spacr/gui_mask_app.py,sha256=Lmz1_PLUSuYYLWp36xnYSkKXqEn2bgaHIpW0uOeq4gQ,10403
+spacr/gui_measure_app.py,sha256=kB-BL0_6vGo5MWND7e2OdLTz4MPa77K9tPYu3eDwBnk,10079
 spacr/gui_sim_app.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-spacr/gui_utils.py,sha256=JRWwmGEEVSPgs0UtZRukdNwIUJepbP675_Fvs5qocPk,49718
+spacr/gui_utils.py,sha256=FFFpDzlNyolv1iQtawwD_acctvUpMsFsbVMCrdwyuCM,53167
 spacr/io.py,sha256=IoERqSwoxJrInYl-E0WfwFOEDZXFdJofk5DmpbyLGWM,112077
 spacr/logger.py,sha256=7Zqr3TuuOQLWT32gYr2q1qvv7x0a2JhLANmZcnBXAW8,670
 spacr/mask_app.py,sha256=jlKmj_evveIkkyH3PYEcAshcLXN0DOPWB1oc4hAwq9E,44201
@@ -32,9 +32,9 @@ spacr/version.py,sha256=axH5tnGwtgSnJHb5IDhiu4Zjk5GhLyAEDRe-rnaoFOA,409
 spacr/models/cp/toxo_plaque_cyto_e25000_X1120_Y1120.CP_model,sha256=z8BbHWZPRnE9D_BHO0fBREE85c1vkltDs-incs2ytXQ,26566572
 spacr/models/cp/toxo_plaque_cyto_e25000_X1120_Y1120.CP_model_settings.csv,sha256=fBAGuL_B8ERVdVizO3BHozTDSbZUh1yFzsYK3wkQN68,420
 spacr/models/cp/toxo_pv_lumen.CP_model,sha256=2y_CindYhmTvVwBH39SNILF3rI3x9SsRn6qrMxHy3l0,26562451
-spacr-0.1.0.dist-info/LICENSE,sha256=SR-2MeGc6SCM1UORJYyarSWY_A-JaOMFDj7ReSs9tRM,1083
-spacr-0.1.0.dist-info/METADATA,sha256=AkkTVCUxEtm5QUQS4c58ZC0eaCx3ctpiFXchwjyRV9o,5157
-spacr-0.1.0.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
-spacr-0.1.0.dist-info/entry_points.txt,sha256=xncHsqD9MI5wj0_p4mgZlrB8dHm_g_qF0Ggo1c78LqY,315
-spacr-0.1.0.dist-info/top_level.txt,sha256=GJPU8FgwRXGzKeut6JopsSRY2R8T3i9lDgya42tLInY,6
-spacr-0.1.0.dist-info/RECORD,,
+spacr-0.1.1.dist-info/LICENSE,sha256=SR-2MeGc6SCM1UORJYyarSWY_A-JaOMFDj7ReSs9tRM,1083
+spacr-0.1.1.dist-info/METADATA,sha256=f4CaWxwjyeC2yAEeYl-3J50QgVGZqTY9dBX9r66LyTM,5157
+spacr-0.1.1.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
+spacr-0.1.1.dist-info/entry_points.txt,sha256=xncHsqD9MI5wj0_p4mgZlrB8dHm_g_qF0Ggo1c78LqY,315
+spacr-0.1.1.dist-info/top_level.txt,sha256=GJPU8FgwRXGzKeut6JopsSRY2R8T3i9lDgya42tLInY,6
+spacr-0.1.1.dist-info/RECORD,,