spacr 0.1.1__py3-none-any.whl → 0.1.12__py3-none-any.whl

spacr/classify_app.py

@@ -0,0 +1,201 @@
+import sys, ctypes, matplotlib
+import tkinter as tk
+from tkinter import ttk, scrolledtext
+from matplotlib.figure import Figure
+from matplotlib.backends.backend_tkagg import FigureCanvasTkAgg
+from matplotlib.figure import Figure
+matplotlib.use('Agg')
+from tkinter import filedialog
+from multiprocessing import Process, Queue, Value
+import traceback
+
+try:
+    ctypes.windll.shcore.SetProcessDpiAwareness(True)
+except AttributeError:
+    pass
+
+from .logger import log_function_call
+from .gui_utils import ScrollableFrame, StdoutRedirector, CustomButton, set_dark_style, set_default_font, generate_fields, process_stdout_stderr, clear_canvas, main_thread_update_function
+from .gui_utils import classify_variables, check_classify_gui_settings, train_test_model_wrapper, read_settings_from_csv, update_settings_from_csv, style_text_boxes, create_menu_bar
+
+thread_control = {"run_thread": None, "stop_requested": False}
+
+#@log_function_call
+def initiate_abort():
+    global thread_control
+    if thread_control.get("stop_requested") is not None:
+        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
+        
+#@log_function_call
+def run_classify_gui(q, fig_queue, stop_requested):
+    global vars_dict
+    process_stdout_stderr(q)
+    try:
+        settings = check_classify_gui_settings(vars_dict)
+        for key in settings:
+            value = settings[key]
+            print(key, value, type(value))
+        train_test_model_wrapper(settings['src'], settings)
+    except Exception as e:
+        q.put(f"Error during processing: {e}")
+        traceback.print_exc()
+    finally:
+        stop_requested.value = 1
+    
+#@log_function_call
+def start_process(q, fig_queue):
+    global thread_control
+    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
+    thread_control["run_thread"] = Process(target=run_classify_gui, args=(q, fig_queue, stop_requested))
+    thread_control["run_thread"].start()
+    
+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 = classify_variables()
+    new_settings = update_settings_from_csv(variables, csv_settings)
+    vars_dict = generate_fields(new_settings, scrollable_frame)
+
+#@log_function_call
+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="Helvetica", size=8)
+
+    parent_frame.configure(bg='#333333')
+    parent_frame.grid_rowconfigure(0, weight=1)
+    parent_frame.grid_columnconfigure(0, weight=1)
+    fig_queue = Queue()
+
+    def _process_fig_queue():
+        global canvas
+        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('#333333')
+                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:
+            canvas_widget.after(100, _process_fig_queue)
+
+    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)
+
+    vertical_container = tk.PanedWindow(parent_frame, orient=tk.HORIZONTAL)
+    vertical_container.grid(row=0, column=0, sticky=tk.NSEW)
+    parent_frame.grid_rowconfigure(0, weight=1)
+    parent_frame.grid_columnconfigure(0, weight=1)
+
+    # Settings Section
+    settings_frame = tk.Frame(vertical_container, bg='#333333')
+    vertical_container.add(settings_frame, stretch="always")
+    settings_label = ttk.Label(settings_frame, text="Settings", background="#333333", foreground="white")
+    settings_label.grid(row=0, column=0, pady=10, padx=10)
+    scrollable_frame = ScrollableFrame(settings_frame, width=500)
+    scrollable_frame.grid(row=1, column=0, sticky="nsew")
+    settings_frame.grid_rowconfigure(1, weight=1)
+    settings_frame.grid_columnconfigure(0, weight=1)
+
+    # Setup for user input fields (variables)
+    variables = classify_variables()
+    vars_dict = generate_fields(variables, scrollable_frame)
+
+    # Button section
+    import_btn = CustomButton(scrollable_frame.scrollable_frame, text="Import", command=lambda: import_settings(scrollable_frame), font=('Helvetica', 10))
+    import_btn.grid(row=47, column=0, pady=20, padx=20)
+    run_button = CustomButton(scrollable_frame.scrollable_frame, text="Run", command=lambda: start_process(q, fig_queue), font=('Helvetica', 10))
+    run_button.grid(row=45, column=0, pady=20, padx=20)
+    abort_button = CustomButton(scrollable_frame.scrollable_frame, text="Abort", command=initiate_abort, font=('Helvetica', 10))
+    abort_button.grid(row=45, column=1, pady=20, padx=20)
+    progress_label = ttk.Label(scrollable_frame.scrollable_frame, text="Processing: 0%", background="black", foreground="white") # Create progress field
+    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)
+    vertical_container.add(plot_frame, stretch="always")
+    figure = Figure(figsize=(30, 4), dpi=100, facecolor='#333333')
+    plot = figure.add_subplot(111)
+    plot.plot([], [])
+    plot.axis('off')
+    canvas = FigureCanvasTkAgg(figure, master=plot_frame)
+    canvas.get_tk_widget().configure(cursor='arrow', background='#333333', highlightthickness=0)
+    canvas_widget = canvas.get_tk_widget()
+    plot_frame.add(canvas_widget, stretch="always")
+    canvas.draw()
+    canvas.figure = figure
+
+    # Console Section
+    console_frame = tk.Frame(vertical_container, bg='#333333')
+    vertical_container.add(console_frame, stretch="always")
+    console_label = ttk.Label(console_frame, text="Console", background="#333333", foreground="white")
+    console_label.grid(row=0, column=0, pady=10, padx=10)
+    console_output = scrolledtext.ScrolledText(console_frame, height=10, bg='#333333', 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)
+
+    q = Queue()
+    sys.stdout = StdoutRedirector(console_output)
+    sys.stderr = StdoutRedirector(console_output)
+
+    _process_console_queue()
+    _process_fig_queue()
+
+    parent_frame.after(100, lambda: main_thread_update_function(parent_frame, q, fig_queue, canvas_widget, progress_label))
+
+    return parent_frame, vars_dict
+
+def gui_classify():
+    root = tk.Tk()
+    width = root.winfo_screenwidth()
+    height = root.winfo_screenheight()
+    root.geometry(f"{width}x{height}") 
+    root.title("SpaCr: classify 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_classify_root(root.content_frame)
+    create_menu_bar(root)
+    root.mainloop()
+
+if __name__ == "__main__":
+    gui_classify()

spacr/gui.py

@@ -6,22 +6,21 @@ import os
 import requests
 
 # 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
+from .app_mask import initiate_mask_root
+from .app_measure import initiate_measure_root
+from .app_annotate import initiate_annotation_app_root
+from .app_make_masks import initiate_mask_app_root
+from .app_classify import initiate_classify_root
+from .gui_utils import CustomButton, style_text_boxes, create_menu_bar
 
 class MainApp(tk.Tk):
     def __init__(self):
         super().__init__()
+        width = self.winfo_screenwidth()
+        height = self.winfo_screenheight()
+        self.geometry(f"{width}x{height}")  
         self.title("SpaCr GUI Collection")
-        self.geometry("1100x1500")
         self.configure(bg="black")
-        #self.attributes('-fullscreen', True)
-
         style = ttk.Style()
         style_text_boxes(style)
 
@@ -38,15 +37,18 @@ class MainApp(tk.Tk):
 
     def create_widgets(self):
         # Create the menu bar
-        #create_menu_bar(self)
+        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 = tk.Canvas(self, bg="black", highlightthickness=0)
         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()
 
@@ -59,10 +61,10 @@ 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=('Helvetica', 24, tkFont.NORMAL)).pack(padx=10, pady=10)
+            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, tkFont.NORMAL)).pack(padx=10, pady=10)
+        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")
@@ -72,10 +74,10 @@ 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), font=('Helvetica', 12))
+            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', 10, tkFont.NORMAL))
+            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
@@ -125,13 +127,14 @@ class MainApp(tk.Tk):
             print(f"An error occurred while processing the logo image: {e}")
             return False
 
-    def load_app(self, app_name):
-        selected_app_func, _ = self.gui_apps[app_name]
+    def load_app(self, app_name, app_func):
+        # Clear the current content frame
         self.clear_frame(self.content_frame)
 
+        # Initialize the selected app
         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())
+        app_func(app_frame)
 
     def clear_frame(self, frame):
         for widget in frame.winfo_children():
@@ -142,4 +145,4 @@ def gui_app():
     app.mainloop()
 
 if __name__ == "__main__":
-    gui_app()
+    gui_app()

spacr/gui_annotate.py

@@ -0,0 +1,145 @@
+import tkinter as tk
+from tkinter import ttk
+from tkinter import font as tkFont
+from PIL import Image, ImageTk
+import os
+import requests
+
+# 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("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):
+        # 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()
+
+    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):
+            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=('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")
+        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), 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', 10, tkFont.NORMAL))
+            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()  # 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)
+                return True
+            except requests.exceptions.RequestException as e:
+                print(f"Failed to download image from {url}: {e}")
+                return False
+
+        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((800, 800), Image.Resampling.LANCZOS)
+            logo_photo = ImageTk.PhotoImage(logo_image)
+            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_app(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)#, self.winfo_width(), self.winfo_height())
+
+    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()

spacr/gui_classify_app.py

@@ -131,11 +131,11 @@ def initiate_classify_root(parent_frame):
     vars_dict = generate_fields(variables, scrollable_frame)
 
     # Button section
-    import_btn = CustomButton(scrollable_frame.scrollable_frame, text="Import Settings", command=lambda: import_settings(scrollable_frame))
+    import_btn = CustomButton(scrollable_frame.scrollable_frame, text="Import", command=lambda: import_settings(scrollable_frame), font=('Helvetica', 10))
     import_btn.grid(row=47, column=0, pady=20, padx=20)
-    run_button = CustomButton(scrollable_frame.scrollable_frame, text="Run", command=lambda: start_process(q, fig_queue))
+    run_button = CustomButton(scrollable_frame.scrollable_frame, text="Run", command=lambda: start_process(q, fig_queue), font=('Helvetica', 10))
     run_button.grid(row=45, column=0, pady=20, padx=20)
-    abort_button = CustomButton(scrollable_frame.scrollable_frame, text="Abort", command=initiate_abort)
+    abort_button = CustomButton(scrollable_frame.scrollable_frame, text="Abort", command=initiate_abort, font=('Helvetica', 10))
     abort_button.grid(row=45, column=1, pady=20, padx=20)
     progress_label = ttk.Label(scrollable_frame.scrollable_frame, text="Processing: 0%", background="black", foreground="white") # Create progress field
     progress_label.grid(row=50, column=0, columnspan=2, sticky="ew", pady=(5, 0), padx=10)
@@ -177,9 +177,23 @@ def initiate_classify_root(parent_frame):
 
 def gui_classify():
     root = tk.Tk()
-    root.geometry("1000x800")
-    root.title("SpaCer: generate masks")
-    initiate_classify_root(root),
+    width = root.winfo_screenwidth()
+    height = root.winfo_screenheight()
+    root.geometry(f"{width}x{height}") 
+    root.title("SpaCr: classify 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_classify_root(root.content_frame)
     create_menu_bar(root)
     root.mainloop()