spacr 0.1.0__py3-none-any.whl → 0.1.6__py3-none-any.whl

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

@@ -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)
@@ -131,11 +131,11 @@ def initiate_classify_root(parent_frame):#, width, height):
     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):#, width, height):
 
 def gui_classify():
     root = tk.Tk()
-    root.geometry("1000x800")
-    root.title("SpaCer: generate masks")
-    initiate_classify_root(root, 1000, 800)
+    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()