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

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)
@@ -164,25 +174,27 @@ def initiate_mask_root(parent_frame, width, height):
     vars_dict['Test mode'] = (None, None, tk.BooleanVar(value=False))
     
     # Button section
-    test_mode_button = CustomButton(scrollable_frame.scrollable_frame, text="Test Mode", command=toggle_test_mode)
+    test_mode_button = CustomButton(scrollable_frame.scrollable_frame, text="Test Mode", command=toggle_test_mode, font=('Helvetica', 10))
+    #CustomButton(buttons_frame, text=app_name, command=lambda app_name=app_name: self.load_app(app_name, app_func), font=('Helvetica', 12))
+
     test_mode_button.grid(row=47, column=1, pady=10, padx=10)
-    import_btn = CustomButton(scrollable_frame.scrollable_frame, text="Import", 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=10, padx=10)
     run_button = CustomButton(scrollable_frame.scrollable_frame, text="Run", command=lambda: start_process(q, fig_queue))
     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 = CustomButton(scrollable_frame.scrollable_frame, text="Abort", command=initiate_abort, font=('Helvetica', 10))
     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 +218,30 @@ 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)
+    width = root.winfo_screenwidth()
+    height = root.winfo_screenheight()
+    root.geometry(f"{width}x{height}")    
+    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

@@ -19,6 +19,15 @@ from .gui_utils import measure_variables, measure_crop_wrapper, clear_canvas, ch
 
 thread_control = {"run_thread": None, "stop_requested": False}
 
+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)
+
 def toggle_test_mode():
     global vars_dict
     current_state = vars_dict['test_mode'][2].get()
@@ -86,29 +95,24 @@ 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 +133,20 @@ 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)
@@ -165,11 +175,11 @@ def initiate_measure_root(parent_frame):#, width, height):
     # Button section
     test_mode_button = CustomButton(scrollable_frame.scrollable_frame, text="Test Mode", command=toggle_test_mode)
     test_mode_button.grid(row=47, column=1, pady=10, padx=10)
-    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)
@@ -205,15 +215,30 @@ 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)
+    width = root.winfo_screenwidth()
+    height = root.winfo_screenheight()
+    root.geometry(f"{width}x{height}") 
+    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_run.py

@@ -0,0 +1,58 @@
+import traceback
+from .gui_wrappers import measure_crop_wrapper, preprocess_generate_masks_wrapper, train_test_model_wrapper, umap_wrapper, sequencing_wrapper
+
+def run_mask_gui(settings, q, fig_queue, stop_requested):
+    from .gui_utils import process_stdout_stderr
+    process_stdout_stderr(q)
+    try:
+        preprocess_generate_masks_wrapper(settings, q, fig_queue)
+    except Exception as e:
+        q.put(f"Error during processing: {e}")
+        traceback.print_exc()
+    finally:
+        stop_requested.value = 1
+
+def run_sequencing_gui(settings, q, fig_queue, stop_requested):
+    from .gui_utils import process_stdout_stderr
+    process_stdout_stderr(q)
+    try:
+        sequencing_wrapper(settings, q, fig_queue)
+    except Exception as e:
+        q.put(f"Error during processing: {e}")
+        traceback.print_exc()
+    finally:
+        stop_requested.value = 1
+
+def run_umap_gui(settings, q, fig_queue, stop_requested):
+    from .gui_utils import process_stdout_stderr
+    process_stdout_stderr(q)
+    try:
+        umap_wrapper(settings, q, fig_queue)
+    except Exception as e:
+        q.put(f"Error during processing: {e}")
+        traceback.print_exc()
+    finally:
+        stop_requested.value = 1
+
+def run_measure_gui(settings, q, fig_queue, stop_requested):
+    from .gui_utils import process_stdout_stderr
+    process_stdout_stderr(q)
+    try:
+        settings['input_folder'] = settings['src']
+        measure_crop_wrapper(settings=settings, q=q, fig_queue=fig_queue)
+    except Exception as e:
+        q.put(f"Error during processing: {e}")
+        traceback.print_exc()
+    finally:
+        stop_requested.value = 1
+
+def run_classify_gui(settings, q, fig_queue, stop_requested):
+    from .gui_utils import process_stdout_stderr
+    process_stdout_stderr(q)
+    try:
+        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