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

spacr/app_mask.py

@@ -0,0 +1,251 @@
+#import customtkinter as ctk
+
+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
+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, ToggleSwitch, CustomButton, ToolTip
+from .gui_utils import clear_canvas, main_thread_update_function, set_dark_style, generate_fields, process_stdout_stderr, set_default_font, style_text_boxes
+from .gui_utils import mask_variables, check_mask_gui_settings, preprocess_generate_masks_wrapper, read_settings_from_csv, update_settings_from_csv, create_menu_bar
+
+thread_control = {"run_thread": None, "stop_requested": False}
+
+test_mode_button = None
+
+def toggle_test_mode():
+    global vars_dict
+    current_state = vars_dict['test_mode'][2].get()
+    new_state = not current_state
+    vars_dict['test_mode'][2].set(new_state)
+    if new_state:
+        test_mode_button.config(bg="blue")
+    else:
+        test_mode_button.config(bg="gray")
+
+def toggle_advanced_settings():
+    global vars_dict
+
+    timelapse_settings = ['timelapse', 'timelapse_memory', 'timelapse_remove_transient', 'timelapse_mode', 'timelapse_objects', 'timelapse_displacement', 'timelapse_frame_limits', 'fps']
+    misc_settings = ['examples_to_plot', 'all_to_mip', 'pick_slice', 'skip_mode']
+    opperational_settings = ['preprocess', 'masks', 'randomize', 'batch_size', 'custom_regex', 'merge', 'normalize_plots', 'workers', 'plot', 'remove_background', 'lower_quantile']
+
+    advanced_settings = timelapse_settings+misc_settings+opperational_settings
+
+    # Toggle visibility of advanced settings
+    for setting in advanced_settings:
+        label, widget, var = vars_dict[setting]
+        if advanced_var.get() is False:
+            label.grid_remove()  # Hide the label
+            widget.grid_remove()  # Hide the widget
+        else:
+            label.grid()  # Show the label
+            widget.grid()  # Show the widget
+
+#@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_mask_gui(q, fig_queue, stop_requested):
+    global vars_dict
+    process_stdout_stderr(q)
+    try:
+        settings = check_mask_gui_settings(vars_dict)
+        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
+
+#@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_mask_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 = mask_variables()
+    new_settings = update_settings_from_csv(variables, csv_settings)
+    vars_dict = generate_fields(new_settings, scrollable_frame)
+
+#@log_function_call
+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="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:
+            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('black')
+                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:
+            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)
+        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)
+    parent_frame.grid_rowconfigure(0, weight=1)
+    parent_frame.grid_columnconfigure(0, weight=1)
+
+    # Settings Section
+    settings_frame = tk.Frame(vertical_container, bg='black')
+    vertical_container.add(settings_frame, stretch="always")
+    settings_label = ttk.Label(settings_frame, text="Settings", style="Custom.TLabel")
+    settings_label.grid(row=0, column=0, pady=10, padx=10)
+    scrollable_frame = ScrollableFrame(settings_frame, width=600)
+    scrollable_frame.grid(row=1, column=0, sticky="nsew")
+    settings_frame.grid_rowconfigure(1, weight=1)
+    settings_frame.grid_columnconfigure(0, weight=1)
+    
+    # Create advanced settings checkbox
+    advanced_var = tk.BooleanVar(value=False)
+    advanced_Toggle = ToggleSwitch(scrollable_frame.scrollable_frame, text="Advanced Settings", variable=advanced_var, command=toggle_advanced_settings)
+    advanced_Toggle.grid(row=48, column=0, pady=10, padx=10)
+    variables = mask_variables()
+    vars_dict = generate_fields(variables, scrollable_frame)
+    toggle_advanced_settings()
+    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, 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), 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, 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")
+    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='black')
+    plot = figure.add_subplot(111)
+    plot.plot([], [])  # This creates an empty plot.
+    plot.axis('off')
+    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")
+    canvas.draw()
+    canvas.figure = figure
+
+    # Console Section
+    console_frame = tk.Frame(vertical_container, bg='black')
+    vertical_container.add(console_frame, stretch="always")
+    console_label = ttk.Label(console_frame, text="Console", background="black", foreground="white")
+    console_label.grid(row=0, column=0, pady=10, padx=10)
+    console_output = scrolledtext.ScrolledText(console_frame, height=10, bg='black', 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()
+    
+    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()
+    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()
+
+if __name__ == "__main__":
+    gui_mask()

spacr/app_measure.py

@@ -0,0 +1,248 @@
+import sys, traceback, matplotlib, ctypes
+import tkinter as tk
+from tkinter import ttk, scrolledtext
+from matplotlib.figure import Figure
+from matplotlib.backends.backend_tkagg import FigureCanvasTkAgg
+matplotlib.use('Agg')  # Use the non-GUI Agg backend
+from multiprocessing import Process, Queue, Value
+from tkinter import filedialog
+
+try:
+    ctypes.windll.shcore.SetProcessDpiAwareness(True)
+except AttributeError:
+    pass
+
+from .logger import log_function_call
+from .gui_utils import ScrollableFrame, StdoutRedirector, CustomButton, ToggleSwitch, ToolTip
+from .gui_utils import process_stdout_stderr, set_dark_style, set_default_font, generate_fields, main_thread_update_function, create_menu_bar
+from .gui_utils import measure_variables, measure_crop_wrapper, clear_canvas, check_measure_gui_settings, read_settings_from_csv, update_settings_from_csv, style_text_boxes
+
+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)
+
+test_mode_button = None
+
+def toggle_test_mode():
+    global vars_dict
+    current_state = vars_dict['test_mode'][2].get()
+    new_state = not current_state
+    vars_dict['test_mode'][2].set(new_state)
+    if new_state:
+        test_mode_button.config(bg="blue")
+    else:
+        test_mode_button.config(bg="gray")
+
+def toggle_advanced_settings():
+    global vars_dict
+
+    timelapse_settings = ['timelapse', 'timelapse_objects']
+    misc_settings = ['representative_images', 'plot', 'plot_filtration', 'include_uninfected', 'dialate_pngs', 'dialate_png_ratios']
+    opperational_settings = ['max_workers','experiment','cells','cell_loc','pathogens','pathogen_loc','treatments','treatment_loc','channel_of_interest','compartments','measurement','nr_imgs', 'um_per_pixel']
+    
+    advanced_settings = timelapse_settings+misc_settings+opperational_settings
+
+    # Toggle visibility of advanced settings
+    for setting in advanced_settings:
+        label, widget, var = vars_dict[setting]
+        if advanced_var.get() is False:
+            label.grid_remove()  # Hide the label
+            widget.grid_remove()  # Hide the widget
+        else:
+            label.grid()  # Show the label
+            widget.grid()  # Show the widget
+
+#@log_function_call
+def run_measure_gui(q, fig_queue, stop_requested):
+    global vars_dict
+    process_stdout_stderr(q)
+    try:
+        print('hello')
+        settings = check_measure_gui_settings(vars_dict)
+        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
+
+#@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_measure_gui, args=(q, fig_queue, stop_requested))
+    thread_control["run_thread"].start()
+
+#@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 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="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:
+            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('black')
+                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:
+            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)
+        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)
+    parent_frame.grid_rowconfigure(0, weight=1)
+    parent_frame.grid_columnconfigure(0, weight=1)
+
+    # Settings Section
+    settings_frame = tk.Frame(vertical_container, bg='black')
+    vertical_container.add(settings_frame, stretch="always")
+    settings_label = ttk.Label(settings_frame, text="Settings", background="black", 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)
+    
+    # Create advanced settings checkbox
+    advanced_var = tk.BooleanVar(value=False)
+    advanced_Toggle = ToggleSwitch(scrollable_frame.scrollable_frame, text="Advanced Settings", variable=advanced_var, command=toggle_advanced_settings)
+    advanced_Toggle.grid(row=48, column=0, pady=10, padx=10)
+    variables = measure_variables()
+    vars_dict = generate_fields(variables, scrollable_frame)
+    toggle_advanced_settings()
+    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.grid(row=47, column=1, pady=10, padx=10)
+    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='black')
+    plot = figure.add_subplot(111)
+    plot.plot([], [])
+    plot.axis('off')
+    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")
+    canvas.draw()
+    canvas.figure = figure
+
+    # Console Section
+    console_frame = tk.Frame(vertical_container, bg='black')
+    vertical_container.add(console_frame, stretch="always")
+    console_label = ttk.Label(console_frame, text="Console", background="black", foreground="white")
+    console_label.grid(row=0, column=0, pady=10, padx=10)
+    console_output = scrolledtext.ScrolledText(console_frame, height=10, bg='black', 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()
+    
+    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()
+    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()
+
+if __name__ == "__main__":
+    gui_measure()