spacr 0.2.2__py3-none-any.whl → 0.2.21__py3-none-any.whl

spacr/mask_app.py

@@ -1,249 +0,0 @@
-#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}
-
-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/measure_app.py

@@ -1,246 +0,0 @@
-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)
-
-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()

spacr/models/cp/toxo_plaque_cyto_e25000_X1120_Y1120.CP_model_settings.csv

@@ -1,23 +0,0 @@
-Key,Value
-img_src,/nas_mnt/carruthers/patrick/Plaque_assay_training/train
-model_name,toxo_plaque
-model_type,cyto
-Signal_to_noise,10
-background,200
-remove_background,False
-learning_rate,0.2
-weight_decay,1e-05
-batch_size,8
-n_epochs,25000
-from_scratch,False
-diameter,30
-resize,True
-width_height,"[1120, 1120]"
-verbose,True
-channels,"[0, 0]"
-normalize,True
-percentiles,
-circular,False
-invert,False
-grayscale,True
-test,False