spacr 0.1.16__py3-none-any.whl → 0.1.50__py3-none-any.whl

spacr/app_annotate.py

@@ -13,7 +13,7 @@ from IPython.display import display, HTML
 from tkinter import font as tkFont
 from tkinter import TclError
 
-from .gui_utils import ScrollableFrame, CustomButton, set_dark_style, set_default_font, set_dark_style, create_menu_bar
+from .gui_utils import ScrollableFrame, CustomButton, set_dark_style, create_menu_bar, set_default_font
 
 class ImageApp:
     def __init__(self, root, db_path, src, image_type=None, channels=None, grid_rows=None, grid_cols=None, image_size=(200, 200), annotation_column='annotate', normalize=False, percentiles=(1,99), measurement=None, threshold=None):

spacr/app_classify.py

@@ -1,206 +1,8 @@
-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
+from .gui import MainApp
 
-try:
-    ctypes.windll.shcore.SetProcessDpiAwareness(True)
-except AttributeError:
-    pass
-
-from .logger import log_function_call
-from .settings import set_default_train_test_model
-from .gui_utils import ScrollableFrame, StdoutRedirector, CustomButton, set_dark_style, set_default_font, generate_fields, process_stdout_stderr, clear_canvas, main_thread_update_function, convert_settings_dict_for_gui
-from .gui_utils import check_classify_gui_settings, train_test_model_wrapper, read_settings_from_csv, update_settings_from_csv, set_dark_style, 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)
-    settings = set_default_train_test_model({})
-    variables = convert_settings_dict_for_gui(settings)
-    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)
-    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()
-
-    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:
-            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='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, bg='black')
-    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)
-    settings = set_default_train_test_model({})
-    variables = convert_settings_dict_for_gui(settings)
-    vars_dict = generate_fields(variables, scrollable_frame)
-
-    # Button section
-    btn_row = 1
-    run_button = CustomButton(scrollable_frame.scrollable_frame, text="Run", command=lambda: start_process(q, fig_queue), font=('Helvetica', 10))
-    run_button.grid(row=btn_row, 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=btn_row, column=1, pady=20, padx=20)
-    btn_row += 1
-    import_btn = CustomButton(scrollable_frame.scrollable_frame, text="Import", command=lambda: import_settings(scrollable_frame), font=('Helvetica', 10))
-    import_btn.grid(row=btn_row, column=0, pady=20, padx=20)
-    btn_row += 1
-    progress_label = ttk.Label(scrollable_frame.scrollable_frame, text="Processing: 0%", background="black", foreground="white") # Create progress field
-    progress_label.grid(row=btn_row, 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()
-
-    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()
+def start_classify_app():
+    app = MainApp(default_app="Classify")
+    app.mainloop()
 
 if __name__ == "__main__":
-    gui_classify()
+    start_classify_app()

spacr/app_make_masks.py

@@ -13,7 +13,7 @@ from ttkthemes import ThemedTk
 
 from .logger import log_function_call
 
-from .gui_utils import ScrollableFrame, CustomButton, set_dark_style, set_default_font, set_dark_style, create_menu_bar
+from .gui_utils import ScrollableFrame, CustomButton, set_dark_style, create_menu_bar, set_default_font
 
 class modify_masks:
 

spacr/app_make_masks_v2.py

@@ -13,7 +13,7 @@ from ttkthemes import ThemedTk
 from pyqtgraph import GraphicsLayoutWidget, ViewBox, ImageItem, mkQApp
 
 from .logger import log_function_call
-from .gui_utils import ScrollableFrame, CustomButton, set_dark_style, set_default_font, create_dark_mode, set_dark_style, create_menu_bar
+from .gui_utils import ScrollableFrame, CustomButton, set_dark_style, create_dark_mode, create_menu_bar, set_default_font
 
 class ModifyMasks:
     def __init__(self, root, folder_path, scale_factor):
@@ -635,7 +635,7 @@ def initiate_mask_app_root(width, height):
     root = ThemedTk(theme=theme)
     style = ttk.Style(root)
     set_dark_style(style)
-    set_default_font(root, font_name="Arial", size=8)
+    #set_default_font(root, font_name="Arial", size=8)
     root.geometry(f"{width}x{height}")
     root.title("Mask App")
     create_menu_bar(root)

spacr/app_mask.py

@@ -1,253 +1,8 @@
-#import customtkinter as ctk
+from .gui import MainApp
 
-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 .settings import set_default_settings_preprocess_generate_masks
-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, set_dark_style, convert_settings_dict_for_gui
-from .gui_utils import 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','fps','timelapse_displacement','timelapse_memory','timelapse_frame_limits','timelapse_remove_transient','timelapse_mode','timelapse_objects']
-    misc_settings = ['all_to_mip','pick_slice','skip_mode','upscale','upscale_factor','adjust_cells','lower_percentile','filter','merge_pathogens','pathogen_model']
-    opperational_settings = ['examples_to_plot','normalize_plots','normalize','cmap','figuresize','plot','pathogen_FT','cell_FT','nucleus_FT','nucleus_CP_prob','nucleus_Signal_to_noise','nucleus_background','cell_CP_prob','cell_Signal_to_noise','cell_background','pathogen_CP_prob','pathogen_Signal_to_noise','pathogen_background','remove_background_pathogen','remove_background_nucleus','remove_background_cell','verbose','randomize','workers','metadata_type','custom_regex','test_images','batch_size','save','masks','preprocess']
-    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)
-    settings = set_default_settings_preprocess_generate_masks({})
-    variables = convert_settings_dict_for_gui(settings)
-    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)
-    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, bg='black')
-    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", background="black", foreground="white")
-    settings_label.grid(row=0, column=0, pady=10, padx=10)
-    scrollable_frame = ScrollableFrame(settings_frame, bg='black')
-    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=4, column=0, pady=10, padx=10)
-    settings = set_default_settings_preprocess_generate_masks({})
-    variables = convert_settings_dict_for_gui(settings)
-    vars_dict = generate_fields(variables, scrollable_frame)
-    toggle_advanced_settings()
-    vars_dict['Test mode'] = (None, None, tk.BooleanVar(value=False))
-
-    # Button section
-    btn_row = 1
-    run_button = CustomButton(scrollable_frame.scrollable_frame, text="Run", command=lambda: start_process(q, fig_queue))
-    run_button.grid(row=btn_row, column=0, pady=5, padx=5)
-    abort_button = CustomButton(scrollable_frame.scrollable_frame, text="Abort", command=initiate_abort, font=('Helvetica', 10))
-    abort_button.grid(row=btn_row, column=1, pady=5, padx=5)
-    btn_row += 1
-    test_mode_button = CustomButton(scrollable_frame.scrollable_frame, text="Test", command=toggle_test_mode, font=('Helvetica', 10))
-    test_mode_button.grid(row=btn_row, column=0, pady=5, padx=5)
-    import_btn = CustomButton(scrollable_frame.scrollable_frame, text="Import", command=lambda: import_settings(scrollable_frame), font=('Helvetica', 10))
-    import_btn.grid(row=btn_row, column=1, pady=5, padx=5)
-    btn_row += 1
-    progress_label = ttk.Label(scrollable_frame.scrollable_frame, text="Processing: 0%", background="black", foreground="white")
-    progress_label.grid(row=btn_row, 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()
+def start_mask_app():
+    app = MainApp(default_app="Mask")
+    app.mainloop()
 
 if __name__ == "__main__":
-    gui_mask()
+    start_mask_app()