spacr 0.2.1__py3-none-any.whl → 0.2.21__py3-none-any.whl

spacr/classify_app.py

@@ -1,201 +0,0 @@
-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
-
-try:
-    ctypes.windll.shcore.SetProcessDpiAwareness(True)
-except AttributeError:
-    pass
-
-from .logger import log_function_call
-from .gui_utils import ScrollableFrame, StdoutRedirector, CustomButton, set_dark_style, set_default_font, generate_fields, process_stdout_stderr, clear_canvas, main_thread_update_function
-from .gui_utils import classify_variables, check_classify_gui_settings, train_test_model_wrapper, read_settings_from_csv, update_settings_from_csv, style_text_boxes, 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)
-    variables = classify_variables()
-    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)
-    style_text_boxes(style)
-    set_default_font(parent_frame, font_name="Helvetica", size=8)
-
-    parent_frame.configure(bg='#333333')
-    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('#333333')
-                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='#333333')
-    vertical_container.add(settings_frame, stretch="always")
-    settings_label = ttk.Label(settings_frame, text="Settings", background="#333333", 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)
-
-    # Setup for user input fields (variables)
-    variables = classify_variables()
-    vars_dict = generate_fields(variables, scrollable_frame)
-
-    # Button section
-    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='#333333')
-    plot = figure.add_subplot(111)
-    plot.plot([], [])
-    plot.axis('off')
-    canvas = FigureCanvasTkAgg(figure, master=plot_frame)
-    canvas.get_tk_widget().configure(cursor='arrow', background='#333333', 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='#333333')
-    vertical_container.add(console_frame, stretch="always")
-    console_label = ttk.Label(console_frame, text="Console", background="#333333", foreground="white")
-    console_label.grid(row=0, column=0, pady=10, padx=10)
-    console_output = scrolledtext.ScrolledText(console_frame, height=10, bg='#333333', 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()
-
-if __name__ == "__main__":
-    gui_classify()

spacr/cli.py

@@ -1,41 +0,0 @@
-"""
-Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu and Michael Rariden.
-"""
-
-import argparse
-
-import argparse
-
-
-def get_arg_parser():
-    """ Parses command line arguments for spacr main functions
-
-    Note: this function has to be in a separate file to allow autodoc to work for CLI.
-    The autodoc_mock_imports in conf.py does not work for sphinx-argparse sometimes,
-    see https://github.com/ashb/sphinx-argparse/issues/9#issue-1097057823
-    """
-    
-    parser = argparse.ArgumentParser(description="SPACR Mask App Command Line Parameters")
-    hardware_args = parser.add_argument_group("Hardware Arguments")
-    input_img_args = parser.add_argument_group("Input Image Arguments")
-    #model_args = parser.add_argument_group("Model Arguments")
-    #algorithm_args = parser.add_argument_group("Algorithm Arguments")
-    #training_args = parser.add_argument_group("Training Arguments")
-    #output_args = parser.add_argument_group("Output Arguments")
-    
-    # misc settings
-    parser.add_argument("--version", action="store_true",
-                        help="show version info")
-    # misc settings
-    parser.add_argument("--headless", action="store_true",
-                        help="run the app without the gui")
-    
-    parser.add_argument("--verbose", action="store_true",
-                        help="show information about running and settings and save to log")
-    
-    hardware_args.add_argument("--gpu_device", required=False, default="0", type=str,
-                               help="which gpu device to use, use an integer for torch, or mps for M1")
-    
-    input_img_args.add_argument("--src", default=[], type=str,
-                                help="folder containing data to run or train on.")
-    return parser