spacr 0.2.31__py3-none-any.whl → 0.2.41__py3-none-any.whl

spacr/gui_core.py

@@ -11,6 +11,13 @@ from matplotlib.figure import Figure
 from matplotlib.backends.backend_tkagg import FigureCanvasTkAgg
 from huggingface_hub import list_repo_files
 import numpy as np
+
+import psutil, gpustat
+import GPUtil
+from threading import Thread
+from time import sleep
+
+
 try:
     ctypes.windll.shcore.SetProcessDpiAwareness(True)
 except AttributeError:
@@ -470,13 +477,12 @@ def download_dataset(repo_id, subfolder, local_dir=None, retries=5, delay=5):
 
     raise Exception("Failed to download files after multiple attempts.")
 
-def setup_button_section(horizontal_container, settings_type='mask', window_dimensions=[500, 1000], run=True, abort=True, download=True, import_btn=True):
-    global button_frame, button_scrollable_frame, run_button, abort_button, download_dataset_button, import_button, q, fig_queue, vars_dict, progress_bar
-    from .settings import descriptions
 
-    width = (window_dimensions[0]) // 8
-    height = window_dimensions[1]
 
+def setup_button_section(horizontal_container, settings_type='mask', run=True, abort=True, download=True, import_btn=True):
+    global button_frame, button_scrollable_frame, run_button, abort_button, download_dataset_button, import_button, q, fig_queue, vars_dict, progress_bar
+    from .gui_utils import set_element_size
+    size_dict = set_element_size(horizontal_container)
     button_frame = tk.Frame(horizontal_container)
     horizontal_container.add(button_frame, stretch="always", sticky="nsew")
     button_frame.grid_rowconfigure(0, weight=0)
@@ -495,25 +501,25 @@ def setup_button_section(horizontal_container, settings_type='mask', window_dime
 
     if run:
         print(f'settings_type: {settings_type}')
-        run_button = spacrButton(button_scrollable_frame.scrollable_frame, text="run", command=lambda: start_process(q, fig_queue, settings_type))
+        run_button = spacrButton(button_scrollable_frame.scrollable_frame, text="run", command=lambda: start_process(q, fig_queue, settings_type), show_text=False, size=size_dict['btn_size'])
         run_button.grid(row=btn_row, column=btn_col, pady=5, padx=5, sticky='ew')
         widgets.append(run_button)
         btn_row += 1
 
     if abort and settings_type in ['mask', 'measure', 'classify', 'sequencing', 'umap']:
-        abort_button = spacrButton(button_scrollable_frame.scrollable_frame, text="abort", command=initiate_abort)
+        abort_button = spacrButton(button_scrollable_frame.scrollable_frame, text="abort", command=initiate_abort, show_text=False, size=size_dict['btn_size'])
         abort_button.grid(row=btn_row, column=btn_col, pady=5, padx=5, sticky='ew')
         widgets.append(abort_button)
         btn_row += 1
 
     if download and settings_type in ['mask']:
-        download_dataset_button = spacrButton(button_scrollable_frame.scrollable_frame, text="download", command=download_hug_dataset)
+        download_dataset_button = spacrButton(button_scrollable_frame.scrollable_frame, text="download", command=download_hug_dataset, show_text=False, size=size_dict['btn_size'])
         download_dataset_button.grid(row=btn_row, column=btn_col, pady=5, padx=5, sticky='ew')
         widgets.append(download_dataset_button)
         btn_row += 1
 
     if import_btn:
-        import_button = spacrButton(button_scrollable_frame.scrollable_frame, text="settings", command=lambda: import_settings(settings_type))
+        import_button = spacrButton(button_scrollable_frame.scrollable_frame, text="settings", command=lambda: import_settings(settings_type),show_text=False, size=size_dict['btn_size'])
         import_button.grid(row=btn_row, column=btn_col, pady=5, padx=5, sticky='ew')
         widgets.append(import_button)
         btn_row += 1
@@ -526,30 +532,44 @@ def setup_button_section(horizontal_container, settings_type='mask', window_dime
     if vars_dict is not None:
         toggle_settings(button_scrollable_frame)
 
+    style = ttk.Style(horizontal_container)
+    _ = set_dark_style(style, containers=[button_frame], widgets=widgets)
+
+    return button_scrollable_frame
+
+def setup_help_section(horizontal_container, settings_type='mask'):
+    from .settings import descriptions
+
     description_frame = tk.Frame(horizontal_container)
     horizontal_container.add(description_frame, stretch="always", sticky="nsew")
     description_frame.grid_columnconfigure(0, weight=1)
-    description_frame.grid_rowconfigure(0, weight=1)  # Add this line to make the row expandable
+    description_frame.grid_rowconfigure(1, weight=1)  # Ensure the text widget row is expandable
+
+    description_label = spacrLabel(description_frame, text=f"{settings_type} Module", anchor='center', justify='center', align="center")
+    description_label.grid(row=0, column=0, pady=10, padx=10, sticky='ew')
+
+    # Set background color directly
+    style_out = set_dark_style(ttk.Style())
+    bg_color = style_out['bg_color']
+    fg_color = style_out['fg_color']
+
+    description_text_widget = tk.Text(description_frame, wrap="word", bg=bg_color, fg=fg_color)
+    description_text_widget.grid(row=1, column=0, sticky="nsew")
 
-    description_label = tk.Label(description_frame, text="Module Description", anchor='nw', justify='left', wraplength=width - 50)
-    description_label.grid(row=0, column=0, pady=50, padx=20, sticky='nsew')
     description_text = descriptions.get(settings_type, "No description available for this module.")
-    description_label.config(text=description_text)
+    description_text_widget.insert("1.0", description_text)
+    description_text_widget.config(state="disabled")  # Make the text widget read-only
 
     def update_wraplength(event):
-        new_width = event.width - 40  # Adjust as needed
-        description_label.config(wraplength=new_width)
+        new_width = event.width - 20  # Adjust as needed
+        description_text_widget.config(width=new_width)
 
-    description_label.bind('<Configure>', update_wraplength)
-
-    containers = [button_frame, description_frame]
-    widgets.extend([description_label])
+    description_text_widget.bind('<Configure>', update_wraplength)
 
     style = ttk.Style(horizontal_container)
-    _ = set_dark_style(style, containers=containers, widgets=widgets)
-
-    return button_scrollable_frame
+    _ = set_dark_style(style, containers=[description_frame], widgets=[description_label, description_text_widget])
 
+    return description_frame
 
 def hide_all_settings(vars_dict, categories):
     """
@@ -707,8 +727,8 @@ def process_console_queue():
     after_id = console_output.after(100, process_console_queue)
     parent_frame.after_tasks.append(after_id)
 
-def set_globals(q_var, console_output_var, parent_frame_var, vars_dict_var, canvas_var, canvas_widget_var, scrollable_frame_var, fig_queue_var, progress_bar_var):
-    global q, console_output, parent_frame, vars_dict, canvas, canvas_widget, scrollable_frame, fig_queue, progress_bar
+def set_globals(q_var, console_output_var, parent_frame_var, vars_dict_var, canvas_var, canvas_widget_var, scrollable_frame_var, fig_queue_var, progress_bar_var, usage_bars_var):
+    global q, console_output, parent_frame, vars_dict, canvas, canvas_widget, scrollable_frame, fig_queue, progress_bar, usage_bars
     q = q_var
     console_output = console_output_var
     parent_frame = parent_frame_var
@@ -718,6 +738,7 @@ def set_globals(q_var, console_output_var, parent_frame_var, vars_dict_var, canv
     scrollable_frame = scrollable_frame_var
     fig_queue = fig_queue_var
     progress_bar = progress_bar_var
+    usage_bars = usage_bars_var
 
 def create_containers(parent_frame):
     vertical_container = tk.PanedWindow(parent_frame, orient=tk.VERTICAL)
@@ -744,6 +765,165 @@ def setup_frame(parent_frame):
     
     return parent_frame, vertical_container, horizontal_container
 
+def setup_usage_panel(horizontal_container):
+    global usage_bars
+    from .gui_utils import set_element_size
+
+    def update_usage(ram_bar, vram_bar, gpu_bar, usage_bars, parent_frame):
+        # Update RAM usage
+        ram_usage = psutil.virtual_memory().percent
+        ram_bar['value'] = ram_usage
+
+        # Update GPU and VRAM usage
+        gpus = GPUtil.getGPUs()
+        if gpus:
+            gpu = gpus[0]
+            vram_usage = gpu.memoryUtil * 100
+            gpu_usage = gpu.load * 100
+            vram_bar['value'] = vram_usage
+            gpu_bar['value'] = gpu_usage
+
+        # Update CPU usage for each core
+        cpu_percentages = psutil.cpu_percent(percpu=True)
+        for bar, usage in zip(usage_bars[3:], cpu_percentages):
+            bar['value'] = usage
+
+        # Schedule the function to run again after 1000 ms (1 second)
+        parent_frame.after(1000, update_usage, ram_bar, vram_bar, gpu_bar, usage_bars, parent_frame)
+
+    size_dict = set_element_size(horizontal_container)
+    print(size_dict)
+
+    usage_frame = tk.Frame(horizontal_container)
+    horizontal_container.add(usage_frame, stretch="always", sticky="nsew")
+    usage_frame.grid_rowconfigure(0, weight=0)
+    usage_frame.grid_rowconfigure(1, weight=1)
+    usage_frame.grid_columnconfigure(0, weight=1)
+    usage_frame.grid_columnconfigure(1, weight=1)
+
+    usage_label = spacrLabel(usage_frame, text="Hardware Stats", anchor='center', justify='center', align="center")
+    usage_label.grid(row=0, column=0, pady=10, padx=10, columnspan=2)
+    
+    usage_scrollable_frame = spacrFrame(usage_frame)
+    usage_scrollable_frame.grid(row=1, column=0, sticky="nsew", columnspan=2)
+    widgets = [usage_label, usage_scrollable_frame.scrollable_frame]
+    usage_bars = []
+    max_elements_per_column = 12
+    row = 0
+    col = 0
+
+    # Initialize RAM, VRAM, and GPU bars as None
+    ram_bar, vram_bar, gpu_bar = None, None, None
+
+    # Try adding RAM bar
+    try:
+        ram_info = psutil.virtual_memory()
+        ram_label_text = f"RAM"
+        label = ttk.Label(usage_scrollable_frame.scrollable_frame, text=ram_label_text, anchor='w')
+        label.grid(row=row, column=2 * col, pady=5, padx=5, sticky='w')
+        ram_bar = spacrProgressBar(usage_scrollable_frame.scrollable_frame, orient='horizontal', mode='determinate', length=size_dict['bar_size'], label=False)
+        ram_bar.grid(row=row, column=2 * col + 1, pady=5, padx=5, sticky='ew')
+        widgets.append(label)
+        widgets.append(ram_bar)
+        usage_bars.append(ram_bar)
+        row += 1
+    except Exception as e:
+        print(f"Could not add RAM usage bar: {e}")
+
+    # Try adding VRAM and GPU usage bars
+    try:
+        gpus = GPUtil.getGPUs()
+        if gpus:
+            gpu = gpus[0]
+            vram_label_text = f"VRAM"
+            label = ttk.Label(usage_scrollable_frame.scrollable_frame, text=vram_label_text, anchor='w')
+            label.grid(row=row, column=2 * col, pady=5, padx=5, sticky='w')
+            vram_bar = spacrProgressBar(usage_scrollable_frame.scrollable_frame, orient='horizontal', mode='determinate', length=size_dict['bar_size'], label=False)
+            vram_bar.grid(row=row, column=2 * col + 1, pady=5, padx=5, sticky='ew')
+            widgets.append(label)
+            widgets.append(vram_bar)
+            usage_bars.append(vram_bar)
+            row += 1
+
+            gpu_label_text = f"GPU"
+            label = ttk.Label(usage_scrollable_frame.scrollable_frame, text=gpu_label_text, anchor='w')
+            label.grid(row=row, column=2 * col, pady=5, padx=5, sticky='w')
+            gpu_bar = spacrProgressBar(usage_scrollable_frame.scrollable_frame, orient='horizontal', mode='determinate', length=size_dict['bar_size'], label=False)
+            gpu_bar.grid(row=row, column=2 * col + 1, pady=5, padx=5, sticky='ew')
+            widgets.append(label)
+            widgets.append(gpu_bar)
+            usage_bars.append(gpu_bar)
+            row += 1
+    except Exception as e:
+        print(f"Could not add VRAM or GPU usage bars: {e}")
+
+    # Add CPU core usage bars
+    try:
+        cpu_cores = psutil.cpu_count(logical=True)
+        cpu_freq = psutil.cpu_freq()
+        
+        for core in range(cpu_cores):
+            if row > 0 and row % max_elements_per_column == 0:
+                col += 1
+                row = 0
+            label = ttk.Label(usage_scrollable_frame.scrollable_frame, text=f"Core {core+1}", anchor='w')
+            label.grid(row=row, column=2 * col, pady=2, padx=5, sticky='w')
+            bar = spacrProgressBar(usage_scrollable_frame.scrollable_frame, orient='horizontal', mode='determinate', length=size_dict['bar_size'], label=False)
+            bar.grid(row=row, column=2 * col + 1, pady=2, padx=5, sticky='ew')
+            widgets.append(label)
+            widgets.append(bar)
+            usage_bars.append(bar)
+            row += 1
+    except Exception as e:
+        print(f"Could not add CPU core usage bars: {e}")
+
+    # Adding the text box for hardware information
+    #hardware_frame = tk.Frame(horizontal_container)
+    #horizontal_container.add(hardware_frame, stretch="always", sticky="nsew")
+    #hardware_frame.grid_columnconfigure(0, weight=1)
+
+    #hardware_info = tk.Text(hardware_frame, height=1, wrap='none', bg='black', fg='white', bd=0)
+    #hardware_info.grid(row=0, column=0, pady=10, padx=5, sticky='ew')
+
+    #hardware_text = ""
+    #try:
+    #    ram_info = psutil.virtual_memory()
+    #    hardware_text += f"RAM: {ram_info.total / (1024 ** 3):.1f} GB  "
+    #except Exception as e:
+    #    hardware_text += f"RAM: Could not retrieve ({e})  "
+
+    #try:
+    #    gpus = GPUtil.getGPUs()
+    #    if gpus:
+    #        gpu = gpus[0]
+    #        hardware_text += f"VRAM: {gpu.memoryTotal / 1024:.1f} GB  "
+    #        hardware_text += f"GPU: {gpu.name}  "
+    #except Exception as e:
+    #    hardware_text += f"VRAM and GPU: Could not retrieve ({e})  "
+
+    #try:
+    #    if cpu_freq:
+    #        hardware_text += f"CPU Max Clock Speed: {cpu_freq.max / 1000:.0f} GHz"
+    #except Exception as e:
+    #    hardware_text += f"CPU Max Clock Speed: Could not retrieve ({e})"
+
+    #hardware_info.insert(tk.END, hardware_text)
+    #hardware_info.configure(state='disabled')
+    #widgets.append(hardware_info)
+
+    style = ttk.Style(horizontal_container)
+    _ = set_dark_style(style, containers=[usage_frame], widgets=widgets) # hardware_frame
+
+    if ram_bar is None:
+        ram_bar = spacrProgressBar(usage_scrollable_frame.scrollable_frame, orient='horizontal', mode='determinate', length=size_dict['bar_size'], label=False)
+    if vram_bar is None:
+        vram_bar = spacrProgressBar(usage_scrollable_frame.scrollable_frame, orient='horizontal', mode='determinate', length=size_dict['bar_size'], label=False)
+    if gpu_bar is None:
+        gpu_bar = spacrProgressBar(usage_scrollable_frame.scrollable_frame, orient='horizontal', mode='determinate', length=size_dict['bar_size'], label=False)
+
+    update_usage(ram_bar, vram_bar, gpu_bar, usage_bars, usage_frame)
+    return usage_scrollable_frame, usage_bars
+
 def initiate_root(parent, settings_type='mask'):
     global q, fig_queue, parent_frame, scrollable_frame, button_frame, vars_dict, canvas, canvas_widget, button_scrollable_frame, progress_bar
     from .gui_utils import main_thread_update_function
@@ -780,11 +960,15 @@ def initiate_root(parent, settings_type='mask'):
         initiate_make_mask_app(horizontal_container)
     else:
         scrollable_frame, vars_dict = setup_settings_panel(horizontal_container, settings_type, window_dimensions=dims)
-        button_scrollable_frame = setup_button_section(horizontal_container, settings_type, window_dimensions=dims)
+        button_scrollable_frame = setup_button_section(horizontal_container, settings_type)
+
+        _, usage_bars = setup_usage_panel(horizontal_container)
+        _ = setup_help_section(horizontal_container, settings_type)
+
         canvas, canvas_widget = setup_plot_section(vertical_container)
         console_output = setup_console(vertical_container)
 
-        set_globals(q, console_output, parent_frame, vars_dict, canvas, canvas_widget, scrollable_frame, fig_queue, progress_bar)
+        set_globals(q, console_output, parent_frame, vars_dict, canvas, canvas_widget, scrollable_frame, fig_queue, progress_bar, usage_bars)
         process_console_queue()
         process_fig_queue()
         after_id = parent_frame.after(100, lambda: main_thread_update_function(parent_frame, q, fig_queue, canvas_widget))

spacr/gui_elements.py

@@ -1,4 +1,4 @@
-import os, threading, time, sqlite3
+import os, threading, time, sqlite3, webbrowser
 import tkinter as tk
 from tkinter import ttk
 import tkinter.font as tkFont
@@ -47,29 +47,11 @@ def set_dark_style(style, parent_frame=None, containers=None, widgets=None, font
     style.configure('TEntry', padding=padding)
     style.configure('Spacr.TEntry', padding=padding)
     style.configure('Custom.TLabel', padding=padding)
-    #style.configure('Spacr.TCheckbutton', padding=padding)
     style.configure('TButton', padding=padding)
-
     style.configure('TFrame', background=bg_color)
     style.configure('TPanedwindow', background=bg_color)
     style.configure('TLabel', background=bg_color, foreground=fg_color, font=font_style)
 
-
-    #style.configure('Custom.TLabel', padding='5 5 5 5', borderwidth=1, relief='flat', background=bg_color, foreground=fg_color, font=font_style)
-    #style.configure('Spacr.TCheckbutton', background=bg_color, foreground=fg_color, indicatoron=False, relief='flat', font="15")
-    #style.map('Spacr.TCheckbutton', background=[('selected', bg_color), ('active', bg_color)], foreground=[('selected', fg_color), ('active', fg_color)])
-    
-
-    #style.configure('TNotebook', background=bg_color, tabmargins=[2, 5, 2, 0])
-    #style.configure('TNotebook.Tab', background=bg_color, foreground=fg_color, padding=[5, 5], font=font_style)
-    #style.map('TNotebook.Tab', background=[('selected', active_color), ('active', active_color)], foreground=[('selected', fg_color), ('active', fg_color)])
-    #style.configure('TButton', background=bg_color, foreground=fg_color, padding='5 5 5 5', font=font_style)
-    #style.map('TButton', background=[('active', active_color), ('disabled', inactive_color)])
-    #style.configure('Vertical.TScrollbar', background=bg_color, troughcolor=bg_color, bordercolor=bg_color)
-    #style.configure('Horizontal.TScrollbar', background=bg_color, troughcolor=bg_color, bordercolor=bg_color)
-    #style.configure('Custom.TLabelFrame', font=(font_family, font_size, 'bold'), background=bg_color, foreground='white', relief='solid', borderwidth=1)
-    #style.configure('Custom.TLabelFrame.Label', background=bg_color, foreground='white', font=(font_family, font_size, 'bold'))
-
     if parent_frame:
         parent_frame.configure(bg=bg_color)
         parent_frame.grid_rowconfigure(0, weight=1)
@@ -363,12 +345,12 @@ class spacrCheckbutton(ttk.Checkbutton):
         _ = set_dark_style(style, widgets=[self])
 
 class spacrProgressBar(ttk.Progressbar):
-    def __init__(self, parent, *args, **kwargs):
+    def __init__(self, parent, label=True, *args, **kwargs):
         super().__init__(parent, *args, **kwargs)
 
         # Get the style colors
         style_out = set_dark_style(ttk.Style())
-       
+
         self.fg_color = style_out['fg_color']
         self.bg_color = style_out['bg_color']
         self.active_color = style_out['active_color']
@@ -389,28 +371,33 @@ class spacrProgressBar(ttk.Progressbar):
         # Set initial value to 0
         self['value'] = 0
 
-        # Create the progress label
-        self.progress_label = tk.Label(parent, text="Processing: 0/0", anchor='w', justify='left', bg=self.inactive_color, fg=self.fg_color)
-        self.progress_label.grid(row=1, column=0, columnspan=2, pady=5, padx=5, sticky='ew')
+        # Track whether to show the progress label
+        self.label = label
+
+        if self.label:
+            # Create the progress label
+            self.progress_label = tk.Label(parent, text="Processing: 0/0", anchor='w', justify='left', bg=self.inactive_color, fg=self.fg_color)
+            self.progress_label.grid(row=1, column=0, columnspan=2, pady=5, padx=5, sticky='ew')
 
-        # Initialize attributes for time and operation
-        self.operation_type = None
-        self.time_image = None
-        self.time_batch = None
-        self.time_left = None
+            # Initialize attributes for time and operation
+            self.operation_type = None
+            self.time_image = None
+            self.time_batch = None
+            self.time_left = None
 
     def update_label(self):
-        # Update the progress label with current progress and additional info
-        label_text = f"Processing: {self['value']}/{self['maximum']}"
-        if self.operation_type:
-            label_text += f", {self.operation_type}"
-        if self.time_image:
-            label_text += f", Time/image: {self.time_image:.3f} sec"
-        if self.time_batch:
-            label_text += f", Time/batch: {self.time_batch:.3f} sec"
-        if self.time_left:
-            label_text += f", Time_left: {self.time_left:.3f} min"
-        self.progress_label.config(text=label_text)
+        if self.label:
+            # Update the progress label with current progress and additional info
+            label_text = f"Processing: {self['value']}/{self['maximum']}"
+            if self.operation_type:
+                label_text += f", {self.operation_type}"
+            if self.time_image:
+                label_text += f", Time/image: {self.time_image:.3f} sec"
+            if self.time_batch:
+                label_text += f", Time/batch: {self.time_batch:.3f} sec"
+            if self.time_left:
+                label_text += f", Time_left: {self.time_left:.3f} min"
+            self.progress_label.config(text=label_text)
 
 class spacrFrame(ttk.Frame):
     def __init__(self, container, width=None, *args, bg='black', **kwargs):
@@ -1591,14 +1578,14 @@ class AnnotateApp:
         self.db_path = db_path
         self.src = src
         self.index = 0
-        
+
         if isinstance(image_size, list):
             self.image_size = (int(image_size[0]), int(image_size[0]))
         elif isinstance(image_size, int):
             self.image_size = (image_size, image_size)
         else:
             raise ValueError("Invalid image size")
-        
+
         self.annotation_column = annotation_column
         self.image_type = image_type
         self.channels = channels
@@ -1613,8 +1600,6 @@ class AnnotateApp:
         self.measurement = measurement
         self.threshold = threshold
 
-        print('self.image_size', self.image_size)
-
         style_out = set_dark_style(ttk.Style())
         self.root.configure(bg=style_out['inactive_color'])
 
@@ -1662,8 +1647,10 @@ class AnnotateApp:
         self.root.grid_columnconfigure(0, weight=1)
         self.root.grid_columnconfigure(1, weight=1)
 
-        self.grid_frame.grid_rowconfigure(0, weight=1)
-        self.grid_frame.grid_columnconfigure(0, weight=1)
+        for row in range(self.grid_rows):
+            self.grid_frame.grid_rowconfigure(row, weight=1)
+        for col in range(self.grid_cols):
+            self.grid_frame.grid_columnconfigure(col, weight=1)
 
     def calculate_grid_dimensions(self):
         window_width = self.root.winfo_width()
@@ -1945,11 +1932,14 @@ class AnnotateApp:
     def shutdown(self):
         self.terminate = True
         self.update_queue.put(self.pending_updates.copy())
-        self.pending_updates.clear()
-        self.db_update_thread.join()
-        self.root.quit()
-        self.root.destroy()
-        print(f'Quit application')
+        if not self.pending_updates:
+            self.pending_updates.clear()
+            self.db_update_thread.join()
+            self.root.quit()
+            self.root.destroy()
+            print(f'Quit application')
+        else:
+            print('Waiting for pending updates to finish before quitting')
 
 def create_menu_bar(root):
     from .gui import initiate_root
@@ -1987,6 +1977,7 @@ def create_menu_bar(root):
 
     # Add a separator and an exit option
     app_menu.add_separator()
+    app_menu.add_command(label="Help", command=lambda: webbrowser.open("https://readthedocs.org/projects/spacr/badge/?version=latest"))
     app_menu.add_command(label="Exit", command=root.quit)
 
     # Configure the menu for the root window

spacr/gui_utils.py

@@ -349,4 +349,14 @@ def annotate_with_image_refs(settings, root, shutdown_callback):
     # Call load_images after setting up the root window
     app.load_images()
 
+def set_element_size(widget):
+    screen_width = widget.winfo_screenwidth()
+    screen_height = widget.winfo_screenheight()
+    btn_size = screen_width/50
+    bar_size = screen_width/75
+
+    size_dict = {'btn_size':btn_size,
+                 'bar_size':bar_size}
+    return size_dict
+
 

spacr/measure.py

@@ -941,14 +941,11 @@ def measure_crop(settings):
     settings = get_measure_crop_settings(settings)
     settings = measure_test_mode(settings)
 
-    #src_fldr = settings['src']
-    #if not os.path.basename(src_fldr).endswith('merged'):
-    #    settings['src'] = os.path.join(src_fldr, 'merged')
-    #    print(f"changed src to {src_fldr}")
-
-    #if not os.path.exists(settings['src']):
-    #    print(f'src: {settings["src"]} does not exist')
-    #    return
+    src_fldr = settings['src']
+    if not os.path.basename(src_fldr).endswith('merged'):
+        print(f"WARNING: Source folder, settings: src: {src_fldr} should end with 'merged'")
+        src_fldr = os.path.join(src_fldr, 'merged')
+        print(f"Changed source folder to: {src_fldr}")
     
     if settings['cell_mask_dim'] is None:
         settings['include_uninfected'] = True
@@ -1009,7 +1006,7 @@ def measure_crop(settings):
                 time.sleep(1)
                 files_processed = len(time_ls)
                 files_to_process = len(files)
-                print_progress(files_processed, files_to_process, n_jobs, time_ls=None)
+                print_progress(files_processed, files_to_process, n_jobs, time_ls=time_ls, operation_type='Measure and Crop')
             result.get()
 
     if settings['representative_images']:

spacr/settings.py

@@ -1114,7 +1114,9 @@ categories = {
 }
 
 descriptions = {
-    'mask': "Generate Cellpose masks for Cells, Nuclei, and Pathogens. Function: preprocess_generate_masks from spacr.core.\n\nKey Features:\n- Automated Mask Generation: Automatically generate accurate masks for various cellular components using Cellpose, a robust deep learning model for cell segmentation.\n- Versatility: Capable of handling different types of biological samples, including cells, nuclei, and pathogens.\n- Integration: Directly integrates with other modules, providing the foundational masks required for subsequent analysis.",
+    'mask': "\n\nHelp:\n- Generate Cells, Nuclei, Pathogens, and Cytoplasm masks from intensity images in src.\n- To ensure that spacr is installed correctly:\n- 1. Downloade the training set (click Download).\n- 2. Import settings (click settings navigate to downloaded dataset settings folder and import preprocess_generate_masks_settings.csv).\n- 3. Run the module.\n- 4. Proceed to the Measure module (click Measure in the menue bar).\n- For further help, click the Help button in the menue bar.",
+
+     #'mask': "Help. Generate masks for Cells, Nuclei, and Pathogens . Function: preprocess_generate_masks from spacr.core.\n\nKey Features:\n- Automated Mask Generation: Automatically generate accurate masks for various cellular components using Cellpose, a robust deep learning model for cell segmentation.\n- Versatility: Capable of handling different types of biological samples, including cells, nuclei, and pathogens.\n- Integration: Directly integrates with other modules, providing the foundational masks required for subsequent analysis.",
     
     'measure': "Capture Measurements from Cells, Nuclei, Pathogens, and Cytoplasm objects. Generate single object PNG images for one or several objects. (Requires masks from the Mask module). Function: measure_crop from spacr.measure.\n\nKey Features:\n- Comprehensive Measurement Capture: Obtain detailed measurements for various cellular components, including area, perimeter, intensity, and more.\n- Image Generation: Create high-resolution PNG images of individual objects, facilitating further analysis and visualization.\n- Mask Dependency: Requires accurate masks generated by the Mask module to ensure precise measurements.",
     

{spacr-0.2.31.dist-info → spacr-0.2.41.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: spacr
-Version: 0.2.31
+Version: 0.2.41
 Summary: Spatial phenotype analysis of crisp screens (SpaCr)
 Home-page: https://github.com/EinarOlafsson/spacr
 Author: Einar Birnir Olafsson
@@ -39,6 +39,9 @@ Requires-Dist: ttf-opensans >=2020.10.30
 Requires-Dist: customtkinter <6.0,>=5.2.2
 Requires-Dist: biopython <2.0,>=1.80
 Requires-Dist: lxml <6.0,>=5.1.0
+Requires-Dist: psutil <6.0,>=5.9.8
+Requires-Dist: gputil <2.0,>=1.4.0
+Requires-Dist: gpustat <2.0,>=1.1.1
 Requires-Dist: huggingface-hub <0.25,>=0.24.0
 Provides-Extra: dev
 Requires-Dist: pytest <3.11,>=3.9 ; extra == 'dev'

{spacr-0.2.31.dist-info → spacr-0.2.41.dist-info}/RECORD

@@ -12,15 +12,15 @@ spacr/core.py,sha256=iAH6de2dW0nKVtVeBjdWOhSW_KoHlVDVOoOsHb6vGC0,148884
 spacr/deep_spacr.py,sha256=ASBsN4JpHp_3S-91JUsB34IWTjTGPYI7jKV2qZnUR5M,37005
 spacr/graph_learning.py,sha256=1tR-ZxvXE3dBz1Saw7BeVFcrsUFu9OlUZeZVifih9eo,13070
 spacr/gui.py,sha256=bA1Qy6D9aeL_Qe0Xeql8bRkbbFajAMGTZZR3uBzIW1Q,8495
-spacr/gui_core.py,sha256=4II8TscaDHDvRXc4D-azQyAeVGNkqyN6_HaNhkjij4s,35546
-spacr/gui_elements.py,sha256=XGM88u7acPO6ulRE4QJwD72-POcN-pKJhseRkJLELzo,96179
-spacr/gui_utils.py,sha256=ySSDDYmY80h_Wk2Nb1oxbugRU2TWt6N7BwusUl_-wRo,14970
+spacr/gui_core.py,sha256=X75_P1pUNiA2B2WAzG20xBqpBygxJ4UU8nPkyBwqBOo,43662
+spacr/gui_elements.py,sha256=XbawiE7JJkY4qRtBLENWQGtbKl7LWTzS7GlQASiXbLw,95149
+spacr/gui_utils.py,sha256=7kD1EB9hqpjoVszJuCcEu_2oSSX6UsTMGrKBT7LhK9A,15255
 spacr/io.py,sha256=Dehuqn_oGo0gcyezQIw9rUUvO7oOHDWuMkPDSCgyrp8,115521
 spacr/logger.py,sha256=7Zqr3TuuOQLWT32gYr2q1qvv7x0a2JhLANmZcnBXAW8,670
-spacr/measure.py,sha256=W5_yuLnsFSafuZNcKzVsCTJSTfpbNgrGTuxG1OVb0iU,55283
+spacr/measure.py,sha256=u7j3z8wJyDQt24vh0nUmrI7uS1hei_9p_zlmAwoT4zI,55295
 spacr/plot.py,sha256=DYJEoK1kz2ih6ZGvKiA3xTqeIeKQNhuQKwgrscopFxA,69101
 spacr/sequencing.py,sha256=fHZRnoMSxmhMdadkei3lUeBdckqFyptWdQyWsDW3aaU,83304
-spacr/settings.py,sha256=deX0pNwTqyHojpCTiF060RSK5oPeSEcS_s6UlVc0x3Q,65442
+spacr/settings.py,sha256=uUiWyeoXEFiybs4JgD0m8THdIQAVxyAA4wSqmpnuRCg,65945
 spacr/sim.py,sha256=FveaVgBi3eypO2oVB5Dx-v0CC1Ny7UPfXkJiiRRodAk,71212
 spacr/sim_app.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 spacr/timelapse.py,sha256=KMYCgHzf9LTZe-lWl5mvH2EjbKRE6OhpwdY13wEumGc,39504
@@ -50,9 +50,9 @@ spacr/resources/icons/umap.png,sha256=dOLF3DeLYy9k0nkUybiZMe1wzHQwLJFRmgccppw-8b
 spacr/resources/models/cp/toxo_plaque_cyto_e25000_X1120_Y1120.CP_model,sha256=z8BbHWZPRnE9D_BHO0fBREE85c1vkltDs-incs2ytXQ,26566572
 spacr/resources/models/cp/toxo_plaque_cyto_e25000_X1120_Y1120.CP_model_settings.csv,sha256=fBAGuL_B8ERVdVizO3BHozTDSbZUh1yFzsYK3wkQN68,420
 spacr/resources/models/cp/toxo_pv_lumen.CP_model,sha256=2y_CindYhmTvVwBH39SNILF3rI3x9SsRn6qrMxHy3l0,26562451
-spacr-0.2.31.dist-info/LICENSE,sha256=SR-2MeGc6SCM1UORJYyarSWY_A-JaOMFDj7ReSs9tRM,1083
-spacr-0.2.31.dist-info/METADATA,sha256=avO1ZcgZs-TVLFdCBmxznpwuIH0Cehk29AuUOmFeVKM,5050
-spacr-0.2.31.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
-spacr-0.2.31.dist-info/entry_points.txt,sha256=BMC0ql9aNNpv8lUZ8sgDLQMsqaVnX5L535gEhKUP5ho,296
-spacr-0.2.31.dist-info/top_level.txt,sha256=GJPU8FgwRXGzKeut6JopsSRY2R8T3i9lDgya42tLInY,6
-spacr-0.2.31.dist-info/RECORD,,
+spacr-0.2.41.dist-info/LICENSE,sha256=SR-2MeGc6SCM1UORJYyarSWY_A-JaOMFDj7ReSs9tRM,1083
+spacr-0.2.41.dist-info/METADATA,sha256=YxsBdTgoarr-fq8Dc7fH0KmZiHYT0e0c-slo7Gjclf0,5156
+spacr-0.2.41.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
+spacr-0.2.41.dist-info/entry_points.txt,sha256=BMC0ql9aNNpv8lUZ8sgDLQMsqaVnX5L535gEhKUP5ho,296
+spacr-0.2.41.dist-info/top_level.txt,sha256=GJPU8FgwRXGzKeut6JopsSRY2R8T3i9lDgya42tLInY,6
+spacr-0.2.41.dist-info/RECORD,,