spacr 0.2.45__tar.gz → 0.2.53__tar.gz

{spacr-0.2.45/spacr.egg-info → spacr-0.2.53}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: spacr
-Version: 0.2.45
+Version: 0.2.53
 Summary: Spatial phenotype analysis of crisp screens (SpaCr)
 Home-page: https://github.com/EinarOlafsson/spacr
 Author: Einar Birnir Olafsson
@@ -9,9 +9,9 @@ Classifier: Programming Language :: Python :: 3
 Classifier: License :: OSI Approved :: MIT License
 Classifier: Operating System :: OS Independent
 License-File: LICENSE
-Requires-Dist: torch<3.0,>=2.2.1
-Requires-Dist: torchvision<1.0,>=0.17.1
-Requires-Dist: torch-geometric<3.0,>=2.5.1
+Requires-Dist: torch<3.0,>=2.0
+Requires-Dist: torchvision<1.0,>=0.1
+Requires-Dist: torch-geometric<3.0,>=2.5
 Requires-Dist: numpy<2.0,>=1.26.4
 Requires-Dist: pandas<3.0,>=2.2.1
 Requires-Dist: statsmodels<1.0,>=0.14.1
@@ -42,6 +42,8 @@ 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: pyautogui<1.0,>=0.9.54
+Requires-Dist: tables<4.0,>=3.8.0
 Requires-Dist: huggingface-hub<0.25,>=0.24.0
 Provides-Extra: dev
 Requires-Dist: pytest<3.11,>=3.9; extra == "dev"

{spacr-0.2.45 → spacr-0.2.53}/setup.py

@@ -15,9 +15,9 @@ with open("README.rst", "r", encoding="utf-8") as fh:
     long_description = fh.read()
 
 dependencies = [
-    'torch>=2.2.1,<3.0',
-    'torchvision>=0.17.1,<1.0',
-    'torch-geometric>=2.5.1,<3.0',
+    'torch>=2.0,<3.0',
+    'torchvision>=0.1,<1.0',
+    'torch-geometric>=2.5,<3.0',
     'numpy>=1.26.4,<2.0',
     'pandas>=2.2.1,<3.0',
     'statsmodels>=0.14.1,<1.0',
@@ -48,12 +48,14 @@ dependencies = [
     'psutil>=5.9.8, <6.0',
     'gputil>=1.4.0, <2.0', 
     'gpustat>=1.1.1,<2.0',
+    'pyautogui>=0.9.54,<1.0',
+    'tables>=3.8.0,<4.0',
     'huggingface-hub>=0.24.0,<0.25'
 ]
 
 setup(
     name="spacr",
-    version="0.2.45",
+    version="0.2.53",
     author="Einar Birnir Olafsson",
     author_email="olafsson@med.umich.com",
     description="Spatial phenotype analysis of crisp screens (SpaCr)",
@@ -61,7 +63,7 @@ setup(
     url="https://github.com/EinarOlafsson/spacr",
     packages=find_packages(exclude=["tests.*", "tests"]),
     include_package_data=True,
-    package_data={'spacr': ['resources/models/cp/*', 'resources/icons/*'],},
+    package_data={'spacr': ['resources/models/cp/*', 'resources/icons/*', 'resources/font/**/*'],},
     install_requires=dependencies,
     entry_points={
         'console_scripts': [

{spacr-0.2.45 → spacr-0.2.53}/spacr/core.py

@@ -1729,20 +1729,43 @@ def preprocess_generate_masks(src, settings={}):
 
     if settings['preprocess']:
         settings, src = preprocess_img_data(settings)
-        
+
+    files_to_process = 3
+    files_processed = 0
     if settings['masks']:
         mask_src = os.path.join(src, 'norm_channel_stack')
         if settings['cell_channel'] != None:
+            time_ls=[]
             if check_mask_folder(src, 'cell_mask_stack'):
+                start = time.time()
                 generate_cellpose_masks(mask_src, settings, 'cell')
+                stop = time.time()
+                duration = (stop - start)
+                time_ls.append(duration)
+                files_processed += 1
+                print_progress(files_processed, files_to_process, n_jobs=1, time_ls=time_ls, batch_size=None, operation_type=f'cell_mask_gen')
             
         if settings['nucleus_channel'] != None:
+            time_ls=[]
             if check_mask_folder(src, 'nucleus_mask_stack'):
+                start = time.time()
                 generate_cellpose_masks(mask_src, settings, 'nucleus')
+                stop = time.time()
+                duration = (stop - start)
+                time_ls.append(duration)
+                files_processed += 1
+                print_progress(files_processed, files_to_process, n_jobs=1, time_ls=time_ls, batch_size=None, operation_type=f'nucleus_mask_gen')
             
         if settings['pathogen_channel'] != None:
+            time_ls=[]
             if check_mask_folder(src, 'pathogen_mask_stack'):
+                start = time.time()
                 generate_cellpose_masks(mask_src, settings, 'pathogen')
+                stop = time.time()
+                duration = (stop - start)
+                time_ls.append(duration)
+                files_processed += 1
+                print_progress(files_processed, files_to_process, n_jobs=1, time_ls=time_ls, batch_size=None, operation_type=f'pathogen_mask_gen')
 
         #if settings['organelle'] != None:
         #    if check_mask_folder(src, 'organelle_mask_stack'):
@@ -1782,7 +1805,7 @@ def preprocess_generate_masks(src, settings={}):
                     
                     for i, file in enumerate(files):
                         start = time.time()
-                        if i <= settings['examples_to_plot']:
+                        if i+1 <= settings['examples_to_plot']:
                             file_path = os.path.join(merged_src, file)
                             plot_image_mask_overlay(file_path, settings['channels'], settings['cell_channel'], settings['nucleus_channel'], settings['pathogen_channel'], figuresize=10, normalize=True, thickness=3, save_pdf=True)
                             stop = time.time()
@@ -2012,9 +2035,7 @@ def generate_cellpose_masks(src, settings, object_type):
     average_sizes = []
     time_ls = []
     
-    files_to_process = len(paths)
     for file_index, path in enumerate(paths):
-        start = time.time()
         name = os.path.basename(path)
         name, ext = os.path.splitext(name)
         output_folder = os.path.join(os.path.dirname(path), object_type+'_mask_stack')
@@ -2062,7 +2083,6 @@ def generate_cellpose_masks(src, settings, object_type):
             if not settings['plot']:
                 batch, batch_filenames = _check_masks(batch, batch_filenames, output_folder)
             if batch.size == 0:
-                #print(f'Processing {file_index}/{len(paths)}: Images/npz {batch.shape[0]}')
                 continue
             
             batch = prepare_batch_for_cellpose(batch)
@@ -2073,16 +2093,6 @@ def generate_cellpose_masks(src, settings, object_type):
                 save_path = os.path.join(movie_path, f'timelapse_{object_type}_{name}.mp4')
                 _npz_to_movie(batch, batch_filenames, save_path, fps=2)
             
-            #if settings['verbose']:
-                #print(f'Processing {file_index}/{len(paths)}: Images/npz {batch.shape[0]}')
-
-            #cellpose_normalize_dict = {'lowhigh':[0.0,1.0], #pass in normalization values for 0.0 and 1.0 as list [low, high] if None all other keys ignored
-            #                           'sharpen':object_settings['diameter']/4, #recommended to be 1/4-1/8 diameter of cells in pixels
-            #                           'normalize':True, #(if False, all following parameters ignored)
-            #                           'percentile':[2,98], #[perc_low, perc_high]
-            #                           'tile_norm':224, #normalize by tile set to e.g. 100 for normailize window to be 100 px
-            #                           'norm3D':True} #compute normalization across entire z-stack rather than plane-by-plane in stitching mode.
-            
             output = model.eval(x=batch,
                                 batch_size=cellpose_batch_size,
                                 normalize=False,
@@ -2204,12 +2214,8 @@ def generate_cellpose_masks(src, settings, object_type):
                 np.save(output_filename, mask)
             mask_stack = []
             batch_filenames = []
-        stop = time.time()
-        duration = (stop - start)
-        time_ls.append(duration)
-        files_processed = file_index+1
-        print_progress(files_processed, files_to_process, n_jobs=1, time_ls=time_ls, batch_size=batch_size, operation_type=f'{object_type}_mask_gen')
-        #gc.collect()
+
+        gc.collect()
     torch.cuda.empty_cache()
     return
 

{spacr-0.2.45 → spacr-0.2.53}/spacr/gui.py

@@ -1,7 +1,5 @@
 import tkinter as tk
 from tkinter import ttk
-from PIL import Image, ImageTk, ImageDraw
-import os
 from multiprocessing import set_start_method
 from .gui_elements import spacrButton, create_menu_bar, set_dark_style
 from .gui_core import initiate_root

{spacr-0.2.45 → spacr-0.2.53}/spacr/gui_core.py

@@ -1,9 +1,8 @@
-import os, traceback, ctypes, requests, csv, time, requests, re
+import traceback, ctypes, csv, re, time
 import tkinter as tk
 from tkinter import ttk
 from tkinter import filedialog
 from multiprocessing import Process, Value, Queue, set_start_method
-from multiprocessing.sharedctypes import Synchronized
 from tkinter import ttk, scrolledtext
 from matplotlib.figure import Figure
 from matplotlib.backends.backend_tkagg import FigureCanvasTkAgg
@@ -44,13 +43,15 @@ def toggle_settings(button_scrollable_frame):
     def toggle_category(settings):
         for setting in settings:
             if setting in vars_dict:
-                label, widget, _ = vars_dict[setting]
+                label, widget, _, frame = vars_dict[setting]
                 if widget.grid_info():
                     label.grid_remove()
                     widget.grid_remove()
+                    frame.grid_remove()
                 else:
                     label.grid()
                     widget.grid()
+                    frame.grid()
 
     def on_category_select(selected_category):
         if selected_category == "Select Category":
@@ -80,15 +81,20 @@ def process_fig_queue():
 
     try:
         while not fig_queue.empty():
+            time.sleep(1)
             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()
+
+            # Adjust layout to minimize spacing between axes
+            fig.subplots_adjust(left=0, right=1, top=1, bottom=0, wspace=0.01, hspace=0.01)
             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)
@@ -96,12 +102,9 @@ def process_fig_queue():
     except Exception as e:
         traceback.print_exc()
     finally:
-        after_id = canvas_widget.after(100, process_fig_queue)
+        after_id = canvas_widget.after(1, process_fig_queue)
         parent_frame.after_tasks.append(after_id)
 
-
-
-
 def set_globals(thread_control_var, 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 thread_control, q, console_output, parent_frame, vars_dict, canvas, canvas_widget, scrollable_frame, fig_queue, progress_bar, usage_bars
     thread_control = thread_control_var
@@ -169,13 +172,14 @@ def import_settings(settings_type='mask'):
 def setup_settings_panel(vertical_container, settings_type='mask'):
     global vars_dict, scrollable_frame
     from .settings import get_identify_masks_finetune_default_settings, set_default_analyze_screen, set_default_settings_preprocess_generate_masks, get_measure_crop_settings, set_default_train_test_model, get_analyze_reads_default_settings, set_default_umap_image_settings, generate_fields, get_perform_regression_default_settings, get_train_cellpose_default_settings, get_map_barcodes_default_settings, get_analyze_recruitment_default_settings, get_check_cellpose_models_default_settings
-    from .gui_utils import convert_settings_dict_for_gui, set_element_size
+    from .gui_utils import convert_settings_dict_for_gui
+    from .gui_elements import set_element_size
 
-    size_dict = set_element_size(vertical_container)
+    size_dict = set_element_size()
     settings_width = size_dict['settings_width']
 
     # Create a PanedWindow for the settings panel
-    settings_paned_window = tk.PanedWindow(vertical_container, orient=tk.HORIZONTAL)
+    settings_paned_window = tk.PanedWindow(vertical_container, orient=tk.HORIZONTAL, width=size_dict['settings_width'])
     vertical_container.add(settings_paned_window, stretch="always")
 
     settings_frame = tk.Frame(settings_paned_window, width=settings_width)
@@ -229,8 +233,12 @@ def setup_settings_panel(vertical_container, settings_type='mask'):
 
 def setup_plot_section(vertical_container):
     global canvas, canvas_widget
-    plot_frame = tk.PanedWindow(vertical_container, orient=tk.VERTICAL)
+
+    # Create a frame for the plot section
+    plot_frame = tk.Frame(vertical_container, bg='lightgrey')
     vertical_container.add(plot_frame, stretch="always")
+
+    # Set up the plot
     figure = Figure(figsize=(30, 4), dpi=100)
     plot = figure.add_subplot(111)
     plot.plot([], [])  # This creates an empty plot.
@@ -238,7 +246,11 @@ def setup_plot_section(vertical_container):
     canvas = FigureCanvasTkAgg(figure, master=plot_frame)
     canvas.get_tk_widget().configure(cursor='arrow', highlightthickness=0)
     canvas_widget = canvas.get_tk_widget()
-    plot_frame.add(canvas_widget, stretch="always")
+    canvas_widget.grid(row=0, column=0, sticky="nsew")  # Use grid for the canvas widget
+
+    plot_frame.grid_rowconfigure(0, weight=1)
+    plot_frame.grid_columnconfigure(0, weight=1)
+
     canvas.draw()
     canvas.figure = figure
     style_out = set_dark_style(ttk.Style())
@@ -249,62 +261,58 @@ def setup_plot_section(vertical_container):
     widgets = [canvas_widget]
     style = ttk.Style(vertical_container)
     _ = set_dark_style(style, containers=containers, widgets=widgets)
+
     return canvas, canvas_widget
 
 def setup_console(vertical_container):
     global console_output
+    from .gui_elements import set_dark_style
 
-    # Create a frame to hold the console and button sections
-    console_button_frame = tk.Frame(vertical_container)
-    vertical_container.add(console_button_frame, stretch="always")
-
-    # Create a PanedWindow for resizing height
-    console_paned_window = tk.PanedWindow(console_button_frame, orient=tk.VERTICAL, bg='black')
-    console_paned_window.pack(fill=tk.BOTH, expand=True)
+    # Apply dark style and get style output
+    style = ttk.Style()
+    style_out = set_dark_style(style)
 
-    # Create the main console frame using spacrFrame with textbox=True
-    console_frame = spacrFrame(console_paned_window, textbox=True)
-    console_paned_window.add(console_frame, stretch="always")
+    # Create a frame for the console section
+    console_frame = tk.Frame(vertical_container, bg=style_out['bg_color'])
+    vertical_container.add(console_frame, stretch="always")
 
-    # Assign the scrollable frame (which is a Text widget) to console_output
-    console_output = console_frame.scrollable_frame
+    # Create a thicker frame at the top for the hover effect
+    top_border = tk.Frame(console_frame, height=5, bg=style_out['bg_color'])
+    top_border.grid(row=0, column=0, sticky="ew", pady=(0, 2))
 
-    # Ensure the Text widget spans the entire console frame
-    console_output.grid(row=0, column=0, sticky="nsew")
+    # Create the scrollable frame (which is a Text widget) with white text
+    family = style_out['font_family']
+    font_size = style_out['font_size'] - 2
+    font_loader = style_out['font_loader']
+    console_output = tk.Text(console_frame, bg=style_out['bg_color'], fg=style_out['fg_color'], font=font_loader.get_font(size=font_size), bd=0, highlightthickness=0)
+    
+    console_output.grid(row=1, column=0, sticky="nsew")  # Use grid for console_output
 
     # Configure the grid to allow expansion
-    console_frame.grid_rowconfigure(0, weight=1)
+    console_frame.grid_rowconfigure(1, weight=1)
     console_frame.grid_columnconfigure(0, weight=1)
 
-    # Create a lower frame to act as the anchor point
-    lower_frame = tk.Frame(console_paned_window)
-    console_paned_window.add(lower_frame, minsize=10)  # Adjust minsize to ensure usability
+    def on_enter(event):
+        top_border.config(bg=style_out['active_color'])
 
-    # Dynamically adjust the height and width of the console_frame
-    def adjust_frame_size(event):
-        console_frame.update_idletasks()
-        new_width = console_paned_window.winfo_width()
-        new_height = console_paned_window.winfo_height()
-        console_frame.config(width=new_width, height=new_height)
-        console_output.config(width=new_width, height=new_height)
+    def on_leave(event):
+        top_border.config(bg=style_out['bg_color'])
 
-    # Bind the configure event to dynamically adjust size
-    console_paned_window.bind("<Configure>", adjust_frame_size)
-
-    # Apply dark style to the PanedWindow and lower frame
-    style = ttk.Style()
-    set_dark_style(style, containers=[console_paned_window, lower_frame])
+    console_output.bind("<Enter>", on_enter)
+    console_output.bind("<Leave>", on_leave)
 
     return console_output, console_frame
 
-
 def setup_progress_frame(vertical_container):
     global progress_output
+    style_out = set_dark_style(ttk.Style())
+    font_loader = style_out['font_loader']
+    font_size = style_out['font_size']
     progress_frame = tk.Frame(vertical_container)
     vertical_container.add(progress_frame, stretch="always")
     label_frame = tk.Frame(progress_frame)
     label_frame.grid(row=0, column=0, sticky="ew", pady=(5, 0), padx=10)
-    progress_label = spacrLabel(label_frame, text="Processing: 0%", font=('Helvetica', 12), anchor='w', justify='left', align="left")
+    progress_label = spacrLabel(label_frame, text="Processing: 0%", font=font_loader.get_font(size=font_size), anchor='w', justify='left', align="left")
     progress_label.grid(row=0, column=0, sticky="w")
     progress_output = scrolledtext.ScrolledText(progress_frame, height=10)
     progress_output.grid(row=1, column=0, sticky="nsew")
@@ -318,16 +326,15 @@ def setup_progress_frame(vertical_container):
 
 def setup_button_section(horizontal_container, settings_type='mask', run=True, abort=True, download=True, import_btn=True):
     global thread_control, parent_frame, 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, download_hug_dataset
-    from .settings import categories
+    from .gui_utils import download_hug_dataset
+    from .gui_elements import set_element_size
 
-
-    size_dict = set_element_size(horizontal_container)
+    size_dict = set_element_size()
     button_section_height = size_dict['panel_height']
     button_frame = tk.Frame(horizontal_container, height=button_section_height)
     
     # Prevent the frame from resizing based on the child widget
-    button_frame.pack_propagate(False)
+    #button_frame.pack_propagate(False)
 
     horizontal_container.add(button_frame, stretch="always", sticky="nsew")
     button_scrollable_frame = spacrFrame(button_frame, scrollbar=False)
@@ -338,7 +345,6 @@ def setup_button_section(horizontal_container, settings_type='mask', run=True, a
     btn_row = 0
 
     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), show_text=False, size=size_dict['btn_size'], animation=False)
         run_button.grid(row=btn_row, column=btn_col, pady=5, padx=5, sticky='ew')
         widgets.append(run_button)
@@ -364,7 +370,7 @@ def setup_button_section(horizontal_container, settings_type='mask', run=True, a
 
     # Add the progress bar under the settings category menu
     progress_bar = spacrProgressBar(button_scrollable_frame.scrollable_frame, orient='horizontal', mode='determinate')
-    progress_bar.grid(row=btn_row, column=0, columnspan=5, pady=5, padx=5, sticky='ew')
+    progress_bar.grid(row=btn_row, column=0, columnspan=7, pady=5, padx=5, sticky='ew')
     progress_bar.set_label_position()  # Set the label position after grid placement
     widgets.append(progress_bar)
 
@@ -374,11 +380,13 @@ def setup_button_section(horizontal_container, settings_type='mask', run=True, a
     style = ttk.Style(horizontal_container)
     _ = set_dark_style(style, containers=[button_frame], widgets=widgets)
 
-    return button_scrollable_frame
+    return button_scrollable_frame, btn_col
 
-def setup_usage_panel(horizontal_container):
+def setup_usage_panel(horizontal_container, btn_col):
     global usage_bars
-    from .gui_utils import set_element_size
+    from .gui_elements import set_dark_style, set_element_size
+
+    usg_col = 1
 
     def update_usage(ram_bar, vram_bar, gpu_bar, usage_bars, parent_frame):
         # Update RAM usage
@@ -402,10 +410,10 @@ def setup_usage_panel(horizontal_container):
         # 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)
+    size_dict = set_element_size()
     usage_panel_height = size_dict['panel_height']
     usage_frame = tk.Frame(horizontal_container, height=usage_panel_height)
-    horizontal_container.add(usage_frame, stretch="always", sticky="nsew")
+    horizontal_container.add(usage_frame)
 
     usage_frame.grid_rowconfigure(0, weight=0)
     usage_frame.grid_rowconfigure(1, weight=1)
@@ -415,19 +423,27 @@ def setup_usage_panel(horizontal_container):
     usage_scrollable_frame = spacrFrame(usage_frame, scrollbar=False)
     usage_scrollable_frame.grid(row=1, column=0, sticky="nsew", columnspan=2)
     widgets = [usage_scrollable_frame.scrollable_frame]
+    
     usage_bars = []
-    max_elements_per_column = 6
+    max_elements_per_column = 4
     row = 0
     col = 0
 
     # Initialize RAM, VRAM, and GPU bars as None
     ram_bar, vram_bar, gpu_bar = None, None, None
+    
+    # Configure the style for the label
+    style = ttk.Style()
+    style_out = set_dark_style(style)
+    font_loader = style_out['font_loader']
+    font_size = style_out['font_size'] - 2
+    style.configure("usage.TLabel", font=font_loader.get_font(size=font_size), foreground=style_out['fg_color'])
 
     # 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 = ttk.Label(usage_scrollable_frame.scrollable_frame, text=ram_label_text, anchor='w', style="usage.TLabel")
         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')
@@ -444,7 +460,7 @@ def setup_usage_panel(horizontal_container):
         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 = ttk.Label(usage_scrollable_frame.scrollable_frame, text=vram_label_text, anchor='w', style="usage.TLabel")
             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')
@@ -454,7 +470,7 @@ def setup_usage_panel(horizontal_container):
             row += 1
 
             gpu_label_text = f"GPU"
-            label = ttk.Label(usage_scrollable_frame.scrollable_frame, text=gpu_label_text, anchor='w')
+            label = ttk.Label(usage_scrollable_frame.scrollable_frame, text=gpu_label_text, anchor='w', style="usage.TLabel")
             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')
@@ -474,7 +490,7 @@ def setup_usage_panel(horizontal_container):
             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 = ttk.Label(usage_scrollable_frame.scrollable_frame, text=f"Core {core+1}", anchor='w', style="usage.TLabel")
             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')
@@ -494,58 +510,9 @@ def setup_usage_panel(horizontal_container):
         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 setup_help_section(horizontal_container, settings_type='mask'):
-    from .settings import descriptions
-    from .gui_utils import set_element_size
-
-    size_dict = set_element_size(horizontal_container)
-    help_section_height = size_dict['panel_height']
-
-    # Create the frame for the help section
-    description_frame = tk.Frame(horizontal_container, height=help_section_height)
-    description_frame.pack_propagate(False)
-
-    # Add the description frame to the 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)  # Ensure the text widget row is expandable
-
-    style_out = set_dark_style(ttk.Style())
-    bg_color = style_out['bg_color']
-    fg_color = style_out['fg_color']
-
-    # Insert the description text
-    description_text = descriptions.get(settings_type, "No description available for this module.")
-    first_line, *rest_of_description = description_text.split('\n', 1)
-
-    # Create the first line label
-    first_line_label = ttk.Label(description_frame, text=first_line, anchor='w', background=bg_color, foreground=fg_color)
-    first_line_label.grid(row=0, column=0, sticky='ew')
-
-    # Create the text widget with the appropriate background and foreground colors
-    description_text_widget = tk.Text(description_frame, wrap="word", bg=bg_color, fg=fg_color, bd=0, highlightthickness=0)
-    description_text_widget.grid(row=1, column=0, sticky="nsew")
-
-    # Insert the rest of the description text
-    if rest_of_description:
-        description_text_widget.insert("1.0", rest_of_description[0].lstrip())
-    description_text_widget.config(state="disabled")  # Make the text widget read-only
-
-    def update_wraplength(event):
-        new_width = event.width - 20  # Adjust as needed
-        description_text_widget.config(width=new_width)
-
-    description_text_widget.bind('<Configure>', update_wraplength)
-
-    # Apply dark style
-    style = ttk.Style(horizontal_container)
-    _ = set_dark_style(style, containers=[description_frame], widgets=[description_text_widget, first_line_label])
-
-    return description_frame
+    
+    update_usage(ram_bar, vram_bar, gpu_bar, usage_bars, usage_frame)    
+    return usage_scrollable_frame, usage_bars, usg_col
 
 def initiate_abort():
     global thread_control, q, parent_frame
@@ -570,7 +537,6 @@ def start_process(q=None, fig_queue=None, settings_type='mask'):
         q = Queue()
     if fig_queue is None:
         fig_queue = Queue()
-
     try:
         settings = check_settings(vars_dict, expected_types, q)
     except ValueError as e:
@@ -602,9 +568,11 @@ def process_console_queue():
     # Initialize function attribute if it doesn't exist
     if not hasattr(process_console_queue, "completed_tasks"):
         process_console_queue.completed_tasks = []
+    if not hasattr(process_console_queue, "current_maximum"):
+        process_console_queue.current_maximum = None
 
     ansi_escape_pattern = re.compile(r'\x1B\[[0-?]*[ -/]*[@-~]')
-    
+
     while not q.empty():
         message = q.get_nowait()
         clean_message = ansi_escape_pattern.sub('', message)
@@ -616,12 +584,18 @@ def process_console_queue():
             try:
                 # Extract the progress information
                 match = re.search(r'Progress: (\d+)/(\d+), operation_type: ([\w\s]*)(.*)', clean_message)
+
                 if match:
                     current_progress = int(match.group(1))
                     total_progress = int(match.group(2))
                     operation_type = match.group(3).strip()
                     time_info = match.group(4).strip()
 
+                    # Check if the maximum value has changed
+                    if process_console_queue.current_maximum != total_progress:
+                        process_console_queue.current_maximum = total_progress
+                        process_console_queue.completed_tasks = []
+
                     # Add the task to the completed set
                     process_console_queue.completed_tasks.append(current_progress)
                     
@@ -656,16 +630,23 @@ def process_console_queue():
                     # Clear completed tasks when progress is complete
                     if unique_progress_count >= total_progress:
                         process_console_queue.completed_tasks.clear()
+
             except Exception as e:
                 print(f"Error parsing progress message: {e}")
-
-    after_id = console_output.after(100, process_console_queue)
+        #else:
+        #    # Only insert messages that do not start with "Progress:"
+        #    console_output.insert(tk.END, clean_message + "\n")
+        #    console_output.see(tk.END)
+        
+    after_id = console_output.after(1, process_console_queue)
     parent_frame.after_tasks.append(after_id)
 
+
 def initiate_root(parent, settings_type='mask'):
     global q, fig_queue, thread_control, parent_frame, scrollable_frame, button_frame, vars_dict, canvas, canvas_widget, button_scrollable_frame, progress_bar
-    from .gui_utils import main_thread_update_function, setup_frame, set_element_size
-    from .gui import gui_app
+    from .gui_utils import main_thread_update_function, setup_frame
+    from .settings import descriptions
+
     set_start_method('spawn', force=True)
     print("Initializing root with settings_type:", settings_type)
 
@@ -693,18 +674,23 @@ def initiate_root(parent, settings_type='mask'):
         initiate_make_mask_app(horizontal_container)
     else:
         scrollable_frame, vars_dict = setup_settings_panel(settings_container, settings_type)
+        print('setup_settings_panel')
         canvas, canvas_widget = setup_plot_section(vertical_container)
-        console_output, console_frame = setup_console(vertical_container)
-        button_scrollable_frame = setup_button_section(horizontal_container, settings_type)
-        _, usage_bars = setup_usage_panel(horizontal_container)
-        _ = setup_help_section(horizontal_container, settings_type)
-        
+        console_output, _ = setup_console(vertical_container)
+        button_scrollable_frame, btn_col = setup_button_section(horizontal_container, settings_type)
+        _, usage_bars, btn_col = setup_usage_panel(horizontal_container, btn_col)
+
         set_globals(thread_control, q, console_output, parent_frame, vars_dict, canvas, canvas_widget, scrollable_frame, fig_queue, progress_bar, usage_bars)
+        description_text = descriptions.get(settings_type, "No description available for this module.")
+        
         q.put(f"Console")
+        q.put(f" ")
+        q.put(description_text)
+        
         process_console_queue()
         process_fig_queue()
         after_id = parent_window.after(100, lambda: main_thread_update_function(parent_window, q, fig_queue, canvas_widget))
         parent_window.after_tasks.append(after_id)
 
     print("Root initialization complete")
-    return parent_frame, vars_dict
+    return parent_frame, vars_dict