spacr 0.2.45__tar.gz → 0.2.46__tar.gz

{spacr-0.2.45/spacr.egg-info → spacr-0.2.46}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: spacr
-Version: 0.2.45
+Version: 0.2.46
 Summary: Spatial phenotype analysis of crisp screens (SpaCr)
 Home-page: https://github.com/EinarOlafsson/spacr
 Author: Einar Birnir Olafsson

{spacr-0.2.45 → spacr-0.2.46}/setup.py

@@ -53,7 +53,7 @@ dependencies = [
 
 setup(
     name="spacr",
-    version="0.2.45",
+    version="0.2.46",
     author="Einar Birnir Olafsson",
     author_email="olafsson@med.umich.com",
     description="Spatial phenotype analysis of crisp screens (SpaCr)",

{spacr-0.2.45 → spacr-0.2.46}/spacr/core.py

@@ -1782,7 +1782,7 @@ 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()
@@ -2014,7 +2014,6 @@ def generate_cellpose_masks(src, settings, object_type):
     
     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')
@@ -2051,6 +2050,7 @@ def generate_cellpose_masks(src, settings, object_type):
                         print(f'Cut batch at indecies: {timelapse_frame_limits}, New batch_size: {batch_size} ')
         
         for i in range(0, stack.shape[0], batch_size):
+            start = time.time()
             mask_stack = []
             if stack.shape[3] == 1:
                 batch = stack[i: i+batch_size, :, :, [0,0]].astype(stack.dtype)
@@ -2062,7 +2062,6 @@ 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 +2072,14 @@ 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.
-            
+            stop = time.time()
+            duration = (stop - start)
+            time_ls.append(duration)
+            files_processed = (file_index+1)*len(batch_filenames)
+            files_processed = len(paths)*batch.shape[0]
+            print('file_index', file_index, 'len(paths)', len(paths), 'batch.shape[0]', batch.shape[0])
+            print_progress(files_processed, files_to_process, n_jobs=1, time_ls=time_ls, batch_size=batch.shape[0], operation_type=f'{object_type}_mask_gen')
+
             output = model.eval(x=batch,
                                 batch_size=cellpose_batch_size,
                                 normalize=False,
@@ -2204,12 +2201,8 @@ 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-0.2.46}/spacr/gui_core.py

@@ -10,6 +10,7 @@ from matplotlib.backends.backend_tkagg import FigureCanvasTkAgg
 import numpy as np
 import psutil
 import GPUtil
+import tkinter.font as tkFont
 
 try:
     ctypes.windll.shcore.SetProcessDpiAwareness(True)
@@ -253,51 +254,45 @@ def setup_plot_section(vertical_container):
 
 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")
+    # Apply dark style and get style output
+    style = ttk.Style()
+    style_out = set_dark_style(style)
+
+    # Create a PanedWindow to hold the main content and console sections
+    main_paned_window = tk.PanedWindow(vertical_container, orient=tk.VERTICAL, bg=style_out['bg_color'])
+    vertical_container.add(main_paned_window, 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)
+    # Create the main content frame
+    main_content_frame = tk.Frame(main_paned_window, bg=style_out['bg_color'])
+    main_paned_window.add(main_content_frame, stretch="always")
 
-    # 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 to hold the console and button sections
+    console_button_frame = tk.Frame(main_paned_window, bg=style_out['bg_color'])
+    main_paned_window.add(console_button_frame, stretch="always")
 
-    # Assign the scrollable frame (which is a Text widget) to console_output
-    console_output = console_frame.scrollable_frame
+    # Create the main console frame
+    console_frame = tk.Frame(console_button_frame, bg=style_out['bg_color'])
+    console_frame.pack(fill=tk.BOTH, expand=True)
 
-    # 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']
+    size = style_out['font_size'] -2
+    font = tkFont.Font(family=family, size=size)
+    console_output = tk.Text(console_frame, bg=style_out['bg_color'], fg=style_out['fg_color'], font=font)
+    console_output.pack(fill=tk.BOTH, expand=True)
 
     # Configure the grid to allow expansion
     console_frame.grid_rowconfigure(0, 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
-
-    # 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)
-
-    # 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])
+    lower_frame = tk.Frame(console_button_frame, bg=style_out['bg_color'])
+    lower_frame.pack(fill=tk.X, expand=False)
 
     return console_output, console_frame
 
-
 def setup_progress_frame(vertical_container):
     global progress_output
     progress_frame = tk.Frame(vertical_container)
@@ -321,13 +316,12 @@ def setup_button_section(horizontal_container, settings_type='mask', run=True, a
     from .gui_utils import set_element_size, download_hug_dataset
     from .settings import categories
 
-
     size_dict = set_element_size(horizontal_container)
     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 +332,6 @@ 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 +357,7 @@ 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=6, pady=5, padx=5, sticky='ew')
     progress_bar.set_label_position()  # Set the label position after grid placement
     widgets.append(progress_bar)
 
@@ -374,11 +367,14 @@ 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
+
+    usg_col = 1
 
     def update_usage(ram_bar, vram_bar, gpu_bar, usage_bars, parent_frame):
         # Update RAM usage
@@ -405,7 +401,7 @@ def setup_usage_panel(horizontal_container):
     size_dict = set_element_size(horizontal_container)
     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)
@@ -415,6 +411,7 @@ 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
     row = 0
@@ -422,12 +419,19 @@ def setup_usage_panel(horizontal_container):
 
     # 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)
+    size = style_out['font_size'] - 2
+    usage_font = tkFont.Font(family=style_out['font_family'], size=size)
+    style.configure("usage.TLabel", font=usage_font, 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 +448,7 @@ 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 +458,7 @@ 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 +478,7 @@ 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 +498,9 @@ 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
@@ -602,9 +557,11 @@ 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 +573,18 @@ def process_console_queue():
             try:
                 # Extract the progress information
                 match = re.search(r'Progress: (\d+)/(\d+), operation_type: ([\w\s]*)(.*)', clean_message)
+                print('match', match)
                 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 +619,19 @@ 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)
+    after_id = console_output.after(10, 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 .settings import descriptions
+
     set_start_method('spawn', force=True)
     print("Initializing root with settings_type:", settings_type)
 
@@ -693,14 +659,19 @@ 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))

{spacr-0.2.45 → spacr-0.2.46}/spacr/gui_utils.py

@@ -314,7 +314,7 @@ def set_element_size(widget):
     screen_height = widget.winfo_screenheight()
     btn_size = screen_width // 40
     bar_size = screen_width // 50
-    settings_width = screen_width // 6
+    settings_width = screen_width // 5
     panel_height = screen_height // 12
     panel_width = settings_width
     size_dict = {
@@ -507,24 +507,38 @@ def hide_all_settings(vars_dict, categories):
 
 def setup_frame(parent_frame):
     from .gui_elements import set_dark_style, set_default_font
+
     style = ttk.Style(parent_frame)
     size_dict = set_element_size(parent_frame)
-    
-    settings_container = tk.PanedWindow(parent_frame, orient=tk.VERTICAL, width=size_dict['settings_width'])
-    vertical_container = tk.PanedWindow(parent_frame, orient=tk.VERTICAL)
-    horizontal_container = tk.PanedWindow(parent_frame, orient=tk.HORIZONTAL, height=size_dict['panel_height'])
+    style_out = set_dark_style(style)
+
+    settings_container = tk.PanedWindow(parent_frame, orient=tk.VERTICAL, width=size_dict['settings_width'], bg=style_out['bg_color'])
+    vertical_container = tk.PanedWindow(parent_frame, orient=tk.VERTICAL, bg=style_out['bg_color'])
+    horizontal_container = tk.PanedWindow(parent_frame, orient=tk.HORIZONTAL, height=size_dict['panel_height'], bg=style_out['bg_color'])
 
     parent_frame.grid_rowconfigure(0, weight=1)
     parent_frame.grid_rowconfigure(1, weight=0)
-    parent_frame.grid_columnconfigure(0, weight=0)  # Change this line
-    parent_frame.grid_columnconfigure(1, weight=1)  # Change this line
+    parent_frame.grid_columnconfigure(0, weight=0)
+    parent_frame.grid_columnconfigure(1, weight=1)
+
+    settings_container.grid(row=0, column=0, rowspan=2, sticky="nsew")
+    vertical_container.grid(row=0, column=1, sticky="nsew")
+    horizontal_container.grid(row=1, column=1, sticky="nsew")
 
-    settings_container.grid(row=0, column=0, rowspan=2, sticky="nsew")  # Change this line
-    vertical_container.grid(row=0, column=1, sticky="nsew")  # Change this line
-    horizontal_container.grid(row=1, column=1, sticky="ew")  # Change this line
+    # Lock the width of the horizontal_container
+    horizontal_container.update_idletasks()  # Ensure geometry manager calculates size
+    fixed_width = horizontal_container.winfo_width()
+    parent_frame.grid_columnconfigure(1, weight=0)
+    horizontal_container.config(width=fixed_width)
+
+    tk.Label(settings_container, text="Settings Container", bg=style_out['bg_color']).pack(fill=tk.BOTH, expand=True)
+    tk.Label(vertical_container, text="Vertical Container", bg=style_out['bg_color']).pack(fill=tk.BOTH, expand=True)
 
     set_dark_style(style, parent_frame, [settings_container, vertical_container, horizontal_container])
-    set_default_font(parent_frame, font_name="Helvetica", size=8)
+    
+    size = style_out['font_size'] - 2
+    
+    set_default_font(parent_frame, font_name=style_out['font_family'], size=size)
 
     return parent_frame, vertical_container, horizontal_container, settings_container
 
@@ -532,7 +546,7 @@ def download_hug_dataset(q, vars_dict):
     dataset_repo_id = "einarolafsson/toxo_mito"
     settings_repo_id = "einarolafsson/spacr_settings"
     dataset_subfolder = "plate1"
-    local_dir = os.path.join(os.path.expanduser("~"), "datasets")  # Set to the home directory
+    local_dir = os.path.join(os.path.expanduser("~"), "datasets")
 
     # Download the dataset
     try:

{spacr-0.2.45 → spacr-0.2.46}/spacr/io.py

@@ -594,9 +594,9 @@ def _rename_and_organize_image_files(src, regex, batch_size=100, pick_slice=Fals
         print(f'All_files: {len(all_filenames)} in {src}')
         time_ls = []
 
-        for i in range(0, len(all_filenames), batch_size):
+        for idx in range(0, len(all_filenames), batch_size):
             start = time.time()
-            batch_filenames = all_filenames[i:i+batch_size]
+            batch_filenames = all_filenames[idx:idx+batch_size]
             files_processed = 0
             for filename in batch_filenames:
                 images_by_key = _extract_filename_metadata(batch_filenames, src, images_by_key, regular_expression, metadata_type, pick_slice, skip_mode)
@@ -610,6 +610,12 @@ def _rename_and_organize_image_files(src, regex, batch_size=100, pick_slice=Fals
                     os.makedirs(output_dir, exist_ok=True)
                     output_filename = f'{plate}_{well}_{field}.tif'
                     output_path = os.path.join(output_dir, output_filename)
+                    files_processed += 1
+                    stop = time.time()
+                    duration = stop - start
+                    time_ls.append(duration)
+                    files_to_process = len(all_filenames)
+                    print_progress(files_processed, files_to_process, n_jobs=1, time_ls=time_ls, batch_size=batch_size, operation_type='Preprocessing filenames')
 
                     if os.path.exists(output_path):                        
                         print(f'WARNING: A file with the same name already exists at location {output_filename}')
@@ -624,18 +630,18 @@ def _rename_and_organize_image_files(src, regex, batch_size=100, pick_slice=Fals
                     os.makedirs(output_dir, exist_ok=True)
                     output_filename = f'{plate}_{well}_{field}.tif'
                     output_path = os.path.join(output_dir, output_filename)
+                    files_processed += 1
+                    stop = time.time()
+                    duration = stop - start
+                    time_ls.append(duration)
+                    files_to_process = len(all_filenames)
+                    print_progress(files_processed, files_to_process, n_jobs=1, time_ls=time_ls, batch_size=batch_size, operation_type='Preprocessing filenames')
 
                     if os.path.exists(output_path):                        
                         print(f'WARNING: A file with the same name already exists at location {output_filename}')
                     else:
                         mip_image.save(output_path)
             images_by_key.clear()
-            stop = time.time()
-            duration = stop - start
-            time_ls.append(duration)
-            files_processed += len(batch_filenames)
-            files_to_process = len(all_filenames)
-            print_progress(files_processed, files_to_process, n_jobs=1, time_ls=time_ls, batch_size=batch_size, operation_type='Preprocessing filenames')
 
         # Move original images to a new directory
         valid_exts = [img_format]
@@ -968,7 +974,7 @@ def _concatenate_channel(src, channels, randomize=True, timelapse=False, batch_s
                 time_ls.append(duration)
                 files_processed = i+1
                 files_to_process = time_stack_path_lists
-                #print_progress(files_processed, files_to_process, n_jobs=1, time_ls=None, batch_size=None, operation_type="Concatinating")
+                print_progress(files_processed, files_to_process, n_jobs=1, time_ls=time_ls, batch_size=None, operation_type="Concatinating")
                 stack = np.stack(stack_region)
                 save_loc = os.path.join(channel_stack_loc, f'{name}.npz')
                 np.savez(save_loc, data=stack, filenames=filenames_region)
@@ -999,7 +1005,7 @@ def _concatenate_channel(src, channels, randomize=True, timelapse=False, batch_s
             time_ls.append(duration)
             files_processed = i+1
             files_to_process = nr_files
-            print_progress(files_processed, files_to_process, n_jobs=1, time_ls=None, batch_size=None, operation_type="Concatinating")
+            print_progress(files_processed, files_to_process, n_jobs=1, time_ls=time_ls, batch_size=None, operation_type="Concatinating")
             if (i+1) % batch_size == 0 or i+1 == nr_files:
                 unique_shapes = {arr.shape[:-1] for arr in stack_ls}
                 if len(unique_shapes) > 1:
@@ -1097,7 +1103,7 @@ def _normalize_img_batch(stack, channels, save_dtype, settings):
         time_ls.append(duration)
         files_processed = i+1
         files_to_process = len(channels)
-        #print_progress(files_processed, files_to_process, n_jobs=1, time_ls=None, batch_size=None, operation_type=f"Normalizing: Channel: {channel}")
+        print_progress(files_processed, files_to_process, n_jobs=1, time_ls=time_ls, batch_size=None, operation_type=f"Normalizing")
 
     return normalized_stack.astype(save_dtype)
 
@@ -1144,7 +1150,6 @@ def concatenate_and_normalize(src, channels, save_dtype=np.float32, settings={})
                         parts = file.split('_')
                         name = parts[0] + '_' + parts[1] + '_' + parts[2]
                     array = np.load(path)
-                    #array = np.take(array, channels, axis=2)
                     stack_region.append(array)
                     filenames_region.append(os.path.basename(path))
                 stop = time.time()
@@ -1152,7 +1157,7 @@ def concatenate_and_normalize(src, channels, save_dtype=np.float32, settings={})
                 time_ls.append(duration)
                 files_processed = i+1
                 files_to_process = len(time_stack_path_lists)
-                print_progress(files_processed, files_to_process, n_jobs=1, time_ls=None, batch_size=None, operation_type="Concatinating")
+                print_progress(files_processed, files_to_process, n_jobs=1, time_ls=time_ls, batch_size=None, operation_type="Concatinating")
                 stack = np.stack(stack_region)
 
                 normalized_stack = _normalize_img_batch(stack=stack,
@@ -1181,6 +1186,7 @@ def concatenate_and_normalize(src, channels, save_dtype=np.float32, settings={})
         stack_ls = []
         filenames_batch = []
         time_ls = []
+        files_processed = 0
         for i, path in enumerate(paths):
             start = time.time()
             array = np.load(path)
@@ -1189,7 +1195,7 @@ def concatenate_and_normalize(src, channels, save_dtype=np.float32, settings={})
             stop = time.time()
             duration = stop - start
             time_ls.append(duration)
-            files_processed = i+1
+            files_processed += 1
             files_to_process = nr_files
             print_progress(files_processed, files_to_process, n_jobs=1, time_ls=time_ls, batch_size=None, operation_type="Concatinating")
 
@@ -1612,8 +1618,8 @@ def preprocess_img_data(settings):
                               save_dtype=np.float32,
                               settings=settings)
 
-    if plot:
-        _plot_4D_arrays(src+'/norm_channel_stack', nr_npz=1, nr=nr)
+    #if plot:
+    #    _plot_4D_arrays(src+'/norm_channel_stack', nr_npz=1, nr=nr)
 
     return settings, src
     
@@ -1943,7 +1949,7 @@ def _load_and_concatenate_arrays(src, channels, cell_chann_dim, nucleus_chann_di
     all_imgs = len(os.listdir(reference_folder))
     time_ls = []
     # Iterate through each file in the reference folder
-    for filename in os.listdir(reference_folder):
+    for idx, filename in enumerate(os.listdir(reference_folder)):
         start = time.time()
         stack_ls = []
         if filename.endswith('.npy'):
@@ -2004,7 +2010,7 @@ def _load_and_concatenate_arrays(src, channels, cell_chann_dim, nucleus_chann_di
         stop = time.time()
         duration = stop - start
         time_ls.append(duration)
-        files_processed = count
+        files_processed = idx+1
         files_to_process = all_imgs
         print_progress(files_processed, files_to_process, n_jobs=1, time_ls=time_ls, batch_size=None, operation_type="Merging Arrays")
 

{spacr-0.2.45 → spacr-0.2.46/spacr.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: spacr
-Version: 0.2.45
+Version: 0.2.46
 Summary: Spatial phenotype analysis of crisp screens (SpaCr)
 Home-page: https://github.com/EinarOlafsson/spacr
 Author: Einar Birnir Olafsson