spacr 0.2.46__tar.gz → 0.2.53__tar.gz

{spacr-0.2.46/spacr.egg-info → spacr-0.2.53}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: spacr
-Version: 0.2.46
+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-0.2.46 → 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="0.2.46",
+    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-0.2.46 → 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'):
@@ -2012,7 +2035,6 @@ def generate_cellpose_masks(src, settings, object_type):
     average_sizes = []
     time_ls = []
     
-    files_to_process = len(paths)
     for file_index, path in enumerate(paths):
         name = os.path.basename(path)
         name, ext = os.path.splitext(name)
@@ -2050,7 +2072,6 @@ 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)
@@ -2072,14 +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)
             
-            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,

{spacr-0.2.46 → 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-0.2.46 → spacr-0.2.53}/spacr/gui_core.py

@@ -1,16 +1,14 @@
-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
 import numpy as np
 import psutil
 import GPUtil
-import tkinter.font as tkFont
 
 try:
     ctypes.windll.shcore.SetProcessDpiAwareness(True)
@@ -45,13 +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":
@@ -81,15 +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)
@@ -97,12 +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
@@ -170,13 +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)
@@ -230,8 +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.
@@ -239,7 +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())
@@ -250,6 +261,7 @@ 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):
@@ -260,46 +272,47 @@ def setup_console(vertical_container):
     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 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 a frame for the console section
+    console_frame = tk.Frame(vertical_container, bg=style_out['bg_color'])
+    vertical_container.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")
-
-    # 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)
+    # 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))
 
     # 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)
+    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_button_frame, bg=style_out['bg_color'])
-    lower_frame.pack(fill=tk.X, expand=False)
+    def on_enter(event):
+        top_border.config(bg=style_out['active_color'])
+
+    def on_leave(event):
+        top_border.config(bg=style_out['bg_color'])
+
+    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")
@@ -313,10 +326,10 @@ 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)
     
@@ -357,7 +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=6, 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)
 
@@ -371,8 +384,7 @@ def setup_button_section(horizontal_container, settings_type='mask', run=True, a
 
 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
+    from .gui_elements import set_dark_style, set_element_size
 
     usg_col = 1
 
@@ -398,7 +410,7 @@ def setup_usage_panel(horizontal_container, btn_col):
         # 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)
@@ -413,7 +425,7 @@ def setup_usage_panel(horizontal_container, btn_col):
     widgets = [usage_scrollable_frame.scrollable_frame]
     
     usage_bars = []
-    max_elements_per_column = 6
+    max_elements_per_column = 4
     row = 0
     col = 0
 
@@ -423,9 +435,9 @@ def setup_usage_panel(horizontal_container, btn_col):
     # 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'])
+    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:
@@ -525,7 +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:
@@ -573,7 +584,7 @@ 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))
@@ -622,14 +633,18 @@ def process_console_queue():
 
             except Exception as e:
                 print(f"Error parsing progress message: {e}")
-
-    after_id = console_output.after(10, 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)
@@ -678,4 +693,4 @@ def initiate_root(parent, settings_type='mask'):
         parent_window.after_tasks.append(after_id)
 
     print("Root initialization complete")
-    return parent_frame, vars_dict
+    return parent_frame, vars_dict