spacr 0.1.16__py3-none-any.whl → 0.1.55__py3-none-any.whl

spacr/app_measure.py

@@ -1,253 +1,8 @@
-import sys, traceback, matplotlib, ctypes
-import tkinter as tk
-from tkinter import ttk, scrolledtext
-from matplotlib.figure import Figure
-from matplotlib.backends.backend_tkagg import FigureCanvasTkAgg
-matplotlib.use('Agg')  # Use the non-GUI Agg backend
-from multiprocessing import Process, Queue, Value
-from tkinter import filedialog
+from .gui import MainApp
 
-try:
-    ctypes.windll.shcore.SetProcessDpiAwareness(True)
-except AttributeError:
-    pass
-
-from .logger import log_function_call
-from .settings import get_measure_crop_settings
-from .gui_utils import ScrollableFrame, StdoutRedirector, CustomButton, ToggleSwitch
-from .gui_utils import process_stdout_stderr, set_dark_style, set_default_font, generate_fields, main_thread_update_function, create_menu_bar, convert_settings_dict_for_gui
-from .gui_utils import measure_crop_wrapper, clear_canvas, check_measure_gui_settings, read_settings_from_csv, update_settings_from_csv, set_dark_style
-
-thread_control = {"run_thread": None, "stop_requested": False}
-
-def import_settings(scrollable_frame):
-    global vars_dict
-
-    csv_file_path = filedialog.askopenfilename(filetypes=[("CSV files", "*.csv")])
-    csv_settings = read_settings_from_csv(csv_file_path)
-    settings = get_measure_crop_settings({})
-    variables = convert_settings_dict_for_gui(settings)
-    new_settings = update_settings_from_csv(variables, csv_settings)
-    vars_dict = generate_fields(new_settings, scrollable_frame)
-
-test_mode_button = None
-
-def toggle_test_mode():
-    global vars_dict
-    current_state = vars_dict['test_mode'][2].get()
-    new_state = not current_state
-    vars_dict['test_mode'][2].set(new_state)
-    if new_state:
-        test_mode_button.config(bg="blue")
-    else:
-        test_mode_button.config(bg="gray")
-
-def toggle_advanced_settings():
-    global vars_dict
-
-    timelapse_settings = ['timelapse', 'timelapse_objects']
-    misc_settings = ['representative_images', 'plot', 'plot_filtration', 'include_uninfected', 'dialate_pngs', 'dialate_png_ratios']
-    opperational_settings = ['max_workers','experiment','cells','cell_loc','pathogens','pathogen_loc','treatments','treatment_loc','channel_of_interest','compartments','measurement','nr_imgs', 'um_per_pixel']
-    
-    advanced_settings = timelapse_settings+misc_settings+opperational_settings
-
-    # Toggle visibility of advanced settings
-    for setting in advanced_settings:
-        label, widget, var = vars_dict[setting]
-        if advanced_var.get() is False:
-            label.grid_remove()  # Hide the label
-            widget.grid_remove()  # Hide the widget
-        else:
-            label.grid()  # Show the label
-            widget.grid()  # Show the widget
-
-#@log_function_call
-def run_measure_gui(q, fig_queue, stop_requested):
-    global vars_dict
-    process_stdout_stderr(q)
-    try:
-        print('hello')
-        settings = check_measure_gui_settings(vars_dict)
-        measure_crop_wrapper(settings=settings, q=q, fig_queue=fig_queue)
-    except Exception as e:
-        q.put(f"Error during processing: {e}")
-        traceback.print_exc()
-    finally:
-        stop_requested.value = 1
-
-#@log_function_call
-def start_process(q, fig_queue):
-    global thread_control
-    if thread_control.get("run_thread") is not None:
-        initiate_abort()
-
-    stop_requested = Value('i', 0)  # multiprocessing shared value for inter-process communication
-    thread_control["stop_requested"] = stop_requested
-    thread_control["run_thread"] = Process(target=run_measure_gui, args=(q, fig_queue, stop_requested))
-    thread_control["run_thread"].start()
-
-#@log_function_call
-def initiate_abort():
-    global thread_control
-    if thread_control.get("stop_requested") is not None:
-        thread_control["stop_requested"].value = 1
-
-    if thread_control.get("run_thread") is not None:
-        thread_control["run_thread"].join(timeout=5)
-        if thread_control["run_thread"].is_alive():
-            thread_control["run_thread"].terminate()
-        thread_control["run_thread"] = None
-
-#@log_function_call
-def initiate_measure_root(parent_frame):
-    global vars_dict, q, canvas, fig_queue, canvas_widget, thread_control, variables, advanced_var, scrollable_frame
-    
-    style = ttk.Style(parent_frame)
-    set_dark_style(style)
-    set_default_font(parent_frame, font_name="Helvetica", size=8)
-
-    parent_frame.configure(bg='black')
-    parent_frame.grid_rowconfigure(0, weight=1)
-    parent_frame.grid_columnconfigure(0, weight=1)
-
-    fig_queue = Queue()
-    
-    # Initialize after_tasks if not already done
-    if not hasattr(parent_frame, 'after_tasks'):
-        parent_frame.after_tasks = []
-
-    def _process_fig_queue():
-        global canvas
-        try:
-            while not fig_queue.empty():
-                clear_canvas(canvas)
-                fig = fig_queue.get_nowait()
-                for ax in fig.get_axes():
-                    ax.set_xticks([])  # Remove x-axis ticks
-                    ax.set_yticks([])  # Remove y-axis ticks
-                    ax.xaxis.set_visible(False)  # Hide the x-axis
-                    ax.yaxis.set_visible(False)  # Hide the y-axis
-                fig.tight_layout()
-                fig.set_facecolor('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)
-                canvas.draw_idle()
-        except Exception as e:
-            traceback.print_exc()
-        finally:
-            after_id = canvas_widget.after(100, _process_fig_queue)
-            parent_frame.after_tasks.append(after_id)
-
-    def _process_console_queue():
-        while not q.empty():
-            message = q.get_nowait()
-            console_output.insert(tk.END, message)
-            console_output.see(tk.END)
-        after_id = console_output.after(100, _process_console_queue)
-        parent_frame.after_tasks.append(after_id)
-
-    # Clear previous content if any
-    for widget in parent_frame.winfo_children():
-        widget.destroy()
-
-    vertical_container = tk.PanedWindow(parent_frame, orient=tk.HORIZONTAL)
-    vertical_container.grid(row=0, column=0, sticky=tk.NSEW)
-    parent_frame.grid_rowconfigure(0, weight=1)
-    parent_frame.grid_columnconfigure(0, weight=1)
-
-    # Settings Section
-    settings_frame = tk.Frame(vertical_container, bg='black')
-    vertical_container.add(settings_frame, stretch="always")
-    settings_label = ttk.Label(settings_frame, text="Settings", background="black", foreground="white")
-    settings_label.grid(row=0, column=0, pady=10, padx=10)
-    scrollable_frame = ScrollableFrame(settings_frame, bg='black')
-    scrollable_frame.grid(row=1, column=0, sticky="nsew")
-    settings_frame.grid_rowconfigure(1, weight=1)
-    settings_frame.grid_columnconfigure(0, weight=1)
-    
-    # Create advanced settings checkbox
-    advanced_var = tk.BooleanVar(value=False)
-    advanced_Toggle = ToggleSwitch(scrollable_frame.scrollable_frame, text="Advanced Settings", variable=advanced_var, command=toggle_advanced_settings)
-    advanced_Toggle.grid(row=4, column=0, pady=10, padx=10)
-    settings = get_measure_crop_settings({})
-    variables = convert_settings_dict_for_gui(settings)
-    vars_dict = generate_fields(variables, scrollable_frame)
-    toggle_advanced_settings()
-    vars_dict['Test mode'] = (None, None, tk.BooleanVar(value=False))
-    
-    # Button section
-    btn_row = 1
-    run_button = CustomButton(scrollable_frame.scrollable_frame, text="Run", command=lambda: start_process(q, fig_queue), font=('Helvetica', 10))
-    run_button.grid(row=btn_row, column=0, pady=5, padx=5)
-    abort_button = CustomButton(scrollable_frame.scrollable_frame, text="Abort", command=initiate_abort, font=('Helvetica', 10))
-    abort_button.grid(row=btn_row, column=1, pady=5, padx=5)
-    btn_row += 1
-    test_mode_button = CustomButton(scrollable_frame.scrollable_frame, text="Test Mode", command=toggle_test_mode)
-    test_mode_button.grid(row=btn_row, column=0, pady=5, padx=5)
-    import_btn = CustomButton(scrollable_frame.scrollable_frame, text="Import", command=lambda: import_settings(scrollable_frame), font=('Helvetica', 10))
-    import_btn.grid(row=btn_row, column=1, pady=5, padx=5)
-    btn_row += 1
-    progress_label = ttk.Label(scrollable_frame.scrollable_frame, text="Processing: 0%", background="black", foreground="white") # Create progress field
-    progress_label.grid(row=btn_row, column=0, columnspan=2, sticky="ew", pady=(5, 0), padx=10)
-
-    # Plot Canvas Section
-    plot_frame = tk.PanedWindow(vertical_container, orient=tk.VERTICAL)
-    vertical_container.add(plot_frame, stretch="always")
-    figure = Figure(figsize=(30, 4), dpi=100, facecolor='black')
-    plot = figure.add_subplot(111)
-    plot.plot([], [])
-    plot.axis('off')
-    canvas = FigureCanvasTkAgg(figure, master=plot_frame)
-    canvas.get_tk_widget().configure(cursor='arrow', background='black', highlightthickness=0)
-    canvas_widget = canvas.get_tk_widget()
-    plot_frame.add(canvas_widget, stretch="always")
-    canvas.draw()
-    canvas.figure = figure
-
-    # Console Section
-    console_frame = tk.Frame(vertical_container, bg='black')
-    vertical_container.add(console_frame, stretch="always")
-    console_label = ttk.Label(console_frame, text="Console", background="black", foreground="white")
-    console_label.grid(row=0, column=0, pady=10, padx=10)
-    console_output = scrolledtext.ScrolledText(console_frame, height=10, bg='black', fg='white', insertbackground='white')
-    console_output.grid(row=1, column=0, sticky="nsew")
-    console_frame.grid_rowconfigure(1, weight=1)
-    console_frame.grid_columnconfigure(0, weight=1)
-
-    q = Queue()
-    sys.stdout = StdoutRedirector(console_output)
-    sys.stderr = StdoutRedirector(console_output)
-    
-    _process_console_queue()
-    _process_fig_queue()
-    
-    after_id = parent_frame.after(100, lambda: main_thread_update_function(parent_frame, q, fig_queue, canvas_widget, progress_label))
-    parent_frame.after_tasks.append(after_id)
-    
-    return parent_frame, vars_dict
-
-def gui_measure():
-    root = tk.Tk()
-    width = root.winfo_screenwidth()
-    height = root.winfo_screenheight()
-    root.geometry(f"{width}x{height}") 
-    root.title("SpaCr: measure objects")
-    
-    # Clear previous content if any
-    if hasattr(root, 'content_frame'):
-        for widget in root.content_frame.winfo_children():
-            widget.destroy()
-        root.content_frame.grid_forget()
-    else:
-        root.content_frame = tk.Frame(root)
-        root.content_frame.grid(row=1, column=0, sticky="nsew")
-        root.grid_rowconfigure(1, weight=1)
-        root.grid_columnconfigure(0, weight=1)
-    
-    initiate_measure_root(root.content_frame)
-    create_menu_bar(root)
-    root.mainloop()
+def start_measure_app():
+    app = MainApp(default_app="Measure")
+    app.mainloop()
 
 if __name__ == "__main__":
-    gui_measure()
+    start_measure_app()

spacr/app_sequencing.py

@@ -0,0 +1,8 @@
+from .gui import MainApp
+
+def start_seq_app():
+    app = MainApp(default_app="Sequencing")
+    app.mainloop()
+
+if __name__ == "__main__":
+    start_seq_app()

spacr/app_umap.py

@@ -0,0 +1,8 @@
+from .gui import MainApp
+
+def start_umap_app():
+    app = MainApp(default_app="Umap")
+    app.mainloop()
+
+if __name__ == "__main__":
+    start_umap_app()

spacr/core.py

@@ -3021,9 +3021,9 @@ def generate_image_umap(settings={}):
     """
  
     from .io import _read_and_join_tables
-    from .utils import get_db_paths, preprocess_data, reduction_and_clustering, remove_noise, generate_colors, correct_paths, plot_embedding, plot_clusters_grid, cluster_feature_analysis, generate_umap_from_images
-    from .settings import get_umap_image_settings
-    settings = get_umap_image_settings(settings)
+    from .utils import get_db_paths, preprocess_data, reduction_and_clustering, remove_noise, generate_colors, correct_paths, plot_embedding, plot_clusters_grid, cluster_feature_analysis #, generate_umap_from_images
+    from .settings import set_default_umap_image_settings
+    settings = set_default_umap_image_settings(settings)
 
     if isinstance(settings['src'], str):
         settings['src'] = [settings['src']]
@@ -3109,7 +3109,9 @@ def generate_image_umap(settings={}):
 
     else:
         if settings['resnet_features']:
-            numeric_data, embedding, labels = generate_umap_from_images(image_paths, settings['n_neighbors'], settings['min_dist'], settings['metric'], settings['clustering'], settings['eps'], settings['min_samples'], settings['n_jobs'], settings['verbose'])
+            # placeholder for resnet features, not implemented yet
+            pass
+            #numeric_data, embedding, labels = generate_umap_from_images(image_paths, settings['n_neighbors'], settings['min_dist'], settings['metric'], settings['clustering'], settings['eps'], settings['min_samples'], settings['n_jobs'], settings['verbose'])
         else:
             # Apply the trained reducer to the entire dataset
             numeric_data = preprocess_data(all_df, settings['filter_by'], settings['remove_highly_correlated'], settings['log_data'], settings['exclude'])
@@ -3205,9 +3207,9 @@ def reducer_hyperparameter_search(settings={}, reduction_params=None, dbscan_par
     
     from .io import _read_and_join_tables
     from .utils import get_db_paths, preprocess_data, search_reduction_and_clustering, generate_colors
-    from .settings import get_umap_image_settings
+    from .settings import set_default_umap_image_settings
 
-    settings = get_umap_image_settings(settings)
+    settings = set_default_umap_image_settings(settings)
     pointsize = settings['dot_size']
     if isinstance(dbscan_params, dict):
         dbscan_params = [dbscan_params]

spacr/deep_spacr.py

@@ -10,6 +10,9 @@ import matplotlib.pyplot as plt
 from PIL import Image
 
 from .logger import log_function_call
+from .utils import close_multiprocessing_processes, reset_mp
+#reset_mp()
+#close_multiprocessing_processes()
 
 def evaluate_model_core(model, loader, loader_name, epoch, loss_type):
     """
@@ -42,7 +45,6 @@ def evaluate_model_core(model, loader, loader_name, epoch, loss_type):
         for batch_idx, (data, target, _) in enumerate(loader, start=1):
             start_time = time.time()
             data, target = data.to(device), target.to(device).float()
-            #data, target = data.to(torch.float).to(device), target.to(device).float()
             output = model(data)
             loss += F.binary_cross_entropy_with_logits(output, target, reduction='sum').item()
             loss = calculate_loss(output, target, loss_type=loss_type)

spacr/gui.py

@@ -1,20 +1,15 @@
 import tkinter as tk
 from tkinter import ttk
-from tkinter import font as tkFont
 from PIL import Image, ImageTk
 import os
 import requests
-
-# Import your GUI apps
-from .app_mask import initiate_mask_root
-from .app_measure import initiate_measure_root
+from multiprocessing import set_start_method
+from .gui_utils import set_dark_style, create_menu_bar, initiate_root, spacrButton
 from .app_annotate import initiate_annotation_app_root
 from .app_make_masks import initiate_mask_app_root
-from .app_classify import initiate_classify_root
-from .gui_utils import CustomButton, set_dark_style, create_menu_bar
 
 class MainApp(tk.Tk):
-    def __init__(self):
+    def __init__(self, default_app=None):
         super().__init__()
         width = self.winfo_screenwidth()
         height = self.winfo_screenheight()
@@ -25,16 +20,34 @@ class MainApp(tk.Tk):
         set_dark_style(style)
 
         self.gui_apps = {
-            "Mask": (initiate_mask_root, "Generate cellpose masks for cells, nuclei and pathogen images."),
-            "Measure": (initiate_measure_root, "Measure single object intensity and morphological feature. Crop and save single object image"),
+            "Mask": (lambda frame: initiate_root(frame, 'mask'), "Generate cellpose masks for cells, nuclei and pathogen images."),
+            "Measure": (lambda frame: initiate_root(frame, 'measure'), "Measure single object intensity and morphological feature. Crop and save single object image"),
             "Annotate": (initiate_annotation_app_root, "Annotation single object images on a grid. Annotations are saved to database."),
             "Make Masks": (initiate_mask_app_root, "Adjust pre-existing Cellpose models to your specific dataset for improved performance"),
-            "Classify": (initiate_classify_root, "Train Torch Convolutional Neural Networks (CNNs) or Transformers to classify single object images.")
+            "Classify": (lambda frame: initiate_root(frame, 'classify'), "Train Torch Convolutional Neural Networks (CNNs) or Transformers to classify single object images."),
+            "Sequencing": (lambda frame: initiate_root(frame, 'sequencing'), "Analyze sequensing data."),
+            "Umap": (lambda frame: initiate_root(frame, 'umap'), "Generate UMAP embedings with datapoints represented as images.")
         }
 
         self.selected_app = tk.StringVar()
         self.create_widgets()
 
+
+        if default_app == "Mask":
+            self.load_app(default_app, self.gui_apps[default_app][0])
+        elif default_app == "Measure":
+            self.load_app(default_app, self.gui_apps[default_app][1])
+        elif default_app == "Annotate":
+            self.load_app(default_app, self.gui_apps[default_app][2])
+        elif default_app == "Make Masks":
+            self.load_app(default_app, self.gui_apps[default_app][3])
+        elif default_app == "Classify":
+            self.load_app(default_app, self.gui_apps[default_app][4])
+        elif default_app == "Sequencing":
+            self.load_app(default_app, self.gui_apps[default_app][5])
+        elif default_app == "Umap":
+            self.load_app(default_app, self.gui_apps[default_app][6])
+
     def create_widgets(self):
         # Create the menu bar
         create_menu_bar(self)
@@ -74,7 +87,8 @@ class MainApp(tk.Tk):
             app_func, app_desc = app_data
 
             # Create custom button with text
-            button = CustomButton(buttons_frame, text=app_name, command=lambda app_name=app_name, app_func=app_func: self.load_app(app_name, app_func), font=('Helvetica', 12))
+            button = spacrButton(buttons_frame, text=app_name, command=lambda app_name=app_name, app_func=app_func: self.load_app(app_name, app_func), font=('Helvetica', 12))
+            #button = ttk.Button(buttons_frame, text=app_name, command=lambda app_name=app_name, app_func=app_func: self.load_app(app_name, app_func), style='Custom.TButton')
             button.grid(row=i, column=0, pady=10, padx=10, sticky="w")
 
             description_label = tk.Label(buttons_frame, text=app_desc, bg="black", fg="white", wraplength=800, justify="left", font=('Helvetica', 12))
@@ -146,4 +160,5 @@ def gui_app():
     app.mainloop()
 
 if __name__ == "__main__":
-    gui_app()
+    set_start_method('spawn', force=True)
+    gui_app()