spacr 0.0.18__py3-none-any.whl → 0.0.21__py3-none-any.whl

spacr/gui_mask_app.py

@@ -1,4 +1,4 @@
-import spacr, sys, ctypes, csv, matplotlib
+import sys, ctypes, matplotlib
 import tkinter as tk
 from tkinter import ttk, scrolledtext
 from ttkthemes import ThemedTk
@@ -16,11 +16,19 @@ except AttributeError:
     pass
 
 from .logger import log_function_call
-from .gui_utils import ScrollableFrame, StdoutRedirector, safe_literal_eval, clear_canvas, main_thread_update_function, create_dark_mode, set_dark_style, set_default_font, generate_fields, process_stdout_stderr
-from .gui_utils import mask_variables, check_mask_gui_settings, add_mask_gui_defaults, preprocess_generate_masks_wrapper
+from .gui_utils import ScrollableFrame, StdoutRedirector, clear_canvas, main_thread_update_function, create_dark_mode, set_dark_style, generate_fields, process_stdout_stderr, set_default_font, style_text_boxes
+from .gui_utils import mask_variables, check_mask_gui_settings, preprocess_generate_masks_wrapper, read_settings_from_csv, update_settings_from_csv#, toggle_advanced_settings
 
 thread_control = {"run_thread": None, "stop_requested": False}
 
+def toggle_advanced_settings():
+    advanced = advanced_var.get()
+    for widget in advanced_widgets:
+        if advanced:
+            widget.grid()
+        else:
+            widget.grid_remove()
+
 @log_function_call
 def initiate_abort():
     global thread_control
@@ -39,7 +47,7 @@ def run_mask_gui(q, fig_queue, stop_requested):
     process_stdout_stderr(q)
     try:
         settings = check_mask_gui_settings(vars_dict)
-        settings = add_mask_gui_defaults(settings)
+        #settings = add_mask_gui_defaults(settings)
         #for key in settings:
         #    value = settings[key]
         #    print(key, value, type(value))
@@ -65,29 +73,15 @@ def import_settings(scrollable_frame):
     global vars_dict
 
     csv_file_path = filedialog.askopenfilename(filetypes=[("CSV files", "*.csv")])
-    
-    if not csv_file_path:
-        return
-    
-    imported_variables = {}
-
-    with open(csv_file_path, newline='') as csvfile:
-        reader = csv.DictReader(csvfile)
-        for row in reader:
-            key = row['Key']
-            value = row['Value']
-            # Evaluate the value safely using safe_literal_eval
-            imported_variables[key] = safe_literal_eval(value)
-
-    # Track changed variables and apply the imported ones, printing changes as we go
-    for key, var in vars_dict.items():
-        if key in imported_variables and var.get() != imported_variables[key]:
-            print(f"Updating '{key}' from '{var.get()}' to '{imported_variables[key]}'")
-            var.set(imported_variables[key])
+    csv_settings = read_settings_from_csv(csv_file_path)
+    variables = mask_variables()
+    #variables = add_mask_gui_defaults(variables)
+    new_settings = update_settings_from_csv(variables, csv_settings)
+    vars_dict = generate_fields(new_settings, scrollable_frame)
     
 @log_function_call
 def initiate_mask_root(width, height):
-    global root, vars_dict, q, canvas, fig_queue, canvas_widget, thread_control
+    global root, vars_dict, q, canvas, fig_queue, canvas_widget, thread_control, advanced_widgets, advanced_var
         
     theme = 'breeze'
     
@@ -101,7 +95,8 @@ def initiate_mask_root(width, height):
         style = ttk.Style(root)
         set_dark_style(style)
         
-    set_default_font(root, font_name="Arial", size=10)
+    style_text_boxes(style)
+    set_default_font(root, font_name="Arial", size=8)
     #root.state('zoomed')  # For Windows to maximize the window
     root.attributes('-fullscreen', True)
     root.geometry(f"{width}x{height}")
@@ -153,6 +148,10 @@ def initiate_mask_root(width, height):
     # Setup for user input fields (variables)
     variables = mask_variables()
     vars_dict = generate_fields(variables, scrollable_frame)
+    #del vars_dict['fps']
+
+    # Debugging: print vars_dict to ensure it is populated correctly
+    #print("vars_dict:", vars_dict)
     
     # Horizontal container for Matplotlib figure and the vertical pane (for settings and console)
     horizontal_container = tk.PanedWindow(vertical_container, orient=tk.VERTICAL) #HORIZONTAL
@@ -181,21 +180,27 @@ def initiate_mask_root(width, height):
     q = Queue()
     sys.stdout = StdoutRedirector(console_output)
     sys.stderr = StdoutRedirector(console_output)
+
+    advanced_var = tk.BooleanVar()
+    advanced_checkbox = ttk.Checkbutton(scrollable_frame.scrollable_frame, text="Advanced Settings", variable=advanced_var, command=toggle_advanced_settings)
+    advanced_checkbox.grid(row=46, column=1, pady=10, padx=10)
     
     # This is your GUI setup where you create the Run button
     run_button = ttk.Button(scrollable_frame.scrollable_frame, text="Run",command=lambda: start_process(q, fig_queue))
-    run_button.grid(row=40, column=0, pady=10)
+    run_button.grid(row=45, column=0, pady=10, padx=10)
     
     abort_button = ttk.Button(scrollable_frame.scrollable_frame, text="Abort", command=initiate_abort)
-    abort_button.grid(row=40, column=1, pady=10)
+    abort_button.grid(row=45, column=1, pady=10, padx=10)
     
     progress_label = ttk.Label(scrollable_frame.scrollable_frame, text="Processing: 0%", background="#333333", foreground="white")
-    progress_label.grid(row=41, column=0, columnspan=2, sticky="ew", pady=(5, 0))
-    
+    progress_label.grid(row=41, column=0, columnspan=2, sticky="ew", pady=(5, 0), padx=10)
+
     # Create the Import Settings button
     import_btn = tk.Button(root, text="Import Settings", command=lambda: import_settings(scrollable_frame))
-    import_btn.pack(pady=20)
+    import_btn.pack(pady=20, padx=10)
+
     
+
     _process_console_queue()
     _process_fig_queue()
     create_dark_mode(root, style, console_output)
@@ -207,6 +212,7 @@ def initiate_mask_root(width, height):
 def gui_mask():
     global vars_dict, root
     root, vars_dict = initiate_mask_root(1000, 1500)
+    
     root.mainloop()
     
 if __name__ == "__main__":

spacr/gui_measure_app.py

@@ -7,7 +7,7 @@ import matplotlib.pyplot as plt
 matplotlib.use('Agg')  # Use the non-GUI Agg backend
 from multiprocessing import Process, Queue, Value
 from ttkthemes import ThemedTk
-from tkinter import filedialog
+from tkinter import filedialog, StringVar, BooleanVar, IntVar, DoubleVar, Tk
 
 try:
     ctypes.windll.shcore.SetProcessDpiAwareness(True)
@@ -16,7 +16,7 @@ except AttributeError:
 
 from .logger import log_function_call
 from .gui_utils import ScrollableFrame, StdoutRedirector, process_stdout_stderr, set_dark_style, set_default_font, generate_fields, create_dark_mode, main_thread_update_function
-from .gui_utils import measure_variables, measure_crop_wrapper, clear_canvas, safe_literal_eval, check_measure_gui_settings, add_measure_gui_defaults
+from .gui_utils import measure_variables, measure_crop_wrapper, clear_canvas, safe_literal_eval, check_measure_gui_settings, read_settings_from_csv, update_settings_from_csv
 
 thread_control = {"run_thread": None, "stop_requested": False}
 
@@ -25,8 +25,8 @@ 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)
-        settings = add_measure_gui_defaults(settings)
         #for key in settings:
         #    value = settings[key]
         #    print(key, value, type(value))
@@ -60,29 +60,15 @@ def initiate_abort():
             thread_control["run_thread"].terminate()
         thread_control["run_thread"] = None
 
+@log_function_call
 def import_settings(scrollable_frame):
-    global vars_dict, original_variables_structure
+    global vars_dict
 
     csv_file_path = filedialog.askopenfilename(filetypes=[("CSV files", "*.csv")])
-    
-    if not csv_file_path:
-        return
-    
-    imported_variables = {}
-
-    with open(csv_file_path, newline='') as csvfile:
-        reader = csv.DictReader(csvfile)
-        for row in reader:
-            key = row['Key']
-            value = row['Value']
-            # Evaluate the value safely using safe_literal_eval
-            imported_variables[key] = safe_literal_eval(value)
-
-    # Track changed variables and apply the imported ones, printing changes as we go
-    for key, var in vars_dict.items():
-        if key in imported_variables and var.get() != imported_variables[key]:
-            print(f"Updating '{key}' from '{var.get()}' to '{imported_variables[key]}'")
-            var.set(imported_variables[key])
+    csv_settings = read_settings_from_csv(csv_file_path)
+    variables = measure_variables()
+    new_settings = update_settings_from_csv(variables, csv_settings)
+    vars_dict = generate_fields(new_settings, scrollable_frame)
 
 @log_function_call
 def initiate_measure_root(width, height):
@@ -201,7 +187,7 @@ def initiate_measure_root(width, height):
     _process_fig_queue()
     create_dark_mode(root, style, console_output)
     
-    root.after(100, lambda: main_thread_update_function(root, q, fig_queue, canvas_widget, progress_label))
+    #root.after(100, lambda: main_thread_update_function(root, q, fig_queue, canvas_widget, progress_label))
     
     return root, vars_dict
 

spacr/gui_utils.py

@@ -1,6 +1,6 @@
-import spacr, inspect, traceback, io, sys, ast, ctypes, matplotlib, re
-matplotlib.use('Agg')
+import spacr, inspect, traceback, io, sys, ast, ctypes, matplotlib, re, csv
 import matplotlib.pyplot as plt
+matplotlib.use('Agg')
 import numpy as np
 import tkinter as tk
 from tkinter import ttk, messagebox
@@ -14,6 +14,41 @@ except AttributeError:
 
 from .logger import log_function_call
 
+def set_default_font(root, font_name="Helvetica", size=12):
+    default_font = (font_name, size)
+    root.option_add("*Font", default_font)
+    root.option_add("*TButton.Font", default_font)
+    root.option_add("*TLabel.Font", default_font)
+    root.option_add("*TEntry.Font", default_font)
+
+def style_text_boxes(style):
+    style.configure('TEntry', padding='5 5 5 5', borderwidth=1, relief='solid', background='#333333', foreground='#ffffff')
+    style.configure('TButton', padding='10 10 10 10', borderwidth=1, relief='solid', background='#444444', foreground='#ffffff', font=('Helvetica', 12, 'bold'))
+    style.map('TButton',
+              background=[('active', '#555555'), ('disabled', '#222222')],
+              foreground=[('active', '#ffffff'), ('disabled', '#888888')])
+    style.configure('TLabel', padding='5 5 5 5', borderwidth=1, relief='flat', background='#2e2e2e', foreground='#ffffff')
+
+def read_settings_from_csv(csv_file_path):
+    settings = {}
+    with open(csv_file_path, newline='') as csvfile:
+        reader = csv.DictReader(csvfile)
+        for row in reader:
+            key = row['Key']
+            value = row['Value']
+            settings[key] = value
+    return settings
+
+def update_settings_from_csv(variables, csv_settings):
+    new_settings = variables.copy()  # Start with a copy of the original settings
+    for key, value in csv_settings.items():
+        if key in new_settings:
+            # Get the variable type and options from the original settings
+            var_type, options, _ = new_settings[key]
+            # Update the default value with the CSV value, keeping the type and options unchanged
+            new_settings[key] = (var_type, options, value)
+    return new_settings
+
 def safe_literal_eval(value):
     try:
         # First, try to evaluate as a literal
@@ -31,7 +66,7 @@ def disable_interactivity(fig):
         for handler_id in list(handlers.keys()):
             fig.canvas.mpl_disconnect(handler_id)
 
-def set_default_font(app, font_name="Arial Bold", size=10):
+def set_default_font_v1(app, font_name="Arial Bold", size=10):
     default_font = nametofont("TkDefaultFont")
     text_font = nametofont("TkTextFont")
     fixed_font = nametofont("TkFixedFont")
@@ -103,62 +138,52 @@ def check_mask_gui_settings(vars_dict):
 def check_measure_gui_settings(vars_dict):
     settings = {}
     for key, var in vars_dict.items():
-        value = var.get()  # This retrieves the string representation for entries or the actual value for checkboxes and combos
+        value = var.get()  # Retrieves the string representation for entries or the actual value for checkboxes and combos.
 
         try:
-            if key == 'channels' or key == 'png_dims':
-                # Converts string representation to a list of integers
+            if key in ['channels', 'png_dims']:
                 settings[key] = [int(chan) for chan in ast.literal_eval(value)] if value else []
                 
             elif key in ['cell_loc', 'pathogen_loc', 'treatment_loc']:
-                settings[key] = ast.literal_eval(value) if value else None
-                
+                # Convert to a list of lists of strings, ensuring all structures are lists.
+                settings[key] = [list(map(str, sublist)) for sublist in ast.literal_eval(value)] if value else []
+
             elif key == 'dialate_png_ratios':
-                settings[key] = [float(num) for num in eval(value)] if value else None
+                settings[key] = [float(num) for num in ast.literal_eval(value)] if value else []
 
             elif key == 'normalize':
-                # Converts 'normalize' into a list of two integers
-                settings[key] = [int(num) for num in ast.literal_eval(value)] if value else None
+                settings[key] = [int(num) for num in ast.literal_eval(value)] if value else []
 
-            elif key == 'normalize_by':
-                # 'normalize_by' is a string, so directly assign the value
+            # Directly assign string values for these specific keys
+            elif key in ['normalize_by', 'experiment', 'measurement', 'input_folder']:
                 settings[key] = value
 
             elif key == 'png_size':
-                # Converts string representation into a list of lists of integers
-                temp_val = ast.literal_eval(value) if value else []
-                settings[key] = [list(map(int, dim)) for dim in temp_val] if temp_val else None
-
-            # Handling for other keys as in your original function...
+                settings[key] = [list(map(int, dim)) for dim in ast.literal_eval(value)] if value else []
             
-            elif key in ['pathogens', 'treatments', 'cells', 'crop_mode', 'timelapse_objects']:
-                # Ensuring these are evaluated correctly as lists or other structures
-                settings[key] = ast.literal_eval(value) if value else None
-
-            elif key == 'timelapse_objects':
-                # Ensure it's a list of strings
-                settings[key] = eval(value) if value else []
-
-            # Handling for keys that should be treated as strings directly
-            elif key in ['normalize_by', 'experiment', 'measurement', 'input_folder']:
-                settings[key] = str(value) if value else None
+            # Ensure these are lists of strings, converting from tuples if necessary
+            elif key in ['timelapse_objects', 'crop_mode', 'cells', 'pathogens', 'treatments']:
+                eval_value = ast.literal_eval(value) if value else []
+                settings[key] = list(map(str, eval_value)) if isinstance(eval_value, (list, tuple)) else [str(eval_value)]
 
-            # Handling for single values that are not strings (int, float, bool)
+            # Handling for single non-string values (int, float, bool)
             elif key in ['cell_mask_dim', 'cell_min_size', 'nucleus_mask_dim', 'nucleus_min_size', 'pathogen_mask_dim', 'pathogen_min_size', 'cytoplasm_min_size', 'max_workers', 'channel_of_interest', 'nr_imgs']:
                 settings[key] = int(value) if value else None
 
             elif key == 'um_per_pixel':
                 settings[key] = float(value) if value else None
 
-            # Direct handling of boolean values based on checkboxes
+            # Handling boolean values based on checkboxes
             elif key in ['save_png', 'use_bounding_box', 'save_measurements', 'plot', 'plot_filtration', 'include_uninfected', 'dialate_pngs', 'timelapse', 'representative_images']:
-                settings[key] = bool(value)
+                settings[key] = var.get()
 
         except SyntaxError as e:
-            messagebox.showerror("Error", f"Syntax error processing {key}: {str(e)}")
+            print(f"Syntax error processing {key}: {str(e)}")
+            #messagebox.showerror("Error", f"Syntax error processing {key}: {str(e)}")
             return None
         except Exception as e:
-            messagebox.showerror("Error", f"Error processing {key}: {str(e)}")
+            print(f"Error processing {key}: {str(e)}")
+            #messagebox.showerror("Error", f"Error processing {key}: {str(e)}")
             return None
 
     return settings
@@ -268,6 +293,10 @@ def sim_variables():
     }
     return variables
 
+def add_measure_gui_defaults(settings):
+    settings['compartments'] = ['pathogen', 'cytoplasm']
+    return settings
+
 def measure_variables():
     variables = {
         'input_folder':('entry', None, '/mnt/data/CellVoyager/40x/einar/mitotrackerHeLaToxoDsRed_20240224_123156/test_gui/merged'),
@@ -304,6 +333,7 @@ def measure_variables():
         'treatments': ('entry', None, '["cm","lovastatin_20uM"]'),
         'treatment_loc': ('entry', None, '[["c1","c2"], ["c3","c4"]]'),
         'channel_of_interest':('entry', None, 3),
+        'compartments':('entry', None, '["pathogen","cytoplasm"]'),
         'measurement':('entry', None, 'mean_intensity'),
         'nr_imgs':('entry', None, 32),
         'um_per_pixel':('entry', None, 0.1)
@@ -352,7 +382,7 @@ def classify_variables():
     return variables
     
 
-@log_function_call
+#@log_function_call
 def create_input_field(frame, label_text, row, var_type='entry', options=None, default_value=None):
     label = ttk.Label(frame, text=label_text, style='TLabel')  # Assuming you have a dark mode style for labels too
     label.grid(column=0, row=row, sticky=tk.W, padx=5, pady=5)
@@ -376,10 +406,6 @@ def create_input_field(frame, label_text, row, var_type='entry', options=None, d
         var = None  # Placeholder in case of an undefined var_type
     
     return var
-
-def add_measure_gui_defaults(settings):
-    settings['compartments'] = ['pathogen', 'cytoplasm']
-    return settings
     
 def mask_variables():
     variables = {
@@ -401,10 +427,10 @@ def mask_variables():
         'pathogen_background': ('entry', None, 100),
         'pathogen_Signal_to_noise': ('entry', None, 3),
         'pathogen_CP_prob': ('entry', None, 0),
-        #'preprocess': ('check', None, True),
-        #'masks': ('check', None, True),
-        #'examples_to_plot': ('entry', None, 1),
-        #'randomize': ('check', None, True),
+        'preprocess': ('check', None, True),
+        'masks': ('check', None, True),
+        'examples_to_plot': ('entry', None, 1),
+        'randomize': ('check', None, True),
         'batch_size': ('entry', None, 50),
         'timelapse': ('check', None, False),
         'timelapse_displacement': ('entry', None, None),
@@ -413,14 +439,14 @@ def mask_variables():
         'timelapse_remove_transient': ('check', None, True),
         'timelapse_mode': ('combo',  ['trackpy', 'btrack'], 'trackpy'),
         'timelapse_objects': ('combo', ['cell','nucleus','pathogen','cytoplasm', None], None),
-        #'fps': ('entry', None, 2),
-        #'remove_background': ('check', None, True),
+        'fps': ('entry', None, 2),
+        'remove_background': ('check', None, True),
         'lower_quantile': ('entry', None, 0.01),
-        #'merge': ('check', None, False),
-        #'normalize_plots': ('check', None, True),
-        #'all_to_mip': ('check', None, False),
-        #'pick_slice': ('check', None, False),
-        #'skip_mode': ('entry', None, None),
+        'merge': ('check', None, False),
+        'normalize_plots': ('check', None, True),
+        'all_to_mip': ('check', None, False),
+        'pick_slice': ('check', None, False),
+        'skip_mode': ('entry', None, None),
         'save': ('check', None, True),
         'plot': ('check', None, True),
         'workers': ('entry', None, 30),
@@ -488,7 +514,7 @@ def set_dark_style(style):
     style.configure('TEntry', background='#333333', foreground='white')
     style.configure('TCheckbutton', background='#333333', foreground='white')
 
-@log_function_call   
+#@log_function_call   
 def main_thread_update_function(root, q, fig_queue, canvas_widget, progress_label):
     try:
         ansi_escape_pattern = re.compile(r'\x1B\[[0-?]*[ -/]*[@-~]')
@@ -497,6 +523,8 @@ def main_thread_update_function(root, q, fig_queue, canvas_widget, progress_labe
             clean_message = ansi_escape_pattern.sub('', message)
             if clean_message.startswith("Progress"):
                 progress_label.config(text=clean_message)
+            if clean_message.startswith("\rProgress"):
+                progress_label.config(text=clean_message)
             elif clean_message.startswith("Successfully"):
                 progress_label.config(text=clean_message)
             elif clean_message.startswith("Processing"):
@@ -543,7 +571,6 @@ def clear_canvas(canvas):
     # Redraw the now empty canvas without changing its size
     canvas.draw_idle()
     
-@log_function_call
 def measure_crop_wrapper(settings, q, fig_queue):
     """
     Wraps the measure_crop function to integrate with GUI processes.
@@ -567,7 +594,8 @@ def measure_crop_wrapper(settings, q, fig_queue):
     plt.show = my_show
 
     try:
-        spacr.measure.measure_crop(settings=settings, annotation_settings={}, advanced_settings={})
+        print('start')
+        spacr.measure.measure_crop(settings=settings)
     except Exception as e:
         errorMessage = f"Error during processing: {e}"
         q.put(errorMessage)  # Send the error message to the GUI via the queue
@@ -599,7 +627,7 @@ def preprocess_generate_masks_wrapper(settings, q, fig_queue):
     plt.show = my_show
 
     try:
-        spacr.core.preprocess_generate_masks(settings['src'], settings=settings, advanced_settings={})
+        spacr.core.preprocess_generate_masks(settings['src'], settings=settings)
     except Exception as e:
         errorMessage = f"Error during processing: {e}"
         q.put(errorMessage)  # Send the error message to the GUI via the queue