spacr 0.1.6__py3-none-any.whl → 0.1.8__py3-none-any.whl

spacr/gui_utils.py

@@ -1,9 +1,9 @@
-import io, sys, ast, ctypes, re, csv, ast
+import os, io, sys, ast, ctypes, re, ast, sqlite3
 import tkinter as tk
 from tkinter import ttk
 
 from . gui_core import initiate_root
-from .gui_elements import spacrLabel, spacrCheckbutton, set_dark_style
+from .gui_elements import spacrLabel, spacrCheckbutton, ImageApp
 
 try:
     ctypes.windll.shcore.SetProcessDpiAwareness(True)
@@ -17,9 +17,7 @@ def set_default_font(root, font_name="Helvetica", size=12):
     root.option_add("*TLabel.Font", default_font)
     root.option_add("*TEntry.Font", default_font)
 
-def proceed_with_app(root, app_name, app_func):
-    from .app_annotate import gui_annotate
-    from .app_make_masks import gui_make_masks
+def proceed_with_app_v1(root, app_name, app_func):
     from .gui import gui_app
 
     # Clear the current content frame
@@ -47,11 +45,23 @@ def proceed_with_app(root, app_name, app_func):
     elif app_name == "Umap":
         initiate_root(root.content_frame, 'umap')
     elif app_name == "Annotate":
-        gui_annotate()
+        initiate_root(root.content_frame, 'annotate')
     elif app_name == "Make Masks":
-        gui_make_masks()
+        initiate_root(root.content_frame, 'make_masks')
     else:
         raise ValueError(f"Invalid app name: {app_name}")
+    
+def proceed_with_app(root, app_name, app_func):
+    # Clear the current content frame
+    if hasattr(root, 'content_frame'):
+        for widget in root.content_frame.winfo_children():
+            try:
+                widget.destroy()
+            except tk.TclError as e:
+                print(f"Error destroying widget: {e}")
+
+    # Initialize the new app in the content frame
+    app_func(root.content_frame)
 
 def load_app(root, app_name, app_func):
     # Cancel all scheduled after tasks
@@ -60,15 +70,15 @@ def load_app(root, app_name, app_func):
             root.after_cancel(task)
     root.after_tasks = []
 
-    # Exit functionality only for the annotation app
-    if app_name != "Annotate" and hasattr(root, 'current_app_exit_func'):
+    # Exit functionality only for the annotation and make_masks apps
+    if app_name not in ["Annotate", "make_masks"] and hasattr(root, 'current_app_exit_func'):
         root.next_app_func = proceed_with_app
         root.next_app_args = (app_name, app_func)  # Ensure correct arguments
         root.current_app_exit_func()
     else:
         proceed_with_app(root, app_name, app_func)
 
-def parse_list(value):
+def parse_list_v1(value):
     try:
         parsed_value = ast.literal_eval(value)
         if isinstance(parsed_value, list):
@@ -78,6 +88,16 @@ def parse_list(value):
     except (ValueError, SyntaxError):
         raise ValueError("Invalid format for list")
     
+def parse_list(value):
+    try:
+        parsed_value = ast.literal_eval(value)
+        if isinstance(parsed_value, list):
+            return parsed_value
+        else:
+            raise ValueError(f"Expected a list but got {type(parsed_value).__name__}")
+    except (ValueError, SyntaxError) as e:
+        raise ValueError(f"Invalid format for list: {value}. Error: {e}")
+    
 def create_input_field(frame, label_text, row, var_type='entry', options=None, default_value=None):
     label_column = 0
     widget_column = 1
@@ -137,3 +157,170 @@ def cancel_after_tasks(frame):
         for task in frame.after_tasks:
             frame.after_cancel(task)
         frame.after_tasks.clear()
+
+def main_thread_update_function(root, q, fig_queue, canvas_widget, progress_label):
+    try:
+        ansi_escape_pattern = re.compile(r'\x1B\[[0-?]*[ -/]*[@-~]')
+        while not q.empty():
+            message = q.get_nowait()
+            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"):
+                progress_label.config(text=clean_message)
+            elif clean_message.startswith("scale"):
+                pass
+            elif clean_message.startswith("plot_cropped_arrays"):
+                pass
+            elif clean_message == "" or clean_message == "\r" or clean_message.strip() == "":
+                pass
+            else:
+                print(clean_message)
+    except Exception as e:
+        print(f"Error updating GUI canvas: {e}")
+    finally:
+        root.after(100, lambda: main_thread_update_function(root, q, fig_queue, canvas_widget, progress_label))
+
+def annotate(settings):
+    from .settings import set_annotate_default_settings
+    settings = set_annotate_default_settings(settings)
+    src  = settings['src']
+
+    db = os.path.join(src, 'measurements/measurements.db')
+    conn = sqlite3.connect(db)
+    c = conn.cursor()
+    c.execute('PRAGMA table_info(png_list)')
+    cols = c.fetchall()
+    if settings['annotation_column'] not in [col[1] for col in cols]:
+        c.execute(f"ALTER TABLE png_list ADD COLUMN {settings['annotation_column']} integer")
+    conn.commit()
+    conn.close()
+
+    root = tk.Tk()
+    root.geometry(settings['geom'])
+    app = ImageApp(root, db, src, image_type=settings['image_type'], channels=settings['channels'], image_size=settings['img_size'], grid_rows=settings['rows'], grid_cols=settings['columns'], annotation_column=settings['annotation_column'], normalize=settings['normalize'], percentiles=settings['percentiles'], measurement=settings['measurement'], threshold=settings['threshold'])
+    next_button = tk.Button(root, text="Next", command=app.next_page)
+    next_button.grid(row=app.grid_rows, column=app.grid_cols - 1)
+    back_button = tk.Button(root, text="Back", command=app.previous_page)
+    back_button.grid(row=app.grid_rows, column=app.grid_cols - 2)
+    exit_button = tk.Button(root, text="Exit", command=app.shutdown)
+    exit_button.grid(row=app.grid_rows, column=app.grid_cols - 3)
+    
+    app.load_images()
+    root.mainloop()
+
+def generate_annotate_fields(frame):
+    from .settings import set_annotate_default_settings
+    vars_dict = {}
+    settings = set_annotate_default_settings(settings={})
+    
+    for setting in settings:
+        vars_dict[setting] = {
+            'entry': ttk.Entry(frame),
+            'value': settings[setting]
+        }
+
+    # Arrange input fields and labels
+    for row, (name, data) in enumerate(vars_dict.items()):
+        ttk.Label(frame, text=f"{name.replace('_', ' ').capitalize()}:",
+                  background="black", foreground="white").grid(row=row, column=0)
+        if isinstance(data['value'], list):
+            # Convert lists to comma-separated strings
+            data['entry'].insert(0, ','.join(map(str, data['value'])))
+        else:
+            data['entry'].insert(0, data['value'])
+        data['entry'].grid(row=row, column=1)
+    
+    return vars_dict
+
+def run_annotate_app(vars_dict, parent_frame):
+    settings = {key: data['entry'].get() for key, data in vars_dict.items()}
+    settings['channels'] = settings['channels'].split(',')
+    settings['img_size'] = list(map(int, settings['img_size'].split(',')))  # Convert string to list of integers
+    settings['percentiles'] = list(map(int, settings['percentiles'].split(',')))  # Convert string to list of integers
+    settings['normalize'] = settings['normalize'].lower() == 'true'
+    settings['rows'] = int(settings['rows'])
+    settings['columns'] = int(settings['columns'])
+    settings['measurement'] = settings['measurement'].split(',')
+    settings['threshold'] = None if settings['threshold'].lower() == 'none' else int(settings['threshold'])
+
+    # Clear previous content instead of destroying the root
+    if hasattr(parent_frame, 'winfo_children'):
+        for widget in parent_frame.winfo_children():
+            widget.destroy()
+
+    # Start the annotate application in the same root window
+    annotate_app(parent_frame, settings)
+
+# Global list to keep references to PhotoImage objects
+global_image_refs = []
+
+def annotate_app(parent_frame, settings):
+    global global_image_refs
+    global_image_refs.clear()
+    root = parent_frame.winfo_toplevel()
+    annotate_with_image_refs(settings, root, lambda: load_next_app(root))
+
+def load_next_app(root):
+    # Get the next app function and arguments
+    next_app_func = root.next_app_func
+    next_app_args = root.next_app_args
+
+    if next_app_func:
+        try:
+            if not root.winfo_exists():
+                raise tk.TclError
+            next_app_func(root, *next_app_args)
+        except tk.TclError:
+            # Reinitialize root if it has been destroyed
+            new_root = tk.Tk()
+            width = new_root.winfo_screenwidth()
+            height = new_root.winfo_screenheight()
+            new_root.geometry(f"{width}x{height}")
+            new_root.title("SpaCr Application")
+            next_app_func(new_root, *next_app_args)
+
+def annotate_with_image_refs(settings, root, shutdown_callback):
+    #from .gui_utils import proceed_with_app
+    from .gui import gui_app
+    from .settings import set_annotate_default_settings
+
+    settings = set_annotate_default_settings(settings)
+    src = settings['src']
+
+    db = os.path.join(src, 'measurements/measurements.db')
+    conn = sqlite3.connect(db)
+    c = conn.cursor()
+    c.execute('PRAGMA table_info(png_list)')
+    cols = c.fetchall()
+    if settings['annotation_column'] not in [col[1] for col in cols]:
+        c.execute(f"ALTER TABLE png_list ADD COLUMN {settings['annotation_column']} integer")
+    conn.commit()
+    conn.close()
+
+    app = ImageApp(root, db, src, image_type=settings['image_type'], channels=settings['channels'], image_size=settings['img_size'], grid_rows=settings['rows'], grid_cols=settings['columns'], annotation_column=settings['annotation_column'], normalize=settings['normalize'], percentiles=settings['percentiles'], measurement=settings['measurement'], threshold=settings['threshold'])
+
+    # Set the canvas background to black
+    root.configure(bg='black')
+
+    next_button = tk.Button(root, text="Next", command=app.next_page, background='black', foreground='white')
+    next_button.grid(row=app.grid_rows, column=app.grid_cols - 1)
+    back_button = tk.Button(root, text="Back", command=app.previous_page, background='black', foreground='white')
+    back_button.grid(row=app.grid_rows, column=app.grid_cols - 2)
+    exit_button = tk.Button(root, text="Exit", command=lambda: [app.shutdown(), shutdown_callback()], background='black', foreground='white')
+    exit_button.grid(row=app.grid_rows, column=app.grid_cols - 3)
+
+    #app.load_images()
+
+    # Store the shutdown function and next app details in the root
+    root.current_app_exit_func = lambda: [app.shutdown(), shutdown_callback()]
+    root.next_app_func = proceed_with_app
+    root.next_app_args = ("Main App", gui_app)
+
+    # Call load_images after setting up the root window
+    app.load_images()
+

spacr/gui_wrappers.py

@@ -4,15 +4,27 @@ matplotlib.use('Agg')
 
 fig_queue = None
 
-def my_show():
+def spacrFigShow_v1():
     """
     Replacement for plt.show() that queues figures instead of displaying them.
     """
+    global fig_queue
     fig = plt.gcf()
     fig_queue.put(fig)
     plt.close(fig)
 
-def measure_crop_wrapper(settings, q, fig_queue):
+def spacrFigShow(fig_queue=None):
+    """
+    Replacement for plt.show() that queues figures instead of displaying them.
+    """
+    fig = plt.gcf()
+    if fig_queue:
+        fig_queue.put(fig)
+    else:
+        fig.show()
+    plt.close(fig)
+
+def preprocess_generate_masks_wrapper(settings, q, fig_queue):
     """
     Wraps the measure_crop function to integrate with GUI processes.
     
@@ -24,19 +36,18 @@ def measure_crop_wrapper(settings, q, fig_queue):
 
     # Temporarily override plt.show
     original_show = plt.show
-    plt.show = my_show
+    plt.show = lambda: spacrFigShow(fig_queue)
 
     try:
-        print('start')
-        spacr.measure.measure_crop(settings=settings)
+        spacr.core.preprocess_generate_masks(src=settings['src'], settings=settings)
     except Exception as e:
         errorMessage = f"Error during processing: {e}"
         q.put(errorMessage)
         traceback.print_exc()
     finally:
-        plt.show = original_show  
-        
-def preprocess_generate_masks_wrapper(settings, q, fig_queue):
+        plt.show = original_show
+
+def measure_crop_wrapper(settings, q, fig_queue):
     """
     Wraps the measure_crop function to integrate with GUI processes.
     
@@ -48,22 +59,23 @@ def preprocess_generate_masks_wrapper(settings, q, fig_queue):
 
     # Temporarily override plt.show
     original_show = plt.show
-    plt.show = my_show
+    plt.show = lambda: spacrFigShow(fig_queue)
 
     try:
-        spacr.core.preprocess_generate_masks(src=settings['src'], settings=settings)
+        print('start')
+        spacr.measure.measure_crop(settings=settings)
     except Exception as e:
         errorMessage = f"Error during processing: {e}"
         q.put(errorMessage)
         traceback.print_exc()
     finally:
-        plt.show = original_show
+        plt.show = original_show  
 
 def sequencing_wrapper(settings, q, fig_queue):
 
     # Temporarily override plt.show
     original_show = plt.show
-    plt.show = my_show
+    plt.show = lambda: spacrFigShow(fig_queue)
 
     try:
         spacr.sequencing.analyze_reads(settings=settings)
@@ -78,7 +90,7 @@ def umap_wrapper(settings, q, fig_queue):
 
     # Temporarily override plt.show
     original_show = plt.show
-    plt.show = my_show
+    plt.show = lambda: spacrFigShow(fig_queue)
 
     try:
         spacr.core.generate_image_umap(settings=settings)
@@ -101,7 +113,7 @@ def train_test_model_wrapper(settings, q, fig_queue):
 
     # Temporarily override plt.show
     original_show = plt.show
-    plt.show = my_show
+    plt.show = lambda: spacrFigShow(fig_queue)
 
     try:
         spacr.core.train_test_model(settings['src'], settings=settings)
@@ -125,7 +137,7 @@ def run_multiple_simulations_wrapper(settings, q, fig_queue):
 
     # Temporarily override plt.show
     original_show = plt.show
-    plt.show = my_show
+    plt.show = lambda: spacrFigShow(fig_queue)
 
     try:
         spacr.sim.run_multiple_simulations(settings=settings)

spacr/measure.py

@@ -16,12 +16,6 @@ from skimage.util import img_as_bool
 
 from .logger import log_function_call
 
-#from .io import create_database, _save_settings_to_db
-#from .timelapse import _timelapse_masks_to_gif, _scmovie
-#from .plot import _plot_cropped_arrays, _save_scimg_plot
-#from .utils import _merge_overlapping_objects, _filter_object, _relabel_parent_with_child_labels, _exclude_objects
-#from .utils import _merge_and_save_to_database, _crop_center, _find_bounding_box, _generate_names, _get_percentiles, normalize_to_dtype, _map_wells_png, _list_endpoint_subdirectories, _generate_representative_images
-
 def get_components(cell_mask, nucleus_mask, pathogen_mask):
     """
     Get the components (nucleus and pathogens) for each cell in the given masks.
@@ -626,8 +620,14 @@ def _measure_crop_core(index, time_ls, file, settings):
 
         file_name = os.path.splitext(file)[0]
         data = np.load(os.path.join(settings['input_folder'], file))
-
         data_type = data.dtype
+        if data_type not in ['uint8','uint16']:
+            data_type_before = data_type
+            data = data.astype(np.uint16)
+            data_type = data.dtype
+            if settings['verbose']:
+                print(f'Converted data from {data_type_before} to {data_type}')
+
         if settings['save_measurements']:
             os.makedirs(source_folder+'/measurements', exist_ok=True)
             _create_database(source_folder+'/measurements/measurements.db')    
@@ -832,7 +832,6 @@ def _measure_crop_core(index, time_ls, file, settings):
                                     png_channels = normalize_to_dtype(png_channels, settings['normalize'][0], settings['normalize'][1], percentile_list=percentile_list)
                             else:
                                 png_channels = normalize_to_dtype(png_channels, 0, 100)
-
                             os.makedirs(png_folder, exist_ok=True)
 
                             if png_channels.shape[2] == 2:
@@ -999,12 +998,12 @@ def measure_crop(settings):
     _save_settings_to_db(settings)
 
     files = [f for f in os.listdir(settings['input_folder']) if f.endswith('.npy')]
-    max_workers = settings['max_workers'] or mp.cpu_count()-4
-    print(f'using {max_workers} cpu cores')
+    n_jobs = settings['n_jobs'] or mp.cpu_count()-4
+    print(f'using {n_jobs} cpu cores')
 
     with mp.Manager() as manager:
         time_ls = manager.list()
-        with mp.Pool(max_workers) as pool:
+        with mp.Pool(n_jobs) as pool:
             result = pool.starmap_async(_measure_crop_core, [(index, time_ls, file, settings) for index, file in enumerate(files)])
 
             # Track progress in the main process
@@ -1013,7 +1012,7 @@ def measure_crop(settings):
                 files_processed = len(time_ls)
                 files_to_process = len(files)
                 average_time = np.mean(time_ls) if len(time_ls) > 0 else 0
-                time_left = (((files_to_process-files_processed)*average_time)/max_workers)/60
+                time_left = (((files_to_process-files_processed)*average_time)/n_jobs)/60
                 print(f'Progress: {files_processed}/{files_to_process} Time/img {average_time:.3f}sec, Time Remaining {time_left:.3f} min.', end='\r', flush=True)
             result.get()
 

spacr/plot.py

@@ -1565,4 +1565,56 @@ def plot_feature_importance(feature_importance_df):
     ax.set_xlabel('Feature Importance', fontsize=font_size)
     ax.tick_params(axis='both', which='major', labelsize=font_size)
     plt.tight_layout()
-    return fig
+    return fig
+
+def read_and_plot__vision_results(base_dir, y_axis='accuracy', name_split='_time', y_lim=[0.8, 0.9]):
+    # List to store data from all CSV files
+    data_frames = []
+
+    dst = os.path.join(base_dir, 'result')
+    os.mkdir(dst,exists=True)
+
+    # Walk through the directory
+    for root, dirs, files in os.walk(base_dir):
+        for file in files:
+            if file.endswith("_test_result.csv"):
+                file_path = os.path.join(root, file)
+                # Extract model information from the file name
+                file_name = os.path.basename(file_path)
+                model = file_name.split(f'{name_split}')[0]
+                
+                # Extract epoch information from the file name
+                epoch_info = file_name.split('_time')[1]
+                base_folder = os.path.dirname(file_path)
+                epoch = os.path.basename(base_folder)
+                
+                # Read the CSV file
+                df = pd.read_csv(file_path)
+                df['model'] = model
+                df['epoch'] = epoch
+                
+                # Append the data frame to the list
+                data_frames.append(df)
+    
+    # Concatenate all data frames
+    if data_frames:
+        result_df = pd.concat(data_frames, ignore_index=True)
+        
+        # Calculate average y_axis per model
+        avg_metric = result_df.groupby('model')[y_axis].mean().reset_index()
+        avg_metric = avg_metric.sort_values(by=y_axis)
+        print(avg_metric)
+        
+        # Plotting the results
+        plt.figure(figsize=(10, 6))
+        plt.bar(avg_metric['model'], avg_metric[y_axis])
+        plt.xlabel('Model')
+        plt.ylabel(f'{y_axis}')
+        plt.title(f'Average {y_axis.capitalize()} per Model')
+        plt.xticks(rotation=45)
+        plt.tight_layout()
+        if y_lim is not None:
+            plt.ylim(y_lim)
+        plt.show()
+    else:
+        print("No CSV files found in the specified directory.")