spacr 0.1.0__py3-none-any.whl → 0.1.11__py3-none-any.whl

spacr/__init__.py

@@ -15,7 +15,8 @@ from . import deep_spacr
 from . import annotate_app
 from . import annotate_app_v2
 from . import gui_utils
-from . import mask_app
+from . import gui_make_masks_app
+from . import gui_make_masks_app_v2
 from . import gui_mask_app
 from . import gui_measure_app
 from . import gui_classify_app
@@ -36,7 +37,8 @@ __all__ = [
     "annotate_app",
     "annotate_app_v2",
     "gui_utils",
-    "mask_app",
+    "gui_make_masks_app",
+    "gui_make_masks_app_v2",
     "gui_mask_app",
     "gui_measure_app",
     "gui_classify_app",

spacr/annotate_app.py

@@ -1,25 +1,21 @@
+import sqlite3
 from queue import Queue
 from tkinter import Label
 import tkinter as tk
+from tkinter import ttk
 import os, threading, time, sqlite3
 import numpy as np
 from PIL import Image, ImageOps
 from concurrent.futures import ThreadPoolExecutor
 from PIL import ImageTk
-from IPython.display import display, HTML
-import tkinter as tk
-from tkinter import ttk
-from ttkthemes import ThemedTk
 from skimage.exposure import rescale_intensity
-import cv2
-import matplotlib.pyplot as plt
-
-from .logger import log_function_call
+from IPython.display import display, HTML
+from tkinter import font as tkFont
 
-from .gui_utils import ScrollableFrame, set_default_font, set_dark_style, create_dark_mode, style_text_boxes, create_menu_bar
+from .gui_utils import ScrollableFrame, CustomButton, set_dark_style, set_default_font, style_text_boxes, create_menu_bar
 
 class ImageApp:
-    def __init__(self, root, db_path, src, image_type=None, channels=None, grid_rows=None, grid_cols=None, image_size=(200, 200), annotation_column='annotate', normalize=False, percentiles=(1,99)):
+    def __init__(self, root, db_path, src, image_type=None, channels=None, grid_rows=None, grid_cols=None, image_size=(200, 200), annotation_column='annotate', normalize=False, percentiles=(1,99), measurement=None, threshold=None):
         """
         Initializes an instance of the ImageApp class.
 
@@ -34,7 +30,10 @@ class ImageApp:
         - image_size (tuple): The size of the displayed images.
         - annotation_column (str): The column name for image annotations in the database.
         - normalize (bool): Whether to normalize images to their 2nd and 98th percentiles. Defaults to False.
+        - measurement (str): The measurement column to filter by.
+        - threshold (float): The threshold value for filtering the measurement column.
         """
+
         self.root = root
         self.db_path = db_path
         self.src = src
@@ -55,20 +54,115 @@ class ImageApp:
         self.update_queue = Queue()
         self.status_label = Label(self.root, text="", font=("Arial", 12))
         self.status_label.grid(row=self.grid_rows + 1, column=0, columnspan=self.grid_cols)
+        self.measurement = measurement
+        self.threshold = threshold
+
+        self.filtered_paths_annotations = []
+        self.prefilter_paths_annotations()
 
         self.db_update_thread = threading.Thread(target=self.update_database_worker)
         self.db_update_thread.start()
-        
+
         for i in range(grid_rows * grid_cols):
             label = Label(root)
             label.grid(row=i // grid_cols, column=i % grid_cols)
             self.labels.append(label)
 
+    def prefilter_paths_annotations(self):
+        """
+        Pre-filters the paths and annotations based on the specified measurement and threshold.
+        """
+        from .io import _read_and_join_tables
+        from .utils import is_list_of_lists
+
+        if self.measurement and self.threshold is not None:
+            df = _read_and_join_tables(self.db_path)
+            df[self.annotation_column] = None
+            before = len(df)
+
+            if is_list_of_lists(self.measurement):
+                if isinstance(self.threshold, list) or is_list_of_lists(self.threshold):
+                    if len(self.measurement) == len(self.threshold):
+                        for idx, var in enumerate(self.measurement):
+                            df = df[df[var[idx]] > self.threshold[idx]]
+                        after = len(df)
+                    elif len(self.measurement) == len(self.threshold)*2:
+                        th_idx = 0
+                        for idx, var in enumerate(self.measurement):
+                            if idx % 2 != 0:
+                                th_idx += 1
+                                thd = self.threshold
+                                if isinstance(thd, list):
+                                    thd = thd[0]
+                                df[f'threshold_measurement_{idx}'] = df[self.measurement[idx]]/df[self.measurement[idx+1]]
+                                print(f"mean threshold_measurement_{idx}: {np.mean(df['threshold_measurement'])}")
+                                print(f"median threshold measurement: {np.median(df[self.measurement])}")
+                                df = df[df[f'threshold_measurement_{idx}'] > thd]
+                        after = len(df)
+            elif isinstance(self.measurement, list):
+                df['threshold_measurement'] = df[self.measurement[0]]/df[self.measurement[1]]
+                print(f"mean threshold measurement: {np.mean(df['threshold_measurement'])}")
+                print(f"median threshold measurement: {np.median(df[self.measurement])}")
+                df = df[df['threshold_measurement'] > self.threshold]
+                after = len(df)
+                self.measurement = 'threshold_measurement'
+                print(f'Removed: {before-after} rows, retained {after}')
+            else:
+                print(f"mean threshold measurement: {np.mean(df[self.measurement])}")
+                print(f"median threshold measurement: {np.median(df[self.measurement])}")
+                before = len(df)
+                if isinstance(self.threshold, str):
+                    if self.threshold == 'q1':
+                        self.threshold = df[self.measurement].quantile(0.1)
+                    if self.threshold == 'q2':
+                        self.threshold = df[self.measurement].quantile(0.2)
+                    if self.threshold == 'q3':
+                        self.threshold = df[self.measurement].quantile(0.3)
+                    if self.threshold == 'q4':
+                        self.threshold = df[self.measurement].quantile(0.4)
+                    if self.threshold == 'q5':
+                        self.threshold = df[self.measurement].quantile(0.5)
+                    if self.threshold == 'q6':
+                        self.threshold = df[self.measurement].quantile(0.6)
+                    if self.threshold == 'q7':
+                        self.threshold = df[self.measurement].quantile(0.7)
+                    if self.threshold == 'q8':
+                        self.threshold = df[self.measurement].quantile(0.8)
+                    if self.threshold == 'q9':
+                        self.threshold = df[self.measurement].quantile(0.9)
+                print(f"threshold: {self.threshold}")
+
+                df = df[df[self.measurement] > self.threshold]
+                after = len(df)
+                print(f'Removed: {before-after} rows, retained {after}')
+
+            df = df.dropna(subset=['png_path'])
+            if self.image_type:
+                before = len(df)
+                if isinstance(self.image_type, list):
+                    for tpe in self.image_type:
+                        df = df[df['png_path'].str.contains(tpe)]
+                else:
+                    df = df[df['png_path'].str.contains(self.image_type)]
+                after = len(df)
+                print(f'image_type: Removed: {before-after} rows, retained {after}')
+
+            self.filtered_paths_annotations = df[['png_path', self.annotation_column]].values.tolist()
+        else:
+            conn = sqlite3.connect(self.db_path)
+            c = conn.cursor()
+            if self.image_type:
+                c.execute(f"SELECT png_path, {self.annotation_column} FROM png_list WHERE png_path LIKE ?", (f"%{self.image_type}%",))
+            else:
+                c.execute(f"SELECT png_path, {self.annotation_column} FROM png_list")
+            self.filtered_paths_annotations = c.fetchall()
+            conn.close()
+
     def load_images(self):
         """
         Loads and displays images with annotations.
 
-        This method retrieves image paths and annotations from a SQLite database,
+        This method retrieves image paths and annotations from a pre-filtered list,
         loads the images using a ThreadPoolExecutor for parallel processing,
         adds colored borders to images based on their annotations,
         and displays the images in the corresponding labels.
@@ -79,23 +173,15 @@ class ImageApp:
         Returns:
             None
         """
+
         for label in self.labels:
             label.config(image='')
 
         self.images = {}
-
-        conn = sqlite3.connect(self.db_path)
-        c = conn.cursor()
-        if self.image_type:
-            c.execute(f"SELECT png_path, {self.annotation_column} FROM png_list WHERE png_path LIKE ? LIMIT ?, ?", (f"%{self.image_type}%", self.index, self.grid_rows * self.grid_cols))
-        else:
-            c.execute(f"SELECT png_path, {self.annotation_column} FROM png_list LIMIT ?, ?", (self.index, self.grid_rows * self.grid_cols))
-        
-        paths = c.fetchall()
-        conn.close()
+        paths_annotations = self.filtered_paths_annotations[self.index:self.index + self.grid_rows * self.grid_cols]
 
         adjusted_paths = []
-        for path, annotation in paths:
+        for path, annotation in paths_annotations:
             if not path.startswith(self.src):
                 parts = path.split('/data/')
                 if len(parts) > 1:
@@ -209,7 +295,6 @@ class ImageApp:
 
         Returns:
             PIL.Image.Image: The filtered image.
-
         """
         r, g, b = img.split()
         if self.channels:
@@ -354,7 +439,7 @@ class ImageApp:
         """
         Shuts down the application.
 
-        This method sets the `terminate` flag to True, clears the pending updates,
+        This method sets the terminate flag to True, clears the pending updates,
         updates the database, and quits the application.
 
         """
@@ -366,10 +451,23 @@ class ImageApp:
         self.root.destroy()
         print(f'Quit application')
 
-def annotate(src, image_type=None, channels=None, geom="1000x1100", img_size=(200, 200), rows=5, columns=5, annotation_column='annotate', normalize=False, percentiles=(1,99)):
-    
-    from .io import _read_and_join_tables
-    
+def get_annotate_default_settings(settings):
+
+    settings.setdefault('image_type', 'cell_png')
+    settings.setdefault('channels', ['r', 'g', 'b'])
+    settings.setdefault('geom', "3200x2000")
+    settings.setdefault('img_size', (200, 200))
+    settings.setdefault('rows', 10)
+    settings.setdefault('columns', 18)
+    settings.setdefault('annotation_column', 'recruited_test')
+    settings.setdefault('normalize', False)
+    settings.setdefault('percentiles', (2,98))
+    settings.setdefault('measurement', ['cytoplasm_channel_3_mean_intensity', 'pathogen_channel_3_mean_intensity'])
+    settings.setdefault('threshold', 2)
+
+    return settings
+
+def annotate(settings):
     """
     Annotates images in a database using a graphical user interface.
 
@@ -384,21 +482,26 @@ def annotate(src, image_type=None, channels=None, geom="1000x1100", img_size=(20
         columns (int, optional): The number of columns in the image grid. Defaults to 5.
         annotation_column (str, optional): The name of the annotation column in the database table. Defaults to 'annotate'.
         normalize (bool, optional): Whether to normalize images to their 2nd and 98th percentiles. Defaults to False.
+        measurement (str, optional): The measurement column to filter by.
+        threshold (float, optional): The threshold value for filtering the measurement column.
     """
+
+    settings = get_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 annotation_column not in [col[1] for col in cols]:
-        c.execute(f'ALTER TABLE png_list ADD COLUMN {annotation_column} integer')
+    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(geom)
-    app = ImageApp(root, db, src, image_type=image_type, channels=channels, image_size=img_size, grid_rows=rows, grid_cols=columns, annotation_column=annotation_column, normalize=normalize, percentiles=percentiles)
+    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)
@@ -409,103 +512,159 @@ def annotate(src, image_type=None, channels=None, geom="1000x1100", img_size=(20
     app.load_images()
     root.mainloop()
 
-def check_for_duplicates(db):
-    """
-    Check for duplicates in the given SQLite database.
+# Global list to keep references to PhotoImage objects
+global_image_refs = []
 
-    Args:
-        db (str): The path to the SQLite database.
-
-    Returns:
-        None
-    """
-    db_path = db
-    conn = sqlite3.connect(db_path)
-    c = conn.cursor()
-    c.execute('SELECT file_name, COUNT(file_name) FROM png_list GROUP BY file_name HAVING COUNT(file_name) > 1')
-    duplicates = c.fetchall()
-    for duplicate in duplicates:
-        file_name = duplicate[0]
-        count = duplicate[1]
-        c.execute('SELECT rowid FROM png_list WHERE file_name = ?', (file_name,))
-        rowids = c.fetchall()
-        for rowid in rowids[:-1]:
-            c.execute('DELETE FROM png_list WHERE rowid = ?', (rowid[0],))
-    conn.commit()
-    conn.close()
-
-#@log_function_call
-def initiate_annotation_app_root(width, height):
-    theme = 'breeze'
-    root = ThemedTk(theme=theme)
-    style = ttk.Style(root)
+def initiate_annotation_app_root(parent_frame):
+    style = ttk.Style(parent_frame)
     set_dark_style(style)
     style_text_boxes(style)
-    set_default_font(root, font_name="Arial", size=8)
-    root.geometry(f"{width}x{height}")
-    root.title("Annotation App")
+    set_default_font(parent_frame, font_name="Arial", size=8)
 
-    container = tk.PanedWindow(root, orient=tk.HORIZONTAL)
+    parent_frame.configure(bg='black')
+    
+    container = tk.PanedWindow(parent_frame, orient=tk.HORIZONTAL, bg='black')
     container.pack(fill=tk.BOTH, expand=True)
 
-    scrollable_frame = ScrollableFrame(container, bg='#333333')
+    scrollable_frame = ScrollableFrame(container, bg='black')
     container.add(scrollable_frame, stretch="always")
 
     # Setup input fields
     vars_dict = {
-        'db': ttk.Entry(scrollable_frame.scrollable_frame),
+        'src': ttk.Entry(scrollable_frame.scrollable_frame),
         'image_type': ttk.Entry(scrollable_frame.scrollable_frame),
         'channels': ttk.Entry(scrollable_frame.scrollable_frame),
-        'annotation_column': ttk.Entry(scrollable_frame.scrollable_frame),
         'geom': ttk.Entry(scrollable_frame.scrollable_frame),
         'img_size': ttk.Entry(scrollable_frame.scrollable_frame),
         'rows': ttk.Entry(scrollable_frame.scrollable_frame),
-        'columns': ttk.Entry(scrollable_frame.scrollable_frame)
+        'columns': ttk.Entry(scrollable_frame.scrollable_frame),
+        'annotation_column': ttk.Entry(scrollable_frame.scrollable_frame),
+        'normalize': ttk.Entry(scrollable_frame.scrollable_frame),
+        'percentiles': ttk.Entry(scrollable_frame.scrollable_frame),
+        'measurement': ttk.Entry(scrollable_frame.scrollable_frame),
+        'threshold': ttk.Entry(scrollable_frame.scrollable_frame),
+    }
+
+    default_settings = {
+        'src': 'path',
+        'image_type': 'cell_png',
+        'channels': 'r,g,b',
+        'geom': "3200x2000",
+        'img_size': '(200, 200)',
+        'rows': '10',
+        'columns': '18',
+        'annotation_column': 'recruited_test',
+        'normalize': 'False',
+        'percentiles': '(2,98)',
+        'measurement': 'None',
+        'threshold': 'None'
     }
 
     # Arrange input fields and labels
     row = 0
     for name, entry in vars_dict.items():
-        ttk.Label(scrollable_frame.scrollable_frame, text=f"{name.replace('_', ' ').capitalize()}:").grid(row=row, column=0)
+        ttk.Label(scrollable_frame.scrollable_frame, text=f"{name.replace('_', ' ').capitalize()}:",
+                  background="black", foreground="white").grid(row=row, column=0)
+        entry.insert(0, default_settings[name])
         entry.grid(row=row, column=1)
         row += 1
 
     # Function to be called when "Run" button is clicked
     def run_app():
-        db = vars_dict['db'].get()
-        image_type = vars_dict['image_type'].get()
-        channels = vars_dict['channels'].get()
-        annotation_column = vars_dict['annotation_column'].get()
-        geom = vars_dict['geom'].get()
-        img_size_str = vars_dict['img_size'].get().split(',')  # Splitting the string by comma
-        img_size = (int(img_size_str[0]), int(img_size_str[1]))  # Converting each part to an integer
-        rows = int(vars_dict['rows'].get())
-        columns = int(vars_dict['columns'].get())
+        settings = {key: entry.get() for key, entry in vars_dict.items()}
+        settings['channels'] = settings['channels'].split(',')
+        settings['img_size'] = tuple(map(int, settings['img_size'][1:-1].split(',')))
+        settings['percentiles'] = tuple(map(int, settings['percentiles'][1:-1].split(',')))
+        settings['normalize'] = settings['normalize'].lower() == 'true'
+        settings['rows'] = int(settings['rows'])
+        settings['columns'] = int(settings['columns'])
+        if settings['measurement'].lower() == 'none':
+            settings['measurement'] = None
+        if settings['threshold'].lower() == 'none':
+            settings['threshold'] = None
         
-        # Destroy the initial settings window
-        root.destroy()
+        # Clear previous content instead of destroying the root
+        if hasattr(parent_frame, 'winfo_children'):
+            for widget in parent_frame.winfo_children():
+                widget.destroy()
         
-        # Create a new root window for the application
-        new_root = tk.Tk()
-        new_root.geometry(f"{width}x{height}")
-        new_root.title("Mask Application")
+        # Start the annotate application in the same root window
+        annotate_app(parent_frame, settings)
         
+    run_button = CustomButton(scrollable_frame.scrollable_frame, text="Run", command=run_app,
+                              font=tkFont.Font(family="Arial", size=12, weight=tkFont.NORMAL))
+    run_button.grid(row=row, column=0, columnspan=2, pady=10, padx=10)
 
-        # Start the annotation application in the new root window
-        app_instance = annotate(db, image_type, channels, annotation_column, geom, img_size, rows, columns)
-        
-        new_root.mainloop()
-        
-    create_dark_mode(root, style, console_output=None)
+    return parent_frame
 
-    run_button = ttk.Button(scrollable_frame.scrollable_frame, text="Run", command=run_app)
-    run_button.grid(row=row, column=0, columnspan=2, pady=10, padx=10)
+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))
 
-    return root
+def annotate_with_image_refs(settings, root, shutdown_callback):
+    settings = get_annotate_default_settings(settings)
+    src = settings['src']
 
-def gui_annotation():
-    root = initiate_annotation_app_root(500, 350)
+    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 = app.shutdown
+    root.next_app_func = None
+    root.next_app_args = ()
+
+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:
+        next_app_func(*next_app_args)
+
+def gui_annotate():
+    root = tk.Tk()
+    width = root.winfo_screenwidth()
+    height = root.winfo_screenheight()
+    root.geometry(f"{width}x{height}")
+    root.title("Annotate Application")
+    
+    # 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_annotation_app_root(root.content_frame)
+    create_menu_bar(root)
     root.mainloop()
 
 if __name__ == "__main__":
-    gui_annotation()
+    gui_annotate()