Source code for spacr.gui_elements

import os, threading, time, sqlite3, webbrowser, pyautogui, random, cv2
import tkinter as tk
from tkinter import ttk
import tkinter.font as tkFont
from tkinter import filedialog
from tkinter import font
from queue import Queue
from tkinter import Label, Frame, Button
import numpy as np
import pandas as pd
from PIL import Image, ImageOps, ImageTk, ImageDraw, ImageFont, ImageEnhance
from concurrent.futures import ThreadPoolExecutor
from skimage.exposure import rescale_intensity
from IPython.display import display, HTML
import imageio.v2 as imageio
from collections import deque
from skimage.draw import polygon, line
from skimage.transform import resize
from scipy.ndimage import binary_fill_holes, label
from tkinter import ttk, scrolledtext
from sklearn.model_selection import train_test_split
from xgboost import XGBClassifier
from sklearn.metrics import classification_report, confusion_matrix

[docs] fig = None
[docs] def restart_gui_app(root): """ Restarts the GUI application by destroying the current instance and launching a fresh one. """ try: # Destroy the current root window root.destroy() # Import and launch a new instance of the application from spacr.gui import gui_app new_root = tk.Tk() # Create a fresh Tkinter root instance gui_app() except Exception as e: print(f"Error restarting GUI application: {e}")
[docs] def create_menu_bar(root): from .gui import initiate_root gui_apps = { "Mask": lambda: initiate_root(root, settings_type='mask'), "Measure": lambda: initiate_root(root, settings_type='measure'), "Annotate": lambda: initiate_root(root, settings_type='annotate'), "Make Masks": lambda: initiate_root(root, settings_type='make_masks'), "Classify": lambda: initiate_root(root, settings_type='classify'), "Umap": lambda: initiate_root(root, settings_type='umap'), "Train Cellpose": lambda: initiate_root(root, settings_type='train_cellpose'), "ML Analyze": lambda: initiate_root(root, settings_type='ml_analyze'), "Cellpose Masks": lambda: initiate_root(root, settings_type='cellpose_masks'), "Cellpose All": lambda: initiate_root(root, settings_type='cellpose_all'), "Map Barcodes": lambda: initiate_root(root, settings_type='map_barcodes'), "Regression": lambda: initiate_root(root, settings_type='regression'), "Activation": lambda: initiate_root(root, settings_type='activation'), "Recruitment": lambda: initiate_root(root, settings_type='recruitment') } # Create the menu bar menu_bar = tk.Menu(root, bg="#008080", fg="white") # Create a "SpaCr Applications" menu app_menu = tk.Menu(menu_bar, tearoff=0, bg="#008080", fg="white") menu_bar.add_cascade(label="SpaCr Applications", menu=app_menu) # Add options to the "SpaCr Applications" menu for app_name, app_func in gui_apps.items(): app_menu.add_command( label=app_name, command=app_func ) # Add a separator and an exit option app_menu.add_separator() #app_menu.add_command(label="Home",command=lambda: restart_gui_app(root)) app_menu.add_command(label="Help", command=lambda: webbrowser.open("https://spacr.readthedocs.io/en/latest/?badge=latest")) app_menu.add_command(label="Exit", command=root.quit) # Configure the menu for the root window root.config(menu=menu_bar)
[docs] def set_element_size(): screen_width, screen_height = pyautogui.size() screen_area = screen_width * screen_height # Calculate sizes based on screen dimensions btn_size = int((screen_area * 0.002) ** 0.5) # Button size as a fraction of screen area bar_size = screen_height // 20 # Bar size based on screen height settings_width = screen_width // 4 # Settings panel width as a fraction of screen width panel_width = screen_width - settings_width # Panel width as a fraction of screen width panel_height = screen_height // 6 # Panel height as a fraction of screen height size_dict = { 'btn_size': btn_size, 'bar_size': bar_size, 'settings_width': settings_width, 'panel_width': panel_width, 'panel_height': panel_height } return size_dict
[docs] def set_dark_style(style, parent_frame=None, containers=None, widgets=None, font_family="OpenSans", font_size=12, bg_color='black', fg_color='white', active_color='blue', inactive_color='dark_gray'): if active_color == 'teal': active_color = '#008080' if inactive_color == 'dark_gray': inactive_color = '#2B2B2B' # '#333333' #'#050505' if bg_color == 'black': bg_color = '#000000' if fg_color == 'white': fg_color = '#ffffff' if active_color == 'blue': active_color = '#007BFF' padding = '5 5 5 5' font_style = tkFont.Font(family=font_family, size=font_size) if font_family == 'OpenSans': font_loader = spacrFont(font_name='OpenSans', font_style='Regular', font_size=12) else: font_loader = None style.theme_use('clam') style.configure('TEntry', padding=padding) style.configure('TCombobox', padding=padding) style.configure('Spacr.TEntry', padding=padding) style.configure('TEntry', padding=padding) style.configure('Spacr.TEntry', padding=padding) style.configure('Custom.TLabel', padding=padding) style.configure('TButton', padding=padding) style.configure('TFrame', background=bg_color) style.configure('TPanedwindow', background=bg_color) if font_loader: style.configure('TLabel', background=bg_color, foreground=fg_color, font=font_loader.get_font(size=font_size)) else: style.configure('TLabel', background=bg_color, foreground=fg_color, font=(font_family, font_size)) if parent_frame: parent_frame.configure(bg=bg_color) parent_frame.grid_rowconfigure(0, weight=1) parent_frame.grid_columnconfigure(0, weight=1) if containers: for container in containers: if isinstance(container, ttk.Frame): container_style = ttk.Style() container_style.configure(f'{container.winfo_class()}.TFrame', background=bg_color) container.configure(style=f'{container.winfo_class()}.TFrame') else: container.configure(bg=bg_color) if widgets: for widget in widgets: if isinstance(widget, (tk.Label, tk.Button, tk.Frame, ttk.LabelFrame, tk.Canvas)): widget.configure(bg=bg_color) if isinstance(widget, (tk.Label, tk.Button)): if font_loader: widget.configure(fg=fg_color, font=font_loader.get_font(size=font_size)) else: widget.configure(fg=fg_color, font=(font_family, font_size)) if isinstance(widget, scrolledtext.ScrolledText): widget.configure(bg=bg_color, fg=fg_color, insertbackground=fg_color) if isinstance(widget, tk.OptionMenu): if font_loader: widget.configure(bg=bg_color, fg=fg_color, font=font_loader.get_font(size=font_size)) else: widget.configure(bg=bg_color, fg=fg_color, font=(font_family, font_size)) menu = widget['menu'] if font_loader: menu.configure(bg=bg_color, fg=fg_color, font=font_loader.get_font(size=font_size)) else: menu.configure(bg=bg_color, fg=fg_color, font=(font_family, font_size)) return {'font_loader':font_loader, 'font_family': font_family, 'font_size': font_size, 'bg_color': bg_color, 'fg_color': fg_color, 'active_color': active_color, 'inactive_color': inactive_color}
[docs] class spacrFont: def __init__(self, font_name, font_style, font_size=12): """ Initializes the FontLoader class. Parameters: - font_name: str, the name of the font (e.g., 'OpenSans'). - font_style: str, the style of the font (e.g., 'Regular', 'Bold'). - font_size: int, the size of the font (default: 12). """
[docs] self.font_name = font_name
[docs] self.font_style = font_style
[docs] self.font_size = font_size
# Determine the path based on the font name and style
[docs] self.font_path = self.get_font_path(font_name, font_style)
# Register the font with Tkinter self.load_font()
[docs] def get_font_path(self, font_name, font_style): """ Returns the font path based on the font name and style. Parameters: - font_name: str, the name of the font. - font_style: str, the style of the font. Returns: - str, the path to the font file. """ base_dir = os.path.dirname(__file__) if font_name == 'OpenSans': if font_style == 'Regular': return os.path.join(base_dir, 'resources/font/open_sans/static/OpenSans-Regular.ttf') elif font_style == 'Bold': return os.path.join(base_dir, 'resources/font/open_sans/static/OpenSans-Bold.ttf') elif font_style == 'Italic': return os.path.join(base_dir, 'resources/font/open_sans/static/OpenSans-Italic.ttf') # Add more styles as needed # Add more fonts as needed raise ValueError(f"Font '{font_name}' with style '{font_style}' not found.")
[docs] def load_font(self): """ Loads the font into Tkinter. """ try: font.Font(family=self.font_name, size=self.font_size) except tk.TclError: # Load the font manually if it's not already loaded self.tk_font = font.Font( name=self.font_name, file=self.font_path, size=self.font_size )
[docs] def get_font(self, size=None): """ Returns the font in the specified size. Parameters: - size: int, the size of the font (optional). Returns: - tkFont.Font object. """ if size is None: size = self.font_size return font.Font(family=self.font_name, size=size)
[docs] class spacrContainer(tk.Frame): def __init__(self, parent, orient=tk.VERTICAL, bg=None, *args, **kwargs): super().__init__(parent, *args, **kwargs)
[docs] self.orient = orient
[docs] self.bg = bg if bg else 'lightgrey'
[docs] self.sash_thickness = 10
[docs] self.panes = []
[docs] self.sashes = []
self.bind("<Configure>", self.on_configure) self.grid_rowconfigure(0, weight=1) self.grid_columnconfigure(0, weight=1)
[docs] def add(self, widget, stretch='always'): print(f"Adding widget: {widget} with stretch: {stretch}") pane = tk.Frame(self, bg=self.bg) pane.grid_propagate(False) widget.grid(in_=pane, sticky="nsew") # Use grid for the widget within the pane self.panes.append((pane, widget)) if len(self.panes) > 1: self.create_sash() self.reposition_panes()
[docs] def create_sash(self): sash = tk.Frame(self, bg=self.bg, cursor='sb_v_double_arrow' if self.orient == tk.VERTICAL else 'sb_h_double_arrow', height=self.sash_thickness, width=self.sash_thickness) sash.bind("<Enter>", self.on_enter_sash) sash.bind("<Leave>", self.on_leave_sash) sash.bind("<ButtonPress-1>", self.start_resize) self.sashes.append(sash)
[docs] def reposition_panes(self): if not self.panes: return total_size = self.winfo_height() if self.orient == tk.VERTICAL else self.winfo_width() pane_size = total_size // len(self.panes) print(f"Total size: {total_size}, Pane size: {pane_size}, Number of panes: {len(self.panes)}") for i, (pane, widget) in enumerate(self.panes): if self.orient == tk.VERTICAL: pane.grid(row=i * 2, column=0, sticky="nsew", pady=(0, self.sash_thickness if i < len(self.panes) - 1 else 0)) else: pane.grid(row=0, column=i * 2, sticky="nsew", padx=(0, self.sash_thickness if i < len(self.panes) - 1 else 0)) for i, sash in enumerate(self.sashes): if self.orient == tk.VERTICAL: sash.grid(row=(i * 2) + 1, column=0, sticky="ew") else: sash.grid(row=0, column=(i * 2) + 1, sticky="ns")
[docs] def on_configure(self, event): print(f"Configuring container: {self}") self.reposition_panes()
[docs] def on_enter_sash(self, event): event.widget.config(bg='blue')
[docs] def on_leave_sash(self, event): event.widget.config(bg=self.bg)
[docs] def start_resize(self, event): sash = event.widget self.start_pos = event.y_root if self.orient == tk.VERTICAL else event.x_root self.start_size = sash.winfo_y() if self.orient == tk.VERTICAL else sash.winfo_x() sash.bind("<B1-Motion>", self.perform_resize)
[docs] def perform_resize(self, event): sash = event.widget delta = (event.y_root - self.start_pos) if self.orient == tk.VERTICAL else (event.x_root - self.start_pos) new_size = self.start_size + delta for i, (pane, widget) in enumerate(self.panes): if self.orient == tk.VERTICAL: new_row = max(0, new_size // self.sash_thickness) if pane.winfo_y() >= new_size: pane.grid_configure(row=new_row) elif pane.winfo_y() < new_size and i > 0: previous_row = max(0, (new_size - pane.winfo_height()) // self.sash_thickness) self.panes[i - 1][0].grid_configure(row=previous_row) else: new_col = max(0, new_size // self.sash_thickness) if pane.winfo_x() >= new_size: pane.grid_configure(column=new_col) elif pane.winfo_x() < new_size and i > 0: previous_col = max(0, (new_size - pane.winfo_width()) // self.sash_thickness) self.panes[i - 1][0].grid_configure(column=previous_col) self.reposition_panes()
[docs] class spacrEntry(tk.Frame): def __init__(self, parent, textvariable=None, outline=False, width=None, *args, **kwargs): super().__init__(parent, *args, **kwargs) # Set dark style style_out = set_dark_style(ttk.Style())
[docs] self.bg_color = style_out['inactive_color']
[docs] self.active_color = style_out['active_color']
[docs] self.fg_color = style_out['fg_color']
[docs] self.outline = outline
[docs] self.font_family = style_out['font_family']
[docs] self.font_size = style_out['font_size']
[docs] self.font_loader = style_out['font_loader']
# Set the background color of the frame self.configure(bg=style_out['bg_color']) # Create a canvas for the rounded rectangle background if width is None: self.canvas_width = 220 # Adjusted for padding else: self.canvas_width = width
[docs] self.canvas_height = 40 # Adjusted for padding
[docs] self.canvas = tk.Canvas(self, width=self.canvas_width, height=self.canvas_height, bd=0, highlightthickness=0, relief='ridge', bg=style_out['bg_color'])
self.canvas.pack() # Create the entry widget if self.font_loader: self.entry = tk.Entry(self, textvariable=textvariable, bd=0, highlightthickness=0, fg=self.fg_color, font=self.font_loader.get_font(size=self.font_size), bg=self.bg_color) else: self.entry = tk.Entry(self, textvariable=textvariable, bd=0, highlightthickness=0, fg=self.fg_color, font=(self.font_family, self.font_size), bg=self.bg_color) self.entry.place(relx=0.5, rely=0.5, anchor=tk.CENTER, width=self.canvas_width - 30, height=20) # Centered positioning # Bind events to change the background color on focus self.entry.bind("<FocusIn>", self.on_focus_in) self.entry.bind("<FocusOut>", self.on_focus_out) self.draw_rounded_rectangle(self.bg_color)
[docs] def draw_rounded_rectangle(self, color): radius = 15 # Increased radius for more rounded corners x0, y0 = 10, 5 x1, y1 = self.canvas_width - 10, self.canvas_height - 5 self.canvas.delete("all") self.canvas.create_arc((x0, y0, x0 + radius, y0 + radius), start=90, extent=90, fill=color, outline=color) self.canvas.create_arc((x1 - radius, y0, x1, y0 + radius), start=0, extent=90, fill=color, outline=color) self.canvas.create_arc((x0, y1 - radius, x0 + radius, y1), start=180, extent=90, fill=color, outline=color) self.canvas.create_arc((x1 - radius, y1 - radius, x1, y1), start=270, extent=90, fill=color, outline=color) self.canvas.create_rectangle((x0 + radius / 2, y0, x1 - radius / 2, y1), fill=color, outline=color) self.canvas.create_rectangle((x0, y0 + radius / 2, x1, y1 - radius / 2), fill=color, outline=color)
[docs] def on_focus_in(self, event): self.draw_rounded_rectangle(self.active_color) self.entry.config(bg=self.active_color)
[docs] def on_focus_out(self, event): self.draw_rounded_rectangle(self.bg_color) self.entry.config(bg=self.bg_color)
[docs] class spacrCheck(tk.Frame): def __init__(self, parent, text="", variable=None, *args, **kwargs): super().__init__(parent, *args, **kwargs) style_out = set_dark_style(ttk.Style())
[docs] self.bg_color = style_out['bg_color']
[docs] self.active_color = style_out['active_color']
[docs] self.fg_color = style_out['fg_color']
[docs] self.inactive_color = style_out['inactive_color']
[docs] self.variable = variable
self.configure(bg=self.bg_color) # Create a canvas for the rounded square background
[docs] self.canvas_width = 20
[docs] self.canvas_height = 20
[docs] self.canvas = tk.Canvas(self, width=self.canvas_width, height=self.canvas_height, bd=0, highlightthickness=0, relief='ridge', bg=self.bg_color)
self.canvas.pack() # Draw the initial rounded square based on the variable's value self.draw_rounded_square(self.active_color if self.variable.get() else self.inactive_color) # Bind variable changes to update the checkbox self.variable.trace_add('write', self.update_check) # Bind click event to toggle the variable self.canvas.bind("<Button-1>", self.toggle_variable)
[docs] def draw_rounded_square(self, color): radius = 5 # Adjust the radius for more rounded corners x0, y0 = 2, 2 x1, y1 = 18, 18 self.canvas.delete("all") self.canvas.create_arc((x0, y0, x0 + radius, y0 + radius), start=90, extent=90, fill=color, outline=self.fg_color) self.canvas.create_arc((x1 - radius, y0, x1, y0 + radius), start=0, extent=90, fill=color, outline=self.fg_color) self.canvas.create_arc((x0, y1 - radius, x0 + radius, y1), start=180, extent=90, fill=color, outline=self.fg_color) self.canvas.create_arc((x1 - radius, y1 - radius, x1, y1), start=270, extent=90, fill=color, outline=self.fg_color) self.canvas.create_rectangle((x0 + radius / 2, y0, x1 - radius / 2, y1), fill=color, outline=color) self.canvas.create_rectangle((x0, y0 + radius / 2, x1, y1 - radius / 2), fill=color, outline=color) self.canvas.create_line(x0 + radius / 2, y0, x1 - radius / 2, y0, fill=self.fg_color) self.canvas.create_line(x0 + radius / 2, y1, x1 - radius / 2, y1, fill=self.fg_color) self.canvas.create_line(x0, y0 + radius / 2, x0, y1 - radius / 2, fill=self.fg_color) self.canvas.create_line(x1, y0 + radius / 2, x1, y1 - radius / 2, fill=self.fg_color)
[docs] def update_check(self, *args): self.draw_rounded_square(self.active_color if self.variable.get() else self.inactive_color)
[docs] def toggle_variable(self, event): self.variable.set(not self.variable.get())
[docs] class spacrCombo(tk.Frame): def __init__(self, parent, textvariable=None, values=None, width=None, *args, **kwargs): super().__init__(parent, *args, **kwargs) # Set dark style style_out = set_dark_style(ttk.Style())
[docs] self.bg_color = style_out['bg_color']
[docs] self.active_color = style_out['active_color']
[docs] self.fg_color = style_out['fg_color']
[docs] self.inactive_color = style_out['inactive_color']
[docs] self.font_family = style_out['font_family']
[docs] self.font_size = style_out['font_size']
[docs] self.font_loader = style_out['font_loader']
[docs] self.values = values or []
# Create a canvas for the rounded rectangle background
[docs] self.canvas_width = width if width is not None else 220 # Adjusted for padding
[docs] self.canvas_height = 40 # Adjusted for padding
[docs] self.canvas = tk.Canvas(self, width=self.canvas_width, height=self.canvas_height, bd=0, highlightthickness=0, relief='ridge', bg=self.bg_color)
self.canvas.pack()
[docs] self.var = textvariable if textvariable else tk.StringVar()
[docs] self.selected_value = self.var.get()
# Create the label to display the selected value if self.font_loader: self.label = tk.Label(self, text=self.selected_value, bg=self.inactive_color, fg=self.fg_color, font=self.font_loader.get_font(size=self.font_size)) else: self.label = tk.Label(self, text=self.selected_value, bg=self.inactive_color, fg=self.fg_color, font=(self.font_family, self.font_size)) self.label.place(relx=0.5, rely=0.5, anchor=tk.CENTER) # Bind events to open the dropdown menu self.canvas.bind("<Button-1>", self.on_click) self.label.bind("<Button-1>", self.on_click) self.draw_rounded_rectangle(self.inactive_color)
[docs] self.dropdown_menu = None
[docs] def draw_rounded_rectangle(self, color): radius = 15 # Increased radius for more rounded corners x0, y0 = 10, 5 x1, y1 = self.canvas_width - 10, self.canvas_height - 5 self.canvas.delete("all") self.canvas.create_arc((x0, y0, x0 + radius, y0 + radius), start=90, extent=90, fill=color, outline=color) self.canvas.create_arc((x1 - radius, y0, x1, y0 + radius), start=0, extent=90, fill=color, outline=color) self.canvas.create_arc((x0, y1 - radius, x0 + radius, y1), start=180, extent=90, fill=color, outline=color) self.canvas.create_arc((x1 - radius, y1 - radius, x1, y1), start=270, extent=90, fill=color, outline=color) self.canvas.create_rectangle((x0 + radius / 2, y0, x1 - radius / 2, y1), fill=color, outline=color) self.canvas.create_rectangle((x0, y0 + radius / 2, x1, y1 - radius / 2), fill=color, outline=color) self.label.config(bg=color) # Update label background to match rectangle color
[docs] def on_click(self, event): if self.dropdown_menu is None: self.open_dropdown() else: self.close_dropdown()
[docs] def open_dropdown(self): self.draw_rounded_rectangle(self.active_color) self.dropdown_menu = tk.Toplevel(self) self.dropdown_menu.wm_overrideredirect(True) x, y, width, height = self.winfo_rootx(), self.winfo_rooty(), self.winfo_width(), self.winfo_height() self.dropdown_menu.geometry(f"{width}x{len(self.values) * 30}+{x}+{y + height}") for index, value in enumerate(self.values): display_text = value if value is not None else 'None' if self.font_loader: item = tk.Label(self.dropdown_menu, text=display_text, bg=self.inactive_color, fg=self.fg_color, font=self.font_loader.get_font(size=self.font_size), anchor='w') else: item = tk.Label(self.dropdown_menu, text=display_text, bg=self.inactive_color, fg=self.fg_color, font=(self.font_family, self.font_size), anchor='w') item.pack(fill='both') item.bind("<Button-1>", lambda e, v=value: self.on_select(v)) item.bind("<Enter>", lambda e, w=item: w.config(bg=self.active_color)) item.bind("<Leave>", lambda e, w=item: w.config(bg=self.inactive_color))
[docs] def close_dropdown(self): self.draw_rounded_rectangle(self.inactive_color) if self.dropdown_menu: self.dropdown_menu.destroy() self.dropdown_menu = None
[docs] def on_select(self, value): display_text = value if value is not None else 'None' self.var.set(value) self.label.config(text=display_text) self.selected_value = value self.close_dropdown()
[docs] def set(self, value): display_text = value if value is not None else 'None' self.var.set(value) self.label.config(text=display_text) self.selected_value = value
[docs] class spacrDropdownMenu(tk.Frame): def __init__(self, parent, variable, options, command=None, font=None, size=50, **kwargs): super().__init__(parent, **kwargs)
[docs] self.variable = variable
[docs] self.options = options
[docs] self.command = command
[docs] self.text = "Settings"
[docs] self.size = size
# Apply dark style and get color settings style_out = set_dark_style(ttk.Style())
[docs] self.font_size = style_out['font_size']
[docs] self.font_loader = style_out['font_loader']
# Button size configuration
[docs] self.button_width = int(size * 3)
[docs] self.canvas_width = self.button_width + 4
[docs] self.canvas_height = self.size + 4
# Create the canvas and rounded button
[docs] self.canvas = tk.Canvas(self, width=self.canvas_width, height=self.canvas_height, highlightthickness=0, bg=style_out['bg_color'])
self.canvas.grid(row=0, column=0) # Apply dark style and get color settings color_settings = set_dark_style(ttk.Style(), containers=[self], widgets=[self.canvas])
[docs] self.inactive_color = color_settings['inactive_color']
[docs] self.active_color = color_settings['active_color']
[docs] self.fg_color = color_settings['fg_color']
[docs] self.bg_color = style_out['bg_color']
# Create the button with rounded edges
[docs] self.button_bg = self.create_rounded_rectangle(2, 2, self.button_width + 2, self.size + 2, radius=20, fill=self.inactive_color, outline=self.inactive_color)
# Create and place the label on the button if self.font_loader: self.font_style = self.font_loader.get_font(size=self.font_size) else: self.font_style = font if font else ("Arial", 12)
[docs] self.button_text = self.canvas.create_text(self.button_width // 2, self.size // 2 + 2, text=self.text, fill=self.fg_color, font=self.font_style, anchor="center")
# Bind events for button behavior self.bind("<Enter>", self.on_enter) self.bind("<Leave>", self.on_leave) self.bind("<Button-1>", self.on_click) self.canvas.bind("<Enter>", self.on_enter) self.canvas.bind("<Leave>", self.on_leave) self.canvas.bind("<Button-1>", self.on_click) # Create a popup menu with the desired background color
[docs] self.menu = tk.Menu(self, tearoff=0, bg=self.bg_color, fg=self.fg_color)
for option in self.options: self.menu.add_command(label=option, command=lambda opt=option: self.on_select(opt))
[docs] def create_rounded_rectangle(self, x1, y1, x2, y2, radius=20, **kwargs): points = [ x1 + radius, y1, x2 - radius, y1, x2 - radius, y1, x2, y1, x2, y1 + radius, x2, y2 - radius, x2, y2 - radius, x2, y2, x2 - radius, y2, x1 + radius, y2, x1 + radius, y2, x1, y2, x1, y2 - radius, x1, y2 - radius, x1, y1 + radius, x1, y1 + radius, x1, y1 ] return self.canvas.create_polygon(points, **kwargs, smooth=True)
[docs] def on_enter(self, event=None): self.canvas.itemconfig(self.button_bg, fill=self.active_color)
[docs] def on_leave(self, event=None): self.canvas.itemconfig(self.button_bg, fill=self.inactive_color)
[docs] def on_click(self, event=None): self.post_menu()
[docs] def post_menu(self): x, y, width, height = self.winfo_rootx(), self.winfo_rooty(), self.winfo_width(), self.winfo_height() self.menu.post(x, y + height)
[docs] def on_select(self, option): if self.command: self.command(option)
[docs] def update_styles(self, active_categories=None): style_out = set_dark_style(ttk.Style(), widgets=[self.menu]) if active_categories is not None: for idx in range(self.menu.index("end") + 1): option = self.menu.entrycget(idx, "label") if option in active_categories: self.menu.entryconfig(idx, background=style_out['active_color'], foreground=style_out['fg_color']) else: self.menu.entryconfig(idx, background=style_out['bg_color'], foreground=style_out['fg_color'])
[docs] class spacrCheckbutton(ttk.Checkbutton): def __init__(self, parent, text="", variable=None, command=None, *args, **kwargs): super().__init__(parent, *args, **kwargs)
[docs] self.text = text
[docs] self.variable = variable if variable else tk.BooleanVar()
[docs] self.command = command
self.configure(text=self.text, variable=self.variable, command=self.command, style='Spacr.TCheckbutton') style = ttk.Style() _ = set_dark_style(style, widgets=[self])
[docs] class spacrProgressBar(ttk.Progressbar): def __init__(self, parent, label=True, *args, **kwargs): super().__init__(parent, *args, **kwargs) # Get the style colors style_out = set_dark_style(ttk.Style())
[docs] self.fg_color = style_out['fg_color']
[docs] self.bg_color = style_out['bg_color']
[docs] self.active_color = style_out['active_color']
[docs] self.inactive_color = style_out['inactive_color']
[docs] self.font_size = style_out['font_size']
[docs] self.font_loader = style_out['font_loader']
# Configure the style for the progress bar
[docs] self.style = ttk.Style()
# Remove any borders and ensure the active color fills the entire space self.style.configure( "spacr.Horizontal.TProgressbar", troughcolor=self.inactive_color, # Set the trough to bg color background=self.active_color, # Active part is the active color borderwidth=0, # Remove border width pbarrelief="flat", # Flat relief for the progress bar troughrelief="flat", # Flat relief for the trough thickness=20, # Set the thickness of the progress bar darkcolor=self.active_color, # Ensure darkcolor matches the active color lightcolor=self.active_color, # Ensure lightcolor matches the active color bordercolor=self.bg_color # Set the border color to the background color to hide it ) self.configure(style="spacr.Horizontal.TProgressbar") # Set initial value to 0 self['value'] = 0 # Track whether to show the progress label
[docs] self.label = label
# Create the progress label with text wrapping if self.label: self.progress_label = tk.Label( parent, text="Processing: 0/0", anchor='w', justify='left', bg=self.inactive_color, fg=self.fg_color, wraplength=300, font=self.font_loader.get_font(size=self.font_size) ) self.progress_label.grid_forget() # Initialize attributes for time and operation
[docs] self.operation_type = None
[docs] self.additional_info = None
[docs] def set_label_position(self): if self.label and self.progress_label: row_info = self.grid_info().get('rowID', 0) col_info = self.grid_info().get('columnID', 0) col_span = self.grid_info().get('columnspan', 1) self.progress_label.grid(row=row_info + 1, column=col_info, columnspan=col_span, pady=5, padx=5, sticky='ew')
[docs] def update_label(self): if self.label and self.progress_label: # Start with the base progress information label_text = f"Processing: {self['value']}/{self['maximum']}" # Include the operation type if it exists if self.operation_type: label_text += f", {self.operation_type}" # Handle additional info without adding newlines if hasattr(self, 'additional_info') and self.additional_info: # Join all additional info items with a space and ensure they're on the same line items = self.additional_info.split(", ") formatted_additional_info = " ".join(items) # Append the additional info to the label_text, ensuring it's all in one line label_text += f" {formatted_additional_info.strip()}" # Update the progress label self.progress_label.config(text=label_text)
[docs] class spacrSlider(tk.Frame): def __init__(self, master=None, length=None, thickness=2, knob_radius=10, position="center", from_=0, to=100, value=None, show_index=False, command=None, **kwargs): super().__init__(master, **kwargs)
[docs] self.specified_length = length # Store the specified length, if any
[docs] self.knob_radius = knob_radius
[docs] self.thickness = thickness
[docs] self.knob_position = knob_radius # Start at the beginning of the slider
[docs] self.slider_line = None
[docs] self.knob = None
[docs] self.position = position.lower() # Store the position option
[docs] self.offset = 0 # Initialize offset
[docs] self.from_ = from_ # Minimum value of the slider
[docs] self.to = to # Maximum value of the slider
[docs] self.value = value if value is not None else from_ # Initial value of the slider
[docs] self.show_index = show_index # Whether to show the index Entry widget
[docs] self.command = command # Callback function to handle value changes
# Initialize the style and colors style_out = set_dark_style(ttk.Style())
[docs] self.fg_color = style_out['fg_color']
[docs] self.bg_color = style_out['bg_color']
[docs] self.active_color = style_out['active_color']
[docs] self.inactive_color = style_out['inactive_color']
# Configure the frame's background color self.configure(bg=self.bg_color) # Create a frame for the slider and entry if needed self.grid_columnconfigure(1, weight=1) # Entry widget for showing and editing index, if enabled if self.show_index: self.index_var = tk.StringVar(value=str(int(self.value))) self.index_entry = tk.Entry(self, textvariable=self.index_var, width=5, bg=self.bg_color, fg=self.fg_color, insertbackground=self.fg_color) self.index_entry.grid(row=0, column=0, padx=5) # Bind the entry to update the slider on change self.index_entry.bind("<Return>", self.update_slider_from_entry) # Create the slider canvas
[docs] self.canvas = tk.Canvas(self, height=knob_radius * 2, bg=self.bg_color, highlightthickness=0)
self.canvas.grid(row=0, column=1, sticky="ew") # Set initial length to specified length or default value
[docs] self.length = self.specified_length if self.specified_length is not None else self.canvas.winfo_reqwidth()
# Calculate initial knob position based on the initial value self.knob_position = self.value_to_position(self.value) # Bind resize event to dynamically adjust the slider length if no length is specified self.canvas.bind("<Configure>", self.resize_slider) # Draw the slider components self.draw_slider(inactive=True) # Bind mouse events to the knob and slider self.canvas.bind("<B1-Motion>", self.move_knob) self.canvas.bind("<Button-1>", self.activate_knob) # Activate knob on click self.canvas.bind("<ButtonRelease-1>", self.release_knob) # Trigger command on release
[docs] def resize_slider(self, event): if self.specified_length is not None: self.length = self.specified_length else: self.length = int(event.width * 0.9) # 90% of the container width # Calculate the horizontal offset based on the position if self.position == "center": self.offset = (event.width - self.length) // 2 elif self.position == "right": self.offset = event.width - self.length else: # position is "left" self.offset = 0 # Update the knob position after resizing self.knob_position = self.value_to_position(self.value) self.draw_slider(inactive=True)
[docs] def value_to_position(self, value): if self.to == self.from_: return self.knob_radius relative_value = (value - self.from_) / (self.to - self.from_) return self.knob_radius + relative_value * (self.length - 2 * self.knob_radius)
[docs] def position_to_value(self, position): if self.to == self.from_: return self.from_ relative_position = (position - self.knob_radius) / (self.length - 2 * self.knob_radius) return self.from_ + relative_position * (self.to - self.from_)
[docs] def draw_slider(self, inactive=False): self.canvas.delete("all") self.slider_line = self.canvas.create_line( self.offset + self.knob_radius, self.knob_radius, self.offset + self.length - self.knob_radius, self.knob_radius, fill=self.fg_color, width=self.thickness ) knob_color = self.inactive_color if inactive else self.active_color self.knob = self.canvas.create_oval( self.offset + self.knob_position - self.knob_radius, self.knob_radius - self.knob_radius, self.offset + self.knob_position + self.knob_radius, self.knob_radius + self.knob_radius, fill=knob_color, outline="" )
[docs] def move_knob(self, event): new_position = min(max(event.x - self.offset, self.knob_radius), self.length - self.knob_radius) self.knob_position = new_position self.value = self.position_to_value(self.knob_position) self.canvas.coords( self.knob, self.offset + self.knob_position - self.knob_radius, self.knob_radius - self.knob_radius, self.offset + self.knob_position + self.knob_radius, self.knob_radius + self.knob_radius ) if self.show_index: self.index_var.set(str(int(self.value)))
[docs] def activate_knob(self, event): self.draw_slider(inactive=False) self.move_knob(event)
[docs] def release_knob(self, event): self.draw_slider(inactive=True) if self.command: self.command(self.value) # Call the command with the final value when the knob is released
[docs] def set_to(self, new_to): self.to = new_to self.knob_position = self.value_to_position(self.value) self.draw_slider(inactive=False)
[docs] def get(self): return self.value
[docs] def set(self, value): """Set the slider's value and update the knob position.""" self.value = max(self.from_, min(value, self.to)) # Ensure the value is within bounds self.knob_position = self.value_to_position(self.value) self.draw_slider(inactive=False) if self.show_index: self.index_var.set(str(int(self.value)))
[docs] def jump_to_click(self, event): self.activate_knob(event)
[docs] def update_slider_from_entry(self, event): """Update the slider's value from the entry.""" try: index = int(self.index_var.get()) self.set(index) if self.command: self.command(self.value) except ValueError: pass
[docs] def spacrScrollbarStyle(style, inactive_color, active_color): # Check if custom elements already exist to avoid duplication if not style.element_names().count('custom.Vertical.Scrollbar.trough'): style.element_create('custom.Vertical.Scrollbar.trough', 'from', 'clam') if not style.element_names().count('custom.Vertical.Scrollbar.thumb'): style.element_create('custom.Vertical.Scrollbar.thumb', 'from', 'clam') style.layout('Custom.Vertical.TScrollbar', [('Vertical.Scrollbar.trough', {'children': [('Vertical.Scrollbar.thumb', {'expand': '1', 'sticky': 'nswe'})], 'sticky': 'ns'})]) style.configure('Custom.Vertical.TScrollbar', background=inactive_color, troughcolor=inactive_color, bordercolor=inactive_color, lightcolor=inactive_color, darkcolor=inactive_color) style.map('Custom.Vertical.TScrollbar', background=[('!active', inactive_color), ('active', active_color)], troughcolor=[('!active', inactive_color), ('active', inactive_color)], bordercolor=[('!active', inactive_color), ('active', inactive_color)], lightcolor=[('!active', inactive_color), ('active', active_color)], darkcolor=[('!active', inactive_color), ('active', active_color)])
[docs] class spacrFrame(ttk.Frame): def __init__(self, container, width=None, *args, bg='black', radius=20, scrollbar=True, textbox=False, **kwargs): super().__init__(container, *args, **kwargs) self.configure(style='TFrame') if width is None: screen_width = self.winfo_screenwidth() width = screen_width // 4 # Create the canvas canvas = tk.Canvas(self, bg=bg, width=width, highlightthickness=0) self.rounded_rectangle(canvas, 0, 0, width, self.winfo_screenheight(), radius, fill=bg) # Define scrollbar styles style_out = set_dark_style(ttk.Style())
[docs] self.inactive_color = style_out['inactive_color']
[docs] self.active_color = style_out['active_color']
[docs] self.fg_color = style_out['fg_color'] # Foreground color for text
# Set custom scrollbar style style = ttk.Style() spacrScrollbarStyle(style, self.inactive_color, self.active_color) # Create scrollbar with custom style if scrollbar option is True if scrollbar: scrollbar_widget = ttk.Scrollbar(self, orient="vertical", command=canvas.yview, style='Custom.Vertical.TScrollbar') if textbox: self.scrollable_frame = tk.Text(canvas, bg=bg, fg=self.fg_color, wrap=tk.WORD) else: self.scrollable_frame = ttk.Frame(canvas, style='TFrame') self.scrollable_frame.bind( "<Configure>", lambda e: canvas.configure(scrollregion=canvas.bbox("all")) ) canvas.create_window((0, 0), window=self.scrollable_frame, anchor="nw") if scrollbar: canvas.configure(yscrollcommand=scrollbar_widget.set) canvas.grid(row=0, column=0, sticky="nsew") if scrollbar: scrollbar_widget.grid(row=0, column=1, sticky="ns") self.grid_rowconfigure(0, weight=1) self.grid_columnconfigure(0, weight=1) if scrollbar: self.grid_columnconfigure(1, weight=0) _ = set_dark_style(style, containers=[self], widgets=[canvas, self.scrollable_frame]) if scrollbar: _ = set_dark_style(style, widgets=[scrollbar_widget])
[docs] def rounded_rectangle(self, canvas, x1, y1, x2, y2, radius=20, **kwargs): points = [ x1 + radius, y1, x2 - radius, y1, x2 - radius, y1, x2, y1, x2, y1 + radius, x2, y2 - radius, x2, y2 - radius, x2, y2, x2 - radius, y2, x1 + radius, y2, x1 + radius, y2, x1, y2, x1, y2 - radius, x1, y2 - radius, x1, y1 + radius, x1, y1 + radius, x1, y1 ] return canvas.create_polygon(points, **kwargs, smooth=True)
[docs] class spacrLabel(tk.Frame): def __init__(self, parent, text="", font=None, style=None, align="right", height=None, **kwargs): valid_kwargs = {k: v for k, v in kwargs.items() if k not in ['foreground', 'background', 'font', 'anchor', 'justify', 'wraplength']} super().__init__(parent, **valid_kwargs)
[docs] self.text = text
[docs] self.align = align
if height is None: screen_height = self.winfo_screenheight() label_height = screen_height // 50 label_width = label_height * 10 else: label_height = height label_width = label_height * 10
[docs] self.style_out = set_dark_style(ttk.Style())
[docs] self.font_style = self.style_out['font_family']
[docs] self.font_size = self.style_out['font_size']
[docs] self.font_family = self.style_out['font_family']
[docs] self.font_loader = self.style_out['font_loader']
[docs] self.canvas = tk.Canvas(self, width=label_width, height=label_height, highlightthickness=0, bg=self.style_out['bg_color'])
self.canvas.grid(row=0, column=0, sticky="ew") if self.style_out['font_family'] != 'OpenSans': self.font_style = font if font else tkFont.Font(family=self.style_out['font_family'], size=self.style_out['font_size'], weight=tkFont.NORMAL)
[docs] self.style = style
if self.align == "center": anchor_value = tk.CENTER text_anchor = 'center' else: # default to right alignment anchor_value = tk.E text_anchor = 'e' if self.style: ttk_style = ttk.Style() if self.font_loader: ttk_style.configure(self.style, font=self.font_loader.get_font(size=self.font_size), background=self.style_out['bg_color'], foreground=self.style_out['fg_color']) else: ttk_style.configure(self.style, font=self.font_style, background=self.style_out['bg_color'], foreground=self.style_out['fg_color']) self.label_text = ttk.Label(self.canvas, text=self.text, style=self.style, anchor=text_anchor) self.label_text.pack(fill=tk.BOTH, expand=True) else: if self.font_loader: self.label_text = self.canvas.create_text(label_width // 2 if self.align == "center" else label_width - 5, label_height // 2, text=self.text, fill=self.style_out['fg_color'], font=self.font_loader.get_font(size=self.font_size), anchor=anchor_value, justify=tk.RIGHT) else: self.label_text = self.canvas.create_text(label_width // 2 if self.align == "center" else label_width - 5, label_height // 2, text=self.text, fill=self.style_out['fg_color'], font=self.font_style, anchor=anchor_value, justify=tk.RIGHT) _ = set_dark_style(ttk.Style(), containers=[self], widgets=[self.canvas])
[docs] def set_text(self, text): if self.style: self.label_text.config(text=text) else: self.canvas.itemconfig(self.label_text, text=text)
[docs] class spacrButton(tk.Frame): def __init__(self, parent, text="", command=None, font=None, icon_name=None, size=50, show_text=True, outline=False, animation=True, *args, **kwargs): super().__init__(parent, *args, **kwargs)
[docs] self.text = text.capitalize() # Capitalize only the first letter of the text
[docs] self.command = command
[docs] self.icon_name = icon_name if icon_name else text.lower()
[docs] self.size = size
[docs] self.show_text = show_text
[docs] self.outline = outline
[docs] self.animation = animation # Add animation attribute
style_out = set_dark_style(ttk.Style())
[docs] self.font_size = style_out['font_size']
[docs] self.font_loader = style_out['font_loader']
if self.show_text: self.button_width = int(size * 3) else: self.button_width = self.size # Make the button width equal to the size if show_text is False # Create the canvas first
[docs] self.canvas = tk.Canvas(self, width=self.button_width + 4, height=self.size + 4, highlightthickness=0, bg=style_out['bg_color'])
self.canvas.grid(row=0, column=0) # Apply dark style and get color settings color_settings = set_dark_style(ttk.Style(), containers=[self], widgets=[self.canvas])
[docs] self.inactive_color = color_settings['inactive_color']
if self.outline: self.button_bg = self.create_rounded_rectangle(2, 2, self.button_width + 2, self.size + 2, radius=20, fill=self.inactive_color, outline=color_settings['fg_color']) else: self.button_bg = self.create_rounded_rectangle(2, 2, self.button_width + 2, self.size + 2, radius=20, fill=self.inactive_color, outline=self.inactive_color) self.load_icon() if self.font_loader: self.font_style = self.font_loader.get_font(size=self.font_size) else: self.font_style = font if font else ("Arial", 12) if self.show_text: self.button_text = self.canvas.create_text(self.size + 10, self.size // 2 + 2, text=self.text, fill=color_settings['fg_color'], font=self.font_style, anchor="w") # Align text to the left of the specified point self.bind("<Enter>", self.on_enter) self.bind("<Leave>", self.on_leave) self.bind("<Button-1>", self.on_click) self.canvas.bind("<Enter>", self.on_enter) self.canvas.bind("<Leave>", self.on_leave) self.canvas.bind("<Button-1>", self.on_click)
[docs] self.bg_color = self.inactive_color
[docs] self.active_color = color_settings['active_color']
[docs] self.fg_color = color_settings['fg_color']
[docs] self.is_zoomed_in = False # Track zoom state for smooth transitions
[docs] def load_icon(self): icon_path = self.get_icon_path(self.icon_name) try: icon_image = Image.open(icon_path) except (FileNotFoundError, Image.UnidentifiedImageError): try: icon_path = icon_path.replace(' ', '_') icon_image = Image.open(icon_path) except (FileNotFoundError, Image.UnidentifiedImageError): icon_image = Image.open(self.get_icon_path("default")) print(f'Icon not found: {icon_path}. Using default icon instead.') initial_size = int(self.size * 0.65) # 65% of button size initially self.original_icon_image = icon_image.resize((initial_size, initial_size), Image.Resampling.LANCZOS) self.icon_photo = ImageTk.PhotoImage(self.original_icon_image) self.button_icon = self.canvas.create_image(self.size // 2 + 2, self.size // 2 + 2, image=self.icon_photo) self.canvas.image = self.icon_photo # Keep a reference to avoid garbage collection
[docs] def get_icon_path(self, icon_name): icon_dir = os.path.join(os.path.dirname(__file__), 'resources', 'icons') return os.path.join(icon_dir, f"{icon_name}.png")
[docs] def on_enter(self, event=None): self.canvas.itemconfig(self.button_bg, fill=self.active_color) self.update_description(event) if self.animation and not self.is_zoomed_in: self.animate_zoom(0.85) # Zoom in the icon to 85% of button size
[docs] def on_leave(self, event=None): self.canvas.itemconfig(self.button_bg, fill=self.inactive_color) self.clear_description(event) if self.animation and self.is_zoomed_in: self.animate_zoom(0.65) # Reset the icon size to 65% of button size
[docs] def on_click(self, event=None): if self.command: self.command()
[docs] def create_rounded_rectangle(self, x1, y1, x2, y2, radius=20, **kwargs): points = [ x1 + radius, y1, x2 - radius, y1, x2 - radius, y1, x2, y1, x2, y1 + radius, x2, y2 - radius, x2, y2 - radius, x2, y2, x2 - radius, y2, x1 + radius, y2, x1 + radius, y2, x1, y2, x1, y2 - radius, x1, y2 - radius, x1, y1 + radius, x1, y1 + radius, x1, y1 ] return self.canvas.create_polygon(points, **kwargs, smooth=True)
[docs] def update_description(self, event): parent = self.master while parent: if hasattr(parent, 'show_description'): parent.show_description(parent.main_buttons.get(self, parent.additional_buttons.get(self, "No description available."))) return parent = parent.master
[docs] def clear_description(self, event): parent = self.master while parent: if hasattr(parent, 'clear_description'): parent.clear_description() return parent = parent.master
[docs] def animate_zoom(self, target_scale, steps=10, delay=10): current_scale = 0.85 if self.is_zoomed_in else 0.65 step_scale = (target_scale - current_scale) / steps self._animate_step(current_scale, step_scale, steps, delay)
def _animate_step(self, current_scale, step_scale, steps, delay): if steps > 0: new_scale = current_scale + step_scale self.zoom_icon(new_scale) self.after(delay, self._animate_step, new_scale, step_scale, steps - 1, delay) else: self.is_zoomed_in = not self.is_zoomed_in
[docs] def zoom_icon(self, scale_factor): # Resize the original icon image new_size = int(self.size * scale_factor) resized_icon = self.original_icon_image.resize((new_size, new_size), Image.Resampling.LANCZOS) self.icon_photo = ImageTk.PhotoImage(resized_icon) # Update the icon on the canvas self.canvas.itemconfig(self.button_icon, image=self.icon_photo) self.canvas.image = self.icon_photo
[docs] class spacrSwitch(ttk.Frame): def __init__(self, parent, text="", variable=None, command=None, *args, **kwargs): super().__init__(parent, *args, **kwargs)
[docs] self.text = text
[docs] self.variable = variable if variable else tk.BooleanVar()
[docs] self.command = command
[docs] self.canvas = tk.Canvas(self, width=40, height=20, highlightthickness=0, bd=0)
self.canvas.grid(row=0, column=1, padx=(10, 0))
[docs] self.switch_bg = self.create_rounded_rectangle(2, 2, 38, 18, radius=9, outline="", fill="#fff")
[docs] self.switch = self.canvas.create_oval(4, 4, 16, 16, outline="", fill="#800080")
[docs] self.label = spacrLabel(self, text=self.text)
self.label.grid(row=0, column=0, padx=(0, 10)) self.bind("<Button-1>", self.toggle) self.canvas.bind("<Button-1>", self.toggle) self.label.bind("<Button-1>", self.toggle) self.update_switch() style = ttk.Style() _ = set_dark_style(style, containers=[self], widgets=[self.canvas, self.label])
[docs] def toggle(self, event=None): self.variable.set(not self.variable.get()) self.animate_switch() if self.command: self.command()
[docs] def update_switch(self): if self.variable.get(): self.canvas.itemconfig(self.switch, fill="#008080") self.canvas.coords(self.switch, 24, 4, 36, 16) else: self.canvas.itemconfig(self.switch, fill="#800080") self.canvas.coords(self.switch, 4, 4, 16, 16)
[docs] def animate_switch(self): if self.variable.get(): start_x, end_x = 4, 24 final_color = "#008080" else: start_x, end_x = 24, 4 final_color = "#800080" self.animate_movement(start_x, end_x, final_color)
[docs] def animate_movement(self, start_x, end_x, final_color): step = 1 if start_x < end_x else -1 for i in range(start_x, end_x, step): self.canvas.coords(self.switch, i, 4, i + 12, 16) self.canvas.update() self.after(10) self.canvas.itemconfig(self.switch, fill=final_color)
[docs] def get(self): return self.variable.get()
[docs] def set(self, value): self.variable.set(value) self.update_switch()
[docs] def create_rounded_rectangle(self, x1, y1, x2, y2, radius=9, **kwargs): points = [x1 + radius, y1, x1 + radius, y1, x2 - radius, y1, x2 - radius, y1, x2, y1, x2, y1 + radius, x2, y1 + radius, x2, y2 - radius, x2, y2 - radius, x2, y2, x2 - radius, y2, x2 - radius, y2, x1 + radius, y2, x1 + radius, y2, x1, y2, x1, y2 - radius, x1, y2 - radius, x1, y1 + radius, x1, y1 + radius, x1, y1] return self.canvas.create_polygon(points, **kwargs, smooth=True)
[docs] class spacrToolTip: def __init__(self, widget, text):
[docs] self.widget = widget
[docs] self.text = text
[docs] self.tooltip_window = None
widget.bind("<Enter>", self.show_tooltip) widget.bind("<Leave>", self.hide_tooltip)
[docs] def show_tooltip(self, event): x = event.x_root + 20 y = event.y_root + 10 self.tooltip_window = tk.Toplevel(self.widget) self.tooltip_window.wm_overrideredirect(True) self.tooltip_window.wm_geometry(f"+{x}+{y}") label = tk.Label(self.tooltip_window, text=self.text, relief='flat', borderwidth=0) label.grid(row=0, column=0, padx=5, pady=5) style = ttk.Style() _ = set_dark_style(style, containers=[self.tooltip_window], widgets=[label])
[docs] def hide_tooltip(self, event): if self.tooltip_window: self.tooltip_window.destroy() self.tooltip_window = None
[docs] class ModifyMaskApp: def __init__(self, root, folder_path, scale_factor):
[docs] self.root = root
[docs] self.folder_path = folder_path
[docs] self.scale_factor = scale_factor
[docs] self.image_filenames = sorted([f for f in os.listdir(folder_path) if f.endswith(('.png', '.jpg', '.jpeg', '.tif', '.tiff'))])
[docs] self.masks_folder = os.path.join(folder_path, 'masks')
[docs] self.current_image_index = 0
self.initialize_flags()
[docs] self.canvas_width = self.root.winfo_screenheight() -100
[docs] self.canvas_height = self.root.winfo_screenheight() -100
self.root.configure(bg='black') self.setup_navigation_toolbar() self.setup_mode_toolbar() self.setup_function_toolbar() self.setup_zoom_toolbar() self.setup_canvas() self.load_first_image() #################################################################################################### # Helper functions# ####################################################################################################
[docs] def update_display(self): if self.zoom_active: self.display_zoomed_image() else: self.display_image()
[docs] def update_original_mask_from_zoom(self): y0, y1, x0, x1 = self.zoom_y0, self.zoom_y1, self.zoom_x0, self.zoom_x1 zoomed_mask_resized = resize(self.zoom_mask, (y1 - y0, x1 - x0), order=0, preserve_range=True).astype(np.uint8) self.mask[y0:y1, x0:x1] = zoomed_mask_resized
[docs] def update_original_mask(self, zoomed_mask, x0, x1, y0, y1): actual_mask_region = self.mask[y0:y1, x0:x1] target_shape = actual_mask_region.shape resized_mask = resize(zoomed_mask, target_shape, order=0, preserve_range=True).astype(np.uint8) if resized_mask.shape != actual_mask_region.shape: raise ValueError(f"Shape mismatch: resized_mask {resized_mask.shape}, actual_mask_region {actual_mask_region.shape}") self.mask[y0:y1, x0:x1] = np.maximum(actual_mask_region, resized_mask) self.mask = self.mask.copy() self.mask[y0:y1, x0:x1] = np.maximum(self.mask[y0:y1, x0:x1], resized_mask) self.mask = self.mask.copy()
[docs] def get_scaling_factors(self, img_width, img_height, canvas_width, canvas_height): x_scale = img_width / canvas_width y_scale = img_height / canvas_height return x_scale, y_scale
[docs] def canvas_to_image(self, x_canvas, y_canvas): x_scale, y_scale = self.get_scaling_factors( self.image.shape[1], self.image.shape[0], self.canvas_width, self.canvas_height ) x_image = int(x_canvas * x_scale) y_image = int(y_canvas * y_scale) return x_image, y_image
[docs] def apply_zoom_on_enter(self, event): if self.zoom_active and self.zoom_rectangle_start is not None: self.set_zoom_rectangle_end(event)
[docs] def normalize_image(self, image, lower_quantile, upper_quantile): lower_bound = np.percentile(image, lower_quantile) upper_bound = np.percentile(image, upper_quantile) normalized = np.clip(image, lower_bound, upper_bound) normalized = (normalized - lower_bound) / (upper_bound - lower_bound) max_value = np.iinfo(image.dtype).max normalized = (normalized * max_value).astype(image.dtype) return normalized
[docs] def resize_arrays(self, img, mask): original_dtype = img.dtype scaled_height = int(img.shape[0] * self.scale_factor) scaled_width = int(img.shape[1] * self.scale_factor) scaled_img = resize(img, (scaled_height, scaled_width), anti_aliasing=True, preserve_range=True) scaled_mask = resize(mask, (scaled_height, scaled_width), order=0, anti_aliasing=False, preserve_range=True) stretched_img = resize(scaled_img, (self.canvas_height, self.canvas_width), anti_aliasing=True, preserve_range=True) stretched_mask = resize(scaled_mask, (self.canvas_height, self.canvas_width), order=0, anti_aliasing=False, preserve_range=True) return stretched_img.astype(original_dtype), stretched_mask.astype(original_dtype)
#################################################################################################### #Initiate canvas elements# ####################################################################################################
[docs] def load_first_image(self): self.image, self.mask = self.load_image_and_mask(self.current_image_index) self.original_size = self.image.shape self.image, self.mask = self.resize_arrays(self.image, self.mask) self.display_image()
[docs] def setup_canvas(self): self.canvas = tk.Canvas(self.root, width=self.canvas_width, height=self.canvas_height, bg='black') self.canvas.pack() self.canvas.bind("<Motion>", self.update_mouse_info)
[docs] def initialize_flags(self): self.zoom_rectangle_start = None self.zoom_rectangle_end = None self.zoom_rectangle_id = None self.zoom_x0 = None self.zoom_y0 = None self.zoom_x1 = None self.zoom_y1 = None self.zoom_mask = None self.zoom_image = None self.zoom_image_orig = None self.zoom_scale = 1 self.drawing = False self.zoom_active = False self.magic_wand_active = False self.brush_active = False self.dividing_line_active = False self.dividing_line_coords = [] self.current_dividing_line = None self.lower_quantile = tk.StringVar(value="1.0") self.upper_quantile = tk.StringVar(value="99.9") self.magic_wand_tolerance = tk.StringVar(value="1000")
[docs] def update_mouse_info(self, event): x, y = event.x, event.y intensity = "N/A" mask_value = "N/A" pixel_count = "N/A" if self.zoom_active: if 0 <= x < self.canvas_width and 0 <= y < self.canvas_height: intensity = self.zoom_image_orig[y, x] if self.zoom_image_orig is not None else "N/A" mask_value = self.zoom_mask[y, x] if self.zoom_mask is not None else "N/A" else: if 0 <= x < self.image.shape[1] and 0 <= y < self.image.shape[0]: intensity = self.image[y, x] mask_value = self.mask[y, x] if mask_value != "N/A" and mask_value != 0: pixel_count = np.sum(self.mask == mask_value) self.intensity_label.config(text=f"Intensity: {intensity}") self.mask_value_label.config(text=f"Mask: {mask_value}, Area: {pixel_count}") self.mask_value_label.config(text=f"Mask: {mask_value}") if mask_value != "N/A" and mask_value != 0: self.pixel_count_label.config(text=f"Area: {pixel_count}") else: self.pixel_count_label.config(text="Area: N/A")
[docs] def setup_navigation_toolbar(self): navigation_toolbar = tk.Frame(self.root, bg='black') navigation_toolbar.pack(side='top', fill='x') prev_btn = tk.Button(navigation_toolbar, text="Previous", command=self.previous_image, bg='black', fg='white') prev_btn.pack(side='left') next_btn = tk.Button(navigation_toolbar, text="Next", command=self.next_image, bg='black', fg='white') next_btn.pack(side='left') save_btn = tk.Button(navigation_toolbar, text="Save", command=self.save_mask, bg='black', fg='white') save_btn.pack(side='left') self.intensity_label = tk.Label(navigation_toolbar, text="Image: N/A", bg='black', fg='white') self.intensity_label.pack(side='right') self.mask_value_label = tk.Label(navigation_toolbar, text="Mask: N/A", bg='black', fg='white') self.mask_value_label.pack(side='right') self.pixel_count_label = tk.Label(navigation_toolbar, text="Area: N/A", bg='black', fg='white') self.pixel_count_label.pack(side='right')
[docs] def setup_mode_toolbar(self): self.mode_toolbar = tk.Frame(self.root, bg='black') self.mode_toolbar.pack(side='top', fill='x') self.draw_btn = tk.Button(self.mode_toolbar, text="Draw", command=self.toggle_draw_mode, bg='black', fg='white') self.draw_btn.pack(side='left') self.magic_wand_btn = tk.Button(self.mode_toolbar, text="Magic Wand", command=self.toggle_magic_wand_mode, bg='black', fg='white') self.magic_wand_btn.pack(side='left') tk.Label(self.mode_toolbar, text="Tolerance:", bg='black', fg='white').pack(side='left') self.tolerance_entry = tk.Entry(self.mode_toolbar, textvariable=self.magic_wand_tolerance, bg='black', fg='white') self.tolerance_entry.pack(side='left') tk.Label(self.mode_toolbar, text="Max Pixels:", bg='black', fg='white').pack(side='left') self.max_pixels_entry = tk.Entry(self.mode_toolbar, bg='black', fg='white') self.max_pixels_entry.insert(0, "1000") self.max_pixels_entry.pack(side='left') self.erase_btn = tk.Button(self.mode_toolbar, text="Erase", command=self.toggle_erase_mode, bg='black', fg='white') self.erase_btn.pack(side='left') self.brush_btn = tk.Button(self.mode_toolbar, text="Brush", command=self.toggle_brush_mode, bg='black', fg='white') self.brush_btn.pack(side='left') self.brush_size_entry = tk.Entry(self.mode_toolbar, bg='black', fg='white') self.brush_size_entry.insert(0, "10") self.brush_size_entry.pack(side='left') tk.Label(self.mode_toolbar, text="Brush Size:", bg='black', fg='white').pack(side='left') self.dividing_line_btn = tk.Button(self.mode_toolbar, text="Dividing Line", command=self.toggle_dividing_line_mode, bg='black', fg='white') self.dividing_line_btn.pack(side='left')
[docs] def setup_function_toolbar(self): self.function_toolbar = tk.Frame(self.root, bg='black') self.function_toolbar.pack(side='top', fill='x') self.fill_btn = tk.Button(self.function_toolbar, text="Fill", command=self.fill_objects, bg='black', fg='white') self.fill_btn.pack(side='left') self.relabel_btn = tk.Button(self.function_toolbar, text="Relabel", command=self.relabel_objects, bg='black', fg='white') self.relabel_btn.pack(side='left') self.clear_btn = tk.Button(self.function_toolbar, text="Clear", command=self.clear_objects, bg='black', fg='white') self.clear_btn.pack(side='left') self.invert_btn = tk.Button(self.function_toolbar, text="Invert", command=self.invert_mask, bg='black', fg='white') self.invert_btn.pack(side='left') remove_small_btn = tk.Button(self.function_toolbar, text="Remove Small", command=self.remove_small_objects, bg='black', fg='white') remove_small_btn.pack(side='left') tk.Label(self.function_toolbar, text="Min Area:", bg='black', fg='white').pack(side='left') self.min_area_entry = tk.Entry(self.function_toolbar, bg='black', fg='white') self.min_area_entry.insert(0, "100") # Default minimum area self.min_area_entry.pack(side='left')
[docs] def setup_zoom_toolbar(self): self.zoom_toolbar = tk.Frame(self.root, bg='black') self.zoom_toolbar.pack(side='top', fill='x') self.zoom_btn = tk.Button(self.zoom_toolbar, text="Zoom", command=self.toggle_zoom_mode, bg='black', fg='white') self.zoom_btn.pack(side='left') self.normalize_btn = tk.Button(self.zoom_toolbar, text="Apply Normalization", command=self.apply_normalization, bg='black', fg='white') self.normalize_btn.pack(side='left') tk.Label(self.zoom_toolbar, text="Lower Percentile:", bg='black', fg='white').pack(side='left') self.lower_entry = tk.Entry(self.zoom_toolbar, textvariable=self.lower_quantile, bg='black', fg='white') self.lower_entry.pack(side='left') tk.Label(self.zoom_toolbar, text="Upper Percentile:", bg='black', fg='white').pack(side='left') self.upper_entry = tk.Entry(self.zoom_toolbar, textvariable=self.upper_quantile, bg='black', fg='white') self.upper_entry.pack(side='left')
[docs] def load_image_and_mask(self, index): # Load the image image_path = os.path.join(self.folder_path, self.image_filenames[index]) image = imageio.imread(image_path) print(f"Original Image shape: {image.shape}, dtype: {image.dtype}") # Handle multi-channel or transparency issues if image.ndim == 3: if image.shape[2] == 4: # If the image has an alpha channel (RGBA) image = image[..., :3] # Remove the alpha channel # Convert RGB to grayscale using weighted average image = np.dot(image[..., :3], [0.2989, 0.5870, 0.1140]).astype(np.uint8) print(f"Converted to grayscale: {image.shape}") # Ensure the shape is (height, width) without extra channel if image.ndim == 3 and image.shape[2] == 1: image = np.squeeze(image, axis=-1) if image.dtype != np.uint16: # Scale the image to fit the 16-bit range (0–65535) image = (image / image.max() * 65535).astype(np.uint16) # eventually remove this images should not have to be 16 bit look into downstream function (non 16bit images are jsut black) # Load the corresponding mask mask_path = os.path.join(self.masks_folder, self.image_filenames[index]) if os.path.exists(mask_path): print(f'Loading mask: {mask_path} for image: {image_path}') mask = imageio.imread(mask_path) # Ensure mask is uint8 if mask.dtype != np.uint8: mask = (mask / mask.max() * 255).astype(np.uint8) else: # Create a new mask with the same size as the image mask = np.zeros(image.shape[:2], dtype=np.uint8) print(f'Loaded new mask for image: {image_path}') return image, mask
#################################################################################################### # Image Display functions# ####################################################################################################
[docs] def display_image(self): if self.zoom_rectangle_id is not None: self.canvas.delete(self.zoom_rectangle_id) self.zoom_rectangle_id = None lower_quantile = float(self.lower_quantile.get()) if self.lower_quantile.get() else 1.0 upper_quantile = float(self.upper_quantile.get()) if self.upper_quantile.get() else 99.9 normalized = self.normalize_image(self.image, lower_quantile, upper_quantile) combined = self.overlay_mask_on_image(normalized, self.mask) self.tk_image = ImageTk.PhotoImage(image=Image.fromarray(combined)) self.canvas.create_image(0, 0, anchor='nw', image=self.tk_image)
[docs] def display_zoomed_image(self): if self.zoom_rectangle_start and self.zoom_rectangle_end: # Convert canvas coordinates to image coordinates x0, y0 = self.canvas_to_image(*self.zoom_rectangle_start) x1, y1 = self.canvas_to_image(*self.zoom_rectangle_end) x0, x1 = min(x0, x1), max(x0, x1) y0, y1 = min(y0, y1), max(y0, y1) self.zoom_x0 = x0 self.zoom_y0 = y0 self.zoom_x1 = x1 self.zoom_y1 = y1 # Normalize the entire image lower_quantile = float(self.lower_quantile.get()) if self.lower_quantile.get() else 1.0 upper_quantile = float(self.upper_quantile.get()) if self.upper_quantile.get() else 99.9 normalized_image = self.normalize_image(self.image, lower_quantile, upper_quantile) # Extract the zoomed portion of the normalized image and mask self.zoom_image = normalized_image[y0:y1, x0:x1] self.zoom_image_orig = self.image[y0:y1, x0:x1] self.zoom_mask = self.mask[y0:y1, x0:x1] original_mask_area = self.mask.shape[0] * self.mask.shape[1] zoom_mask_area = self.zoom_mask.shape[0] * self.zoom_mask.shape[1] if original_mask_area > 0: self.zoom_scale = original_mask_area/zoom_mask_area # Resize the zoomed image and mask to fit the canvas canvas_height = self.canvas.winfo_height() canvas_width = self.canvas.winfo_width() if self.zoom_image.size > 0 and canvas_height > 0 and canvas_width > 0: self.zoom_image = resize(self.zoom_image, (canvas_height, canvas_width), preserve_range=True).astype(self.zoom_image.dtype) self.zoom_image_orig = resize(self.zoom_image_orig, (canvas_height, canvas_width), preserve_range=True).astype(self.zoom_image_orig.dtype) #self.zoom_mask = resize(self.zoom_mask, (canvas_height, canvas_width), preserve_range=True).astype(np.uint8) self.zoom_mask = resize(self.zoom_mask, (canvas_height, canvas_width), order=0, preserve_range=True).astype(np.uint8) combined = self.overlay_mask_on_image(self.zoom_image, self.zoom_mask) self.tk_image = ImageTk.PhotoImage(image=Image.fromarray(combined)) self.canvas.create_image(0, 0, anchor='nw', image=self.tk_image)
[docs] def overlay_mask_on_image(self, image, mask, alpha=0.5): if len(image.shape) == 2: image = np.stack((image,) * 3, axis=-1) mask = mask.astype(np.int32) max_label = np.max(mask) np.random.seed(0) colors = np.random.randint(0, 255, size=(max_label + 1, 3), dtype=np.uint8) colors[0] = [0, 0, 0] # background color colored_mask = colors[mask] image_8bit = (image / 256).astype(np.uint8) # Blend the mask and the image with transparency combined_image = np.where(mask[..., None] > 0, np.clip(image_8bit * (1 - alpha) + colored_mask * alpha, 0, 255), image_8bit) # Convert the final image back to uint8 combined_image = combined_image.astype(np.uint8) return combined_image
#################################################################################################### # Navigation functions# ####################################################################################################
[docs] def previous_image(self): if self.current_image_index > 0: self.current_image_index -= 1 self.initialize_flags() self.image, self.mask = self.load_image_and_mask(self.current_image_index) self.original_size = self.image.shape self.image, self.mask = self.resize_arrays(self.image, self.mask) self.display_image()
[docs] def next_image(self): if self.current_image_index < len(self.image_filenames) - 1: self.current_image_index += 1 self.initialize_flags() self.image, self.mask = self.load_image_and_mask(self.current_image_index) self.original_size = self.image.shape self.image, self.mask = self.resize_arrays(self.image, self.mask) self.display_image()
[docs] def save_mask(self): if self.current_image_index < len(self.image_filenames): original_size = self.original_size if self.mask.shape != original_size: resized_mask = resize(self.mask, original_size, order=0, preserve_range=True).astype(np.uint16) else: resized_mask = self.mask resized_mask, _ = label(resized_mask > 0) save_folder = os.path.join(self.folder_path, 'masks') if not os.path.exists(save_folder): os.makedirs(save_folder) image_filename = os.path.splitext(self.image_filenames[self.current_image_index])[0] + '.tif' save_path = os.path.join(save_folder, image_filename) print(f"Saving mask to: {save_path}") # Debug print imageio.imwrite(save_path, resized_mask)
#################################################################################################### # Zoom Functions # ####################################################################################################
[docs] def set_zoom_rectangle_start(self, event): if self.zoom_active: self.zoom_rectangle_start = (event.x, event.y)
[docs] def set_zoom_rectangle_end(self, event): if self.zoom_active: self.zoom_rectangle_end = (event.x, event.y) if self.zoom_rectangle_id is not None: self.canvas.delete(self.zoom_rectangle_id) self.zoom_rectangle_id = None self.display_zoomed_image() self.canvas.unbind("<Motion>") self.canvas.unbind("<Button-1>") self.canvas.unbind("<Button-3>") self.canvas.bind("<Motion>", self.update_mouse_info)
[docs] def update_zoom_box(self, event): if self.zoom_active and self.zoom_rectangle_start is not None: if self.zoom_rectangle_id is not None: self.canvas.delete(self.zoom_rectangle_id) # Assuming event.x and event.y are already in image coordinates self.zoom_rectangle_end = (event.x, event.y) x0, y0 = self.zoom_rectangle_start x1, y1 = self.zoom_rectangle_end self.zoom_rectangle_id = self.canvas.create_rectangle(x0, y0, x1, y1, outline="red", width=2)
#################################################################################################### # Mode activation# ####################################################################################################
[docs] def toggle_zoom_mode(self): if not self.zoom_active: self.brush_btn.config(text="Brush") self.canvas.unbind("<B1-Motion>") self.canvas.unbind("<B3-Motion>") self.canvas.unbind("<ButtonRelease-1>") self.canvas.unbind("<ButtonRelease-3>") self.zoom_active = True self.drawing = False self.magic_wand_active = False self.erase_active = False self.brush_active = False self.dividing_line_active = False self.draw_btn.config(text="Draw") self.erase_btn.config(text="Erase") self.magic_wand_btn.config(text="Magic Wand") self.zoom_btn.config(text="Zoom ON") self.dividing_line_btn.config(text="Dividing Line") self.canvas.unbind("<Button-1>") self.canvas.unbind("<Button-3>") self.canvas.unbind("<Motion>") self.canvas.bind("<Button-1>", self.set_zoom_rectangle_start) self.canvas.bind("<Button-3>", self.set_zoom_rectangle_end) self.canvas.bind("<Motion>", self.update_zoom_box) else: self.zoom_active = False self.zoom_btn.config(text="Zoom") self.canvas.unbind("<Button-1>") self.canvas.unbind("<Button-3>") self.canvas.unbind("<Motion>") self.zoom_rectangle_start = self.zoom_rectangle_end = None self.zoom_rectangle_id = None self.display_image() self.canvas.bind("<Motion>", self.update_mouse_info) self.zoom_rectangle_start = None self.zoom_rectangle_end = None self.zoom_rectangle_id = None self.zoom_x0 = None self.zoom_y0 = None self.zoom_x1 = None self.zoom_y1 = None self.zoom_mask = None self.zoom_image = None self.zoom_image_orig = None
[docs] def toggle_brush_mode(self): self.brush_active = not self.brush_active if self.brush_active: self.drawing = False self.magic_wand_active = False self.erase_active = False self.brush_btn.config(text="Brush ON") self.draw_btn.config(text="Draw") self.erase_btn.config(text="Erase") self.magic_wand_btn.config(text="Magic Wand") self.canvas.unbind("<Button-1>") self.canvas.unbind("<Button-3>") self.canvas.unbind("<Motion>") self.canvas.bind("<B1-Motion>", self.apply_brush) # Left click and drag to apply brush self.canvas.bind("<B3-Motion>", self.erase_brush) # Right click and drag to erase with brush self.canvas.bind("<ButtonRelease-1>", self.apply_brush_release) # Left button release self.canvas.bind("<ButtonRelease-3>", self.erase_brush_release) # Right button release else: self.brush_active = False self.brush_btn.config(text="Brush") self.canvas.unbind("<B1-Motion>") self.canvas.unbind("<B3-Motion>") self.canvas.unbind("<ButtonRelease-1>") self.canvas.unbind("<ButtonRelease-3>")
[docs] def image_to_canvas(self, x_image, y_image): x_scale, y_scale = self.get_scaling_factors( self.image.shape[1], self.image.shape[0], self.canvas_width, self.canvas_height ) x_canvas = int(x_image / x_scale) y_canvas = int(y_image / y_scale) return x_canvas, y_canvas
[docs] def toggle_dividing_line_mode(self): self.dividing_line_active = not self.dividing_line_active if self.dividing_line_active: self.drawing = False self.magic_wand_active = False self.erase_active = False self.brush_active = False self.draw_btn.config(text="Draw") self.erase_btn.config(text="Erase") self.magic_wand_btn.config(text="Magic Wand") self.brush_btn.config(text="Brush") self.dividing_line_btn.config(text="Dividing Line ON") self.canvas.unbind("<Button-1>") self.canvas.unbind("<ButtonRelease-1>") self.canvas.unbind("<Motion>") self.canvas.bind("<Button-1>", self.start_dividing_line) self.canvas.bind("<ButtonRelease-1>", self.finish_dividing_line) self.canvas.bind("<Motion>", self.update_dividing_line_preview) else: print("Dividing Line Mode: OFF") self.dividing_line_active = False self.dividing_line_btn.config(text="Dividing Line") self.canvas.unbind("<Button-1>") self.canvas.unbind("<ButtonRelease-1>") self.canvas.unbind("<Motion>") self.display_image()
[docs] def start_dividing_line(self, event): if self.dividing_line_active: self.dividing_line_coords = [(event.x, event.y)] self.current_dividing_line = self.canvas.create_line(event.x, event.y, event.x, event.y, fill="red", width=2)
[docs] def finish_dividing_line(self, event): if self.dividing_line_active: self.dividing_line_coords.append((event.x, event.y)) if self.zoom_active: self.dividing_line_coords = [self.canvas_to_image(x, y) for x, y in self.dividing_line_coords] self.apply_dividing_line() self.canvas.delete(self.current_dividing_line) self.current_dividing_line = None
[docs] def update_dividing_line_preview(self, event): if self.dividing_line_active and self.dividing_line_coords: x, y = event.x, event.y if self.zoom_active: x, y = self.canvas_to_image(x, y) self.dividing_line_coords.append((x, y)) canvas_coords = [(self.image_to_canvas(*pt) if self.zoom_active else pt) for pt in self.dividing_line_coords] flat_canvas_coords = [coord for pt in canvas_coords for coord in pt] self.canvas.coords(self.current_dividing_line, *flat_canvas_coords)
[docs] def apply_dividing_line(self): if self.dividing_line_coords: coords = self.dividing_line_coords if self.zoom_active: coords = [self.canvas_to_image(x, y) for x, y in coords] rr, cc = [], [] for (x0, y0), (x1, y1) in zip(coords[:-1], coords[1:]): line_rr, line_cc = line(y0, x0, y1, x1) rr.extend(line_rr) cc.extend(line_cc) rr, cc = np.array(rr), np.array(cc) mask_copy = self.mask.copy() if self.zoom_active: # Update the zoomed mask self.zoom_mask[rr, cc] = 0 # Reflect changes to the original mask y0, y1, x0, x1 = self.zoom_y0, self.zoom_y1, self.zoom_x0, self.zoom_x1 zoomed_mask_resized_back = resize(self.zoom_mask, (y1 - y0, x1 - x0), order=0, preserve_range=True).astype(np.uint8) self.mask[y0:y1, x0:x1] = zoomed_mask_resized_back else: # Directly update the original mask mask_copy[rr, cc] = 0 self.mask = mask_copy labeled_mask, num_labels = label(self.mask > 0) self.mask = labeled_mask self.update_display() self.dividing_line_coords = [] self.canvas.unbind("<Button-1>") self.canvas.unbind("<ButtonRelease-1>") self.canvas.unbind("<Motion>") self.dividing_line_active = False self.dividing_line_btn.config(text="Dividing Line")
[docs] def toggle_draw_mode(self): self.drawing = not self.drawing if self.drawing: self.brush_btn.config(text="Brush") self.canvas.unbind("<B1-Motion>") self.canvas.unbind("<B3-Motion>") self.canvas.unbind("<ButtonRelease-1>") self.canvas.unbind("<ButtonRelease-3>") self.magic_wand_active = False self.erase_active = False self.brush_active = False self.draw_btn.config(text="Draw ON") self.magic_wand_btn.config(text="Magic Wand") self.erase_btn.config(text="Erase") self.draw_coordinates = [] self.canvas.unbind("<Button-1>") self.canvas.unbind("<Motion>") self.canvas.bind("<B1-Motion>", self.draw) self.canvas.bind("<ButtonRelease-1>", self.finish_drawing) else: self.drawing = False self.draw_btn.config(text="Draw") self.canvas.unbind("<B1-Motion>") self.canvas.unbind("<ButtonRelease-1>")
[docs] def toggle_magic_wand_mode(self): self.magic_wand_active = not self.magic_wand_active if self.magic_wand_active: self.brush_btn.config(text="Brush") self.canvas.unbind("<B1-Motion>") self.canvas.unbind("<B3-Motion>") self.canvas.unbind("<ButtonRelease-1>") self.canvas.unbind("<ButtonRelease-3>") self.drawing = False self.erase_active = False self.brush_active = False self.draw_btn.config(text="Draw") self.erase_btn.config(text="Erase") self.magic_wand_btn.config(text="Magic Wand ON") self.canvas.bind("<Button-1>", self.use_magic_wand) self.canvas.bind("<Button-3>", self.use_magic_wand) else: self.magic_wand_btn.config(text="Magic Wand") self.canvas.unbind("<Button-1>") self.canvas.unbind("<Button-3>")
[docs] def toggle_erase_mode(self): self.erase_active = not self.erase_active if self.erase_active: self.brush_btn.config(text="Brush") self.canvas.unbind("<B1-Motion>") self.canvas.unbind("<B3-Motion>") self.canvas.unbind("<ButtonRelease-1>") self.canvas.unbind("<ButtonRelease-3>") self.erase_btn.config(text="Erase ON") self.canvas.bind("<Button-1>", self.erase_object) self.drawing = False self.magic_wand_active = False self.brush_active = False self.draw_btn.config(text="Draw") self.magic_wand_btn.config(text="Magic Wand") else: self.erase_active = False self.erase_btn.config(text="Erase") self.canvas.unbind("<Button-1>")
#################################################################################################### # Mode functions# ####################################################################################################
[docs] def apply_brush_release(self, event): if hasattr(self, 'brush_path'): for x, y, brush_size in self.brush_path: img_x, img_y = (x, y) if self.zoom_active else self.canvas_to_image(x, y) x0 = max(img_x - brush_size // 2, 0) y0 = max(img_y - brush_size // 2, 0) x1 = min(img_x + brush_size // 2, self.zoom_mask.shape[1] if self.zoom_active else self.mask.shape[1]) y1 = min(img_y + brush_size // 2, self.zoom_mask.shape[0] if self.zoom_active else self.mask.shape[0]) if self.zoom_active: self.zoom_mask[y0:y1, x0:x1] = 255 self.update_original_mask_from_zoom() else: self.mask[y0:y1, x0:x1] = 255 del self.brush_path self.canvas.delete("temp_line") self.update_display()
[docs] def erase_brush_release(self, event): if hasattr(self, 'erase_path'): for x, y, brush_size in self.erase_path: img_x, img_y = (x, y) if self.zoom_active else self.canvas_to_image(x, y) x0 = max(img_x - brush_size // 2, 0) y0 = max(img_y - brush_size // 2, 0) x1 = min(img_x + brush_size // 2, self.zoom_mask.shape[1] if self.zoom_active else self.mask.shape[1]) y1 = min(img_y + brush_size // 2, self.zoom_mask.shape[0] if self.zoom_active else self.mask.shape[0]) if self.zoom_active: self.zoom_mask[y0:y1, x0:x1] = 0 self.update_original_mask_from_zoom() else: self.mask[y0:y1, x0:x1] = 0 del self.erase_path self.canvas.delete("temp_line") self.update_display()
[docs] def apply_brush(self, event): brush_size = int(self.brush_size_entry.get()) x, y = event.x, event.y if not hasattr(self, 'brush_path'): self.brush_path = [] self.last_brush_coord = (x, y) if self.last_brush_coord: last_x, last_y = self.last_brush_coord rr, cc = line(last_y, last_x, y, x) for ry, rx in zip(rr, cc): self.brush_path.append((rx, ry, brush_size)) self.canvas.create_line(self.last_brush_coord[0], self.last_brush_coord[1], x, y, width=brush_size, fill="blue", tag="temp_line") self.last_brush_coord = (x, y)
[docs] def erase_brush(self, event): brush_size = int(self.brush_size_entry.get()) x, y = event.x, event.y if not hasattr(self, 'erase_path'): self.erase_path = [] self.last_erase_coord = (x, y) if self.last_erase_coord: last_x, last_y = self.last_erase_coord rr, cc = line(last_y, last_x, y, x) for ry, rx in zip(rr, cc): self.erase_path.append((rx, ry, brush_size)) self.canvas.create_line(self.last_erase_coord[0], self.last_erase_coord[1], x, y, width=brush_size, fill="white", tag="temp_line") self.last_erase_coord = (x, y)
[docs] def erase_object(self, event): x, y = event.x, event.y if self.zoom_active: canvas_x, canvas_y = x, y zoomed_x = int(canvas_x * (self.zoom_image.shape[1] / self.canvas_width)) zoomed_y = int(canvas_y * (self.zoom_image.shape[0] / self.canvas_height)) orig_x = int(zoomed_x * ((self.zoom_x1 - self.zoom_x0) / self.canvas_width) + self.zoom_x0) orig_y = int(zoomed_y * ((self.zoom_y1 - self.zoom_y0) / self.canvas_height) + self.zoom_y0) if orig_x < 0 or orig_y < 0 or orig_x >= self.image.shape[1] or orig_y >= self.image.shape[0]: print("Point is out of bounds in the original image.") return else: orig_x, orig_y = x, y label_to_remove = self.mask[orig_y, orig_x] if label_to_remove > 0: self.mask[self.mask == label_to_remove] = 0 self.update_display()
[docs] def use_magic_wand(self, event): x, y = event.x, event.y tolerance = int(self.magic_wand_tolerance.get()) maximum = int(self.max_pixels_entry.get()) action = 'add' if event.num == 1 else 'erase' if self.zoom_active: self.magic_wand_zoomed((x, y), tolerance, action) else: self.magic_wand_normal((x, y), tolerance, action)
[docs] def apply_magic_wand(self, image, mask, seed_point, tolerance, maximum, action='add'): x, y = seed_point initial_value = image[y, x].astype(np.float32) visited = np.zeros_like(image, dtype=bool) queue = deque([(x, y)]) added_pixels = 0 while queue and added_pixels < maximum: cx, cy = queue.popleft() if visited[cy, cx]: continue visited[cy, cx] = True current_value = image[cy, cx].astype(np.float32) if np.linalg.norm(abs(current_value - initial_value)) <= tolerance: if mask[cy, cx] == 0: added_pixels += 1 mask[cy, cx] = 255 if action == 'add' else 0 if added_pixels >= maximum: break for dx, dy in [(-1, 0), (1, 0), (0, -1), (0, 1)]: nx, ny = cx + dx, cy + dy if 0 <= nx < image.shape[1] and 0 <= ny < image.shape[0] and not visited[ny, nx]: queue.append((nx, ny)) return mask
[docs] def magic_wand_normal(self, seed_point, tolerance, action): try: maximum = int(self.max_pixels_entry.get()) except ValueError: print("Invalid maximum value; using default of 1000") maximum = 1000 self.mask = self.apply_magic_wand(self.image, self.mask, seed_point, tolerance, maximum, action) self.display_image()
[docs] def magic_wand_zoomed(self, seed_point, tolerance, action): if self.zoom_image_orig is None or self.zoom_mask is None: print("Zoomed image or mask not initialized") return try: maximum = int(self.max_pixels_entry.get()) maximum = maximum * self.zoom_scale except ValueError: print("Invalid maximum value; using default of 1000") maximum = 1000 canvas_x, canvas_y = seed_point if canvas_x < 0 or canvas_y < 0 or canvas_x >= self.zoom_image_orig.shape[1] or canvas_y >= self.zoom_image_orig.shape[0]: print("Selected point is out of bounds in the zoomed image.") return self.zoom_mask = self.apply_magic_wand(self.zoom_image_orig, self.zoom_mask, (canvas_x, canvas_y), tolerance, maximum, action) y0, y1, x0, x1 = self.zoom_y0, self.zoom_y1, self.zoom_x0, self.zoom_x1 zoomed_mask_resized_back = resize(self.zoom_mask, (y1 - y0, x1 - x0), order=0, preserve_range=True).astype(np.uint8) if action == 'erase': self.mask[y0:y1, x0:x1] = np.where(zoomed_mask_resized_back == 0, 0, self.mask[y0:y1, x0:x1]) else: self.mask[y0:y1, x0:x1] = np.where(zoomed_mask_resized_back > 0, zoomed_mask_resized_back, self.mask[y0:y1, x0:x1]) self.update_display()
[docs] def draw(self, event): if self.drawing: x, y = event.x, event.y if self.draw_coordinates: last_x, last_y = self.draw_coordinates[-1] self.current_line = self.canvas.create_line(last_x, last_y, x, y, fill="yellow", width=3) self.draw_coordinates.append((x, y))
[docs] def draw_on_zoomed_mask(self, draw_coordinates): canvas_height = self.canvas.winfo_height() canvas_width = self.canvas.winfo_width() zoomed_mask = np.zeros((canvas_height, canvas_width), dtype=np.uint8) rr, cc = polygon(np.array(draw_coordinates)[:, 1], np.array(draw_coordinates)[:, 0], shape=zoomed_mask.shape) zoomed_mask[rr, cc] = 255 return zoomed_mask
[docs] def finish_drawing(self, event): if len(self.draw_coordinates) > 2: self.draw_coordinates.append(self.draw_coordinates[0]) if self.zoom_active: x0, x1, y0, y1 = self.zoom_x0, self.zoom_x1, self.zoom_y0, self.zoom_y1 zoomed_mask = self.draw_on_zoomed_mask(self.draw_coordinates) self.update_original_mask(zoomed_mask, x0, x1, y0, y1) else: rr, cc = polygon(np.array(self.draw_coordinates)[:, 1], np.array(self.draw_coordinates)[:, 0], shape=self.mask.shape) self.mask[rr, cc] = np.maximum(self.mask[rr, cc], 255) self.mask = self.mask.copy() self.canvas.delete(self.current_line) self.draw_coordinates.clear() self.update_display()
[docs] def finish_drawing_if_active(self, event): if self.drawing and len(self.draw_coordinates) > 2: self.finish_drawing(event)
#################################################################################################### # Single function butons# ####################################################################################################
[docs] def apply_normalization(self): self.lower_quantile.set(self.lower_entry.get()) self.upper_quantile.set(self.upper_entry.get()) self.update_display()
[docs] def fill_objects(self): binary_mask = self.mask > 0 filled_mask = binary_fill_holes(binary_mask) self.mask = filled_mask.astype(np.uint8) * 255 labeled_mask, _ = label(filled_mask) self.mask = labeled_mask self.update_display()
[docs] def relabel_objects(self): mask = self.mask labeled_mask, num_labels = label(mask > 0) self.mask = labeled_mask self.update_display()
[docs] def clear_objects(self): self.mask = np.zeros_like(self.mask) self.update_display()
[docs] def invert_mask(self): self.mask = np.where(self.mask > 0, 0, 1) self.relabel_objects() self.update_display()
[docs] def remove_small_objects(self): try: min_area = int(self.min_area_entry.get()) except ValueError: print("Invalid minimum area value; using default of 100") min_area = 100 labeled_mask, num_labels = label(self.mask > 0) for i in range(1, num_labels + 1): # Skip background if np.sum(labeled_mask == i) < min_area: self.mask[labeled_mask == i] = 0 # Remove small objects self.update_display()
[docs] class AnnotateApp: def __init__(self, root, db_path, src, image_type=None, channels=None, image_size=200, annotation_column='annotate', normalize=False, percentiles=(1, 99), measurement=None, threshold=None, normalize_channels=None):
[docs] self.root = root
[docs] self.db_path = db_path
[docs] self.src = src
[docs] self.index = 0
if isinstance(image_size, list): self.image_size = (int(image_size[0]), int(image_size[0])) elif isinstance(image_size, int): self.image_size = (image_size, image_size) else: raise ValueError("Invalid image size")
[docs] self.orig_annotation_columns = annotation_column
[docs] self.annotation_column = annotation_column
[docs] self.image_type = image_type
[docs] self.channels = channels
[docs] self.normalize = normalize
[docs] self.percentiles = percentiles
[docs] self.images = {}
[docs] self.pending_updates = {}
[docs] self.labels = []
[docs] self.adjusted_to_original_paths = {}
[docs] self.terminate = False
[docs] self.update_queue = Queue()
[docs] self.measurement = measurement
[docs] self.threshold = threshold
[docs] self.normalize_channels = normalize_channels
print('self.normalize_channels',self.normalize_channels) style_out = set_dark_style(ttk.Style())
[docs] self.font_loader = style_out['font_loader']
[docs] self.font_size = style_out['font_size']
[docs] self.bg_color = style_out['bg_color']
[docs] self.fg_color = style_out['fg_color']
[docs] self.active_color = style_out['active_color']
[docs] self.inactive_color = style_out['inactive_color']
if self.font_loader: self.font_style = self.font_loader.get_font(size=self.font_size) else: self.font_style = ("Arial", 12) self.root.configure(bg=style_out['inactive_color'])
[docs] self.filtered_paths_annotations = []
self.prefilter_paths_annotations()
[docs] self.db_update_thread = threading.Thread(target=self.update_database_worker)
self.db_update_thread.start() # Set the initial window size and make it fit the screen size self.root.geometry(f"{self.root.winfo_screenwidth()}x{self.root.winfo_screenheight()}") self.root.update_idletasks() # Create the status label
[docs] self.status_label = Label(root, text="", font=self.font_style, bg=self.root.cget('bg'))
self.status_label.grid(row=2, column=0, padx=10, pady=10, sticky="w") # Place the buttons at the bottom right
[docs] self.button_frame = Frame(root, bg=self.root.cget('bg'))
self.button_frame.grid(row=2, column=1, padx=10, pady=10, sticky="se")
[docs] self.next_button = Button(self.button_frame, text="Next", command=self.next_page, bg=self.bg_color, fg=self.fg_color, highlightbackground=self.fg_color, highlightcolor=self.fg_color, highlightthickness=1)
self.next_button.pack(side="right", padx=5)
[docs] self.previous_button = Button(self.button_frame, text="Back", command=self.previous_page, bg=self.bg_color, fg=self.fg_color, highlightbackground=self.fg_color, highlightcolor=self.fg_color, highlightthickness=1)
self.previous_button.pack(side="right", padx=5)
[docs] self.exit_button = Button(self.button_frame, text="Exit", command=self.shutdown, bg=self.bg_color, fg=self.fg_color, highlightbackground=self.fg_color, highlightcolor=self.fg_color, highlightthickness=1)
self.exit_button.pack(side="right", padx=5)
[docs] self.train_button = Button(self.button_frame,text="Train & Classify (beta)",command=self.train_and_classify,bg=self.bg_color,fg=self.fg_color,highlightbackground=self.fg_color,highlightcolor=self.fg_color,highlightthickness=1)
self.train_button.pack(side="right", padx=5) self.train_button = Button(self.button_frame,text="orig.",command=self.swich_back_annotation_column,bg=self.bg_color,fg=self.fg_color,highlightbackground=self.fg_color,highlightcolor=self.fg_color,highlightthickness=1) self.train_button.pack(side="right", padx=5)
[docs] self.settings_button = Button(self.button_frame, text="Settings", command=self.open_settings_window, bg=self.bg_color, fg=self.fg_color, highlightbackground=self.fg_color,highlightcolor=self.fg_color,highlightthickness=1)
self.settings_button.pack(side="right", padx=5) # Calculate grid rows and columns based on the root window size and image size self.calculate_grid_dimensions() # Create a frame to hold the image grid
[docs] self.grid_frame = Frame(root, bg=self.root.cget('bg'))
self.grid_frame.grid(row=0, column=0, columnspan=2, padx=0, pady=0, sticky="nsew") for i in range(self.grid_rows * self.grid_cols): label = Label(self.grid_frame, bg=self.root.cget('bg')) label.grid(row=i // self.grid_cols, column=i % self.grid_cols, padx=2, pady=2, sticky="nsew") self.labels.append(label) # Make the grid frame resize with the window self.root.grid_rowconfigure(0, weight=1) self.root.grid_columnconfigure(0, weight=1) self.root.grid_columnconfigure(1, weight=1) for row in range(self.grid_rows): self.grid_frame.grid_rowconfigure(row, weight=1) for col in range(self.grid_cols): self.grid_frame.grid_columnconfigure(col, weight=1)
[docs] def open_settings_window(self): from .gui_utils import generate_annotate_fields, convert_to_number # Create settings window settings_window = tk.Toplevel(self.root) settings_window.title("Modify Annotation Settings") style_out = set_dark_style(ttk.Style()) settings_window.configure(bg=style_out['bg_color']) settings_frame = tk.Frame(settings_window, bg=style_out['bg_color']) settings_frame.pack(fill=tk.BOTH, expand=True) # Generate fields with current settings pre-filled vars_dict = generate_annotate_fields(settings_frame) # Pre-fill the current settings into vars_dict current_settings = { 'image_type': self.image_type or '', 'channels': ','.join(self.channels) if self.channels else '', 'img_size': f"{self.image_size[0]},{self.image_size[1]}", 'annotation_column': self.annotation_column or '', 'normalize': str(self.normalize), 'percentiles': ','.join(map(str, self.percentiles)), 'measurement': ','.join(self.measurement) if self.measurement else '', 'threshold': str(self.threshold) if self.threshold is not None else '', 'normalize_channels': ','.join(self.normalize_channels) if self.normalize_channels else '' } for key, data in vars_dict.items(): if key in current_settings: data['entry'].delete(0, tk.END) data['entry'].insert(0, current_settings[key]) def apply_new_settings(): settings = {key: data['entry'].get() for key, data in vars_dict.items()} # Process settings exactly as your original initiation function does settings['channels'] = settings['channels'].split(',') if settings['channels'] else None settings['img_size'] = list(map(int, settings['img_size'].split(','))) settings['percentiles'] = list(map(convert_to_number, settings['percentiles'].split(','))) if settings['percentiles'] else [1, 99] settings['normalize'] = settings['normalize'].lower() == 'true' settings['normalize_channels'] = settings['normalize_channels'].split(',') if settings['normalize_channels'] else None try: settings['measurement'] = settings['measurement'].split(',') if settings['measurement'] else None settings['threshold'] = None if settings['threshold'].lower() == 'none' else int(settings['threshold']) except: settings['measurement'] = None settings['threshold'] = None # Convert empty strings to None for key, value in settings.items(): if isinstance(value, list): settings[key] = [v if v != '' else None for v in value] elif value == '': settings[key] = None # Apply these settings dynamically using update_settings method self.update_settings(**{ 'image_type': settings.get('image_type'), 'channels': settings.get('channels'), 'image_size': settings.get('img_size'), 'annotation_column': settings.get('annotation_column'), 'normalize': settings.get('normalize'), 'percentiles': settings.get('percentiles'), 'measurement': settings.get('measurement'), 'threshold': settings.get('threshold'), 'normalize_channels': settings.get('normalize_channels') }) settings_window.destroy() apply_button = spacrButton(settings_window, text="Apply Settings", command=apply_new_settings,show_text=False) apply_button.pack(pady=10)
[docs] def update_settings(self, **kwargs): allowed_attributes = { 'image_type', 'channels', 'image_size', 'annotation_column', 'normalize', 'percentiles', 'measurement', 'threshold', 'normalize_channels' } updated = False for attr, value in kwargs.items(): if attr in allowed_attributes and value is not None: setattr(self, attr, value) updated = True if 'image_size' in kwargs: if isinstance(self.image_size, list): self.image_size = (int(self.image_size[0]), int(self.image_size[0])) elif isinstance(self.image_size, int): self.image_size = (self.image_size, self.image_size) else: raise ValueError("Invalid image size") self.calculate_grid_dimensions() self.recreate_image_grid() if updated: current_index = self.index # Retain current index self.prefilter_paths_annotations() # Ensure the retained index is still valid (not out of bounds) max_index = len(self.filtered_paths_annotations) - 1 self.index = min(current_index, max_index := max(0, max(0, max(len(self.filtered_paths_annotations) - self.grid_rows * self.grid_cols, 0)))) self.load_images()
[docs] def recreate_image_grid(self): # Remove current labels for label in self.labels: label.destroy() self.labels.clear() # Recreate the labels grid with updated dimensions for i in range(self.grid_rows * self.grid_cols): label = Label(self.grid_frame, bg=self.root.cget('bg')) label.grid(row=i // self.grid_cols, column=i % self.grid_cols, padx=2, pady=2, sticky="nsew") self.labels.append(label) # Reconfigure grid weights for row in range(self.grid_rows): self.grid_frame.grid_rowconfigure(row, weight=1) for col in range(self.grid_cols): self.grid_frame.grid_columnconfigure(col, weight=1)
[docs] def swich_back_annotation_column(self): self.annotation_column = self.orig_annotation_columns self.prefilter_paths_annotations() self.update_display()
[docs] def calculate_grid_dimensions(self): window_width = self.root.winfo_width() window_height = self.root.winfo_height() self.grid_cols = window_width // (self.image_size[0] + 4) self.grid_rows = (window_height - self.button_frame.winfo_height() - 4) // (self.image_size[1] + 4) # Update to make sure grid_rows and grid_cols are at least 1 self.grid_cols = max(1, self.grid_cols) self.grid_rows = max(1, self.grid_rows)
[docs] def prefilter_paths_annotations(self): from .io import _read_and_join_tables, _read_db from .utils import is_list_of_lists if self.measurement and self.threshold is not None: df = _read_and_join_tables(self.db_path) png_list_df = _read_db(self.db_path, tables=['png_list'])[0] png_list_df = png_list_df.set_index('prcfo') df = df.merge(png_list_df, left_index=True, right_index=True) df[self.annotation_column] = None before = len(df) if isinstance(self.threshold, int): if isinstance(self.measurement, list): mes = self.measurement[0] if isinstance(self.measurement, str): mes = self.measurement df = df[df[f'{mes}'] == self.threshold] 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()
[docs] def load_images(self): for label in self.labels: label.config(image='') self.images = {} paths_annotations = self.filtered_paths_annotations[self.index:self.index + self.grid_rows * self.grid_cols] adjusted_paths = [] for path, annotation in paths_annotations: if not path.startswith(self.src): parts = path.split('/data/') if len(parts) > 1: new_path = os.path.join(self.src, 'data', parts[1]) self.adjusted_to_original_paths[new_path] = path adjusted_paths.append((new_path, annotation)) else: adjusted_paths.append((path, annotation)) else: adjusted_paths.append((path, annotation)) with ThreadPoolExecutor() as executor: loaded_images = list(executor.map(self.load_single_image, adjusted_paths)) for i, (img, annotation) in enumerate(loaded_images): if annotation: border_color = self.active_color if annotation == 1 else 'red' img = self.add_colored_border(img, border_width=5, border_color=border_color) photo = ImageTk.PhotoImage(img) label = self.labels[i] self.images[label] = photo label.config(image=photo) path = adjusted_paths[i][0] label.bind('<Button-1>', self.get_on_image_click(path, label, img)) label.bind('<Button-3>', self.get_on_image_click(path, label, img)) self.root.update()
[docs] def load_single_image(self, path_annotation_tuple): path, annotation = path_annotation_tuple img = Image.open(path) img = self.normalize_image(img, self.normalize, self.percentiles, self.normalize_channels) img = img.convert('RGB') img = self.filter_channels(img) img = img.resize(self.image_size) return img, annotation
@staticmethod
[docs] def normalize_image(img, normalize=False, percentiles=(1, 99), normalize_channels=None): """ Normalize an image based on specific channels (R, G, B). Args: img (PIL.Image or np.array): Input image. normalize (bool): Whether to normalize the image or not. percentiles (tuple): Percentiles to use for intensity rescaling. normalize_channels (list): List of channels to normalize. E.g., ['r', 'g', 'b'], ['r'], ['g'], etc. Returns: PIL.Image: Normalized image. """ img_array = np.array(img) if normalize: if img_array.ndim == 2: # Grayscale image p2, p98 = np.percentile(img_array, percentiles) img_array = rescale_intensity(img_array, in_range=(p2, p98), out_range=(0, 255)) else: # Color image or multi-channel image # Create a map for the color channels channel_map = {'r': 0, 'g': 1, 'b': 2} # If normalize_channels is not specified, normalize all channels if normalize_channels is None: normalize_channels = ['r', 'g', 'b'] for channel_name in normalize_channels: if channel_name in channel_map: channel_idx = channel_map[channel_name] p2, p98 = np.percentile(img_array[:, :, channel_idx], percentiles) img_array[:, :, channel_idx] = rescale_intensity(img_array[:, :, channel_idx], in_range=(p2, p98), out_range=(0, 255)) img_array = np.clip(img_array, 0, 255).astype('uint8') return Image.fromarray(img_array)
[docs] def add_colored_border(self, img, border_width, border_color): top_border = Image.new('RGB', (img.width, border_width), color=border_color) bottom_border = Image.new('RGB', (img.width, border_width), color=border_color) left_border = Image.new('RGB', (border_width, img.height), color=border_color) right_border = Image.new('RGB', (border_width, img.height), color=border_color) bordered_img = Image.new('RGB', (img.width + 2 * border_width, img.height + 2 * border_width), color=self.fg_color) bordered_img.paste(top_border, (border_width, 0)) bordered_img.paste(bottom_border, (border_width, img.height + border_width)) bordered_img.paste(left_border, (0, border_width)) bordered_img.paste(right_border, (img.width + border_width, border_width)) bordered_img.paste(img, (border_width, border_width)) return bordered_img
[docs] def filter_channels(self, img): r, g, b = img.split() if self.channels: if 'r' not in self.channels: r = r.point(lambda _: 0) if 'g' not in self.channels: g = g.point(lambda _: 0) if 'b' not in self.channels: b = b.point(lambda _: 0) if len(self.channels) == 1: channel_img = r if 'r' in self.channels else (g if 'g' in self.channels else b) return ImageOps.grayscale(channel_img) return Image.merge("RGB", (r, g, b))
[docs] def get_on_image_click(self, path, label, img): def on_image_click(event): new_annotation = 1 if event.num == 1 else (2 if event.num == 3 else None) original_path = self.adjusted_to_original_paths.get(path, path) if original_path in self.pending_updates and self.pending_updates[original_path] == new_annotation: self.pending_updates[original_path] = None new_annotation = None else: self.pending_updates[original_path] = new_annotation print(f"Image {os.path.split(path)[1]} annotated: {new_annotation}") img_ = img.crop((5, 5, img.width-5, img.height-5)) border_fill = self.active_color if new_annotation == 1 else ('red' if new_annotation == 2 else None) img_ = ImageOps.expand(img_, border=5, fill=border_fill) if border_fill else img_ photo = ImageTk.PhotoImage(img_) self.images[label] = photo label.config(image=photo) self.root.update() return on_image_click
@staticmethod
[docs] def update_html(text): display(HTML(f""" <script> document.getElementById('unique_id').innerHTML = '{text}'; </script> """))
[docs] def update_database_worker(self): conn = sqlite3.connect(self.db_path) c = conn.cursor() display(HTML("<div id='unique_id'>Initial Text</div>")) while True: if self.terminate: conn.close() break if not self.update_queue.empty(): AnnotateApp.update_html("Do not exit, Updating database...") self.status_label.config(text='Do not exit, Updating database...') pending_updates = self.update_queue.get() for path, new_annotation in pending_updates.items(): if new_annotation is None: c.execute(f'UPDATE png_list SET {self.annotation_column} = NULL WHERE png_path = ?', (path,)) else: c.execute(f'UPDATE png_list SET {self.annotation_column} = ? WHERE png_path = ?', (new_annotation, path)) conn.commit() AnnotateApp.update_html('') self.status_label.config(text='') self.root.update() time.sleep(0.1)
[docs] def update_gui_text(self, text): self.status_label.config(text=text) self.root.update()
[docs] def next_page(self): if self.pending_updates: self.update_queue.put(self.pending_updates.copy()) self.pending_updates.clear() self.index += self.grid_rows * self.grid_cols self.prefilter_paths_annotations() # Re-fetch annotations from the database self.load_images()
[docs] def previous_page(self): if self.pending_updates: self.update_queue.put(self.pending_updates.copy()) self.pending_updates.clear() self.index -= self.grid_rows * self.grid_cols if self.index < 0: self.index = 0 self.prefilter_paths_annotations() # Re-fetch annotations from the database self.load_images()
[docs] def shutdown(self): self.terminate = True self.update_queue.put(self.pending_updates.copy()) if not self.pending_updates: self.pending_updates.clear() self.db_update_thread.join() self.root.quit() self.root.destroy() print(f'Quit application') else: print('Waiting for pending updates to finish before quitting')
[docs] def train_and_classify(self): """ 1) Merge data from the relevant DB tables (including png_list). 2) Collect manual annotations from png_list.<annotation_column> => 'manual_annotation'. - 1 => class=1, 2 => class=0 (for training). 3) If only one class is present, randomly sample unannotated images as the other class. 4) Train an XGBoost model. 5) Classify *all* rows -> fill XGboost_score (prob of class=1) & XGboost_annotation (1 or 2 if high confidence). 6) Write those columns back to sqlite, so every row in png_list has a score (and possibly an annotation). 7) Refresh the UI (prefilter_paths_annotations + load_images). """ # Optionally, update your GUI status label self.update_gui_text("Merging data...") from spacr.io import _read_and_merge_data # Adapt to your actual import # (1) Merge data merged_df, obj_df_ls = _read_and_merge_data( locs=[self.db_path], tables=['cell', 'cytoplasm', 'nucleus', 'pathogen', 'png_list'], verbose=False ) # (2) Load manual annotations from the DB conn = sqlite3.connect(self.db_path) c = conn.cursor() c.execute(f"SELECT png_path, {self.annotation_column} FROM png_list WHERE {self.annotation_column} IS NOT NULL") annotated_rows = c.fetchall() # e.g. [(png_path, 1 or 2), ...] conn.close() # dict {png_path -> 1 or 2} annot_dict = dict(annotated_rows) # Add 'manual_annotation' to merged_df merged_df['manual_annotation'] = merged_df['png_path'].map(annot_dict) # Subset with manual labels annotated_df = merged_df.dropna(subset=['manual_annotation']).copy() # Convert "2" => "0" for binary classification annotated_df['manual_annotation'] = annotated_df['manual_annotation'].replace({2: 0}).astype(int) # (3) Handle single-class scenario class_counts = annotated_df['manual_annotation'].value_counts() if len(class_counts) == 1: single_class = class_counts.index[0] # 0 or 1 needed = class_counts.iloc[0] other_class = 1 if single_class == 0 else 0 unannotated_df_all = merged_df[merged_df['manual_annotation'].isna()].copy() if len(unannotated_df_all) == 0: print("No unannotated rows to sample for the other class. Cannot proceed.") self.update_gui_text("Not enough data to train (no second class).") return sample_size = min(needed, len(unannotated_df_all)) artificially_labeled = unannotated_df_all.sample(n=sample_size, replace=False).copy() artificially_labeled['manual_annotation'] = other_class annotated_df = pd.concat([annotated_df, artificially_labeled], ignore_index=True) print(f"Only one class was present => randomly labeled {sample_size} unannotated rows as {other_class}.") if len(annotated_df) < 2: print("Not enough annotated data to train (need at least 2).") self.update_gui_text("Not enough data to train.") return # (4) Train XGBoost self.update_gui_text("Training XGBoost model...") # Identify numeric columns ignore_cols = {'png_path', 'manual_annotation'} feature_cols = [ col for col in annotated_df.columns if col not in ignore_cols and (annotated_df[col].dtype == float or annotated_df[col].dtype == int) ] X_data = annotated_df[feature_cols].fillna(0).values y_data = annotated_df['manual_annotation'].values # standard train/test X_train, X_test, y_train, y_test = train_test_split( X_data, y_data, test_size=0.1, random_state=42 ) model = XGBClassifier(use_label_encoder=False, eval_metric='logloss') model.fit(X_train, y_train) # Evaluate preds = model.predict(X_test) print("=== Classification Report ===") print(classification_report(y_test, preds)) print("=== Confusion Matrix ===") print(confusion_matrix(y_test, preds)) # (5) Classify ALL rows all_df = merged_df.copy() X_all = all_df[feature_cols].fillna(0).values probs_all = model.predict_proba(X_all)[:, 1] # Probability => XGboost_score all_df['XGboost_score'] = probs_all # Decide XGboost_annotation def get_annotation_from_prob(prob): if prob > 0.9: return 1 # class=1 elif prob < 0.1: return 0 # class=0 return None # uncertain xgb_anno_col = [get_annotation_from_prob(p) for p in probs_all] # Convert 0 => 2 if your DB uses "2" for the negative class xgb_anno_col = [2 if x == 0 else x for x in xgb_anno_col] all_df['XGboost_annotation'] = xgb_anno_col # (6) Write results back to png_list self.update_gui_text("Updating the database with XGBoost predictions...") conn = sqlite3.connect(self.db_path) c = conn.cursor() # Ensure columns exist try: c.execute("ALTER TABLE png_list ADD COLUMN XGboost_annotation INTEGER") except sqlite3.OperationalError: pass try: c.execute("ALTER TABLE png_list ADD COLUMN XGboost_score FLOAT") except sqlite3.OperationalError: pass # Update each row for idx, row in all_df.iterrows(): score_val = float(row['XGboost_score']) anno_val = row['XGboost_annotation'] the_path = row['png_path'] if pd.isna(the_path): continue # skip if no path if pd.isna(anno_val): # We set annotation=NULL but do set the score c.execute(""" UPDATE png_list SET XGboost_annotation = NULL, XGboost_score = ? WHERE png_path = ? """, (score_val, the_path)) else: # numeric annotation + numeric score c.execute(""" UPDATE png_list SET XGboost_annotation = ?, XGboost_score = ? WHERE png_path = ? """, (int(anno_val), score_val, the_path)) self.annotation_column = 'XGboost_annotation'
[docs] def standardize_figure(fig): from .gui_elements import set_dark_style from matplotlib.font_manager import FontProperties style_out = set_dark_style(ttk.Style()) bg_color = style_out['bg_color'] fg_color = style_out['fg_color'] font_size = style_out['font_size'] font_loader = style_out['font_loader'] # Get the custom font path from the font loader font_path = font_loader.font_path font_prop = FontProperties(fname=font_path, size=font_size) """ Standardizes the appearance of the figure: - Font size: from style - Font color: from style - Font family: custom OpenSans from font_loader - Removes top and right spines - Figure and subplot background: from style - Line width: 1 - Line color: from style """ for ax in fig.get_axes(): # Set font properties for title and labels ax.title.set_fontsize(font_size) ax.title.set_color(fg_color) ax.title.set_fontproperties(font_prop) ax.xaxis.label.set_fontsize(font_size) ax.xaxis.label.set_color(fg_color) ax.xaxis.label.set_fontproperties(font_prop) ax.yaxis.label.set_fontsize(font_size) ax.yaxis.label.set_color(fg_color) ax.yaxis.label.set_fontproperties(font_prop) # Set font properties for tick labels for label in ax.get_xticklabels() + ax.get_yticklabels(): label.set_fontsize(font_size) label.set_color(fg_color) label.set_fontproperties(font_prop) # Remove top and right spines ax.spines['top'].set_visible(False) ax.spines['right'].set_visible(False) ax.spines['left'].set_visible(True) ax.spines['bottom'].set_visible(True) # Set spine line width and color for spine in ax.spines.values(): spine.set_linewidth(1) spine.set_edgecolor(fg_color) # Set line width and color for line in ax.get_lines(): line.set_linewidth(1) line.set_color(fg_color) # Set subplot background color ax.set_facecolor(bg_color) # Adjust the grid if needed ax.grid(True, color='gray', linestyle='--', linewidth=0.5) # Set figure background color fig.patch.set_facecolor(bg_color) fig.canvas.draw_idle() return fig
[docs] def modify_figure_properties(fig, scale_x=None, scale_y=None, line_width=None, font_size=None, x_lim=None, y_lim=None, grid=False, legend=None, title=None, x_label_rotation=None, remove_axes=False, bg_color=None, text_color=None, line_color=None): """ Modifies the properties of the figure, including scaling, line widths, font sizes, axis limits, x-axis label rotation, background color, text color, line color, and other common options. Parameters: - fig: The Matplotlib figure object to modify. - scale_x: Scaling factor for the width of subplots (optional). - scale_y: Scaling factor for the height of subplots (optional). - line_width: Desired line width for all lines (optional). - font_size: Desired font size for all text (optional). - x_lim: Tuple specifying the x-axis limits (min, max) (optional). - y_lim: Tuple specifying the y-axis limits (min, max) (optional). - grid: Boolean to add grid lines to the plot (optional). - legend: Boolean to show/hide the legend (optional). - title: String to set as the title of the plot (optional). - x_label_rotation: Angle to rotate the x-axis labels (optional). - remove_axes: Boolean to remove or show the axes labels (optional). - bg_color: Color for the figure and subplot background (optional). - text_color: Color for all text in the figure (optional). - line_color: Color for all lines in the figure (optional). """ if fig is None: print("Error: The figure provided is None.") return for ax in fig.get_axes(): # Rescale subplots if scaling factors are provided if scale_x is not None or scale_y is not None: bbox = ax.get_position() width = bbox.width * (scale_x if scale_x else 1) height = bbox.height * (scale_y if scale_y else 1) new_bbox = [bbox.x0, bbox.y0, width, height] ax.set_position(new_bbox) # Set axis limits if provided if x_lim is not None: ax.set_xlim(x_lim) if y_lim is not None: ax.set_ylim(y_lim) # Set grid visibility only ax.grid(grid) # Adjust line width and color if specified if line_width is not None or line_color is not None: for line in ax.get_lines(): if line_width is not None: line.set_linewidth(line_width) if line_color is not None: line.set_color(line_color) for spine in ax.spines.values(): # Modify width and color of spines (e.g., scale bars) if line_width is not None: spine.set_linewidth(line_width) if line_color is not None: spine.set_edgecolor(line_color) ax.tick_params(width=line_width, colors=text_color if text_color else 'black') # Adjust font size if specified if font_size is not None: for label in ax.get_xticklabels() + ax.get_yticklabels(): label.set_fontsize(font_size) ax.title.set_fontsize(font_size) ax.xaxis.label.set_fontsize(font_size) ax.yaxis.label.set_fontsize(font_size) if ax.legend_: for text in ax.legend_.get_texts(): text.set_fontsize(font_size) # Rotate x-axis labels if rotation is specified if x_label_rotation is not None: for label in ax.get_xticklabels(): label.set_rotation(x_label_rotation) if 0 <= x_label_rotation <= 90: label.set_ha('center') # Toggle axes labels visibility without affecting the grid or spines if remove_axes: ax.xaxis.set_visible(False) ax.yaxis.set_visible(False) else: ax.xaxis.set_visible(True) ax.yaxis.set_visible(True) # Set text color if specified if text_color: ax.title.set_color(text_color) ax.xaxis.label.set_color(text_color) ax.yaxis.label.set_color(text_color) ax.tick_params(colors=text_color) for label in ax.get_xticklabels() + ax.get_yticklabels(): label.set_color(text_color) # Set background color for subplots if specified if bg_color: ax.set_facecolor(bg_color) # Set figure background color if specified if bg_color: fig.patch.set_facecolor(bg_color) fig.canvas.draw_idle()
[docs] def save_figure_as_format(fig, file_format): file_path = filedialog.asksaveasfilename(defaultextension=f".{file_format}", filetypes=[(f"{file_format.upper()} files", f"*.{file_format}"), ("All files", "*.*")]) if file_path: try: fig.savefig(file_path, format=file_format) print(f"Figure saved as {file_format.upper()} at {file_path}") except Exception as e: print(f"Error saving figure: {e}")
[docs] def modify_figure(fig): from .gui_core import display_figure def apply_modifications(): try: # Only apply changes if the fields are filled scale_x = float(scale_x_var.get()) if scale_x_var.get() else None scale_y = float(scale_y_var.get()) if scale_y_var.get() else None line_width = float(line_width_var.get()) if line_width_var.get() else None font_size = int(font_size_var.get()) if font_size_var.get() else None x_lim = eval(x_lim_var.get()) if x_lim_var.get() else None y_lim = eval(y_lim_var.get()) if y_lim_var.get() else None title = title_var.get() if title_var.get() else None bg_color = bg_color_var.get() if bg_color_var.get() else None text_color = text_color_var.get() if text_color_var.get() else None line_color = line_color_var.get() if line_color_var.get() else None x_label_rotation = int(x_label_rotation_var.get()) if x_label_rotation_var.get() else None modify_figure_properties( fig, scale_x=scale_x, scale_y=scale_y, line_width=line_width, font_size=font_size, x_lim=x_lim, y_lim=y_lim, grid=grid_var.get(), legend=legend_var.get(), title=title, x_label_rotation=x_label_rotation, remove_axes=remove_axes_var.get(), bg_color=bg_color, text_color=text_color, line_color=line_color ) display_figure(fig) except ValueError: print("Invalid input; please enter numeric values.") def toggle_spleens(): for ax in fig.get_axes(): if spleens_var.get(): ax.spines['top'].set_visible(False) ax.spines['right'].set_visible(False) ax.spines['left'].set_visible(True) ax.spines['bottom'].set_visible(True) ax.spines['top'].set_linewidth(2) ax.spines['right'].set_linewidth(2) else: ax.spines['top'].set_visible(True) ax.spines['right'].set_visible(True) display_figure(fig) # Create a new window for user input modify_window = tk.Toplevel() modify_window.title("Modify Figure Properties") # Apply dark style to the popup window style = ttk.Style() style.configure("TCheckbutton", background="#2E2E2E", foreground="white", selectcolor="blue") modify_window.configure(bg="#2E2E2E") # Create and style the input fields scale_x_var = tk.StringVar() scale_y_var = tk.StringVar() line_width_var = tk.StringVar() font_size_var = tk.StringVar() x_lim_var = tk.StringVar() y_lim_var = tk.StringVar() title_var = tk.StringVar() bg_color_var = tk.StringVar() text_color_var = tk.StringVar() line_color_var = tk.StringVar() x_label_rotation_var = tk.StringVar() remove_axes_var = tk.BooleanVar() grid_var = tk.BooleanVar() legend_var = tk.BooleanVar() spleens_var = tk.BooleanVar() options = [ ("Rescale X:", scale_x_var), ("Rescale Y:", scale_y_var), ("Line Width:", line_width_var), ("Font Size:", font_size_var), ("X Axis Limits (tuple):", x_lim_var), ("Y Axis Limits (tuple):", y_lim_var), ("Title:", title_var), ("X Label Rotation (degrees):", x_label_rotation_var), ("Background Color:", bg_color_var), ("Text Color:", text_color_var), ("Line Color:", line_color_var) ] for i, (label_text, var) in enumerate(options): tk.Label(modify_window, text=label_text, bg="#2E2E2E", fg="white").grid(row=i, column=0, padx=10, pady=5) tk.Entry(modify_window, textvariable=var, bg="#2E2E2E", fg="white").grid(row=i, column=1, padx=10, pady=5) checkboxes = [ ("Grid", grid_var), ("Legend", legend_var), ("Spleens", spleens_var), ("Remove Axes", remove_axes_var) ] for i, (label_text, var) in enumerate(checkboxes, start=len(options)): ttk.Checkbutton(modify_window, text=label_text, variable=var, style="TCheckbutton").grid(row=i, column=0, padx=10, pady=5, columnspan=2, sticky='w') spleens_var.trace_add("write", lambda *args: toggle_spleens()) # Apply button apply_button = tk.Button(modify_window, text="Apply", command=apply_modifications, bg="#2E2E2E", fg="white") apply_button.grid(row=len(options) + len(checkboxes), column=0, columnspan=2, pady=10)
[docs] def generate_dna_matrix(output_path='dna_matrix.gif', canvas_width=1500, canvas_height=1000, duration=30, fps=20, base_size=20, transition_frames=30, font_type='arial.ttf', enhance=[1.1, 1.5, 1.2, 1.5], lowercase_prob=0.3): """ Generate a DNA matrix animation and save it as GIF, MP4, or AVI using OpenCV for videos. """ def save_output(frames, output_path, fps, output_format): """Save the animation based on output format.""" if output_format in ['.mp4', '.avi']: images = [np.array(img.convert('RGB')) for img in frames] fourcc = cv2.VideoWriter_fourcc(*('mp4v' if output_format == '.mp4' else 'XVID')) out = cv2.VideoWriter(output_path, fourcc, fps, (canvas_width, canvas_height)) for img in images: out.write(cv2.cvtColor(img, cv2.COLOR_RGB2BGR)) out.release() elif output_format == '.gif': frames[0].save(output_path, save_all=True, append_images=frames[1:], duration=int(1000/fps), loop=0) def draw_base(draw, col_idx, base_position, base, font, alpha=255, fill_color=None): """Draws a DNA base at the specified position.""" draw.text((col_idx * base_size, base_position * base_size), base, fill=(*fill_color, alpha), font=font) # Setup variables num_frames = duration * fps num_columns = canvas_width // base_size bases = ['A', 'T', 'C', 'G'] active_color = (155, 55, 155) color = (255, 255, 255) base_colors = {'A': color, 'T': color, 'C': color, 'G': color} _, output_format = os.path.splitext(output_path) # Initialize font try: font = ImageFont.truetype(font_type, base_size) except IOError: font = ImageFont.load_default() # DNA string and positions string_lengths = [random.randint(10, 100) for _ in range(num_columns)] visible_bases = [0] * num_columns base_positions = [random.randint(-canvas_height // base_size, 0) for _ in range(num_columns)] column_strings = [[''] * 100 for _ in range(num_columns)] random_white_sequences = [None] * num_columns frames = [] end_frame_start = int(num_frames * 0.8) for frame_idx in range(num_frames): img = Image.new('RGBA', (canvas_width, canvas_height), color=(0, 0, 0, 255)) draw = ImageDraw.Draw(img) for col_idx in range(num_columns): if base_positions[col_idx] >= canvas_height // base_size and frame_idx < end_frame_start: string_lengths[col_idx] = random.randint(10, 100) base_positions[col_idx] = -string_lengths[col_idx] visible_bases[col_idx] = 0 # Randomly choose whether to make each base lowercase column_strings[col_idx] = [ random.choice([base.lower(), base]) if random.random() < lowercase_prob else base for base in [random.choice(bases) for _ in range(string_lengths[col_idx])] ] if string_lengths[col_idx] > 8: random_start = random.randint(0, string_lengths[col_idx] - 8) random_white_sequences[col_idx] = range(random_start, random_start + 8) last_10_percent_start = max(0, int(string_lengths[col_idx] * 0.9)) for row_idx in range(min(visible_bases[col_idx], string_lengths[col_idx])): base_position = base_positions[col_idx] + row_idx if 0 <= base_position * base_size < canvas_height: base = column_strings[col_idx][row_idx] if base: if row_idx == visible_bases[col_idx] - 1: draw_base(draw, col_idx, base_position, base, font, fill_color=active_color) elif row_idx >= last_10_percent_start: alpha = 255 - int(((row_idx - last_10_percent_start) / (string_lengths[col_idx] - last_10_percent_start)) * 127) draw_base(draw, col_idx, base_position, base, font, alpha=alpha, fill_color=base_colors[base.upper()]) elif random_white_sequences[col_idx] and row_idx in random_white_sequences[col_idx]: draw_base(draw, col_idx, base_position, base, font, fill_color=active_color) else: draw_base(draw, col_idx, base_position, base, font, fill_color=base_colors[base.upper()]) if visible_bases[col_idx] < string_lengths[col_idx]: visible_bases[col_idx] += 1 base_positions[col_idx] += 2 # Convert the image to numpy array to check unique pixel values img_array = np.array(img) if len(np.unique(img_array)) > 2: # Only append frames with more than two unique pixel values (avoid black frames) # Enhance contrast and saturation if enhance: img = ImageEnhance.Brightness(img).enhance(enhance[0]) # Slightly increase brightness img = ImageEnhance.Sharpness(img).enhance(enhance[1]) # Sharpen the image img = ImageEnhance.Contrast(img).enhance(enhance[2]) # Enhance contrast img = ImageEnhance.Color(img).enhance(enhance[3]) # Boost color saturation frames.append(img) for i in range(transition_frames): alpha = i / float(transition_frames) transition_frame = Image.blend(frames[-1], frames[0], alpha) frames.append(transition_frame) save_output(frames, output_path, fps, output_format)