spacr 0.1.0__tar.gz → 0.1.11__tar.gz

{spacr-0.1.0/spacr.egg-info → spacr-0.1.11}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: spacr
-Version: 0.1.0
+Version: 0.1.11
 Summary: Spatial phenotype analysis of crisp screens (SpaCr)
 Home-page: https://github.com/EinarOlafsson/spacr
 Author: Einar Birnir Olafsson
@@ -40,6 +40,10 @@ Requires-Dist: ttf_opensans>=2020.10.30
 Requires-Dist: customtkinter<6.0,>=5.2.2
 Requires-Dist: biopython<2.0,>=1.80
 Requires-Dist: lxml<6.0,>=5.1.0
+Requires-Dist: qtpy<2.5,>=2.4.1
+Requires-Dist: superqt<0.7,>=0.6.7
+Requires-Dist: pyqt6<6.8,>=6.7.1
+Requires-Dist: pyqtgraph<0.14,>=0.13.7
 Provides-Extra: dev
 Requires-Dist: pytest>=3.9; extra == "dev"
 Provides-Extra: headless

{spacr-0.1.0 → spacr-0.1.11}/setup.py

@@ -52,12 +52,16 @@ dependencies = [
     'ttf_opensans>=2020.10.30',
     'customtkinter>=5.2.2,<6.0', 
     'biopython>=1.80,<2.0',
-    'lxml>=5.1.0,<6.0'
+    'lxml>=5.1.0,<6.0', 
+    'qtpy>=2.4.1,<2.5',
+    'superqt>=0.6.7,<0.7',
+    'pyqt6>=6.7.1,<6.8',
+    'pyqtgraph>=0.13.7,<0.14'
 ]
 
 setup(
     name="spacr",
-    version="0.1.0",
+    version="0.1.11",
     author="Einar Birnir Olafsson",
     author_email="olafsson@med.umich.com",
     description="Spatial phenotype analysis of crisp screens (SpaCr)",
@@ -71,12 +75,12 @@ setup(
         'console_scripts': [
             'mask=spacr.gui_mask_app:gui_mask',
             'measure=spacr.gui_measure_app:gui_measure',
-            'make_masks=spacr.mask_app:gui_make_masks',
-            'annotate=spacr.annotate_app:gui_annotation',
+            'make_masks=spacr.gui_make_mask_app:gui_make_masks',
+            'make_masks2=spacr.gui_make_mask_app_v2:gui_make_masks',
+            'annotate=spacr.annotate_app_v2:gui_annotate',
             'classify=spacr.gui_classify_app:gui_classify',
             'sim=spacr.gui_sim_app:gui_sim',
             'gui=spacr.gui:gui_app',
-            'gui2=spacr.gui_2:gui_app',
         ],
     },
     extras_require={

{spacr-0.1.0 → spacr-0.1.11}/spacr/__init__.py

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

spacr-0.1.0/spacr/annotate_app_v2.py → spacr-0.1.11/spacr/annotate_app.py

@@ -1,16 +1,18 @@
+import sqlite3
 from queue import Queue
-from tkinter import Label, Entry, Button
+from tkinter import Label
 import tkinter as tk
+from tkinter import ttk
 import os, threading, time, sqlite3
 import numpy as np
 from PIL import Image, ImageOps
 from concurrent.futures import ThreadPoolExecutor
 from PIL import ImageTk
-import pandas as pd
 from skimage.exposure import rescale_intensity
-import cv2
-import matplotlib.pyplot as plt
 from IPython.display import display, HTML
+from tkinter import font as tkFont
+
+from .gui_utils import ScrollableFrame, CustomButton, set_dark_style, set_default_font, style_text_boxes, create_menu_bar
 
 class ImageApp:
     def __init__(self, root, db_path, src, image_type=None, channels=None, grid_rows=None, grid_cols=None, image_size=(200, 200), annotation_column='annotate', normalize=False, percentiles=(1,99), measurement=None, threshold=None):
@@ -509,3 +511,160 @@ def annotate(settings):
     
     app.load_images()
     root.mainloop()
+
+# Global list to keep references to PhotoImage objects
+global_image_refs = []
+
+def initiate_annotation_app_root(parent_frame):
+    style = ttk.Style(parent_frame)
+    set_dark_style(style)
+    style_text_boxes(style)
+    set_default_font(parent_frame, font_name="Arial", size=8)
+
+    parent_frame.configure(bg='black')
+    
+    container = tk.PanedWindow(parent_frame, orient=tk.HORIZONTAL, bg='black')
+    container.pack(fill=tk.BOTH, expand=True)
+
+    scrollable_frame = ScrollableFrame(container, bg='black')
+    container.add(scrollable_frame, stretch="always")
+
+    # Setup input fields
+    vars_dict = {
+        'src': ttk.Entry(scrollable_frame.scrollable_frame),
+        'image_type': ttk.Entry(scrollable_frame.scrollable_frame),
+        'channels': ttk.Entry(scrollable_frame.scrollable_frame),
+        'geom': ttk.Entry(scrollable_frame.scrollable_frame),
+        'img_size': ttk.Entry(scrollable_frame.scrollable_frame),
+        'rows': ttk.Entry(scrollable_frame.scrollable_frame),
+        'columns': ttk.Entry(scrollable_frame.scrollable_frame),
+        'annotation_column': ttk.Entry(scrollable_frame.scrollable_frame),
+        'normalize': ttk.Entry(scrollable_frame.scrollable_frame),
+        'percentiles': ttk.Entry(scrollable_frame.scrollable_frame),
+        'measurement': ttk.Entry(scrollable_frame.scrollable_frame),
+        'threshold': ttk.Entry(scrollable_frame.scrollable_frame),
+    }
+
+    default_settings = {
+        'src': 'path',
+        'image_type': 'cell_png',
+        'channels': 'r,g,b',
+        'geom': "3200x2000",
+        'img_size': '(200, 200)',
+        'rows': '10',
+        'columns': '18',
+        'annotation_column': 'recruited_test',
+        'normalize': 'False',
+        'percentiles': '(2,98)',
+        'measurement': 'None',
+        'threshold': 'None'
+    }
+
+    # Arrange input fields and labels
+    row = 0
+    for name, entry in vars_dict.items():
+        ttk.Label(scrollable_frame.scrollable_frame, text=f"{name.replace('_', ' ').capitalize()}:",
+                  background="black", foreground="white").grid(row=row, column=0)
+        entry.insert(0, default_settings[name])
+        entry.grid(row=row, column=1)
+        row += 1
+
+    # Function to be called when "Run" button is clicked
+    def run_app():
+        settings = {key: entry.get() for key, entry in vars_dict.items()}
+        settings['channels'] = settings['channels'].split(',')
+        settings['img_size'] = tuple(map(int, settings['img_size'][1:-1].split(',')))
+        settings['percentiles'] = tuple(map(int, settings['percentiles'][1:-1].split(',')))
+        settings['normalize'] = settings['normalize'].lower() == 'true'
+        settings['rows'] = int(settings['rows'])
+        settings['columns'] = int(settings['columns'])
+        if settings['measurement'].lower() == 'none':
+            settings['measurement'] = None
+        if settings['threshold'].lower() == 'none':
+            settings['threshold'] = None
+        
+        # Clear previous content instead of destroying the root
+        if hasattr(parent_frame, 'winfo_children'):
+            for widget in parent_frame.winfo_children():
+                widget.destroy()
+        
+        # Start the annotate application in the same root window
+        annotate_app(parent_frame, settings)
+        
+    run_button = CustomButton(scrollable_frame.scrollable_frame, text="Run", command=run_app,
+                              font=tkFont.Font(family="Arial", size=12, weight=tkFont.NORMAL))
+    run_button.grid(row=row, column=0, columnspan=2, pady=10, padx=10)
+
+    return parent_frame
+
+def annotate_app(parent_frame, settings):
+    global global_image_refs
+    global_image_refs.clear()
+    root = parent_frame.winfo_toplevel()
+    annotate_with_image_refs(settings, root, lambda: load_next_app(root))
+
+def annotate_with_image_refs(settings, root, shutdown_callback):
+    settings = get_annotate_default_settings(settings)
+    src = settings['src']
+
+    db = os.path.join(src, 'measurements/measurements.db')
+    conn = sqlite3.connect(db)
+    c = conn.cursor()
+    c.execute('PRAGMA table_info(png_list)')
+    cols = c.fetchall()
+    if settings['annotation_column'] not in [col[1] for col in cols]:
+        c.execute(f"ALTER TABLE png_list ADD COLUMN {settings['annotation_column']} integer")
+    conn.commit()
+    conn.close()
+
+    app = ImageApp(root, db, src, image_type=settings['image_type'], channels=settings['channels'], image_size=settings['img_size'], grid_rows=settings['rows'], grid_cols=settings['columns'], annotation_column=settings['annotation_column'], normalize=settings['normalize'], percentiles=settings['percentiles'], measurement=settings['measurement'], threshold=settings['threshold'])
+
+    # Set the canvas background to black
+    root.configure(bg='black')
+
+    next_button = tk.Button(root, text="Next", command=app.next_page, background='black', foreground='white')
+    next_button.grid(row=app.grid_rows, column=app.grid_cols - 1)
+    back_button = tk.Button(root, text="Back", command=app.previous_page, background='black', foreground='white')
+    back_button.grid(row=app.grid_rows, column=app.grid_cols - 2)
+    exit_button = tk.Button(root, text="Exit", command=lambda: [app.shutdown(), shutdown_callback()], background='black', foreground='white')
+    exit_button.grid(row=app.grid_rows, column=app.grid_cols - 3)
+
+    app.load_images()
+
+    # Store the shutdown function and next app details in the root
+    root.current_app_exit_func = app.shutdown
+    root.next_app_func = None
+    root.next_app_args = ()
+
+def load_next_app(root):
+    # Get the next app function and arguments
+    next_app_func = root.next_app_func
+    next_app_args = root.next_app_args
+
+    if next_app_func:
+        next_app_func(*next_app_args)
+
+def gui_annotate():
+    root = tk.Tk()
+    width = root.winfo_screenwidth()
+    height = root.winfo_screenheight()
+    root.geometry(f"{width}x{height}")
+    root.title("Annotate Application")
+    
+    # Clear previous content if any
+    if hasattr(root, 'content_frame'):
+        for widget in root.content_frame.winfo_children():
+            widget.destroy()
+        root.content_frame.grid_forget()
+    else:
+        root.content_frame = tk.Frame(root)
+        root.content_frame.grid(row=1, column=0, sticky="nsew")
+        root.grid_rowconfigure(1, weight=1)
+        root.grid_columnconfigure(0, weight=1)
+    
+    initiate_annotation_app_root(root.content_frame)
+    create_menu_bar(root)
+    root.mainloop()
+
+if __name__ == "__main__":
+    gui_annotate()

spacr-0.1.0/spacr/gui_classify_app.py → spacr-0.1.11/spacr/classify_app.py

@@ -69,13 +69,13 @@ def import_settings(scrollable_frame):
     vars_dict = generate_fields(new_settings, scrollable_frame)
 
 #@log_function_call
-def initiate_classify_root(parent_frame):#, width, height):
+def initiate_classify_root(parent_frame):
     global vars_dict, q, canvas, fig_queue, canvas_widget, thread_control
     
     style = ttk.Style(parent_frame)
     set_dark_style(style)
     style_text_boxes(style)
-    set_default_font(parent_frame, font_name="Arial", size=8)
+    set_default_font(parent_frame, font_name="Helvetica", size=8)
 
     parent_frame.configure(bg='#333333')
     parent_frame.grid_rowconfigure(0, weight=1)
@@ -131,11 +131,11 @@ def initiate_classify_root(parent_frame):#, width, height):
     vars_dict = generate_fields(variables, scrollable_frame)
 
     # Button section
-    import_btn = CustomButton(scrollable_frame.scrollable_frame, text="Import Settings", command=lambda: import_settings(scrollable_frame))
+    import_btn = CustomButton(scrollable_frame.scrollable_frame, text="Import", command=lambda: import_settings(scrollable_frame), font=('Helvetica', 10))
     import_btn.grid(row=47, column=0, pady=20, padx=20)
-    run_button = CustomButton(scrollable_frame.scrollable_frame, text="Run", command=lambda: start_process(q, fig_queue))
+    run_button = CustomButton(scrollable_frame.scrollable_frame, text="Run", command=lambda: start_process(q, fig_queue), font=('Helvetica', 10))
     run_button.grid(row=45, column=0, pady=20, padx=20)
-    abort_button = CustomButton(scrollable_frame.scrollable_frame, text="Abort", command=initiate_abort)
+    abort_button = CustomButton(scrollable_frame.scrollable_frame, text="Abort", command=initiate_abort, font=('Helvetica', 10))
     abort_button.grid(row=45, column=1, pady=20, padx=20)
     progress_label = ttk.Label(scrollable_frame.scrollable_frame, text="Processing: 0%", background="black", foreground="white") # Create progress field
     progress_label.grid(row=50, column=0, columnspan=2, sticky="ew", pady=(5, 0), padx=10)
@@ -177,9 +177,23 @@ def initiate_classify_root(parent_frame):#, width, height):
 
 def gui_classify():
     root = tk.Tk()
-    root.geometry("1000x800")
-    root.title("SpaCer: generate masks")
-    initiate_classify_root(root, 1000, 800)
+    width = root.winfo_screenwidth()
+    height = root.winfo_screenheight()
+    root.geometry(f"{width}x{height}") 
+    root.title("SpaCr: classify objects")
+    
+    # Clear previous content if any
+    if hasattr(root, 'content_frame'):
+        for widget in root.content_frame.winfo_children():
+            widget.destroy()
+        root.content_frame.grid_forget()
+    else:
+        root.content_frame = tk.Frame(root)
+        root.content_frame.grid(row=1, column=0, sticky="nsew")
+        root.grid_rowconfigure(1, weight=1)
+        root.grid_columnconfigure(0, weight=1)
+    
+    initiate_classify_root(root.content_frame)
     create_menu_bar(root)
     root.mainloop()
 

{spacr-0.1.0 → spacr-0.1.11}/spacr/gui.py

@@ -9,10 +9,9 @@ import requests
 from .gui_mask_app import initiate_mask_root
 from .gui_measure_app import initiate_measure_root
 from .annotate_app import initiate_annotation_app_root
-from .mask_app import initiate_mask_app_root
+from .gui_make_masks_app import initiate_mask_app_root
 from .gui_classify_app import initiate_classify_root
-
-from .gui_utils import CustomButton, style_text_boxes
+from .gui_utils import CustomButton, style_text_boxes, create_menu_bar
 
 class MainApp(tk.Tk):
     def __init__(self):
@@ -38,18 +37,24 @@ class MainApp(tk.Tk):
 
     def create_widgets(self):
         # Create the menu bar
-        #create_menu_bar(self)
+        self.gui_create_menu_bar()
+
         # Create a canvas to hold the selected app and other elements
-        self.canvas = tk.Canvas(self, bg="black", highlightthickness=0, width=4000, height=4000)
+        self.canvas = tk.Canvas(self, bg="black", highlightthickness=0)
         self.canvas.grid(row=0, column=0, sticky="nsew")
         self.grid_rowconfigure(0, weight=1)
         self.grid_columnconfigure(0, weight=1)
+
         # Create a frame inside the canvas to hold the main content
         self.content_frame = tk.Frame(self.canvas, bg="black")
         self.content_frame.pack(fill=tk.BOTH, expand=True)
+
         # Create startup screen with buttons for each GUI app
         self.create_startup_screen()
 
+    def gui_create_menu_bar(self):
+        create_menu_bar(self)
+
     def create_startup_screen(self):
         self.clear_frame(self.content_frame)
 
@@ -59,10 +64,10 @@ class MainApp(tk.Tk):
 
         # Load the logo image
         if not self.load_logo(logo_frame):
-            tk.Label(logo_frame, text="Logo not found", bg="black", fg="white", font=('Arial', 24, tkFont.NORMAL)).pack(padx=10, pady=10)
+            tk.Label(logo_frame, text="Logo not found", bg="black", fg="white", font=('Helvetica', 24)).pack(padx=10, pady=10)
 
         # Add SpaCr text below the logo with padding for sharper text
-        tk.Label(logo_frame, text="SpaCr", bg="black", fg="#008080", font=('Arial', 24, tkFont.NORMAL)).pack(padx=10, pady=10)
+        tk.Label(logo_frame, text="SpaCr", bg="black", fg="#008080", font=('Helvetica', 24)).pack(padx=10, pady=10)
 
         # Create a frame for the buttons and descriptions
         buttons_frame = tk.Frame(self.content_frame, bg="black")
@@ -72,10 +77,10 @@ class MainApp(tk.Tk):
             app_func, app_desc = app_data
 
             # Create custom button with text
-            button = CustomButton(buttons_frame, text=app_name, command=lambda app_name=app_name: self.load_app(app_name))
+            button = CustomButton(buttons_frame, text=app_name, command=lambda app_name=app_name: self.load_app(app_name, app_func), font=('Helvetica', 12))
             button.grid(row=i, column=0, pady=10, padx=10, sticky="w")
 
-            description_label = tk.Label(buttons_frame, text=app_desc, bg="black", fg="white", wraplength=800, justify="left", font=('Arial', 10, tkFont.NORMAL))
+            description_label = tk.Label(buttons_frame, text=app_desc, bg="black", fg="white", wraplength=800, justify="left", font=('Helvetica', 12))
             description_label.grid(row=i, column=1, pady=10, padx=10, sticky="w")
 
         # Ensure buttons have a fixed width
@@ -125,13 +130,14 @@ class MainApp(tk.Tk):
             print(f"An error occurred while processing the logo image: {e}")
             return False
 
-    def load_app(self, app_name):
-        selected_app_func, _ = self.gui_apps[app_name]
+    def load_app(self, app_name, app_func):
+        # Clear the current content frame
         self.clear_frame(self.content_frame)
 
+        # Initialize the selected app
         app_frame = tk.Frame(self.content_frame, bg="black")
         app_frame.pack(fill=tk.BOTH, expand=True)
-        selected_app_func(app_frame, self.winfo_width(), self.winfo_height())
+        app_func(app_frame)
 
     def clear_frame(self, frame):
         for widget in frame.winfo_children():
@@ -142,4 +148,4 @@ def gui_app():
     app.mainloop()
 
 if __name__ == "__main__":
-    gui_app()
+    gui_app()