spacr 0.1.11__tar.gz → 0.1.12__tar.gz

{spacr-0.1.11/spacr.egg-info → spacr-0.1.12}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: spacr
-Version: 0.1.11
+Version: 0.1.12
 Summary: Spatial phenotype analysis of crisp screens (SpaCr)
 Home-page: https://github.com/EinarOlafsson/spacr
 Author: Einar Birnir Olafsson

{spacr-0.1.11 → spacr-0.1.12}/setup.py

@@ -61,7 +61,7 @@ dependencies = [
 
 setup(
     name="spacr",
-    version="0.1.11",
+    version="0.1.12",
     author="Einar Birnir Olafsson",
     author_email="olafsson@med.umich.com",
     description="Spatial phenotype analysis of crisp screens (SpaCr)",

{spacr-0.1.11 → spacr-0.1.12}/spacr/__init__.py

@@ -12,14 +12,13 @@ from . import sim
 from . import sequencing
 from . import timelapse
 from . import deep_spacr
-from . import annotate_app
-from . import annotate_app_v2
+from . import app_annotate
 from . import gui_utils
-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
+from . import app_make_masks
+from . import app_make_masks_v2
+from . import app_mask
+from . import app_measure
+from . import app_classify
 from . import logger
 
 
@@ -34,14 +33,13 @@ __all__ = [
     "sequencing"
     "timelapse",
     "deep_spacr",
-    "annotate_app",
-    "annotate_app_v2",
+    "app_annotate",
     "gui_utils",
-    "gui_make_masks_app",
-    "gui_make_masks_app_v2",
-    "gui_mask_app",
-    "gui_measure_app",
-    "gui_classify_app",
+    "app_make_masks",
+    "app_make_masks_v2",
+    "app_mask",
+    "app_measure",
+    "app_classify",
     "logger"
 ]
 

spacr-0.1.11/spacr/annotate_app.py → spacr-0.1.12/spacr/app_annotate.py

@@ -11,29 +11,12 @@ from PIL import ImageTk
 from skimage.exposure import rescale_intensity
 from IPython.display import display, HTML
 from tkinter import font as tkFont
+from tkinter import TclError
 
 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):
-        """
-        Initializes an instance of the ImageApp class.
-
-        Parameters:
-        - root (tkinter.Tk): The root window of the application.
-        - db_path (str): The path to the SQLite database.
-        - src (str): The source directory that should be upstream of 'data' in the paths.
-        - image_type (str): The type of images to display.
-        - channels (list): The channels to filter in the images.
-        - grid_rows (int): The number of rows in the image grid.
-        - grid_cols (int): The number of columns in the image grid.
-        - image_size (tuple): The size of the displayed images.
-        - annotation_column (str): The column name for image annotations in the database.
-        - normalize (bool): Whether to normalize images to their 2nd and 98th percentiles. Defaults to False.
-        - measurement (str): The measurement column to filter by.
-        - threshold (float): The threshold value for filtering the measurement column.
-        """
-
         self.root = root
         self.db_path = db_path
         self.src = src
@@ -69,9 +52,6 @@ class ImageApp:
             self.labels.append(label)
 
     def prefilter_paths_annotations(self):
-        """
-        Pre-filters the paths and annotations based on the specified measurement and threshold.
-        """
         from .io import _read_and_join_tables
         from .utils import is_list_of_lists
 
@@ -159,21 +139,6 @@ class ImageApp:
             conn.close()
 
     def load_images(self):
-        """
-        Loads and displays images with annotations.
-
-        This method retrieves image paths and annotations from a pre-filtered list,
-        loads the images using a ThreadPoolExecutor for parallel processing,
-        adds colored borders to images based on their annotations,
-        and displays the images in the corresponding labels.
-
-        Args:
-            None
-
-        Returns:
-            None
-        """
-
         for label in self.labels:
             label.config(image='')
 
@@ -213,16 +178,6 @@ class ImageApp:
         self.root.update()
 
     def load_single_image(self, path_annotation_tuple):
-        """
-        Loads a single image from the given path and annotation tuple.
-
-        Args:
-            path_annotation_tuple (tuple): A tuple containing the image path and its annotation.
-
-        Returns:
-            img (PIL.Image.Image): The loaded image.
-            annotation: The annotation associated with the image.
-        """
         path, annotation = path_annotation_tuple
         img = Image.open(path)
         img = self.normalize_image(img, self.normalize, self.percentiles)
@@ -233,18 +188,6 @@ class ImageApp:
 
     @staticmethod
     def normalize_image(img, normalize=False, percentiles=(1, 99)):
-        """
-        Normalize the pixel values of an image based on the 2nd and 98th percentiles or the image min and max values,
-        and ensure the image is exported as 8-bit.
-
-        Parameters:
-        - img: PIL.Image.Image. The input image to be normalized.
-        - normalize: bool. Whether to normalize based on the 2nd and 98th percentiles.
-        - percentiles: tuple. The percentiles to use for normalization.
-
-        Returns:
-        - PIL.Image.Image. The normalized and 8-bit converted image.
-        """
         img_array = np.array(img)
 
         if normalize:
@@ -261,17 +204,6 @@ class ImageApp:
         return Image.fromarray(img_array)
     
     def add_colored_border(self, img, border_width, border_color):
-        """
-        Adds a colored border to an image.
-
-        Args:
-            img (PIL.Image.Image): The input image.
-            border_width (int): The width of the border in pixels.
-            border_color (str): The color of the border in RGB format.
-
-        Returns:
-            PIL.Image.Image: The image with the colored border.
-        """
         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)
@@ -287,15 +219,6 @@ class ImageApp:
         return bordered_img
     
     def filter_channels(self, img):
-        """
-        Filters the channels of an image based on the specified channels.
-
-        Args:
-            img (PIL.Image.Image): The input image.
-
-        Returns:
-            PIL.Image.Image: The filtered image.
-        """
         r, g, b = img.split()
         if self.channels:
             if 'r' not in self.channels:
@@ -312,17 +235,6 @@ class ImageApp:
         return Image.merge("RGB", (r, g, b))
 
     def get_on_image_click(self, path, label, img):
-        """
-        Returns a callback function that handles the click event on an image.
-
-        Parameters:
-        path (str): The path of the image file.
-        label (tkinter.Label): The label widget to update with the annotated image.
-        img (PIL.Image.Image): The image object.
-
-        Returns:
-        function: The callback function for the image click event.
-        """
         def on_image_click(event):
             new_annotation = 1 if event.num == 1 else (2 if event.num == 3 else None)
             
@@ -356,11 +268,6 @@ class ImageApp:
         """))
 
     def update_database_worker(self):
-        """
-        Worker function that continuously updates the database with pending updates from the update queue.
-        It retrieves the pending updates from the queue, updates the corresponding records in the database,
-        and resets the text in the HTML and status label.
-        """
         conn = sqlite3.connect(self.db_path)
         c = conn.cursor()
 
@@ -383,51 +290,24 @@ class ImageApp:
                         c.execute(f'UPDATE png_list SET {self.annotation_column} = ? WHERE png_path = ?', (new_annotation, path))
                 conn.commit()
 
-                # Reset the text
                 ImageApp.update_html('')
                 self.status_label.config(text='')
                 self.root.update()
             time.sleep(0.1)
 
     def update_gui_text(self, text):
-        """
-        Update the text of the status label in the GUI.
-
-        Args:
-            text (str): The new text to be displayed in the status label.
-
-        Returns:
-            None
-        """
         self.status_label.config(text=text)
         self.root.update()
 
     def next_page(self):
-        """
-        Moves to the next page of images in the grid.
-
-        If there are pending updates in the dictionary, they are added to the update queue.
-        The pending updates dictionary is then cleared.
-        The index is incremented by the number of rows multiplied by the number of columns in the grid.
-        Finally, the images are loaded for the new page.
-        """
-        if self.pending_updates:  # Check if the dictionary is not empty
+        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.load_images()
 
     def previous_page(self):
-        """
-        Move to the previous page in the grid.
-
-        If there are pending updates in the dictionary, they are added to the update queue.
-        The dictionary of pending updates is then cleared.
-        The index is decremented by the number of rows multiplied by the number of columns in the grid.
-        If the index becomes negative, it is set to 0.
-        Finally, the images are loaded for the new page.
-        """
-        if self.pending_updates:  # Check if the dictionary is not empty
+        if self.pending_updates:
             self.update_queue.put(self.pending_updates.copy())
         self.pending_updates.clear()
         self.index -= self.grid_rows * self.grid_cols
@@ -436,23 +316,15 @@ class ImageApp:
         self.load_images()
 
     def shutdown(self):
-        """
-        Shuts down the application.
-
-        This method sets the terminate flag to True, clears the pending updates,
-        updates the database, and quits the application.
-
-        """
-        self.terminate = True  # Set terminate first
+        self.terminate = True
         self.update_queue.put(self.pending_updates.copy())
         self.pending_updates.clear()
-        self.db_update_thread.join()  # Join the thread to make sure database is updated
+        self.db_update_thread.join()
         self.root.quit()
         self.root.destroy()
         print(f'Quit application')
 
 def get_annotate_default_settings(settings):
-
     settings.setdefault('image_type', 'cell_png')
     settings.setdefault('channels', ['r', 'g', 'b'])
     settings.setdefault('geom', "3200x2000")
@@ -468,24 +340,6 @@ def get_annotate_default_settings(settings):
     return settings
 
 def annotate(settings):
-    """
-    Annotates images in a database using a graphical user interface.
-
-    Args:
-        db (str): The path to the SQLite database.
-        src (str): The source directory that should be upstream of 'data' in the paths.
-        image_type (str, optional): The type of images to load from the database. Defaults to None.
-        channels (str, optional): The channels of the images to load from the database. Defaults to None.
-        geom (str, optional): The geometry of the GUI window. Defaults to "1000x1100".
-        img_size (tuple, optional): The size of the images to display in the GUI. Defaults to (200, 200).
-        rows (int, optional): The number of rows in the image grid. Defaults to 5.
-        columns (int, optional): The number of columns in the image grid. Defaults to 5.
-        annotation_column (str, optional): The name of the annotation column in the database table. Defaults to 'annotate'.
-        normalize (bool, optional): Whether to normalize images to their 2nd and 98th percentiles. Defaults to False.
-        measurement (str, optional): The measurement column to filter by.
-        threshold (float, optional): The threshold value for filtering the measurement column.
-    """
-
     settings = get_annotate_default_settings(settings)
     src  = settings['src']
 
@@ -604,6 +458,9 @@ def annotate_app(parent_frame, settings):
     annotate_with_image_refs(settings, root, lambda: load_next_app(root))
 
 def annotate_with_image_refs(settings, root, shutdown_callback):
+    from .gui_utils import proceed_with_app
+    from .gui import gui_app
+
     settings = get_annotate_default_settings(settings)
     src = settings['src']
 
@@ -632,9 +489,9 @@ def annotate_with_image_refs(settings, root, shutdown_callback):
     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 = ()
+    root.current_app_exit_func = lambda: [app.shutdown(), shutdown_callback()]
+    root.next_app_func = proceed_with_app
+    root.next_app_args = ("Main App", gui_app)  # Specify the main app function
 
 def load_next_app(root):
     # Get the next app function and arguments
@@ -642,7 +499,19 @@ def load_next_app(root):
     next_app_args = root.next_app_args
 
     if next_app_func:
-        next_app_func(*next_app_args)
+        try:
+            if not root.winfo_exists():
+                raise tk.TclError
+            next_app_func(root, *next_app_args)
+        except tk.TclError:
+            # Reinitialize root if it has been destroyed
+            new_root = tk.Tk()
+            width = new_root.winfo_screenwidth()
+            height = new_root.winfo_screenheight()
+            new_root.geometry(f"{width}x{height}")
+            new_root.title("SpaCr Application")
+            next_app_func(new_root, *next_app_args)
+
 
 def gui_annotate():
     root = tk.Tk()
@@ -667,4 +536,4 @@ def gui_annotate():
     root.mainloop()
 
 if __name__ == "__main__":
-    gui_annotate()
+    gui_annotate()

spacr-0.1.11/spacr/classify_app.py → spacr-0.1.12/spacr/app_classify.py

@@ -77,7 +77,7 @@ def initiate_classify_root(parent_frame):
     style_text_boxes(style)
     set_default_font(parent_frame, font_name="Helvetica", size=8)
 
-    parent_frame.configure(bg='#333333')
+    parent_frame.configure(bg='black')
     parent_frame.grid_rowconfigure(0, weight=1)
     parent_frame.grid_columnconfigure(0, weight=1)
     fig_queue = Queue()
@@ -94,7 +94,7 @@ def initiate_classify_root(parent_frame):
                     ax.xaxis.set_visible(False)  # Hide the x-axis
                     ax.yaxis.set_visible(False)  # Hide the y-axis
                 fig.tight_layout()
-                fig.set_facecolor('#333333')
+                fig.set_facecolor('black')
                 canvas.figure = fig
                 fig_width, fig_height = canvas_widget.winfo_width(), canvas_widget.winfo_height()
                 fig.set_size_inches(fig_width / fig.dpi, fig_height / fig.dpi, forward=True)
@@ -117,9 +117,9 @@ def initiate_classify_root(parent_frame):
     parent_frame.grid_columnconfigure(0, weight=1)
 
     # Settings Section
-    settings_frame = tk.Frame(vertical_container, bg='#333333')
+    settings_frame = tk.Frame(vertical_container, bg='black')
     vertical_container.add(settings_frame, stretch="always")
-    settings_label = ttk.Label(settings_frame, text="Settings", background="#333333", foreground="white")
+    settings_label = ttk.Label(settings_frame, text="Settings", background="black", foreground="white")
     settings_label.grid(row=0, column=0, pady=10, padx=10)
     scrollable_frame = ScrollableFrame(settings_frame, width=500)
     scrollable_frame.grid(row=1, column=0, sticky="nsew")
@@ -143,23 +143,23 @@ def initiate_classify_root(parent_frame):
     # Plot Canvas Section
     plot_frame = tk.PanedWindow(vertical_container, orient=tk.VERTICAL)
     vertical_container.add(plot_frame, stretch="always")
-    figure = Figure(figsize=(30, 4), dpi=100, facecolor='#333333')
+    figure = Figure(figsize=(30, 4), dpi=100, facecolor='black')
     plot = figure.add_subplot(111)
     plot.plot([], [])
     plot.axis('off')
     canvas = FigureCanvasTkAgg(figure, master=plot_frame)
-    canvas.get_tk_widget().configure(cursor='arrow', background='#333333', highlightthickness=0)
+    canvas.get_tk_widget().configure(cursor='arrow', background='black', highlightthickness=0)
     canvas_widget = canvas.get_tk_widget()
     plot_frame.add(canvas_widget, stretch="always")
     canvas.draw()
     canvas.figure = figure
 
     # Console Section
-    console_frame = tk.Frame(vertical_container, bg='#333333')
+    console_frame = tk.Frame(vertical_container, bg='black')
     vertical_container.add(console_frame, stretch="always")
-    console_label = ttk.Label(console_frame, text="Console", background="#333333", foreground="white")
+    console_label = ttk.Label(console_frame, text="Console", background="black", foreground="white")
     console_label.grid(row=0, column=0, pady=10, padx=10)
-    console_output = scrolledtext.ScrolledText(console_frame, height=10, bg='#333333', fg='white', insertbackground='white')
+    console_output = scrolledtext.ScrolledText(console_frame, height=10, bg='black', fg='white', insertbackground='white')
     console_output.grid(row=1, column=0, sticky="nsew")
     console_frame.grid_rowconfigure(1, weight=1)
     console_frame.grid_columnconfigure(0, weight=1)

spacr-0.1.11/spacr/make_masks_app.py → spacr-0.1.12/spacr/app_make_masks.py

@@ -870,7 +870,7 @@ def initiate_mask_app_root(parent_frame):
     container = tk.PanedWindow(parent_frame, orient=tk.HORIZONTAL)
     container.pack(fill=tk.BOTH, expand=True)
 
-    scrollable_frame = ScrollableFrame(container, bg='#333333')
+    scrollable_frame = ScrollableFrame(container, bg='black')
     container.add(scrollable_frame, stretch="always")
 
     # Setup input fields
@@ -905,7 +905,9 @@ def initiate_mask_app_root(parent_frame):
 
 def gui_make_masks():
     root = tk.Tk()
-    root.geometry("1000x800")
+    width = root.winfo_screenwidth()
+    height = root.winfo_screenheight()
+    root.geometry(f"{width}x{height}")
     root.title("Mask Application")
     
     # Clear previous content if any

spacr-0.1.11/spacr/make_masks_app_v2.py → spacr-0.1.12/spacr/app_make_masks_v2.py

@@ -645,7 +645,7 @@ def initiate_mask_app_root(width, height):
     container = tk.PanedWindow(root, orient=tk.HORIZONTAL)
     container.pack(fill=tk.BOTH, expand=True)
 
-    scrollable_frame = ScrollableFrame(container, bg='#333333')
+    scrollable_frame = ScrollableFrame(container, bg='black')
     container.add(scrollable_frame, stretch="always")
 
     vars_dict = {

spacr-0.1.11/spacr/mask_app.py → spacr-0.1.12/spacr/app_mask.py

@@ -22,6 +22,8 @@ from .gui_utils import mask_variables, check_mask_gui_settings, preprocess_gener
 
 thread_control = {"run_thread": None, "stop_requested": False}
 
+test_mode_button = None
+
 def toggle_test_mode():
     global vars_dict
     current_state = vars_dict['test_mode'][2].get()

spacr-0.1.11/spacr/measure_app.py → spacr-0.1.12/spacr/app_measure.py

@@ -28,6 +28,8 @@ def import_settings(scrollable_frame):
     new_settings = update_settings_from_csv(variables, csv_settings)
     vars_dict = generate_fields(new_settings, scrollable_frame)
 
+test_mode_button = None
+
 def toggle_test_mode():
     global vars_dict
     current_state = vars_dict['test_mode'][2].get()

{spacr-0.1.11 → spacr-0.1.12}/spacr/gui.py

@@ -6,21 +6,21 @@ import os
 import requests
 
 # Import your GUI apps
-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 .gui_make_masks_app import initiate_mask_app_root
-from .gui_classify_app import initiate_classify_root
+from .app_mask import initiate_mask_root
+from .app_measure import initiate_measure_root
+from .app_annotate import initiate_annotation_app_root
+from .app_make_masks import initiate_mask_app_root
+from .app_classify import initiate_classify_root
 from .gui_utils import CustomButton, style_text_boxes, create_menu_bar
 
 class MainApp(tk.Tk):
     def __init__(self):
         super().__init__()
+        width = self.winfo_screenwidth()
+        height = self.winfo_screenheight()
+        self.geometry(f"{width}x{height}")  
         self.title("SpaCr GUI Collection")
-        self.geometry("1100x1500")
         self.configure(bg="black")
-        #self.attributes('-fullscreen', True)
-
         style = ttk.Style()
         style_text_boxes(style)
 
@@ -37,7 +37,7 @@ class MainApp(tk.Tk):
 
     def create_widgets(self):
         # Create the menu bar
-        self.gui_create_menu_bar()
+        create_menu_bar(self)
 
         # Create a canvas to hold the selected app and other elements
         self.canvas = tk.Canvas(self, bg="black", highlightthickness=0)
@@ -52,9 +52,6 @@ class MainApp(tk.Tk):
         # 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)
 

{spacr-0.1.11 → spacr-0.1.12}/spacr/gui_utils.py

@@ -65,11 +65,11 @@ def load_app(root, app_name, app_func):
     app_func(root.content_frame)
 
 def create_menu_bar(root):
-    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 .gui_make_masks_app import initiate_mask_app_root
-    from .gui_classify_app import initiate_classify_root
+    from .app_mask import initiate_mask_root
+    from .app_measure import initiate_measure_root
+    from .app_annotate import initiate_annotation_app_root
+    from .app_make_masks import initiate_mask_app_root
+    from .app_classify import initiate_classify_root
 
     gui_apps = {
         "Mask": initiate_mask_root,
@@ -96,6 +96,42 @@ def create_menu_bar(root):
     # Configure the menu for the root window
     root.config(menu=menu_bar)
 
+def proceed_with_app(root, app_name, app_func):
+
+    from .app_mask import gui_mask
+    from .app_measure import gui_measure
+    from .app_annotate import gui_annotate
+    from .app_make_masks import gui_make_masks
+    from .app_classify import gui_classify
+    from .gui import gui_app
+
+    # Clear the current content frame
+    if hasattr(root, 'content_frame'):
+        for widget in root.content_frame.winfo_children():
+            widget.destroy()
+    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)
+
+    # Initialize the new app in the content frame
+    if app_name == "Main App":
+        root.destroy()  # Close the current window
+        gui_app()  # Open the main app window
+    elif app_name == "Mask":
+        gui_mask()
+    elif app_name == "Measure":
+        gui_measure()
+    elif app_name == "Annotate":
+        gui_annotate()
+    elif app_name == "Make Masks":
+        gui_make_masks()
+    elif app_name == "Classify":
+        gui_classify()
+    else:
+        raise ValueError(f"Invalid app name: {app_name}")
+
 def load_app(root, app_name, app_func):
     # Cancel all scheduled after tasks
     if hasattr(root, 'after_tasks'):
@@ -103,35 +139,25 @@ def load_app(root, app_name, app_func):
             root.after_cancel(task)
     root.after_tasks = []
 
-    def proceed_with_app():
-        # Clear the current content frame
-        if hasattr(root, 'content_frame'):
-            for widget in root.content_frame.winfo_children():
-                widget.destroy()
-        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)
-
-        # Initialize the new app in the content frame
-        app_func(root.content_frame)
-
     # Exit functionality only for the annotation app
     if app_name != "Annotate" and hasattr(root, 'current_app_exit_func'):
         root.next_app_func = proceed_with_app
+        root.next_app_args = (app_name, app_func)  # Ensure correct arguments
         root.current_app_exit_func()
     else:
-        proceed_with_app()
+        proceed_with_app(root, app_name, app_func)
+
 
 def create_menu_bar(root):
-    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 .gui_make_masks_app import initiate_mask_app_root
-    from .gui_classify_app import initiate_classify_root
+    from .app_mask import initiate_mask_root
+    from .app_measure import initiate_measure_root
+    from .app_annotate import initiate_annotation_app_root
+    from .app_make_masks import initiate_mask_app_root
+    from .app_classify import initiate_classify_root
+    from .gui import gui_app 
 
     gui_apps = {
+        "Main App": gui_app,
         "Mask": initiate_mask_root,
         "Measure": initiate_measure_root,
         "Annotate": initiate_annotation_app_root,
@@ -381,19 +407,19 @@ def style_text_boxes_v1(style):
               background=[('active', '#66b2b2'), ('disabled', '#004d4d'), ('!disabled', '#008080')],
               foreground=[('active', '#ffffff'), ('disabled', '#888888')])
     style.configure('Custom.TLabel', padding='5 5 5 5', borderwidth=1, relief='flat', background='#000000', foreground='#ffffff', font=font_style)
-    style.configure('TCheckbutton', background='#333333', foreground='#ffffff', indicatoron=False, relief='flat', font=font_style)
+    style.configure('TCheckbutton', background='black', foreground='#ffffff', indicatoron=False, relief='flat', font=font_style)
     style.map('TCheckbutton', background=[('selected', '#555555'), ('active', '#555555')])
 
 def style_text_boxes(style):
     font_style = tkFont.Font(family="Helvetica", size=10) 
-    style.configure('TEntry', padding='5 5 5 5', borderwidth=1, relief='solid', fieldbackground='#333333', foreground='#ffffff', font=font_style)
-    style.configure('TCombobox', fieldbackground='#333333', background='#333333', foreground='#ffffff', font=font_style)
+    style.configure('TEntry', padding='5 5 5 5', borderwidth=1, relief='solid', fieldbackground='black', foreground='#ffffff', font=font_style)
+    style.configure('TCombobox', fieldbackground='black', background='black', foreground='#ffffff', font=font_style)
     style.configure('Custom.TButton', padding='10 10 10 10', borderwidth=1, relief='solid', background='#008080', foreground='#ffffff', font=font_style)
     style.map('Custom.TButton',
               background=[('active', '#66b2b2'), ('disabled', '#004d4d'), ('!disabled', '#008080')],
               foreground=[('active', '#ffffff'), ('disabled', '#888888')])
     style.configure('Custom.TLabel', padding='5 5 5 5', borderwidth=1, relief='flat', background='#000000', foreground='#ffffff', font=font_style)
-    style.configure('TCheckbutton', background='#333333', foreground='#ffffff', indicatoron=False, relief='flat', font=font_style)
+    style.configure('TCheckbutton', background='black', foreground='#ffffff', indicatoron=False, relief='flat', font=font_style)
     style.map('TCheckbutton', background=[('selected', '#555555'), ('active', '#555555')])
 
 

{spacr-0.1.11 → spacr-0.1.12/spacr.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: spacr
-Version: 0.1.11
+Version: 0.1.12
 Summary: Spatial phenotype analysis of crisp screens (SpaCr)
 Home-page: https://github.com/EinarOlafsson/spacr
 Author: Einar Birnir Olafsson

{spacr-0.1.11 → spacr-0.1.12}/spacr.egg-info/SOURCES.txt

@@ -4,9 +4,13 @@ README.rst
 setup.py
 spacr/__init__.py
 spacr/__main__.py
-spacr/annotate_app.py
+spacr/app_annotate.py
+spacr/app_classify.py
+spacr/app_make_masks.py
+spacr/app_make_masks_v2.py
+spacr/app_mask.py
+spacr/app_measure.py
 spacr/chris.py
-spacr/classify_app.py
 spacr/core.py
 spacr/deep_spacr.py
 spacr/graph_learning.py
@@ -14,11 +18,7 @@ spacr/gui.py
 spacr/gui_utils.py
 spacr/io.py
 spacr/logger.py
-spacr/make_masks_app.py
-spacr/make_masks_app_v2.py
-spacr/mask_app.py
 spacr/measure.py
-spacr/measure_app.py
 spacr/plot.py
 spacr/sequencing.py
 spacr/settings.py

{spacr-0.1.11 → spacr-0.1.12}/tests/test_annotate_app.py

@@ -1,6 +1,6 @@
 import unittest
 from unittest.mock import MagicMock
-from spacr.annotate_app import ImageApp
+from spacr.app_annotate import ImageApp
 from PIL import Image
 
 class TestImageApp(unittest.TestCase):

{spacr-0.1.11 → spacr-0.1.12}/tests/test_gui_classify_app.py

@@ -1,6 +1,6 @@
 import unittest
 from unittest.mock import MagicMock
-from spacr.gui_classify_app import initiate_classify_root
+from spacr.app_classify import initiate_classify_root
 
 class TestInitiateClassifyRoot(unittest.TestCase):
     def setUp(self):

{spacr-0.1.11 → spacr-0.1.12}/tests/test_gui_mask_app.py

@@ -1,6 +1,6 @@
 import unittest
 from unittest.mock import MagicMock
-from spacr.gui_mask_app import initiate_mask_root
+from spacr.app_mask import initiate_mask_root
 
 class TestInitiateMaskRoot(unittest.TestCase):
     def setUp(self):

{spacr-0.1.11 → spacr-0.1.12}/tests/test_gui_measure_app.py

@@ -1,6 +1,6 @@
 import unittest
 from unittest.mock import MagicMock
-from spacr.gui_measure_app import initiate_measure_root
+from spacr.app_measure import initiate_measure_root
 
 class TestInitiateMeasureRoot(unittest.TestCase):
     def setUp(self):

{spacr-0.1.11 → spacr-0.1.12}/tests/test_gui_sim_app.py

@@ -1,6 +1,6 @@
 import unittest
 from unittest.mock import MagicMock
-from spacr.gui_sim_app import initiate_sim_root
+from spacr.sim_app import initiate_sim_root
 
 class TestInitiateSimRoot(unittest.TestCase):
     def setUp(self):

{spacr-0.1.11 → spacr-0.1.12}/tests/test_mask_app.py

@@ -1,6 +1,6 @@
 import unittest
 from unittest.mock import MagicMock
-from spacr.mask_app import modify_masks
+from spacr.app_make_masks import modify_masks
 
 class TestModifyMasks(unittest.TestCase):
     def setUp(self):