spacr 0.3.30__py3-none-any.whl → 0.3.31__py3-none-any.whl

spacr/app_annotate.py

@@ -20,7 +20,7 @@ def initiate_annotation_app(parent_frame):
         settings['img_size'] = list(map(int, settings['img_size'].split(',')))  # Convert string to list of integers
         settings['percentiles'] = list(map(int, settings['percentiles'].split(',')))  # Convert string to list of integers
         settings['normalize'] = settings['normalize'].lower() == 'true'
-
+        settings['normalize_channels'] = settings['normalize_channels'].split(',')
         try:
             settings['measurement'] = settings['measurement'].split(',') if settings['measurement'] else None
             settings['threshold'] = None if settings['threshold'].lower() == 'none' else int(settings['threshold'])
@@ -38,7 +38,6 @@ def initiate_annotation_app(parent_frame):
                 settings[key] = None
 
         settings_window.destroy()
-
         annotate_app(parent_frame, settings)
     
     start_button = spacrButton(settings_window, text="annotate", command=start_annotation_app, show_text=False)

spacr/gui_elements.py

@@ -20,6 +20,47 @@ from tkinter import ttk, scrolledtext
 
 fig = None
 
+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="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)
+
 def set_element_size():
 
     screen_width, screen_height = pyautogui.size()
@@ -2122,7 +2163,7 @@ class ModifyMaskApp:
         self.update_display()
 
 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):
+    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):
         self.root = root
         self.db_path = db_path
         self.src = src
@@ -2148,7 +2189,8 @@ class AnnotateApp:
         self.update_queue = Queue()
         self.measurement = measurement
         self.threshold = threshold
-
+        self.normalize_channels = normalize_channels
+        print('self.normalize_channels',self.normalize_channels)
         style_out = set_dark_style(ttk.Style())
         self.font_loader = style_out['font_loader']
         self.font_size = style_out['font_size']
@@ -2157,7 +2199,6 @@ class AnnotateApp:
         self.active_color = style_out['active_color']
         self.inactive_color = style_out['inactive_color']
 
-
         if self.font_loader:
             self.font_style = self.font_loader.get_font(size=self.font_size)
         else:
@@ -2356,14 +2397,26 @@ class AnnotateApp:
     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)
+        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
-    def normalize_image(img, normalize=False, percentiles=(1, 99)):
+    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:
@@ -2371,13 +2424,23 @@ class AnnotateApp:
                 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
-                for channel in range(img_array.shape[2]):
-                    p2, p98 = np.percentile(img_array[:, :, channel], percentiles)
-                    img_array[:, :, channel] = rescale_intensity(img_array[:, :, channel], in_range=(p2, p98), out_range=(0, 255))
+                # 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)
+
     
     def add_colored_border(self, img, border_width, border_color):
         top_border = Image.new('RGB', (img.width, border_width), color=border_color)
@@ -2505,46 +2568,6 @@ class AnnotateApp:
         else:
             print('Waiting for pending updates to finish before quitting')
 
-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'),
-        "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="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)
-
 def standardize_figure(fig):
     from .gui_elements import set_dark_style
     from matplotlib.font_manager import FontProperties

spacr/gui_utils.py

@@ -253,7 +253,7 @@ def annotate(settings):
 
     root = tk.Tk()
     root.geometry(settings['geom'])
-    app = AnnotateApp(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'])
+    app = AnnotateApp(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'], normalize_channels=settings['normalize_channels'])
     next_button = tk.Button(root, text="Next", command=app.next_page)
     next_button.grid(row=app.grid_rows, column=app.grid_cols - 1)
     back_button = tk.Button(root, text="Back", command=app.previous_page)
@@ -284,7 +284,6 @@ def generate_annotate_fields(frame):
     # Arrange input fields and labels
     for row, (name, data) in enumerate(vars_dict.items()):
         tk.Label(frame, text=f"{name.replace('_', ' ').capitalize()}:", bg=style_out['bg_color'], fg=style_out['fg_color'], font=font_loader.get_font(size=font_size)).grid(row=row, column=0)
-        #ttk.Label(frame, text=f"{name.replace('_', ' ').capitalize()}:", background="black", foreground="white").grid(row=row, column=0)
         if isinstance(data['value'], list):
             # Convert lists to comma-separated strings
             data['entry'].insert(0, ','.join(map(str, data['value'])))
@@ -300,6 +299,7 @@ def run_annotate_app(vars_dict, parent_frame):
     settings['img_size'] = list(map(int, settings['img_size'].split(',')))  # Convert string to list of integers
     settings['percentiles'] = list(map(int, settings['percentiles'].split(',')))  # Convert string to list of integers
     settings['normalize'] = settings['normalize'].lower() == 'true'
+    settings['normalize_channels'] = settings['channels'].split(',')
     settings['rows'] = int(settings['rows'])
     settings['columns'] = int(settings['columns'])
     settings['measurement'] = settings['measurement'].split(',')
@@ -320,6 +320,7 @@ def annotate_app(parent_frame, settings):
     global global_image_refs
     global_image_refs.clear()
     root = parent_frame.winfo_toplevel()
+    print('annotate_app',settings)
     annotate_with_image_refs(settings, root, lambda: load_next_app(root))
 
 def load_next_app(root):
@@ -341,46 +342,6 @@ def load_next_app(root):
             new_root.title("SpaCr Application")
             next_app_func(new_root, *next_app_args)
 
-def annotate_with_image_refs(settings, root, shutdown_callback):
-    #from .gui_utils import proceed_with_app
-    from .gui import gui_app
-    from .settings import set_annotate_default_settings
-
-    settings = set_annotate_default_settings(settings)
-    src = settings['src']
-
-    db = os.path.join(src, 'measurements/measurements.db')
-    conn = sqlite3.connect(db)
-    c = conn.cursor()
-    c.execute('PRAGMA table_info(png_list)')
-    cols = c.fetchall()
-    if settings['annotation_column'] not in [col[1] for col in cols]:
-        c.execute(f"ALTER TABLE png_list ADD COLUMN {settings['annotation_column']} integer")
-    conn.commit()
-    conn.close()
-
-    app = AnnotateApp(root, db, src, image_type=settings['image_type'], channels=settings['channels'], image_size=settings['img_size'], grid_rows=settings['rows'], grid_cols=settings['columns'], annotation_column=settings['annotation_column'], normalize=settings['normalize'], percentiles=settings['percentiles'], measurement=settings['measurement'], threshold=settings['threshold'])
-
-    # Set the canvas background to black
-    root.configure(bg='black')
-
-    next_button = tk.Button(root, text="Next", command=app.next_page, background='black', foreground='white')
-    next_button.grid(row=app.grid_rows, column=app.grid_cols - 1)
-    back_button = tk.Button(root, text="Back", command=app.previous_page, background='black', foreground='white')
-    back_button.grid(row=app.grid_rows, column=app.grid_cols - 2)
-    exit_button = tk.Button(root, text="Exit", command=lambda: [app.shutdown(), shutdown_callback()], background='black', foreground='white')
-    exit_button.grid(row=app.grid_rows, column=app.grid_cols - 3)
-
-    #app.load_images()
-
-    # Store the shutdown function and next app details in the root
-    root.current_app_exit_func = lambda: [app.shutdown(), shutdown_callback()]
-    root.next_app_func = proceed_with_app
-    root.next_app_args = ("Main App", gui_app)
-
-    # Call load_images after setting up the root window
-    app.load_images()
-
 def annotate_with_image_refs(settings, root, shutdown_callback):
     from .settings import set_annotate_default_settings
 
@@ -401,7 +362,7 @@ def annotate_with_image_refs(settings, root, shutdown_callback):
     screen_height = root.winfo_screenheight()
     root.geometry(f"{screen_width}x{screen_height}")
 
-    app = AnnotateApp(root, db, src, image_type=settings['image_type'], channels=settings['channels'], image_size=settings['img_size'], annotation_column=settings['annotation_column'], normalize=settings['normalize'], percentiles=settings['percentiles'], measurement=settings['measurement'], threshold=settings['threshold'])
+    app = AnnotateApp(root, db, src, image_type=settings['image_type'], channels=settings['channels'], image_size=settings['img_size'], annotation_column=settings['annotation_column'], normalize=settings['normalize'], percentiles=settings['percentiles'], measurement=settings['measurement'], threshold=settings['threshold'], normalize_channels=settings['normalize_channels'])
 
     # Set the canvas background to black
     root.configure(bg='black')

spacr/plot.py

@@ -1020,8 +1020,6 @@ def _plot_recruitment_v2(df, df_type, channel_of_interest, columns=[], figuresiz
         None
     """
 
-    from .plot import spacrGraph
-
     color_list = [(55/255, 155/255, 155/255), 
                   (155/255, 55/255, 155/255), 
                   (55/255, 155/255, 255/255), 

spacr/settings.py

@@ -1315,6 +1315,7 @@ def set_annotate_default_settings(settings):
     settings.setdefault('img_size', 200)
     settings.setdefault('annotation_column', 'test')
     settings.setdefault('normalize', 'False')
+    settings.setdefault('normalize_channels', "r,g,b")
     settings.setdefault('percentiles', [2, 98])
     settings.setdefault('measurement', '')#'cytoplasm_channel_3_mean_intensity,pathogen_channel_3_mean_intensity')
     settings.setdefault('threshold', '')#'2')

{spacr-0.3.30.dist-info → spacr-0.3.31.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: spacr
-Version: 0.3.30
+Version: 0.3.31
 Summary: Spatial phenotype analysis of crisp screens (SpaCr)
 Home-page: https://github.com/EinarOlafsson/spacr
 Author: Einar Birnir Olafsson

{spacr-0.3.30.dist-info → spacr-0.3.31.dist-info}/RECORD

@@ -1,6 +1,6 @@
 spacr/__init__.py,sha256=3TNo4PgxHZTHOhyPc8AORvG3tzdPFEc30KAtsOou174,1618
 spacr/__main__.py,sha256=bkAJJD2kjIqOP-u1kLvct9jQQCeUXzlEjdgitwi1Lm8,75
-spacr/app_annotate.py,sha256=nEIL7Fle9CDKGo3sucG_03DgjUQt5W1M1IHBIpVBr08,2171
+spacr/app_annotate.py,sha256=XxGpapg71099aVjb5ZEqgpKTBc_1OIb6_y8yzWfqrsM,2252
 spacr/app_classify.py,sha256=urTP_wlZ58hSyM5a19slYlBxN0PdC-9-ga0hvq8CGWc,165
 spacr/app_make_masks.py,sha256=pqDhRpluiHZz-kPX2Zh_KbYe4TsU43qYBa_7f-rsjpw,1694
 spacr/app_mask.py,sha256=l-dBY8ftzCMdDe6-pXc2Nh_u-idNL9G7UOARiLJBtds,153
@@ -12,17 +12,17 @@ spacr/core.py,sha256=G_x-w7FRIHNfSOoPaIZPSf_A7mVj7PA7o9HQZ4nIu5o,48231
 spacr/deep_spacr.py,sha256=HdOcNU8cHcE_19nP7_5uTz-ih3E169ffr2Hm--NvMvA,43255
 spacr/gui.py,sha256=ARyn9Q_g8HoP-cXh1nzMLVFCKqthY4v2u9yORyaQqQE,8230
 spacr/gui_core.py,sha256=LV_HX5zreu3Bye6sQFDbOuk8Dfj4StMoohy6hsrDEXA,41363
-spacr/gui_elements.py,sha256=3ru8FPZtXCZSj7167GJj18-Zo6TVebhAzkit-mmqmTI,135342
-spacr/gui_utils.py,sha256=hY7JC8HMlyKa9d7tDjkgXgRILgBYTw85jAkRsexO0P0,46960
+spacr/gui_elements.py,sha256=puDqf7PJJ_UMA01fjqODk-zsfSmvzVXpvaZ1BYV988w,136554
+spacr/gui_utils.py,sha256=TFY3zNyTk-FkJ0mjSrWsE2DpHWBbGuQoi1rh2AkXQyQ,45007
 spacr/io.py,sha256=AARmqn1fMmTgVDwWy8bEYK6SjH-6DZIulgCSPdBTyf0,143370
 spacr/logger.py,sha256=lJhTqt-_wfAunCPl93xE65Wr9Y1oIHJWaZMjunHUeIw,1538
 spacr/measure.py,sha256=BThn_sALgKrwGKnLOGpT4FyoJeRVoTZoP9SXbCtCMRw,54857
 spacr/mediar.py,sha256=FwLvbLQW5LQzPgvJZG8Lw7GniA2vbZx6Jv6vIKu7I5c,14743
 spacr/ml.py,sha256=3XiQUfhhseCz9cZXhaVkCCv_qfqoZCdXGnO_p3ulwo4,47131
 spacr/openai.py,sha256=5vBZ3Jl2llYcW3oaTEXgdyCB2aJujMUIO5K038z7w_A,1246
-spacr/plot.py,sha256=eZcs-CQrDTENXVeMY8y8N8VZnmPePO-kAWdoaweFmW8,105540
+spacr/plot.py,sha256=Lv-QFD_NwP9pdsUIiJ--XHJN-jQBkFz_AI9y4i36jEA,105506
 spacr/sequencing.py,sha256=t18mgpK6rhWuB1LtFOsPxqgpFXxuUmrD06ecsaVQ0Gw,19655
-spacr/settings.py,sha256=BUQv8mSQLaw3yT08cKB0x5Y5gl0-S7AxmV6TABoPQlk,75773
+spacr/settings.py,sha256=uTTR6pmwBHbZ_uLLWE4cXplGK7q6K_OmZnsXH-HAFW0,75828
 spacr/sim.py,sha256=1xKhXimNU3ukzIw-3l9cF3Znc_brW8h20yv8fSTzvss,71173
 spacr/submodules.py,sha256=AB7s6-cULsaqz-haAaCtXfGEIi8uPZGT4xoCslUJC3Y,18391
 spacr/timelapse.py,sha256=FSYpUtAVy6xc3lwprRYgyDTT9ysUhfRQ4zrP9_h2mvg,39465
@@ -150,9 +150,9 @@ spacr/resources/icons/umap.png,sha256=dOLF3DeLYy9k0nkUybiZMe1wzHQwLJFRmgccppw-8b
 spacr/resources/images/plate1_E01_T0001F001L01A01Z01C02.tif,sha256=Tl0ZUfZ_AYAbu0up_nO0tPRtF1BxXhWQ3T3pURBCCRo,7958528
 spacr/resources/images/plate1_E01_T0001F001L01A02Z01C01.tif,sha256=m8N-V71rA1TT4dFlENNg8s0Q0YEXXs8slIn7yObmZJQ,7958528
 spacr/resources/images/plate1_E01_T0001F001L01A03Z01C03.tif,sha256=Pbhk7xn-KUP6RSIhJsxQcrHFImBm3GEpLkzx7WOc-5M,7958528
-spacr-0.3.30.dist-info/LICENSE,sha256=SR-2MeGc6SCM1UORJYyarSWY_A-JaOMFDj7ReSs9tRM,1083
-spacr-0.3.30.dist-info/METADATA,sha256=pi7DGlwhEsgk3YMKEDCiATIXZC1ku_PuEo_CKGjDUE4,5949
-spacr-0.3.30.dist-info/WHEEL,sha256=HiCZjzuy6Dw0hdX5R3LCFPDmFS4BWl8H-8W39XfmgX4,91
-spacr-0.3.30.dist-info/entry_points.txt,sha256=BMC0ql9aNNpv8lUZ8sgDLQMsqaVnX5L535gEhKUP5ho,296
-spacr-0.3.30.dist-info/top_level.txt,sha256=GJPU8FgwRXGzKeut6JopsSRY2R8T3i9lDgya42tLInY,6
-spacr-0.3.30.dist-info/RECORD,,
+spacr-0.3.31.dist-info/LICENSE,sha256=SR-2MeGc6SCM1UORJYyarSWY_A-JaOMFDj7ReSs9tRM,1083
+spacr-0.3.31.dist-info/METADATA,sha256=-U4SqumPkRAW6fWg7hsKsgq7tTVPvwtH8um0ZEXca1c,5949
+spacr-0.3.31.dist-info/WHEEL,sha256=HiCZjzuy6Dw0hdX5R3LCFPDmFS4BWl8H-8W39XfmgX4,91
+spacr-0.3.31.dist-info/entry_points.txt,sha256=BMC0ql9aNNpv8lUZ8sgDLQMsqaVnX5L535gEhKUP5ho,296
+spacr-0.3.31.dist-info/top_level.txt,sha256=GJPU8FgwRXGzKeut6JopsSRY2R8T3i9lDgya42tLInY,6
+spacr-0.3.31.dist-info/RECORD,,