spacr 0.1.11__py3-none-any.whl → 0.1.16__py3-none-any.whl

spacr/gui_utils.py

@@ -10,7 +10,6 @@ from torchvision import models
 
 from tkinter import font as tkFont
 
-
 from .logger import log_function_call
 
 try:
@@ -65,11 +64,11 @@ 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 +95,42 @@ 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 +138,24 @@ 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,
@@ -162,14 +186,19 @@ class CustomButton(tk.Frame):
         self.text = text
         self.command = command
 
-        self.canvas = tk.Canvas(self, width=150, height=50, highlightthickness=0, bg="black")
+        # Detect screen height and calculate button dimensions
+        screen_height = self.winfo_screenheight()
+        button_height = screen_height // 50
+        button_width = button_height * 3
+
+        self.canvas = tk.Canvas(self, width=button_width, height=button_height, highlightthickness=0, bg="black")
         self.canvas.grid(row=0, column=0)
 
-        self.button_bg = self.create_rounded_rectangle(0, 0, 150, 50, radius=20, fill="#800080")
+        self.button_bg = self.create_rounded_rectangle(0, 0, button_width, button_height, radius=20, fill="#800080")
 
         # Use the passed font or default to Helvetica if not provided
         self.font_style = font if font else tkFont.Font(family="Helvetica", size=12, weight=tkFont.NORMAL)
-        self.button_text = self.canvas.create_text(75, 25, text=self.text, fill="white", font=self.font_style)
+        self.button_text = self.canvas.create_text(button_width // 2, button_height // 2, text=self.text, fill="white", font=self.font_style)
 
         self.bind("<Enter>", self.on_enter)
         self.bind("<Leave>", self.on_leave)
@@ -307,38 +336,6 @@ def set_default_font(root, font_name="Helvetica", size=12):
     root.option_add("*TLabel.Font", default_font)
     root.option_add("*TEntry.Font", default_font)
 
-def check_and_download_font_v1():
-    font_name = "Helvetica"
-    font_dir = "fonts"
-    font_path = os.path.join(font_dir, "OpenSans-Regular.ttf")
-
-    # Check if the font is already available
-    available_fonts = list(tkFont.families())
-    if font_name not in available_fonts:
-        print(f"Font '{font_name}' not found. Downloading...")
-        if not os.path.exists(font_dir):
-            os.makedirs(font_dir)
-
-        if not os.path.exists(font_path):
-            url = "https://github.com/google/fonts/blob/main/apache/opensans/OpenSans-Regular.ttf?raw=true"
-            response = requests.get(url)
-            with open(font_path, "wb") as f:
-                f.write(response.content)
-
-        # Load the font
-        try:
-            tkFont.nametofont("TkDefaultFont").configure(family=font_name, size=10)
-            tkFont.nametofont("TkTextFont").configure(family=font_name, size=10)
-            tkFont.nametofont("TkHeadingFont").configure(family=font_name, size=12)
-        except tk.TclError:
-            tkFont.nametofont("TkDefaultFont").configure(family="Helvetica", size=10)
-            tkFont.nametofont("TkTextFont").configure(family="Helvetica", size=10)
-            tkFont.nametofont("TkHeadingFont").configure(family="Helvetica", size=12)
-    else:
-        tkFont.nametofont("TkDefaultFont").configure(family=font_name, size=10)
-        tkFont.nametofont("TkTextFont").configure(family=font_name, size=10)
-        tkFont.nametofont("TkHeadingFont").configure(family=font_name, size=12)
-
 def check_and_download_font():
     font_name = "Helvetica"
     font_dir = "fonts"
@@ -356,8 +353,6 @@ def check_and_download_font():
             response = requests.get(url)
             with open(font_path, "wb") as f:
                 f.write(response.content)
-
-        # Load the font
         try:
             tkFont.nametofont("TkDefaultFont").configure(family=font_name, size=10)
             tkFont.nametofont("TkTextFont").configure(family=font_name, size=10)
@@ -371,32 +366,39 @@ def check_and_download_font():
         tkFont.nametofont("TkTextFont").configure(family=font_name, size=10)
         tkFont.nametofont("TkHeadingFont").configure(family=font_name, size=12)
 
-def style_text_boxes_v1(style):
-    check_and_download_font()
-    font_style = tkFont.Font(family="Helvetica", size=10)  # Define the Helvetica font
-    style.configure('TEntry', padding='5 5 5 5', borderwidth=1, relief='solid', fieldbackground='#000000', foreground='#ffffff', font=font_style)
-    style.configure('TCombobox', fieldbackground='#000000', background='#000000', foreground='#ffffff', font=font_style)
+def set_dark_style_v1(style):
+    font_style = tkFont.Font(family="Helvetica", size=10) 
+    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('Custom.TLabel', padding='5 5 5 5', borderwidth=1, relief='flat', background='black', foreground='#ffffff', 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):
+def set_dark_style(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('Custom.TButton', padding='10 10 10 10', borderwidth=1, relief='solid', background='#008080', foreground='#ffffff', font=font_style)
+    style.configure('TEntry', padding='5 5 5 5', borderwidth=1, relief='solid', fieldbackground='black', foreground='#ffffff', font=font_style)  # Entry
+    style.configure('TCombobox', fieldbackground='black', background='black', foreground='#ffffff', font=font_style)  # Combobox
+    style.configure('Custom.TButton', padding='10 10 10 10', borderwidth=1, relief='solid', background='#008080', foreground='#ffffff', font=font_style)  # Custom Button
     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('Custom.TLabel', padding='5 5 5 5', borderwidth=1, relief='flat', background='black', foreground='#ffffff', font=font_style) # Custom Label
+    style.configure('TCheckbutton', background='black', foreground='#ffffff', indicatoron=False, relief='flat', font=font_style)  # Checkbutton
     style.map('TCheckbutton', background=[('selected', '#555555'), ('active', '#555555')])
-
-
+    style.configure('TLabel', background='black', foreground='#ffffff', font=font_style) # Label
+    style.configure('TFrame', background='black') # Frame
+    style.configure('TPanedwindow', background='black') # PanedWindow
+    style.configure('TNotebook', background='black', tabmargins=[2, 5, 2, 0]) # Notebook
+    style.configure('TNotebook.Tab', background='black', foreground='#ffffff', padding=[5, 5], font=font_style)
+    style.map('TNotebook.Tab', background=[('selected', '#555555'), ('active', '#555555')])
+    style.configure('TButton', background='black', foreground='#ffffff', padding='5 5 5 5', font=font_style) # Button (regular)
+    style.map('TButton', background=[('active', '#555555'), ('disabled', '#333333')])
+    style.configure('Vertical.TScrollbar', background='black', troughcolor='black', bordercolor='black') # Scrollbar
+    style.configure('Horizontal.TScrollbar', background='black', troughcolor='black', bordercolor='black')
 
 def read_settings_from_csv(csv_file_path):
     settings = {}
@@ -435,36 +437,45 @@ def disable_interactivity(fig):
         for handler_id in list(handlers.keys()):
             fig.canvas.mpl_disconnect(handler_id)
 
-class ScrollableFrame(ttk.Frame):
+class ScrollableFrame_v1(ttk.Frame):
     def __init__(self, container, *args, bg='black', **kwargs):
         super().__init__(container, *args, **kwargs)
-        self.configure(style='TFrame')  # Ensure this uses the styled frame from dark mode
-        
-        canvas = tk.Canvas(self, bg=bg)  # Set canvas background to match dark mode
+        self.configure(style='TFrame')
+        screen_width = self.winfo_screenwidth()
+        frame_width = screen_width // 4  # Set the frame width to 1/4th of the screen width
+        canvas = tk.Canvas(self, bg=bg, width=frame_width)  # Set canvas background to match dark mode
         scrollbar = ttk.Scrollbar(self, orient="vertical", command=canvas.yview)
-        
-        self.scrollable_frame = ttk.Frame(canvas, style='TFrame')  # Ensure it uses the styled frame
+        self.scrollable_frame = ttk.Frame(canvas, style='TFrame', padding=5)  # Ensure it uses the styled frame
         self.scrollable_frame.bind(
             "<Configure>",
             lambda e: canvas.configure(scrollregion=canvas.bbox("all"))
         )
-        
         canvas.create_window((0, 0), window=self.scrollable_frame, anchor="nw")
         canvas.configure(yscrollcommand=scrollbar.set)
-        
         canvas.pack(side="left", fill="both", expand=True)
         scrollbar.pack(side="right", fill="y")
 
-class StdoutRedirector_v1(object):
-    def __init__(self, text_widget):
-        self.text_widget = text_widget
-
-    def write(self, string):
-        self.text_widget.insert(tk.END, string)
-        self.text_widget.see(tk.END)
-
-    def flush(self):
-        pass
+class ScrollableFrame(ttk.Frame):
+    def __init__(self, container, width=None, *args, bg='black', **kwargs):
+        super().__init__(container, *args, **kwargs)
+        self.configure(style='TFrame')
+        if width is None:
+            screen_width = self.winfo_screenwidth()
+            width = screen_width // 4
+        canvas = tk.Canvas(self, bg=bg, width=width)
+        scrollbar = ttk.Scrollbar(self, orient="vertical", command=canvas.yview)
+        
+        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")
+        canvas.configure(yscrollcommand=scrollbar.set)
+        canvas.pack(side="left", fill="both", expand=True)
+        scrollbar.pack(side="right", fill="y")
+        for child in self.scrollable_frame.winfo_children():
+            child.configure(bg='black')
 
 class StdoutRedirector:
     def __init__(self, text_widget):
@@ -767,7 +778,7 @@ def create_input_field(frame, label_text, row, var_type='entry', options=None, d
         return (label, entry, var)  # Return both the label and the entry, and the variable
     elif var_type == 'check':
         var = tk.BooleanVar(value=default_value)  # Set default value (True/False)
-        check = ToggleSwitch(frame, text=label_text, variable=var)  # Use ToggleSwitch class
+        check = ToggleSwitch(frame, text="", variable=var)  # Use ToggleSwitch class
         check.grid(column=1, row=row, sticky=tk.W, padx=5)
         return (label, check, var)  # Return both the label and the checkbutton, and the variable
     elif var_type == 'combo':
@@ -780,10 +791,43 @@ def create_input_field(frame, label_text, row, var_type='entry', options=None, d
     else:
         var = None  # Placeholder in case of an undefined var_type
         return (label, None, var)
+    
+def convert_settings_dict_for_gui(settings):
+    variables = {}
+    special_cases = {
+        'metadata_type': ('combo', ['cellvoyager', 'cq1', 'nikon', 'zeis', 'custom'], 'cellvoyager'),
+        'channels': ('combo', ['[0,1,2,3]', '[0,1,2]', '[0,1]', '[0]'], '[0,1,2,3]'),
+        'magnification': ('combo', [20, 40, 60], 20),
+        'nucleus_channel': ('combo', [0, 1, 2, 3, None], None),
+        'cell_channel': ('combo', [0, 1, 2, 3, None], None),
+        'pathogen_channel': ('combo', [0, 1, 2, 3, None], None),
+        'timelapse_mode': ('combo', ['trackpy', 'btrack'], 'trackpy'),
+        'timelapse_objects': ('combo', ['cell', 'nucleus', 'pathogen', 'cytoplasm', None], None),
+        'model_type': ('combo', ['resnet50', 'other_model'], 'resnet50'),
+        'optimizer_type': ('combo', ['adamw', 'adam'], 'adamw'),
+        'schedule': ('combo', ['reduce_lr_on_plateau', 'step_lr'], 'reduce_lr_on_plateau'),
+        'loss_type': ('combo', ['focal_loss', 'binary_cross_entropy_with_logits'], 'focal_loss'),
+        'normalize_by': ('combo', ['fov', 'png'], 'png'),
+    }
+    for key, value in settings.items():
+        if key in special_cases:
+            variables[key] = special_cases[key]
+        elif isinstance(value, bool):
+            variables[key] = ('check', None, value)
+        elif isinstance(value, int) or isinstance(value, float):
+            variables[key] = ('entry', None, value)
+        elif isinstance(value, str):
+            variables[key] = ('entry', None, value)
+        elif value is None:
+            variables[key] = ('entry', None, value)
+        elif isinstance(value, list):
+            variables[key] = ('entry', None, str(value))
+    return variables
 
 def mask_variables():
     variables = {
-        'src': ('entry', None, '/mnt/data/CellVoyager/40x/einar/mitotrackerHeLaToxoDsRed_20240224_123156/test_gui'),
+        'src': ('entry', None, 'path/to/images'),
+        'pathogen_model': ('entry', None, 'path/to/model'),
         'metadata_type': ('combo', ['cellvoyager', 'cq1', 'nikon', 'zeis', 'custom'], 'cellvoyager'),
         'custom_regex': ('entry', None, None),
         'experiment': ('entry', None, 'exp'),
@@ -793,14 +837,17 @@ def mask_variables():
         'nucleus_background': ('entry', None, 100),
         'nucleus_Signal_to_noise': ('entry', None, 5),
         'nucleus_CP_prob': ('entry', None, 0),
+        'remove_background_nucleus': ('check', None, False),
         'cell_channel': ('combo', [0,1,2,3, None], 3),
         'cell_background': ('entry', None, 100),
         'cell_Signal_to_noise': ('entry', None, 5),
         'cell_CP_prob': ('entry', None, 0),
+        'remove_background_cell': ('check', None, False),
         'pathogen_channel': ('combo', [0,1,2,3, None], 2),
         'pathogen_background': ('entry', None, 100),
         'pathogen_Signal_to_noise': ('entry', None, 3),
         'pathogen_CP_prob': ('entry', None, 0),
+        'remove_background_pathogen': ('check', None, False),
         'preprocess': ('check', None, True),
         'masks': ('check', None, True),
         'examples_to_plot': ('entry', None, 1),
@@ -816,7 +863,7 @@ def mask_variables():
         'fps': ('entry', None, 2),
         'remove_background': ('check', None, True),
         'lower_quantile': ('entry', None, 0.01),
-        'merge': ('check', None, False),
+        #'merge': ('check', None, False),
         'normalize_plots': ('check', None, True),
         'all_to_mip': ('check', None, False),
         'pick_slice': ('check', None, False),
@@ -825,6 +872,11 @@ def mask_variables():
         'plot': ('check', None, True),
         'workers': ('entry', None, 30),
         'verbose': ('check', None, True),
+        'filter': ('check', None, True),
+        'merge_pathogens': ('check', None, True),
+        'adjust_cells': ('check', None, True),
+        'test_images': ('entry', None, 10),
+        'random_test': ('check', None, True),
     }
     return variables
 
@@ -845,7 +897,7 @@ def add_mask_gui_defaults(settings):
 
 def generate_fields(variables, scrollable_frame):
     vars_dict = {}
-    row = 0
+    row = 5
     tooltips = {
         "src": "Path to the folder containing the images.",
         "metadata_type": "Type of metadata to expect in the images. This will determine how the images are processed. If 'custom' is selected, you can provide a custom regex pattern to extract metadata from the image names",
@@ -967,12 +1019,6 @@ def create_dark_mode(root, style, console_output):
     if console_output != None:
         console_output.config(bg=dark_bg, fg=light_text, insertbackground=light_text) #, font=("Helvetica", 12)
     root.configure(bg=dark_bg)
-    
-def set_dark_style(style):
-    style.configure('TFrame', background='black')
-    style.configure('TLabel', background='black', foreground='white')
-    style.configure('TEntry', background='black', foreground='white')
-    style.configure('TCheckbutton', background='black', foreground='white')
 
 ##@log_function_call   
 def main_thread_update_function(root, q, fig_queue, canvas_widget, progress_label):

spacr/make_masks_app.py

@@ -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.dist-info → spacr-0.1.16.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: spacr
-Version: 0.1.11
+Version: 0.1.16
 Summary: Spatial phenotype analysis of crisp screens (SpaCr)
 Home-page: https://github.com/EinarOlafsson/spacr
 Author: Einar Birnir Olafsson
@@ -9,7 +9,6 @@ Classifier: Programming Language :: Python :: 3
 Classifier: License :: OSI Approved :: MIT License
 Classifier: Operating System :: OS Independent
 License-File: LICENSE
-Requires-Dist: dgl ==0.9.1
 Requires-Dist: torch <3.0,>=2.2.1
 Requires-Dist: torchvision <1.0,>=0.17.1
 Requires-Dist: torch-geometric <3.0,>=2.5.1
@@ -40,12 +39,8 @@ 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'
+Requires-Dist: pytest <3.11,>=3.9 ; extra == 'dev'
 Provides-Extra: full
 Requires-Dist: opencv-python ; extra == 'full'
 Provides-Extra: headless
@@ -67,7 +62,7 @@ Requires-Dist: opencv-python-headless ; extra == 'headless'
 SpaCr
 =====
 
-Spatial phenotype analysis of CRISPR-Cas9 screens (SpaCr). The spatial organization of organelles and proteins within cells constitutes a key level of functional regulation. In the context of infectious disease, the spatial relationships between host cell structures and intracellular pathogens are critical to understand host clearance mechanisms and how pathogens evade them. SpaCr is a Python-based software package for generating single-cell image data for deep-learning sub-cellular/cellular phenotypic classification from pooled genetic CRISPR-Cas9 screens. SpaCr provides a flexible toolset to extract single-cell images and measurements from high-content cell painting experiments, train deep-learning models to classify cellular/subcellular phenotypes, simulate, and analyze pooled CRISPR-Cas9 imaging screens.
+Spatial phenotype analysis of CRISPR-Cas9 screens (SpaCr). The spatial organization of organelles and proteins within cells constitutes a key level of functional regulation. In the context of infectious disease, the spatial relationships between host cell structures and intracellular pathogens are critical to understanding host clearance mechanisms and how pathogens evade them. SpaCr is a Python-based software package for generating single-cell image data for deep-learning sub-cellular/cellular phenotypic classification from pooled genetic CRISPR-Cas9 screens. SpaCr provides a flexible toolset to extract single-cell images and measurements from high-content cell painting experiments, train deep-learning models to classify cellular/subcellular phenotypes, simulate, and analyze pooled CRISPR-Cas9 imaging screens.
 
 Features
 --------
@@ -76,9 +71,9 @@ Features
 
 -  **Object Measurements:** Measurements for each object including scikit-image-regionprops, intensity percentiles, shannon-entropy, pearsons and manders correlations, homogeneity, and radial distribution. Measurements are saved to a SQL database in object-level tables.
 
--  **Crop Images:** Objects (e.g., cells) can be saved as PNGs from the object area or bounding box area of each object. Object paths are saved in a SQL database that can be annotated and used to train CNNs/Transformer models for classification tasks.
+-  **Crop Images:** Save objects (cells, nuclei, pathogen, cytoplasm) as images. Object image paths are saved in a SQL database.
 
--  **Train CNNs or Transformers:** Train Torch Convolutional Neural Networks (CNNs) or Transformers to classify single object images. Train Torch models with IRM/ERM, checkpointing.
+-  **Train CNNs or Transformers:** Train Torch models to classify single object images.
 
 -  **Manual Annotation:** Supports manual annotation of single-cell images and segmentation to refine training datasets for training CNNs/Transformers or cellpose, respectively.
 
@@ -95,29 +90,20 @@ Features
 Installation
 ------------
 
-Requires Tkinter for graphical user interface features.
+If using Windows, switch to Linux—it's free, open-source, and better.
 
-Ubuntu
-~~~~~~
+Before installing SpaCr on OSX ensure OpenMP is installed::
 
-Before installing SpaCr, ensure Tkinter is installed:
+   brew install libomp
 
-(Tkinter is included with the standard Python installation on macOS, and Windows)
-
-On Linux:
-
-::
+SpaCr GUI requires Tkinter. On Linux, ensure Tkinter is installed. (Tkinter is included with the standard Python installation on macOS and Windows)::
 
    sudo apt-get install python3-tk
 
-Install spacr with pip
-
-::
+Install SpaCr with pip::
 
    pip install spacr
 
-Run spacr GUI:
-
-::
+Run SpaCr GUI::
 
-   gui
+   spacr

{spacr-0.1.11.dist-info → spacr-0.1.16.dist-info}/RECORD

@@ -1,8 +1,14 @@
-spacr/__init__.py,sha256=M16gIwyDInyfifwm0w9F0RKEbIoG0O4TMO_bdFYtfBc,1373
+spacr/__init__.py,sha256=xu2zNv8A523YvDACynkThH2CYqN5mafsu9lfKGjMmIM,1278
 spacr/__main__.py,sha256=bkAJJD2kjIqOP-u1kLvct9jQQCeUXzlEjdgitwi1Lm8,75
 spacr/alpha.py,sha256=Y95sLEfpK2OSYKRn3M8eUOU33JJeXfV8zhrC4KnwSTY,35244
 spacr/annotate_app.py,sha256=imQ7ZEXDyM6ce1dxZ1xUS1-KequuF_NCI4xCaPLjvco,29275
 spacr/annotate_app_v2.py,sha256=imQ7ZEXDyM6ce1dxZ1xUS1-KequuF_NCI4xCaPLjvco,29275
+spacr/app_annotate.py,sha256=27NzovmbcSa-zdqo9WrFfBcggybhVQmKbgSBDTFnSvU,23588
+spacr/app_classify.py,sha256=7UKRGW245Chtxc_oCmyS-4omQpffvzzBvsHmC5ey4v8,8665
+spacr/app_make_masks.py,sha256=ksggY0xBWt7Fgbd451JOabA064kcjiDm8MTslUq1FLo,45088
+spacr/app_make_masks_v2.py,sha256=csZbUFhOfdHCQ1Wi21bgC1PG8ll5InMqUVmY3-90xlc,30543
+spacr/app_mask.py,sha256=dDZyIlI71vSMqBT3tC9I3BN8J0kxRf9-h5gBiI7pWZk,11357
+spacr/app_measure.py,sha256=jOhtqpO6BQSEpeUZA3taR9jThmo0J7BXMq1URzrdyjA,10841
 spacr/chris.py,sha256=YlBjSgeZaY8HPy6jkrT_ISAnCMAKVfvCxF0I9eAZLFM,2418
 spacr/classify_app.py,sha256=Zi15ryc1ocYitRF4kyxlC27XxGyzfSPdvj2d6ZrSh7E,8446
 spacr/cli.py,sha256=507jfOOEV8BoL4eeUcblvH-iiDHdBrEVJLu1ghAAPSc,1800
@@ -11,7 +17,7 @@ spacr/deep_spacr.py,sha256=N0o7ILD2p1FTfU4DFxnpjs00xjLhwib-ev0XGqA6muU,37035
 spacr/foldseek.py,sha256=YIP1d4Ci6CeA9jSyiv-HTDbNmAmcSM9Y_DaOs7wYzLY,33546
 spacr/get_alfafold_structures.py,sha256=ehx_MQgb12k3hFecP6cYVlm5TLO8iWjgevy8ESyS3cw,3544
 spacr/graph_learning.py,sha256=1tR-ZxvXE3dBz1Saw7BeVFcrsUFu9OlUZeZVifih9eo,13070
-spacr/gui.py,sha256=5kKGKa-iZ5DxAOquW2IkNCP8C87nVKNOA3eONOa7iHo,6559
+spacr/gui.py,sha256=xyf2bmAck8OrbYlvNLpY6rs4EuhuCOxff3f8ZcEZHBQ,6594
 spacr/gui_2.py,sha256=ZAI5quQYbhQJ40vK0NCqU_UMSPLkpfeQpomBWUSM0fc,6946
 spacr/gui_annotate.py,sha256=ugBksLGOHdtOLlEuRyyc59TrkYKu3rDf8JxEgiBSVao,6536
 spacr/gui_classify_app.py,sha256=Zi15ryc1ocYitRF4kyxlC27XxGyzfSPdvj2d6ZrSh7E,8446
@@ -20,10 +26,10 @@ spacr/gui_make_masks_app_v2.py,sha256=X3izTBXdCZDlkVe-fbG-jmCQtcAbmK0OIivjyWaLhu
 spacr/gui_mask_app.py,sha256=mhTl_XzXLFl8Tx3WYEMpdYB_qw9u5JJa0EdkvlcIzAE,10706
 spacr/gui_measure_app.py,sha256=_C1-XFL5HSquUEEbM_NcxdvHx-socPFCx85MBG4d6xo,10598
 spacr/gui_sim_app.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-spacr/gui_utils.py,sha256=elvnIAd-bqVmwzDihg-g_RqWayvkrVpZJGDMskdn-HE,55663
+spacr/gui_utils.py,sha256=emUGYxxk9LOsYk2ozLc6mfglzeb4WqBwYhXwitLLJBA,58746
 spacr/io.py,sha256=IoERqSwoxJrInYl-E0WfwFOEDZXFdJofk5DmpbyLGWM,112077
 spacr/logger.py,sha256=7Zqr3TuuOQLWT32gYr2q1qvv7x0a2JhLANmZcnBXAW8,670
-spacr/make_masks_app.py,sha256=tl4M4Q2WQgrrwjRBJVevxJxpNowqzPhWkdCOm2UfRbw,45053
+spacr/make_masks_app.py,sha256=iGaTwhowoe2JMOSOf8bJwQZTooRhLQx7KO0ewnAmqDY,45138
 spacr/make_masks_app_v2.py,sha256=X3izTBXdCZDlkVe-fbG-jmCQtcAbmK0OIivjyWaLhug,30576
 spacr/mask_app.py,sha256=mhTl_XzXLFl8Tx3WYEMpdYB_qw9u5JJa0EdkvlcIzAE,10706
 spacr/measure.py,sha256=0FRsHF5ftar4JZ0B_6Nq-NlyP5t6aiO0IrskyikIBEE,55000
@@ -40,9 +46,9 @@ spacr/version.py,sha256=axH5tnGwtgSnJHb5IDhiu4Zjk5GhLyAEDRe-rnaoFOA,409
 spacr/models/cp/toxo_plaque_cyto_e25000_X1120_Y1120.CP_model,sha256=z8BbHWZPRnE9D_BHO0fBREE85c1vkltDs-incs2ytXQ,26566572
 spacr/models/cp/toxo_plaque_cyto_e25000_X1120_Y1120.CP_model_settings.csv,sha256=fBAGuL_B8ERVdVizO3BHozTDSbZUh1yFzsYK3wkQN68,420
 spacr/models/cp/toxo_pv_lumen.CP_model,sha256=2y_CindYhmTvVwBH39SNILF3rI3x9SsRn6qrMxHy3l0,26562451
-spacr-0.1.11.dist-info/LICENSE,sha256=SR-2MeGc6SCM1UORJYyarSWY_A-JaOMFDj7ReSs9tRM,1083
-spacr-0.1.11.dist-info/METADATA,sha256=FykpqeYP5uOY3XnsUaqwe2tSctPILiguTqqPNOJZ4Vg,5301
-spacr-0.1.11.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
-spacr-0.1.11.dist-info/entry_points.txt,sha256=PxmdWbth1nQzQfE0s2M3XST_of47tBtlBPH20KJrvkE,354
-spacr-0.1.11.dist-info/top_level.txt,sha256=GJPU8FgwRXGzKeut6JopsSRY2R8T3i9lDgya42tLInY,6
-spacr-0.1.11.dist-info/RECORD,,
+spacr-0.1.16.dist-info/LICENSE,sha256=SR-2MeGc6SCM1UORJYyarSWY_A-JaOMFDj7ReSs9tRM,1083
+spacr-0.1.16.dist-info/METADATA,sha256=-VoJLJbzVVNvGhVmWA2uh5DydW0W4KjiCnz5WYwgLlQ,5004
+spacr-0.1.16.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
+spacr-0.1.16.dist-info/entry_points.txt,sha256=e6tBSk-bac5ypML_iWIROnQ-hDSLZT_sGpGviPNHG4g,277
+spacr-0.1.16.dist-info/top_level.txt,sha256=GJPU8FgwRXGzKeut6JopsSRY2R8T3i9lDgya42tLInY,6
+spacr-0.1.16.dist-info/RECORD,,

spacr-0.1.16.dist-info/entry_points.txt

@@ -0,0 +1,8 @@
+[console_scripts]
+annotate = spacr.app_annotate:gui_annotate
+classify = spacr.app_classify:gui_classify
+make_masks = spacr.app_make_mask:gui_make_masks
+mask = spacr.app_mask:gui_mask
+measure = spacr.app_measure:gui_measure
+sim = spacr.app_sim:gui_sim
+spacr = spacr.gui:gui_app

spacr-0.1.11.dist-info/entry_points.txt

@@ -1,9 +0,0 @@
-[console_scripts]
-annotate = spacr.annotate_app_v2:gui_annotate
-classify = spacr.gui_classify_app:gui_classify
-gui = spacr.gui:gui_app
-make_masks = spacr.gui_make_mask_app:gui_make_masks
-make_masks2 = spacr.gui_make_mask_app_v2:gui_make_masks
-mask = spacr.gui_mask_app:gui_mask
-measure = spacr.gui_measure_app:gui_measure
-sim = spacr.gui_sim_app:gui_sim