spacr 0.1.85__tar.gz → 0.2.1__tar.gz

{spacr-0.1.85/spacr.egg-info → spacr-0.2.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: spacr
-Version: 0.1.85
+Version: 0.2.1
 Summary: Spatial phenotype analysis of crisp screens (SpaCr)
 Home-page: https://github.com/EinarOlafsson/spacr
 Author: Einar Birnir Olafsson

{spacr-0.1.85 → spacr-0.2.1}/setup.py

@@ -50,7 +50,7 @@ dependencies = [
 
 setup(
     name="spacr",
-    version="0.1.85",
+    version="0.2.1",
     author="Einar Birnir Olafsson",
     author_email="olafsson@med.umich.com",
     description="Spatial phenotype analysis of crisp screens (SpaCr)",
@@ -58,7 +58,7 @@ setup(
     url="https://github.com/EinarOlafsson/spacr",
     packages=find_packages(exclude=["tests.*", "tests"]),
     include_package_data=True,
-    package_data={'spacr': ['models/cp/*'],},
+    package_data={'spacr': ['resources/models/cp/*', 'resources/icons/*'],},
     install_requires=dependencies,
     entry_points={
         'console_scripts': [

{spacr-0.1.85 → spacr-0.2.1}/spacr/__init__.py

@@ -16,8 +16,8 @@ from . import app_annotate
 from . import gui_utils
 from . import gui_elements
 from . import gui_core
-from . import gui_run
-from . import gui_wrappers
+from . import gui
+from . import gui
 from . import app_make_masks
 from . import app_mask
 from . import app_measure
@@ -40,6 +40,10 @@ __all__ = [
     "deep_spacr",
     "app_annotate",
     "gui_utils",
+    "gui_elements",
+    "gui_core",
+    "gui",
+    "gui",
     "app_make_masks",
     "app_mask",
     "app_measure",

{spacr-0.1.85 → spacr-0.2.1}/spacr/app_annotate.py

@@ -1,15 +1,16 @@
 import tkinter as tk
+from tkinter import ttk
 from .gui import MainApp
+from .gui_elements import set_dark_style
 
 def initiate_annotation_app(parent_frame):
     from .gui_utils import generate_annotate_fields, annotate_app
     # Set up the settings window
     settings_window = tk.Toplevel(parent_frame)
     settings_window.title("Annotation Settings")
-    settings_window.configure(bg='black')  # Set the background color to black
-    
-    # Use the existing function to create the settings UI
-    settings_frame = tk.Frame(settings_window, bg='black')  # Set the background color to black
+    style_out = set_dark_style(ttk.Style())
+    settings_window.configure(bg=style_out['bg_color'])
+    settings_frame = tk.Frame(settings_window, bg=style_out['bg_color'])
     settings_frame.pack(fill=tk.BOTH, expand=True)
     vars_dict = generate_annotate_fields(settings_frame)
     
@@ -41,7 +42,7 @@ def initiate_annotation_app(parent_frame):
         settings_window.destroy()
         annotate_app(parent_frame, settings)
     
-    start_button = tk.Button(settings_window, text="Start Annotation", command=start_annotation_app, bg='black', fg='white')
+    start_button = tk.Button(settings_window, text="Start Annotation", command=start_annotation_app, bg=style_out['bg_color'], fg=style_out['bg_color'])
     start_button.pack(pady=10)
 
 def start_annotate_app():

{spacr-0.1.85 → spacr-0.2.1}/spacr/app_make_masks.py

@@ -3,26 +3,22 @@ from tkinter import ttk
 from .gui import MainApp
 
 def initiate_make_mask_app(parent_frame):
-    from .gui_elements import modify_masks
-    # Set up the settings window
+    from .gui_elements import ModifyMaskApp, set_dark_style
     settings_window = tk.Toplevel(parent_frame)
     settings_window.title("Make Masks Settings")
-    settings_window.configure(bg='black')  # Set the background color to black
-    
-    # Use the existing function to create the settings UI
-    settings_frame = tk.Frame(settings_window, bg='black')  # Set the background color to black
+    style_out = set_dark_style(ttk.Style())
+    settings_window.configure(bg=style_out['bg_color'])
+    settings_frame = tk.Frame(settings_window, bg=style_out['bg_color'])
     settings_frame.pack(fill=tk.BOTH, expand=True)
     
     vars_dict = {
         'folder_path': ttk.Entry(settings_frame),
         'scale_factor': ttk.Entry(settings_frame)
     }
-
-    # Arrange input fields and labels
     row = 0
     for name, entry in vars_dict.items():
         ttk.Label(settings_frame, text=f"{name.replace('_', ' ').capitalize()}:",
-                  background="black", foreground="white").grid(row=row, column=0)
+                  background=style_out['bg_color'], foreground=style_out['fg_color']).grid(row=row, column=0)
         entry.grid(row=row, column=1)
         row += 1
 
@@ -32,15 +28,12 @@ def initiate_make_mask_app(parent_frame):
         try:
             scale_factor = float(vars_dict['scale_factor'].get())
         except ValueError:
-            scale_factor = None  # Handle invalid input gracefully
-
-        # Convert empty strings to None
+            scale_factor = None
         folder_path = folder_path if folder_path != '' else None
-
         settings_window.destroy()
-        modify_masks(parent_frame, folder_path, scale_factor)
+        ModifyMaskApp(parent_frame, folder_path, scale_factor)
     
-    run_button = tk.Button(settings_window, text="Start Make Masks", command=start_make_mask_app, bg='black', fg='white')
+    run_button = tk.Button(settings_window, text="Start Make Masks", command=start_make_mask_app, bg=style_out['bg_color'], fg=style_out['fg_color'])
     run_button.pack(pady=10)
 
 def start_make_mask_app():

{spacr-0.1.85 → spacr-0.2.1}/spacr/core.py

@@ -1738,7 +1738,7 @@ def preprocess_generate_masks(src, settings={}):
         if os.path.exists(os.path.join(src,'measurements')):
             _pivot_counts_table(db_path=os.path.join(src,'measurements', 'measurements.db'))
 
-        #Concatinate stack with masks
+        #Concatenate stack with masks
         _load_and_concatenate_arrays(src, settings['channels'], settings['cell_channel'], settings['nucleus_channel'], settings['pathogen_channel'])
         
         if settings['plot']:

spacr-0.2.1/spacr/gui.py

@@ -0,0 +1,157 @@
+import tkinter as tk
+from tkinter import ttk
+from PIL import Image, ImageTk, ImageDraw
+import os
+from multiprocessing import set_start_method
+from .gui_elements import spacrButton, create_menu_bar, set_dark_style
+from .gui_core import initiate_root
+
+class MainApp(tk.Tk):
+    def __init__(self, default_app=None):
+        super().__init__()
+        width = self.winfo_screenwidth()
+        height = self.winfo_screenheight()
+        self.geometry(f"{width}x{height}")
+        self.title("SpaCr GUI Collection")
+        self.configure(bg='#333333')  # Set window background to dark gray
+
+        # Initialize style and apply dark style to the main window
+        style = ttk.Style()
+        self.color_settings = set_dark_style(style, parent_frame=self)
+        self.main_buttons = {}  # Initialize main_buttons dictionary here
+        self.additional_buttons = {}  # Initialize additional_buttons dictionary here
+
+        self.main_gui_apps = {
+            "Mask": (lambda frame: initiate_root(frame, 'mask'), "Generate cellpose masks for cells, nuclei and pathogen images."),
+            "Measure": (lambda frame: initiate_root(frame, 'measure'), "Measure single object intensity and morphological feature. Crop and save single object image"),
+            "Annotate": (lambda frame: initiate_root(frame, 'annotate'), "Annotation single object images on a grid. Annotations are saved to database."),
+            "Make Masks": (lambda frame: initiate_root(frame, 'make_masks'), "Adjust pre-existing Cellpose models to your specific dataset for improved performance"),
+            "Classify": (lambda frame: initiate_root(frame, 'classify'), "Train Torch Convolutional Neural Networks (CNNs) or Transformers to classify single object images."),
+        }
+
+        self.additional_gui_apps = {
+            "Sequencing": (lambda frame: initiate_root(frame, 'sequencing'), "Analyze sequencing data."),
+            "Umap": (lambda frame: initiate_root(frame, 'umap'), "Generate UMAP embeddings with datapoints represented as images."),
+            "Train Cellpose": (lambda frame: initiate_root(frame, 'train_cellpose'), "Train custom Cellpose models."),
+            "ML Analyze": (lambda frame: initiate_root(frame, 'ml_analyze'), "Machine learning analysis of data."),
+            "Cellpose Masks": (lambda frame: initiate_root(frame, 'cellpose_masks'), "Generate Cellpose masks."),
+            "Cellpose All": (lambda frame: initiate_root(frame, 'cellpose_all'), "Run Cellpose on all images."),
+            "Map Barcodes": (lambda frame: initiate_root(frame, 'map_barcodes'), "Map barcodes to data."),
+            "Regression": (lambda frame: initiate_root(frame, 'regression'), "Perform regression analysis."),
+            "Recruitment": (lambda frame: initiate_root(frame, 'recruitment'), "Analyze recruitment data.")
+        }
+
+        self.selected_app = tk.StringVar()
+        self.create_widgets()
+
+        if default_app in self.main_gui_apps:
+            self.load_app(default_app, self.main_gui_apps[default_app][0])
+        elif default_app in self.additional_gui_apps:
+            self.load_app(default_app, self.additional_gui_apps[default_app][0])
+
+    def create_widgets(self):
+        # Create the menu bar
+        create_menu_bar(self)
+
+        # Create a canvas to hold the selected app and other elements
+        self.canvas = tk.Canvas(self, 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)
+        self.content_frame.grid(row=0, column=0, sticky="nsew")
+
+        # Center the content frame within the canvas
+        self.canvas.create_window((self.winfo_screenwidth() // 2, self.winfo_screenheight() // 2), window=self.content_frame, anchor="center")
+
+        # Apply dark style to canvas and content_frame
+        set_dark_style(ttk.Style(), containers=[self.canvas, self.content_frame])
+
+        # Create startup screen with buttons for each main GUI app and drop-down for additional apps
+        self.create_startup_screen()
+
+    def create_startup_screen(self):
+        self.clear_frame(self.content_frame)
+
+        # Create frames for the grids
+        main_buttons_frame = tk.Frame(self.content_frame)
+        main_buttons_frame.pack(pady=10)
+        set_dark_style(ttk.Style(), containers=[main_buttons_frame])
+
+        additional_buttons_frame = tk.Frame(self.content_frame)
+        additional_buttons_frame.pack(pady=10)
+        set_dark_style(ttk.Style(), containers=[additional_buttons_frame])
+
+        # Create a frame for the description below the icon grids
+        description_frame = tk.Frame(self.content_frame, height=70)
+        description_frame.pack(fill=tk.X, pady=10)
+        description_frame.pack_propagate(False)  # Prevent the frame from resizing based on its content
+        set_dark_style(ttk.Style(), containers=[description_frame])
+
+        # Use a Label widget to display descriptions
+        self.description_label = tk.Label(description_frame, text="", wraplength=800, justify="center", font=('Helvetica', 12), fg=self.color_settings['fg_color'], bg=self.color_settings['bg_color'])
+        self.description_label.pack(fill=tk.BOTH, pady=10)
+
+        # Load the logo image and place it in the main apps row
+        logo_button = spacrButton(main_buttons_frame, text="SpaCr", command=lambda: self.load_app("logo_spacr", initiate_root), icon_name="logo_spacr", size=100, show_text=False)
+        logo_button.grid(row=0, column=0, padx=5, pady=5)
+        self.main_buttons[logo_button] = "SpaCr: An advanced application suite for cellpose masks, measurements, annotations, and more."
+
+        # Create icon buttons for the main apps
+        for i, (app_name, app_data) in enumerate(self.main_gui_apps.items()):
+            app_func, app_desc = app_data
+            button = spacrButton(main_buttons_frame, text=app_name, command=lambda app_name=app_name, app_func=app_func: self.load_app(app_name, app_func), icon_name=app_name.lower(), size=100, show_text=False)
+            button.grid(row=0, column=i + 1, padx=5, pady=5)
+            self.main_buttons[button] = app_desc
+
+        # Create icon buttons for the additional apps
+        for i, (app_name, app_data) in enumerate(self.additional_gui_apps.items()):
+            app_func, app_desc = app_data
+            button = spacrButton(additional_buttons_frame, text=app_name, command=lambda app_name=app_name, app_func=app_func: self.load_app(app_name, app_func), icon_name=app_name.lower(), size=75, show_text=False)
+            button.grid(row=0, column=i, padx=5, pady=5)
+            self.additional_buttons[button] = app_desc
+
+        # Update description initially
+        self.update_description()
+
+    def update_description(self):
+        # Check all buttons and update description if any has the active color
+        for button, desc in {**self.main_buttons, **self.additional_buttons}.items():
+            if button.canvas.itemcget(button.button_bg, "fill") == self.color_settings['active_color']:
+                self.show_description(desc)
+                return
+        self.clear_description()
+
+    def show_description(self, description):
+        if self.description_label.winfo_exists():
+            self.description_label.config(text=description)
+            self.description_label.update_idletasks()  # Ensure the label updates immediately
+
+    def clear_description(self):
+        if self.description_label.winfo_exists():
+            self.description_label.config(text="")
+            self.description_label.update_idletasks()  # Ensure the label updates immediately
+
+    def load_app(self, app_name, app_func):
+        # Clear the current content frame
+        self.clear_frame(self.canvas)
+
+        # Initialize the selected app
+        app_frame = tk.Frame(self.canvas)
+        app_frame.pack(fill=tk.BOTH, expand=True)
+        set_dark_style(ttk.Style(), containers=[app_frame])
+        app_func(app_frame)
+
+    def clear_frame(self, frame):
+        for widget in frame.winfo_children():
+            widget.destroy()
+
+def gui_app():
+    app = MainApp()
+    app.mainloop()
+
+if __name__ == "__main__":
+    set_start_method('spawn', force=True)
+    gui_app()

{spacr-0.1.85 → spacr-0.2.1}/spacr/gui_core.py

@@ -231,25 +231,43 @@ def import_settings(settings_type='mask'):
     vars_dict = hide_all_settings(vars_dict, categories=None)
 
 def convert_settings_dict_for_gui(settings):
+    from torchvision import models as torch_models
+    torchvision_models = [name for name, obj in torch_models.__dict__.items() if callable(obj)]
+    chans = ['0', '1', '2', '3', '4', '5', '6', '7', '8', None]
+    chans_v2 = [0, 1, 2, 3, None]
     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]'),
-        'cell_mask_dim': ('combo', ['0', '1', '2', '3', '4', '5', '6', '7', '8', None], None),
-        'nucleus_mask_dim': ('combo', ['0', '1', '2', '3', '4', '5', '6', '7', '8', None], None),
-        'pathogen_mask_dim': ('combo', ['0', '1', '2', '3', '4', '5', '6', '7', '8', None], None),
-        #'crop_mode': ('combo', ['cell', 'nucleus', 'pathogen', '[cell, nucleus, pathogen]', '[cell,nucleus, pathogen]'], ['cell']),
+        'channel_dims': ('combo', ['[0,1,2,3]', '[0,1,2]', '[0,1]', '[0]'], '[0,1,2,3]'),
+        'cell_mask_dim': ('combo', chans, None),
+        'cell_chann_dim': ('combo', chans, None),
+        'nucleus_mask_dim': ('combo', chans, None),
+        'nucleus_chann_dim': ('combo', chans, None),
+        'pathogen_mask_dim': ('combo', chans, None),
+        'pathogen_chann_dim': ('combo', chans, None),
+        'crop_mode': ('combo', ['cell', 'nucleus', 'pathogen', '[cell, nucleus, pathogen]', '[cell,nucleus, pathogen]'], ['cell']),
         '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),
+        'nucleus_channel': ('combo', chans_v2, None),
+        'cell_channel': ('combo', chans_v2, None),
+        'channel_of_interest': ('combo', chans_v2, None),
+        'pathogen_channel': ('combo', chans_v2, None),
         'timelapse_mode': ('combo', ['trackpy', 'btrack'], 'trackpy'),
+        'train_mode': ('combo', ['erm', 'irm'], 'erm'),
+        'clustering': ('combo', ['dbscan', 'kmean'], 'dbscan'),
+        'reduction_method': ('combo', ['umap', 'tsne'], 'umap'),
+        'model_name': ('combo', ['cyto', 'cyto_2', 'cyto_3', 'nuclei'], 'cyto'),
+        'regression_type': ('combo', ['ols','gls','wls','rlm','glm','mixed','quantile','logit','probit','poisson','lasso','ridge'], 'ols'),
         'timelapse_objects': ('combo', ['cell', 'nucleus', 'pathogen', 'cytoplasm', None], None),
-        'model_type': ('combo', ['resnet50', 'other_model'], 'resnet50'),
+        'model_type': ('combo', torchvision_models, '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'),
+        'agg_type': ('combo', ['mean', 'median'], 'mean'),
+        'grouping': ('combo', ['mean', 'median'], 'mean'),
+        'min_max': ('combo', ['allq', 'all'], 'allq'),
+        'transform': ('combo', ['log', 'sqrt', 'square', None], None)
     }
 
     for key, value in settings.items():
@@ -338,9 +356,10 @@ def setup_plot_section(vertical_container):
     plot_frame.add(canvas_widget, stretch="always")
     canvas.draw()
     canvas.figure = figure
-    # Set the figure and axes background to black
-    figure.patch.set_facecolor('black')
-    plot.set_facecolor('black')
+    style_out = set_dark_style(ttk.Style())
+
+    figure.patch.set_facecolor(style_out['bg_color'])
+    plot.set_facecolor(style_out['bg_color'])
     containers = [plot_frame]
     widgets = [canvas_widget]
     style = ttk.Style(vertical_container)
@@ -488,25 +507,25 @@ def setup_button_section(horizontal_container, settings_type='mask', window_dime
     btn_row = 1
 
     if run:
-        run_button = spacrButton(button_scrollable_frame.scrollable_frame, text="Run", command=lambda: start_process(q, fig_queue, settings_type))
+        run_button = spacrButton(button_scrollable_frame.scrollable_frame, text="run", command=lambda: start_process(q, fig_queue, settings_type))
         run_button.grid(row=btn_row, column=btn_col, pady=5, padx=5, sticky='ew')
         widgets.append(run_button)
         btn_row += 1
 
     if abort and settings_type in ['mask', 'measure', 'classify', 'sequencing', 'umap']:
-        abort_button = spacrButton(button_scrollable_frame.scrollable_frame, text="Abort", command=initiate_abort)
+        abort_button = spacrButton(button_scrollable_frame.scrollable_frame, text="abort", command=initiate_abort)
         abort_button.grid(row=btn_row, column=btn_col, pady=5, padx=5, sticky='ew')
         widgets.append(abort_button)
         btn_row += 1
 
     if download and settings_type in ['mask']:
-        download_dataset_button = spacrButton(button_scrollable_frame.scrollable_frame, text="Download", command=download_hug_dataset)
+        download_dataset_button = spacrButton(button_scrollable_frame.scrollable_frame, text="download", command=download_hug_dataset)
         download_dataset_button.grid(row=btn_row, column=btn_col, pady=5, padx=5, sticky='ew')
         widgets.append(download_dataset_button)
         btn_row += 1
 
     if import_btn:
-        import_button = spacrButton(button_scrollable_frame.scrollable_frame, text="Import", command=lambda: import_settings(settings_type))
+        import_button = spacrButton(button_scrollable_frame.scrollable_frame, text="settings", command=lambda: import_settings(settings_type))
         import_button.grid(row=btn_row, column=btn_col, pady=5, padx=5, sticky='ew')
         widgets.append(import_button)
 
@@ -516,11 +535,19 @@ def setup_button_section(horizontal_container, settings_type='mask', window_dime
     description_frame = tk.Frame(horizontal_container)
     horizontal_container.add(description_frame, stretch="always", sticky="nsew")
     description_frame.grid_columnconfigure(0, weight=1)
+    description_frame.grid_rowconfigure(0, weight=1)  # Add this line to make the row expandable
+
     description_label = tk.Label(description_frame, text="Module Description", anchor='nw', justify='left', wraplength=width - 50)
     description_label.grid(row=0, column=0, pady=50, padx=20, sticky='nsew')
     description_text = descriptions.get(settings_type, "No description available for this module.")
     description_label.config(text=description_text)
 
+    def update_wraplength(event):
+        new_width = event.width - 40  # Adjust as needed
+        description_label.config(wraplength=new_width)
+
+    description_label.bind('<Configure>', update_wraplength)
+
     containers = [button_frame, description_frame]
     widgets.extend([description_label])
 
@@ -588,7 +615,7 @@ def toggle_settings(button_scrollable_frame):
     category_var = tk.StringVar()
     non_empty_categories = [category for category, settings in categories.items() if any(setting in vars_dict for setting in settings)]
     category_dropdown = spacrDropdownMenu(button_scrollable_frame.scrollable_frame, category_var, non_empty_categories, command=on_category_select)
-    category_dropdown.grid(row=1, column=3, sticky="ew", pady=2, padx=2)
+    category_dropdown.grid(row=5, column=0, sticky="ew", pady=2, padx=2)
     vars_dict = hide_all_settings(vars_dict, categories)
 
 def process_fig_queue():