spacr 0.1.16__tar.gz → 0.1.55__tar.gz

{spacr-0.1.16/spacr.egg-info → spacr-0.1.55}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: spacr
-Version: 0.1.16
+Version: 0.1.55
 Summary: Spatial phenotype analysis of crisp screens (SpaCr)
 Home-page: https://github.com/EinarOlafsson/spacr
 Author: Einar Birnir Olafsson
@@ -39,6 +39,7 @@ 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: huggingface-hub<0.25,>=0.24.0
 Provides-Extra: dev
 Requires-Dist: pytest<3.11,>=3.9; extra == "dev"
 Provides-Extra: headless

{spacr-0.1.16 → spacr-0.1.55}/setup.py

@@ -44,12 +44,13 @@ dependencies = [
     'ttf_opensans>=2020.10.30',
     'customtkinter>=5.2.2,<6.0', 
     'biopython>=1.80,<2.0',
-    'lxml>=5.1.0,<6.0'
+    'lxml>=5.1.0,<6.0',
+    'huggingface-hub>=0.24.0,<0.25'
 ]
 
 setup(
     name="spacr",
-    version="0.1.16",
+    version="0.1.55",
     author="Einar Birnir Olafsson",
     author_email="olafsson@med.umich.com",
     description="Spatial phenotype analysis of crisp screens (SpaCr)",
@@ -61,11 +62,11 @@ setup(
     install_requires=dependencies,
     entry_points={
         'console_scripts': [
-            'mask=spacr.app_mask:gui_mask',
-            'measure=spacr.app_measure:gui_measure',
-            'make_masks=spacr.app_make_mask:gui_make_masks',
+            'mask=spacr.app_mask:start_mask_app',
+            'measure=spacr.app_measure:start_measure_app',
+            'make_masks=spacr.app_make_masks:gui_make_masks',
             'annotate=spacr.app_annotate:gui_annotate',
-            'classify=spacr.app_classify:gui_classify',
+            'classify=spacr.app_classify:start_classify_app',
             'sim=spacr.app_sim:gui_sim',
             'spacr=spacr.gui:gui_app',
         ],

{spacr-0.1.16 → spacr-0.1.55}/spacr/__init__.py

@@ -15,10 +15,11 @@ from . import deep_spacr
 from . import app_annotate
 from . import gui_utils
 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 app_sequencing
+from . import app_umap
 from . import logger
 
 
@@ -40,6 +41,8 @@ __all__ = [
     "app_mask",
     "app_measure",
     "app_classify",
+    "app_sequencing",
+    "app_umap",
     "logger"
 ]
 

{spacr-0.1.16 → spacr-0.1.55}/spacr/app_annotate.py

@@ -13,7 +13,7 @@ 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, set_dark_style, create_menu_bar
+from .gui_utils import spacrFrame, spacrButton, set_dark_style, create_menu_bar, set_default_font
 
 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):
@@ -379,7 +379,7 @@ def initiate_annotation_app_root(parent_frame):
     container = tk.PanedWindow(parent_frame, orient=tk.HORIZONTAL, bg='black')
     container.pack(fill=tk.BOTH, expand=True)
 
-    scrollable_frame = ScrollableFrame(container, bg='black')
+    scrollable_frame = spacrFrame(container, bg='black')
     container.add(scrollable_frame, stretch="always")
 
     # Setup input fields
@@ -444,7 +444,7 @@ def initiate_annotation_app_root(parent_frame):
         # Start the annotate application in the same root window
         annotate_app(parent_frame, settings)
         
-    run_button = CustomButton(scrollable_frame.scrollable_frame, text="Run", command=run_app,
+    run_button = spacrButton(scrollable_frame.scrollable_frame, text="Run", command=run_app,
                               font=tkFont.Font(family="Arial", size=12, weight=tkFont.NORMAL))
     run_button.grid(row=row, column=0, columnspan=2, pady=10, padx=10)
 

spacr-0.1.55/spacr/app_classify.py

@@ -0,0 +1,8 @@
+from .gui import MainApp
+
+def start_classify_app():
+    app = MainApp(default_app="Classify")
+    app.mainloop()
+
+if __name__ == "__main__":
+    start_classify_app()

{spacr-0.1.16 → spacr-0.1.55}/spacr/app_make_masks.py

@@ -13,7 +13,7 @@ from ttkthemes import ThemedTk
 
 from .logger import log_function_call
 
-from .gui_utils import ScrollableFrame, CustomButton, set_dark_style, set_default_font, set_dark_style, create_menu_bar
+from .gui_utils import spacrFrame, spacrButton, set_dark_style, create_menu_bar, set_default_font
 
 class modify_masks:
 
@@ -869,7 +869,7 @@ 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='black')
+    scrollable_frame = spacrFrame(container, bg='black')
     container.add(scrollable_frame, stretch="always")
 
     # Setup input fields
@@ -897,7 +897,7 @@ def initiate_mask_app_root(parent_frame):
         # Start the modify_masks application in the same root window
         app_instance = modify_masks(parent_frame, folder_path, scale_factor)
         
-    run_button = CustomButton(scrollable_frame.scrollable_frame, text="Run", command=run_app)
+    run_button = spacrButton(scrollable_frame.scrollable_frame, text="Run", command=run_app)
     run_button.grid(row=row, column=0, columnspan=2, pady=10, padx=10)
 
     return parent_frame

spacr-0.1.55/spacr/app_mask.py

@@ -0,0 +1,8 @@
+from .gui import MainApp
+
+def start_mask_app():
+    app = MainApp(default_app="Mask")
+    app.mainloop()
+
+if __name__ == "__main__":
+    start_mask_app()

spacr-0.1.55/spacr/app_measure.py

@@ -0,0 +1,8 @@
+from .gui import MainApp
+
+def start_measure_app():
+    app = MainApp(default_app="Measure")
+    app.mainloop()
+
+if __name__ == "__main__":
+    start_measure_app()

spacr-0.1.55/spacr/app_sequencing.py

@@ -0,0 +1,8 @@
+from .gui import MainApp
+
+def start_seq_app():
+    app = MainApp(default_app="Sequencing")
+    app.mainloop()
+
+if __name__ == "__main__":
+    start_seq_app()

spacr-0.1.55/spacr/app_umap.py

@@ -0,0 +1,8 @@
+from .gui import MainApp
+
+def start_umap_app():
+    app = MainApp(default_app="Umap")
+    app.mainloop()
+
+if __name__ == "__main__":
+    start_umap_app()

{spacr-0.1.16 → spacr-0.1.55}/spacr/core.py

@@ -3021,9 +3021,9 @@ def generate_image_umap(settings={}):
     """
  
     from .io import _read_and_join_tables
-    from .utils import get_db_paths, preprocess_data, reduction_and_clustering, remove_noise, generate_colors, correct_paths, plot_embedding, plot_clusters_grid, cluster_feature_analysis, generate_umap_from_images
-    from .settings import get_umap_image_settings
-    settings = get_umap_image_settings(settings)
+    from .utils import get_db_paths, preprocess_data, reduction_and_clustering, remove_noise, generate_colors, correct_paths, plot_embedding, plot_clusters_grid, cluster_feature_analysis #, generate_umap_from_images
+    from .settings import set_default_umap_image_settings
+    settings = set_default_umap_image_settings(settings)
 
     if isinstance(settings['src'], str):
         settings['src'] = [settings['src']]
@@ -3109,7 +3109,9 @@ def generate_image_umap(settings={}):
 
     else:
         if settings['resnet_features']:
-            numeric_data, embedding, labels = generate_umap_from_images(image_paths, settings['n_neighbors'], settings['min_dist'], settings['metric'], settings['clustering'], settings['eps'], settings['min_samples'], settings['n_jobs'], settings['verbose'])
+            # placeholder for resnet features, not implemented yet
+            pass
+            #numeric_data, embedding, labels = generate_umap_from_images(image_paths, settings['n_neighbors'], settings['min_dist'], settings['metric'], settings['clustering'], settings['eps'], settings['min_samples'], settings['n_jobs'], settings['verbose'])
         else:
             # Apply the trained reducer to the entire dataset
             numeric_data = preprocess_data(all_df, settings['filter_by'], settings['remove_highly_correlated'], settings['log_data'], settings['exclude'])
@@ -3205,9 +3207,9 @@ def reducer_hyperparameter_search(settings={}, reduction_params=None, dbscan_par
     
     from .io import _read_and_join_tables
     from .utils import get_db_paths, preprocess_data, search_reduction_and_clustering, generate_colors
-    from .settings import get_umap_image_settings
+    from .settings import set_default_umap_image_settings
 
-    settings = get_umap_image_settings(settings)
+    settings = set_default_umap_image_settings(settings)
     pointsize = settings['dot_size']
     if isinstance(dbscan_params, dict):
         dbscan_params = [dbscan_params]

{spacr-0.1.16 → spacr-0.1.55}/spacr/deep_spacr.py

@@ -10,6 +10,9 @@ import matplotlib.pyplot as plt
 from PIL import Image
 
 from .logger import log_function_call
+from .utils import close_multiprocessing_processes, reset_mp
+#reset_mp()
+#close_multiprocessing_processes()
 
 def evaluate_model_core(model, loader, loader_name, epoch, loss_type):
     """
@@ -42,7 +45,6 @@ def evaluate_model_core(model, loader, loader_name, epoch, loss_type):
         for batch_idx, (data, target, _) in enumerate(loader, start=1):
             start_time = time.time()
             data, target = data.to(device), target.to(device).float()
-            #data, target = data.to(torch.float).to(device), target.to(device).float()
             output = model(data)
             loss += F.binary_cross_entropy_with_logits(output, target, reduction='sum').item()
             loss = calculate_loss(output, target, loss_type=loss_type)

{spacr-0.1.16 → spacr-0.1.55}/spacr/gui.py

@@ -1,20 +1,15 @@
 import tkinter as tk
 from tkinter import ttk
-from tkinter import font as tkFont
 from PIL import Image, ImageTk
 import os
 import requests
-
-# Import your GUI apps
-from .app_mask import initiate_mask_root
-from .app_measure import initiate_measure_root
+from multiprocessing import set_start_method
+from .gui_utils import set_dark_style, create_menu_bar, initiate_root, spacrButton
 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, set_dark_style, create_menu_bar
 
 class MainApp(tk.Tk):
-    def __init__(self):
+    def __init__(self, default_app=None):
         super().__init__()
         width = self.winfo_screenwidth()
         height = self.winfo_screenheight()
@@ -25,16 +20,34 @@ class MainApp(tk.Tk):
         set_dark_style(style)
 
         self.gui_apps = {
-            "Mask": (initiate_mask_root, "Generate cellpose masks for cells, nuclei and pathogen images."),
-            "Measure": (initiate_measure_root, "Measure single object intensity and morphological feature. Crop and save single object image"),
+            "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": (initiate_annotation_app_root, "Annotation single object images on a grid. Annotations are saved to database."),
             "Make Masks": (initiate_mask_app_root, "Adjust pre-existing Cellpose models to your specific dataset for improved performance"),
-            "Classify": (initiate_classify_root, "Train Torch Convolutional Neural Networks (CNNs) or Transformers to classify single object images.")
+            "Classify": (lambda frame: initiate_root(frame, 'classify'), "Train Torch Convolutional Neural Networks (CNNs) or Transformers to classify single object images."),
+            "Sequencing": (lambda frame: initiate_root(frame, 'sequencing'), "Analyze sequensing data."),
+            "Umap": (lambda frame: initiate_root(frame, 'umap'), "Generate UMAP embedings with datapoints represented as images.")
         }
 
         self.selected_app = tk.StringVar()
         self.create_widgets()
 
+
+        if default_app == "Mask":
+            self.load_app(default_app, self.gui_apps[default_app][0])
+        elif default_app == "Measure":
+            self.load_app(default_app, self.gui_apps[default_app][1])
+        elif default_app == "Annotate":
+            self.load_app(default_app, self.gui_apps[default_app][2])
+        elif default_app == "Make Masks":
+            self.load_app(default_app, self.gui_apps[default_app][3])
+        elif default_app == "Classify":
+            self.load_app(default_app, self.gui_apps[default_app][4])
+        elif default_app == "Sequencing":
+            self.load_app(default_app, self.gui_apps[default_app][5])
+        elif default_app == "Umap":
+            self.load_app(default_app, self.gui_apps[default_app][6])
+
     def create_widgets(self):
         # Create the menu bar
         create_menu_bar(self)
@@ -74,7 +87,8 @@ class MainApp(tk.Tk):
             app_func, app_desc = app_data
 
             # Create custom button with text
-            button = CustomButton(buttons_frame, text=app_name, command=lambda app_name=app_name, app_func=app_func: self.load_app(app_name, app_func), font=('Helvetica', 12))
+            button = spacrButton(buttons_frame, text=app_name, command=lambda app_name=app_name, app_func=app_func: self.load_app(app_name, app_func), font=('Helvetica', 12))
+            #button = ttk.Button(buttons_frame, text=app_name, command=lambda app_name=app_name, app_func=app_func: self.load_app(app_name, app_func), style='Custom.TButton')
             button.grid(row=i, column=0, pady=10, padx=10, sticky="w")
 
             description_label = tk.Label(buttons_frame, text=app_desc, bg="black", fg="white", wraplength=800, justify="left", font=('Helvetica', 12))
@@ -146,4 +160,5 @@ def gui_app():
     app.mainloop()
 
 if __name__ == "__main__":
-    gui_app()
+    set_start_method('spawn', force=True)
+    gui_app()