spacr 0.1.12__tar.gz → 0.1.50__tar.gz

{spacr-0.1.12/spacr.egg-info → spacr-0.1.50}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: spacr
-Version: 0.1.12
+Version: 0.1.50
 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 +39,9 @@ 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
+Requires-Dist: huggingface-hub<0.25,>=0.24.0
 Provides-Extra: dev
-Requires-Dist: pytest>=3.9; extra == "dev"
+Requires-Dist: pytest<3.11,>=3.9; extra == "dev"
 Provides-Extra: headless
 Requires-Dist: opencv-python-headless; extra == "headless"
 Provides-Extra: full
@@ -67,7 +63,7 @@ Requires-Dist: opencv-python; extra == "full"
 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 +72,9 @@ 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 +91,20 @@ 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-0.1.12 → spacr-0.1.50}/README.rst

@@ -14,7 +14,7 @@
 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
 --------
@@ -23,9 +23,9 @@ 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.
 
@@ -42,29 +42,20 @@ 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-0.1.12 → spacr-0.1.50}/setup.py

@@ -10,19 +10,11 @@ def get_cuda_version():
     except (subprocess.CalledProcessError, FileNotFoundError):
         return None
 
-cuda_version = get_cuda_version()
-
-if cuda_version:
-    dgl_dependency = f'dgl-cu{cuda_version}==0.9.1'  # Specify the version of DGL compatible with your setup
-else:
-    dgl_dependency = 'dgl==0.9.1'  # Fallback to CPU version if no CUDA is detected
-
 # Ensure you have read the README.rst content into a variable, e.g., `long_description`
 with open("README.rst", "r", encoding="utf-8") as fh:
     long_description = fh.read()
 
 dependencies = [
-    dgl_dependency,
     'torch>=2.2.1,<3.0',
     'torchvision>=0.17.1,<1.0',
     'torch-geometric>=2.5.1,<3.0',
@@ -52,16 +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', 
-    'qtpy>=2.4.1,<2.5',
-    'superqt>=0.6.7,<0.7',
-    'pyqt6>=6.7.1,<6.8',
-    'pyqtgraph>=0.13.7,<0.14'
+    'lxml>=5.1.0,<6.0',
+    'huggingface-hub>=0.24.0,<0.25'
 ]
 
 setup(
     name="spacr",
-    version="0.1.12",
+    version="0.1.50",
     author="Einar Birnir Olafsson",
     author_email="olafsson@med.umich.com",
     description="Spatial phenotype analysis of crisp screens (SpaCr)",
@@ -73,18 +62,17 @@ setup(
     install_requires=dependencies,
     entry_points={
         'console_scripts': [
-            'mask=spacr.gui_mask_app:gui_mask',
-            'measure=spacr.gui_measure_app:gui_measure',
-            'make_masks=spacr.gui_make_mask_app:gui_make_masks',
-            'make_masks2=spacr.gui_make_mask_app_v2:gui_make_masks',
-            'annotate=spacr.annotate_app_v2:gui_annotate',
-            'classify=spacr.gui_classify_app:gui_classify',
-            'sim=spacr.gui_sim_app:gui_sim',
-            'gui=spacr.gui:gui_app',
+            '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:start_classify_app',
+            'sim=spacr.app_sim:gui_sim',
+            'spacr=spacr.gui:gui_app',
         ],
     },
     extras_require={
-        'dev': ['pytest>=3.9'],
+        'dev': ['pytest>=3.9,<3.11'],
         'headless': ['opencv-python-headless'],
         'full': ['opencv-python'],
     },
@@ -93,4 +81,32 @@ setup(
         "License :: OSI Approved :: MIT License",
         "Operating System :: OS Independent",
     ]
-)
+)
+
+cuda_version = get_cuda_version()
+
+if cuda_version:
+    dgl = f'dgl-cu{cuda_version}==0.9.1'
+else:
+    dgl = 'dgl==0.9.1'  # Fallback to CPU version if no CUDA is detected
+try:
+    subprocess.run(['pip', 'install', dgl], check=True)
+except subprocess.CalledProcessError:
+    subprocess.run(['pip', 'install', 'dgl'], check=True)
+
+deps = ['pyqtgraph>=0.13.7,<0.14',
+        'pyqt6>=6.7.1,<6.8',
+        'pyqt6.sip',
+        'qtpy>=2.4.1,<2.5',
+        'superqt>=0.6.7,<0.7',
+        'pyqtgraph',
+        'pyqt6',
+        'pyqt6.sip',
+        'qtpy',
+        'superqt']
+
+for dep in deps:
+    try:
+        subprocess.run(['pip', 'install', dep], check=True)
+    except subprocess.CalledProcessError:
+        pass

{spacr-0.1.12 → spacr-0.1.50}/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, style_text_boxes, create_menu_bar
+from .gui_utils import ScrollableFrame, CustomButton, 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):
@@ -372,7 +372,6 @@ global_image_refs = []
 def initiate_annotation_app_root(parent_frame):
     style = ttk.Style(parent_frame)
     set_dark_style(style)
-    style_text_boxes(style)
     set_default_font(parent_frame, font_name="Arial", size=8)
 
     parent_frame.configure(bg='black')
@@ -536,4 +535,4 @@ def gui_annotate():
     root.mainloop()
 
 if __name__ == "__main__":
-    gui_annotate()
+    gui_annotate()

spacr-0.1.50/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-0.1.12 → spacr-0.1.50}/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, create_dark_mode, style_text_boxes, create_menu_bar
+from .gui_utils import ScrollableFrame, CustomButton, set_dark_style, create_menu_bar, set_default_font
 
 class modify_masks:
 
@@ -864,7 +864,6 @@ class modify_masks:
 def initiate_mask_app_root(parent_frame):
     style = ttk.Style(parent_frame)
     set_dark_style(style)
-    style_text_boxes(style)
     set_default_font(parent_frame, font_name="Arial", size=8)
     
     container = tk.PanedWindow(parent_frame, orient=tk.HORIZONTAL)

{spacr-0.1.12 → spacr-0.1.50}/spacr/app_make_masks_v2.py

@@ -13,7 +13,7 @@ from ttkthemes import ThemedTk
 from pyqtgraph import GraphicsLayoutWidget, ViewBox, ImageItem, mkQApp
 
 from .logger import log_function_call
-from .gui_utils import ScrollableFrame, CustomButton, set_dark_style, set_default_font, create_dark_mode, style_text_boxes, create_menu_bar
+from .gui_utils import ScrollableFrame, CustomButton, set_dark_style, create_dark_mode, create_menu_bar, set_default_font
 
 class ModifyMasks:
     def __init__(self, root, folder_path, scale_factor):
@@ -635,9 +635,7 @@ def initiate_mask_app_root(width, height):
     root = ThemedTk(theme=theme)
     style = ttk.Style(root)
     set_dark_style(style)
-
-    style_text_boxes(style)
-    set_default_font(root, font_name="Arial", size=8)
+    #set_default_font(root, font_name="Arial", size=8)
     root.geometry(f"{width}x{height}")
     root.title("Mask App")
     create_menu_bar(root)

spacr-0.1.50/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-0.1.50/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-0.1.12 → spacr-0.1.50}/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-0.1.12 → spacr-0.1.50}/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
 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):
+    def __init__(self, default_app=None):
         super().__init__()
         width = self.winfo_screenwidth()
         height = self.winfo_screenheight()
@@ -22,19 +17,31 @@ class MainApp(tk.Tk):
         self.title("SpaCr GUI Collection")
         self.configure(bg="black")
         style = ttk.Style()
-        style_text_boxes(style)
+        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.")
         }
 
         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])
+
     def create_widgets(self):
         # Create the menu bar
         create_menu_bar(self)
@@ -74,7 +81,8 @@ 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: self.load_app(app_name, app_func), font=('Helvetica', 12))
+            #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 = 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))
@@ -100,7 +108,6 @@ class MainApp(tk.Tk):
 
         try:
             img_path = os.path.join(os.path.dirname(__file__), 'logo_spacr.png')
-            print(f"Trying to load logo from {img_path}")
             logo_image = Image.open(img_path)
         except (FileNotFoundError, Image.UnidentifiedImageError):
             print(f"File {img_path} not found or is not a valid image. Attempting to download from GitHub.")
@@ -117,7 +124,9 @@ class MainApp(tk.Tk):
             print(f"An error occurred while loading the logo: {e}")
             return False
         try:
-            logo_image = logo_image.resize((800, 800), Image.Resampling.LANCZOS)
+            screen_height = frame.winfo_screenheight()
+            new_height = int(screen_height // 4)
+            logo_image = logo_image.resize((new_height, new_height), Image.Resampling.LANCZOS)
             logo_photo = ImageTk.PhotoImage(logo_image)
             logo_label = tk.Label(frame, image=logo_photo, bg="black")
             logo_label.image = logo_photo  # Keep a reference to avoid garbage collection
@@ -145,4 +154,5 @@ def gui_app():
     app.mainloop()
 
 if __name__ == "__main__":
-    gui_app()
+    set_start_method('spawn', force=True)
+    gui_app()