spacr 0.1.12__tar.gz → 0.1.16__tar.gz

{spacr-0.1.12/spacr.egg-info → spacr-0.1.16}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: spacr
-Version: 0.1.12
+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: headless
 Requires-Dist: opencv-python-headless; extra == "headless"
 Provides-Extra: full
@@ -67,7 +62,7 @@ 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 +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-0.1.12 → spacr-0.1.16}/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-0.1.16}/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 +44,12 @@ 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'
 ]
 
 setup(
     name="spacr",
-    version="0.1.12",
+    version="0.1.16",
     author="Einar Birnir Olafsson",
     author_email="olafsson@med.umich.com",
     description="Spatial phenotype analysis of crisp screens (SpaCr)",
@@ -73,18 +61,17 @@ 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:gui_mask',
+            'measure=spacr.app_measure:gui_measure',
+            'make_masks=spacr.app_make_mask:gui_make_masks',
+            'annotate=spacr.app_annotate:gui_annotate',
+            'classify=spacr.app_classify:gui_classify',
+            '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 +80,32 @@ 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-0.1.16}/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, set_default_font, set_dark_style, create_menu_bar
 
 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-0.1.12 → spacr-0.1.16}/spacr/app_classify.py

@@ -15,8 +15,9 @@ except AttributeError:
     pass
 
 from .logger import log_function_call
-from .gui_utils import ScrollableFrame, StdoutRedirector, CustomButton, set_dark_style, set_default_font, generate_fields, process_stdout_stderr, clear_canvas, main_thread_update_function
-from .gui_utils import classify_variables, check_classify_gui_settings, train_test_model_wrapper, read_settings_from_csv, update_settings_from_csv, style_text_boxes, create_menu_bar
+from .settings import set_default_train_test_model
+from .gui_utils import ScrollableFrame, StdoutRedirector, CustomButton, set_dark_style, set_default_font, generate_fields, process_stdout_stderr, clear_canvas, main_thread_update_function, convert_settings_dict_for_gui
+from .gui_utils import check_classify_gui_settings, train_test_model_wrapper, read_settings_from_csv, update_settings_from_csv, set_dark_style, create_menu_bar
 
 thread_control = {"run_thread": None, "stop_requested": False}
 
@@ -64,7 +65,8 @@ def import_settings(scrollable_frame):
 
     csv_file_path = filedialog.askopenfilename(filetypes=[("CSV files", "*.csv")])
     csv_settings = read_settings_from_csv(csv_file_path)
-    variables = classify_variables()
+    settings = set_default_train_test_model({})
+    variables = convert_settings_dict_for_gui(settings)
     new_settings = update_settings_from_csv(variables, csv_settings)
     vars_dict = generate_fields(new_settings, scrollable_frame)
 
@@ -74,7 +76,6 @@ def initiate_classify_root(parent_frame):
     
     style = ttk.Style(parent_frame)
     set_dark_style(style)
-    style_text_boxes(style)
     set_default_font(parent_frame, font_name="Helvetica", size=8)
 
     parent_frame.configure(bg='black')
@@ -121,24 +122,28 @@ def initiate_classify_root(parent_frame):
     vertical_container.add(settings_frame, stretch="always")
     settings_label = ttk.Label(settings_frame, text="Settings", background="black", foreground="white")
     settings_label.grid(row=0, column=0, pady=10, padx=10)
-    scrollable_frame = ScrollableFrame(settings_frame, width=500)
+    scrollable_frame = ScrollableFrame(settings_frame, bg='black')
     scrollable_frame.grid(row=1, column=0, sticky="nsew")
     settings_frame.grid_rowconfigure(1, weight=1)
     settings_frame.grid_columnconfigure(0, weight=1)
 
     # Setup for user input fields (variables)
-    variables = classify_variables()
+    settings = set_default_train_test_model({})
+    variables = convert_settings_dict_for_gui(settings)
     vars_dict = generate_fields(variables, scrollable_frame)
 
     # Button section
-    import_btn = CustomButton(scrollable_frame.scrollable_frame, text="Import", command=lambda: import_settings(scrollable_frame), font=('Helvetica', 10))
-    import_btn.grid(row=47, column=0, pady=20, padx=20)
+    btn_row = 1
     run_button = CustomButton(scrollable_frame.scrollable_frame, text="Run", command=lambda: start_process(q, fig_queue), font=('Helvetica', 10))
-    run_button.grid(row=45, column=0, pady=20, padx=20)
+    run_button.grid(row=btn_row, column=0, pady=20, padx=20)
     abort_button = CustomButton(scrollable_frame.scrollable_frame, text="Abort", command=initiate_abort, font=('Helvetica', 10))
-    abort_button.grid(row=45, column=1, pady=20, padx=20)
+    abort_button.grid(row=btn_row, column=1, pady=20, padx=20)
+    btn_row += 1
+    import_btn = CustomButton(scrollable_frame.scrollable_frame, text="Import", command=lambda: import_settings(scrollable_frame), font=('Helvetica', 10))
+    import_btn.grid(row=btn_row, column=0, pady=20, padx=20)
+    btn_row += 1
     progress_label = ttk.Label(scrollable_frame.scrollable_frame, text="Processing: 0%", background="black", foreground="white") # Create progress field
-    progress_label.grid(row=50, column=0, columnspan=2, sticky="ew", pady=(5, 0), padx=10)
+    progress_label.grid(row=btn_row, column=0, columnspan=2, sticky="ew", pady=(5, 0), padx=10)
 
     # Plot Canvas Section
     plot_frame = tk.PanedWindow(vertical_container, orient=tk.VERTICAL)

{spacr-0.1.12 → spacr-0.1.16}/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, set_default_font, set_dark_style, create_menu_bar
 
 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-0.1.16}/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, set_default_font, create_dark_mode, set_dark_style, create_menu_bar
 
 class ModifyMasks:
     def __init__(self, root, folder_path, scale_factor):
@@ -635,8 +635,6 @@ 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)
     root.geometry(f"{width}x{height}")
     root.title("Mask App")

{spacr-0.1.12 → spacr-0.1.16}/spacr/app_mask.py

@@ -16,9 +16,10 @@ except AttributeError:
     pass
 
 from .logger import log_function_call
+from .settings import set_default_settings_preprocess_generate_masks
 from .gui_utils import ScrollableFrame, StdoutRedirector, ToggleSwitch, CustomButton, ToolTip
-from .gui_utils import clear_canvas, main_thread_update_function, set_dark_style, generate_fields, process_stdout_stderr, set_default_font, style_text_boxes
-from .gui_utils import mask_variables, check_mask_gui_settings, preprocess_generate_masks_wrapper, read_settings_from_csv, update_settings_from_csv, create_menu_bar
+from .gui_utils import clear_canvas, main_thread_update_function, set_dark_style, generate_fields, process_stdout_stderr, set_default_font, set_dark_style, convert_settings_dict_for_gui
+from .gui_utils import check_mask_gui_settings, preprocess_generate_masks_wrapper, read_settings_from_csv, update_settings_from_csv, create_menu_bar
 
 thread_control = {"run_thread": None, "stop_requested": False}
 
@@ -37,10 +38,9 @@ def toggle_test_mode():
 def toggle_advanced_settings():
     global vars_dict
 
-    timelapse_settings = ['timelapse', 'timelapse_memory', 'timelapse_remove_transient', 'timelapse_mode', 'timelapse_objects', 'timelapse_displacement', 'timelapse_frame_limits', 'fps']
-    misc_settings = ['examples_to_plot', 'all_to_mip', 'pick_slice', 'skip_mode']
-    opperational_settings = ['preprocess', 'masks', 'randomize', 'batch_size', 'custom_regex', 'merge', 'normalize_plots', 'workers', 'plot', 'remove_background', 'lower_quantile']
-
+    timelapse_settings = ['timelapse','fps','timelapse_displacement','timelapse_memory','timelapse_frame_limits','timelapse_remove_transient','timelapse_mode','timelapse_objects']
+    misc_settings = ['all_to_mip','pick_slice','skip_mode','upscale','upscale_factor','adjust_cells','lower_percentile','filter','merge_pathogens','pathogen_model']
+    opperational_settings = ['examples_to_plot','normalize_plots','normalize','cmap','figuresize','plot','pathogen_FT','cell_FT','nucleus_FT','nucleus_CP_prob','nucleus_Signal_to_noise','nucleus_background','cell_CP_prob','cell_Signal_to_noise','cell_background','pathogen_CP_prob','pathogen_Signal_to_noise','pathogen_background','remove_background_pathogen','remove_background_nucleus','remove_background_cell','verbose','randomize','workers','metadata_type','custom_regex','test_images','batch_size','save','masks','preprocess']
     advanced_settings = timelapse_settings+misc_settings+opperational_settings
 
     # Toggle visibility of advanced settings
@@ -94,7 +94,8 @@ def import_settings(scrollable_frame):
 
     csv_file_path = filedialog.askopenfilename(filetypes=[("CSV files", "*.csv")])
     csv_settings = read_settings_from_csv(csv_file_path)
-    variables = mask_variables()
+    settings = set_default_settings_preprocess_generate_masks({})
+    variables = convert_settings_dict_for_gui(settings)
     new_settings = update_settings_from_csv(variables, csv_settings)
     vars_dict = generate_fields(new_settings, scrollable_frame)
 
@@ -104,7 +105,6 @@ def initiate_mask_root(parent_frame):
 
     style = ttk.Style(parent_frame)
     set_dark_style(style)
-    style_text_boxes(style)
     set_default_font(parent_frame, font_name="Helvetica", size=8)
     parent_frame.configure(bg='black')
     parent_frame.grid_rowconfigure(0, weight=1)
@@ -151,7 +151,7 @@ def initiate_mask_root(parent_frame):
     for widget in parent_frame.winfo_children():
         widget.destroy()
 
-    vertical_container = tk.PanedWindow(parent_frame, orient=tk.HORIZONTAL)
+    vertical_container = tk.PanedWindow(parent_frame, orient=tk.HORIZONTAL, bg='black')
     vertical_container.grid(row=0, column=0, sticky=tk.NSEW)
     parent_frame.grid_rowconfigure(0, weight=1)
     parent_frame.grid_columnconfigure(0, weight=1)
@@ -159,9 +159,9 @@ def initiate_mask_root(parent_frame):
     # Settings Section
     settings_frame = tk.Frame(vertical_container, bg='black')
     vertical_container.add(settings_frame, stretch="always")
-    settings_label = ttk.Label(settings_frame, text="Settings", style="Custom.TLabel")
+    settings_label = ttk.Label(settings_frame, text="Settings", style="Custom.TLabel", background="black", foreground="white")
     settings_label.grid(row=0, column=0, pady=10, padx=10)
-    scrollable_frame = ScrollableFrame(settings_frame, width=600)
+    scrollable_frame = ScrollableFrame(settings_frame, bg='black')
     scrollable_frame.grid(row=1, column=0, sticky="nsew")
     settings_frame.grid_rowconfigure(1, weight=1)
     settings_frame.grid_columnconfigure(0, weight=1)
@@ -169,25 +169,27 @@ def initiate_mask_root(parent_frame):
     # Create advanced settings checkbox
     advanced_var = tk.BooleanVar(value=False)
     advanced_Toggle = ToggleSwitch(scrollable_frame.scrollable_frame, text="Advanced Settings", variable=advanced_var, command=toggle_advanced_settings)
-    advanced_Toggle.grid(row=48, column=0, pady=10, padx=10)
-    variables = mask_variables()
+    advanced_Toggle.grid(row=4, column=0, pady=10, padx=10)
+    settings = set_default_settings_preprocess_generate_masks({})
+    variables = convert_settings_dict_for_gui(settings)
     vars_dict = generate_fields(variables, scrollable_frame)
     toggle_advanced_settings()
     vars_dict['Test mode'] = (None, None, tk.BooleanVar(value=False))
-    
-    # Button section
-    test_mode_button = CustomButton(scrollable_frame.scrollable_frame, text="Test Mode", command=toggle_test_mode, font=('Helvetica', 10))
-    #CustomButton(buttons_frame, text=app_name, command=lambda app_name=app_name: self.load_app(app_name, app_func), font=('Helvetica', 12))
 
-    test_mode_button.grid(row=47, column=1, pady=10, padx=10)
-    import_btn = CustomButton(scrollable_frame.scrollable_frame, text="Import", command=lambda: import_settings(scrollable_frame), font=('Helvetica', 10))
-    import_btn.grid(row=47, column=0, pady=10, padx=10)
+    # Button section
+    btn_row = 1
     run_button = CustomButton(scrollable_frame.scrollable_frame, text="Run", command=lambda: start_process(q, fig_queue))
-    run_button.grid(row=45, column=0, pady=10, padx=10)
+    run_button.grid(row=btn_row, column=0, pady=5, padx=5)
     abort_button = CustomButton(scrollable_frame.scrollable_frame, text="Abort", command=initiate_abort, font=('Helvetica', 10))
-    abort_button.grid(row=45, column=1, pady=10, padx=10)
+    abort_button.grid(row=btn_row, column=1, pady=5, padx=5)
+    btn_row += 1
+    test_mode_button = CustomButton(scrollable_frame.scrollable_frame, text="Test", command=toggle_test_mode, font=('Helvetica', 10))
+    test_mode_button.grid(row=btn_row, column=0, pady=5, padx=5)
+    import_btn = CustomButton(scrollable_frame.scrollable_frame, text="Import", command=lambda: import_settings(scrollable_frame), font=('Helvetica', 10))
+    import_btn.grid(row=btn_row, column=1, pady=5, padx=5)
+    btn_row += 1
     progress_label = ttk.Label(scrollable_frame.scrollable_frame, text="Processing: 0%", background="black", foreground="white")
-    progress_label.grid(row=50, column=0, columnspan=2, sticky="ew", pady=(5, 0), padx=10)
+    progress_label.grid(row=btn_row, column=0, columnspan=2, sticky="ew", pady=(5, 0), padx=10)
 
     # Plot Canvas Section
     plot_frame = tk.PanedWindow(vertical_container, orient=tk.VERTICAL)

{spacr-0.1.12 → spacr-0.1.16}/spacr/app_measure.py

@@ -13,9 +13,10 @@ except AttributeError:
     pass
 
 from .logger import log_function_call
-from .gui_utils import ScrollableFrame, StdoutRedirector, CustomButton, ToggleSwitch, ToolTip
-from .gui_utils import process_stdout_stderr, set_dark_style, set_default_font, generate_fields, main_thread_update_function, create_menu_bar
-from .gui_utils import measure_variables, measure_crop_wrapper, clear_canvas, check_measure_gui_settings, read_settings_from_csv, update_settings_from_csv, style_text_boxes
+from .settings import get_measure_crop_settings
+from .gui_utils import ScrollableFrame, StdoutRedirector, CustomButton, ToggleSwitch
+from .gui_utils import process_stdout_stderr, set_dark_style, set_default_font, generate_fields, main_thread_update_function, create_menu_bar, convert_settings_dict_for_gui
+from .gui_utils import measure_crop_wrapper, clear_canvas, check_measure_gui_settings, read_settings_from_csv, update_settings_from_csv, set_dark_style
 
 thread_control = {"run_thread": None, "stop_requested": False}
 
@@ -24,7 +25,8 @@ def import_settings(scrollable_frame):
 
     csv_file_path = filedialog.askopenfilename(filetypes=[("CSV files", "*.csv")])
     csv_settings = read_settings_from_csv(csv_file_path)
-    variables = measure_variables()
+    settings = get_measure_crop_settings({})
+    variables = convert_settings_dict_for_gui(settings)
     new_settings = update_settings_from_csv(variables, csv_settings)
     vars_dict = generate_fields(new_settings, scrollable_frame)
 
@@ -102,7 +104,6 @@ def initiate_measure_root(parent_frame):
     
     style = ttk.Style(parent_frame)
     set_dark_style(style)
-    style_text_boxes(style)
     set_default_font(parent_frame, font_name="Helvetica", size=8)
 
     parent_frame.configure(bg='black')
@@ -160,7 +161,7 @@ def initiate_measure_root(parent_frame):
     vertical_container.add(settings_frame, stretch="always")
     settings_label = ttk.Label(settings_frame, text="Settings", background="black", foreground="white")
     settings_label.grid(row=0, column=0, pady=10, padx=10)
-    scrollable_frame = ScrollableFrame(settings_frame, width=500)
+    scrollable_frame = ScrollableFrame(settings_frame, bg='black')
     scrollable_frame.grid(row=1, column=0, sticky="nsew")
     settings_frame.grid_rowconfigure(1, weight=1)
     settings_frame.grid_columnconfigure(0, weight=1)
@@ -168,23 +169,27 @@ def initiate_measure_root(parent_frame):
     # Create advanced settings checkbox
     advanced_var = tk.BooleanVar(value=False)
     advanced_Toggle = ToggleSwitch(scrollable_frame.scrollable_frame, text="Advanced Settings", variable=advanced_var, command=toggle_advanced_settings)
-    advanced_Toggle.grid(row=48, column=0, pady=10, padx=10)
-    variables = measure_variables()
+    advanced_Toggle.grid(row=4, column=0, pady=10, padx=10)
+    settings = get_measure_crop_settings({})
+    variables = convert_settings_dict_for_gui(settings)
     vars_dict = generate_fields(variables, scrollable_frame)
     toggle_advanced_settings()
     vars_dict['Test mode'] = (None, None, tk.BooleanVar(value=False))
     
     # Button section
-    test_mode_button = CustomButton(scrollable_frame.scrollable_frame, text="Test Mode", command=toggle_test_mode)
-    test_mode_button.grid(row=47, column=1, pady=10, padx=10)
-    import_btn = CustomButton(scrollable_frame.scrollable_frame, text="Import", command=lambda: import_settings(scrollable_frame), font=('Helvetica', 10))
-    import_btn.grid(row=47, column=0, pady=20, padx=20)
+    btn_row = 1
     run_button = CustomButton(scrollable_frame.scrollable_frame, text="Run", command=lambda: start_process(q, fig_queue), font=('Helvetica', 10))
-    run_button.grid(row=45, column=0, pady=20, padx=20)
+    run_button.grid(row=btn_row, column=0, pady=5, padx=5)
     abort_button = CustomButton(scrollable_frame.scrollable_frame, text="Abort", command=initiate_abort, font=('Helvetica', 10))
-    abort_button.grid(row=45, column=1, pady=20, padx=20)
+    abort_button.grid(row=btn_row, column=1, pady=5, padx=5)
+    btn_row += 1
+    test_mode_button = CustomButton(scrollable_frame.scrollable_frame, text="Test Mode", command=toggle_test_mode)
+    test_mode_button.grid(row=btn_row, column=0, pady=5, padx=5)
+    import_btn = CustomButton(scrollable_frame.scrollable_frame, text="Import", command=lambda: import_settings(scrollable_frame), font=('Helvetica', 10))
+    import_btn.grid(row=btn_row, column=1, pady=5, padx=5)
+    btn_row += 1
     progress_label = ttk.Label(scrollable_frame.scrollable_frame, text="Processing: 0%", background="black", foreground="white") # Create progress field
-    progress_label.grid(row=50, column=0, columnspan=2, sticky="ew", pady=(5, 0), padx=10)
+    progress_label.grid(row=btn_row, column=0, columnspan=2, sticky="ew", pady=(5, 0), padx=10)
 
     # Plot Canvas Section
     plot_frame = tk.PanedWindow(vertical_container, orient=tk.VERTICAL)

{spacr-0.1.12 → spacr-0.1.16}/spacr/gui.py

@@ -11,7 +11,7 @@ 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_utils import CustomButton, style_text_boxes, create_menu_bar
+from .gui_utils import CustomButton, set_dark_style, create_menu_bar
 
 class MainApp(tk.Tk):
     def __init__(self):
@@ -22,7 +22,7 @@ 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."),
@@ -74,7 +74,7 @@ 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.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 +100,6 @@ 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 +116,9 @@ 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

{spacr-0.1.12 → spacr-0.1.16}/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:
@@ -147,7 +146,6 @@ def load_app(root, app_name, app_func):
     else:
         proceed_with_app(root, app_name, app_func)
 
-
 def create_menu_bar(root):
     from .app_mask import initiate_mask_root
     from .app_measure import initiate_measure_root
@@ -188,14 +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)
@@ -333,38 +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"
@@ -382,8 +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)
@@ -397,32 +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('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='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.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='black', 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 = {}
@@ -461,36 +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):
@@ -793,7 +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':
@@ -806,10 +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'),
@@ -819,14 +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),
@@ -842,7 +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),
@@ -851,6 +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
 
@@ -871,7 +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",
@@ -993,12 +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-0.1.12 → spacr-0.1.16/spacr.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: spacr
-Version: 0.1.12
+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: headless
 Requires-Dist: opencv-python-headless; extra == "headless"
 Provides-Extra: full
@@ -67,7 +62,7 @@ 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 +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-0.1.16/spacr.egg-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-0.1.12 → spacr-0.1.16}/spacr.egg-info/requires.txt

@@ -1,4 +1,3 @@
-dgl==0.9.1
 torch<3.0,>=2.2.1
 torchvision<1.0,>=0.17.1
 torch-geometric<3.0,>=2.5.1
@@ -29,13 +28,9 @@ ttf_opensans>=2020.10.30
 customtkinter<6.0,>=5.2.2
 biopython<2.0,>=1.80
 lxml<6.0,>=5.1.0
-qtpy<2.5,>=2.4.1
-superqt<0.7,>=0.6.7
-pyqt6<6.8,>=6.7.1
-pyqtgraph<0.14,>=0.13.7
 
 [dev]
-pytest>=3.9
+pytest<3.11,>=3.9
 
 [full]
 opencv-python

spacr-0.1.12/spacr.egg-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