spacr 0.1.50__py3-none-any.whl → 0.1.61__py3-none-any.whl

spacr/__init__.py

@@ -14,11 +14,16 @@ from . import timelapse
 from . import deep_spacr
 from . import app_annotate
 from . import gui_utils
+from . import gui_elements
+from . import gui_core
+from . import gui_run
+from . import gui_wrappers
 from . import 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
 
 
@@ -36,10 +41,11 @@ __all__ = [
     "app_annotate",
     "gui_utils",
     "app_make_masks",
-    "app_make_masks_v2",
     "app_mask",
     "app_measure",
     "app_classify",
+    "app_sequencing",
+    "app_umap",
     "logger"
 ]
 

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, create_menu_bar, set_default_font
+from .gui_elements 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/app_make_masks.py

@@ -9,11 +9,8 @@ from skimage.transform import resize
 from scipy.ndimage import binary_fill_holes, label
 import tkinter as tk
 from tkinter import ttk
-from ttkthemes import ThemedTk
 
-from .logger import log_function_call
-
-from .gui_utils import ScrollableFrame, CustomButton, set_dark_style, create_menu_bar, set_default_font
+from .gui_elements import spacrFrame, spacrButton, set_dark_style, create_menu_bar, set_default_font
 
 class modify_masks:
 
@@ -869,7 +866,7 @@ 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 +894,7 @@ 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/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, create_dark_mode, create_menu_bar, set_default_font
+from .gui_utils import spacrFrame, spacrButton, set_dark_style, create_menu_bar, set_default_font
 
 class ModifyMasks:
     def __init__(self, root, folder_path, scale_factor):
@@ -635,7 +635,7 @@ def initiate_mask_app_root(width, height):
     root = ThemedTk(theme=theme)
     style = ttk.Style(root)
     set_dark_style(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)
@@ -643,7 +643,7 @@ def initiate_mask_app_root(width, height):
     container = tk.PanedWindow(root, 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")
 
     vars_dict = {
@@ -673,7 +673,7 @@ def initiate_mask_app_root(width, height):
 
     create_dark_mode(root, style, console_output=None)
 
-    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 root

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/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/core.py

@@ -1668,7 +1668,7 @@ def preprocess_generate_masks(src, settings={}):
 
     from .io import preprocess_img_data, _load_and_concatenate_arrays
     from .plot import plot_merged, plot_arrays
-    from .utils import _pivot_counts_table, check_mask_folder, adjust_cell_masks, _merge_cells_based_on_parasite_overlap, process_masks
+    from .utils import _pivot_counts_table, check_mask_folder, adjust_cell_masks
     from .settings import set_default_settings_preprocess_generate_masks, set_default_plot_merge_settings
     
     settings = set_default_settings_preprocess_generate_masks(src, settings)
@@ -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/gui.py

@@ -1,10 +1,10 @@
 import tkinter as tk
 from tkinter import ttk
 from PIL import Image, ImageTk
-import os
-import requests
+import os, requests
 from multiprocessing import set_start_method
-from .gui_utils import set_dark_style, create_menu_bar, initiate_root
+from .gui_elements import spacrButton, create_menu_bar, set_dark_style
+from .gui_core import initiate_root
 from .app_annotate import initiate_annotation_app_root
 from .app_make_masks import initiate_mask_app_root
 
@@ -24,7 +24,9 @@ class MainApp(tk.Tk):
             "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": (lambda frame: initiate_root(frame, 'classify'), "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()
@@ -41,6 +43,10 @@ class MainApp(tk.Tk):
             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
@@ -81,8 +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 = 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 = 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))