spacr 0.1.75__py3-none-any.whl → 0.1.77__py3-none-any.whl

spacr/app_annotate.py

@@ -41,8 +41,7 @@ def initiate_annotation_app(parent_frame):
         settings_window.destroy()
         annotate_app(parent_frame, settings)
     
-    #start_button = spacrButton(settings_window, text="Start Annotation", command=lambda: start_annotation_app, font=('Helvetica', 12))
-    start_button = tk.Button(settings_window, text="Start Annotation", command=start_annotation_app)
+    start_button = tk.Button(settings_window, text="Start Annotation", command=start_annotation_app, bg='black', fg='white')
     start_button.pack(pady=10)
 
 def start_annotate_app():

spacr/core.py

@@ -971,7 +971,7 @@ def generate_dataset(src, file_metadata=None, experiment='TSG101_screen', sample
     shutil.rmtree(temp_dir)
     print(f"\nSaved {total_images} images to {tar_name}")
 
-def apply_model_to_tar(tar_path, model_path, file_type='cell_png', image_size=224, batch_size=64, normalize=True, preload='images', n_job=10, threshold=0.5, verbose=False):
+def apply_model_to_tar(tar_path, model_path, file_type='cell_png', image_size=224, batch_size=64, normalize=True, preload='images', n_jobs=10, threshold=0.5, verbose=False):
     
     from .io import TarImageDataset
     from .utils import process_vision_results
@@ -994,7 +994,7 @@ def apply_model_to_tar(tar_path, model_path, file_type='cell_png', image_size=22
     model = torch.load(model_path)
     
     dataset = TarImageDataset(tar_path, transform=transform)
-    data_loader = DataLoader(dataset, batch_size=batch_size, shuffle=True, n_job=n_job, pin_memory=True)
+    data_loader = DataLoader(dataset, batch_size=batch_size, shuffle=True, num_workers=n_jobs, pin_memory=True)
     
     model_name = os.path.splitext(os.path.basename(model_path))[0] 
     dataset_name = os.path.splitext(os.path.basename(tar_path))[0]  
@@ -1034,7 +1034,7 @@ def apply_model_to_tar(tar_path, model_path, file_type='cell_png', image_size=22
     torch.cuda.memory.empty_cache()
     return df
 
-def apply_model(src, model_path, image_size=224, batch_size=64, normalize=True, n_job=10):
+def apply_model(src, model_path, image_size=224, batch_size=64, normalize=True, n_jobs=10):
     
     from .io import NoClassDataset
     
@@ -1055,7 +1055,7 @@ def apply_model(src, model_path, image_size=224, batch_size=64, normalize=True,
     
     print(f'Loading dataset in {src} with {len(src)} images')
     dataset = NoClassDataset(data_dir=src, transform=transform, shuffle=True, load_to_memory=False)
-    data_loader = DataLoader(dataset, batch_size=batch_size, shuffle=True, n_job=n_job)
+    data_loader = DataLoader(dataset, batch_size=batch_size, shuffle=True, num_workers=n_jobs)
     print(f'Loaded {len(src)} images')
     
     result_loc = os.path.splitext(model_path)[0]+datetime.date.today().strftime('%y%m%d')+'_'+os.path.splitext(model_path)[1]+'_test_result.csv'
@@ -1302,7 +1302,7 @@ def generate_training_dataset(src, mode='annotation', annotation_column='test',
     
     return
 
-def generate_loaders(src, train_mode='erm', mode='train', image_size=224, batch_size=32, classes=['nc','pc'], n_job=None, validation_split=0.0, max_show=2, pin_memory=False, normalize=False, channels=[1, 2, 3], augment=False, verbose=False):
+def generate_loaders(src, train_mode='erm', mode='train', image_size=224, batch_size=32, classes=['nc','pc'], n_jobs=None, validation_split=0.0, max_show=2, pin_memory=False, normalize=False, channels=[1, 2, 3], augment=False, verbose=False):
     
     """
     Generate data loaders for training and validation/test datasets.
@@ -1314,7 +1314,7 @@ def generate_loaders(src, train_mode='erm', mode='train', image_size=224, batch_
     - image_size (int): The size of the input images.
     - batch_size (int): The batch size for the data loaders.
     - classes (list): The list of classes to consider.
-    - n_job (int): The number of worker threads for data loading.
+    - n_jobs (int): The number of worker threads for data loading.
     - validation_split (float): The fraction of data to use for validation when train_mode is 'erm'.
     - max_show (int): The maximum number of images to show when verbose is True.
     - pin_memory (bool): Whether to pin memory for faster data transfer.
@@ -1404,10 +1404,10 @@ def generate_loaders(src, train_mode='erm', mode='train', image_size=224, batch_
                 #val_dataset = augment_dataset(val_dataset, is_grayscale=(len(channels) == 1))
                 print(f'Data after augmentation: Train: {len(train_dataset)}')#, Validataion:{len(val_dataset)}')
 
-            train_loaders = DataLoader(train_dataset, batch_size=batch_size, shuffle=shuffle, n_job=n_job if n_job is not None else 0, pin_memory=pin_memory)
-            val_loaders = DataLoader(val_dataset, batch_size=batch_size, shuffle=shuffle, n_job=n_job if n_job is not None else 0, pin_memory=pin_memory)
+            train_loaders = DataLoader(train_dataset, batch_size=batch_size, shuffle=shuffle, num_workers=n_jobs if n_jobs is not None else 0, pin_memory=pin_memory)
+            val_loaders = DataLoader(val_dataset, batch_size=batch_size, shuffle=shuffle, num_workers=n_jobs if n_jobs is not None else 0, pin_memory=pin_memory)
         else:
-            train_loaders = DataLoader(data, batch_size=batch_size, shuffle=shuffle, n_job=n_job if n_job is not None else 0, pin_memory=pin_memory)
+            train_loaders = DataLoader(data, batch_size=batch_size, shuffle=shuffle, num_workers=n_jobs if n_jobs is not None else 0, pin_memory=pin_memory)
         
     elif train_mode == 'irm':
         data = MyDataset(data_dir, classes, transform=transform, shuffle=shuffle, pin_memory=pin_memory)
@@ -1436,13 +1436,13 @@ def generate_loaders(src, train_mode='erm', mode='train', image_size=224, batch_
                     #val_dataset = augment_dataset(val_dataset, is_grayscale=(len(channels) == 1))
                     print(f'Data after augmentation: Train: {len(train_dataset)}')#, Validataion:{len(val_dataset)}')
 
-                train_loader = DataLoader(train_dataset, batch_size=batch_size, shuffle=shuffle, n_job=n_job if n_job is not None else 0, pin_memory=pin_memory)
-                val_loader = DataLoader(val_dataset, batch_size=batch_size, shuffle=shuffle, n_job=n_job if n_job is not None else 0, pin_memory=pin_memory)
+                train_loader = DataLoader(train_dataset, batch_size=batch_size, shuffle=shuffle, num_workers=n_jobs if n_jobs is not None else 0, pin_memory=pin_memory)
+                val_loader = DataLoader(val_dataset, batch_size=batch_size, shuffle=shuffle, num_workers=n_jobs if n_jobs is not None else 0, pin_memory=pin_memory)
 
                 train_loaders.append(train_loader)
                 val_loaders.append(val_loader)
             else:
-                train_loader = DataLoader(plate_data, batch_size=batch_size, shuffle=shuffle, n_job=n_job if n_job is not None else 0, pin_memory=pin_memory)
+                train_loader = DataLoader(plate_data, batch_size=batch_size, shuffle=shuffle, num_workers=n_jobs if n_jobs is not None else 0, pin_memory=pin_memory)
                 train_loaders.append(train_loader)
                 val_loaders.append(None)
     
@@ -2078,11 +2078,11 @@ def identify_masks(src, object_type, model_name, batch_size, channels, diameter,
                             else:
                                 radius = 100
 
-                            n_job = os.cpu_count()-2
-                            if n_job < 1:
-                                n_job = 1
+                            n_jobs = os.cpu_count()-2
+                            if n_jobs < 1:
+                                n_jobs = 1
 
-                            mask_stack = _btrack_track_cells(src, name, batch_filenames, object_type, plot, save, masks_3D=masks, mode=timelapse_mode, timelapse_remove_transient=timelapse_remove_transient, radius=radius, n_job=n_job)
+                            mask_stack = _btrack_track_cells(src, name, batch_filenames, object_type, plot, save, masks_3D=masks, mode=timelapse_mode, timelapse_remove_transient=timelapse_remove_transient, radius=radius, n_jobs=n_jobs)
                         if timelapse_mode == 'trackpy':
                             mask_stack = _trackpy_track_cells(src, name, batch_filenames, object_type, masks, timelapse_displacement, timelapse_memory, timelapse_remove_transient, plot, save, timelapse_mode)
                             
@@ -2303,9 +2303,9 @@ def generate_cellpose_masks(src, settings, object_type):
                         else:
                             radius = 100
 
-                        n_job = os.cpu_count()-2
-                        if n_job < 1:
-                            n_job = 1
+                        n_jobs = os.cpu_count()-2
+                        if n_jobs < 1:
+                            n_jobs = 1
 
                         mask_stack = _btrack_track_cells(src=src,
                                                          name=name,
@@ -2317,7 +2317,7 @@ def generate_cellpose_masks(src, settings, object_type):
                                                          mode=timelapse_mode,
                                                          timelapse_remove_transient=timelapse_remove_transient,
                                                          radius=radius,
-                                                         n_job=n_job)
+                                                         n_jobs=n_jobs)
                     if timelapse_mode == 'trackpy':
                         mask_stack = _trackpy_track_cells(src=src,
                                                           name=name,
@@ -2551,7 +2551,7 @@ def compare_cellpose_masks(src, verbose=False, processes=None, save=True):
         common_files.intersection_update(os.listdir(d))
     common_files = list(common_files)
 
-    # Create a pool of n_job
+    # Create a pool of n_jobs
     with Pool(processes=processes) as pool:
         args = [(src, filename, dirs, conditions) for filename in common_files]
         results = pool.map(compare_mask, args)

spacr/deep_spacr.py

@@ -230,7 +230,7 @@ def train_test_model(src, settings, custom_model=False, custom_model_path=None):
                                                     image_size=settings['image_size'],
                                                     batch_size=settings['batch_size'], 
                                                     classes=settings['classes'], 
-                                                    n_job=settings['n_job'],
+                                                    n_jobs=settings['n_jobs'],
                                                     validation_split=settings['val_split'],
                                                     pin_memory=settings['pin_memory'],
                                                     normalize=settings['normalize'],
@@ -255,7 +255,7 @@ def train_test_model(src, settings, custom_model=False, custom_model_path=None):
                             optimizer_type = settings['optimizer_type'], 
                             use_checkpoint = settings['use_checkpoint'], 
                             dropout_rate = settings['dropout_rate'], 
-                            n_job = settings['n_job'], 
+                            n_jobs = settings['n_jobs'], 
                             val_loaders = val, 
                             test_loaders = None, 
                             intermedeate_save = settings['intermedeate_save'],
@@ -276,7 +276,7 @@ def train_test_model(src, settings, custom_model=False, custom_model_path=None):
                                                      image_size=settings['image_size'],
                                                      batch_size=settings['batch_size'], 
                                                      classes=settings['classes'], 
-                                                     n_job=settings['n_job'],
+                                                     n_jobs=settings['n_jobs'],
                                                      validation_split=0.0,
                                                      pin_memory=settings['pin_memory'],
                                                      normalize=settings['normalize'],
@@ -315,7 +315,7 @@ def train_test_model(src, settings, custom_model=False, custom_model_path=None):
     torch.cuda.memory.empty_cache()
     gc.collect()
     
-def train_model(dst, model_type, train_loaders, train_loader_names, train_mode='erm', epochs=100, learning_rate=0.0001, weight_decay=0.05, amsgrad=False, optimizer_type='adamw', use_checkpoint=False, dropout_rate=0, n_job=20, val_loaders=None, test_loaders=None, init_weights='imagenet', intermedeate_save=None, chan_dict=None, schedule = None, loss_type='binary_cross_entropy_with_logits', gradient_accumulation=False, gradient_accumulation_steps=4, channels=['r','g','b']):
+def train_model(dst, model_type, train_loaders, train_loader_names, train_mode='erm', epochs=100, learning_rate=0.0001, weight_decay=0.05, amsgrad=False, optimizer_type='adamw', use_checkpoint=False, dropout_rate=0, n_jobs=20, val_loaders=None, test_loaders=None, init_weights='imagenet', intermedeate_save=None, chan_dict=None, schedule = None, loss_type='binary_cross_entropy_with_logits', gradient_accumulation=False, gradient_accumulation_steps=4, channels=['r','g','b']):
     """
     Trains a model using the specified parameters.
 
@@ -332,7 +332,7 @@ def train_model(dst, model_type, train_loaders, train_loader_names, train_mode='
         optimizer_type (str, optional): The type of optimizer to use. Defaults to 'adamw'.
         use_checkpoint (bool, optional): Whether to use checkpointing during training. Defaults to False.
         dropout_rate (float, optional): The dropout rate for the model. Defaults to 0.
-        n_job (int, optional): The number of n_job for data loading. Defaults to 20.
+        n_jobs (int, optional): The number of n_jobs for data loading. Defaults to 20.
         val_loaders (list, optional): A list of validation data loaders. Defaults to None.
         test_loaders (list, optional): A list of test data loaders. Defaults to None.
         init_weights (str, optional): The initialization weights for the model. Defaults to 'imagenet'.
@@ -357,7 +357,7 @@ def train_model(dst, model_type, train_loaders, train_loader_names, train_mode='
         
     use_cuda = torch.cuda.is_available()
     device = torch.device("cuda" if use_cuda else "cpu")
-    kwargs = {'n_job': n_job, 'pin_memory': True} if use_cuda else {}
+    kwargs = {'n_jobs': n_jobs, 'pin_memory': True} if use_cuda else {}
     
     for idx, (images, labels, filenames) in enumerate(train_loaders):
         batch, chans, height, width = images.shape

spacr/gui_core.py

@@ -192,15 +192,19 @@ def convert_settings_dict_for_gui(settings):
             variables[key] = ('entry', None, str(value))
     return variables
 
-def setup_settings_panel(vertical_container, settings_type='mask', frame_height=500, frame_width=1000):
+def setup_settings_panel(vertical_container, settings_type='mask', window_dimensions=[500, 1000]):
     global vars_dict, scrollable_frame
-    from .settings import set_default_settings_preprocess_generate_masks, get_measure_crop_settings, set_default_train_test_model, get_analyze_reads_default_settings, set_default_umap_image_settings, generate_fields
+    from .settings import set_default_settings_preprocess_generate_masks, get_measure_crop_settings, set_default_train_test_model, get_analyze_reads_default_settings, set_default_umap_image_settings, generate_fields, descriptions
 
-    settings_frame = tk.Frame(vertical_container, bg='black', height=frame_height, width=frame_width)
+    width = (window_dimensions[0])//6
+    height = window_dimensions[1]
+
+    # Settings Frame
+    settings_frame = tk.Frame(vertical_container, bg='black', height=height, width=width)
     vertical_container.add(settings_frame, stretch="always")
     settings_label = spacrLabel(settings_frame, text="Settings", background="black", foreground="white", anchor='center', justify='center', align="center")
     settings_label.grid(row=0, column=0, pady=10, padx=10)
-    scrollable_frame = spacrFrame(settings_frame, bg='black', width=frame_width)
+    scrollable_frame = spacrFrame(settings_frame, bg='black', width=width)
     scrollable_frame.grid(row=1, column=0, sticky="nsew")
     settings_frame.grid_rowconfigure(1, weight=1)
     settings_frame.grid_columnconfigure(0, weight=1)
@@ -351,18 +355,21 @@ def download_dataset(repo_id, subfolder, local_dir=None, retries=5, delay=5):
 
     raise Exception("Failed to download files after multiple attempts.")
 
-def setup_button_section(horizontal_container, settings_type='mask', settings_row=5, run=True, abort=True, download=True, import_btn=True):
+def setup_button_section(horizontal_container, settings_type='mask',  window_dimensions=[500, 1000], run=True, abort=True, download=True, import_btn=True):
     global button_frame, button_scrollable_frame, run_button, abort_button, download_dataset_button, import_button, q, fig_queue, vars_dict
+    from .settings import descriptions
+
+    width = (window_dimensions[0])//8
+    height = window_dimensions[1]
 
-    button_frame = tk.Frame(horizontal_container, bg='black')
+    button_frame = tk.Frame(horizontal_container, bg='black', height=height, width=width)
     horizontal_container.add(button_frame, stretch="always", sticky="nsew")
     button_frame.grid_rowconfigure(0, weight=0)
     button_frame.grid_rowconfigure(1, weight=1)
     button_frame.grid_columnconfigure(0, weight=1)
 
-    categories_label = spacrLabel(button_frame, text="Categories", background="black", foreground="white", font=('Helvetica', 12), anchor='center', justify='center', align="center")  # Increase font size
+    categories_label = spacrLabel(button_frame, text="Categories", background="black", foreground="white", font=('Helvetica', 12), anchor='center', justify='center', align="center")
     categories_label.grid(row=0, column=0, pady=10, padx=10)
-
     button_scrollable_frame = spacrFrame(button_frame, bg='black')
     button_scrollable_frame.grid(row=1, column=0, sticky="nsew")
 
@@ -391,6 +398,15 @@ def setup_button_section(horizontal_container, settings_type='mask', settings_ro
     # Call toggle_settings after vars_dict is initialized
     if vars_dict is not None:
         toggle_settings(button_scrollable_frame)
+
+    # Description frame
+    description_frame = tk.Frame(horizontal_container, bg='black', height=height, width=width)
+    horizontal_container.add(description_frame, stretch="always", sticky="nsew")
+    description_label = tk.Label(description_frame, text="Module Description", bg='black', fg='white', anchor='nw', justify='left', wraplength=width//2-100)
+    description_label.pack(pady=10, padx=10)
+    description_text = descriptions.get(settings_type, "No description available for this module.")
+    description_label.config(text=description_text)
+
     return button_scrollable_frame
 
 def hide_all_settings(vars_dict, categories):
@@ -527,13 +543,18 @@ def setup_frame(parent_frame):
     return parent_frame, vertical_container, horizontal_container
 
 def initiate_root(parent, settings_type='mask'):
-    global q, fig_queue, parent_frame, scrollable_frame, button_frame, vars_dict, canvas, canvas_widget, progress_label, button_scrollable_frame
+    global q, fig_queue, parent_frame, scrollable_frame, button_frame, vars_dict, canvas, canvas_widget, progress_label, progress_output, button_scrollable_frame
     from .gui_utils import main_thread_update_function
     from .gui import gui_app
     set_start_method('spawn', force=True)
-    
     print("Initializing root with settings_type:", settings_type)
+
     parent_frame = parent
+    parent_frame.update_idletasks()
+    frame_width = int(parent_frame.winfo_width())
+    frame_height = int(parent_frame.winfo_height())
+    print(frame_width, frame_height)
+    dims = [frame_width, frame_height]
 
     if not hasattr(parent_frame, 'after_tasks'):
         parent_frame.after_tasks = []
@@ -555,13 +576,9 @@ def initiate_root(parent, settings_type='mask'):
     elif settings_type == 'make_masks':
         from .app_make_masks import initiate_make_mask_app
         initiate_make_mask_app(horizontal_container)
-    elif settings_type is None:
-        #parent.quit()
-        parent_frame.destroy()
-        gui_app()
     else:
-        scrollable_frame, vars_dict = setup_settings_panel(horizontal_container, settings_type)
-        button_scrollable_frame = setup_button_section(horizontal_container, settings_type)
+        scrollable_frame, vars_dict = setup_settings_panel(horizontal_container, settings_type, window_dimensions=dims)
+        button_scrollable_frame = setup_button_section(horizontal_container, settings_type, window_dimensions=dims)
         canvas, canvas_widget = setup_plot_section(vertical_container)
         console_output = setup_console(vertical_container)
 
@@ -578,16 +595,3 @@ def initiate_root(parent, settings_type='mask'):
 
     print("Root initialization complete")
     return parent_frame, vars_dict
-
-def start_gui_app(settings_type='mask'):
-    global q, fig_queue, parent_frame, scrollable_frame, vars_dict, canvas, canvas_widget, progress_label
-    root = tk.Tk()
-    width = root.winfo_screenwidth()
-    height = root.winfo_screenheight()
-    root.geometry(f"{width}x{height}")
-    root.title(f"SpaCr: {settings_type.capitalize()}")
-    root.content_frame = tk.Frame(root)
-    print("Starting GUI app with settings_type:", settings_type)
-    initiate_root(root.content_frame, settings_type)
-    create_menu_bar(root)
-    root.mainloop()

spacr/gui_elements.py

@@ -1433,7 +1433,6 @@ def create_menu_bar(root):
     from .gui_core import initiate_root
 
     gui_apps = {
-        "Main": (lambda frame: initiate_root(frame, None), "Main GUI window."),
         "Mask": (lambda frame: initiate_root(frame, 'mask'), "Generate cellpose masks for cells, nuclei and pathogen images."),
         "Measure": (lambda frame: initiate_root(frame, 'measure'), "Measure single object intensity and morphological feature. Crop and save single object image"),
         "Annotate": (lambda frame: initiate_root(frame, 'annotate'), "Annotation single object images on a grid. Annotations are saved to database."),

spacr/measure.py

@@ -998,12 +998,12 @@ def measure_crop(settings):
     _save_settings_to_db(settings)
 
     files = [f for f in os.listdir(settings['input_folder']) if f.endswith('.npy')]
-    n_job = settings['n_job'] or mp.cpu_count()-4
-    print(f'using {n_job} cpu cores')
+    n_jobs = settings['n_jobs'] or mp.cpu_count()-4
+    print(f'using {n_jobs} cpu cores')
 
     with mp.Manager() as manager:
         time_ls = manager.list()
-        with mp.Pool(n_job) as pool:
+        with mp.Pool(n_jobs) as pool:
             result = pool.starmap_async(_measure_crop_core, [(index, time_ls, file, settings) for index, file in enumerate(files)])
 
             # Track progress in the main process
@@ -1012,7 +1012,7 @@ def measure_crop(settings):
                 files_processed = len(time_ls)
                 files_to_process = len(files)
                 average_time = np.mean(time_ls) if len(time_ls) > 0 else 0
-                time_left = (((files_to_process-files_processed)*average_time)/n_job)/60
+                time_left = (((files_to_process-files_processed)*average_time)/n_jobs)/60
                 print(f'Progress: {files_processed}/{files_to_process} Time/img {average_time:.3f}sec, Time Remaining {time_left:.3f} min.', end='\r', flush=True)
             result.get()
 

spacr/settings.py

@@ -43,7 +43,7 @@ def set_default_settings_preprocess_generate_masks(src, settings={}):
     settings.setdefault('magnification', 20)
     settings.setdefault('custom_regex', None)
     settings.setdefault('metadata_type', 'cellvoyager')
-    settings.setdefault('n_job', os.cpu_count()-4)
+    settings.setdefault('n_jobs', os.cpu_count()-4)
     settings.setdefault('randomize', True)
     settings.setdefault('verbose', True)
     settings.setdefault('remove_background_cell', False)
@@ -254,7 +254,7 @@ def get_measure_crop_settings(settings):
     settings.setdefault('plot',False)
     settings.setdefault('plot_filtration',False)
     settings.setdefault('representative_images', False)
-    settings.setdefault('n_job', os.cpu_count()-2)
+    settings.setdefault('n_jobs', os.cpu_count()-2)
 
     # Object settings
     settings.setdefault('cell_mask_dim',None)
@@ -340,7 +340,7 @@ def set_default_train_test_model(settings):
     settings.setdefault('gradient_accumulation_steps',4)
     settings.setdefault('intermedeate_save',True)
     settings.setdefault('pin_memory',True)
-    settings.setdefault('n_job',cores)
+    settings.setdefault('n_jobs',cores)
     settings.setdefault('channels',['r','g','b'])
     settings.setdefault('augment',False)
     settings.setdefault('verbose',False)
@@ -534,7 +534,7 @@ expected_types = {
     "skip_mode": str,
     "save": bool,
     "plot": bool,
-    "n_job": int,
+    "n_jobs": int,
     "verbose": bool,
     "input_folder": str,
     "cell_mask_dim": int,
@@ -557,7 +557,7 @@ expected_types = {
     "include_uninfected": bool,
     "dialate_pngs": bool,
     "dialate_png_ratios": list,
-    "n_job": int,
+    "n_jobs": int,
     "cells": list,
     "cell_loc": list,
     "pathogens": list,
@@ -677,7 +677,7 @@ expected_types = {
     "gradient_accumulation_steps": int,
     "intermedeate_save": bool,
     "pin_memory": bool,
-    "n_job": int,
+    "n_jobs": int,
     "augment": bool,
     "target": str,
     "cell_types": list,
@@ -902,7 +902,7 @@ def generate_fields(variables, scrollable_frame):
         "save": "Whether to save the results to disk.",
         "merge_edge_pathogen_cells": "Whether to merge cells that share pathogen objects.",
         "plot": "Whether to plot the results.",
-        "n_job": "The number of n_job to use for processing the images. This will determine how many images are processed in parallel. Increase to speed up processing.",
+        "n_jobs": "The number of n_jobs to use for processing the images. This will determine how many images are processed in parallel. Increase to speed up processing.",
         "verbose": "Whether to print verbose output during processing.",
         "input_folder": "Path to the folder containing the images.",
         "cell_mask_dim": "The dimension of the array the cell mask is saved in.",
@@ -926,7 +926,7 @@ def generate_fields(variables, scrollable_frame):
         "include_uninfected": "Whether to include uninfected cells in the analysis.",
         "dialate_pngs": "Whether to dilate the PNG images before saving.",
         "dialate_png_ratios": "The ratios to use for dilating the PNG images. This will determine the amount of dilation applied to the images before cropping.",
-        "n_job": "The number of n_job to use for processing the images. This will determine how many images are processed in parallel. Increase to speed up processing.",
+        "n_jobs": "The number of n_jobs to use for processing the images. This will determine how many images are processed in parallel. Increase to speed up processing.",
         "cells": "The cell types to include in the analysis.",
         "cell_loc": "The locations of the cell types in the images.",
         "pathogens": "The pathogen types to include in the analysis.",
@@ -960,7 +960,7 @@ categories = {
     "Object Image": ["save_png", "dialate_pngs", "dialate_png_ratios", "png_size", "png_dims", "save_arrays", "normalize_by", "dialate_png_ratios", "crop_mode", "dialate_pngs", "normalize", "use_bounding_box"],
     "Annotate Data": ["positive_control","negative_control", "location_column", "treatment_loc", "cells", "cell_loc", "pathogens", "pathogen_loc", "channel_of_interest", "measurement", "treatments", "representative_images", "um_per_pixel", "nr_imgs", "exclude", "exclude_conditions", "mix", "pos", "neg"],
     "Measurements": ["remove_image_canvas", "remove_highly_correlated", "homogeneity", "homogeneity_distances", "radial_dist", "calculate_correlation", "manders_thresholds", "save_measurements", "tables", "image_nr", "dot_size", "filter_by", "remove_highly_correlated_features", "remove_low_variance_features", "channel_of_interest"],
-    "Advanced": ["plot", "timelapse", "schedule", "test_size","exclude","n_repeats","top_features", "model_type","minimum_cell_count","n_estimators","preprocess", "remove_background", "normalize", "lower_percentile", "merge_pathogens", "batch_size", "filter", "save", "masks", "verbose", "randomize", "n_job", "train_mode","amsgrad","use_checkpoint","gradient_accumulation","gradient_accumulation_steps","intermedeate_save","pin_memory","n_job","channels","augment"],
+    "Advanced": ["plot", "timelapse", "schedule", "test_size","exclude","n_repeats","top_features", "model_type","minimum_cell_count","n_estimators","preprocess", "remove_background", "normalize", "lower_percentile", "merge_pathogens", "batch_size", "filter", "save", "masks", "verbose", "randomize", "n_jobs", "train_mode","amsgrad","use_checkpoint","gradient_accumulation","gradient_accumulation_steps","intermedeate_save","pin_memory","n_jobs","channels","augment"],
     "Clustering": ["eps","min_samples","analyze_clusters","clustering","remove_cluster_noise"],
     "Embedding": ["visualize","n_neighbors","min_dist","metric","resnet_features","reduction_method","embedding_by_controls","col_to_compare","log_data"],
     "Train DL Model": ["epochs", "loss_type", "optimizer_type","image_size","val_split","learning_rate","weight_decay","dropout_rate","init_weights", "train", "classes"],
@@ -969,6 +969,15 @@ categories = {
     "Sequencing": ["upstream", "downstream", "barecode_length_1", "barecode_length_2", "chunk_size", "test"]
 }
 
+descriptions = {
+    'mask': "This module allows you to set default settings for preprocessing and generating masks.",
+    'measure': "This module allows you to set default settings for measuring and cropping images.",
+    'classify': "This module allows you to set default settings for training and testing classification models.",
+    'sequencing': "This module allows you to set default settings for analyzing sequencing reads.",
+    'umap': "This module allows you to set default settings for UMAP image analysis."
+}
+
+
 def set_annotate_default_settings(settings):
     settings.setdefault('src', 'path')
     settings.setdefault('image_type', 'cell_png')
@@ -982,4 +991,5 @@ def set_annotate_default_settings(settings):
     settings.setdefault('percentiles', [2, 98])
     settings.setdefault('measurement', 'cytoplasm_channel_3_mean_intensity,pathogen_channel_3_mean_intensity')
     settings.setdefault('threshold', '2')
-    return settings
+    return settings
+

spacr/utils.py

@@ -74,9 +74,18 @@ from scipy import stats
 from .logger import log_function_call
 from multiprocessing import set_start_method, get_start_method
 
-import tkinter as tk
-from tkinter import ttk
-import tkinter.font as tkFont
+import torch
+import torchvision.transforms as transforms
+from torchvision.models import resnet50
+from PIL import Image
+import numpy as np
+import umap
+import pandas as pd
+from sklearn.ensemble import RandomForestClassifier
+from sklearn.preprocessing import StandardScaler
+from scipy.stats import f_oneway, kruskal
+from sklearn.cluster import KMeans
+from scipy import stats
 
 def reset_mp():
     current_method = get_start_method()
@@ -3853,18 +3862,6 @@ def search_reduction_and_clustering(numeric_data, n_neighbors, min_dist, metric,
     if verbose:
         print(f'Embedding shape: {embedding.shape}')
     return embedding, labels
-import torch
-import torchvision.transforms as transforms
-from torchvision.models import resnet50
-from PIL import Image
-import numpy as np
-import umap
-import pandas as pd
-from sklearn.ensemble import RandomForestClassifier
-from sklearn.preprocessing import StandardScaler
-from scipy.stats import f_oneway, kruskal
-from sklearn.cluster import KMeans
-from scipy import stats
 
 def load_image(image_path):
     """Load and preprocess an image."""

{spacr-0.1.75.dist-info → spacr-0.1.77.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: spacr
-Version: 0.1.75
+Version: 0.1.77
 Summary: Spatial phenotype analysis of crisp screens (SpaCr)
 Home-page: https://github.com/EinarOlafsson/spacr
 Author: Einar Birnir Olafsson

{spacr-0.1.75.dist-info → spacr-0.1.77.dist-info}/RECORD

@@ -3,7 +3,7 @@ spacr/__main__.py,sha256=bkAJJD2kjIqOP-u1kLvct9jQQCeUXzlEjdgitwi1Lm8,75
 spacr/alpha.py,sha256=Y95sLEfpK2OSYKRn3M8eUOU33JJeXfV8zhrC4KnwSTY,35244
 spacr/annotate_app.py,sha256=imQ7ZEXDyM6ce1dxZ1xUS1-KequuF_NCI4xCaPLjvco,29275
 spacr/annotate_app_v2.py,sha256=imQ7ZEXDyM6ce1dxZ1xUS1-KequuF_NCI4xCaPLjvco,29275
-spacr/app_annotate.py,sha256=CW7gW5qXIElCJdr1dhXyCBlV8sB-GlPNjOEY471udcs,2386
+spacr/app_annotate.py,sha256=FhyDBsLdo6etOSvz6et2AhhJn67SwdeYUVDzBJzdw1E,2274
 spacr/app_classify.py,sha256=urTP_wlZ58hSyM5a19slYlBxN0PdC-9-ga0hvq8CGWc,165
 spacr/app_make_masks.py,sha256=qV3L_2TilGZBAUyBrzaWAayei_tf3XvJdUUDyzEI6hA,1834
 spacr/app_make_masks_v2.py,sha256=OkNeskNbgep8wQa4ES3jpJjZLfn4yIkGwQOd9r0spfA,30497
@@ -14,8 +14,8 @@ spacr/app_umap.py,sha256=ZWAmf_OsIKbYvolYuWPMYhdlVe-n2CADoJulAizMiEo,153
 spacr/chris.py,sha256=YlBjSgeZaY8HPy6jkrT_ISAnCMAKVfvCxF0I9eAZLFM,2418
 spacr/classify_app.py,sha256=Zi15ryc1ocYitRF4kyxlC27XxGyzfSPdvj2d6ZrSh7E,8446
 spacr/cli.py,sha256=507jfOOEV8BoL4eeUcblvH-iiDHdBrEVJLu1ghAAPSc,1800
-spacr/core.py,sha256=jNlDk-0vb0fpteNT3bsNpfLRLAuwsx7SPlcajT1eCuw,160139
-spacr/deep_spacr.py,sha256=bIa_txVJBy9zrKyqX0tpNQw0nNCUo77pSSUJiYy1egE,36994
+spacr/core.py,sha256=bm1cApGVTE218Ds3FqqWD5TsF5FF8kclHwPlvdOolzc,160216
+spacr/deep_spacr.py,sha256=ASBsN4JpHp_3S-91JUsB34IWTjTGPYI7jKV2qZnUR5M,37005
 spacr/foldseek.py,sha256=YIP1d4Ci6CeA9jSyiv-HTDbNmAmcSM9Y_DaOs7wYzLY,33546
 spacr/get_alfafold_structures.py,sha256=ehx_MQgb12k3hFecP6cYVlm5TLO8iWjgevy8ESyS3cw,3544
 spacr/graph_learning.py,sha256=1tR-ZxvXE3dBz1Saw7BeVFcrsUFu9OlUZeZVifih9eo,13070
@@ -23,8 +23,8 @@ spacr/gui.py,sha256=9psWiXMna1ebi-I55H0vQ3lad_923fhq_LB13lMSEg4,6893
 spacr/gui_2.py,sha256=ZAI5quQYbhQJ40vK0NCqU_UMSPLkpfeQpomBWUSM0fc,6946
 spacr/gui_annotate.py,sha256=ugBksLGOHdtOLlEuRyyc59TrkYKu3rDf8JxEgiBSVao,6536
 spacr/gui_classify_app.py,sha256=Zi15ryc1ocYitRF4kyxlC27XxGyzfSPdvj2d6ZrSh7E,8446
-spacr/gui_core.py,sha256=EGcSvroOLsktdaXs_7RVC8vAfqP3YjUnoxWfr4LCiWY,27508
-spacr/gui_elements.py,sha256=L1usJ9kCWLvO9UWIGxV3KKVtT-5BTboyqRdH1xeDLPg,72624
+spacr/gui_core.py,sha256=VkcYV8gE8Bc1fKcuZSJ1plS8agS_386ZxjqudRMLhG0,27912
+spacr/gui_elements.py,sha256=fgRaG7THe95jyaIaqJqe05syQ9apo9ZIwkRR2u9vMnY,72544
 spacr/gui_make_masks_app.py,sha256=tl4M4Q2WQgrrwjRBJVevxJxpNowqzPhWkdCOm2UfRbw,45053
 spacr/gui_make_masks_app_v2.py,sha256=X3izTBXdCZDlkVe-fbG-jmCQtcAbmK0OIivjyWaLhug,30576
 spacr/gui_mask_app.py,sha256=mhTl_XzXLFl8Tx3WYEMpdYB_qw9u5JJa0EdkvlcIzAE,10706
@@ -38,23 +38,23 @@ spacr/logger.py,sha256=7Zqr3TuuOQLWT32gYr2q1qvv7x0a2JhLANmZcnBXAW8,670
 spacr/make_masks_app.py,sha256=iGaTwhowoe2JMOSOf8bJwQZTooRhLQx7KO0ewnAmqDY,45138
 spacr/make_masks_app_v2.py,sha256=X3izTBXdCZDlkVe-fbG-jmCQtcAbmK0OIivjyWaLhug,30576
 spacr/mask_app.py,sha256=mhTl_XzXLFl8Tx3WYEMpdYB_qw9u5JJa0EdkvlcIzAE,10706
-spacr/measure.py,sha256=CL8bI3ujtQxsRuQJUVSXmThQFPzQvTEDK38DSELpSQo,55746
+spacr/measure.py,sha256=e36NR8raCkvKHZXvTJgPDwObsmsegvc1dAiCqD3oljk,55751
 spacr/measure_app.py,sha256=_C1-XFL5HSquUEEbM_NcxdvHx-socPFCx85MBG4d6xo,10598
 spacr/old_code.py,sha256=jw67DAGoLBd7mWofVzRJSEmCI1Qrff26zIo65SEkV00,13817
 spacr/plot.py,sha256=DYJEoK1kz2ih6ZGvKiA3xTqeIeKQNhuQKwgrscopFxA,69101
 spacr/sequencing.py,sha256=fHZRnoMSxmhMdadkei3lUeBdckqFyptWdQyWsDW3aaU,83304
-spacr/settings.py,sha256=VNEt7WWf_cpLCpkcfE6o0m3te2b4IuUlDS_j1mhP_s4,48131
+spacr/settings.py,sha256=PQ-VJSTlBMxfQuz35MiipoGmBjq56jqepViUvOjov0k,48668
 spacr/sim.py,sha256=FveaVgBi3eypO2oVB5Dx-v0CC1Ny7UPfXkJiiRRodAk,71212
 spacr/sim_app.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 spacr/timelapse.py,sha256=KMYCgHzf9LTZe-lWl5mvH2EjbKRE6OhpwdY13wEumGc,39504
-spacr/utils.py,sha256=149Bbha9OXAKyDwABgHz5h4O7Gqy6aeFLA1pMSq311s,186966
+spacr/utils.py,sha256=OQ8sSBH6VWx2xP_vh4ILJT71B46DFFhsq-Y6WxYdGhI,186891
 spacr/version.py,sha256=axH5tnGwtgSnJHb5IDhiu4Zjk5GhLyAEDRe-rnaoFOA,409
 spacr/models/cp/toxo_plaque_cyto_e25000_X1120_Y1120.CP_model,sha256=z8BbHWZPRnE9D_BHO0fBREE85c1vkltDs-incs2ytXQ,26566572
 spacr/models/cp/toxo_plaque_cyto_e25000_X1120_Y1120.CP_model_settings.csv,sha256=fBAGuL_B8ERVdVizO3BHozTDSbZUh1yFzsYK3wkQN68,420
 spacr/models/cp/toxo_pv_lumen.CP_model,sha256=2y_CindYhmTvVwBH39SNILF3rI3x9SsRn6qrMxHy3l0,26562451
-spacr-0.1.75.dist-info/LICENSE,sha256=SR-2MeGc6SCM1UORJYyarSWY_A-JaOMFDj7ReSs9tRM,1083
-spacr-0.1.75.dist-info/METADATA,sha256=xaKRgGtsxGpRudRxKq8F02eI0T0dJRVcpLzY1GRTaBY,5050
-spacr-0.1.75.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
-spacr-0.1.75.dist-info/entry_points.txt,sha256=BMC0ql9aNNpv8lUZ8sgDLQMsqaVnX5L535gEhKUP5ho,296
-spacr-0.1.75.dist-info/top_level.txt,sha256=GJPU8FgwRXGzKeut6JopsSRY2R8T3i9lDgya42tLInY,6
-spacr-0.1.75.dist-info/RECORD,,
+spacr-0.1.77.dist-info/LICENSE,sha256=SR-2MeGc6SCM1UORJYyarSWY_A-JaOMFDj7ReSs9tRM,1083
+spacr-0.1.77.dist-info/METADATA,sha256=FEEy3ZRedFlkX0jIEsC7MZ1qlDRCahOWGrtmzE7Mj3g,5050
+spacr-0.1.77.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
+spacr-0.1.77.dist-info/entry_points.txt,sha256=BMC0ql9aNNpv8lUZ8sgDLQMsqaVnX5L535gEhKUP5ho,296
+spacr-0.1.77.dist-info/top_level.txt,sha256=GJPU8FgwRXGzKeut6JopsSRY2R8T3i9lDgya42tLInY,6
+spacr-0.1.77.dist-info/RECORD,,