spacr 1.0.5__py3-none-any.whl → 1.0.6__py3-none-any.whl

spacr/app_annotate.py

@@ -11,7 +11,7 @@ def convert_to_number(value):
             return float(value)
         except ValueError:
             raise ValueError(f"Unable to convert '{value}' to an integer or float.")
-
+    
 def initiate_annotation_app(parent_frame):
     from .gui_utils import generate_annotate_fields, annotate_app, convert_to_number
     # Set up the settings window

spacr/core.py

@@ -238,6 +238,7 @@ def generate_cellpose_masks(src, settings, object_type):
     model_name = object_settings['model_name']
     
     cellpose_channels = _get_cellpose_channels(src, settings['nucleus_channel'], settings['pathogen_channel'], settings['cell_channel'])
+    
     if settings['verbose']:
         print(cellpose_channels)
         

spacr/deep_spacr.py

@@ -1,10 +1,8 @@
-import os, torch, time, gc, datetime, cv2
+import os, torch, time, gc, datetime
 torch.backends.cudnn.benchmark = True
-
 import numpy as np
 import pandas as pd
 from torch.optim import Adagrad, AdamW
-from torch.autograd import grad
 from torch.optim.lr_scheduler import StepLR
 import torch.nn.functional as F
 import matplotlib.pyplot as plt

spacr/gui.py

@@ -4,6 +4,7 @@ from multiprocessing import set_start_method
 from .gui_elements import spacrButton, create_menu_bar, set_dark_style
 from .gui_core import initiate_root
 from screeninfo import get_monitors
+import webbrowser
 
 class MainApp(tk.Tk):
     def __init__(self, default_app=None):
@@ -22,6 +23,7 @@ class MainApp(tk.Tk):
         for monitor in get_monitors():
             if monitor.x <= x < monitor.x + monitor.width and monitor.y <= y < monitor.y + monitor.height:
                 width = monitor.width
+                self.width = width
                 height = monitor.height
                 break
         else:
@@ -42,22 +44,22 @@ class MainApp(tk.Tk):
         self.main_gui_apps = {
             "Mask": (lambda frame: initiate_root(self, 'mask'), "Generate cellpose masks for cells, nuclei and pathogen images."),
             "Measure": (lambda frame: initiate_root(self, 'measure'), "Measure single object intensity and morphological feature. Crop and save single object image"),
-            "Annotate": (lambda frame: initiate_root(self, 'annotate'), "Annotation single object images on a grid. Annotations are saved to database."),
-            "Make Masks": (lambda frame: initiate_root(self, 'make_masks'), "Adjust pre-existing Cellpose models to your specific dataset for improved performance"),
+            #"Annotate": (lambda frame: initiate_root(self, 'annotate'), "Annotation single object images on a grid. Annotations are saved to database."),
+            #"Make Masks": (lambda frame: initiate_root(self, 'make_masks'), "Adjust pre-existing Cellpose models to your specific dataset for improved performance"),
             "Classify": (lambda frame: initiate_root(self, 'classify'), "Train Torch Convolutional Neural Networks (CNNs) or Transformers to classify single object images."),
         }
 
         self.additional_gui_apps = {
-            "Umap": (lambda frame: initiate_root(self, 'umap'), "Generate UMAP embeddings with datapoints represented as images."),
-            "Train Cellpose": (lambda frame: initiate_root(self, 'train_cellpose'), "Train custom Cellpose models."),
-            "ML Analyze": (lambda frame: initiate_root(self, 'ml_analyze'), "Machine learning analysis of data."),
-            "Cellpose Masks": (lambda frame: initiate_root(self, 'cellpose_masks'), "Generate Cellpose masks."),
-            "Cellpose All": (lambda frame: initiate_root(self, 'cellpose_all'), "Run Cellpose on all images."),
+            #"Umap": (lambda frame: initiate_root(self, 'umap'), "Generate UMAP embeddings with datapoints represented as images."),
+            #"Train Cellpose": (lambda frame: initiate_root(self, 'train_cellpose'), "Train custom Cellpose models."),
+            #"ML Analyze": (lambda frame: initiate_root(self, 'ml_analyze'), "Machine learning analysis of data."),
+            #"Cellpose Masks": (lambda frame: initiate_root(self, 'cellpose_masks'), "Generate Cellpose masks."),
+            #"Cellpose All": (lambda frame: initiate_root(self, 'cellpose_all'), "Run Cellpose on all images."),
             "Map Barcodes": (lambda frame: initiate_root(self, 'map_barcodes'), "Map barcodes to data."),
             "Regression": (lambda frame: initiate_root(self, 'regression'), "Perform regression analysis."),
-            "Recruitment": (lambda frame: initiate_root(self, 'recruitment'), "Analyze recruitment data."),
+            #"Recruitment": (lambda frame: initiate_root(self, 'recruitment'), "Analyze recruitment data."),
             "Activation": (lambda frame: initiate_root(self, 'activation'), "Generate activation maps of computer vision models and measure channel-activation correlation."),
-            "Plaque": (lambda frame: initiate_root(self, 'analyze_plaques'), "Analyze plaque data.")
+            #"Plaque": (lambda frame: initiate_root(self, 'analyze_plaques'), "Analyze plaque data.")
         }
 
         self.selected_app = tk.StringVar()
@@ -88,6 +90,13 @@ class MainApp(tk.Tk):
         set_dark_style(ttk.Style(), containers=[self.content_frame, self.inner_frame])
 
         self.create_startup_screen()
+        
+    def _update_wraplength(self, event):
+        if self.description_label.winfo_exists():
+            # Use the actual width of the inner_frame as a proxy for full width
+            available_width = self.inner_frame.winfo_width()
+            if available_width > 0:
+                self.description_label.config(wraplength=int(available_width * 0.9))  # or 0.9
 
     def create_startup_screen(self):
         self.clear_frame(self.inner_frame)
@@ -99,18 +108,30 @@ class MainApp(tk.Tk):
         additional_buttons_frame = tk.Frame(self.inner_frame)
         additional_buttons_frame.pack(pady=10)
         set_dark_style(ttk.Style(), containers=[additional_buttons_frame])
-
-        description_frame = tk.Frame(self.inner_frame, height=70)
+        
+        description_frame = tk.Frame(self.inner_frame)
         description_frame.pack(fill=tk.X, pady=10)
-        description_frame.pack_propagate(False)
+        description_frame.columnconfigure(0, weight=1)
+        
         set_dark_style(ttk.Style(), containers=[description_frame])
+        style_out = set_dark_style(ttk.Style())
+        font_loader = style_out['font_loader']
+        font_size = style_out['font_size']
+        
+        self.description_label = tk.Label( description_frame, text="", wraplength=int(self.width * 0.9), justify="center", font=font_loader.get_font(size=font_size), fg=self.color_settings['fg_color'], bg=self.color_settings['bg_color'])
+        
+        # Pack it without expanding
+        self.description_label.pack(pady=10)
 
-        self.description_label = tk.Label(description_frame, text="", wraplength=800, justify="center", font=('Helvetica', 12), fg=self.color_settings['fg_color'], bg=self.color_settings['bg_color'])
-        self.description_label.pack(fill=tk.BOTH, pady=10)
-
-        logo_button = spacrButton(main_buttons_frame, text="SpaCr", command=lambda: self.load_app("logo_spacr", initiate_root), icon_name="logo_spacr", size=100, show_text=False)
+        # Force character width and center it
+        self.description_label.configure(width=int(self.width * 0.5 // 7))
+        self.description_label.pack_configure(anchor='center')
+        
+        #logo_button = spacrButton(main_buttons_frame, text="SpaCR", command=lambda: self.load_app("logo_spacr", initiate_root), icon_name="logo_spacr", size=100, show_text=False)
+        logo_button = spacrButton(main_buttons_frame,text="SpaCR",command=lambda: webbrowser.open_new("https://einarolafsson.github.io/spacr/tutorial/"),icon_name="logo_spacr",size=100,show_text=False)
+        
         logo_button.grid(row=0, column=0, padx=5, pady=5)
-        self.main_buttons[logo_button] = "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."
+        self.main_buttons[logo_button] = "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. Click to open the spaCR tutorial in your browser."
 
         for i, (app_name, app_data) in enumerate(self.main_gui_apps.items()):
             app_func, app_desc = app_data
@@ -125,6 +146,7 @@ class MainApp(tk.Tk):
             self.additional_buttons[button] = app_desc
 
         self.update_description()
+        self.inner_frame.bind("<Configure>", self._update_wraplength)
 
     def update_description(self):
         for button, desc in {**self.main_buttons, **self.additional_buttons}.items():

spacr/gui_elements.py

@@ -50,18 +50,18 @@ def create_menu_bar(root):
     gui_apps = {
         "Mask": lambda: initiate_root(root, settings_type='mask'),
         "Measure": lambda: initiate_root(root, settings_type='measure'),
-        "Annotate": lambda: initiate_root(root, settings_type='annotate'),
-        "Make Masks": lambda: initiate_root(root, settings_type='make_masks'),
+        "Annotate (Beta)": lambda: initiate_root(root, settings_type='annotate'),
+        #"Make Masks": lambda: initiate_root(root, settings_type='make_masks'),
         "Classify": lambda: initiate_root(root, settings_type='classify'),
-        "Umap": lambda: initiate_root(root, settings_type='umap'),
-        "Train Cellpose": lambda: initiate_root(root, settings_type='train_cellpose'),
+        #"Umap": lambda: initiate_root(root, settings_type='umap'),
+        #"Train Cellpose": lambda: initiate_root(root, settings_type='train_cellpose'),
         "ML Analyze": lambda: initiate_root(root, settings_type='ml_analyze'),
-        "Cellpose Masks": lambda: initiate_root(root, settings_type='cellpose_masks'),
-        "Cellpose All": lambda: initiate_root(root, settings_type='cellpose_all'),
+        #"Cellpose Masks": lambda: initiate_root(root, settings_type='cellpose_masks'),
+        #"Cellpose All": lambda: initiate_root(root, settings_type='cellpose_all'),
         "Map Barcodes": lambda: initiate_root(root, settings_type='map_barcodes'),
         "Regression": lambda: initiate_root(root, settings_type='regression'),
         "Activation": lambda: initiate_root(root, settings_type='activation'),
-        "Recruitment": lambda: initiate_root(root, settings_type='recruitment')
+        "Recruitment (Beta)": lambda: initiate_root(root, settings_type='recruitment')
     }
 
     # Create the menu bar

spacr/io.py

@@ -1,4 +1,4 @@
-import os, re, sqlite3, gc, torch, time, random, shutil, cv2, tarfile, cellpose, glob, queue, tifffile, czifile, atexit, datetime
+import os, re, sqlite3, gc, torch, time, random, shutil, cv2, tarfile, cellpose, glob, queue, tifffile, czifile, atexit, datetime, readlif
 import numpy as np
 import pandas as pd
 from PIL import Image, ImageOps
@@ -22,7 +22,6 @@ import seaborn as sns
 from nd2reader import ND2Reader
 from torchvision import transforms
 from sklearn.model_selection import train_test_split
-import readlif
 from pylibCZIrw import czi as pyczi
 
 def process_non_tif_non_2D_images(folder):
@@ -1133,6 +1132,7 @@ def _normalize_img_batch(stack, channels, save_dtype, settings):
 
 def concatenate_and_normalize(src, channels, save_dtype=np.float32, settings={}):
     from .utils import print_progress
+    from .plot import plot_arrays
 
     """
     Concatenates and normalizes channel data from multiple files and saves the normalized data.
@@ -1155,6 +1155,8 @@ def concatenate_and_normalize(src, channels, save_dtype=np.float32, settings={})
     """
 
     channels = [item for item in channels if item is not None]
+    
+    print(f"Generating concatenated and normalized channel data for channels: {channels}")
 
     paths = []
     time_ls = []
@@ -1175,7 +1177,7 @@ def concatenate_and_normalize(src, channels, save_dtype=np.float32, settings={})
                         name = parts[0] + '_' + parts[1] + '_' + parts[2]
                     array = np.load(path)
                     stack_region.append(array)
-                    filenames_region.append(os.path.basename(path))
+                    filenames_region.append(os.path.basename(path))                    
                 stop = time.time()
                 duration = stop - start
                 time_ls.append(duration)
@@ -1193,6 +1195,10 @@ def concatenate_and_normalize(src, channels, save_dtype=np.float32, settings={})
                 
                 save_loc = os.path.join(output_fldr, f'{name}_norm_timelapse.npz')
                 np.savez(save_loc, data=normalized_stack, filenames=filenames_region)
+                
+                if i == 0:
+                    plot_arrays(save_loc, settings['figuresize'], settings['cmap'], nr=settings['nr'], normalize=False)
+                
                 print(save_loc)
                 del stack, normalized_stack
         except Exception as e:
@@ -1250,7 +1256,11 @@ def concatenate_and_normalize(src, channels, save_dtype=np.float32, settings={})
                 normalized_stack = normalized_stack[..., channels]
 
                 save_loc = os.path.join(output_fldr, f'stack_{batch_index}_norm.npz')
-                np.savez(save_loc, data=normalized_stack, filenames=filenames_batch)
+                np.savez(save_loc, data=normalized_stack, filenames=filenames_batch)                
+                if batch_index == 0:
+                    print(f"plotting: {save_loc}")
+                    plot_arrays(save_loc, settings['figuresize'], settings['cmap'], nr=settings['nr'], normalize=False)
+                
                 batch_index += 1
                 del stack, normalized_stack
                 stack_ls = []

spacr/plot.py

@@ -760,7 +760,63 @@ def _filter_objects_in_plot(stack, cell_mask_dim, nucleus_mask_dim, pathogen_mas
 
     return stack
 
+
 def plot_arrays(src, figuresize=10, cmap='inferno', nr=1, normalize=True, q1=1, q2=99):
+    """
+    Plot randomly selected arrays from a given directory or a single .npz/.npy file.
+
+    Parameters:
+    - src (str): The directory path or file path containing the arrays.
+    - figuresize (int): The size of the figure (default: 10).
+    - cmap (str): The colormap to use for displaying the arrays (default: 'inferno').
+    - nr (int): The number of arrays to plot (default: 1).
+    - normalize (bool): Whether to normalize the arrays (default: True).
+    - q1 (int): The lower percentile for normalization (default: 1).
+    - q2 (int): The upper percentile for normalization (default: 99).
+    """
+    from .utils import normalize_to_dtype
+
+    mask_cmap = random_cmap()
+    paths = []
+
+    if src.endswith('.npz') or src.endswith('.npy'):
+        paths = [src]
+    else:
+        paths = [os.path.join(src, f) for f in os.listdir(src) if f.endswith(('.npy', '.npz'))]
+        paths = random.sample(paths, min(nr, len(paths)))
+
+    for path in paths:
+        print(f'Image path: {path}')
+        if path.endswith('.npz'):
+            with np.load(path) as data:
+                key = list(data.keys())[0]  # assume first key
+                img = data[key][0]          # get first image in batch
+        else:
+            img = np.load(path)
+
+        if normalize:
+            img = normalize_to_dtype(array=img, p1=q1, p2=q2)
+
+        if img.ndim == 3:
+            array_nr = img.shape[2]
+            fig, axs = plt.subplots(1, array_nr, figsize=(figuresize, figuresize))
+            if array_nr == 1:
+                axs = [axs]  # ensure iterable
+            for channel in range(array_nr):
+                i = img[:, :, channel]
+                axs[channel].imshow(i, cmap=plt.get_cmap(cmap))
+                axs[channel].set_title(f'Channel {channel}', size=24)
+                axs[channel].axis('off')
+        else:
+            fig, ax = plt.subplots(1, 1, figsize=(figuresize, figuresize))
+            ax.imshow(img, cmap=plt.get_cmap(cmap))
+            ax.set_title('Channel 0', size=24)
+            ax.axis('off')
+
+        fig.tight_layout()
+        plt.show()
+
+def plot_arrays_v1(src, figuresize=10, cmap='inferno', nr=1, normalize=True, q1=1, q2=99):
     """
     Plot randomly selected arrays from a given directory.
 
@@ -780,6 +836,7 @@ def plot_arrays(src, figuresize=10, cmap='inferno', nr=1, normalize=True, q1=1,
     
     mask_cmap = random_cmap()
     paths = []
+
     for file in os.listdir(src):
         if file.endswith('.npy'):
             path = os.path.join(src, file)