spacr 1.0.5__py3-none-any.whl → 1.0.7__py3-none-any.whl

spacr/gui_utils.py

@@ -463,14 +463,13 @@ def function_gui_wrapper(function=None, settings={}, q=None, fig_queue=None, imp
 def run_function_gui(settings_type, settings, q, fig_queue, stop_requested):
     
     from .core import generate_image_umap, preprocess_generate_masks
-    from .spacr_cellpose import identify_masks_finetune, check_cellpose_models, compare_cellpose_masks
+    from .spacr_cellpose import identify_masks_finetune, check_cellpose_models
     from .submodules import analyze_recruitment
     from .ml import generate_ml_scores, perform_regression
     from .submodules import train_cellpose, analyze_plaques
-    from .io import process_non_tif_non_2D_images, generate_cellpose_train_test, generate_dataset
+    from .io import process_non_tif_non_2D_images
     from .measure import measure_crop
-    from .sim import run_multiple_simulations
-    from .deep_spacr import deep_spacr, apply_model_to_tar
+    from .deep_spacr import deep_spacr
     from .sequencing import generate_barecode_mapping
     
     process_stdout_stderr(q)
@@ -483,9 +482,6 @@ def run_function_gui(settings_type, settings, q, fig_queue, stop_requested):
     elif settings_type == 'measure':
         function = measure_crop
         imports = 1
-    elif settings_type == 'simulation':
-        function = run_multiple_simulations
-        imports = 1
     elif settings_type == 'classify':
         function = deep_spacr
         imports = 1

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)