spacr 0.0.80__tar.gz → 0.0.82__tar.gz

{spacr-0.0.80/spacr.egg-info → spacr-0.0.82}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: spacr
-Version: 0.0.80
+Version: 0.0.82
 Summary: Spatial phenotype analysis of crisp screens (SpaCr)
 Home-page: https://github.com/EinarOlafsson/spacr
 Author: Einar Birnir Olafsson
@@ -38,6 +38,7 @@ Requires-Dist: PyWavelets<2.0,>=1.6.0
 Requires-Dist: torchcam<1.0,>=0.4.0
 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
 Provides-Extra: dev
 Requires-Dist: pytest>=3.9; extra == "dev"

{spacr-0.0.80 → spacr-0.0.82}/setup.py

@@ -50,13 +50,14 @@ dependencies = [
     'PyWavelets>=1.6.0,<2.0',
     'torchcam>=0.4.0,<1.0',
     'ttf_opensans>=2020.10.30',
-    'customtkinter>=5.2.2,<6.0',  
+    'customtkinter>=5.2.2,<6.0', 
+    'biopython>=1.80,<2.0',
     'lxml>=5.1.0,<6.0'
 ]
 
 setup(
     name="spacr",
-    version="0.0.80",
+    version="0.0.82",
     author="Einar Birnir Olafsson",
     author_email="olafsson@med.umich.com",
     description="Spatial phenotype analysis of crisp screens (SpaCr)",

{spacr-0.0.80 → spacr-0.0.82}/spacr/core.py

@@ -77,7 +77,7 @@ def analyze_plaques(folder):
 def train_cellpose(settings):
     
     from .io import _load_normalized_images_and_labels, _load_images_and_labels
-    from .utils import resize_images_and_labels
+    #from .utils import resize_images_and_labels
 
     img_src = settings['img_src'] 
     mask_src = os.path.join(img_src, 'masks')
@@ -99,7 +99,6 @@ def train_cellpose(settings):
     Signal_to_noise = settings.setdefault( 'Signal_to_noise', 10)
     verbose = settings.setdefault( 'verbose', False)
 
-    
     channels = settings.setdefault( 'channels', [0,0])
     normalize = settings.setdefault( 'normalize', True)
     percentiles = settings.setdefault( 'percentiles', None)
@@ -119,7 +118,7 @@ def train_cellpose(settings):
         test_img_src = os.path.join(os.path.dirname(img_src), 'test')
         test_mask_src = os.path.join(test_img_src, 'mask')
 
-    test_images, test_masks, test_image_names, test_mask_names = None,None,None,None,
+    test_images, test_masks, test_image_names, test_mask_names = None,None,None,None
     print(settings)
 
     if from_scratch:
@@ -147,13 +146,13 @@ def train_cellpose(settings):
 
         image_files = [os.path.join(img_src, f) for f in os.listdir(img_src) if f.endswith('.tif')]
         label_files = [os.path.join(mask_src, f) for f in os.listdir(mask_src) if f.endswith('.tif')]
-        images, masks, image_names, mask_names = _load_normalized_images_and_labels(image_files, label_files, channels, percentiles,  circular, invert, verbose, remove_background, background, Signal_to_noise)
+        images, masks, image_names, mask_names = _load_normalized_images_and_labels(image_files, label_files, channels, percentiles,  circular, invert, verbose, remove_background, background, Signal_to_noise, target_height, target_width)        
         images = [np.squeeze(img) if img.shape[-1] == 1 else img for img in images]
         
         if test:
             test_image_files = [os.path.join(test_img_src, f) for f in os.listdir(test_img_src) if f.endswith('.tif')]
             test_label_files = [os.path.join(test_mask_src, f) for f in os.listdir(test_mask_src) if f.endswith('.tif')]
-            test_images, test_masks, test_image_names, test_mask_names = _load_normalized_images_and_labels(test_image_files, test_label_files, channels, percentiles,  circular, invert, verbose, remove_background, background, Signal_to_noise)
+            test_images, test_masks, test_image_names, test_mask_names = _load_normalized_images_and_labels(test_image_files, test_label_files, channels, percentiles,  circular, invert, verbose, remove_background, background, Signal_to_noise, target_height, target_width)
             test_images = [np.squeeze(img) if img.shape[-1] == 1 else img for img in test_images]
             
     else:
@@ -164,8 +163,8 @@ def train_cellpose(settings):
             test_images, test_masks, test_image_names, test_mask_names = _load_images_and_labels(img_src=test_img_src, mask_src=test_mask_src, circular=circular, invert=invert)
             test_images = [np.squeeze(img) if img.shape[-1] == 1 else img for img in test_images]
     
-    if resize:
-        images, masks = resize_images_and_labels(images, masks, target_height, target_width, show_example=True)
+    #if resize:
+    #    images, masks = resize_images_and_labels(images, masks, target_height, target_width, show_example=True)
 
     if model_type == 'cyto':
         cp_channels = [0,1]

{spacr-0.0.80 → spacr-0.0.82}/spacr/io.py

@@ -87,7 +87,7 @@ def _load_images_and_labels(image_files, label_files, circular=False, invert=Fal
         print(f'image shape: {images[0].shape}, image type: images[0].shape mask shape: {labels[0].shape}, image type: labels[0].shape')
     return images, labels, image_names, label_names
 
-def _load_normalized_images_and_labels(image_files, label_files, channels=None, percentiles=None,  circular=False, invert=False, visualize=False, remove_background=False, background=0, Signal_to_noise=10):
+def _load_normalized_images_and_labels_v1(image_files, label_files, channels=None, percentiles=None,  circular=False, invert=False, visualize=False, remove_background=False, background=0, Signal_to_noise=10):
     
     from .plot import normalize_and_visualize
     from .utils import invert_image, apply_mask
@@ -182,6 +182,113 @@ def _load_normalized_images_and_labels(image_files, label_files, channels=None,
     
     return normalized_images, labels, image_names, label_names
 
+def _load_normalized_images_and_labels(image_files, label_files, channels=None, percentiles=None,  circular=False, invert=False, visualize=False, remove_background=False, background=0, Signal_to_noise=10, target_height=None, target_width=None):
+    
+    from .plot import normalize_and_visualize, plot_resize
+    from .utils import invert_image, apply_mask
+    from skimage.transform import resize as resizescikit
+
+    signal_thresholds = background * Signal_to_noise
+    lower_percentile = 2
+
+    images = []
+    labels = []
+    
+    num_channels = 4
+    percentiles_1 = [[] for _ in range(num_channels)]
+    percentiles_99 = [[] for _ in range(num_channels)]
+
+    image_names = [os.path.basename(f) for f in image_files]
+    image_dir = os.path.dirname(image_files[0])
+    
+    if label_files is not None:
+        label_names = [os.path.basename(f) for f in label_files]
+        label_dir = os.path.dirname(label_files[0])
+
+    # Load, normalize, and resize images
+    for i, img_file in enumerate(image_files):
+        image = cellpose.io.imread(img_file)
+        if invert:
+            image = invert_image(image)
+        if circular:
+            image = apply_mask(image, output_value=0)
+
+        # If specific channels are specified, select them
+        if channels is not None and image.ndim == 3:
+            image = image[..., channels]
+
+        if remove_background:
+            image[image < background] = 0
+        
+        if image.ndim < 3:
+            image = np.expand_dims(image, axis=-1)
+        
+        if percentiles is None:
+            for c in range(image.shape[-1]):
+                p1 = np.percentile(image[..., c], lower_percentile)
+                percentiles_1[c].append(p1)
+                for percentile in [98, 99, 99.9, 99.99, 99.999]:
+                    p = np.percentile(image[..., c], percentile)
+                    if p > signal_thresholds:
+                        percentiles_99[c].append(p)
+                        break
+        
+        # Resize image
+        if target_height is not None and target_width is not None:
+            if image.ndim == 2:
+                image_shape = (target_height, target_width)
+            elif image.ndim == 3:
+                image_shape = (target_height, target_width, image.shape[-1])
+                
+            image = resizescikit(image, image_shape, preserve_range=True, anti_aliasing=True).astype(image.dtype)
+        
+        images.append(image)
+    
+    if percentiles is None:
+        # Calculate average percentiles for normalization
+        avg_p1 = [np.mean(p) for p in percentiles_1]
+        avg_p99 = [np.mean(p) if len(p) > 0 else np.mean(percentiles_1[i]) for i, p in enumerate(percentiles_99)]
+
+        print(f'Average 1st percentiles: {avg_p1}, Average 99th percentiles: {avg_p99}')
+
+        normalized_images = []
+        for image in images:
+            normalized_image = np.zeros_like(image, dtype=np.float32)
+            for c in range(image.shape[-1]):
+                normalized_image[..., c] = rescale_intensity(image[..., c], in_range=(avg_p1[c], avg_p99[c]), out_range=(0, 1))
+            normalized_images.append(normalized_image)
+            if visualize:
+                normalize_and_visualize(image, normalized_image, title=f"Channel {c+1} Normalized")
+    else:
+        normalized_images = []
+        for image in images:
+            normalized_image = np.zeros_like(image, dtype=np.float32)
+            for c in range(image.shape[-1]):
+                low_p = np.percentile(image[..., c], percentiles[0])
+                high_p = np.percentile(image[..., c], percentiles[1])
+                normalized_image[..., c] = rescale_intensity(image[..., c], in_range=(low_p, high_p), out_range=(0, 1))
+            normalized_images.append(normalized_image)
+            if visualize:
+                normalize_and_visualize(image, normalized_image, title=f"Channel {c+1} Normalized")
+
+    if label_files is not None:
+        for lbl_file in label_files:
+            label = cellpose.io.imread(lbl_file)
+            # Resize label
+            if target_height is not None and target_width is not None:
+                label = resizescikit(label, (target_height, target_width), order=0, preserve_range=True, anti_aliasing=False).astype(label.dtype)
+            labels.append(label)
+    else:
+        label_names = []
+        label_dir = None
+
+    print(f'Loaded and normalized {len(normalized_images)} images and {len(labels)} labels from {image_dir} and {label_dir}')
+
+    if visualize and images and labels:
+        plot_resize(images, normalized_images, labels, labels)
+    
+    return normalized_images, labels, image_names, label_names
+
 class CombineLoaders:
 
     """