fix show augs with alpha

Author: mluerig

bioencoder/core/utils.py

@@ -681,7 +681,7 @@ def save_augmented_sample(data_dir, transform, n_samples, seed):
         ## apply augmentations and save
         for i, idx in enumerate(selected_indices):
             path, _ = dataset.samples[idx]
-            image = Image.open(path)
+            image = Image.open(path).convert("RGB")
             image_name = os.path.basename(path)
             augmented_image = transform(image=np.asarray(image))["image"]   
             to_pil_image = transforms.ToPILImage()

bioencoder/scripts/interactive_plots.py

@@ -139,7 +139,7 @@ def interactive_plots(
 
     helpers.bokeh_plot(df_plot, out_path=plot_path, **plot_config)
 
-    # Return logic: either one or both
+    # return embeddings and plot coords
     if return_results:
         return df_embeddings, df_plot