Synthetic collection generation

Refactoring of synthetic blob generation

• Created new generate module in library and corresponding page in the documentation
• Moved generate_volume function from qim3d/utils/img.py to qim3d/generate/blob_.py, and re-named function to blob
• Moved overlay_rgb_images function from qim3d/utils/img.py to qim3d/processing/operations.py
• Optimized qim3d.generate.blob function with vectorized approach for faster computations
• Added auto_clip boolean parameter for allowing automatic threshold computation to ensure blobs without straight cuts

Implementation of synthetic collection generation

• Created new collection function in the generate module (qim3d/generate/collection_.py), and corresponding page in the documentation
• The collection function generates and returns a 3D volume with a collection of blobs from specified parameter ranges, along with a connected components CC object. Blobs are placed without overlap, and can either be placed randomly or at specific positions within the collection.

qim3d/generate/collection_.py

@@ -226,7 +226,7 @@ def collection(
             angle = rng.uniform(low = 0, high = max_rotation_degrees)    # Sample rotation angle
             axes = rng.choice([(0, 1), (0, 2), (1, 2)]) # Sample the two axes to rotate around
 
-            blob = scipy.ndimage.rotate(blob, angle, axes, order=0)
+            blob = scipy.ndimage.rotate(blob, angle, axes, order=1)
 
         # Place synthetic object into the collection
         # If positions are specified, place blob at one of the specified positions
@@ -243,7 +243,7 @@ def collection(
             break
 
         # Update labels
-        new_labels = np.where(collection > collection_before, i, 0).astype(labels.dtype)
+        new_labels = np.where(collection > collection_before, i+1, 0).astype(labels.dtype)
         labels += new_labels
 
     if not placed: