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

@@ -194,7 +194,7 @@ def collection(
     rng = np.random.default_rng(seed)
 
     # Initialize the 3D array for the shape
-    collection = np.empty((collection_shape[0], collection_shape[1], collection_shape[2]), dtype=np.uint8)
+    collection = np.empty((collection_shape[0], collection_shape[1], collection_shape[2]), dtype=np.uint8).copy()
 
     # Fill the 3D array with synthetic blobs
     for i in tqdm(range(num_blobs), desc = 'Blobs placed'):