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

@@ -197,6 +197,7 @@ def collection(
 
     # Initialize the 3D array for the shape
     collection = np.zeros((collection_shape[0], collection_shape[1], collection_shape[2]), dtype=np.uint8)
+    labels = np.zeros_like(collection)
 
 
     # Fill the 3D array with synthetic blobs
@@ -225,10 +226,11 @@ 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)
+            blob = scipy.ndimage.rotate(blob, angle, axes, order=0)
 
         # Place synthetic object into the collection
         # If positions are specified, place blob at one of the specified positions
+        collection_before = collection.copy()
         if positions:
             collection, placed, positions = specific_placement(collection, blob, positions)
 
@@ -237,17 +239,21 @@ def collection(
             collection, placed = random_placement(collection, blob, rng)
 
         # Break if blob could not be placed
-        if not placed: 
+        if not placed:
             break
-    
+
+        # Update labels
+        new_labels = np.where(collection > collection_before, i, 0).astype(labels.dtype)
+        labels += new_labels
+
     if not placed:
         # Log error if not all num_objects could be placed (this line of code has to be here, otherwise it will interfere with tqdm progress bar)
         log.error(f"Object #{i+1} could not be placed in the collection, so no more blobs are added. Collection contains {i}/{num_objects} objects.")
 
-    # Compute binary mask of collection based on Li thresholding
-    mask = collection > threshold_li(collection)
+    # # Compute binary mask of collection based on Li thresholding
+    # mask = collection > threshold_li(collection)
 
-    # Find connected components in the mask
-    CC = get_3d_cc(mask)
+    # # Find connected components in the mask
+    # CC = get_3d_cc(mask)
 
-    return collection, CC
\ No newline at end of file
+    return collection, labels
\ No newline at end of file