nettracer3d 0.5.3__py3-none-any.whl → 0.5.5__py3-none-any.whl

nettracer3d/community_extractor.py

@@ -9,6 +9,7 @@ from scipy import ndimage
 from scipy.ndimage import zoom
 from networkx.algorithms import community
 from community import community_louvain
+import random
 from . import node_draw
 
 
@@ -781,6 +782,47 @@ def generate_distinct_colors(n_colors: int) -> List[Tuple[int, int, int]]:
         colors.append(rgb)
     return colors
 
+def assign_node_colors(node_list: List[int], labeled_array: np.ndarray) -> Tuple[np.ndarray, Dict[int, str]]:
+    """
+    Assign distinct colors to nodes and create an RGBA image.
+    
+    Args:
+        node_list: List of node IDs
+        labeled_array: 3D numpy array with labels corresponding to node IDs
+    
+    Returns:
+        Tuple of (RGBA-coded numpy array (H, W, D, 4), dictionary mapping nodes to color names)
+    """
+    
+    # Sort communities by size (descending)
+    sorted_nodes= sorted(node_list, reverse=True)
+    
+    # Generate distinct colors
+    colors = generate_distinct_colors(len(node_list))
+    random.shuffle(colors) #Randomly sorted to make adjacent structures likely stand out
+    
+    # Convert RGB colors to RGBA by adding alpha channel
+    colors_rgba = [(r, g, b, 255) for r, g, b in colors]  # Full opacity for colored regions
+    
+    # Create mapping from community to color
+    node_to_color = {node: colors_rgba[i] for i, node in enumerate(sorted_nodes)}
+    
+    # Create RGBA array (initialize with transparent background)
+    rgba_array = np.zeros((*labeled_array.shape, 4), dtype=np.uint8)
+    
+    # Assign colors to each voxel based on its label
+    for label in np.unique(labeled_array):
+        if label in node_to_color:  # Skip background (usually label 0)
+            mask = labeled_array == label
+            for i in range(4):  # RGBA channels
+                rgba_array[mask, i] = node_to_color[label][i]
+
+    # Convert the RGB portion of community_to_color back to RGB for color naming
+    node_to_color_rgb = {k: tuple(v[:3]) for k, v in node_to_color.items()}
+    node_to_color_names = convert_node_colors_to_names(node_to_color_rgb)
+    
+    return rgba_array, node_to_color_names
+
 def assign_community_colors(community_dict: Dict[int, int], labeled_array: np.ndarray) -> Tuple[np.ndarray, Dict[int, str]]:
     """
     Assign distinct colors to communities and create an RGBA image.

nettracer3d/nettracer.py

@@ -4091,6 +4091,29 @@ class Network_3D:
 
 
         return image, output
+
+    def node_to_color(self, down_factor = None, mode = 0):
+
+        if mode == 0:
+            array = self._nodes
+        elif mode == 1:
+            array = self._edges
+
+        items = list(np.unique(array))
+        if 0 in items:
+            del items[0]
+
+
+        if down_factor is not None:
+            original_shape = array.shape
+            array = downsample(array, down_factor)
+
+        array, output = community_extractor.assign_node_colors(items, array)
+
+        if down_factor is not None:
+            array = upsample_with_padding(array, down_factor, original_shape)
+
+        return array, output