nettracer3d 0.7.9__py3-none-any.whl → 0.8.1__py3-none-any.whl

nettracer3d/node_draw.py

@@ -201,18 +201,28 @@ def degree_draw(degree_dict, centroid_dict, nodes):
     return draw_array
 
 def degree_infect(degree_dict, nodes):
-
-    num_nodes = int(np.max(nodes))
-    return_nodes = nodes.copy()
-
-    for node in range(1, num_nodes + 1):
-        if node not in degree_dict:
-            continue
-        else:
-            idxs = np.argwhere(nodes == node)
-            for idx in idxs:
-                return_nodes[tuple(idx)] = degree_dict[node]
-
+    return_nodes = np.zeros_like(nodes)  # Start with all zeros
+    
+    if not degree_dict:  # Handle empty dict
+        return return_nodes
+    
+    # Create arrays for old and new values
+    old_vals = np.array(list(degree_dict.keys()))
+    new_vals = np.array(list(degree_dict.values()))
+    
+    # Sort for searchsorted to work correctly
+    sort_idx = np.argsort(old_vals)
+    old_vals_sorted = old_vals[sort_idx]
+    new_vals_sorted = new_vals[sort_idx]
+    
+    # Find which nodes exist in the dictionary
+    mask = np.isin(nodes, old_vals_sorted)
+    
+    # Only process nodes that exist in the dictionary
+    if np.any(mask):
+        indices = np.searchsorted(old_vals_sorted, nodes[mask])
+        return_nodes[mask] = new_vals_sorted[indices]
+    
     return return_nodes
 
 

nettracer3d/proximity.py

@@ -296,6 +296,69 @@ def extract_pairwise_connections(connections):
     return output
 
 
+def average_nearest_neighbor_distances(point_centroids, root_set, compare_set, xy_scale=1.0, z_scale=1.0, num = 1):
+    """
+    Calculate the average distance between each point in root_set and its nearest neighbor in compare_set.
+    
+    Args:
+        point_centroids (dict): Dictionary mapping point IDs to [Z, Y, X] coordinates
+        root_set (set): Set of point IDs to find nearest neighbors for
+        compare_set (set): Set of point IDs to search for nearest neighbors in
+        xy_scale (float): Scaling factor for X and Y coordinates
+        z_scale (float): Scaling factor for Z coordinate
+    
+    Returns:
+        float: Average distance to nearest neighbors
+    """
+    
+    # Extract and scale coordinates for compare_set
+    compare_coords = []
+    compare_ids = list(compare_set)
+    
+    for point_id in compare_ids:
+        z, y, x = point_centroids[point_id]
+        compare_coords.append([z * z_scale, y * xy_scale, x * xy_scale])
+    
+    compare_coords = np.array(compare_coords)
+    
+    # Build KDTree for efficient nearest neighbor search
+    tree = KDTree(compare_coords)
+    
+    distances = {}
+    same_sets = root_set == compare_set
+    
+    for root_id in root_set:
+        # Get scaled coordinates for root point
+        z, y, x = point_centroids[root_id]
+        root_coord = np.array([z * z_scale, y * xy_scale, x * xy_scale])
+        
+        if same_sets:
+            # When sets are the same, find 2 nearest neighbors and take the second one
+            # (first one would be the point itself)
+            distances_to_all, indices = tree.query(root_coord, k= (num + 1))
+
+            temp_dist = 0
+            for i in range(1, len(distances_to_all)):
+                temp_dist += distances_to_all[i]
+
+            distances[root_id] = temp_dist/(len(distances_to_all) - 1)
+
+        else:
+            # Different sets, find nearest neighbors
+            distances_to_all, _ = tree.query(root_coord, k=num)
+            temp_dist = 0
+            for val in distances_to_all:
+                temp_dist += val
+
+            distances[root_id] = temp_dist/(len(distances_to_all))
+
+    avg = np.mean(list(distances.values())) if list(distances.values()) else 0.0
+
+    
+    # Return average distance
+    return avg, distances
+
+
 
 #voronois:
 def create_voronoi_3d_kdtree(centroids: Dict[Union[int, str], Union[Tuple[int, int, int], List[int]]], 
@@ -361,7 +424,7 @@ def convert_centroids_to_array(centroids_list, xy_scale = 1, z_scale = 1):
     """
     # Determine how many centroids we have
     n_points = len(centroids_list)
-    
+
     # Get dimensionality from the first centroid
     dim = len(list(centroids_list)[0])
     
@@ -404,7 +467,12 @@ def generate_r_values(points_array, step_size, bounds = None, dim = 2, max_propo
 
     
     # Calculate the longest dimension
-    dimensions = max_coords - min_coords
+    try:
+        dimensions = max_coords - min_coords
+    except: # Presume dimension mismatch
+        min_coords = np.array([0,0,0])
+        dimensions = max_coords - min_coords
+
     max_dimension = np.max(dimensions)
     
     # Calculate maximum r value (typically half the shortest side for 2D,
@@ -459,7 +527,10 @@ def optimized_ripleys_k(reference_points, subset_points, r_values, bounds=None,
     # Calculate volume of study area
     min_bounds, max_bounds = bounds
     sides = max_bounds - min_bounds
-    volume = np.prod(sides)
+    if dim == 2:
+        volume = sides[0] * sides[1]
+    else:
+        volume = np.prod(sides)
     
     # Point intensity (points per unit volume)
     intensity = n_ref / volume
@@ -618,7 +689,7 @@ def compute_ripleys_h(k_values, r_values, dimension=2):
     else:
         raise ValueError("Dimension must be 2 or 3")
 
-def plot_ripley_functions(r_values, k_values, h_values, dimension=2, figsize=(12, 5)):
+def plot_ripley_functions(r_values, k_values, h_values, dimension=2, rootiden = None, compiden = None, figsize=(12, 5)):
     """
     Plot Ripley's K and H functions with theoretical Poisson distribution references
     adjusted for edge effects.
@@ -651,7 +722,10 @@ def plot_ripley_functions(r_values, k_values, h_values, dimension=2, figsize=(12
     ax1.plot(r_values, theo_k, 'r--', label='Theoretical K(r) for CSR')
     ax1.set_xlabel('Distance (r)')
     ax1.set_ylabel('L(r)')
-    ax1.set_title("Ripley's K Function")
+    if rootiden is None or compiden is None:
+        ax1.set_title("Ripley's K Function")
+    else:
+        ax1.set_title(f"Ripley's K Function for {compiden} Clustering Around {rootiden}")
     ax1.legend()
     ax1.grid(True, alpha=0.3)
     
@@ -660,7 +734,10 @@ def plot_ripley_functions(r_values, k_values, h_values, dimension=2, figsize=(12
     ax2.plot(r_values, theo_h, 'r--', label='Theoretical H(r) for CSR')
     ax2.set_xlabel('Distance (r)')
     ax2.set_ylabel('L(r) Normalized')
-    ax2.set_title("Ripley's H Function")
+    if rootiden is None or compiden is None:
+        ax2.set_title("Ripley's H Function")
+    else:
+        ax2.set_title(f"Ripley's H Function for {compiden} Clustering Around {rootiden}")
     ax2.axhline(y=0, color='k', linestyle='-', alpha=0.3)
     ax2.legend()
     ax2.grid(True, alpha=0.3)

nettracer3d/segmenter.py

@@ -1412,7 +1412,7 @@ class InteractiveSegmenter:
                  use_two=self.use_two,
                  mem_lock=self.mem_lock)
 
-        print(f"Model data saved to {file_name}")
+        print(f"Model data saved to {file_name}. Please retrain current model prior to segmentation.")
 
 
     def load_model(self, file_name):

nettracer3d/segmenter_GPU.py

@@ -1221,7 +1221,7 @@ class InteractiveSegmenter:
                  use_two=self.use_two,
                  mem_lock=self.mem_lock)
 
-        print(f"Model data saved to {file_name}")
+        print(f"Model data saved to {file_name}. Please retrain current model prior to segmentation.")
 
 
     def load_model(self, file_name):

nettracer3d/simple_network.py

@@ -174,32 +174,50 @@ def show_identity_network(excel_file_path, node_identities, geometric=False, geo
     G = nx.Graph()
     G.add_edges_from(edges)
 
-    # Create a more sophisticated color palette using a combination of colormap sequences
+    # ENHANCED COLOR LOGIC - Generate bright, contrasting colors
     unique_categories = list(set(identity_dict.values()))
     num_categories = len(unique_categories)
     
-    # Create a color palette that combines multiple colormaps for more distinct colors
-    if num_categories <= 10:
-        colors = plt.cm.tab10(np.linspace(0, 1, num_categories))
-    elif num_categories <= 20:
-        colors1 = plt.cm.tab20(np.linspace(0, 1, min(num_categories, 20)))
-        colors = colors1[:num_categories]
-    else:
-        # For large number of categories, combine multiple distinct colormaps
-        colors1 = plt.cm.tab20(np.linspace(0, 1, 20))
-        colors2 = plt.cm.Set3(np.linspace(0, 1, 12))
-        colors3 = plt.cm.Pastel1(np.linspace(0, 1, 9))
-        colors4 = plt.cm.Paired(np.linspace(0, 1, 12))
-        
-        # Combine and take needed number of colors
-        all_colors = np.vstack([colors1, colors2, colors3, colors4])
-        # Shuffle the colors to ensure adjacent categories have distinct colors
-        np.random.seed(42)  # For consistency
-        np.random.shuffle(all_colors)
-        colors = all_colors[:num_categories]
-
-    color_map = {category: mcolors.to_hex(color[:3]) 
-                 for category, color in zip(unique_categories, colors)}
+    def generate_distinct_colors(n):
+        """Generate visually distinct, bright colors with maximum contrast"""
+        if n <= 12:
+            # Use carefully selected high-contrast colors for small sets
+            base_colors = [
+                '#FF0000',  # Bright Red
+                '#0066FF',  # Bright Blue
+                '#00CC00',  # Bright Green
+                '#FF8800',  # Bright Orange
+                '#8800FF',  # Bright Purple
+                '#FFFF00',  # Bright Yellow
+                '#FF0088',  # Bright Pink
+                '#00FFFF',  # Bright Cyan
+                '#88FF00',  # Bright Lime
+                '#FF4400',  # Red-Orange
+                '#0088FF',  # Sky Blue
+                '#CC00FF'   # Magenta
+            ]
+            return base_colors[:n]
+        else:
+            # For larger sets, use HSV color space for maximum separation
+            colors = []
+            import colorsys
+            for i in range(n):
+                hue = (i * 360 / n) % 360
+                # Alternate saturation and value to create more distinction
+                sat = 0.85 if i % 2 == 0 else 0.95
+                val = 0.95 if i % 3 != 0 else 0.85
+                
+                # Convert HSV to RGB
+                rgb = colorsys.hsv_to_rgb(hue/360, sat, val)
+                hex_color = '#{:02x}{:02x}{:02x}'.format(
+                    int(rgb[0]*255), int(rgb[1]*255), int(rgb[2]*255)
+                )
+                colors.append(hex_color)
+            return colors
+    
+    # Generate the enhanced color palette
+    colors = generate_distinct_colors(num_categories)
+    color_map = dict(zip(unique_categories, colors))
 
     # Node size handling
     node_dict = {node: 30 if identity_dict[node] == 'Edge' else 100 
@@ -225,11 +243,11 @@ def show_identity_network(excel_file_path, node_identities, geometric=False, geo
     # Create separate axes for the graph and legend
     graph_ax = plt.gca()
     
-    # Draw the network
+    # Draw the network with enhanced font styling
     node_colors = [color_map[identity_dict[node]] for node in G.nodes()]
     nx.draw(G, pos, ax=graph_ax, with_labels=True, font_color='black', 
             font_weight='bold', node_size=node_sizes_list, 
-            node_color=node_colors, alpha=0.8, font_size=12)
+            node_color=node_colors, alpha=0.8, font_size=11, font_family='sans-serif')
 
     # Create custom legend with multiple columns if needed
     legend_handles = [Patch(color=color, label=category) 

{nettracer3d-0.7.9.dist-info → nettracer3d-0.8.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nettracer3d
-Version: 0.7.9
+Version: 0.8.1
 Summary: Scripts for intializing and analyzing networks from segmentations of three dimensional images.
 Author-email: Liam McLaughlin <liamm@wustl.edu>
 Project-URL: Documentation, https://nettracer3d.readthedocs.io/en/latest/
@@ -73,6 +73,8 @@ NetTracer3D is free to use/fork for academic/nonprofit use so long as citation i
 
 NetTracer3D was developed by Liam McLaughlin while working under Dr. Sanjay Jain at Washington University School of Medicine.
 
--- Version 0.7.9 Updates -- 
+-- Version 0.8.1 Updates -- 
 
-	* The GPU segmenter was being imported regardless of GPU status, causing the program to fail without cupy (which should be optional), fixed that.
+	* Added nearest neighbor evaluation function (Analysis -> Stats -> Avg Nearest Neighbor)
+	* Added heatmap outputs for node degrees (Analysis -> Data/Overlays -> Get Degree Information).
+	* Bug fixes and misc improvements.

nettracer3d-0.8.1.dist-info/RECORD

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+nettracer3d/community_extractor.py,sha256=ZOz97Au4k7dHK8azarWQtxCPyvwzGmDHNL8kTIC9by8,22670
+nettracer3d/excelotron.py,sha256=lS5vnpoOGZWp7fdqVpTPqeC-mUKrfwDrWHfx4PQ7Uzg,71384
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+nettracer3d/neighborhoods.py,sha256=LnflCJdlNOuILal_fsT-idp1IROQH2PvLG-Ro3m55vo,26757
+nettracer3d/nettracer.py,sha256=F91vCLJ-OB5qGLjOXRjNh2qE3vFkXYh_VPpFud2Cu4o,231437
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nettracer3d-0.7.9.dist-info/RECORD

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