nettracer3d 0.8.9__py3-none-any.whl → 0.9.0__py3-none-any.whl

nettracer3d/proximity.py

@@ -469,68 +469,121 @@ 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):
+def average_nearest_neighbor_distances(point_centroids, root_set, compare_set, xy_scale=1.0, z_scale=1.0, num=1, do_borders=False):
     """
     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
+        point_centroids (dict): Dictionary mapping point IDs to [Z, Y, X] coordinates (when do_borders=False)
+                               OR dictionary mapping labels to border coordinates (when do_borders=True)
+        root_set (set or dict): Set of point IDs (when do_borders=False) 
+                               OR dict {label: border_coords} (when do_borders=True)
+        compare_set (set or numpy.ndarray): Set of point IDs (when do_borders=False)
+                                           OR 1D array of border coordinates (when do_borders=True)
         xy_scale (float): Scaling factor for X and Y coordinates
         z_scale (float): Scaling factor for Z coordinate
+        num (int): Number of nearest neighbors (ignored when do_borders=True, always uses 1)
+        do_borders (bool): If True, perform border-to-border distance calculation
     
     Returns:
-        float: Average distance to nearest neighbors
+        tuple: (average_distance, distances_dict)
     """
     
-    # 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
+    if do_borders:
+        # Border comparison mode
+        if not isinstance(compare_set, np.ndarray):
+            raise ValueError("When do_borders=True, compare_set must be a numpy array of coordinates")
+        
+        # Vectorized scaling for compare coordinates
+        compare_coords_scaled = compare_set.astype(float)
+        compare_coords_scaled[:, 0] *= z_scale  # Z coordinates
+        compare_coords_scaled[:, 1:] *= xy_scale  # Y and X coordinates
+        
+        distances = {}
+        
+        for label, border_coords in root_set.items():
+            if len(border_coords) == 0:
+                continue
+                
+            # Vectorized scaling for border coordinates
+            border_coords_scaled = border_coords.astype(float)
+            border_coords_scaled[:, 0] *= z_scale  # Z coordinates
+            border_coords_scaled[:, 1:] *= xy_scale  # Y and X coordinates
+            
+            # Remove overlapping coordinates to avoid distance = 0
+            # Create a set of tuples for fast membership testing
+            border_coords_set = set(map(tuple, border_coords_scaled))
+            
+            # Filter out overlapping coordinates from compare set
+            non_overlapping_mask = np.array([
+                tuple(coord) not in border_coords_set 
+                for coord in compare_coords_scaled
+            ])
+            
+            if not np.any(non_overlapping_mask):
+                # All compare coordinates overlap - skip this object or set to NaN
+                distances[label] = np.nan
+                continue
+            
+            filtered_compare_coords = compare_coords_scaled[non_overlapping_mask]
+            
+            # Build KDTree with filtered coordinates
+            tree = KDTree(filtered_compare_coords)
+            
+            # Vectorized nearest neighbor search for all border points at once
+            distances_to_all, _ = tree.query(border_coords_scaled, k=1)
+            
+            # Find minimum distance for this object
+            distances[label] = np.min(distances_to_all)
+        
+        # Calculate average excluding NaN values
+        valid_distances = [d for d in distances.values() if not np.isnan(d)]
+        avg = np.mean(valid_distances) if valid_distances else np.nan
+        return avg, distances
     
-    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])
+    else:
+        # Original centroid comparison mode (unchanged)
+        # Extract coordinates for compare_set
+        compare_coords = np.array([point_centroids[point_id] for point_id in compare_set])
         
+        # Vectorized scaling for compare coordinates
+        compare_coords_scaled = compare_coords.astype(float)
+        compare_coords_scaled[:, 0] *= z_scale  # Z coordinates
+        compare_coords_scaled[:, 1:] *= xy_scale  # Y and X coordinates
+        
+        # Build KDTree for efficient nearest neighbor search
+        tree = KDTree(compare_coords_scaled)
+        
+        distances = {}
+        same_sets = root_set == compare_set
+        
+        # Extract and scale root coordinates all at once
+        root_coords = np.array([point_centroids[root_id] for root_id in root_set])
+        root_coords_scaled = root_coords.astype(float)
+        root_coords_scaled[:, 0] *= z_scale  # Z coordinates
+        root_coords_scaled[:, 1:] *= xy_scale  # Y and X coordinates
+        
+        # Vectorized nearest neighbor search for all root points
         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)
-
+            distances_to_all, indices = tree.query(root_coords_scaled, k=(num + 1))
+            # Remove self-matches (first column) and average the rest
+            if num == 1:
+                distances_array = distances_to_all[:, 1]  # Just take second nearest
+            else:
+                distances_array = np.mean(distances_to_all[:, 1:], axis=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
-
+            distances_to_all, _ = tree.query(root_coords_scaled, k=num)
+            if num == 1:
+                distances_array = distances_to_all.flatten()
+            else:
+                distances_array = np.mean(distances_to_all, axis=1)
+        
+        # Map back to root_ids
+        for i, root_id in enumerate(root_set):
+            distances[root_id] = distances_array[i]
+        
+        avg = np.mean(distances_array) if len(distances_array) > 0 else 0.0
+        return avg, distances
 
 
 #voronois:

{nettracer3d-0.8.9.dist-info → nettracer3d-0.9.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nettracer3d
-Version: 0.8.9
+Version: 0.9.0
 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/
@@ -110,6 +110,16 @@ McLaughlin, L., Zhang, B., Sharma, S. et al. Three dimensional multiscalar neuro
 
 NetTracer3D was developed by Liam McLaughlin while working under Dr. Sanjay Jain at Washington University School of Medicine.
 
--- Version 0.8.9 Updates -- 
-
-	* See Documentation Once Updated
+-- Version 0.9.0 Updates --
+	* Note that this includes updates for 0.8.3 - 0.9.0
+	* Bug Fixes
+	* Updated network histogram statistics menu, and moved degree distribution here
+	* Added gray watershed
+	* Updated binary watershed
+	* Improved branch labelling method
+	* Updated branch removal in skeletonization method to no longer trim branches that do not reach their node.
+	* Added default branchpoint and branch-adjacency calculation options.
+	* Improved speed of painting and panning.
+	* Enabled the nearest neighbor method to handle non-centroid objects, for the first neighbor at least. And updated it to actually predict theoretical clustering when coloring the heatmap.
+	* Improved segmenter.
+	* Added centroids UMAP method.

{nettracer3d-0.8.9.dist-info → nettracer3d-0.9.0.dist-info}/RECORD

@@ -1,25 +1,25 @@
 nettracer3d/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-nettracer3d/cellpose_manager.py,sha256=qZpTxSkmPb38Pru8TmjJ88xxcD_wM02EfJB5Mw9Xx4Y,6021
+nettracer3d/cellpose_manager.py,sha256=NfRqW6Zl7yRU4qHCS_KjmR0R6QANSSgCO0_dr-eivxg,6694
 nettracer3d/community_extractor.py,sha256=QG2v2y9lKb07LRU0zXCAlA_z-96BNqLHh5xP17KLmYA,28147
 nettracer3d/excelotron.py,sha256=X9v_mte8gJBPNGdj6NJNUYja0Z6eorVoKAFx4nHiMnU,72058
-nettracer3d/modularity.py,sha256=O9OeKbjD3v6gSFz9K2GzP6LsxlpQaPfeJbM1pyIEigw,21788
+nettracer3d/modularity.py,sha256=pborVcDBvICB2-g8lNoSVZbIReIBlfeBmjFbPYmtq7Y,22443
 nettracer3d/morphology.py,sha256=jyDjYzrZ4LvI5jOyw8DLsxmo-i5lpqHsejYpW7Tq7Mo,19786
-nettracer3d/neighborhoods.py,sha256=VWubD5CBu9aNPhUea7FbAk9aTOq0FLKR9y-1VT7YkAc,39677
-nettracer3d/nettracer.py,sha256=TEV-nDmkcGP3UjWEor1LtEwm5mFBQu2nB0VRyz9Lt08,253649
-nettracer3d/nettracer_gui.py,sha256=aYU4r8HLLNiKPOpQIjdvRu2BRtvx18Z6OXa8N7g27Xg,546298
+nettracer3d/neighborhoods.py,sha256=qOmN8gDZM-J5zsFFaQ772obj6PzsiISXzVZgnlmGGS8,41349
+nettracer3d/nettracer.py,sha256=cuHc0djb6auNgZ6c38kow9N4zTN7ve00gGBnBSUgEAc,263183
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 nettracer3d/network_analysis.py,sha256=kBzsVaq4dZkMe0k-VGvQIUvM-tK0ZZ8bvb-wtsugZRQ,46150
 nettracer3d/network_draw.py,sha256=F7fw6Pcf4qWOhdKwLmhwqWdschbDlHzwCVolQC9imeU,14117
 nettracer3d/node_draw.py,sha256=kZcR1PekLg0riioNeGcALIXQyZ5PtHA_9MT6z7Zovdk,10401
 nettracer3d/painting.py,sha256=K_dwngivw80r-Yyg4btKMsWGn566ZE9PnrQl986uxJE,23497
-nettracer3d/proximity.py,sha256=bTaucn_InQ-v1GIk8ug-dXvDhIO59rnBMl5nIwAmNyw,35335
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 nettracer3d/run.py,sha256=xYeaAc8FCx8MuzTGyL3NR3mK7WZzffAYAH23bNRZYO4,127
 nettracer3d/segmenter.py,sha256=_ZBLe2eqV9c5yxuyfN69XR5mBoc_OD-CZjwdTCUV0YQ,67045
 nettracer3d/segmenter_GPU.py,sha256=SGOsy8tSRlxAnD1OrJmjhiQ3k6CWiUFZZdrN6pkkgeU,69057
 nettracer3d/simple_network.py,sha256=dkG4jpc4zzdeuoaQobgGfL3PNo6N8dGKQ5hEEubFIvA,9947
 nettracer3d/smart_dilate.py,sha256=TvRUh6B4q4zIdCO1BWH-xgTdND5OUNmo99eyxG9oIAU,27145
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-nettracer3d-0.8.9.dist-info/top_level.txt,sha256=zsYy9rZwirfCEOubolhee4TyzqBAL5gSUeFMzhFTX8c,12
-nettracer3d-0.8.9.dist-info/RECORD,,
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