nettracer3d 0.8.3__py3-none-any.whl → 0.8.5__py3-none-any.whl

nettracer3d/smart_dilate.py

@@ -223,6 +223,7 @@ def dilate_3D_dt(array, search_distance, xy_scaling=1.0, z_scaling=1.0, GPU = Fa
             inv, indices = compute_distance_transform_GPU(inv, return_dists = True, sampling = [z_scaling, xy_scaling, xy_scaling])
         except:
             print("Failed, attempting on CPU...")
+            cleanup()
             #Who would have seen this coming?:
             inv, indices = compute_distance_transform(inv, return_dists = True, sampling = [z_scaling, xy_scaling, xy_scaling])
     else:
@@ -251,15 +252,37 @@ def process_chunk(start_idx, end_idx, nodes, ring_mask, nearest_label_indices):
     nodes_chunk = nodes[:, start_idx:end_idx, :]
     ring_mask_chunk = ring_mask[:, start_idx:end_idx, :]
     dilated_nodes_with_labels_chunk = np.copy(nodes_chunk)
+    
+    # Get all ring indices at once
     ring_indices = np.argwhere(ring_mask_chunk)
-
-    for index in ring_indices:
-        z, y, x = index
-        nearest_z, nearest_y, nearest_x = nearest_label_indices[:, z, y + start_idx, x]
-        try: #There was an index error here once on the highest val of the second axis. I could not understand why because it usually doesnt hence the try block.
-            dilated_nodes_with_labels_chunk[z, y, x] = nodes[nearest_z, nearest_y, nearest_x]
-        except:
-            pass
+    
+    if len(ring_indices) > 0:
+        # Extract coordinates
+        z_coords = ring_indices[:, 0]
+        y_coords = ring_indices[:, 1] 
+        x_coords = ring_indices[:, 2]
+        
+        # Get nearest label coordinates (adjust y for chunk offset)
+        nearest_coords = nearest_label_indices[:, z_coords, y_coords + start_idx, x_coords]
+        nearest_z = nearest_coords[0, :]
+        nearest_y = nearest_coords[1, :]
+        nearest_x = nearest_coords[2, :]
+        
+        # Vectorized assignment
+        try:
+            dilated_nodes_with_labels_chunk[z_coords, y_coords, x_coords] = \
+                nodes[nearest_z, nearest_y, nearest_x]
+        except IndexError:
+            # Fallback for any problematic indices
+            valid_mask = (nearest_z < nodes.shape[0]) & \
+                        (nearest_y < nodes.shape[1]) & \
+                        (nearest_x < nodes.shape[2]) & \
+                        (nearest_z >= 0) & (nearest_y >= 0) & (nearest_x >= 0)
+            
+            valid_indices = valid_mask.nonzero()[0]
+            if len(valid_indices) > 0:
+                dilated_nodes_with_labels_chunk[z_coords[valid_indices], y_coords[valid_indices], x_coords[valid_indices]] = \
+                    nodes[nearest_z[valid_indices], nearest_y[valid_indices], nearest_x[valid_indices]]
     
     return dilated_nodes_with_labels_chunk
 
@@ -506,6 +529,7 @@ def compute_distance_transform_GPU(nodes, return_dists = False, sampling = [1, 1
 
 
 def compute_distance_transform(nodes, return_dists = False, sampling = [1, 1, 1]):
+    #print("(Now doing distance transform...)")
     is_pseudo_3d = nodes.shape[0] == 1
     if is_pseudo_3d:
         nodes = np.squeeze(nodes)  # Convert to 2D for processing
@@ -548,13 +572,15 @@ def compute_distance_transform_distance_GPU(nodes, sampling = [1, 1, 1]):
     distance = cp.asnumpy(distance)
 
     if is_pseudo_3d:
-        np.expand_dims(distance, axis = 0)
+        distance = np.expand_dims(distance, axis = 0)
     
     return distance    
 
 
 def compute_distance_transform_distance(nodes, sampling = [1, 1, 1]):
 
+    #print("(Now doing distance transform...)")
+
     is_pseudo_3d = nodes.shape[0] == 1
     if is_pseudo_3d:
         nodes = np.squeeze(nodes)  # Convert to 2D for processing
@@ -563,7 +589,7 @@ def compute_distance_transform_distance(nodes, sampling = [1, 1, 1]):
     # Fallback to CPU if there's an issue with GPU computation
     distance = distance_transform_edt(nodes, sampling = sampling)
     if is_pseudo_3d:
-        np.expand_dims(distance, axis = 0)
+        distance = np.expand_dims(distance, axis = 0)
     return distance
 
 
@@ -621,6 +647,14 @@ def catch_memory(e):
         downsample_needed = (memory_required/total_memory)
         return (downsample_needed)
 
+def cleanup():
+
+    try:
+        cp.get_default_memory_pool().free_all_blocks()
+    except:
+        pass
+
+
 
 if __name__ == "__main__":
     nodes = input("Labelled Nodes tiff?: ")

{nettracer3d-0.8.3.dist-info → nettracer3d-0.8.5.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nettracer3d
-Version: 0.8.3
+Version: 0.8.5
 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/
@@ -104,9 +104,12 @@ This gui is built from the PyQt6 package and therefore may not function on docke
 For a (slightly outdated) video tutorial on using the GUI: https://www.youtube.com/watch?v=cRatn5VTWDY
 
 NetTracer3D is free to use/fork for academic/nonprofit use so long as citation is provided, and is available for commercial use at a fee (see license file for information).
+The current citation is here: 
+
+McLaughlin, L., Zhang, B., Sharma, S. et al. Three dimensional multiscalar neurovascular nephron connectivity map of the human kidney across the lifespan. Nat Commun 16, 5161 (2025). https://doi.org/10.1038/s41467-025-60435-8
 
 NetTracer3D was developed by Liam McLaughlin while working under Dr. Sanjay Jain at Washington University School of Medicine.
 
--- Version 0.8.3 Updates -- 
+-- Version 0.8.5 Updates -- 
 
-	* Added better color legend display
+	* See Documentation Once Updated

nettracer3d-0.8.5.dist-info/RECORD

@@ -0,0 +1,25 @@
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+nettracer3d/cellpose_manager.py,sha256=qZpTxSkmPb38Pru8TmjJ88xxcD_wM02EfJB5Mw9Xx4Y,6021
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+nettracer3d/smart_dilate.py,sha256=TvRUh6B4q4zIdCO1BWH-xgTdND5OUNmo99eyxG9oIAU,27145
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+nettracer3d-0.8.5.dist-info/RECORD,,

{nettracer3d-0.8.3.dist-info → nettracer3d-0.8.5.dist-info}/licenses/LICENSE

@@ -1,7 +1,5 @@
-NetTracer3D is freely available for academic and nonprofit use and can be obtained from Liam McLaughlin (boom2449@gmail.com) OR at pip (pip install nettracer3d), provided that the following citation is included in any abstract, paper, or presentation utilizing NetTracer3D.
+NetTracer3D is freely available for academic and nonprofit use and can be obtained from Liam McLaughlin (boom2449@gmail.com) OR at pip (pip install nettracer3d), provided that the following citation is included in any abstract, paper, or presentation utilizing NetTracer3D:
 
-Three Dimensional Multiscalar Neurovascular Nephron Connectivity Map of the Human Kidney Across the Lifespan
-Liam McLaughlin, Bo Zhang, Siddharth Sharma, Amanda L. Knoten, Madhurima Kaushal, Jeffrey M. Purkerson, Heidy Huyck, Gloria S. Pryhuber, Joseph P. Gaut, Sanjay Jain
-bioRxiv 2024.07.29.605633; doi: https://doi.org/10.1101/2024.07.29.605633
+McLaughlin, L., Zhang, B., Sharma, S. et al. Three dimensional multiscalar neurovascular nephron connectivity map of the human kidney across the lifespan. Nat Commun 16, 5161 (2025). https://doi.org/10.1038/s41467-025-60435-8
 
 Commercial use is available for a fee. Copyright © is held by Washington University. Please direct all commercial requests for licensing, information, and limited evaluation copies to Washington University's Office of Technology Management at OTM@wustl.edu.

nettracer3d-0.8.3.dist-info/RECORD

@@ -1,24 +0,0 @@
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