nettracer3d 0.9.5__py3-none-any.whl → 0.9.6__py3-none-any.whl

nettracer3d/proximity.py

@@ -966,4 +966,94 @@ def partition_objects_into_cells(object_centroids, cell_size):
         cell_assignments[int(cell_number)].append(int(label))
     
     # Convert defaultdict to regular dict and sort keys
-    return dict(sorted(cell_assignments.items()))
+    return dict(sorted(cell_assignments.items()))
+
+
+
+# To use with the merge node identities manual calculation: 
+
+def get_reslice_indices_for_id(slice_obj, array_shape):
+    """Convert slice object to padded indices accounting for dilation and boundaries"""
+    if slice_obj is None:
+        return None, None, None
+        
+    z_slice, y_slice, x_slice = slice_obj
+    
+    # Extract min/max from slices
+    z_min, z_max = z_slice.start, z_slice.stop - 1
+    y_min, y_max = y_slice.start, y_slice.stop - 1
+    x_min, x_max = x_slice.start, x_slice.stop - 1
+
+    # Boundary checks
+    y_max = min(y_max, array_shape[1] - 1)
+    x_max = min(x_max, array_shape[2] - 1)
+    z_max = min(z_max, array_shape[0] - 1)
+    y_min = max(y_min, 0)
+    x_min = max(x_min, 0)
+    z_min = max(z_min, 0)
+
+    return [z_min, z_max], [y_min, y_max], [x_min, x_max]
+
+
+def _get_node_edge_dict_id(label_array, edge_array, label):
+    """Internal method used for the secondary algorithm to find which nodes interact with which edges."""
+    
+    # Create compound condition: label matches AND edge value > 0
+    valid_mask = (label_array == label) & (edge_array > 0)
+    valid_edges = edge_array[valid_mask]
+    
+    if len(valid_edges) > 0:
+        edge_val = np.mean(valid_edges)
+    else:
+        edge_val = 0  
+    
+    return edge_val
+    
+def process_label_id(args):
+    """Modified to use pre-computed bounding boxes instead of argwhere"""
+    nodes, edges, label, array_shape, bounding_boxes = args
+    
+    # Get the pre-computed bounding box for this label
+    slice_obj = bounding_boxes[int(label)-1]  # -1 because label numbers start at 1
+    if slice_obj is None:
+        return None, None, None
+        
+    z_vals, y_vals, x_vals = get_reslice_indices_for_id(slice_obj, array_shape)
+    if z_vals is None:
+        return None, None, None
+        
+    sub_nodes = reslice_3d_array((nodes, z_vals, y_vals, x_vals))
+    sub_edges = reslice_3d_array((edges, z_vals, y_vals, x_vals))
+    return label, sub_nodes, sub_edges
+
+
+def create_node_dictionary_id(nodes, edges, num_nodes):
+    """Modified to pre-compute all bounding boxes using find_objects"""
+    node_dict = {}
+    array_shape = nodes.shape
+    
+    # Get all bounding boxes at once
+    bounding_boxes = ndimage.find_objects(nodes)
+    
+    # Use ThreadPoolExecutor for parallel execution
+    with ThreadPoolExecutor(max_workers=mp.cpu_count()) as executor:
+        # Create args list with bounding_boxes included
+        args_list = [(nodes, edges, i, array_shape, bounding_boxes) 
+                    for i in range(1, int(num_nodes) + 1)]
+
+        # Execute parallel tasks to process labels
+        results = executor.map(process_label_id, args_list)
+
+        # Process results in parallel
+        for label, sub_nodes, sub_edges in results:
+            executor.submit(create_dict_entry_id, node_dict, label, sub_nodes, sub_edges)
+
+    return node_dict
+
+def create_dict_entry_id(node_dict, label, sub_nodes, sub_edges):
+    """Internal method used for the secondary algorithm to pass around args in parallel."""
+
+    if label is None:
+        pass
+    else:
+        node_dict[label] = _get_node_edge_dict_id(sub_nodes, sub_edges, label)

{nettracer3d-0.9.5.dist-info → nettracer3d-0.9.6.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nettracer3d
-Version: 0.9.5
+Version: 0.9.6
 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/
@@ -110,8 +110,10 @@ 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 0.9.5 Updates --
+-- Version 0.9.6 Updates --
 
-	* Adjusted how pan mode works a little bit.
+	* Moved some file menu options around.
+	* The 'merge node id' option now offers interactive support for assisted thresholding for any new identity channels the user is trying to merge with.
 	* Bug Fixes
-	* Erode can now optionally preserve object labels.
+	* The 'merge nodes' option now can provide centroids prior to the merge, since oftentimes objects end up on top of each other.
+	* A few other minor adjustments.

{nettracer3d-0.9.5.dist-info → nettracer3d-0.9.6.dist-info}/RECORD

@@ -4,22 +4,22 @@ nettracer3d/community_extractor.py,sha256=yFHwygfeK-p0bjUMaIpeq_v6LbsKZiVAvPD6nh
 nettracer3d/excelotron.py,sha256=aNof6k-DgMxVyFgsl3ltSCxG4vZW49cuvCBzfzhYhUY,75072
 nettracer3d/modularity.py,sha256=pborVcDBvICB2-g8lNoSVZbIReIBlfeBmjFbPYmtq7Y,22443
 nettracer3d/morphology.py,sha256=jyDjYzrZ4LvI5jOyw8DLsxmo-i5lpqHsejYpW7Tq7Mo,19786
-nettracer3d/neighborhoods.py,sha256=2QzGKkQCSUerxigkcHF4iN7ys8kv-KHTbkD_9_2Krgo,58365
-nettracer3d/nettracer.py,sha256=Yse2gTI_WaITRJmJxUttqAgsxUzUq5wcvFdGPOw-7r4,266988
-nettracer3d/nettracer_gui.py,sha256=J3vVucTa3HIzfdspHJRQ2cJTD4xTOmxEqbapvMPCy8U,617103
+nettracer3d/neighborhoods.py,sha256=iIaHU1COIdRtzRpAuIQKfLGLNKYFK3dL8Vb_EeJIlEA,46459
+nettracer3d/nettracer.py,sha256=d9Mhz-pHox5OfGGUSTrkTBJzCWCrbQvClTu2ANt-jUE,267943
+nettracer3d/nettracer_gui.py,sha256=ZJzW3-P3m18LPhoIkCqLVTqsRb8nRFzzwYmQ-vfIs5Y,628407
 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=ZCfthYpQbDBwXBcVioxyzgO9PZACu6mQ8pSXdldP1TM,38592
+nettracer3d/proximity.py,sha256=WaHPwE6ypeInFO_LnMT0zaVE53jX3TJx6h7nmtYtr8U,41824
 nettracer3d/run.py,sha256=xYeaAc8FCx8MuzTGyL3NR3mK7WZzffAYAH23bNRZYO4,127
 nettracer3d/segmenter.py,sha256=-Llkhp3TlAIBXZNhcfMFQRdg0vec1xtlOm0c4_bSU9U,75761
 nettracer3d/segmenter_GPU.py,sha256=optCZ_zLIfe99rgqmyKWUZlWW5TF5jEC_C3keu1m7VQ,77771
 nettracer3d/simple_network.py,sha256=dkG4jpc4zzdeuoaQobgGfL3PNo6N8dGKQ5hEEubFIvA,9947
 nettracer3d/smart_dilate.py,sha256=TvRUh6B4q4zIdCO1BWH-xgTdND5OUNmo99eyxG9oIAU,27145
-nettracer3d-0.9.5.dist-info/licenses/LICENSE,sha256=jnNT-yBeIAKAHpYthPvLeqCzJ6nSurgnKmloVnfsjCI,764
-nettracer3d-0.9.5.dist-info/METADATA,sha256=OD9KdN1NkyKgm97r4jiU-sLRE5EQkg5egzf5xolEzUI,7085
-nettracer3d-0.9.5.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-nettracer3d-0.9.5.dist-info/entry_points.txt,sha256=Nx1rr_0QhJXDBHAQg2vcqCzLMKBzSHfwy3xwGkueVyc,53
-nettracer3d-0.9.5.dist-info/top_level.txt,sha256=zsYy9rZwirfCEOubolhee4TyzqBAL5gSUeFMzhFTX8c,12
-nettracer3d-0.9.5.dist-info/RECORD,,
+nettracer3d-0.9.6.dist-info/licenses/LICENSE,sha256=jnNT-yBeIAKAHpYthPvLeqCzJ6nSurgnKmloVnfsjCI,764
+nettracer3d-0.9.6.dist-info/METADATA,sha256=MHM0yBkUeOtSk_cdnD6-5KEmgS7oiQaLBBDGg4ZMbE8,7343
+nettracer3d-0.9.6.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+nettracer3d-0.9.6.dist-info/entry_points.txt,sha256=Nx1rr_0QhJXDBHAQg2vcqCzLMKBzSHfwy3xwGkueVyc,53
+nettracer3d-0.9.6.dist-info/top_level.txt,sha256=zsYy9rZwirfCEOubolhee4TyzqBAL5gSUeFMzhFTX8c,12
+nettracer3d-0.9.6.dist-info/RECORD,,