nettracer3d 0.5.2__py3-none-any.whl → 0.5.4__py3-none-any.whl

nettracer3d/proximity.py

@@ -3,6 +3,7 @@ from . import nettracer
 import multiprocessing as mp
 from concurrent.futures import ThreadPoolExecutor, as_completed
 from scipy.spatial import KDTree
+from scipy import ndimage
 import concurrent.futures
 import multiprocessing as mp
 import pandas as pd
@@ -11,41 +12,35 @@ from typing import Dict, Union, Tuple, List, Optional
 
 # Related to morphological border searching:
 
-def get_reslice_indices(args):
-    """Internal method used for the secondary algorithm that finds dimensions for subarrays around nodes"""
-
-    indices, dilate_xy, dilate_z, array_shape = args
-    try:
-        max_indices = np.amax(indices, axis = 0) #Get the max/min of each index.
-    except ValueError: #Return Nones if this error is encountered
+def get_reslice_indices(slice_obj, dilate_xy, dilate_z, array_shape):
+    """Convert slice object to padded indices accounting for dilation and boundaries"""
+    if slice_obj is None:
         return None, None, None
-    min_indices = np.amin(indices, axis = 0)
-
-    z_max, y_max, x_max = max_indices[0], max_indices[1], max_indices[2]
-
-    z_min, y_min, x_min = min_indices[0], min_indices[1], min_indices[2]
-
-    y_max = y_max + ((dilate_xy-1)/2) + 1 #Establish dimensions of intended subarray, expanding the max/min indices to include
-    y_min = y_min - ((dilate_xy-1)/2) - 1 #the future dilation space (by adding/subtracting half the dilation kernel for each axis)
-    x_max = x_max + ((dilate_xy-1)/2) + 1 #an additional index is added in each direction to make sure nothing is discluded.
+        
+    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
+
+    # Add dilation padding
+    y_max = y_max + ((dilate_xy-1)/2) + 1
+    y_min = y_min - ((dilate_xy-1)/2) - 1
+    x_max = x_max + ((dilate_xy-1)/2) + 1
     x_min = x_min - ((dilate_xy-1)/2) - 1
     z_max = z_max + ((dilate_z-1)/2) + 1
     z_min = z_min - ((dilate_z-1)/2) - 1
 
-    if y_max > (array_shape[1] - 1): #Some if statements to make sure the subarray will not cause an indexerror
-        y_max = (array_shape[1] - 1)
-    if x_max > (array_shape[2] - 1):
-        x_max = (array_shape[2] - 1)
-    if z_max > (array_shape[0] - 1):
-        z_max = (array_shape[0] - 1)
-    if y_min < 0:
-        y_min = 0
-    if x_min < 0:
-        x_min = 0
-    if z_min < 0:
-        z_min = 0
-
-    y_vals = [y_min, y_max] #Return the subarray dimensions as lists
+    # 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)
+
+    y_vals = [y_min, y_max]
     x_vals = [x_min, x_max]
     z_vals = [z_min, z_max]
 
@@ -85,40 +80,43 @@ def _get_node_node_dict(label_array, label, dilate_xy, dilate_z):
     return label_array
 
 def process_label(args):
-    """Internal method used for the secondary algorithm to process a particular node."""
-    nodes, label, dilate_xy, dilate_z, array_shape = args
+    """Modified to use pre-computed bounding boxes instead of argwhere"""
+    nodes, label, dilate_xy, dilate_z, array_shape, bounding_boxes = args
     print(f"Processing node {label}")
-    indices = np.argwhere(nodes == label)
-    if len(indices) == 0:
+    
+    # Get the pre-computed bounding box for this label
+    slice_obj = bounding_boxes[label-1]  # -1 because label numbers start at 1
+    if slice_obj is None:
         return None, None
-    z_vals, y_vals, x_vals = get_reslice_indices((indices, dilate_xy, dilate_z, array_shape))
-    if z_vals is None: #If get_reslice_indices ran into a ValueError, nothing is returned.
+        
+    z_vals, y_vals, x_vals = get_reslice_indices(slice_obj, dilate_xy, dilate_z, array_shape)
+    if z_vals is None:
         return None, None
+        
     sub_nodes = reslice_3d_array((nodes, z_vals, y_vals, x_vals))
     return label, sub_nodes
 
 
-def create_node_dictionary(nodes, num_nodes, dilate_xy, dilate_z, targets = None):
-    """Internal method used for the secondary algorithm to process nodes in parallel."""
-    # Initialize the dictionary to be returned
+def create_node_dictionary(nodes, num_nodes, dilate_xy, dilate_z, targets=None):
+    """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:
-        # First parallel section to process labels
-        # List of arguments for each parallel task
-        args_list = [(nodes, i, dilate_xy, dilate_z, array_shape) for i in range(1, num_nodes + 1)]
+        # Create args list with bounding_boxes included
+        args_list = [(nodes, i, dilate_xy, dilate_z, array_shape, bounding_boxes) 
+                    for i in range(1, num_nodes + 1)]
 
         if targets is not None:
             args_list = [tup for tup in args_list if tup[1] in targets]
 
         results = executor.map(process_label, args_list)
 
-
-        # Second parallel section to create dictionary entries
+        # Process results in parallel
         for label, sub_nodes in results:
             executor.submit(create_dict_entry, node_dict, label, sub_nodes, dilate_xy, dilate_z)
 

nettracer3d/segmenter.py

@@ -401,7 +401,7 @@ class InteractiveSegmenter:
         
         return foreground, background
 
-    def segment_volume(self, chunk_size=64, gpu=False):
+    def segment_volume(self, chunk_size=None, gpu=False):
         """Segment volume using parallel processing of chunks with vectorized chunk creation"""
         #Change the above chunk size to None to have it auto-compute largest chunks (not sure which is faster, 64 seems reasonable in test cases)
 

{nettracer3d-0.5.2.dist-info → nettracer3d-0.5.4.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: nettracer3d
-Version: 0.5.2
+Version: 0.5.4
 Summary: Scripts for intializing and analyzing networks from segmentations of three dimensional images.
 Author-email: Liam McLaughlin <mclaughlinliam99@gmail.com>
 Project-URL: User_Tutorial, https://www.youtube.com/watch?v=cRatn5VTWDY
@@ -26,6 +26,7 @@ Requires-Dist: tifffile==2023.7.18
 Requires-Dist: qtrangeslider==0.1.5
 Requires-Dist: PyQt6==6.8.0
 Requires-Dist: scikit-learn==1.6.1
+Requires-Dist: nibabel==5.2.0
 Provides-Extra: cuda11
 Requires-Dist: cupy-cuda11x; extra == "cuda11"
 Provides-Extra: cuda12
@@ -42,3 +43,11 @@ for a video tutorial on using the GUI.
 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).
 
 NetTracer3D was developed by Liam McLaughlin while working under Dr. Sanjay Jain at Washington University School of Medicine.
+
+-- Version 0.5.4 updates --
+
+1. Added new function to GUI in image -> overlays -> color nodes/edges. Generates a rgb array corresponding to the nodes/edge labels where each node/edge (depending which array is selected) is randomly assigned a unique rgb color in an overlay channel. This can be used, for example, to color code labeled branches for easy identification of which branch is which.
+
+2. Improved highlight overlay general functionality (for selecting nodes/edges). Previously selecting a node/edge had the program attempting to create an equal sized array as an overlay, find all objects corresponding to the selected ones, fill those into the new highlight overlay, then overlay that image. This was understandably quite slow in big arrays where the system was wasting a lot of time searching the entire array every time something was selected. New version retains this functionality for arrays below 125 million voxels, since search time is rather manageable at that size. For larger arrays, it instead draws the highlight for the selected objects only into the current slice, rendering a new slice whenever the user scrolls in the stack (although the entire highlight overlay is still initialized as a placeholder). Functions that require the use of the entire highlight overlay (such as masking) are correspondingly updated to draw the entirety of the highlight overlay before executing (when the system has up until that point been drawing slices one at a time). This will likely be the retained behavior moving forward, although to eliminate this behavior, one can open nettracer_gui.py and set self.mini_thresh to some comically large value. The new highlight overlay seems to work effectively the same but faster in my testing although it is possible a bug slipped through, which I will fix if informed about (or if I find it myself).
+
+3. For the machine learning segmenter, changed the system to attempt to segment the image by chunking the array into the largest possible chunks that can be divided across all CPU cores. Previously the system split the array into 64^3 voxel sized chunks and passed those to the CPU cores until everything was processed. I am not sure which version is more efficient/faster so this is somewhat of a test. In theory the new behavior could be faster because it asking Python to interpret less stuff. 

nettracer3d-0.5.4.dist-info/RECORD

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+nettracer3d/node_draw.py,sha256=k3sCTfUCJs3aH1C1q1gTNxDz9EAQbBd1hsUIJajxRx8,9823
+nettracer3d/proximity.py,sha256=FnIiI_AzfXd22HwCIFIyQRZxKYJ8YscIDdPnIv-wsO4,10560
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+nettracer3d-0.5.4.dist-info/RECORD,,

nettracer3d-0.5.2.dist-info/RECORD

@@ -1,21 +0,0 @@
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-nettracer3d/nettracer.py,sha256=hDccGy6RybSJFvY6dsN1l5eM3wKZW93CizlTvgEeyNs,209690
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-nettracer3d/network_analysis.py,sha256=MJBBjslA1k_R8ymid77U-qGSgzxFVfzGVQhE0IdhnbE,48046
-nettracer3d/network_draw.py,sha256=F7fw6Pcf4qWOhdKwLmhwqWdschbDlHzwCVolQC9imeU,14117
-nettracer3d/node_draw.py,sha256=k3sCTfUCJs3aH1C1q1gTNxDz9EAQbBd1hsUIJajxRx8,9823
-nettracer3d/proximity.py,sha256=B1pmFegx5Wb0JKI5rvpILv2VRU09f6M2iljAQAqBja0,11059
-nettracer3d/run.py,sha256=xYeaAc8FCx8MuzTGyL3NR3mK7WZzffAYAH23bNRZYO4,127
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