nettracer3d 0.7.5__tar.gz → 0.7.7__tar.gz

{nettracer3d-0.7.5/src/nettracer3d.egg-info → nettracer3d-0.7.7}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nettracer3d
-Version: 0.7.5
+Version: 0.7.7
 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/
@@ -28,6 +28,7 @@ Requires-Dist: PyQt6
 Requires-Dist: scikit-learn
 Requires-Dist: nibabel
 Requires-Dist: setuptools
+Requires-Dist: umap-learn
 Provides-Extra: cuda11
 Requires-Dist: cupy-cuda11x; extra == "cuda11"
 Provides-Extra: cuda12
@@ -72,11 +73,6 @@ 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 0.7.5 Updates -- 
+-- Version 0.7.7 Updates -- 
 
-	* Bug fixes
-	* The segmenter GPU option has been updated to include 2D segmentation and to also be able to load/save models.
-	* A new function (Analyze -> Stats -> Calculate Generic Network Histograms has been added (gives a few histograms about the network and their corresponding tables. Previously stats mostly gave averages).
-	* The function 'Analyze -> Data/Overlays -> Get Hub Information' now looks for the upper hubs unique to each separate network component. It will also ignore smaller components that have too few nodes to be reasonably considered having hubs relative to the threshold the user sets.
-	* The function to split non-connected nodes has been improved a bit (its faster albeit still slowish - its a tough operation)
-	* Removed python-louvain dependence, now uses networkx for Louvain partitioning. (On top of this, now the user can set the random seed they desire for partitioning for reproducibility purposes).
+	* See documentation once updated

{nettracer3d-0.7.5 → nettracer3d-0.7.7}/README.md

@@ -34,11 +34,6 @@ 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 0.7.5 Updates -- 
-
-	* Bug fixes
-	* The segmenter GPU option has been updated to include 2D segmentation and to also be able to load/save models.
-	* A new function (Analyze -> Stats -> Calculate Generic Network Histograms has been added (gives a few histograms about the network and their corresponding tables. Previously stats mostly gave averages).
-	* The function 'Analyze -> Data/Overlays -> Get Hub Information' now looks for the upper hubs unique to each separate network component. It will also ignore smaller components that have too few nodes to be reasonably considered having hubs relative to the threshold the user sets.
-	* The function to split non-connected nodes has been improved a bit (its faster albeit still slowish - its a tough operation)
-	* Removed python-louvain dependence, now uses networkx for Louvain partitioning. (On top of this, now the user can set the random seed they desire for partitioning for reproducibility purposes).
+-- Version 0.7.7 Updates -- 
+
+	* See documentation once updated

{nettracer3d-0.7.5 → nettracer3d-0.7.7}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "nettracer3d"
-version = "0.7.5"
+version = "0.7.7"
 authors = [
   { name="Liam McLaughlin", email="liamm@wustl.edu" },
 ]
@@ -22,7 +22,8 @@ dependencies = [
     "PyQt6",
     "scikit-learn",
     "nibabel",
-    "setuptools"
+    "setuptools",
+    "umap-learn"
 ]
 
 readme = "README.md"

{nettracer3d-0.7.5 → nettracer3d-0.7.7}/src/nettracer3d/community_extractor.py

@@ -533,46 +533,30 @@ def assign_node_colors(node_list: List[int], labeled_array: np.ndarray) -> Tuple
     return rgba_array, node_to_color_names
 
 def assign_community_colors(community_dict: Dict[int, int], labeled_array: np.ndarray) -> Tuple[np.ndarray, Dict[int, str]]:
-    """
-    Assign distinct colors to communities and create an RGBA image.
-    
-    Args:
-        community_dict: Dictionary mapping node IDs to community numbers
-        labeled_array: 3D numpy array with labels corresponding to node IDs
+    """Ultra-fast version using lookup table approach."""
     
-    Returns:
-        Tuple of (RGBA-coded numpy array (H, W, D, 4), dictionary mapping nodes to color names)
-    """
-    # Get unique communities and their sizes
+    # Same setup as before
     communities = set(community_dict.values())
     community_sizes = Counter(community_dict.values())
-    
-    # Sort communities by size (descending)
     sorted_communities = sorted(communities, key=lambda x: community_sizes[x], reverse=True)
     
-    # Generate distinct colors
     colors = generate_distinct_colors(len(communities))
+    colors_rgba = np.array([(r, g, b, 255) for r, g, b in colors], dtype=np.uint8)
     
-    # Convert RGB colors to RGBA by adding alpha channel
-    colors_rgba = [(r, g, b, 255) for r, g, b in colors]  # Full opacity for colored regions
-    
-    # Create mapping from community to color
     community_to_color = {comm: colors_rgba[i] for i, comm in enumerate(sorted_communities)}
-    
-    # Create mapping from node ID to color
     node_to_color = {node: community_to_color[comm] for node, comm in community_dict.items()}
     
-    # Create RGBA array (initialize with transparent background)
-    rgba_array = np.zeros((*labeled_array.shape, 4), dtype=np.uint8)
+    # Create lookup table - this is the key optimization
+    max_label = max(max(labeled_array.flat), max(node_to_color.keys()) if node_to_color else 0)
+    color_lut = np.zeros((max_label + 1, 4), dtype=np.uint8)  # Transparent by default
     
-    # Assign colors to each voxel based on its label
-    for label in np.unique(labeled_array):
-        if label in node_to_color:  # Skip background (usually label 0)
-            mask = labeled_array == label
-            for i in range(4):  # RGBA channels
-                rgba_array[mask, i] = node_to_color[label][i]
-
-    # Convert the RGB portion of community_to_color back to RGB for color naming
+    for node_id, color in node_to_color.items():
+        color_lut[node_id] = color
+    
+    # Single vectorized operation - this is much faster!
+    rgba_array = color_lut[labeled_array]
+    
+    # Rest remains the same
     community_to_color_rgb = {k: tuple(v[:3]) for k, v in community_to_color.items()}
     node_to_color_names = convert_node_colors_to_names(community_to_color_rgb)