nettracer3d 0.6.8__tar.gz → 0.7.0__tar.gz

{nettracer3d-0.6.8/src/nettracer3d.egg-info → nettracer3d-0.7.0}/PKG-INFO

@@ -1,14 +1,15 @@
 Metadata-Version: 2.4
 Name: nettracer3d
-Version: 0.6.8
+Version: 0.7.0
 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
+Author-email: Liam McLaughlin <liamm@wustl.edu>
+Project-URL: Documentation, https://nettracer3d.readthedocs.io/en/latest/
+Project-URL: Video_Tutorial, https://www.youtube.com/watch?v=cRatn5VTWDY
 Project-URL: Reference_Citation_For_Use, https://doi.org/10.1101/2024.07.29.605633
 Classifier: Programming Language :: Python :: 3
 Classifier: License :: Other/Proprietary License
 Classifier: Operating System :: OS Independent
-Requires-Python: >=3.8
+Requires-Python: ==3.11
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: numpy==1.26.4
@@ -38,16 +39,48 @@ Dynamic: license-file
 
 NetTracer3D is a python package developed for both 2D and 3D analysis of microscopic images in the .tif file format. It supports generation of 3D networks showing the relationships between objects (or nodes) in three dimensional space, either based on their own proximity or connectivity via connecting objects such as nerves or blood vessels. In addition to these functionalities are several advanced 3D data processing algorithms, such as labeling of branched structures or abstraction of branched structures into networks. Note that nettracer3d uses segmented data, which can be segmented from other softwares such as ImageJ and imported into NetTracer3D, although it does offer its own segmentation via intensity and volumetric thresholding, or random forest machine learning segmentation. NetTracer3D currently has a fully functional GUI. To use the GUI, after installing the nettracer3d package via pip, enter the command 'nettracer3d' in your command prompt:
 
+--- Documentation ---
 
-This gui is built from the PyQt6 package and therefore may not function on dockers or virtual envs that are unable to support PyQt6 displays. More advanced documentation is coming down the line, but for now please see: https://www.youtube.com/watch?v=cRatn5VTWDY
-for a video tutorial on using the GUI.
+Please see: https://nettracer3d.readthedocs.io/en/latest/
+
+--- Installation ---
+
+To install nettracer3d, simply install Python and use this command in your command terminal:
+
+pip install nettracer3d
+
+I recommend installing the program as an Anaconda package to ensure its modules are work together on your specific system:
+(Install anaconda at the link below, set up a new python env for nettracer3d, then use the same pip command).
+
+https://www.anaconda.com/download?utm_source=anacondadocs&utm_medium=documentation&utm_campaign=download&utm_content=installwindows
+
+nettracer3d mostly utilizes the CPU for processing and visualization, although it does have a few GPU-aided options. If you would like to use the GPU for these, you will need an NVIDIA GPU and a corresponding CUDA toolkit which can be installed here:
+https://developer.nvidia.com/cuda-toolkit
+
+To install nettracer3d with associated GPU-supporting packages, please use:
+
+If your CUDA toolkit is version 11: pip install nettracer3d[CUDA11]
+If your CUDA toolkit is version 12: pip install nettracer3d[CUDA12]
+If you just want the entire cupy library: pip install nettracer3d[cupy]
+
+
+This gui is built from the PyQt6 package and therefore may not function on dockers or virtual envs that are unable to support PyQt6 displays.
+
+
+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).
 
 NetTracer3D was developed by Liam McLaughlin while working under Dr. Sanjay Jain at Washington University School of Medicine.
 
--- Version 0.6.8 updates --
+-- Version 0.7.0 Updates -- 
+
+1. Added new function in 'Analyze -> Stats -> Cluster Analysis'
+    * This function allows the user to create a ripley's K or H function to compare the relative clustering of two types of nodes, or of one type of node vs itself.
 
-1. Added new fill-can and 3D-brush functionalities to the brush mode (press f in brush mode to toggle the fill can. Press d while in brush mode to use the 3D painting tools. Standard Mouse wheel scrolling in the 3D painter will change how many frames you paint on - ie. 5 lets you paint 2 above and 2 below).
+2. Added new function in 'Analyze -> Randomize -> Scramble Nodes'
+    * This function randomly rearranges the node (centroids) for comparison with other centroid-using methods, as a possible way to demonstrate non-random behavior.
+    * The randomize menu is likewise new and the 'Generate Equivalent Random Network' method was moved there.
 
-1.5. Added single-use ctrl-z functionality to the fill can only because of how easily it can mess up. (Leaving the fill can mode will garbage collect the backup image though).
+3. Bug fixes.
+    * Importantly fixed a bug with dt-based dilation not working in 2D, which I had accidentally introduced recently.

nettracer3d-0.7.0/README.md

@@ -0,0 +1,47 @@
+NetTracer3D is a python package developed for both 2D and 3D analysis of microscopic images in the .tif file format. It supports generation of 3D networks showing the relationships between objects (or nodes) in three dimensional space, either based on their own proximity or connectivity via connecting objects such as nerves or blood vessels. In addition to these functionalities are several advanced 3D data processing algorithms, such as labeling of branched structures or abstraction of branched structures into networks. Note that nettracer3d uses segmented data, which can be segmented from other softwares such as ImageJ and imported into NetTracer3D, although it does offer its own segmentation via intensity and volumetric thresholding, or random forest machine learning segmentation. NetTracer3D currently has a fully functional GUI. To use the GUI, after installing the nettracer3d package via pip, enter the command 'nettracer3d' in your command prompt:
+
+--- Documentation ---
+
+Please see: https://nettracer3d.readthedocs.io/en/latest/
+
+--- Installation ---
+
+To install nettracer3d, simply install Python and use this command in your command terminal:
+
+pip install nettracer3d
+
+I recommend installing the program as an Anaconda package to ensure its modules are work together on your specific system:
+(Install anaconda at the link below, set up a new python env for nettracer3d, then use the same pip command).
+
+https://www.anaconda.com/download?utm_source=anacondadocs&utm_medium=documentation&utm_campaign=download&utm_content=installwindows
+
+nettracer3d mostly utilizes the CPU for processing and visualization, although it does have a few GPU-aided options. If you would like to use the GPU for these, you will need an NVIDIA GPU and a corresponding CUDA toolkit which can be installed here:
+https://developer.nvidia.com/cuda-toolkit
+
+To install nettracer3d with associated GPU-supporting packages, please use:
+
+If your CUDA toolkit is version 11: pip install nettracer3d[CUDA11]
+If your CUDA toolkit is version 12: pip install nettracer3d[CUDA12]
+If you just want the entire cupy library: pip install nettracer3d[cupy]
+
+
+This gui is built from the PyQt6 package and therefore may not function on dockers or virtual envs that are unable to support PyQt6 displays.
+
+
+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).
+
+NetTracer3D was developed by Liam McLaughlin while working under Dr. Sanjay Jain at Washington University School of Medicine.
+
+-- Version 0.7.0 Updates -- 
+
+1. Added new function in 'Analyze -> Stats -> Cluster Analysis'
+    * This function allows the user to create a ripley's K or H function to compare the relative clustering of two types of nodes, or of one type of node vs itself.
+
+2. Added new function in 'Analyze -> Randomize -> Scramble Nodes'
+    * This function randomly rearranges the node (centroids) for comparison with other centroid-using methods, as a possible way to demonstrate non-random behavior.
+    * The randomize menu is likewise new and the 'Generate Equivalent Random Network' method was moved there.
+
+3. Bug fixes.
+    * Importantly fixed a bug with dt-based dilation not working in 2D, which I had accidentally introduced recently.

{nettracer3d-0.6.8 → nettracer3d-0.7.0}/pyproject.toml

@@ -1,8 +1,8 @@
 [project]
 name = "nettracer3d"
-version = "0.6.8"
+version = "0.7.0"
 authors = [
-  { name="Liam McLaughlin", email="mclaughlinliam99@gmail.com" },
+  { name="Liam McLaughlin", email="liamm@wustl.edu" },
 ]
 description = "Scripts for intializing and analyzing networks from segmentations of three dimensional images."
 
@@ -27,7 +27,7 @@ dependencies = [
 ]
 
 readme = "README.md"
-requires-python = ">=3.8"
+requires-python = "==3.11"
 classifiers = [
     "Programming Language :: Python :: 3",
     "License :: Other/Proprietary License",
@@ -49,5 +49,6 @@ cupy = [
 nettracer3d = "nettracer3d.run:main"
 
 [project.urls]
-User_Tutorial = "https://www.youtube.com/watch?v=cRatn5VTWDY"
+Documentation = "https://nettracer3d.readthedocs.io/en/latest/"
+Video_Tutorial = "https://www.youtube.com/watch?v=cRatn5VTWDY"
 Reference_Citation_For_Use = "https://doi.org/10.1101/2024.07.29.605633"

{nettracer3d-0.6.8 → nettracer3d-0.7.0}/src/nettracer3d/modularity.py

@@ -446,31 +446,11 @@ def community_partition(master_list, weighted = False, style = 0, dostats = True
         except:
             pass
 
-        try:        
-            # Per-community statistics
-            for i, com in enumerate(communities):
-                subgraph = G.subgraph(com)
-                
-                # Basic community metrics
-                stats[f'Community {i+1} Density'] = nx.density(subgraph)
-                stats[f'Community {i+1} Conductance'] = nx.conductance(G, com)
-                stats[f'Community {i+1} Avg Clustering'] = nx.average_clustering(subgraph)
-                
-                # Degree centrality
-                degree_cent = nx.degree_centrality(subgraph)
-                stats[f'Community {i+1} Avg Degree Centrality'] = np.mean(list(degree_cent.values()))
-                
-                # Average path length (only for connected subgraphs)
-                if nx.is_connected(subgraph):
-                    stats[f'Community {i+1} Avg Path Length'] = nx.average_shortest_path_length(subgraph)
-        except:
-            pass
-
-        try:        
+        #try:        
             # Add some Louvain-specific statistics
-            stats['Partition Resolution'] = 1.0  # Default resolution parameter
-        except:
-            pass
+            #stats['Partition Resolution'] = 1.0  # Default resolution parameter
+        #except:
+            #pass
         try:
             stats['Number of Iterations'] = len(set(partition.values()))
         except:
@@ -514,6 +494,25 @@ def community_partition(master_list, weighted = False, style = 0, dostats = True
         except:
             pass
 
+        try:        
+            # Per-community statistics
+            for i, com in enumerate(communities):
+                subgraph = G.subgraph(com)
+                
+                # Basic community metrics
+                stats[f'Community {i+1} Density'] = nx.density(subgraph)
+                stats[f'Community {i+1} Conductance'] = nx.conductance(G, com)
+                stats[f'Community {i+1} Avg Clustering'] = nx.average_clustering(subgraph)
+                
+                # Degree centrality
+                degree_cent = nx.degree_centrality(subgraph)
+                stats[f'Community {i+1} Avg Degree Centrality'] = np.mean(list(degree_cent.values()))
+                
+                # Average path length (only for connected subgraphs)
+                if nx.is_connected(subgraph):
+                    stats[f'Community {i+1} Avg Path Length'] = nx.average_shortest_path_length(subgraph)
+        except:
+            pass
         
         return stats
 

{nettracer3d-0.6.8 → nettracer3d-0.7.0}/src/nettracer3d/morphology.py

@@ -354,6 +354,7 @@ def process_object_cpu(label, objects, labeled_array, xy_scale = 1, z_scale = 1)
     mask = (subarray == label)
 
 
+    """
     # Determine which dimension needs resampling
     if (z_scale > xy_scale) and mask.shape[0] != 1:
         # Z dimension needs to be stretched
@@ -371,13 +372,13 @@ def process_object_cpu(label, objects, labeled_array, xy_scale = 1, z_scale = 1)
     # Resample the mask if needed
     if zoom_factor:
         mask = ndimage.zoom(mask, zoom_factor, order=0)  # Use order=0 for binary masks
-
+    """
     
     # Compute distance transform on the smaller mask
-    dist_transform = compute_distance_transform_distance(mask)
+    dist_transform = compute_distance_transform_distance(mask, sampling = [z_scale, xy_scale, xy_scale])
     
     # Filter out small values near the edge to focus on more central regions
-    radius = np.max(dist_transform) * cardinal
+    radius = np.max(dist_transform)
     
     return label, radius
 
@@ -474,6 +475,7 @@ def estimate_object_radii_gpu(labeled_array, xy_scale = 1, z_scale = 1):
             # Create binary mask for this object (directly on GPU)
             mask_gpu = (labeled_array_gpu[tuple(padded_slices)] == label)
 
+            """
             # Determine which dimension needs resampling
             if (z_scale > xy_scale) and mask_gpu.shape[0] != 1:
                 # Z dimension needs to be stretched
@@ -491,11 +493,12 @@ def estimate_object_radii_gpu(labeled_array, xy_scale = 1, z_scale = 1):
             # Resample the mask if needed
             if zoom_factor:
                 mask_gpu = cpx.zoom(mask_gpu, zoom_factor, order=0)  # Use order=0 for binary masks
+            """
             
             # Compute distance transform on GPU
-            dist_transform_gpu = compute_distance_transform_distance_GPU(mask_gpu)
+            dist_transform_gpu = compute_distance_transform_distance_GPU(mask_gpu, sampling = [z_scale, xy_scale, xy_scale])
         
-            radius = float(cp.max(dist_transform_gpu).get()) * cardinal
+            radius = float(cp.max(dist_transform_gpu).get())
 
 
             # Store the radius and the scaled radius
@@ -510,14 +513,15 @@ def estimate_object_radii_gpu(labeled_array, xy_scale = 1, z_scale = 1):
         print(f"GPU calculation failed, trying CPU instead -> {e}")
         return estimate_object_radii_cpu(labeled_array)
 
-def compute_distance_transform_distance_GPU(nodes):
+def compute_distance_transform_distance_GPU(nodes, sampling = [1,1,1]):
 
     is_pseudo_3d = nodes.shape[0] == 1
     if is_pseudo_3d:
         nodes = cp.squeeze(nodes)  # Convert to 2D for processing
+        del sampling[0]
     
     # Compute the distance transform on the GPU
-    distance = cpx.distance_transform_edt(nodes)
+    distance = cpx.distance_transform_edt(nodes, sampling = sampling)
 
     if is_pseudo_3d:
         cp.expand_dims(distance, axis = 0)
@@ -525,14 +529,15 @@ def compute_distance_transform_distance_GPU(nodes):
     return distance    
 
 
-def compute_distance_transform_distance(nodes):
+def compute_distance_transform_distance(nodes, sampling = [1,1,1]):
 
     is_pseudo_3d = nodes.shape[0] == 1
     if is_pseudo_3d:
         nodes = np.squeeze(nodes)  # Convert to 2D for processing
+        del sampling[0]
 
     # Fallback to CPU if there's an issue with GPU computation
-    distance = ndimage.distance_transform_edt(nodes)
+    distance = ndimage.distance_transform_edt(nodes, sampling = sampling)
     if is_pseudo_3d:
         np.expand_dims(distance, axis = 0)
     return distance