nettracer3d 0.7.5__tar.gz → 0.7.6__tar.gz

{nettracer3d-0.7.5/src/nettracer3d.egg-info → nettracer3d-0.7.6}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nettracer3d
-Version: 0.7.5
+Version: 0.7.6
 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/
@@ -72,11 +72,6 @@ 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 0.7.6 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).
+	* Bug Fixes

{nettracer3d-0.7.5 → nettracer3d-0.7.6}/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 0.7.6 Updates -- 
+
+	* Bug Fixes

{nettracer3d-0.7.5 → nettracer3d-0.7.6}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "nettracer3d"
-version = "0.7.5"
+version = "0.7.6"
 authors = [
   { name="Liam McLaughlin", email="liamm@wustl.edu" },
 ]

{nettracer3d-0.7.5 → nettracer3d-0.7.6}/src/nettracer3d/nettracer_gui.py

@@ -1448,7 +1448,7 @@ class ImageViewerWindow(QMainWindow):
 
         print("Note, this method is a tad slow...")
 
-        def separate_nontouching_objects(input_array):
+        def separate_nontouching_objects(input_array, max_val = 0):
             """
             Efficiently separate non-touching objects in a labeled array.
             
@@ -1483,7 +1483,7 @@ class ImageViewerWindow(QMainWindow):
             
             # Step 3: Create a new output array with unique labels for each connected component
             output_array = np.zeros_like(input_array)
-            next_label = 1
+            next_label = 1 + max_val
             
             # Map of (original_label, connected_component) -> new_unique_label
             unique_label_map = {}
@@ -1512,9 +1512,14 @@ class ImageViewerWindow(QMainWindow):
                 
                 # Get non-highlighted part of the array
                 non_highlighted = my_network.nodes * (~self.highlight_overlay)
+
+                if (highlighted_nodes==non_highlighted).all():
+                    max_val = 0
+                else:
+                    max_val = np.max(non_highlighted)
                 
                 # Process highlighted part
-                processed_highlights = separate_nontouching_objects(highlighted_nodes)
+                processed_highlights = separate_nontouching_objects(highlighted_nodes, max_val)
                 
                 # Combine back with non-highlighted parts
                 my_network.nodes = non_highlighted + processed_highlights
@@ -1534,9 +1539,14 @@ class ImageViewerWindow(QMainWindow):
                 
                 # Get non-highlighted part of the array
                 non_highlighted = my_network.edges * (~self.highlight_overlay)
+
+                if (highlighted_nodes==non_highlighted).all():
+                    max_val = 0
+                else:
+                    max_val = np.max(non_highlighted)
                 
                 # Process highlighted part
-                processed_highlights = separate_nontouching_objects(highlighted_edges)
+                processed_highlights = separate_nontouching_objects(highlighted_edges, max_val)
                 
                 # Combine back with non-highlighted parts
                 my_network.edges = non_highlighted + processed_highlights
@@ -1545,7 +1555,7 @@ class ImageViewerWindow(QMainWindow):
             
             self.highlight_overlay = None
             self.update_display()
-            print("Network is not updated automatically, please recompute if necessary. Identities are not automatically updated.")
+            print("Network is not updated automatically, please recompute if necessary - this method has a high chance of disrupting the network. Identities are not automatically updated.")
             self.show_centroid_dialog()
         except Exception as e:
             print(f"Error separating: {e}")
@@ -2837,99 +2847,103 @@ class ImageViewerWindow(QMainWindow):
 
         """from networkx documentation"""
 
-        G = my_network.network
+        try:
 
-        shortest_path_lengths = dict(nx.all_pairs_shortest_path_length(G))
-        diameter = max(nx.eccentricity(G, sp=shortest_path_lengths).values())
-        # We know the maximum shortest path length (the diameter), so create an array
-        # to store values from 0 up to (and including) diameter
-        path_lengths = np.zeros(diameter + 1, dtype=int)
+            G = my_network.network
 
+            shortest_path_lengths = dict(nx.all_pairs_shortest_path_length(G))
+            diameter = max(nx.eccentricity(G, sp=shortest_path_lengths).values())
+            # We know the maximum shortest path length (the diameter), so create an array
+            # to store values from 0 up to (and including) diameter
+            path_lengths = np.zeros(diameter + 1, dtype=int)
 
 
-        # Extract the frequency of shortest path lengths between two nodes
-        for pls in shortest_path_lengths.values():
-            pl, cnts = np.unique(list(pls.values()), return_counts=True)
-            path_lengths[pl] += cnts
 
-        # Express frequency distribution as a percentage (ignoring path lengths of 0)
-        freq_percent = 100 * path_lengths[1:] / path_lengths[1:].sum()
+            # Extract the frequency of shortest path lengths between two nodes
+            for pls in shortest_path_lengths.values():
+                pl, cnts = np.unique(list(pls.values()), return_counts=True)
+                path_lengths[pl] += cnts
 
-        # Plot the frequency distribution (ignoring path lengths of 0) as a percentage
-        fig, ax = plt.subplots(figsize=(15, 8))
-        ax.bar(np.arange(1, diameter + 1), height=freq_percent)
-        ax.set_title(
-            "Distribution of shortest path length in G", fontdict={"size": 35}, loc="center"
-        )
-        ax.set_xlabel("Shortest Path Length", fontdict={"size": 22})
-        ax.set_ylabel("Frequency (%)", fontdict={"size": 22})
-
-        plt.show()
-        freq_dict = {freq: length for length, freq in enumerate(freq_percent, start=1)}
-        self.format_for_upperright_table(freq_dict, metric='Frequency (%)', value='Shortest Path Length', title="Distribution of shortest path length in G")
-
-        degree_centrality = nx.centrality.degree_centrality(G)
-        plt.figure(figsize=(15, 8))
-        plt.hist(degree_centrality.values(), bins=25)
-        plt.xticks(ticks=[0, 0.025, 0.05, 0.1, 0.15, 0.2])  # set the x axis ticks
-        plt.title("Degree Centrality Histogram ", fontdict={"size": 35}, loc="center")
-        plt.xlabel("Degree Centrality", fontdict={"size": 20})
-        plt.ylabel("Counts", fontdict={"size": 20})
-        plt.show()
-        self.format_for_upperright_table(degree_centrality, metric='Node', value='Degree Centrality', title="Degree Centrality Table")
-
-
-        betweenness_centrality = nx.centrality.betweenness_centrality(
-            G
-        )
-        plt.figure(figsize=(15, 8))
-        plt.hist(betweenness_centrality.values(), bins=100)
-        plt.xticks(ticks=[0, 0.02, 0.1, 0.2, 0.3, 0.4, 0.5])  # set the x axis ticks
-        plt.title("Betweenness Centrality Histogram ", fontdict={"size": 35}, loc="center")
-        plt.xlabel("Betweenness Centrality", fontdict={"size": 20})
-        plt.ylabel("Counts", fontdict={"size": 20})
-        plt.show()
-        self.format_for_upperright_table(betweenness_centrality, metric='Node', value='Betweenness Centrality', title="Betweenness Centrality Table")
-
-
-        closeness_centrality = nx.centrality.closeness_centrality(
-            G
-        )
-        plt.figure(figsize=(15, 8))
-        plt.hist(closeness_centrality.values(), bins=60)
-        plt.title("Closeness Centrality Histogram ", fontdict={"size": 35}, loc="center")
-        plt.xlabel("Closeness Centrality", fontdict={"size": 20})
-        plt.ylabel("Counts", fontdict={"size": 20})
-        plt.show()
-        self.format_for_upperright_table(closeness_centrality, metric='Node', value='Closeness Centrality', title="Closeness Centrality Table")
+            # Express frequency distribution as a percentage (ignoring path lengths of 0)
+            freq_percent = 100 * path_lengths[1:] / path_lengths[1:].sum()
 
+            # Plot the frequency distribution (ignoring path lengths of 0) as a percentage
+            fig, ax = plt.subplots(figsize=(15, 8))
+            ax.bar(np.arange(1, diameter + 1), height=freq_percent)
+            ax.set_title(
+                "Distribution of shortest path length in G", fontdict={"size": 35}, loc="center"
+            )
+            ax.set_xlabel("Shortest Path Length", fontdict={"size": 22})
+            ax.set_ylabel("Frequency (%)", fontdict={"size": 22})
+
+            plt.show()
+            freq_dict = {freq: length for length, freq in enumerate(freq_percent, start=1)}
+            self.format_for_upperright_table(freq_dict, metric='Frequency (%)', value='Shortest Path Length', title="Distribution of shortest path length in G")
+
+            degree_centrality = nx.centrality.degree_centrality(G)
+            plt.figure(figsize=(15, 8))
+            plt.hist(degree_centrality.values(), bins=25)
+            plt.xticks(ticks=[0, 0.025, 0.05, 0.1, 0.15, 0.2])  # set the x axis ticks
+            plt.title("Degree Centrality Histogram ", fontdict={"size": 35}, loc="center")
+            plt.xlabel("Degree Centrality", fontdict={"size": 20})
+            plt.ylabel("Counts", fontdict={"size": 20})
+            plt.show()
+            self.format_for_upperright_table(degree_centrality, metric='Node', value='Degree Centrality', title="Degree Centrality Table")
+
+
+            betweenness_centrality = nx.centrality.betweenness_centrality(
+                G
+            )
+            plt.figure(figsize=(15, 8))
+            plt.hist(betweenness_centrality.values(), bins=100)
+            plt.xticks(ticks=[0, 0.02, 0.1, 0.2, 0.3, 0.4, 0.5])  # set the x axis ticks
+            plt.title("Betweenness Centrality Histogram ", fontdict={"size": 35}, loc="center")
+            plt.xlabel("Betweenness Centrality", fontdict={"size": 20})
+            plt.ylabel("Counts", fontdict={"size": 20})
+            plt.show()
+            self.format_for_upperright_table(betweenness_centrality, metric='Node', value='Betweenness Centrality', title="Betweenness Centrality Table")
+
+
+            closeness_centrality = nx.centrality.closeness_centrality(
+                G
+            )
+            plt.figure(figsize=(15, 8))
+            plt.hist(closeness_centrality.values(), bins=60)
+            plt.title("Closeness Centrality Histogram ", fontdict={"size": 35}, loc="center")
+            plt.xlabel("Closeness Centrality", fontdict={"size": 20})
+            plt.ylabel("Counts", fontdict={"size": 20})
+            plt.show()
+            self.format_for_upperright_table(closeness_centrality, metric='Node', value='Closeness Centrality', title="Closeness Centrality Table")
 
-        eigenvector_centrality = nx.centrality.eigenvector_centrality(
-            G
-        )
-        plt.figure(figsize=(15, 8))
-        plt.hist(eigenvector_centrality.values(), bins=60)
-        plt.xticks(ticks=[0, 0.01, 0.02, 0.04, 0.06, 0.08])  # set the x axis ticks
-        plt.title("Eigenvector Centrality Histogram ", fontdict={"size": 35}, loc="center")
-        plt.xlabel("Eigenvector Centrality", fontdict={"size": 20})
-        plt.ylabel("Counts", fontdict={"size": 20})
-        plt.show()
-        self.format_for_upperright_table(eigenvector_centrality, metric='Node', value='Eigenvector Centrality', title="Eigenvector Centrality Table")
+
+            eigenvector_centrality = nx.centrality.eigenvector_centrality(
+                G
+            )
+            plt.figure(figsize=(15, 8))
+            plt.hist(eigenvector_centrality.values(), bins=60)
+            plt.xticks(ticks=[0, 0.01, 0.02, 0.04, 0.06, 0.08])  # set the x axis ticks
+            plt.title("Eigenvector Centrality Histogram ", fontdict={"size": 35}, loc="center")
+            plt.xlabel("Eigenvector Centrality", fontdict={"size": 20})
+            plt.ylabel("Counts", fontdict={"size": 20})
+            plt.show()
+            self.format_for_upperright_table(eigenvector_centrality, metric='Node', value='Eigenvector Centrality', title="Eigenvector Centrality Table")
 
 
 
-        clusters = nx.clustering(G)
-        plt.figure(figsize=(15, 8))
-        plt.hist(clusters.values(), bins=50)
-        plt.title("Clustering Coefficient Histogram ", fontdict={"size": 35}, loc="center")
-        plt.xlabel("Clustering Coefficient", fontdict={"size": 20})
-        plt.ylabel("Counts", fontdict={"size": 20})
-        plt.show()
-        self.format_for_upperright_table(clusters, metric='Node', value='Clustering Coefficient', title="Clustering Coefficient Table")
+            clusters = nx.clustering(G)
+            plt.figure(figsize=(15, 8))
+            plt.hist(clusters.values(), bins=50)
+            plt.title("Clustering Coefficient Histogram ", fontdict={"size": 35}, loc="center")
+            plt.xlabel("Clustering Coefficient", fontdict={"size": 20})
+            plt.ylabel("Counts", fontdict={"size": 20})
+            plt.show()
+            self.format_for_upperright_table(clusters, metric='Node', value='Clustering Coefficient', title="Clustering Coefficient Table")
 
-        bridges = list(nx.bridges(G))
-        self.format_for_upperright_table(bridges, metric = 'Node Pair', title="Bridges")
+            bridges = list(nx.bridges(G))
+            self.format_for_upperright_table(bridges, metric = 'Node Pair', title="Bridges")
 
+        except Exception as e:
+            print(f"Error generating histograms: {e}")
 
     def volumes(self):
 

{nettracer3d-0.7.5 → nettracer3d-0.7.6/src/nettracer3d.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nettracer3d
-Version: 0.7.5
+Version: 0.7.6
 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/
@@ -72,11 +72,6 @@ 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 0.7.6 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).
+	* Bug Fixes