nettracer3d 0.6.3__tar.gz → 0.6.4__tar.gz

{nettracer3d-0.6.3/src/nettracer3d.egg-info → nettracer3d-0.6.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nettracer3d
-Version: 0.6.3
+Version: 0.6.4
 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
@@ -45,10 +45,15 @@ 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 0.6.3 updates --
+-- Version 0.6.4 updates --
 
-1. Fixed bug with the active channel indicator on the GUI not always updating when the active channel was changed by internal loading.
+1. Fixed bug with tabulated data in top right having a right click window corresponding to the bottom left.
 
-2. Updated ram_lock mode in the segmenter to garbage collect better... again.
+2. Fixed bug when converting communities to nodes that let the same community connect to itself in the new network.
 
-3. Added new function (Label neighborhoods). Find it in process -> image -> label neighborhoods. Allows a 3d labeled array to act as a kernel and extend its labels along a secondary binary array. This can be useful in evaluating nearest neighbors en-masse. The method behind this (smart label) was previously used internally for some methods (ie watershedding) but I thought I'd include it as an actual function since it has some more general uses.
+3. Removed attempted trendline fitting from degree distribution
+
+4. Added new feature to skeletonization (and corresponding branch labeler/gennodes)
+	Now you can have the program attempt to auto-correct 3D skeletonization loop artifacts through a method that just runs the 3d fill holes algo and then attempts to reskeletonize the output. This worked well in my own testing. 
+
+5. Other minor fixes/improvements

{nettracer3d-0.6.3 → nettracer3d-0.6.4}/README.md

@@ -8,10 +8,15 @@ 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 0.6.3 updates --
+-- Version 0.6.4 updates --
 
-1. Fixed bug with the active channel indicator on the GUI not always updating when the active channel was changed by internal loading.
+1. Fixed bug with tabulated data in top right having a right click window corresponding to the bottom left.
 
-2. Updated ram_lock mode in the segmenter to garbage collect better... again.
+2. Fixed bug when converting communities to nodes that let the same community connect to itself in the new network.
 
-3. Added new function (Label neighborhoods). Find it in process -> image -> label neighborhoods. Allows a 3d labeled array to act as a kernel and extend its labels along a secondary binary array. This can be useful in evaluating nearest neighbors en-masse. The method behind this (smart label) was previously used internally for some methods (ie watershedding) but I thought I'd include it as an actual function since it has some more general uses.
+3. Removed attempted trendline fitting from degree distribution
+
+4. Added new feature to skeletonization (and corresponding branch labeler/gennodes)
+	Now you can have the program attempt to auto-correct 3D skeletonization loop artifacts through a method that just runs the 3d fill holes algo and then attempts to reskeletonize the output. This worked well in my own testing. 
+
+5. Other minor fixes/improvements

{nettracer3d-0.6.3 → nettracer3d-0.6.4}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "nettracer3d"
-version = "0.6.3"
+version = "0.6.4"
 authors = [
   { name="Liam McLaughlin", email="mclaughlinliam99@gmail.com" },
 ]

{nettracer3d-0.6.3 → nettracer3d-0.6.4}/src/nettracer3d/nettracer.py

@@ -751,6 +751,8 @@ def fill_holes_3d(array):
         
         return holes_mask
 
+    print("Filling Holes...")
+    
     array = binarize(array)
     inv_array = invert_array(array)
 
@@ -3270,7 +3272,10 @@ class Network_3D:
         self._xy_scale = xy_scale
         self._z_scale = z_scale
 
-        self.save_scaling(directory)
+        try:
+            self.save_scaling(directory)
+        except:
+            pass
 
         if search is None and ignore_search_region == False:
             search = 0
@@ -3286,29 +3291,51 @@ class Network_3D:
         if other_nodes is not None:
             self.merge_nodes(other_nodes, label_nodes)
 
-        self.save_nodes(directory)
-        self.save_node_identities(directory)
+        try:
+            self.save_nodes(directory)
+        except:
+            pass
+        try:
+            self.save_node_identities(directory)
+        except:
+            pass
 
         if not ignore_search_region:
             self.calculate_search_region(search, GPU = GPU, fast_dil = fast_dil, GPU_downsample = GPU_downsample)
-            self._nodes = None
+            #self._nodes = None # I originally put this here to micromanage RAM a little bit (it writes it to disk so I wanted to purge it from mem briefly but now idt thats necessary and I'd rather give it flexibility when lacking write permissions)
             search = None
-            self.save_search_region(directory)
+            try:
+                self.save_search_region(directory)
+            except:
+                pass
 
         self.calculate_edges(edges, diledge = diledge, inners = inners, hash_inner_edges = hash_inners, search = search, remove_edgetrunk = remove_trunk, GPU = GPU, fast_dil = fast_dil, skeletonized = skeletonize)
         del edges
-        self.save_edges(directory)
+        try:
+            self.save_edges(directory)
+        except:
+            pass
 
         self.calculate_network(search = search, ignore_search_region = ignore_search_region)
-        self.save_network(directory)
+
+        try:
+            self.save_network(directory)
+        except:
+            pass
 
         if self._nodes is None:
             self.load_nodes(directory)
 
         self.calculate_node_centroids(down_factor)
-        self.save_node_centroids(directory)
+        try:
+            self.save_node_centroids(directory)
+        except:
+            pass
         self.calculate_edge_centroids(down_factor)
-        self.save_edge_centroids(directory)
+        try:
+            self.save_edge_centroids(directory)
+        except:
+            pass
 
 
     def draw_network(self, directory = None, down_factor = None, GPU = False):
@@ -3557,15 +3584,21 @@ class Network_3D:
         list1 = self._network_lists[0] #Get network lists to change
         list2 = self._network_lists[1]
         list3 = self._network_lists[2]
+        return1 = []
+        return2 = []
+        return3 = []
 
         for i in range(len(list1)):
             list1[i] = self.communities[list1[i]] #Set node at network list spot to its community instead
             list2[i] = self.communities[list2[i]]
-            if list1[i] == list2[i]: #If the  edge corresponding there joins different communities, it will not be set to 0
-                list3[i] = 0
+            if list1[i] != list2[i]: #Avoid self - self connections
+                return1.append(list1[i])
+                return2.append(list2[i])
+                return3.append(list3[i])
+
 
 
-        self.network_lists = [list1, list2, list3]
+        self.network_lists = [return1, return2, return3]
 
         if self._nodes is not None:
             self._nodes = update_array(self._nodes, inverted, targets = targets) #Set the array to match the new network

{nettracer3d-0.6.3 → nettracer3d-0.6.4}/src/nettracer3d/nettracer_gui.py

@@ -325,7 +325,7 @@ class ImageViewerWindow(QMainWindow):
         self.tabbed_data = TabbedDataWidget(self)
         right_layout.addWidget(self.tabbed_data)
         # Initialize data_table property to None - it will be set when tabs are added
-        self.data_table = None
+        self.data_table = []
         
         # Create table control panel
         table_control = QWidget()
@@ -1814,6 +1814,7 @@ class ImageViewerWindow(QMainWindow):
                 new_xlim = [xdata - x_range, xdata + x_range]
                 new_ylim = [ydata - y_range, ydata + y_range]
                 
+                
                 if (new_xlim[0] <= self.original_xlim[0] or 
                     new_xlim[1] >= self.original_xlim[1] or
                     new_ylim[0] <= self.original_ylim[0] or
@@ -3228,6 +3229,9 @@ class ImageViewerWindow(QMainWindow):
                                 self.highlight_overlay = None
                         except:
                             pass
+                    if not data:
+                        self.original_xlim = None
+                        self.original_ylim = None
                     continue
                 else:
                     old_shape = self.channel_data[i].shape[:3] #Ask user to resize images that are shaped differently
@@ -3987,7 +3991,7 @@ class CustomTableView(QTableView):
                     desc_action.triggered.connect(lambda checked, c=col: self.sort_table(c, ascending=False))
             
             # Different menus for top and bottom tables
-            if self == self.parent.data_table:  # Top table
+            if self in self.parent.data_table:  # Top table
                 save_menu = context_menu.addMenu("Save As")
                 save_csv = save_menu.addAction("CSV")
                 save_excel = save_menu.addAction("Excel")
@@ -4096,7 +4100,7 @@ class CustomTableView(QTableView):
         df = self.model()._data
         
         # Get table name for the file dialog title
-        if self == self.parent.data_table:
+        if self in self.parent.data_table:
             table_name = "Statistics"
         elif self == self.parent.network_table:
             table_name = "Network"
@@ -4105,7 +4109,7 @@ class CustomTableView(QTableView):
         
         # Get save file name
         file_filter = ("CSV Files (*.csv)" if file_type == 'csv' else 
-                      "Excel Files (*.xlsx)" if file_type == 'excel' else 
+                      "Excel Files (*.xlsx)" if file_type == 'xlsx' else 
                       "Gephi Graph (*.gexf)" if file_type == 'gexf' else
                       "GraphML (*.graphml)" if file_type == 'graphml' else
                       "Pajek Network (*.net)")
@@ -4490,7 +4494,13 @@ class TabbedDataWidget(QTabWidget):
         """Add a new table with the given name"""
         if name in self.tables:
             # If tab already exists, update its content
-            idx = self.indexOf(self.tables[name])
+            old_table = self.tables[name]
+            idx = self.indexOf(old_table)
+            
+            # Remove the old table reference from parent's data_table
+            if self.parent_window and old_table in self.parent_window.data_table:
+                self.parent_window.data_table.remove(old_table)
+                
             self.removeTab(idx)
             
         # Create a new CustomTableView with is_top_table=True
@@ -4510,7 +4520,7 @@ class TabbedDataWidget(QTabWidget):
             
         # Update parent's data_table reference
         if self.parent_window:
-            self.parent_window.data_table = new_table
+            self.parent_window.data_table.append(new_table)
             
     def close_tab(self, index):
         """Close the tab at the given index"""
@@ -4525,12 +4535,12 @@ class TabbedDataWidget(QTabWidget):
         if name_to_remove:
             del self.tables[name_to_remove]
             
-        self.removeTab(index)
-        
-        # Update parent's data_table reference to current table
-        if self.parent_window and self.count() > 0:
-            self.parent_window.data_table = self.currentWidget()
+        # Update parent's data_table reference by removing the widget
+        if self.parent_window and widget in self.parent_window.data_table:
+            self.parent_window.data_table.remove(widget)
             
+        self.removeTab(index)
+                
     def clear_all_tabs(self):
         """Remove all tabs"""
         while self.count() > 0:
@@ -5433,18 +5443,23 @@ class RadialDialog(QDialog):
 
     def radial(self):
 
-        distance = float(self.distance.text()) if self.distance.text().strip() else 50
+        try:
 
-        directory = str(self.distance.text()) if self.directory.text().strip() else None
+            distance = float(self.distance.text()) if self.distance.text().strip() else 50
 
-        if my_network.node_centroids is None:
-            self.parent().show_centroid_dialog()
+            directory = str(self.distance.text()) if self.directory.text().strip() else None
 
-        radial = my_network.radial_distribution(distance, directory = directory)
+            if my_network.node_centroids is None:
+                self.parent().show_centroid_dialog()
 
-        self.parent().format_for_upperright_table(radial, 'Radial Distance From Any Node', 'Average Number of Neighboring Nodes', title = 'Radial Distribution Analysis')
+            radial = my_network.radial_distribution(distance, directory = directory)
 
-        self.accept()
+            self.parent().format_for_upperright_table(radial, 'Radial Distance From Any Node', 'Average Number of Neighboring Nodes', title = 'Radial Distribution Analysis')
+
+            self.accept()
+
+        except Exception as e:
+            print(f"An error occurred: {e}")
 
 class DegreeDistDialog(QDialog):
 
@@ -5477,7 +5492,7 @@ class DegreeDistDialog(QDialog):
 
             self.accept()
 
-        except Excpetion as e:
+        except Exception as e:
             print(f"An error occurred: {e}")
 
 class NeighborIdentityDialog(QDialog):
@@ -7783,6 +7798,12 @@ class SkeletonizeDialog(QDialog):
         self.remove = QLineEdit("0")
         layout.addRow("Remove Branches Pixel Length (int):", self.remove)
 
+        # auto checkbox (default True)
+        self.auto = QPushButton("Auto")
+        self.auto.setCheckable(True)
+        self.auto.setChecked(False)
+        layout.addRow("Attempt to Auto Correct Skeleton Looping:", self.auto)
+
        # Add Run button
         run_button = QPushButton("Run Skeletonize")
         run_button.clicked.connect(self.run_skeletonize)
@@ -7796,11 +7817,17 @@ class SkeletonizeDialog(QDialog):
                 remove = int(self.remove.text()) if self.remove.text() else 0
             except ValueError:
                 remove = 0
+
+            auto = self.auto.isChecked()
             
             # Get the active channel data from parent
             active_data = self.parent().channel_data[self.parent().active_channel]
             if active_data is None:
                 raise ValueError("No active image selected")
+
+            if auto:
+                active_data = n3d.skeletonize(active_data)
+                active_data = n3d.fill_holes_3d(active_data)
             
             # Call dilate method with parameters
             result = n3d.skeletonize(
@@ -8112,11 +8139,17 @@ class GenNodesDialog(QDialog):
         self.branch_removal = QLineEdit("0")
         layout.addRow("Skeleton Voxel Branch Length to Remove (int) (Compensates for spines off medial axis):", self.branch_removal)
 
+        self.comp_dil = QLineEdit("0")
+        layout.addRow("Voxel distance to merge nearby nodes (Int - compensates for multi-branch identification along thick branch regions):", self.comp_dil)
+
         self.max_vol = QLineEdit("0")
         layout.addRow("Maximum Voxel Volume of Vertices to Retain (int - Compensates for skeleton looping - occurs before any node merging - the smallest objects are always 27 voxels):", self.max_vol)
 
-        self.comp_dil = QLineEdit("0")
-        layout.addRow("Voxel distance to merge nearby nodes (Int - compensates for multi-branch identification along thick branch regions):", self.comp_dil)
+        # auto checkbox (default True)
+        self.auto = QPushButton("Auto")
+        self.auto.setCheckable(True)
+        self.auto.setChecked(False)
+        layout.addRow("Attempt to Auto Correct Skeleton Looping:", self.auto)
 
         if not down_factor:
             down_factor = None
@@ -8194,6 +8227,13 @@ class GenNodesDialog(QDialog):
             else:
                 order = 0
 
+            auto = self.auto.isChecked()
+
+
+            if auto:
+                my_network.edges = n3d.skeletonize(my_network.edges)
+                my_network.edges = n3d.fill_holes_3d(my_network.edges)
+
             
             result, skele = n3d.label_vertices(
                 my_network.edges,
@@ -8248,6 +8288,7 @@ class GenNodesDialog(QDialog):
             )
 
 
+
 class BranchDialog(QDialog):
 
     def __init__(self, parent=None):
@@ -8275,8 +8316,7 @@ class BranchDialog(QDialog):
         self.fix.setChecked(False)
         layout.addRow("Attempt to auto-correct branch labels:", self.fix)
 
-        self.fix_val = QLineEdit()
-        self.fix_val.setPlaceholderText("Empty = default value...")
+        self.fix_val = QLineEdit('4')
         layout.addRow("If checked above - Avg Degree of Nearby Branch Communities to Merge (Attempt to fix branch labeling - try 4 to 6 to start or leave empty):", self.fix_val)
 
         self.down_factor = QLineEdit("0")

{nettracer3d-0.6.3 → nettracer3d-0.6.4}/src/nettracer3d/network_analysis.py

@@ -1024,11 +1024,8 @@ def histogram(counts, y_vals, directory = None):
     plt.ylabel('Avg Number of Neigbhoring Vertices')
 
     try:
-
         if directory is not None:
             plt.savefig(f'{directory}/radial_plot.png')
-        else:
-            plt.savefig('radial_plot.png')
     except:
         pass
 
@@ -1439,6 +1436,7 @@ def degree_distribution(G, directory = None):
 
 def power_trendline(x, y, directory = None):
     # Handle zeros in y for logarithmic transformations
+    """
     y = np.array(y)
     x = np.array(x)
     y[y == 0] += 0.001
@@ -1460,6 +1458,8 @@ def power_trendline(x, y, directory = None):
     ss_res = np.sum((y - y_pred) ** 2)
     ss_tot = np.sum((y - np.mean(y)) ** 2)
     r2 = 1 - (ss_res / ss_tot)
+    """
+    # ^ I commented out this power trendline stuff because I decided I no longer want it to do that so.
 
     # Create a scatterplot
     plt.scatter(x, y, label='Data')
@@ -1468,9 +1468,10 @@ def power_trendline(x, y, directory = None):
     plt.title('Degree Distribution of Network')
 
     # Plot the power trendline
-    plt.plot(x_fit, y_fit, color='red', label=f'Power Trendline: $y = {a:.2f}x^{{{b:.2f}}}$')
+    #plt.plot(x_fit, y_fit, color='red', label=f'Power Trendline: $y = {a:.2f}x^{{{b:.2f}}}$')
 
     # Annotate the plot with the trendline equation and R-squared value
+    """
     plt.text(
         0.05, 0.95, 
         f'$y = {a:.2f}x^{{{b:.2f}}}$\n$R^2 = {r2:.2f}$',
@@ -1478,13 +1479,12 @@ def power_trendline(x, y, directory = None):
         fontsize=12,
         verticalalignment='top'
     )
+    """
 
     try:
 
         if directory is not None:
             plt.savefig(f'{directory}/degree_plot.png')
-        else:
-            plt.savefig('degree_plot.png')
     except:
         pass
 

{nettracer3d-0.6.3 → nettracer3d-0.6.4/src/nettracer3d.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nettracer3d
-Version: 0.6.3
+Version: 0.6.4
 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
@@ -45,10 +45,15 @@ 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 0.6.3 updates --
+-- Version 0.6.4 updates --
 
-1. Fixed bug with the active channel indicator on the GUI not always updating when the active channel was changed by internal loading.
+1. Fixed bug with tabulated data in top right having a right click window corresponding to the bottom left.
 
-2. Updated ram_lock mode in the segmenter to garbage collect better... again.
+2. Fixed bug when converting communities to nodes that let the same community connect to itself in the new network.
 
-3. Added new function (Label neighborhoods). Find it in process -> image -> label neighborhoods. Allows a 3d labeled array to act as a kernel and extend its labels along a secondary binary array. This can be useful in evaluating nearest neighbors en-masse. The method behind this (smart label) was previously used internally for some methods (ie watershedding) but I thought I'd include it as an actual function since it has some more general uses.
+3. Removed attempted trendline fitting from degree distribution
+
+4. Added new feature to skeletonization (and corresponding branch labeler/gennodes)
+	Now you can have the program attempt to auto-correct 3D skeletonization loop artifacts through a method that just runs the 3d fill holes algo and then attempts to reskeletonize the output. This worked well in my own testing. 
+
+5. Other minor fixes/improvements