nettracer3d 0.6.2__tar.gz → 0.6.4__tar.gz

{nettracer3d-0.6.2/src/nettracer3d.egg-info → nettracer3d-0.6.4}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.2
+Metadata-Version: 2.4
 Name: nettracer3d
-Version: 0.6.2
+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
@@ -33,6 +33,7 @@ Provides-Extra: cuda12
 Requires-Dist: cupy-cuda12x; extra == "cuda12"
 Provides-Extra: cupy
 Requires-Dist: cupy; extra == "cupy"
+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:
 
@@ -44,8 +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 0.6.2 updates --
+-- Version 0.6.4 updates --
 
-1. Fixed bug with performing 2D distance transforms on CPU
+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 use smaller chunks and garbage collect better.
+2. Fixed bug when converting communities to nodes that let the same community connect to itself in the new network.
+
+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-0.6.2 → nettracer3d-0.6.4}/README.md

@@ -8,8 +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 0.6.2 updates --
+-- Version 0.6.4 updates --
 
-1. Fixed bug with performing 2D distance transforms on CPU
+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 use smaller chunks and garbage collect better.
+2. Fixed bug when converting communities to nodes that let the same community connect to itself in the new network.
+
+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-0.6.2 → nettracer3d-0.6.4}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "nettracer3d"
-version = "0.6.2"
+version = "0.6.4"
 authors = [
   { name="Liam McLaughlin", email="mclaughlinliam99@gmail.com" },
 ]

{nettracer3d-0.6.2 → 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-0.6.2 → 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
@@ -2429,10 +2430,14 @@ class ImageViewerWindow(QMainWindow):
         binarize_action.triggered.connect(self.show_binarize_dialog)
         label_action = image_menu.addAction("Label Objects")
         label_action.triggered.connect(self.show_label_dialog)
+        slabel_action = image_menu.addAction("Neighborhood Labels")
+        slabel_action.triggered.connect(self.show_slabel_dialog)
         thresh_action = image_menu.addAction("Threshold/Segment")
         thresh_action.triggered.connect(self.show_thresh_dialog)
         mask_action = image_menu.addAction("Mask Channel")
         mask_action.triggered.connect(self.show_mask_dialog)
+        type_action = image_menu.addAction("Channel dtype")
+        type_action.triggered.connect(self.show_type_dialog)
         skeletonize_action = image_menu.addAction("Skeletonize")
         skeletonize_action.triggered.connect(self.show_skeletonize_dialog)
         watershed_action = image_menu.addAction("Watershed")
@@ -2657,6 +2662,11 @@ class ImageViewerWindow(QMainWindow):
         dialog = LabelDialog(self)
         dialog.exec()
 
+    def show_slabel_dialog(self):
+        """Show the slabel dialog"""
+        dialog = SLabelDialog(self)
+        dialog.exec()
+
     def show_thresh_dialog(self):
         """Show threshold dialog"""
         if self.machine_window is not None:
@@ -2671,6 +2681,11 @@ class ImageViewerWindow(QMainWindow):
         dialog = MaskDialog(self)
         dialog.exec()
 
+    def show_type_dialog(self):
+        """Show the type dialog"""
+        dialog = TypeDialog(self)
+        dialog.exec()
+
     def show_skeletonize_dialog(self):
         """show the skeletonize dialog"""
         dialog = SkeletonizeDialog(self)
@@ -3066,6 +3081,7 @@ class ImageViewerWindow(QMainWindow):
     def set_active_channel(self, index):
         """Set the active channel and update UI accordingly."""
         self.active_channel = index
+        self.active_channel_combo.setCurrentIndex(index)
         # Update button appearances to show active channel
         for i, btn in enumerate(self.channel_buttons):
             if i == index and btn.isEnabled():
@@ -3213,6 +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
@@ -3972,7 +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")
@@ -4081,7 +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"
@@ -4090,7 +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)")
@@ -4475,7 +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
@@ -4495,7 +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"""
@@ -4510,12 +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:
@@ -5418,18 +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):
 
@@ -5462,7 +5492,7 @@ class DegreeDistDialog(QDialog):
 
             self.accept()
 
-        except Excpetion as e:
+        except Exception as e:
             print(f"An error occurred: {e}")
 
 class NeighborIdentityDialog(QDialog):
@@ -6261,6 +6291,91 @@ class LabelDialog(QDialog):
                 f"Error running label: {str(e)}"
             )
 
+
+class SLabelDialog(QDialog):
+    def __init__(self, parent=None):
+        super().__init__(parent)
+        self.setWindowTitle("Smart Label (Use label array to assign label neighborhoods to binary array)?")
+        self.setModal(True)
+        
+        layout = QFormLayout(self)
+
+
+        # Add mode selection dropdown
+        self.mode_selector = QComboBox()
+        self.mode_selector.addItems(["Nodes", "Edges", "Overlay 1", "Overlay 2"])
+        self.mode_selector.setCurrentIndex(0)  # Default to Mode 1
+        layout.addRow("Prelabeled Array:", self.mode_selector)
+
+        layout.addRow(QLabel("Will Label Neighborhoods in: "))
+
+        # Add mode selection dropdown
+        self.target_selector = QComboBox()
+        self.target_selector.addItems(["Nodes", "Edges", "Overlay 1", "Overlay 2"])
+        self.target_selector.setCurrentIndex(1)  # Default to Mode 1
+        layout.addRow("Binary Array:", self.target_selector)
+
+        # GPU checkbox (default True)
+        self.GPU = QPushButton("GPU")
+        self.GPU.setCheckable(True)
+        self.GPU.setChecked(True)
+        layout.addRow("Use GPU:", self.GPU)
+
+        self.down_factor = QLineEdit("")
+        layout.addRow("Internal Downsample for GPU (if needed):", self.down_factor)
+
+       # Add Run button
+        run_button = QPushButton("Run Smart Label")
+        run_button.clicked.connect(self.run_slabel)
+        layout.addRow(run_button)
+
+    def run_slabel(self):
+
+        try:
+
+            accepted_source = self.mode_selector.currentIndex()
+            accepted_target = self.target_selector.currentIndex()
+            GPU = self.GPU.isChecked()
+
+
+            if accepted_source == accepted_target:
+                return
+
+            binary_array = self.parent().channel_data[accepted_target]
+
+            label_array = self.parent().channel_data[accepted_source]
+
+            down_factor = float(self.down_factor.text()) if self.down_factor.text().strip() else None
+
+
+            try:
+
+                # Update both the display data and the network object
+                binary_array = sdl.smart_label(binary_array, label_array, directory = None, GPU = GPU, predownsample = down_factor)
+
+                label_array = sdl.invert_array(label_array)
+
+                binary_array = binary_array * label_array
+
+                self.parent().load_channel(accepted_target, binary_array, True)
+
+                self.accept()
+                
+            except Exception as e:
+                QMessageBox.critical(
+                    self,
+                    "Error",
+                    f"Error running smart label: {str(e)}"
+                )
+
+        except Exception as e:
+            QMessageBox.critical(
+                self,
+                "Error",
+                f"Error running smart label: {str(e)}"
+            )
+
+
 class ThresholdDialog(QDialog):
     def __init__(self, parent=None):
         super().__init__(parent)
@@ -6380,9 +6495,8 @@ class MachineWindow(QMainWindow):
                 act_channel = 1
 
 
-        array1 = np.zeros_like(active_data)
-        array2 = np.zeros_like(active_data)
-        array3 = np.zeros_like(active_data)
+        array1 = np.zeros_like(active_data).astype(np.uint8)
+        array3 = np.zeros_like(active_data).astype(np.uint8)
         self.parent().highlight_overlay = array3 #Clear this out for the segmenter to use
 
         self.parent().load_channel(2, array1, True)
@@ -6460,7 +6574,7 @@ class MachineWindow(QMainWindow):
 
         # Group 3: Training Options
         training_group = QGroupBox("Training")
-        training_layout = QVBoxLayout()
+        training_layout = QHBoxLayout()
         train_quick = QPushButton("Train Quick Model")
         train_quick.clicked.connect(lambda: self.train_model(speed=True))
         train_detailed = QPushButton("Train More Detailed Model")
@@ -6471,11 +6585,13 @@ class MachineWindow(QMainWindow):
 
         # Group 4: Segmentation Options
         segmentation_group = QGroupBox("Segmentation")
-        segmentation_layout = QVBoxLayout()
+        segmentation_layout = QHBoxLayout()
         seg_button = QPushButton("Preview Segment")
         self.seg_button = seg_button
         seg_button.clicked.connect(self.start_segmentation)
-        self.lock_button = QPushButton("🔒 Memory lock - (Prioritize RAM. Recommended unless you have a lot)")
+        self.pause_button = QPushButton("▶/⏸️")
+        self.pause_button.clicked.connect(self.pause)
+        self.lock_button = QPushButton("🔒 Memory lock - (Prioritize RAM)")
         self.lock_button.setCheckable(True)
         self.lock_button.setChecked(True)
         self.lock_button.clicked.connect(self.toggle_lock)
@@ -6483,6 +6599,7 @@ class MachineWindow(QMainWindow):
         full_button = QPushButton("Segment All")
         full_button.clicked.connect(self.segment)
         segmentation_layout.addWidget(seg_button)
+        #segmentation_layout.addWidget(self.pause_button)   # <--- for some reason the segmenter preview is still running even when killed, may be regenerating itself somewhere. May or may not actually try to resolve this because this feature isnt that necessary.
         segmentation_layout.addWidget(self.lock_button)
         segmentation_layout.addWidget(full_button)
         segmentation_group.setLayout(segmentation_layout)
@@ -6507,6 +6624,27 @@ class MachineWindow(QMainWindow):
 
         self.mem_lock = self.lock_button.isChecked()
 
+    def pause(self):
+
+        if self.segmentation_worker is not None:
+            try:
+                print("Pausing segmenter")
+                self.previewing = False
+                self.segmentation_finished
+                del self.segmentation_worker
+                self.segmentation_worker = None
+            except:
+                pass
+
+        else:
+            try:
+                print("Restarting segmenter")
+                self.previewing = True
+                self.start_segmentation
+            except:
+                pass
+
+
 
     def toggle_GPU(self):
 
@@ -6615,7 +6753,7 @@ class MachineWindow(QMainWindow):
             else:
                 active_data = self.parent().channel_data[1]
 
-        array3 = np.zeros_like(active_data)
+        array3 = np.zeros_like(active_data).astype(np.uint8)
         self.parent().highlight_overlay = array3 #Clear this out for the segmenter to use
 
         if not self.trained:
@@ -6801,7 +6939,7 @@ class MachineWindow(QMainWindow):
                 else:
                     active_data = self.parent().channel_data[1]
 
-            array3 = np.zeros_like(active_data)
+            array3 = np.zeros_like(active_data).astype(np.uint8)
             self.parent().highlight_overlay = array3 #Clear this out for the segmenter to use
 
             print("Segmenting entire volume with model...")
@@ -7589,6 +7727,65 @@ class MaskDialog(QDialog):
             print(f"Error masking: {e}")
 
 
+class TypeDialog(QDialog):
+
+    def __init__(self, parent=None):
+
+        super().__init__(parent)
+        self.setWindowTitle("Active Channel dtype")
+        self.setModal(True)
+
+        layout = QFormLayout(self)
+
+        self.active_chan = self.parent().active_channel
+
+        active_data = self.parent().channel_data[self.active_chan]
+
+        layout.addRow("Info:", QLabel(f"Active dtype (Channel {self.active_chan}): {active_data.dtype}"))
+
+        # Add mode selection dropdown
+        self.mode_selector = QComboBox()
+        self.mode_selector.addItems(["8bit int", "16bit int", "32bit int", "32bit float", "64bit float"])
+        self.mode_selector.setCurrentIndex(0)  # Default to Mode 1
+        layout.addRow("Change to?:", self.mode_selector)
+
+        # Add Run button
+        run_button = QPushButton("Run")
+        run_button.clicked.connect(lambda: self.run_type(active_data))
+        layout.addRow(run_button)
+
+    def run_type(self, active_data):
+
+        mode = self.mode_selector.currentIndex()
+
+        if mode == 0:
+
+            active_data = active_data.astype(np.uint8)
+
+        elif mode == 1:
+
+            active_data = active_data.astype(np.uint16)
+
+        elif mode == 2:
+
+            active_data = active_data.astype(np.uint32)
+
+        elif mode == 3:
+
+            active_data = active_data.astype(np.float32)
+
+        elif mode == 4:
+
+            active_data = active_data.astype(np.float64)
+
+        self.parent().load_channel(self.active_chan, active_data, True)
+
+
+        print(f"Channel {self.active_chan}) dtype now: {self.parent().channel_data[self.active_chan].dtype}")
+        self.accept()
+
+
+
 
 class SkeletonizeDialog(QDialog):
     def __init__(self, parent=None):
@@ -7601,6 +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)
@@ -7614,11 +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(
@@ -7930,11 +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
@@ -8012,6 +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,
@@ -8066,6 +8288,7 @@ class GenNodesDialog(QDialog):
             )
 
 
+
 class BranchDialog(QDialog):
 
     def __init__(self, parent=None):
@@ -8093,8 +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-0.6.2 → 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-0.6.2 → nettracer3d-0.6.4}/src/nettracer3d/segmenter.py

@@ -1289,6 +1289,9 @@ class InteractiveSegmenter:
         """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)
 
+        self.realtimechunks = None # Presumably no longer need this.
+        self.map_slice = None
+
         if self.mem_lock:
             chunk_size = 32 #memory efficient chunk
 
@@ -1302,7 +1305,7 @@ class InteractiveSegmenter:
             Returns:
                 List of chunks, where each chunk contains the coordinates for one z-slice or subchunk
             """
-            MAX_CHUNK_SIZE = 32768000
+            MAX_CHUNK_SIZE = 32768
             chunks = []
             
             for z in range(self.image_3d.shape[0]):
@@ -1690,6 +1693,7 @@ class InteractiveSegmenter:
     def train_batch(self, foreground_array, speed = True, use_gpu = False, use_two = False, mem_lock = False):
         """Train directly on foreground and background arrays"""
 
+        print("Training model...")
         self.speed = speed
         self.cur_gpu = use_gpu
         if mem_lock != self.mem_lock:

{nettracer3d-0.6.2 → nettracer3d-0.6.4/src/nettracer3d.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.2
+Metadata-Version: 2.4
 Name: nettracer3d
-Version: 0.6.2
+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
@@ -33,6 +33,7 @@ Provides-Extra: cuda12
 Requires-Dist: cupy-cuda12x; extra == "cuda12"
 Provides-Extra: cupy
 Requires-Dist: cupy; extra == "cupy"
+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:
 
@@ -44,8 +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 0.6.2 updates --
+-- Version 0.6.4 updates --
 
-1. Fixed bug with performing 2D distance transforms on CPU
+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 use smaller chunks and garbage collect better.
+2. Fixed bug when converting communities to nodes that let the same community connect to itself in the new network.
+
+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