nettracer3d 1.0.2__py3-none-any.whl → 1.0.3__py3-none-any.whl

nettracer3d/nettracer.py

@@ -3933,7 +3933,7 @@ class Network_3D:
         """
         self._nodes, num_nodes = label_objects(nodes, structure_3d)
 
-    def combine_nodes(self, root_nodes, other_nodes, other_ID, identity_dict, root_ID = None, centroids = False):
+    def combine_nodes(self, root_nodes, other_nodes, other_ID, identity_dict, root_ID = None, centroids = False, down_factor = None):
 
         """Internal method to merge two labelled node arrays into one"""
 
@@ -3944,7 +3944,10 @@ class Network_3D:
             max_val = np.max(root_nodes)
             other_nodes[:] = np.where(mask, other_nodes + max_val, 0)
         if centroids:
-            new_dict = network_analysis._find_centroids(other_nodes)
+            new_dict = network_analysis._find_centroids(other_nodes, down_factor = down_factor)
+            if down_factor is not None:
+                for item in new_dict:
+                    new_dict[item] = down_factor * new_dict[item]
             self.node_centroids.update(new_dict)
 
         if root_ID is not None:
@@ -3984,7 +3987,7 @@ class Network_3D:
 
         return nodes, identity_dict
 
-    def merge_nodes(self, addn_nodes_name, label_nodes = True, root_id = "Root_Nodes", centroids = False):
+    def merge_nodes(self, addn_nodes_name, label_nodes = True, root_id = "Root_Nodes", centroids = False, down_factor = None):
         """
         Merges the self._nodes attribute with alternate labelled node images. The alternate nodes can be inputted as a string for a filepath to a tif,
         or as a directory address containing only tif images, which will merge the _nodes attribute with all tifs in the folder. The _node_identities attribute
@@ -4005,19 +4008,21 @@ class Network_3D:
         identity_dict = {} #A dictionary to deliniate the node identities
 
         if centroids:
-            self.node_centroids = network_analysis._find_centroids(self._nodes)
-
+            self.node_centroids = network_analysis._find_centroids(self._nodes, down_factor = down_factor)
+            if down_factor is not None:
+                for item in self.node_centroids:
+                    self.node_centroids[item] = down_factor * self.node_centroids[item]
 
         try: #Try presumes the input is a tif
             addn_nodes = tifffile.imread(addn_nodes_name) #If not this will fail and activate the except block
 
             if label_nodes is True:
                 addn_nodes, num_nodes2 = label_objects(addn_nodes) # Label the node objects. Note this presumes no overlap between node masks.
-                node_labels, identity_dict = self.combine_nodes(self._nodes, addn_nodes, addn_nodes_name, identity_dict, nodes_name, centroids = centroids) #This method stacks labelled arrays
+                node_labels, identity_dict = self.combine_nodes(self._nodes, addn_nodes, addn_nodes_name, identity_dict, nodes_name, centroids = centroids, down_factor = down_factor) #This method stacks labelled arrays
                 num_nodes = np.max(node_labels)
 
             else: #If nodes already labelled
-                node_labels, identity_dict = self.combine_nodes(self._nodes, addn_nodes, addn_nodes_name, identity_dict, nodes_name, centroids = centroids)
+                node_labels, identity_dict = self.combine_nodes(self._nodes, addn_nodes, addn_nodes_name, identity_dict, nodes_name, centroids = centroids, down_factor = down_factor)
                 num_nodes = int(np.max(node_labels))
 
         except: #Exception presumes the input is a directory containing multiple tifs, to allow multi-node stackage.
@@ -4035,15 +4040,15 @@ class Network_3D:
                     if label_nodes is True:
                         addn_nodes, num_nodes2 = label_objects(addn_nodes)  # Label the node objects. Note this presumes no overlap between node masks.
                         if i == 0:
-                            node_labels, identity_dict = self.combine_nodes(self._nodes, addn_nodes, addn_nodes_ID, identity_dict, nodes_name, centroids = centroids)
+                            node_labels, identity_dict = self.combine_nodes(self._nodes, addn_nodes, addn_nodes_ID, identity_dict, nodes_name, centroids = centroids, down_factor = down_factor)
                         else:
-                            node_labels, identity_dict = self.combine_nodes(node_labels, addn_nodes, addn_nodes_ID, identity_dict, centroids = centroids)
+                            node_labels, identity_dict = self.combine_nodes(node_labels, addn_nodes, addn_nodes_ID, identity_dict, centroids = centroids, down_factor = down_factor)
 
                     else:
                         if i == 0:
-                            node_labels, identity_dict = self.combine_nodes(self._nodes, addn_nodes, addn_nodes_ID, identity_dict, nodes_name, centroids = centroids)
+                            node_labels, identity_dict = self.combine_nodes(self._nodes, addn_nodes, addn_nodes_ID, identity_dict, nodes_name, centroids = centroids, down_factor = down_factor)
                         else:
-                            node_labels, identity_dict = self.combine_nodes(node_labels, addn_nodes, addn_nodes_ID, identity_dict, centroids = centroids)
+                            node_labels, identity_dict = self.combine_nodes(node_labels, addn_nodes, addn_nodes_ID, identity_dict, centroids = centroids, down_factor = down_factor)
                 except Exception as e:
                     print("Could not open additional nodes, verify they are being inputted correctly...")
 

nettracer3d/nettracer_gui.py

@@ -4,7 +4,7 @@ from PyQt6.QtWidgets import (QApplication, QMainWindow, QWidget, QVBoxLayout, QG
                             QHBoxLayout, QSlider, QMenuBar, QMenu, QDialog, 
                             QFormLayout, QLineEdit, QPushButton, QFileDialog,
                             QLabel, QComboBox, QMessageBox, QTableView, QInputDialog,
-                            QMenu, QTabWidget, QGroupBox)
+                            QMenu, QTabWidget, QGroupBox, QCheckBox)
 from PyQt6.QtCore import (QPoint, Qt, QAbstractTableModel, QTimer,  QThread, pyqtSignal, QObject, QCoreApplication, QEvent, QEventLoop)
 import numpy as np
 import time
@@ -5471,7 +5471,6 @@ class ImageViewerWindow(QMainWindow):
 
         elif sort == 'Merge Nodes':
             try:
-
                 if my_network.nodes is None:
                     QMessageBox.critical(
                         self,
@@ -5479,72 +5478,118 @@ class ImageViewerWindow(QMainWindow):
                         "Please load your first set of nodes into the 'Nodes' channel first"
                     )
                     return
-
                 if len(np.unique(my_network.nodes)) < 3:
                     self.show_label_dialog()
-
-                # First ask user what they want to select
-                msg = QMessageBox()
-                msg.setWindowTitle("Selection Type")
-                msg.setText("Would you like to select a TIFF file or a directory?")
-                tiff_button = msg.addButton("TIFF File", QMessageBox.ButtonRole.AcceptRole)
-                dir_button = msg.addButton("Directory", QMessageBox.ButtonRole.AcceptRole)
-                msg.addButton("Cancel", QMessageBox.ButtonRole.RejectRole)
-
-                msg.exec()
-
-                # Also if they want centroids:
-                msg2 = QMessageBox()
-                msg2.setWindowTitle("Selection Type")
-                msg2.setText("Would you like to compute node centroids for each image prior to merging?")
-                yes_button = msg2.addButton("Yes", QMessageBox.ButtonRole.AcceptRole)
-                no_button = msg2.addButton("No", QMessageBox.ButtonRole.AcceptRole)
-                msg2.addButton("Cancel", QMessageBox.ButtonRole.RejectRole)
-
-                msg2.exec()
-
-                if msg2.clickedButton() == yes_button:
-                    centroids = True
-                else:
-                    centroids = False
-
-                if msg.clickedButton() == tiff_button:
-                    # Code for selecting TIFF files
-                    filename, _ = QFileDialog.getOpenFileName(
-                        self,
-                        "Select TIFF file",
-                        "",
-                        "TIFF files (*.tiff *.tif)"
-                    )
-                    if filename:
-                        selected_path = filename
-
-                elif msg.clickedButton() == dir_button:
-                    # Code for selecting directories
-                    dialog = QFileDialog(self)
-                    dialog.setOption(QFileDialog.Option.DontUseNativeDialog)
-                    dialog.setOption(QFileDialog.Option.ReadOnly)
-                    dialog.setFileMode(QFileDialog.FileMode.Directory)
-                    dialog.setViewMode(QFileDialog.ViewMode.Detail)
-
-                    if dialog.exec() == QFileDialog.DialogCode.Accepted:
-                        selected_path = dialog.directory().absolutePath()
-
-                my_network.merge_nodes(selected_path, root_id = self.node_name, centroids = centroids)
-                self.load_channel(0, my_network.nodes, True)
-
-
-                if hasattr(my_network, 'node_identities') and my_network.node_identities is not None:
+                
+                # Create custom dialog
+                dialog = QDialog(self)
+                dialog.setWindowTitle("Merge Nodes Configuration")
+                dialog.setModal(True)
+                dialog.resize(400, 200)
+                
+                layout = QVBoxLayout(dialog)
+                
+                # Selection type
+                type_layout = QHBoxLayout()
+                type_label = QLabel("Selection Type:")
+                type_combo = QComboBox()
+                type_combo.addItems(["TIFF File", "Directory"])
+                type_layout.addWidget(type_label)
+                type_layout.addWidget(type_combo)
+                layout.addLayout(type_layout)
+                
+                # Centroids checkbox
+                centroids_layout = QHBoxLayout()
+                centroids_check = QCheckBox("Compute node centroids for each image prior to merging")
+                centroids_layout.addWidget(centroids_check)
+                layout.addLayout(centroids_layout)
+                
+                # Down factor for centroid calculation
+                down_factor_layout = QHBoxLayout()
+                down_factor_label = QLabel("Down Factor (for centroid calculation downsampling):")
+                down_factor_edit = QLineEdit()
+                down_factor_edit.setText("1")  # Default value
+                down_factor_edit.setPlaceholderText("Enter down factor (e.g., 1, 2, 4)")
+                down_factor_layout.addWidget(down_factor_label)
+                down_factor_layout.addWidget(down_factor_edit)
+                layout.addLayout(down_factor_layout)
+                
+                # Buttons
+                button_layout = QHBoxLayout()
+                accept_button = QPushButton("Accept")
+                cancel_button = QPushButton("Cancel")
+                button_layout.addWidget(accept_button)
+                button_layout.addWidget(cancel_button)
+                layout.addLayout(button_layout)
+                
+                # Connect buttons
+                accept_button.clicked.connect(dialog.accept)
+                cancel_button.clicked.connect(dialog.reject)
+                
+                # Execute dialog
+                if dialog.exec() == QDialog.DialogCode.Accepted:
+                    # Get values from dialog
+                    selection_type = type_combo.currentText()
+                    centroids = centroids_check.isChecked()
+                    
+                    # Validate and get down_factor
                     try:
-                        self.format_for_upperright_table(my_network.node_identities, 'NodeID', 'Identity', 'Node Identities')
-                    except Exception as e:
-                        print(f"Error loading node identity table: {e}")
-                if centroids:
-                    self.format_for_upperright_table(my_network.node_centroids, 'NodeID', ['Z', 'Y', 'X'], 'Node Centroids')
-
-
+                        down_factor = int(down_factor_edit.text())
+                        if down_factor <= 0:
+                            raise ValueError("Down factor must be positive")
+                    except ValueError as e:
+                        QMessageBox.critical(
+                            self,
+                            "Invalid Input",
+                            f"Invalid down factor: {str(e)}"
+                        )
+                        return
+                    
+                    # Handle file/directory selection based on combo box choice
+                    if selection_type == "TIFF File":
+                        filename, _ = QFileDialog.getOpenFileName(
+                            self,
+                            "Select TIFF file",
+                            "",
+                            "TIFF files (*.tiff *.tif)"
+                        )
+                        if filename:
+                            selected_path = filename
+                        else:
+                            return  # User cancelled file selection
+                    else:  # Directory
+                        file_dialog = QFileDialog(self)
+                        file_dialog.setOption(QFileDialog.Option.DontUseNativeDialog)
+                        file_dialog.setOption(QFileDialog.Option.ReadOnly)
+                        file_dialog.setFileMode(QFileDialog.FileMode.Directory)
+                        file_dialog.setViewMode(QFileDialog.ViewMode.Detail)
+                        if file_dialog.exec() == QFileDialog.DialogCode.Accepted:
+                            selected_path = file_dialog.directory().absolutePath()
+                        else:
+                            return  # User cancelled directory selection
+                    
+                    if down_factor == 1:
+                        down_factor = None
+                    # Call merge_nodes with all parameters
+                    my_network.merge_nodes(
+                        selected_path, 
+                        root_id=self.node_name, 
+                        centroids=centroids,
+                        down_factor=down_factor
+                    )
+                    
+                    self.load_channel(0, my_network.nodes, True)
+                    
+                    if hasattr(my_network, 'node_identities') and my_network.node_identities is not None:
+                        try:
+                            self.format_for_upperright_table(my_network.node_identities, 'NodeID', 'Identity', 'Node Identities')
+                        except Exception as e:
+                            print(f"Error loading node identity table: {e}")
+                    
+                    if centroids:
+                        self.format_for_upperright_table(my_network.node_centroids, 'NodeID', ['Z', 'Y', 'X'], 'Node Centroids')
+                
             except Exception as e:
-
                 QMessageBox.critical(
                     self,
                     "Error Merging",
@@ -10064,9 +10109,33 @@ class ViolinDialog(QDialog):
         
         return df_normalized
 
+    def show_in_table(self, df, metric, title):
+
+        # Create new table
+        table = CustomTableView(self.parent())
+        table.setModel(PandasModel(df))
+
+        try:
+            first_column_name = table.model()._data.columns[0]
+            table.sort_table(first_column_name, ascending=True)
+        except:
+             pass
+        
+        # Add to tabbed widget
+        if title is None:
+            self.parent().tabbed_data.add_table(f"{metric} Analysis", table)
+        else:
+            self.parent().tabbed_data.add_table(f"{title}", table)
+        
+
+
+        # Adjust column widths to content
+        for column in range(table.model().columnCount(None)):
+            table.resizeColumnToContents(column)
+
     def run(self):
 
-        def df_to_dict_by_rows(df, row_indices):
+        def df_to_dict_by_rows(df, row_indices, title):
             """
             Convert a pandas DataFrame to a dictionary by selecting specific rows.
             No normalization - dataframe is already normalized.
@@ -10095,6 +10164,10 @@ class ViolinDialog(QDialog):
             for column in masked_df.columns:
                 result_dict[column] = masked_df[column].tolist()
             
+            masked_df.insert(0, "NodeIDs", row_indices)
+            self.show_in_table(masked_df, metric = "NodeID", title = title)
+
+
             return result_dict
 
         from . import neighborhoods
@@ -10112,10 +10185,10 @@ class ViolinDialog(QDialog):
                     if iden in parse:
                         iden_list.append(item)
                 except:
-                    if iden == item:
+                    if (iden == my_network.node_identities[item]):
                         iden_list.append(item)
 
-            violin_dict = df_to_dict_by_rows(self.df, iden_list)
+            violin_dict = df_to_dict_by_rows(self.df, iden_list, f"Z-Score-like Channel Intensities of Identity {iden}, {len(iden_list)} Nodes")
 
             neighborhoods.create_violin_plots(violin_dict, graph_title=f"Z-Score-like Channel Intensities of Identity {iden}, {len(iden_list)} Nodes")
 
@@ -10124,11 +10197,11 @@ class ViolinDialog(QDialog):
 
             com = self.coms.currentText()
 
-            com_dict = n3d.invert_dict(my_network.communities)  # Fixed: should be communities
+            com_dict = n3d.invert_dict(my_network.communities)
 
             com_list = com_dict[int(com)]
 
-            violin_dict = df_to_dict_by_rows(self.df, com_list)
+            violin_dict = df_to_dict_by_rows(self.df, com_list, f"Z-Score-like Channel Intensities of Community/Neighborhood {com}, {len(com_list)} Nodes")
 
             neighborhoods.create_violin_plots(violin_dict, graph_title=f"Z-Score-like Channel Intensities of Community/Neighborhood {com}, {len(com_list)} Nodes")
 

{nettracer3d-1.0.2.dist-info → nettracer3d-1.0.3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nettracer3d
-Version: 1.0.2
+Version: 1.0.3
 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/
@@ -110,7 +110,6 @@ McLaughlin, L., Zhang, B., Sharma, S. et al. Three dimensional multiscalar neuro
 
 NetTracer3D was developed by Liam McLaughlin while working under Dr. Sanjay Jain at Washington University School of Medicine.
 
--- Version 1.0.2 Updates --
+-- Version 1.0.3 Updates --
 
-	* Minor fixes
-	* Added ability to generate violin plots using the table generated from merging node identities, showing the relative expression of markers for multiple channels for the nodes belonging to some channel or community/neighborhood
+	* Some small bug fixes and adjustments

{nettracer3d-1.0.2.dist-info → nettracer3d-1.0.3.dist-info}/RECORD

@@ -5,8 +5,8 @@ nettracer3d/excelotron.py,sha256=aNof6k-DgMxVyFgsl3ltSCxG4vZW49cuvCBzfzhYhUY,750
 nettracer3d/modularity.py,sha256=pborVcDBvICB2-g8lNoSVZbIReIBlfeBmjFbPYmtq7Y,22443
 nettracer3d/morphology.py,sha256=jyDjYzrZ4LvI5jOyw8DLsxmo-i5lpqHsejYpW7Tq7Mo,19786
 nettracer3d/neighborhoods.py,sha256=lh4_zuTwgTq-u8VHy72buBfZf58FEJo9sH3IIBuZr68,52735
-nettracer3d/nettracer.py,sha256=dZR8wOFUDNmfsn1M615FKbg1n4C_RhtwLh9vtjCryBg,270737
-nettracer3d/nettracer_gui.py,sha256=m1V7S1YMw17YBgcAdE3lRmCbvoBsTZyUl7dOmQ6N6OI,661601
+nettracer3d/nettracer.py,sha256=_K_npg50qrXU1kj8NeFnlQY0oRMnD_PyvNi23hoQDow,271318
+nettracer3d/nettracer_gui.py,sha256=3nUjgPi2H-OKqBB7PP35kQVXLJNzPJN9wx9Ay_9pt50,665218
 nettracer3d/network_analysis.py,sha256=kBzsVaq4dZkMe0k-VGvQIUvM-tK0ZZ8bvb-wtsugZRQ,46150
 nettracer3d/network_draw.py,sha256=F7fw6Pcf4qWOhdKwLmhwqWdschbDlHzwCVolQC9imeU,14117
 nettracer3d/node_draw.py,sha256=kZcR1PekLg0riioNeGcALIXQyZ5PtHA_9MT6z7Zovdk,10401
@@ -17,9 +17,9 @@ nettracer3d/segmenter.py,sha256=aOO3PwZ2UeizEIFX7N8midwzTzbEDzgM2jQ7WTdbrUg,7067
 nettracer3d/segmenter_GPU.py,sha256=OUekQljLKPiC4d4hNZmqrRa9HSVQ6HcCnILiAfHE5Hg,78051
 nettracer3d/simple_network.py,sha256=dkG4jpc4zzdeuoaQobgGfL3PNo6N8dGKQ5hEEubFIvA,9947
 nettracer3d/smart_dilate.py,sha256=TvRUh6B4q4zIdCO1BWH-xgTdND5OUNmo99eyxG9oIAU,27145
-nettracer3d-1.0.2.dist-info/licenses/LICENSE,sha256=jnNT-yBeIAKAHpYthPvLeqCzJ6nSurgnKmloVnfsjCI,764
-nettracer3d-1.0.2.dist-info/METADATA,sha256=1LixOhZlmUtLcP9OrX6WK_mS0M2tuzo3tjGbw4FZrEE,7218
-nettracer3d-1.0.2.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-nettracer3d-1.0.2.dist-info/entry_points.txt,sha256=Nx1rr_0QhJXDBHAQg2vcqCzLMKBzSHfwy3xwGkueVyc,53
-nettracer3d-1.0.2.dist-info/top_level.txt,sha256=zsYy9rZwirfCEOubolhee4TyzqBAL5gSUeFMzhFTX8c,12
-nettracer3d-1.0.2.dist-info/RECORD,,
+nettracer3d-1.0.3.dist-info/licenses/LICENSE,sha256=jnNT-yBeIAKAHpYthPvLeqCzJ6nSurgnKmloVnfsjCI,764
+nettracer3d-1.0.3.dist-info/METADATA,sha256=jXFL5Ol1kS56twkSbK7qat2uYIFrnw9E7fRwOcojqLs,7013
+nettracer3d-1.0.3.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+nettracer3d-1.0.3.dist-info/entry_points.txt,sha256=Nx1rr_0QhJXDBHAQg2vcqCzLMKBzSHfwy3xwGkueVyc,53
+nettracer3d-1.0.3.dist-info/top_level.txt,sha256=zsYy9rZwirfCEOubolhee4TyzqBAL5gSUeFMzhFTX8c,12
+nettracer3d-1.0.3.dist-info/RECORD,,