nettracer3d 0.9.8__tar.gz → 1.0.0__tar.gz

{nettracer3d-0.9.8/src/nettracer3d.egg-info → nettracer3d-1.0.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nettracer3d
-Version: 0.9.8
+Version: 1.0.0
 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/
@@ -110,6 +110,7 @@ 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 0.9.8 Updates --
+-- Version 1.0.0 Updates --
 
-	* Some minor bug fixes
+	* The 'network selection' table is now auto-populated when using the multiple-identity selector, and when using the node thresholder.
+	* And other minor adjustments/bug fixes

{nettracer3d-0.9.8 → nettracer3d-1.0.0}/README.md

@@ -65,6 +65,7 @@ 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 0.9.8 Updates --
+-- Version 1.0.0 Updates --
 
-	* Some minor bug fixes
+	* The 'network selection' table is now auto-populated when using the multiple-identity selector, and when using the node thresholder.
+	* And other minor adjustments/bug fixes

{nettracer3d-0.9.8 → nettracer3d-1.0.0}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "nettracer3d"
-version = "0.9.8"
+version = "1.0.0"
 authors = [
   { name="Liam McLaughlin", email="liamm@wustl.edu" },
 ]

{nettracer3d-0.9.8 → nettracer3d-1.0.0}/src/nettracer3d/nettracer_gui.py

@@ -466,6 +466,102 @@ class ImageViewerWindow(QMainWindow):
         self.hold_update = False
         self._first_pan_done = False
 
+
+    def load_file(self):
+        """Load CSV or Excel file and convert to dictionary format."""
+        try:
+            # Open file dialog
+            file_filter = "Spreadsheet Files (*.csv *.xlsx);;CSV Files (*.csv);;Excel Files (*.xlsx)"
+            filename, _ = QFileDialog.getOpenFileName(
+                self,
+                "Load File",
+                "",
+                file_filter
+            )
+            
+            if not filename:
+                return
+            
+            # Read the file
+            if filename.endswith('.csv'):
+                df = pd.read_csv(filename)
+            elif filename.endswith('.xlsx'):
+                df = pd.read_excel(filename)
+            else:
+                QMessageBox.warning(self, "Error", "Please select a CSV or Excel file.")
+                return
+            
+            if df.empty:
+                QMessageBox.warning(self, "Error", "The file appears to be empty.")
+                return
+            
+            # Extract headers
+            headers = df.columns.tolist()
+            if len(headers) < 1:
+                QMessageBox.warning(self, "Error", "File must have at least 1 column.")
+                return
+            
+            # Extract filename without extension for title
+            import os
+            title = os.path.splitext(os.path.basename(filename))[0]
+            
+            if len(headers) == 1:
+                # Single column: pass header to metric, column data as list to data, nothing to value
+                metric = headers[0]
+                data = df.iloc[:, 0].tolist()  # First column as list
+                value = None
+                
+                self.format_for_upperright_table(
+                    data=data,
+                    metric=metric,
+                    value=value,
+                    title=title
+                )
+            else:
+                # Multiple columns: create dictionary as before
+                # First column header (for metric parameter)
+                metric = headers[0]
+                
+                # Remaining headers (for value parameter)
+                value = headers[1:]
+                
+                # Create dictionary
+                data_dict = {}
+                
+                for index, row in df.iterrows():
+                    key = row.iloc[0]  # First column value as key
+                    
+                    if len(headers) == 2:
+                        # If only 2 columns, store single value
+                        data_dict[key] = row.iloc[1]
+                    else:
+                        # If more than 2 columns, store as list
+                        data_dict[key] = row.iloc[1:].tolist()
+                
+                if len(value) == 1:
+                    value = value[0]
+                
+                # Call the parent method
+                self.format_for_upperright_table(
+                    data=data_dict,
+                    metric=metric,
+                    value=value,
+                    title=title
+                )
+            
+            QMessageBox.information(
+                self,
+                "Success",
+                f"File '{title}' loaded successfully with {len(df)} entries."
+            )
+            
+        except Exception as e:
+            QMessageBox.critical(
+                self,
+                "Error",
+                f"Failed to load file: {str(e)}"
+            )
+        
     def popup_canvas(self):
         """Pop the canvas out into its own window"""
         if hasattr(self, 'popup_window') and self.popup_window.isVisible():
@@ -931,7 +1027,6 @@ class ImageViewerWindow(QMainWindow):
 
         """Highlight overlay generation method specific for the segmenter interactive mode"""
 
-
         def process_chunk_bounds(chunk_data, indices_to_check):
             """Process a single chunk of the array to create highlight mask"""
             mask = (chunk_data >= indices_to_check[0]) & (chunk_data <= indices_to_check[1])
@@ -1010,6 +1105,30 @@ class ImageViewerWindow(QMainWindow):
             current_ylim = self.ax.get_ylim()
             self.update_display_pan_mode(current_xlim, current_ylim)
 
+        if my_network.network is not None:
+            try:
+                if self.active_channel == 0:
+
+                    # Get the existing DataFrame from the model
+                    original_df = self.network_table.model()._data
+                    
+                    # Create mask for rows where one column is any original node AND the other column is any neighbor
+                    mask = (
+                        (original_df.iloc[:, 0].isin(indices)) &
+                        (original_df.iloc[:, 1].isin(indices)))
+                    
+                    # Filter the DataFrame to only include direct connections
+                    filtered_df = original_df[mask].copy()
+                    
+                    # Create new model with filtered DataFrame and update selection table
+                    new_model = PandasModel(filtered_df)
+                    self.selection_table.setModel(new_model)
+                    
+                    # Switch to selection table
+                    self.selection_button.click()
+            except:
+                pass
+
 
 
     def create_mini_overlay(self, node_indices = None, edge_indices = None):
@@ -3872,6 +3991,30 @@ class ImageViewerWindow(QMainWindow):
                         if len(self.clicked_values['edges']):
                             self.highlight_value_in_tables(self.clicked_values['edges'][-1])
                             self.handle_info('edge')
+
+                    if len(self.clicked_values['nodes']) > 0 or len(self.clicked_values['edges']) > 0:  # Check if we have any nodes selected
+
+                        old_nodes = copy.deepcopy(self.clicked_values['nodes']) 
+
+                        # Get the existing DataFrame from the model
+                        original_df = self.network_table.model()._data
+                        
+                        # Create mask for rows where one column is any original node AND the other column is any neighbor
+                        mask = (
+                            ((original_df.iloc[:, 0].isin(self.clicked_values['nodes'])) &
+                            (original_df.iloc[:, 1].isin(self.clicked_values['nodes']))) |
+                            (original_df.iloc[:, 2].isin(self.clicked_values['edges']))
+                            )
+                        
+                        # Filter the DataFrame to only include direct connections
+                        filtered_df = original_df[mask].copy()
+                        
+                        # Create new model with filtered DataFrame and update selection table
+                        new_model = PandasModel(filtered_df)
+                        self.selection_table.setModel(new_model)
+                        
+                        # Switch to selection table
+                        self.selection_button.click()
             
             elif not self.selecting and self.selection_start:  # If we had a click but never started selection
                 # Handle as a normal click
@@ -4418,7 +4561,7 @@ class ImageViewerWindow(QMainWindow):
         
         
         # Add after your other buttons
-        self.popup_button = QPushButton("⤴")  # or "🔗" or "⤴"
+        self.popup_button = QPushButton("⤴") 
         self.popup_button.setFixedSize(40, 40)
         self.popup_button.setToolTip("Pop out canvas")
         self.popup_button.clicked.connect(self.popup_canvas)
@@ -4433,6 +4576,12 @@ class ImageViewerWindow(QMainWindow):
         cam_button.setStyleSheet("font-size: 24px;")
         cam_button.clicked.connect(self.snap)
         corner_layout.addWidget(cam_button)
+
+        load_button = QPushButton("📁")
+        load_button.setFixedSize(40, 40)
+        load_button.setStyleSheet("font-size: 24px;")
+        load_button.clicked.connect(self.load_file)
+        corner_layout.addWidget(load_button)
         
         # Set as corner widget
         menubar.setCornerWidget(corner_widget, Qt.Corner.TopRightCorner)
@@ -6073,8 +6222,6 @@ class ImageViewerWindow(QMainWindow):
                 if self.resume:
                     self.machine_window.segmentation_worker.resume()
                     self.resume = False
-                if self.prev_down != self.downsample_factor:
-                    self.validate_downsample_input(text = self.prev_down)
            
             if self.static_background is not None:
                 # Your existing virtual strokes conversion logic
@@ -6131,8 +6278,6 @@ class ImageViewerWindow(QMainWindow):
                 for img in list(self.ax.get_images()):
                     img.remove()
                 # Clear measurement points
-                for artist in self.measurement_artists:
-                    artist.remove()
                 self.measurement_artists.clear()
 
             # Determine the current view bounds (either from preserve_zoom or current state)
@@ -6347,9 +6492,10 @@ class ImageViewerWindow(QMainWindow):
             if reset_resize:
                 self.resizing = False
             
-            # Use draw_idle for better performance
+            # draw_idle
             self.canvas.draw_idle()
 
+
         except Exception as e:
             pass
             #import traceback
@@ -6655,15 +6801,19 @@ 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 in self.parent.data_table:  # Top table
+            if self.is_top_table:  # Use the flag instead of checking membership
                 save_menu = context_menu.addMenu("Save As")
                 save_csv = save_menu.addAction("CSV")
                 save_excel = save_menu.addAction("Excel")
+                
+                if self.model() and len(self.model()._data.columns) == 2:
+                    thresh_action = context_menu.addAction("Use to Threshold Nodes")
+                    thresh_action.triggered.connect(lambda: self.thresh(self.create_threshold_dict()))
+                
                 close_action = context_menu.addAction("Close All")
-
                 close_action.triggered.connect(self.close_all)
                 
-                # Connect the actions
+                # Connect the save actions
                 save_csv.triggered.connect(lambda: self.save_table_as('csv'))
                 save_excel.triggered.connect(lambda: self.save_table_as('xlsx'))
             else:  # Bottom tables
@@ -6707,6 +6857,38 @@ class CustomTableView(QTableView):
             cursor_pos = QCursor.pos()
             context_menu.exec(cursor_pos)
 
+
+
+    def thresh(self, special_dict):
+        try:
+            self.parent.special_dict = special_dict
+            thresh_window = ThresholdWindow(self.parent, 4)
+            thresh_window.show()
+        except:
+            pass
+
+    def create_threshold_dict(self):
+        try:
+            """Create a dictionary from the 2-column table data."""
+            if not self.model() or not hasattr(self.model(), '_data'):
+                return {}
+            
+            df = self.model()._data
+            if len(df.columns) != 2:
+                return {}
+            
+            # Create dictionary: {column_0_value: column_1_value}
+            threshold_dict = {}
+            for index, row in df.iterrows():
+                key = row.iloc[0]    # Column 0 value
+                value = row.iloc[1]  # Column 1 value
+                threshold_dict[int(key)] = float(value)
+            
+            return threshold_dict
+        except:
+            pass
+
+
     def sort_table(self, column, ascending=True):
         """Sort the table by the specified column."""
         try:
@@ -12970,7 +13152,7 @@ class GenNodesDialog(QDialog):
 
             if my_network.edges is None and my_network.nodes is not None:
                 self.parent().load_channel(1, my_network.nodes, data = True)
-                self.parent().delete_channel(0, True)
+                self.parent().delete_channel(0, False)
             # Get directory (None if empty)
             #directory = self.directory.text() if self.directory.text() else None
             
@@ -13202,7 +13384,7 @@ class BranchDialog(QDialog):
 
             if my_network.edges is None and my_network.nodes is not None:
                 self.parent().load_channel(1, my_network.nodes, data = True)
-                self.parent().delete_channel(0, True)
+                self.parent().delete_channel(0, False)
 
             original_shape = my_network.edges.shape
             original_array = copy.deepcopy(my_network.edges)

{nettracer3d-0.9.8 → nettracer3d-1.0.0/src/nettracer3d.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nettracer3d
-Version: 0.9.8
+Version: 1.0.0
 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/
@@ -110,6 +110,7 @@ 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 0.9.8 Updates --
+-- Version 1.0.0 Updates --
 
-	* Some minor bug fixes
+	* The 'network selection' table is now auto-populated when using the multiple-identity selector, and when using the node thresholder.
+	* And other minor adjustments/bug fixes