nettracer3d 0.9.7__py3-none-any.whl → 0.9.9__py3-none-any.whl

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():
@@ -2494,6 +2590,12 @@ class ImageViewerWindow(QMainWindow):
         
         self.update_display(preserve_zoom=(current_xlim, current_ylim))
 
+        if self.pan_mode:
+            self.create_pan_background()
+            current_xlim = self.ax.get_xlim()
+            current_ylim = self.ax.get_ylim()
+            self.update_display_pan_mode(current_xlim, current_ylim)
+
         
     def toggle_zoom_mode(self):
         """Toggle zoom mode on/off."""
@@ -2501,7 +2603,9 @@ class ImageViewerWindow(QMainWindow):
 
         if self.zoom_mode:
             if self.pan_mode:
-                self.pan_button.click()
+                self.update_display(preserve_zoom=(self.ax.get_xlim(), self.ax.get_ylim()))
+                self.pan_mode = False
+                self.pan_button.setChecked(False)
 
             self.pen_button.setChecked(False)
             self.brush_mode = False
@@ -2522,11 +2626,6 @@ class ImageViewerWindow(QMainWindow):
                 current_xlim = self.ax.get_xlim()
                 current_ylim = self.ax.get_ylim()
                 self.update_display(preserve_zoom=(current_xlim, current_ylim))
-            if self.pan_mode:
-                current_xlim = self.ax.get_xlim()
-                current_ylim = self.ax.get_ylim()
-                self.update_display(preserve_zoom=(current_xlim, current_ylim))
-            self.pan_mode = False
 
         else:
             if self.machine_window is None:
@@ -2605,7 +2704,9 @@ class ImageViewerWindow(QMainWindow):
         if self.brush_mode:
 
             if self.pan_mode:
-                self.pan_button.click()
+                self.update_display(preserve_zoom=(self.ax.get_xlim(), self.ax.get_ylim()))
+                self.pan_mode = False
+                self.pan_button.setChecked(False)
 
             self.pm = painting.PaintManager(parent = self)
 
@@ -3594,8 +3695,8 @@ class ImageViewerWindow(QMainWindow):
             # Multi-color highlight for machine window
             mask_1 = (highlight_data == 1)
             mask_2 = (highlight_data == 2)
-            rgba[mask_1] = [1, 1, 0, 0.5]      # Yellow for 1
-            rgba[mask_2] = [0, 0.7, 1, 0.5]    # Blue for 2
+            rgba[mask_1] = [1, 1, 0, 0.3]      # Yellow for 1
+            rgba[mask_2] = [0, 0.7, 1, 0.3]    # Blue for 2
         
         return rgba
 
@@ -4428,6 +4529,12 @@ 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)
@@ -6088,17 +6195,6 @@ class ImageViewerWindow(QMainWindow):
                     pass
                 self.static_background = None
                 
-                # Your existing machine_window logic
-                if self.machine_window is None:
-                    try:
-                        self.channel_data[4][self.current_slice, :, :] = n3d.overlay_arrays_simple(
-                            self.channel_data[self.temp_chan][self.current_slice, :, :], 
-                            self.channel_data[4][self.current_slice, :, :])
-                        self.load_channel(self.temp_chan, self.channel_data[4], data=True, end_paint=True)
-                        self.channel_data[4] = None
-                        self.channel_visible[4] = False
-                    except:
-                        pass
 
             # Get dimensions
             active_channels = [i for i in range(4) if self.channel_data[i] is not None]
@@ -6661,15 +6757,19 @@ 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
@@ -6713,6 +6813,38 @@ 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:
@@ -10991,6 +11123,8 @@ class MachineWindow(QMainWindow):
     def toggle_brush_mode(self):
         """Toggle brush mode on/off"""
         self.parent().brush_mode = self.brush_button.isChecked()
+        if self.parent().pan_mode:
+            self.parent().update_display(preserve_zoom=(self.parent().ax.get_xlim(), self.parent().ax.get_ylim()))
 
         if self.parent().brush_mode:
 

{nettracer3d-0.9.7.dist-info → nettracer3d-0.9.9.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nettracer3d
-Version: 0.9.7
+Version: 0.9.9
 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 +110,7 @@ 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 0.9.7 Updates --
+-- Version 0.9.9 Updates --
 
-	* Fixed a bug with the segmenter and color images.
-	* The overlay 2 is now cyan by default.
+	* Tables can now be opened to the rightside upper widget if they are the right format.
+	* Similarly, tables that have the format node id column:numerical values can now be used liberally to threshold the nodes, meaning most outputs of network analysis can be used to threshold nodes.

{nettracer3d-0.9.7.dist-info → nettracer3d-0.9.9.dist-info}/RECORD

@@ -6,7 +6,7 @@ nettracer3d/modularity.py,sha256=pborVcDBvICB2-g8lNoSVZbIReIBlfeBmjFbPYmtq7Y,224
 nettracer3d/morphology.py,sha256=jyDjYzrZ4LvI5jOyw8DLsxmo-i5lpqHsejYpW7Tq7Mo,19786
 nettracer3d/neighborhoods.py,sha256=iIaHU1COIdRtzRpAuIQKfLGLNKYFK3dL8Vb_EeJIlEA,46459
 nettracer3d/nettracer.py,sha256=d9Mhz-pHox5OfGGUSTrkTBJzCWCrbQvClTu2ANt-jUE,267943
-nettracer3d/nettracer_gui.py,sha256=VsZep2sgES10ZePVJDoUoFGgsg3wGRW-rAp1NMgQQwQ,628409
+nettracer3d/nettracer_gui.py,sha256=ckTjhIutYwnh7qwvgCmcKs2DCCODKICsiCxd1sD77gA,633247
 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-0.9.7.dist-info/licenses/LICENSE,sha256=jnNT-yBeIAKAHpYthPvLeqCzJ6nSurgnKmloVnfsjCI,764
-nettracer3d-0.9.7.dist-info/METADATA,sha256=oJJZS4YPNc21NZd5sFUY6doxe5vpgzZwdEObUGIwswg,7067
-nettracer3d-0.9.7.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-nettracer3d-0.9.7.dist-info/entry_points.txt,sha256=Nx1rr_0QhJXDBHAQg2vcqCzLMKBzSHfwy3xwGkueVyc,53
-nettracer3d-0.9.7.dist-info/top_level.txt,sha256=zsYy9rZwirfCEOubolhee4TyzqBAL5gSUeFMzhFTX8c,12
-nettracer3d-0.9.7.dist-info/RECORD,,
+nettracer3d-0.9.9.dist-info/licenses/LICENSE,sha256=jnNT-yBeIAKAHpYthPvLeqCzJ6nSurgnKmloVnfsjCI,764
+nettracer3d-0.9.9.dist-info/METADATA,sha256=0T7rx2BBeAwH0NxEczmM0TeOaL6y0VmHMJlIDKkPu9g,7259
+nettracer3d-0.9.9.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+nettracer3d-0.9.9.dist-info/entry_points.txt,sha256=Nx1rr_0QhJXDBHAQg2vcqCzLMKBzSHfwy3xwGkueVyc,53
+nettracer3d-0.9.9.dist-info/top_level.txt,sha256=zsYy9rZwirfCEOubolhee4TyzqBAL5gSUeFMzhFTX8c,12
+nettracer3d-0.9.9.dist-info/RECORD,,