nettracer3d 1.2.7__py3-none-any.whl → 1.3.1__py3-none-any.whl

nettracer3d/painting.py

@@ -1,32 +1,29 @@
 from PyQt6.QtWidgets import QApplication, QMainWindow
-import matplotlib.pyplot as plt
+from PyQt6.QtCore import Qt
+import pyqtgraph as pg
 import copy
 import numpy as np
 
 
 class PaintManager(QMainWindow):
-    def __init__(self, parent = None):
+    def __init__(self, parent=None):
         super().__init__(parent)
         self.resume = False
         
         # Initialize stroke tracking storage once
         if parent is not None:
             if not hasattr(parent, 'completed_paint_strokes'):
-                parent.completed_paint_strokes = []  # List of individual completed strokes
+                parent.completed_paint_strokes = []
             if not hasattr(parent, 'current_stroke_points'):
-                parent.current_stroke_points = []    # Current stroke being drawn
+                parent.current_stroke_points = []
             if not hasattr(parent, 'current_stroke_type'):
-                parent.current_stroke_type = None    # 'draw' or 'erase'
+                parent.current_stroke_type = None
             
-            # Keep the old properties for display purposes
-            if not hasattr(parent, 'virtual_draw_operations'):
-                parent.virtual_draw_operations = []
-            if not hasattr(parent, 'virtual_erase_operations'):
-                parent.virtual_erase_operations = []
-            if not hasattr(parent, 'current_operation'):
-                parent.current_operation = []
-            if not hasattr(parent, 'current_operation_type'):
-                parent.current_operation_type = None
+            # PyQtGraph visual items
+            if not hasattr(parent, 'virtual_paint_items'):
+                parent.virtual_paint_items = []  # Store all visual items
+            if not hasattr(parent, 'current_paint_items'):
+                parent.current_paint_items = []  # Current stroke visuals
 
     def get_line_points(self, x0, y0, x1, y1):
         """Get all points in a line between (x0,y0) and (x1,y1) using Bresenham's algorithm."""
@@ -60,27 +57,19 @@ class PaintManager(QMainWindow):
         return points
 
     def initiate_paint_session(self, channel, current_xlim, current_ylim):
-        # Create static background (same as selection rectangle)
-
         if self.parent().machine_window is not None:
             if self.parent().machine_window.segmentation_worker is not None:
                 if not self.parent().machine_window.segmentation_worker._paused:
                     self.resume = True
                 self.parent().machine_window.segmentation_worker.pause()
 
-
         if not self.parent().channel_visible[channel]:
             self.parent().channel_visible[channel] = True
-            
-        # Capture the background once
-        self.parent().static_background = self.parent().canvas.copy_from_bbox(self.parent().ax.bbox)
 
         if self.resume:
             self.parent().machine_window.segmentation_worker.resume()
             self.resume = False
 
-
-
     def start_virtual_paint_session(self, channel, current_xlim, current_ylim):
         """Start a virtual paint session that doesn't modify arrays until the end."""
         self.parent().painting = True
@@ -90,7 +79,7 @@ class PaintManager(QMainWindow):
         if not self.parent().channel_visible[channel]:
             self.parent().channel_visible[channel] = True
             
-        # Initialize stroke tracking storage ONLY if they don't exist
+        # Initialize stroke tracking storage
         if not hasattr(self.parent(), 'completed_paint_strokes'):
             self.parent().completed_paint_strokes = []
         if not hasattr(self.parent(), 'current_stroke_points'):
@@ -98,50 +87,53 @@ class PaintManager(QMainWindow):
         if not hasattr(self.parent(), 'current_stroke_type'):
             self.parent().current_stroke_type = None
             
-        # Initialize display storage ONLY if they don't exist
-        if not hasattr(self.parent(), 'virtual_draw_operations'):
-            self.parent().virtual_draw_operations = []
-        if not hasattr(self.parent(), 'virtual_erase_operations'):
-            self.parent().virtual_erase_operations = []
-        if not hasattr(self.parent(), 'current_operation'):
-            self.parent().current_operation = []
-        if not hasattr(self.parent(), 'current_operation_type'):
-            self.parent().current_operation_type = None
+        # Initialize PyQtGraph visual storage
+        if not hasattr(self.parent(), 'virtual_paint_items'):
+            self.parent().virtual_paint_items = []
+        if not hasattr(self.parent(), 'current_paint_items'):
+            self.parent().current_paint_items = []
 
     def reset_all_paint_storage(self):
-        """Reset all paint storage - call this when you want to start completely fresh."""
+        """Reset all paint storage."""
+        # Clear visual items from view
+        if hasattr(self.parent(), 'virtual_paint_items'):
+            for item in self.parent().virtual_paint_items:
+                try:
+                    self.parent().view.removeItem(item)
+                except:
+                    pass
+        
+        if hasattr(self.parent(), 'current_paint_items'):
+            for item in self.parent().current_paint_items:
+                try:
+                    self.parent().view.removeItem(item)
+                except:
+                    pass
+        
         self.parent().completed_paint_strokes = []
         self.parent().current_stroke_points = []
         self.parent().current_stroke_type = None
-        self.parent().virtual_draw_operations = []
-        self.parent().virtual_erase_operations = []
-        self.parent().current_operation = []
-        self.parent().current_operation_type = None
-
-    
+        self.parent().virtual_paint_items = []
+        self.parent().current_paint_items = []
 
     def add_virtual_paint_point(self, x, y, brush_size, erase=False, foreground=True):
-        """Add a single paint point to the virtual layer."""
+        """Add a single paint point to the virtual layer using PyQtGraph."""
         
         # Determine operation type and visual properties
         if erase:
-            paint_color = 'black'  # Visual indicator for erase
-            alpha = 0.5
+            paint_color = (0, 0, 0)  # Black for erase
             operation_type = 'erase'
         else:
             if self.parent().machine_window is not None:
                 if foreground:
-                    paint_color = 'green'  # Visual for foreground (value 1)
-                    alpha = 0.7
+                    paint_color = (0, 255, 0)  # Green for foreground (value 1)
                 else:
-                    paint_color = 'red'  # Visual for background (value 2)
-                    alpha = 0.7
+                    paint_color = (255, 0, 0)  # Red for background (value 2)
             else:
-                paint_color = 'white'  # Normal paint
-                alpha = 0.7
+                paint_color = (255, 255, 255)  # White for normal paint
             operation_type = 'draw'
-                
-        # Store the operation data (for later conversion to real paint)
+        
+        # Store the operation data
         operation_data = {
             'x': x,
             'y': y,
@@ -153,229 +145,156 @@ class PaintManager(QMainWindow):
             'threedthresh': getattr(self.parent(), 'threedthresh', 1)
         }
         
-        # Add to stroke tracking (NEW - separate stroke tracking)
+        # Add to stroke tracking
         if self.parent().current_stroke_type != operation_type:
-            # Finish previous stroke if switching between draw/erase
             self.finish_current_stroke()
             self.parent().current_stroke_type = operation_type
         
         self.parent().current_stroke_points.append(operation_data)
         
-        # Create visual circle for display
-        circle = plt.Circle((x, y), brush_size/2, 
-                           color=paint_color, alpha=alpha, animated=True)
-        
-        # Add to display operations (OLD - for visual display)
-        if self.parent().current_operation_type != operation_type:
-            # Finish previous operation if switching between draw/erase
-            self.finish_current_virtual_operation()
-            self.parent().current_operation_type = operation_type
-        
-        self.parent().current_operation.append({
-            'circle': circle,
-            'data': operation_data
-        })
-        
-        self.parent().ax.add_patch(circle)
+        # Create visual circle using ScatterPlotItem
+        scatter = pg.ScatterPlotItem(
+            [x], [y], 
+            size=brush_size,
+            pen=pg.mkPen(paint_color, width=1),
+            brush=pg.mkBrush(*paint_color, 127)  # 50% alpha
+        )
+        
+        # Add to view
+        self.parent().view.addItem(scatter)
+        self.parent().current_paint_items.append(scatter)
 
     def finish_current_stroke(self):
         """Finish the current stroke and add it to completed strokes."""
         if not self.parent().current_stroke_points:
             return
-            
-        # Store the completed stroke with its type
+        
+        # Store the completed stroke with its type AND visual items
         stroke_data = {
             'points': self.parent().current_stroke_points.copy(),
-            'type': self.parent().current_stroke_type
+            'type': self.parent().current_stroke_type,
+            'visual_items': self.parent().current_paint_items.copy()  # Store visual items with stroke
         }
         
         self.parent().completed_paint_strokes.append(stroke_data)
         
-        # Clear current stroke
+        # Move current visual items to completed
+        self.parent().virtual_paint_items.extend(self.parent().current_paint_items)
+        self.parent().current_paint_items = []
+        
+        # Clear current stroke data
         self.parent().current_stroke_points = []
         self.parent().current_stroke_type = None
 
+    def undo_last_virtual_stroke(self):
+        """Undo the most recent virtual paint stroke (not yet converted to data)."""
+        
+        # First try to undo the current stroke in progress
+        if hasattr(self.parent(), 'current_stroke_points') and self.parent().current_stroke_points:
+            # Remove visual items for current stroke
+            if hasattr(self.parent(), 'current_paint_items'):
+                for item in self.parent().current_paint_items:
+                    try:
+                        self.parent().view.removeItem(item)
+                    except:
+                        pass
+                self.parent().current_paint_items = []
+            
+            # Clear current stroke data
+            self.parent().current_stroke_points = []
+            self.parent().current_stroke_type = None
+            return True  # Successfully undid current stroke
+        
+        # If no current stroke, undo the most recent completed stroke
+        if hasattr(self.parent(), 'completed_paint_strokes') and self.parent().completed_paint_strokes:
+            # Get the last completed stroke
+            last_stroke = self.parent().completed_paint_strokes.pop()
+            
+            # Remove its visual items from the view
+            visual_items = last_stroke.get('visual_items', [])
+            for item in visual_items:
+                try:
+                    self.parent().view.removeItem(item)
+                    # Also remove from virtual_paint_items list
+                    if item in self.parent().virtual_paint_items:
+                        self.parent().virtual_paint_items.remove(item)
+                except:
+                    pass
+            
+            return True  # Successfully undid completed stroke
+        
+        # Nothing to undo
+        return False
+
     def add_virtual_paint_stroke(self, x, y, brush_size, erase=False, foreground=True):
-        """Add a paint stroke - simple visual, interpolation happens during data conversion."""
-        # Just add the current point for visual display (no interpolation yet)
+        """Add a paint stroke."""
         self.add_virtual_paint_point(x, y, brush_size, erase, foreground)
-        
-        # Store the last position for data conversion later
         self.parent().last_virtual_pos = (x, y)
 
     def connect_virtual_paint_points(self):
-        """Connect points with lines matching the circle size by converting to screen coordinates."""
-        
-        if not hasattr(self.parent(), 'current_operation') or len(self.parent().current_operation) < 2:
+        """Connect points with lines matching the brush size."""
+        if not hasattr(self.parent(), 'current_stroke_points') or len(self.parent().current_stroke_points) < 2:
             return
         
-        # Get existing points but DON'T remove them
-        existing_points = self.parent().current_operation.copy()
-        point_data = [item['data'] for item in existing_points if 'data' in item]
+        point_data = self.parent().current_stroke_points
         
         if len(point_data) < 2:
             return
         
-        # Get visual properties and brush size from first point
+        # Get visual properties from first point
         first_data = point_data[0]
-        brush_size_data = first_data['brush_size']  # This is in data coordinates
-        
-        # Convert brush size from data coordinates to points for linewidth
-        # Get the transformation from data to display coordinates
-        ax = self.parent().ax
-        
-        # Transform two points to see the scaling
-        p1_data = [0, 0]
-        p2_data = [brush_size_data, 0]  # One brush_size unit away
-        
-        p1_display = ax.transData.transform(p1_data)
-        p2_display = ax.transData.transform(p2_data)
-        
-        # Calculate pixels per data unit
-        pixels_per_data_unit = abs(p2_display[0] - p1_display[0])
-        
-        # Convert to points (matplotlib uses 72 points per inch, figure.dpi pixels per inch)
-        fig = ax.figure
-        points_per_pixel = 72.0 / fig.dpi
-        brush_size_points = pixels_per_data_unit * points_per_pixel
+        brush_size = first_data['brush_size']
         
         if first_data['erase']:
-            line_color = 'black'
-            alpha = 0.5
+            line_color = (0, 0, 0)  # Black
         else:
             if self.parent().machine_window is not None:
                 if first_data['foreground']:
-                    line_color = 'green'
-                    alpha = 0.7
+                    line_color = (0, 255, 0)  # Green
                 else:
-                    line_color = 'red'
-                    alpha = 0.7
+                    line_color = (255, 0, 0)  # Red
             else:
-                line_color = 'white'
-                alpha = 0.7
-        
-        # Create line segments for connections using LineCollection
-        from matplotlib.collections import LineCollection
-        
-        segments = []
-        for i in range(len(point_data) - 1):
-            x1, y1 = point_data[i]['x'], point_data[i]['y']
-            x2, y2 = point_data[i+1]['x'], point_data[i+1]['y']
-            segments.append([(x1, y1), (x2, y2)])
-        
-        # Create line collection with converted linewidth
-        if segments:
-            lc = LineCollection(segments, 
-                               colors=line_color, 
-                               alpha=alpha,
-                               linewidths=brush_size_points,  # Now in points, matching circles
-                               animated=True)
-            self.parent().ax.add_collection(lc)
-            
-            # Add the line collection as a visual-only element
-            self.parent().current_operation.append({
-                'line_collection': lc,
-                'is_connection_visual': True
-            })
+                line_color = (255, 255, 255)  # White
+        
+        # Create line segments
+        x_coords = [p['x'] for p in point_data]
+        y_coords = [p['y'] for p in point_data]
+        
+        # Create connected line
+        line = pg.PlotDataItem(
+            x_coords, y_coords,
+            pen=pg.mkPen(color=line_color, width=brush_size)
+        )
+        line.setOpacity(0.5)
+        
+        # Add to view
+        self.parent().view.addItem(line)
+        self.parent().current_paint_items.append(line)
 
     def finish_current_virtual_operation(self):
-       """Finish the current operation (draw or erase) and add it to the appropriate list."""
-       
-       if not self.parent().current_operation:
-           return
-       
-       # Filter out connection visuals from the operation before storing
-       data_items = []
-       visual_items = []
-       
-       for item in self.parent().current_operation:
-           if item.get('is_connection_visual', False):
-               visual_items.append(item)
-           else:
-               data_items.append(item)
-       
-       # Only store the data items for this specific stroke
-       if data_items:
-           if self.parent().current_operation_type == 'draw':
-               self.parent().virtual_draw_operations.append(data_items)
-           elif self.parent().current_operation_type == 'erase':
-               self.parent().virtual_erase_operations.append(data_items)
-       
-       # Clean up visual items that are connection-only
-       for item in visual_items:
-           try:
-               if 'line_collection' in item:
-                   item['line_collection'].remove()
-               elif 'line' in item:
-                   item['line'].remove()
-           except:
-               pass
-       
-       self.parent().current_operation = []
-       self.parent().current_operation_type = None
-
-    def update_virtual_paint_display(self):
-        """Update display with virtual paint strokes - handles different object types."""
-        if not hasattr(self.parent(), 'static_background') or self.parent().static_background is None:
-            return
-        
-        # Restore the clean background
-        self.parent().canvas.restore_region(self.parent().static_background)
-        
-        # Draw all completed operations
-        for operation_list in [self.parent().virtual_draw_operations, self.parent().virtual_erase_operations]:
-            for operation in operation_list:
-                for item in operation:
-                    self._draw_virtual_item(item)
-        
-        # Draw current operation being painted
-        if hasattr(self.parent(), 'current_operation'):
-            for item in self.parent().current_operation:
-                self._draw_virtual_item(item)
-        
-        # Blit everything at once
-        self.parent().canvas.blit(self.parent().ax.bbox)
-
-    def _draw_virtual_item(self, item):
-        """Helper method to draw different types of virtual paint items."""
-        try:
-            # Skip items that are marked as visual-only connections
-            if item.get('is_connection_visual', False):
-                if 'line' in item:
-                    self.parent().ax.draw_artist(item['line'])
-                elif 'line_collection' in item:
-                    self.parent().ax.draw_artist(item['line_collection'])
-            elif 'circle' in item:
-                self.parent().ax.draw_artist(item['circle'])
-            elif 'line' in item:
-                self.parent().ax.draw_artist(item['line'])
-            elif 'line_collection' in item:
-                self.parent().ax.draw_artist(item['line_collection'])
-        except Exception as e:
-            # Skip items that can't be drawn (might have been removed)
-            pass
+        """Finish the current operation."""
+        self.finish_current_stroke()
 
     def convert_virtual_strokes_to_data(self):
-        """Convert each stroke separately to actual array data using ONLY the new stroke tracking system."""
+        """Convert each stroke separately to actual array data."""
         
         # Finish the current stroke first
         self.finish_current_stroke()
         
-        # Process ONLY the completed_paint_strokes (ignore old display operations)
+        # Process completed strokes
         for stroke in self.parent().completed_paint_strokes:
             stroke_points = stroke['points']
-            stroke_type = stroke['type']
             
             if len(stroke_points) == 0:
                 continue
-                
-            # Apply interpolation within this stroke only
+            
+            # Apply interpolation within this stroke
             last_pos = None
             for point_data in stroke_points:
                 current_pos = (point_data['x'], point_data['y'])
                 
                 if last_pos is not None:
-                    # Interpolate between consecutive points in this stroke
+                    # Interpolate between consecutive points
                     points = self.get_line_points(last_pos[0], last_pos[1], current_pos[0], current_pos[1])
                     for px, py in points:
                         self.paint_at_position_vectorized(
@@ -403,74 +322,25 @@ class PaintManager(QMainWindow):
                 
                 last_pos = current_pos
         
-        # Clean up ALL visual elements (both old and new systems)
-        for operation_list in [self.parent().virtual_draw_operations, self.parent().virtual_erase_operations]:
-            for operation in operation_list:
-                for item in operation:
-                    try:
-                        if 'circle' in item:
-                            item['circle'].remove()
-                        elif 'line_collection' in item:
-                            item['line_collection'].remove()
-                        elif 'line' in item:
-                            item['line'].remove()
-                    except:
-                        pass
+        # Clean up visual elements
+        for item in self.parent().virtual_paint_items:
+            try:
+                self.parent().view.removeItem(item)
+            except:
+                pass
         
-        if hasattr(self.parent(), 'current_operation'):
-            for item in self.parent().current_operation:
-                try:
-                    if 'circle' in item:
-                        item['circle'].remove()
-                    elif 'line_collection' in item:
-                        item['line_collection'].remove()
-                    elif 'line' in item:
-                        item['line'].remove()
-                except:
-                    pass
+        for item in self.parent().current_paint_items:
+            try:
+                self.parent().view.removeItem(item)
+            except:
+                pass
         
-        # Reset all storage for next paint session
+        # Reset storage
         self.parent().completed_paint_strokes = []
         self.parent().current_stroke_points = []
         self.parent().current_stroke_type = None
-        self.parent().virtual_draw_operations = []
-        self.parent().virtual_erase_operations = []
-        self.parent().current_operation = []
-        self.parent().current_operation_type = None
-
-    def end_virtual_paint_session(self):
-        """Convert virtual paint to actual array modifications when exiting paint mode."""
-        if not hasattr(self.parent(), 'virtual_paint_strokes'):
-            return
-        
-        # Now apply all the virtual strokes to the actual arrays
-        for stroke in self.parent().virtual_paint_strokes:
-            for circle in stroke:
-                center = circle.center
-                radius = circle.radius
-                is_erase = circle.get_facecolor()[0] == 0  # Black = erase
-                
-                # Apply to actual array
-                self.paint_at_position_vectorized(
-                    int(center[0]), int(center[1]), 
-                    erase=is_erase, 
-                    channel=self.paint_channel,
-                    brush_size=int(radius * 2)
-                )
-                
-                # Remove the virtual circle
-                circle.remove()
-        
-        # Clean up virtual paint data
-        self.virtual_paint_strokes = []
-        self.current_stroke = []
-        
-        # Reset background
-        self.static_background = None
-        self.painting = False
-        
-        # Full refresh to show final result
-        self.update_display()
+        self.parent().virtual_paint_items = []
+        self.parent().current_paint_items = []
 
     def paint_at_position_vectorized(self, center_x, center_y, erase=False, channel=2, 
                                    slice_idx=None, brush_size=None, threed=None, 
@@ -478,46 +348,37 @@ class PaintManager(QMainWindow):
         """Vectorized paint operation for better performance."""
         if self.parent().channel_data[channel] is None:
             return
-        
-        # Use provided parameters or fall back to instance variables
         slice_idx = slice_idx if slice_idx is not None else self.parent().current_slice
         brush_size = brush_size if brush_size is not None else getattr(self.parent(), 'brush_size', 5)
         threed = threed if threed is not None else getattr(self.parent(), 'threed', False)
         threedthresh = threedthresh if threedthresh is not None else getattr(self.parent(), 'threedthresh', 1)
         
-        # Handle 3D painting by recursively calling for each slice
+        # Handle 3D painting
         if threed and threedthresh > 1:
             half_range = (threedthresh - 1) // 2
             low = max(0, slice_idx - half_range)
             high = min(self.parent().channel_data[channel].shape[0] - 1, slice_idx + half_range)
             
-            
             for i in range(low, high + 1):
-                
-                # Recursive call for each slice, but with threed=False to avoid infinite recursion
                 self.paint_at_position_vectorized(
                     center_x, center_y, 
                     erase=erase, 
                     channel=channel,
-                    slice_idx=i,  # Paint on slice i
+                    slice_idx=i,
                     brush_size=brush_size,
-                    threed=False,  # Important: turn off 3D for recursive calls
+                    threed=False,
                     threedthresh=1,
                     foreground=foreground,
                     machine_window=machine_window
                 )
-                
-                
-            return  # Exit early, recursive calls handle everything
-        
-        # Regular 2D painting (single slice)
+            return
         
         # Determine paint value
         if erase:
             val = 0
         elif machine_window is None:
             try:
-                val = self.parent().min_max[channel][1]
+                val = max(1, self.parent().min_max[channel][1])
             except:
                 val = 255
         elif foreground:
@@ -535,15 +396,14 @@ class PaintManager(QMainWindow):
         x_max = min(width, center_x + radius + 1)
         
         if y_min >= y_max or x_min >= x_max:
-            return  # No valid region to paint
+            return
         
-        # Create coordinate grids for the affected region
+        # Create coordinate grids
         y_coords, x_coords = np.mgrid[y_min:y_max, x_min:x_max]
         
-        # Calculate distances squared (avoid sqrt for performance)
+        # Calculate distances and create mask
         distances_sq = (x_coords - center_x) ** 2 + (y_coords - center_y) ** 2
         mask = distances_sq <= radius ** 2
         
-        # Paint on this single slice
-        
+        # Paint on this slice
         self.parent().channel_data[channel][slice_idx][y_min:y_max, x_min:x_max][mask] = val

nettracer3d/simple_network.py

@@ -222,13 +222,13 @@ def show_identity_network(excel_file_path, node_identities, geometric=False, geo
     # Node size handling
     node_dict = {}
     for node in G.nodes():
-        try:
+        try: #Perhaps remove this
             if identity_dict[node] == 'Edge':
-                node_dict[node] = 30
+                node_dict[node] = 10
             else:
-                node_dict[node] = 100
+                node_dict[node] = 10
         except:
-            node_dict[node] = 100
+            node_dict[node] = 10
 
     if geometric:
         # Handle geometric positioning