nettracer3d 0.6.7__tar.gz → 0.6.8__tar.gz

{nettracer3d-0.6.7/src/nettracer3d.egg-info → nettracer3d-0.6.8}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nettracer3d
-Version: 0.6.7
+Version: 0.6.8
 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
@@ -46,12 +46,8 @@ 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 0.6.7 updates --
+-- Version 0.6.8 updates --
 
-1. Updated all methods to use dilation to allow the user to select between perfect distance transform based dilation (which can be slower but allows for perfect searching - and is designed to account for scaling differences), or the current pseudo-3d kernel method.
+1. Added new fill-can and 3D-brush functionalities to the brush mode (press f in brush mode to toggle the fill can. Press d while in brush mode to use the 3D painting tools. Standard Mouse wheel scrolling in the 3D painter will change how many frames you paint on - ie. 5 lets you paint 2 above and 2 below).
 
-1.5. The dt dilator accounts for scaling by stretching (upsampling) images to equivalent scales before dilating with the distance transform. It will not attempt to downsample. This admittedly will ask for greater memory and some more processing. To give the user the option to use the dt dilator without dealing with this, I added two new options to the resize method. You can now have it upsample your image until its equivalently scaled, or, if you don't need the fidelity, downsample your image until it's equivalently scaled. When the scaling is equivalent, the dt dilator will always just use the regular distance transform without attempting to resize the array.
-
-2. Fixed radius finding method to also account for scaling correctly. Previous method scaled wrong. New method predictably accounts for differing scaling in xy vs z dims as well.
-
-3. Bug fixes.
+1.5. Added single-use ctrl-z functionality to the fill can only because of how easily it can mess up. (Leaving the fill can mode will garbage collect the backup image though).

{nettracer3d-0.6.7 → nettracer3d-0.6.8}/README.md

@@ -8,12 +8,8 @@ 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 0.6.7 updates --
+-- Version 0.6.8 updates --
 
-1. Updated all methods to use dilation to allow the user to select between perfect distance transform based dilation (which can be slower but allows for perfect searching - and is designed to account for scaling differences), or the current pseudo-3d kernel method.
+1. Added new fill-can and 3D-brush functionalities to the brush mode (press f in brush mode to toggle the fill can. Press d while in brush mode to use the 3D painting tools. Standard Mouse wheel scrolling in the 3D painter will change how many frames you paint on - ie. 5 lets you paint 2 above and 2 below).
 
-1.5. The dt dilator accounts for scaling by stretching (upsampling) images to equivalent scales before dilating with the distance transform. It will not attempt to downsample. This admittedly will ask for greater memory and some more processing. To give the user the option to use the dt dilator without dealing with this, I added two new options to the resize method. You can now have it upsample your image until its equivalently scaled, or, if you don't need the fidelity, downsample your image until it's equivalently scaled. When the scaling is equivalent, the dt dilator will always just use the regular distance transform without attempting to resize the array.
-
-2. Fixed radius finding method to also account for scaling correctly. Previous method scaled wrong. New method predictably accounts for differing scaling in xy vs z dims as well.
-
-3. Bug fixes.
+1.5. Added single-use ctrl-z functionality to the fill can only because of how easily it can mess up. (Leaving the fill can mode will garbage collect the backup image though).

{nettracer3d-0.6.7 → nettracer3d-0.6.8}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "nettracer3d"
-version = "0.6.7"
+version = "0.6.8"
 authors = [
   { name="Liam McLaughlin", email="mclaughlinliam99@gmail.com" },
 ]

{nettracer3d-0.6.7 → nettracer3d-0.6.8}/src/nettracer3d/nettracer_gui.py

@@ -18,7 +18,7 @@ from nettracer3d import smart_dilate as sdl
 from matplotlib.colors import LinearSegmentedColormap
 from matplotlib.backends.backend_qt5agg import FigureCanvasQTAgg as FigureCanvas
 import pandas as pd
-from PyQt6.QtGui import (QFont, QCursor, QColor, QPixmap, QPainter, QPen)
+from PyQt6.QtGui import (QFont, QCursor, QColor, QPixmap, QFontMetrics, QPainter, QPen)
 import tifffile
 import copy
 import multiprocessing as mp
@@ -118,6 +118,9 @@ class ImageViewerWindow(QMainWindow):
 
         #For ML segmenting mode
         self.brush_mode = False
+        self.can = False
+        self.threed = False
+        self.threedthresh = 5
         self.painting = False
         self.foreground = True
         self.machine_window = None
@@ -1712,6 +1715,9 @@ class ImageViewerWindow(QMainWindow):
             self.pen_button.setChecked(False)
             self.pan_mode = False
             self.brush_mode = False
+            self.can = False
+            self.threed = False
+            self.last_change = None
             if self.machine_window is not None:
                 self.machine_window.silence_button()
             self.canvas.setCursor(Qt.CursorShape.CrossCursor)
@@ -1729,6 +1735,9 @@ class ImageViewerWindow(QMainWindow):
             self.zoom_button.setChecked(False)
             self.pen_button.setChecked(False)
             self.zoom_mode = False
+            self.can = False
+            self.threed = False
+            self.last_change = None
             self.brush_mode = False
             if self.machine_window is not None:
                 self.machine_window.silence_button()
@@ -1749,14 +1758,69 @@ class ImageViewerWindow(QMainWindow):
             self.zoom_mode = False
             self.update_brush_cursor()
         else:
+            self.last_change = None
+            self.can = False
+            self.threed = False
             self.canvas.setCursor(Qt.CursorShape.ArrowCursor)
 
+    def toggle_can(self):
+
+        if not self.can:
+            self.can = True
+            self.update_brush_cursor()
+        else:
+            self.can = False
+            self.last_change = None
+            self.update_brush_cursor()
+
+    def toggle_threed(self):
+
+        if not self.threed:
+            self.threed = True
+            self.threedthresh = 5
+            self.update_brush_cursor()
+        else:
+            self.threed = False
+            self.update_brush_cursor()
+
 
     def on_mpl_scroll(self, event):
         """Handle matplotlib canvas scroll events"""
         #Wheel events
         if self.brush_mode and event.inaxes == self.ax:
+
+            # Get modifiers
+            modifiers = event.guiEvent.modifiers()
+            ctrl_pressed = bool(modifiers & Qt.ControlModifier)
+            shift_pressed = bool(modifiers & Qt.ShiftModifier)
+            alt_pressed = bool(modifiers & Qt.AltModifier)
+            
+            # Check if threed is enabled and ONLY if no specific modifiers are pressed
+            if self.threed and not ctrl_pressed and not shift_pressed and not alt_pressed:
+                import math
+                step = 1 if event.button == 'up' else -1
+                self.threedthresh += step
+                
+                # Round to appropriate odd integer based on scroll direction
+                if event.button == 'up':
+                    # Round up to nearest odd
+                    self.threedthresh = math.ceil(self.threedthresh)
+                    if self.threedthresh % 2 == 0:
+                        self.threedthresh += 1
+                else:  # event.button == 'down'
+                    # Round down to nearest odd, but not below 1
+                    self.threedthresh = math.floor(self.threedthresh)
+                    if self.threedthresh % 2 == 0:
+                        self.threedthresh -= 1
+                    # Ensure not below minimum value of 1
+                    self.threedthresh = max(1, self.threedthresh)
+                
+                # Update the brush cursor to show the new threshold
+                self.update_brush_cursor()
+                return
+                
             # Check if Ctrl is pressed
+
             if event.guiEvent.modifiers() & Qt.ShiftModifier:
                 pass
 
@@ -1793,6 +1857,15 @@ class ImageViewerWindow(QMainWindow):
             self.update_display(preserve_zoom=(current_xlim, current_ylim))
 
     def keyPressEvent(self, event):
+
+        if event.key() == Qt.Key_Z and event.modifiers() & Qt.ControlModifier:
+            try:
+                self.load_channel(self.last_change[1], self.last_change[0], True)
+            except:
+                pass
+
+            return  # Return to prevent triggering the regular Z key action below
+
         if event.key() == Qt.Key_Z:
             self.zoom_button.click()
         if self.machine_window is not None:
@@ -1800,28 +1873,65 @@ class ImageViewerWindow(QMainWindow):
                 self.machine_window.switch_foreground()
         if event.key() == Qt.Key_X:
             self.high_button.click()
+        if self.brush_mode and self.machine_window is None:
+            if event.key() == Qt.Key_F:
+                self.toggle_can()
+            elif event.key() == Qt.Key_D:
+                self.toggle_threed()
 
 
     def update_brush_cursor(self):
         """Update the cursor to show brush size"""
         if not self.brush_mode:
             return
-            
-        # Create a pixmap for the cursor
-        size = self.brush_size * 2 + 2  # Add padding for border
-        pixmap = QPixmap(size, size)
+        
+        # Get font metrics first to determine text size
+        font = QFont()
+        font.setPointSize(14)
+        font_metrics = QFontMetrics(font)
+        thresh_text = str(self.threedthresh)
+        text_rect = font_metrics.boundingRect(thresh_text)
+        
+        # Create a pixmap for the cursor - ensure it's large enough for text
+        brush_size = self.brush_size * 2 + 2  # Add padding for border
+        extra_width = max(0, text_rect.width() + 4 - brush_size)  # Extra width for text if needed
+        extra_height = max(0, text_rect.height() + 4 - brush_size)  # Extra height for text if needed
+        
+        # Make sure pixmap is large enough for both brush and text
+        total_width = brush_size + extra_width
+        total_height = brush_size + extra_height
+        pixmap = QPixmap(total_width, total_height)
         pixmap.fill(Qt.transparent)
         
         # Create painter for the pixmap
         painter = QPainter(pixmap)
         painter.setRenderHint(QPainter.RenderHint.Antialiasing) 
         
+        # Calculate center offset for brush ellipse to accommodate text
+        x_offset = extra_width // 2
+        y_offset = extra_height // 2
+        
         # Draw circle
-        pen = QPen(Qt.white)
+        if not self.threed:
+            pen = QPen(Qt.white)
+        else:
+            pen = QPen(Qt.red)
         pen.setWidth(1)
         painter.setPen(pen)
         painter.setBrush(Qt.transparent)
-        painter.drawEllipse(1, 1, size-2, size-2)
+        if not self.can:
+            painter.drawEllipse(1 + x_offset, 1 + y_offset, brush_size-2, brush_size-2)
+            
+            # Draw threshold number when threed is True and can is False
+            if self.threed:
+                # Set text properties
+                painter.setFont(font)
+                painter.setPen(QPen(Qt.white))  # White text for visibility
+                
+                # Draw the text
+                painter.drawText(2, font_metrics.ascent() + 2, thresh_text)
+        else:
+            painter.drawRect(1 + x_offset, 1 + y_offset, 8, 8) 
         
         # Create cursor from pixmap
         cursor = QCursor(pixmap)
@@ -1929,13 +2039,20 @@ class ImageViewerWindow(QMainWindow):
 
             if event.button == 1 or event.button == 3:
 
+                x, y = int(event.xdata), int(event.ydata)
+
+
+                if event.button == 1 and self.can:
+                    self.handle_can(x, y)
+                    return
+
+
                 if event.button == 3:
                     self.erase = True
                 else:
                     self.erase = False
 
                 self.painting = True
-                x, y = int(event.xdata), int(event.ydata)
                 self.last_paint_pos = (x, y)
 
                 if self.pen_button.isChecked():
@@ -1995,7 +2112,77 @@ class ImageViewerWindow(QMainWindow):
             for x in range(max(0, center_x - radius), min(width, center_x + radius + 1)):
                 # Check if point is within circular brush area
                 if (x - center_x) ** 2 + (y - center_y) ** 2 <= radius ** 2:
-                    self.channel_data[channel][self.current_slice][y, x] = val
+
+                    if self.threed and self.threedthresh > 1:
+                        amount = (self.threedthresh - 1) / 2
+                        low = max(0, self.current_slice - amount)
+                        high = min(self.channel_data[channel].shape[0] - 1, self.current_slice + amount)
+
+                        for i in range(int(low), int(high + 1)):
+                            self.channel_data[channel][i][y, x] = val
+                    else:
+                        self.channel_data[channel][self.current_slice][y, x] = val
+
+    def handle_can(self, x, y):
+
+
+        if self.threed:
+            ref = copy.deepcopy(self.channel_data[self.active_channel])
+            the_slice = self.channel_data[self.active_channel]
+            
+            # First invert the boolean array
+            inv = n3d.invert_boolean(the_slice)
+            
+            # Label the connected components in the inverted array
+            labeled_array, num_features = n3d.label_objects(inv)
+            
+            # Get the target label at the clicked point
+            target_label = labeled_array[self.current_slice][y][x]
+            
+            # Only fill if we clicked on a valid region (target_label > 0)
+            if target_label > 0:
+                # Create a mask of the connected component we clicked on
+                fill_mask = (labeled_array == target_label) * 255
+
+                self.last_change = [ref, self.active_channel]
+
+                # Add this mask to the original slice
+                the_slice = the_slice | fill_mask  # Use logical OR to add the filled region
+            
+            # Update the channel data
+            self.load_channel(self.active_channel, the_slice, True)
+        else:
+
+            ref = copy.deepcopy(self.channel_data[self.active_channel])
+
+            the_slice = self.channel_data[self.active_channel][self.current_slice]
+
+            # First invert the boolean array
+            inv = n3d.invert_boolean(the_slice)
+            
+            # Label the connected components in the inverted array
+            labeled_array, num_features = n3d.label_objects(inv)
+            
+            # Get the target label at the clicked point
+            target_label = labeled_array[y][x]
+            
+            # Only fill if we clicked on a valid region (target_label > 0)
+            if target_label > 0:
+                # Create a mask of the connected component we clicked on
+                fill_mask = (labeled_array == target_label) * 255
+
+                self.last_change = [ref, self.active_channel]
+                
+                # Add this mask to the original slice
+                the_slice = the_slice | fill_mask  # Use logical OR to add the filled region
+            
+            # Update the channel data
+            self.channel_data[self.active_channel][self.current_slice] = the_slice
+            self.load_channel(self.active_channel, self.channel_data[self.active_channel], True)
+
+
+
+
 
     def on_mouse_move(self, event):
         """Handle mouse movement events."""
@@ -2082,6 +2269,7 @@ class ImageViewerWindow(QMainWindow):
                     points = self.get_line_points(last_x, last_y, x, y)
                     
                     # Paint at each point along the line
+
                     for px, py in points:
                         if 0 <= px < width and 0 <= py < height:
                             self.paint_at_position(px, py, self.erase, channel)
@@ -6776,6 +6964,9 @@ class MachineWindow(QMainWindow):
 
         if self.parent().pen_button.isChecked(): #Disable the pen mode if the user is in it because the segmenter pen forks it
             self.parent().pen_button.click()
+        self.parent().threed = False
+        self.parent().can = False
+        self.parent().last_change = None
 
         self.parent().pen_button.setEnabled(False)
 
@@ -7002,6 +7193,8 @@ class MachineWindow(QMainWindow):
             self.parent().zoom_mode = False
             self.parent().update_brush_cursor()
         else:
+            self.threed = False
+            self.can = False
             self.parent().zoom_button.click()
 
     def silence_button(self):

{nettracer3d-0.6.7 → nettracer3d-0.6.8}/src/nettracer3d/proximity.py

@@ -82,7 +82,7 @@ def _get_node_node_dict(label_array, label, dilate_xy, dilate_z, fastdil = False
 def process_label(args):
     """Modified to use pre-computed bounding boxes instead of argwhere"""
     nodes, label, dilate_xy, dilate_z, array_shape, bounding_boxes = args
-    #print(f"Processing node {label}")
+    print(f"Processing node {label}")
     
     # Get the pre-computed bounding box for this label
     slice_obj = bounding_boxes[label-1]  # -1 because label numbers start at 1

{nettracer3d-0.6.7 → nettracer3d-0.6.8/src/nettracer3d.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nettracer3d
-Version: 0.6.7
+Version: 0.6.8
 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
@@ -46,12 +46,8 @@ 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 0.6.7 updates --
+-- Version 0.6.8 updates --
 
-1. Updated all methods to use dilation to allow the user to select between perfect distance transform based dilation (which can be slower but allows for perfect searching - and is designed to account for scaling differences), or the current pseudo-3d kernel method.
+1. Added new fill-can and 3D-brush functionalities to the brush mode (press f in brush mode to toggle the fill can. Press d while in brush mode to use the 3D painting tools. Standard Mouse wheel scrolling in the 3D painter will change how many frames you paint on - ie. 5 lets you paint 2 above and 2 below).
 
-1.5. The dt dilator accounts for scaling by stretching (upsampling) images to equivalent scales before dilating with the distance transform. It will not attempt to downsample. This admittedly will ask for greater memory and some more processing. To give the user the option to use the dt dilator without dealing with this, I added two new options to the resize method. You can now have it upsample your image until its equivalently scaled, or, if you don't need the fidelity, downsample your image until it's equivalently scaled. When the scaling is equivalent, the dt dilator will always just use the regular distance transform without attempting to resize the array.
-
-2. Fixed radius finding method to also account for scaling correctly. Previous method scaled wrong. New method predictably accounts for differing scaling in xy vs z dims as well.
-
-3. Bug fixes.
+1.5. Added single-use ctrl-z functionality to the fill can only because of how easily it can mess up. (Leaving the fill can mode will garbage collect the backup image though).