nettracer3d 1.3.2__tar.gz → 1.3.4__tar.gz

{nettracer3d-1.3.2/src/nettracer3d.egg-info → nettracer3d-1.3.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nettracer3d
-Version: 1.3.2
+Version: 1.3.4
 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/
@@ -155,7 +155,9 @@ NetTracer3D is freely available for academic and nonprofit use and can obtained
 
 NetTracer3D was developed by Liam McLaughlin while working under Dr. Sanjay Jain at Washington University School of Medicine.
 
--- Version 1.3.2 Updates --
+-- Version 1.3.4 Updates --
 
-	* Some minor tweaks and bug fixes
+	* Added option to view network in a concentric-shell like manner
+	* Added way to batch compute the histogram statistics
+	* Updated the slice refresh rate to be much faster
 	

{nettracer3d-1.3.2 → nettracer3d-1.3.4}/README.md

@@ -104,7 +104,9 @@ NetTracer3D is freely available for academic and nonprofit use and can obtained
 
 NetTracer3D was developed by Liam McLaughlin while working under Dr. Sanjay Jain at Washington University School of Medicine.
 
--- Version 1.3.2 Updates --
+-- Version 1.3.4 Updates --
 
-	* Some minor tweaks and bug fixes
+	* Added option to view network in a concentric-shell like manner
+	* Added way to batch compute the histogram statistics
+	* Updated the slice refresh rate to be much faster
 	

{nettracer3d-1.3.2 → nettracer3d-1.3.4}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "nettracer3d"
-version = "1.3.2"
+version = "1.3.4"
 authors = [
   { name="Liam McLaughlin", email="liamm@wustl.edu" },
 ]

nettracer3d-1.3.4/src/nettracer3d/endpoint_joiner.py

@@ -0,0 +1,286 @@
+import numpy as np
+from scipy.spatial import cKDTree
+import warnings
+from . import nettracer as n3d
+from . import smart_dilate as sdl
+warnings.filterwarnings('ignore')
+
+
+class EndpointConnector:
+    """
+    Simple endpoint connector - finds skeleton endpoints and connects them
+    if they're within a specified distance.
+    """
+    
+    def __init__(self, connection_distance=20, spine_removal = 0):
+        """
+        Parameters:
+        -----------
+        connection_distance : float
+            Maximum distance to connect two endpoints
+        """
+        self.connection_distance = connection_distance
+        self._sphere_cache = {}  # Cache sphere masks for different radii
+        self.spine_removal = spine_removal
+
+    def _get_sphere_mask(self, radius):
+        """Get a cached sphere mask for the given radius"""
+        cache_key = round(radius * 2) / 2
+        
+        if cache_key not in self._sphere_cache:
+            r = max(1, int(np.ceil(cache_key)))
+            
+            size = 2 * r + 1
+            center = r
+            zz, yy, xx = np.ogrid[-r:r+1, -r:r+1, -r:r+1]
+            
+            dist_sq = zz**2 + yy**2 + xx**2
+            mask = dist_sq <= cache_key**2
+            
+            self._sphere_cache[cache_key] = {
+                'mask': mask,
+                'radius_int': r,
+                'center': center
+            }
+        
+        return self._sphere_cache[cache_key]
+
+    def _draw_sphere_3d_cached(self, array, center, radius):
+        """Draw a filled sphere using cached mask"""
+        sphere_data = self._get_sphere_mask(radius)
+        mask = sphere_data['mask']
+        r = sphere_data['radius_int']
+        
+        z, y, x = center
+        
+        # Bounding box in the array
+        z_min = max(0, int(z - r))
+        z_max = min(array.shape[0], int(z + r + 1))
+        y_min = max(0, int(y - r))
+        y_max = min(array.shape[1], int(y + r + 1))
+        x_min = max(0, int(x - r))
+        x_max = min(array.shape[2], int(x + r + 1))
+        
+        # Calculate actual slice sizes
+        array_z_size = z_max - z_min
+        array_y_size = y_max - y_min
+        array_x_size = x_max - x_min
+        
+        if array_z_size <= 0 or array_y_size <= 0 or array_x_size <= 0:
+            return
+        
+        # Calculate mask offset
+        mask_z_start = max(0, r - int(z) + z_min)
+        mask_y_start = max(0, r - int(y) + y_min)
+        mask_x_start = max(0, r - int(x) + x_min)
+        
+        mask_z_end = mask_z_start + array_z_size
+        mask_y_end = mask_y_start + array_y_size
+        mask_x_end = mask_x_start + array_x_size
+        
+        mask_z_end = min(mask_z_end, mask.shape[0])
+        mask_y_end = min(mask_y_end, mask.shape[1])
+        mask_x_end = min(mask_x_end, mask.shape[2])
+        
+        actual_z_size = mask_z_end - mask_z_start
+        actual_y_size = mask_y_end - mask_y_start
+        actual_x_size = mask_x_end - mask_x_start
+        
+        z_max = z_min + actual_z_size
+        y_max = y_min + actual_y_size
+        x_max = x_min + actual_x_size
+        
+        try:
+            array[z_min:z_max, y_min:y_max, x_min:x_max] |= \
+                mask[mask_z_start:mask_z_end, mask_y_start:mask_y_end, mask_x_start:mask_x_end]
+        except ValueError:
+            pass
+
+    def _draw_cylinder_3d_cached(self, array, pos1, pos2, radius1, radius2):
+        """Draw a tapered cylinder using cached sphere masks"""
+        distance = np.linalg.norm(pos2 - pos1)
+        if distance < 0.5:
+            self._draw_sphere_3d_cached(array, pos1, max(radius1, radius2))
+            return
+        
+        radius_change = abs(radius2 - radius1)
+        samples_per_unit = 2.0
+        if radius_change > 2:
+            samples_per_unit = 3.0
+        
+        num_samples = max(3, int(distance * samples_per_unit))
+        t_values = np.linspace(0, 1, num_samples)
+        
+        for t in t_values:
+            pos = pos1 * (1 - t) + pos2 * t
+            radius = radius1 * (1 - t) + radius2 * t
+            self._draw_sphere_3d_cached(array, pos, radius)
+
+    def _find_endpoints(self, skeleton):
+        """
+        Find skeleton endpoints by checking connectivity
+        Endpoints have degree 1 (only one neighbor)
+        """
+        endpoints = []
+        skeleton_coords = np.argwhere(skeleton)
+        
+        if len(skeleton_coords) == 0:
+            return np.array([])
+        
+        # 26-connectivity offsets
+        nbr_offsets = [(dz, dy, dx)
+                       for dz in (-1, 0, 1)
+                       for dy in (-1, 0, 1)
+                       for dx in (-1, 0, 1)
+                       if not (dz == dy == dx == 0)]
+        
+        for coord in skeleton_coords:
+            z, y, x = coord
+            
+            # Count neighbors
+            neighbor_count = 0
+            for dz, dy, dx in nbr_offsets:
+                nz, ny, nx = z + dz, y + dy, x + dx
+                
+                if (0 <= nz < skeleton.shape[0] and
+                    0 <= ny < skeleton.shape[1] and
+                    0 <= nx < skeleton.shape[2]):
+                    if skeleton[nz, ny, nx]:
+                        neighbor_count += 1
+            
+            # Endpoint has exactly 1 neighbor
+            if neighbor_count == 1:
+                endpoints.append(coord)
+        
+        return np.array(endpoints)
+
+    def connect_endpoints(self, binary_image, verbose=True):
+        """
+        Main function: connect endpoints within specified distance
+        
+        Parameters:
+        -----------
+        binary_image : ndarray
+            3D binary segmentation
+        verbose : bool
+            Print progress information
+            
+        Returns:
+        --------
+        result : ndarray
+            Original image with endpoint connections drawn
+        """
+        if verbose:
+            print(f"Starting endpoint connector...")
+            print(f"Input shape: {binary_image.shape}")
+        
+        # Make a copy to modify
+        result = binary_image.copy()
+        
+        # Compute skeleton
+        if verbose:
+            print("Computing skeleton...")
+        skeleton = n3d.skeletonize(binary_image)
+        if len(skeleton.shape) == 3 and skeleton.shape[0] != 1:
+            skeleton = n3d.fill_holes_3d(skeleton)
+            skeleton = n3d.skeletonize(skeleton)
+        if self.spine_removal > 0:
+            print(f"removing spines: {self.spine_removal}")
+            skeleton = n3d.remove_branches_new(skeleton, self.spine_removal)
+            skeleton = n3d.dilate_3D(skeleton, 3, 3, 3)
+            skeleton = n3d.skeletonize(skeleton)
+
+
+        # Compute distance transform (for radii)
+        if verbose:
+            print("Computing distance transform...")
+        distance_map = sdl.compute_distance_transform_distance(binary_image, fast_dil = True)
+        
+        # Find endpoints
+        if verbose:
+            print("Finding skeleton endpoints...")
+        endpoints = self._find_endpoints(skeleton)
+        
+        if len(endpoints) == 0:
+            if verbose:
+                print("No endpoints found!")
+            return result
+        
+        if verbose:
+            print(f"Found {len(endpoints)} endpoints")
+        
+        # Get radius at each endpoint
+        endpoint_radii = []
+        for ep in endpoints:
+            radius = distance_map[tuple(ep)]
+            endpoint_radii.append(radius)
+        endpoint_radii = np.array(endpoint_radii)
+        
+        # Build KD-tree for fast distance queries
+        if verbose:
+            print(f"Connecting endpoints within {self.connection_distance} voxels...")
+        tree = cKDTree(endpoints)
+        
+        # Find all pairs within connection distance
+        connections_made = 0
+        for i, ep1 in enumerate(endpoints):
+            # Query all points within connection distance
+            nearby_indices = tree.query_ball_point(ep1, self.connection_distance)
+            
+            for j in nearby_indices:
+                if j <= i:  # Skip self and already processed pairs
+                    continue
+                
+                ep2 = endpoints[j]
+                radius1 = endpoint_radii[i]
+                radius2 = endpoint_radii[j]
+                
+                # Draw tapered cylinder connection
+                self._draw_cylinder_3d_cached(
+                    result,
+                    ep1.astype(float),
+                    ep2.astype(float),
+                    radius1,
+                    radius2
+                )
+                connections_made += 1
+        
+        if verbose:
+            print(f"Made {connections_made} connections")
+            print(f"Done! Output voxels: {np.sum(result)} (input: {np.sum(binary_image)})")
+        
+        return result
+
+
+def connect_endpoints(binary_image, connection_distance=20, spine_removal = 0, verbose=True):
+    """
+    Simple function to connect skeleton endpoints
+    
+    Parameters:
+    -----------
+    binary_image : ndarray
+        3D binary segmentation
+    connection_distance : float
+        Maximum distance to connect endpoints
+    verbose : bool
+        Print progress
+        
+    Returns:
+    --------
+    result : ndarray
+        Image with endpoint connections
+    """
+    # Convert to binary if needed
+    if verbose:
+        print("Converting to binary...")
+    binary_image = (binary_image > 0).astype(np.uint8)
+    
+    # Create connector and run
+    connector = EndpointConnector(connection_distance=connection_distance, spine_removal = spine_removal)
+    result = connector.connect_endpoints(binary_image, verbose=verbose)
+    
+    return result
+
+
+if __name__ == "__main__":
+    print("Endpoint connector ready")