nettracer3d 1.2.5__py3-none-any.whl → 1.3.1__py3-none-any.whl

nettracer3d/branch_stitcher.py

@@ -1,126 +1,177 @@
 import numpy as np
 import networkx as nx
-from . import nettracer as n3d
-from scipy.ndimage import distance_transform_edt, gaussian_filter, binary_fill_holes
 from scipy.spatial import cKDTree
-from skimage.morphology import remove_small_objects, skeletonize
-import warnings
-warnings.filterwarnings('ignore')
+from collections import deque
+from . import smart_dilate as sdl
 
 
 class VesselDenoiser:
     """
     Denoise vessel segmentations using graph-based geometric features
+    IMPROVED: Uses skeleton topology to compute endpoint directions
     """
     
     def __init__(self, 
-                 score_thresh = 2):
-
+                 score_thresh = 2,
+                 xy_scale = 1,
+                 z_scale = 1,
+                 trace_length = 10):
         self.score_thresh = score_thresh
+        self.xy_scale = xy_scale
+        self.z_scale = z_scale
+        self.trace_length = trace_length  # How far to trace from endpoint
 
-
-    def select_kernel_points_topology(self, data, skeleton):
+    def _build_skeleton_graph(self, skeleton):
         """
-        ENDPOINTS ONLY version: Returns only skeleton endpoints (degree=1 nodes)
+        Build a graph from skeleton where nodes are voxel coordinates
+        and edges connect 26-connected neighbors
         """
         skeleton_coords = np.argwhere(skeleton)
         if len(skeleton_coords) == 0:
-            return skeleton_coords
+            return None, None
         
-        # Map coord -> index
+        # Map coordinate tuple -> node index
         coord_to_idx = {tuple(c): i for i, c in enumerate(skeleton_coords)}
         
-        # Build full 26-connected skeleton graph
+        # Build graph
         skel_graph = nx.Graph()
         for i, c in enumerate(skeleton_coords):
             skel_graph.add_node(i, pos=c)
         
+        # 26-connected neighborhood
         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)]
         
+        # Add edges
         for i, c in enumerate(skeleton_coords):
             cz, cy, cx = c
             for dz, dy, dx in nbr_offsets:
                 nb = (cz + dz, cy + dy, cx + dx)
-                j = coord_to_idx.get(nb, None)
+                j = coord_to_idx.get(nb)
                 if j is not None and j > i:
                     skel_graph.add_edge(i, j)
         
-        # Get degree per voxel
+        return skel_graph, coord_to_idx
+
+    def select_kernel_points_topology(self, data, skeleton):
+        """
+        Returns only skeleton endpoints (degree=1 nodes)
+        """
+        skel_graph, coord_to_idx = self._build_skeleton_graph(skeleton)
+        
+        if skel_graph is None:
+            return np.array([]), None, None
+        
+        # Get degree per node
         deg = dict(skel_graph.degree())
         
         # ONLY keep endpoints (degree=1)
-        endpoints = {i for i, d in deg.items() if d == 1}
+        endpoints = [i for i, d in deg.items() if d == 1]
         
-        # Return endpoint coordinates
+        # Get coordinates
+        skeleton_coords = np.argwhere(skeleton)
         kernel_coords = np.array([skeleton_coords[i] for i in endpoints])
-        return kernel_coords
         
-    
-    def extract_kernel_features(self, skeleton, distance_map, kernel_pos, radius=5):
-        """Extract geometric features for a kernel at a skeleton point"""
+        return kernel_coords, skel_graph, coord_to_idx
+
+    def _compute_endpoint_direction(self, skel_graph, endpoint_idx, trace_length=None):
+        """
+        Compute direction by tracing along skeleton from endpoint.
+        Returns direction vector pointing INTO the skeleton (away from endpoint).
+        
+        Parameters:
+        -----------
+        skel_graph : networkx.Graph
+            Skeleton graph with node positions
+        endpoint_idx : int
+            Node index of the endpoint
+        trace_length : int
+            How many steps to trace along skeleton
+            
+        Returns:
+        --------
+        direction : ndarray
+            Normalized direction vector pointing into skeleton from endpoint
+        """
+        if trace_length is None:
+            trace_length = self.trace_length
+        
+        # Get endpoint position
+        endpoint_pos = skel_graph.nodes[endpoint_idx]['pos']
+        
+        # BFS from endpoint to collect positions along skeleton path
+        visited = {endpoint_idx}
+        queue = deque([endpoint_idx])
+        path_positions = []
+        
+        while queue and len(path_positions) < trace_length:
+            current = queue.popleft()
+            
+            # Get neighbors
+            for neighbor in skel_graph.neighbors(current):
+                if neighbor not in visited:
+                    visited.add(neighbor)
+                    queue.append(neighbor)
+                    
+                    # Add this position to path
+                    neighbor_pos = skel_graph.nodes[neighbor]['pos']
+                    path_positions.append(neighbor_pos)
+                    
+                    if len(path_positions) >= trace_length:
+                        break
+        
+        # If we couldn't trace far enough, use what we have
+        if len(path_positions) == 0:
+            # Isolated endpoint, return arbitrary direction
+            return np.array([0., 0., 1.])
+        
+        # Compute direction as average vector from endpoint to traced positions
+        # This gives us the direction the skeleton is "extending" from the endpoint
+        path_positions = np.array(path_positions)
+        
+        # Weight more distant points more heavily (they better represent overall direction)
+        weights = np.linspace(1.0, 2.0, len(path_positions))
+        weights = weights / weights.sum()
+        
+        # Weighted average position along the path
+        weighted_target = np.sum(path_positions * weights[:, None], axis=0)
+        
+        # Direction from endpoint toward this position
+        direction = weighted_target - endpoint_pos
+        
+        # Normalize
+        norm = np.linalg.norm(direction)
+        if norm < 1e-10:
+            return np.array([0., 0., 1.])
+        
+        return direction / norm
+
+    def extract_kernel_features(self, skeleton, distance_map, kernel_pos, 
+                                skel_graph, coord_to_idx, endpoint_idx):
+        """Extract geometric features for a kernel at a skeleton endpoint"""
         z, y, x = kernel_pos
-        shape = skeleton.shape
         
         features = {}
         
         # Vessel radius at this point
         features['radius'] = distance_map[z, y, x]
-        
-        # Local skeleton density (connectivity measure)
-        z_min = max(0, z - radius)
-        z_max = min(shape[0], z + radius + 1)
-        y_min = max(0, y - radius)
-        y_max = min(shape[1], y + radius + 1)
-        x_min = max(0, x - radius)
-        x_max = min(shape[2], x + radius + 1)
-        
-        local_region = skeleton[z_min:z_max, y_min:y_max, x_min:x_max]
-        features['local_density'] = np.sum(local_region) / max(local_region.size, 1)
-        
-        # Local direction vector
-        features['direction'] = self._compute_local_direction(
-            skeleton, kernel_pos, radius
+                        
+        # Direction vector using topology-based tracing
+        features['direction'] = self._compute_endpoint_direction(
+            skel_graph, endpoint_idx, self.trace_length
         )
         
         # Position
         features['pos'] = np.array(kernel_pos)
         
-        # ALL kernels are endpoints in this version
+        # All kernels are endpoints
         features['is_endpoint'] = True
         
         return features
 
-    
-    def _compute_local_direction(self, skeleton, pos, radius=5):
-        """Compute principal direction of skeleton in local neighborhood"""
-        z, y, x = pos
-        shape = skeleton.shape
-        
-        z_min = max(0, z - radius)
-        z_max = min(shape[0], z + radius + 1)
-        y_min = max(0, y - radius)
-        y_max = min(shape[1], y + radius + 1)
-        x_min = max(0, x - radius)
-        x_max = min(shape[2], x + radius + 1)
-        
-        local_skel = skeleton[z_min:z_max, y_min:y_max, x_min:x_max]
-        coords = np.argwhere(local_skel)
-        
-        if len(coords) < 2:
-            return np.array([0., 0., 1.])
-        
-        # PCA to find principal direction
-        centered = coords - coords.mean(axis=0)
-        cov = np.cov(centered.T)
-        eigenvalues, eigenvectors = np.linalg.eigh(cov)
-        principal_direction = eigenvectors[:, -1]  # largest eigenvalue
-        
-        return principal_direction / (np.linalg.norm(principal_direction) + 1e-10)
-    
     def group_endpoints_by_vertex(self, skeleton_points, verts):
         """
         Group endpoints by which vertex (labeled blob) they belong to
@@ -149,66 +200,106 @@ class VesselDenoiser:
     
     def compute_edge_features(self, feat_i, feat_j):
         """
-        Compute features for potential connection between two endpoints
-        NO DISTANCE-BASED FEATURES - only radius and direction
+        Compute features for potential connection between two endpoints.
+        IMPROVED: Uses proper directional alignment (not abs value).
+        
+        Two endpoints should connect if:
+        - Their skeletons are pointing TOWARD each other (negative dot product of directions)
+        - They have similar radii
+        - The connection vector aligns with both skeleton directions
         """
         features = {}
         
-        # Euclidean distance (for reference only, not used in scoring)
+        # Vector from endpoint i to endpoint j
         pos_diff = feat_j['pos'] - feat_i['pos']
         features['distance'] = np.linalg.norm(pos_diff)
         
+        if features['distance'] < 1e-10:
+            # Same point, shouldn't happen
+            features['connection_vector'] = np.array([0., 0., 1.])
+        else:
+            features['connection_vector'] = pos_diff / features['distance']
+        
         # Radius similarity
         r_i, r_j = feat_i['radius'], feat_j['radius']
         features['radius_diff'] = abs(r_i - r_j)
         features['radius_ratio'] = min(r_i, r_j) / (max(r_i, r_j) + 1e-10)
         features['mean_radius'] = (r_i + r_j) / 2.0
         
-        # Direction alignment
-        direction_vec = pos_diff / (features['distance'] + 1e-10)
+        # CRITICAL: Check if skeletons point toward each other
+        # If both directions point into their skeletons (away from endpoints),
+        # they should point in OPPOSITE directions across the gap
+        dir_i = feat_i['direction']
+        dir_j = feat_j['direction']
+        connection_vec = features['connection_vector']
         
-        # Alignment with both local directions
-        align_i = abs(np.dot(feat_i['direction'], direction_vec))
-        align_j = abs(np.dot(feat_j['direction'], direction_vec))
-        features['alignment'] = (align_i + align_j) / 2.0
+        # How well does endpoint i's skeleton direction align with the gap vector?
+        # (positive = pointing toward j)
+        align_i = np.dot(dir_i, connection_vec)
         
-        # Smoothness: how well does connection align with both local directions
-        features['smoothness'] = min(align_i, align_j)
+        # How well does endpoint j's skeleton direction align AGAINST the gap vector?
+        # (negative = pointing toward i)
+        align_j = np.dot(dir_j, connection_vec)
         
-        # Density similarity
-        features['density_diff'] = abs(feat_i['local_density'] - feat_j['local_density'])
+        # For good connection: align_i should be positive (i pointing toward j)
+        # and align_j should be negative (j pointing toward i)
+        # So align_i - align_j should be large and positive
+        features['approach_score'] = align_i - align_j
+        
+        # Individual alignment scores (for diagnostics)
+        features['align_i'] = align_i
+        features['align_j'] = align_j
+        
+        # How parallel/antiparallel are the two skeleton directions?
+        # -1 = pointing toward each other (good for connection)
+        # +1 = pointing in same direction (bad, parallel branches)
+        features['direction_similarity'] = np.dot(dir_i, dir_j)
         
         return features
     
     def score_connection(self, edge_features):
+        """
+        Score potential connection between two endpoints.
+        FIXED: Directions point INTO skeletons (away from endpoints)
+        """
         score = 0.0
-
-        # HARD REJECT for definite forks/sharp turns
-        if edge_features['smoothness'] < 0.5:  # At least one endpoint pointing away
+        
+        # For good connections when directions point INTO skeletons:
+        # - align_i should be NEGATIVE (skeleton i extends away from j)
+        # - align_j should be POSITIVE (skeleton j extends away from i)  
+        # - Both skeletons extend away from the gap (good!)
+        
+        # HARD REJECT: If skeletons point in same direction (parallel branches)
+        if edge_features['direction_similarity'] > 0.7:
+            return -999
+        
+        # HARD REJECT: If both skeletons extend TOWARD the gap (diverging structure)
+        # This means: align_i > 0 and align_j < 0 (both point at gap = fork/divergence)
+        if edge_features['align_i'] > 0.3 and edge_features['align_j'] < -0.3:
+            return -999
+        
+        # HARD REJECT: If either skeleton extends the wrong way
+        # align_i should be negative, align_j should be positive
+        if edge_features['align_i'] > 0.3 or edge_features['align_j'] < -0.3:
             return -999
         
         # Base similarity scoring
-        score += edge_features['radius_ratio'] * 10.0
-        score += edge_features['alignment'] * 8.0
-        score += edge_features['smoothness'] * 6.0
-        score -= edge_features['density_diff'] * 0.5
-        
-        # PENALTY for poor directional alignment (punish forks!)
-        # Alignment < 0.5 means vessels are pointing in different directions
-        # This doesn't trigger that often so it might be redundant with the above step
-        if edge_features['alignment'] < 0.5:
-            penalty = (0.5 - edge_features['alignment']) * 15.0
-            score -= penalty
-        
-        # ADDITIONAL PENALTY for sharp turns/forks --- no longer in use since we now hard reject these, but I left this in here to reverse it later potentially
-        # Smoothness < 0.4 means at least one endpoint points away
-        #if edge_features['smoothness'] < 0.4:
-         #   penalty = (0.4 - edge_features['smoothness']) * 20.0
-          #  score -= penalty
-        
-        # Size bonus: ONLY if vessels already match well
-        
-        if edge_features['radius_ratio'] > 0.7 and edge_features['alignment'] > 0.5:
+        score += edge_features['radius_ratio'] * 15.0
+        
+        # REWARD: Skeletons extending away from each other across gap
+        # When directions point into skeletons:
+        # Good connection has align_i < 0 and align_j > 0
+        # So we want to MAXIMIZE: -align_i + align_j (both terms positive)
+        extension_score = (-edge_features['align_i'] + edge_features['align_j'])
+        score += extension_score * 10.0
+        
+        # REWARD: Skeletons pointing in opposite directions (antiparallel)
+        # direction_similarity should be negative
+        antiparallel_bonus = max(0, -edge_features['direction_similarity']) * 5.0
+        score += antiparallel_bonus
+
+        # SIZE BONUS: Reward large, well-matched vessels
+        if edge_features['radius_ratio'] > 0.7 and extension_score > 1.0:
             mean_radius = edge_features['mean_radius']
             score += mean_radius * 1.5
         
@@ -217,8 +308,8 @@ class VesselDenoiser:
     def connect_vertices_across_gaps(self, skeleton_points, kernel_features, 
                                      labeled_skeleton, vertex_to_endpoints, verbose=False):
         """
-        Connect vertices by finding best endpoint pair across each vertex
-        Each vertex makes at most one connection
+        Connect vertices by finding best endpoint pair across each vertex.
+        Each vertex makes at most one connection.
         """
         # Initialize label dictionary: label -> label (identity mapping)
         unique_labels = np.unique(labeled_skeleton[labeled_skeleton > 0])
@@ -241,7 +332,6 @@ class VesselDenoiser:
         # Iterate through each vertex
         for vertex_label, endpoint_indices in vertex_to_endpoints.items():
             if len(endpoint_indices) < 2:
-                # Need at least 2 endpoints to make a connection
                 continue
             
             if verbose and len(endpoint_indices) > 0:
@@ -271,11 +361,17 @@ class VesselDenoiser:
                     if root_i == root_j:
                         continue
                     
-                    # Compute edge features (no skeleton needed, no distance penalty)
+                    # Compute edge features
                     edge_feat = self.compute_edge_features(feat_i, feat_j)
                     
                     # Score this connection
                     score = self.score_connection(edge_feat)
+                    #print(score)
+                    
+                    if verbose and score > -900:
+                        print(f"  Pair {idx_i}-{idx_j}: score={score:.2f}, "
+                              f"approach={edge_feat['approach_score']:.2f}, "
+                              f"dir_sim={edge_feat['direction_similarity']:.2f}")
                     
                     # Apply threshold
                     if score > self.score_thresh and score > best_score:
@@ -291,7 +387,7 @@ class VesselDenoiser:
                 root_i = find_root(label_i)
                 root_j = find_root(label_j)
                 
-                # Unify labels: point larger label to smaller label
+                # Unify labels
                 if root_i < root_j:
                     label_dict[root_j] = root_i
                     unified_label = root_i
@@ -310,42 +406,29 @@ class VesselDenoiser:
     def denoise(self, data, skeleton, labeled_skeleton, verts, verbose=False):
         """
         Main pipeline: unify skeleton labels by connecting endpoints at vertices
-        
-        Parameters:
-        -----------
-        data : ndarray
-            3D binary segmentation (for distance transform)
-        skeleton : ndarray
-            3D binary skeleton
-        labeled_skeleton : ndarray
-            Labeled skeleton (each branch has unique label)
-        verts : ndarray
-            Labeled vertices (blobs where branches meet)
-        verbose : bool
-            Print progress
-            
-        Returns:
-        --------
-        label_dict : dict
-            Dictionary mapping old labels to unified labels
         """
         if verbose:
-            print("Starting skeleton label unification...")
+            print("Starting skeleton label unification (IMPROVED VERSION)...")
             print(f"Initial unique labels: {len(np.unique(labeled_skeleton[labeled_skeleton > 0]))}")
         
         # Compute distance transform
         if verbose:
             print("Computing distance transform...")
-        distance_map = distance_transform_edt(data)
+        distance_map = sdl.compute_distance_transform_distance(data, fast_dil = True)
         
-        # Extract endpoints
+        # Extract endpoints and build skeleton graph
         if verbose:
-            print("Extracting skeleton endpoints...")
-        kernel_points = self.select_kernel_points_topology(data, skeleton)
+            print("Extracting skeleton endpoints and building graph...")
+        kernel_points, skel_graph, coord_to_idx = self.select_kernel_points_topology(data, skeleton)
         
         if verbose:
             print(f"Found {len(kernel_points)} endpoints")
         
+        if len(kernel_points) == 0:
+            # No endpoints, return identity mapping
+            unique_labels = np.unique(labeled_skeleton[labeled_skeleton > 0])
+            return {int(label): int(label) for label in unique_labels}
+        
         # Group endpoints by vertex
         if verbose:
             print("Grouping endpoints by vertex...")
@@ -358,10 +441,25 @@ class VesselDenoiser:
         
         # Extract features for each endpoint
         if verbose:
-            print("Extracting endpoint features...")
+            print("Extracting endpoint features with topology-based directions...")
+        
+        # Create reverse mapping: position -> node index in graph
+        skeleton_coords = np.argwhere(skeleton)
         kernel_features = []
+        
         for pt in kernel_points:
-            feat = self.extract_kernel_features(skeleton, distance_map, pt)
+            # Find this endpoint in the graph
+            pt_tuple = tuple(pt)
+            endpoint_idx = coord_to_idx.get(pt_tuple)
+            
+            if endpoint_idx is None:
+                # Shouldn't happen, but handle gracefully
+                print(f"Warning: Endpoint {pt} not found in graph")
+                continue
+            
+            feat = self.extract_kernel_features(
+                skeleton, distance_map, pt, skel_graph, coord_to_idx, endpoint_idx
+            )
             kernel_features.append(feat)
         
         # Connect vertices
@@ -372,7 +470,7 @@ class VesselDenoiser:
             vertex_to_endpoints, verbose
         )
         
-        # Compress label dictionary (path compression for union-find)
+        # Compress label dictionary
         if verbose:
             print("\nCompressing label mappings...")
         for label in list(label_dict.keys()):
@@ -390,31 +488,41 @@ class VesselDenoiser:
         return label_dict
 
 
-def trace(data, labeled_skeleton, verts, score_thresh=10, verbose=False):
+def trace(data, labeled_skeleton, verts, score_thresh=10, xy_scale=1, z_scale=1, 
+          trace_length=10, verbose=False):
     """
-    Trace and unify skeleton labels using vertex-based endpoint grouping
+    Trace and unify skeleton labels using vertex-based endpoint grouping.
+    IMPROVED: Uses topology-based direction calculation.
+    
+    Parameters:
+    -----------
+    trace_length : int
+        How many voxels to trace from each endpoint to determine direction
     """
-    skeleton = n3d.binarize(labeled_skeleton)
+    skeleton = (labeled_skeleton > 0).astype(np.uint8)
     
-    # Create denoiser
-    denoiser = VesselDenoiser(score_thresh=score_thresh)
+    # Create denoiser with trace_length parameter
+    denoiser = VesselDenoiser(
+        score_thresh=score_thresh, 
+        xy_scale=xy_scale, 
+        z_scale=z_scale,
+        trace_length=trace_length
+    )
     
     # Run label unification
     label_dict = denoiser.denoise(data, skeleton, labeled_skeleton, verts, verbose=verbose)
     
-    # Apply unified labels efficiently (SINGLE PASS)
-    # Create lookup array: index by old label, get new label
+    # Apply unified labels
     max_label = np.max(labeled_skeleton)
-    label_map = np.arange(max_label + 1)  # Identity mapping by default
+    label_map = np.arange(max_label + 1)
     
     for old_label, new_label in label_dict.items():
         label_map[old_label] = new_label
     
-    # Single array indexing operation
     relabeled_skeleton = label_map[labeled_skeleton]
     
     return relabeled_skeleton
 
 
 if __name__ == "__main__":
-    print("Test area")
+    print("Improved branch stitcher with topology-based direction calculation")

nettracer3d/filaments.py

@@ -1,10 +1,11 @@
 import numpy as np
 import networkx as nx
 from . import nettracer as n3d
-from scipy.ndimage import distance_transform_edt, gaussian_filter, binary_fill_holes
+from scipy.ndimage import gaussian_filter, binary_fill_holes
 from scipy.spatial import cKDTree
 from skimage.morphology import remove_small_objects, skeletonize
 import warnings
+from . import smart_dilate as sdl
 warnings.filterwarnings('ignore')
 
 
@@ -22,6 +23,8 @@ class VesselDenoiser:
                  blob_volume = 200,
                  spine_removal=0,
                  score_thresh = 2,
+                 xy_scale = 1,
+                 z_scale = 1,
                  radius_aware_distance=True):
         """
         Parameters:
@@ -46,6 +49,8 @@ class VesselDenoiser:
         self.spine_removal = spine_removal
         self.radius_aware_distance = radius_aware_distance
         self.score_thresh = score_thresh
+        self.xy_scale = xy_scale
+        self.z_scale = z_scale
 
         self._sphere_cache = {}  # Cache sphere masks for different radii
 
@@ -939,7 +944,7 @@ class VesselDenoiser:
         
         if verbose:
             print("Step 3: Computing distance transform...")
-        distance_map = distance_transform_edt(cleaned)
+        distance_map = sdl.compute_distance_transform_distance(cleaned, fast_dil = True)
         
         # Step 3: Sample kernels along skeleton
         if verbose:
@@ -1036,7 +1041,7 @@ class VesselDenoiser:
         return result
 
 
-def trace(data, kernel_spacing = 1, max_distance = 20, min_component = 20, gap_tolerance = 5, blob_sphericity = 1.0, blob_volume = 200, spine_removal = 0, score_thresh = 2):
+def trace(data, kernel_spacing = 1, max_distance = 20, min_component = 20, gap_tolerance = 5, blob_sphericity = 1.0, blob_volume = 200, spine_removal = 0, score_thresh = 2, xy_scale = 1, z_scale = 1):
 
     """Main function with user prompts"""
     
@@ -1054,7 +1059,9 @@ def trace(data, kernel_spacing = 1, max_distance = 20, min_component = 20, gap_t
         blob_sphericity = blob_sphericity,
         blob_volume = blob_volume,
         spine_removal = spine_removal,
-        score_thresh = score_thresh
+        score_thresh = score_thresh,
+        xy_scale = xy_scale,
+        z_scale = z_scale
     )
     
     # Run denoising