moved conncomp from laplace_beltrami.py to gen_isosurface.py

Author: Jordan DeKraker

hippunfold/workflow/scripts/gen_isosurface.py

@@ -2,6 +2,7 @@
 import nibabel as nib
 import numpy as np
 from copy import deepcopy
+import networkx as nx
 
 
 def write_surface_to_gifti(points, faces, out_surf_gii):
@@ -21,6 +22,48 @@ def write_surface_to_gifti(points, faces, out_surf_gii):
     gifti.to_filename(out_surf_gii)
 
 
+def largest_connected_component(vertices: np.ndarray, faces: np.ndarray):
+    """
+    Returns the vertices, faces, and original indices of the largest connected component of a 3D surface mesh.
+
+    Parameters:
+    vertices (np.ndarray): Array of vertex coordinates (N x 3).
+    faces (np.ndarray): Array of face indices (M x 3).
+
+    Returns:
+    tuple: (new_vertices, new_faces, largest_component), where new_vertices are the vertex coordinates of the largest component,
+           new_faces are the face indices adjusted to the new vertex order, and largest_component contains the indices of the original vertices.
+    """
+    # Build adjacency graph from face connectivity
+    G = nx.Graph()
+    for face in faces:
+        G.add_edges_from(
+            [(face[i], face[j]) for i in range(3) for j in range(i + 1, 3)]
+        )
+
+    # Find connected components
+    components = list(nx.connected_components(G))
+
+    # Select the largest connected component
+    largest_component = max(components, key=len)
+    largest_component = np.array(list(largest_component))
+
+    # Create a mapping from old vertex indices to new ones
+    index_map = {old_idx: new_idx for new_idx, old_idx in enumerate(largest_component)}
+
+    # Filter the vertices and faces
+    new_vertices = vertices[largest_component]
+    new_faces = np.array(
+        [
+            [index_map[v] for v in face]
+            for face in faces
+            if all(v in index_map for v in face)
+        ]
+    )
+
+    return new_vertices, new_faces, largest_component
+
+
 def remove_nan_vertices(vertices, faces):
     """
     Removes vertices containing NaNs and updates faces accordingly.
@@ -186,5 +229,9 @@ def compute_geodesic_distances(vertices, faces, source_indices):
 points, faces = remove_nan_vertices(points, faces)
 
 
+# apply largest connected component
+points, faces, i_concomp = largest_connected_component(vertices_orig, faces)
+
+
 # write to gifti
 write_surface_to_gifti(points, faces, snakemake.output.surf_gii)

hippunfold/workflow/scripts/laplace_beltrami.py

@@ -3,49 +3,6 @@
 import nibabel as nib
 from scipy.interpolate import NearestNDInterpolator
 from collections import defaultdict
-import networkx as nx
-
-
-def largest_connected_component(vertices: np.ndarray, faces: np.ndarray):
-    """
-    Returns the vertices, faces, and original indices of the largest connected component of a 3D surface mesh.
-
-    Parameters:
-    vertices (np.ndarray): Array of vertex coordinates (N x 3).
-    faces (np.ndarray): Array of face indices (M x 3).
-
-    Returns:
-    tuple: (new_vertices, new_faces, largest_component), where new_vertices are the vertex coordinates of the largest component,
-           new_faces are the face indices adjusted to the new vertex order, and largest_component contains the indices of the original vertices.
-    """
-    # Build adjacency graph from face connectivity
-    G = nx.Graph()
-    for face in faces:
-        G.add_edges_from(
-            [(face[i], face[j]) for i in range(3) for j in range(i + 1, 3)]
-        )
-
-    # Find connected components
-    components = list(nx.connected_components(G))
-
-    # Select the largest connected component
-    largest_component = max(components, key=len)
-    largest_component = np.array(list(largest_component))
-
-    # Create a mapping from old vertex indices to new ones
-    index_map = {old_idx: new_idx for new_idx, old_idx in enumerate(largest_component)}
-
-    # Filter the vertices and faces
-    new_vertices = vertices[largest_component]
-    new_faces = np.array(
-        [
-            [index_map[v] for v in face]
-            for face in faces
-            if all(v in index_map for v in face)
-        ]
-    )
-
-    return new_vertices, new_faces, largest_component
 
 
 def find_boundary_vertices(vertices, faces):
@@ -154,11 +111,9 @@ def solve_laplace_beltrami_open_mesh(vertices, faces, boundary_conditions=None):
 
 
 surf = nib.load(snakemake.input.surf_gii)
-vertices_orig = surf.agg_data("NIFTI_INTENT_POINTSET")
+vertices = surf.agg_data("NIFTI_INTENT_POINTSET")
 faces = surf.agg_data("NIFTI_INTENT_TRIANGLE")
 
-vertices, faces, i_concomp = largest_connected_component(vertices_orig, faces)
-
 
 # get source/sink vertices by nearest neighbour (only of edge vertices)
 boundary_vertices = np.array(find_boundary_vertices(vertices, faces))