used sanitized faces for geodesics

Author: jo-mueller

src/napari_stress/_measurements/geodesics.py

@@ -26,10 +26,12 @@ def geodesic_distance_matrix(surface: SurfaceData) -> np.ndarray:
 
     """
     import gdist
+    from .._utils import sanitize_faces
 
     # Reorder the faces of the surface to ensure consistent orientation
-    faces = np.asarray(surface[1], dtype=np.int32)
-    vertices = np.asarray(surface[0], dtype=np.float64)
+    sanitized_surface = sanitize_faces(surface)
+    vertices = sanitized_surface[0]
+    faces = sanitized_surface[1]
 
     distance_matrix = gdist.local_gdist_matrix(
         vertices, faces, max_distance=1e9).toarray()
@@ -62,8 +64,13 @@ def geodesic_path(
 
     """
     import potpourri3d as pp3d
+    from .._utils import sanitize_faces
 
-    path_solver = pp3d.EdgeFlipGeodesicSolver(surface[0], surface[1])
+    sanitized_surface = sanitize_faces(surface)
+    vertices = sanitized_surface[0]
+    faces = sanitized_surface[1]
+
+    path_solver = pp3d.EdgeFlipGeodesicSolver(vertices, faces)
     path = path_solver.find_geodesic_path(index_1, index_2)
 
     # convert points to vectors from point to point
@@ -224,8 +231,10 @@ def local_extrema_analysis(
             - `min_max_pair_distances`: Distances between all pairs of local minima and maxima.
             - `min_max_pair_anisotropies`: Difference in input value `(vertices, faces, values)` between all pairs of local minima and maxima.
     """
-    triangles = surface[1]
+    from .._utils import sanitize_faces
     feature = surface[2]
+    surface = sanitize_faces(surface)
+    triangles = surface[1]
 
     quad_fit = len(feature)
 

src/napari_stress/_reconstruction/reconstruct_surface.py

@@ -21,12 +21,12 @@ def reconstruct_surface_from_quadrature_points(
 
     Returns
     -------
-    Sphere_Triangulation_Array : TYPE
-        DESCRIPTION.
+    tuple
+        Tuple of points and faces
 
     """
     from scipy.spatial import Delaunay
-
+    from .._utils import sanitize_faces
     from .._stress import lebedev_write_SPB as lebedev_write
 
     n_quadrature_points = len(points)
@@ -52,15 +52,4 @@ def reconstruct_surface_from_quadrature_points(
                 delauney_triangles[tri_i, vert_ind] = vertex
                 vert_ind = vert_ind + 1
 
-    # go through every triangle and make sure that they are all oriented
-    # counter-clockwise with respect to the center point
-    for i in range(num_tris):
-        p1 = points[int(delauney_triangles[i, 0])]
-        p2 = points[int(delauney_triangles[i, 1])]
-        p3 = points[int(delauney_triangles[i, 2])]
-
-        # check if the triangle is oriented clockwise
-        if np.cross(p2 - p1, p3 - p1)[2] < 0:
-            delauney_triangles[i] = delauney_triangles[i][::-1]
-
-    return (points, delauney_triangles.astype(int))
+    return sanitize_faces((points, delauney_triangles.astype(int)))