Sphericity

Create a method to compute sphericity using a mesh based approach

qim3d/processing/mesh.py

@@ -9,6 +9,7 @@ def create_mesh(
     volume: np.ndarray,
     level: float = None,
     step_size=1,
+    allow_degenerate=False,
     padding: Tuple[int, int, int] = (2, 2, 2),
     **kwargs: Any,
 ) -> trimesh.Trimesh:
@@ -18,6 +19,9 @@ def create_mesh(
     Args:
         volume (np.ndarray): The 3D numpy array representing the volume.
         level (float, optional): The threshold value for Marching Cubes. If None, Otsu's method is used.
+        step_size (int, optional): The step size for the Marching Cubes algorithm.
+        allow_degenerate (bool, optional): Whether to allow degenerate (i.e. zero-area) triangles in the end-result.
+        If False, degenerate triangles are removed, at the cost of making the algorithm slower. Default False.
         padding (tuple of int, optional): Padding to add around the volume.
         **kwargs: Additional keyword arguments to pass to `skimage.measure.marching_cubes`.
 
@@ -39,7 +43,7 @@ def create_mesh(
         mesh = qim3d.processing.create_mesh(vol, step_size=3)
         qim3d.viz.mesh(mesh.vertices, mesh.faces)
         ```
-
+        <iframe src="https://platform.qim.dk/k3d/mesh_visualization.html" width="100%" height="500" frameborder="0"></iframe>
     """
     if volume.ndim != 3:
         raise ValueError("The input volume must be a 3D numpy array.")
@@ -63,10 +67,13 @@ def create_mesh(
 
     # Call skimage.measure.marching_cubes with user-provided kwargs
     verts, faces, normals, values = measure.marching_cubes(
-        volume, level=level, step_size=step_size, **kwargs
+        volume, level=level, step_size=step_size, allow_degenerate=allow_degenerate, **kwargs
     )
 
     # Create the Trimesh object
     mesh = trimesh.Trimesh(vertices=verts, faces=faces)
 
+    # Fix face orientation to ensure normals point outwards
+    trimesh.repair.fix_inversion(mesh, multibody=True) 
+
     return mesh