pyhaze

Fast smoothing of per-vertex data on triangular meshes for Python.

About

This package package performs smoothing of per-vertex data on triangular meshes. Such smoothing is typically used to reduce high-frequency noise and improve signal-to-noise ration (SNR). The algorithm for iterative nearest-neighbor smoothing is trivial, but involves nested tight loops, which are very slow in Python, so this package calls into C++ via pybind11 to achieve high performance.

Fig.1: Noisy per-vertex data on a brain mesh (left), and the same data after smoothing (right). White represents NA values.

This is a Python implementation of the haze package for R. The haze website offers a more detailed explanation of the motivation and use cases.

Installation

Via pip:

pip install pyhaze

Alternatively, if you want to use conda:

conda install -c dfspspirit pyhaze

Usage

Example 1: Smooth data on a mesh given as a vertex index list

Here is a simple example using the pyhaze.smooth_pvd function.

import pyhaze
import numpy as np

vertices, faces = pyhaze.construct_cube()

pvd_data = np.arange(len(vertices), dtype=float)
smoothed_data = pyhaze.smooth_pvd(vertices, faces, pvd_data.tolist(), num_iter=5)

A note on the mesh representation used, so you can replace the vertices and faces with your own triangular mesh:

• vertices is a list of lists of float, with dimension N, 3 for N vertices. So the outer list has length N. The 3 columns (length of all inner lists) are the x,y,z coordinates for each vertex.
• faces is a list of lists of int, with dimension M, 3 for M faces. So the outer list has length M. The 3 columns (length of all inner lists) are the 3 vertices (given as indices into vertices) making up the respective triangular face.

Example 2: Smooth data on a mesh given as an adjacency list

For very large meshes, it pays off to pre-compute the adjacency list of the mesh with a fast method, such as with the igl Python package, which provides Python bindings for libigl, and use the pyhaze.smooth_pvd_adj function.

import pyhaze
import numpy as np
import igl

vertices, faces = pyhaze.construct_cube()

pvd_data = np.arange(len(vertices), dtype=float)
faces_igl = np.array(faces).reshape(-1, 3).astype(np.int64)
mesh_adj = igl.adjacency_list(faces_igl)  # Compute adjacency list with igl.
res = pyhaze.smooth_pvd_adj(mesh_adj, pvd_data.tolist(), num_iter=5)

See the unit tests for more examples.