lacunr

lacunr is an R package for calculating 3D lacunarity from voxel data. It is designed to be used with LiDAR point clouds to measure the heterogeneity or “gappiness” of 3-dimensional structures such as forest stands. It provides fast C++ functions to efficiently convert point cloud data to voxels and calculate lacunarity using different variants of Allain & Cloitre’s well-known gliding-box algorithm.

Installation

You can install lacunr from CRAN with:

install.packages("lacunr")

Or you can install the development version of lacunr from GitHub with:

# install.packages("devtools")
devtools::install_github("ElliottSmeds/lacunr")

Basic Usage

The standard workflow for lacunr is fairly simple:

1. Convert point cloud data to voxels using voxelize()
2. Arrange the voxels into a 3-dimensional binary map using bounding_box()
3. Calculate a lacunarity curve using lacunarity()

library(lacunr)
# create a data.frame of simulated point cloud data
pc <- data.frame(X = rnorm(1000, 10), Y = rnorm(1000, 50), Z = rnorm(1000, 25))
# convert to voxels of size 0.5
vox <- voxelize(pc, edge_length = c(0.5, 0.5, 0.5))
# generate binary map
box <- bounding_box(vox)
# calculate lacunarity curve
lac_curve <- lacunarity(box)

Interfacing with lidR

The lidr package offers a robust suite of tools for processing LiDAR data. While lacunr does not require lidR as a dependency, it is assumed that most users will be working with point cloud data imported using lidR, and the package is designed to mesh well with lidR’s data objects. The following tips will help make combining these packages as seamless as possible.

Working with LAS objects

Users should take special care when using a lidR LAS object as input for the voxelize() function. Since LAS is an S4 class, it is important to extract the point cloud data from the LAS object using @data, otherwise voxelize() will throw an error:

library(lidR)
# read in LAS point cloud file
las <- readLAS("<file.las>")
# voxelize the LAS point cloud, taking care to input the correct S4 slot
vox <- voxelize(las@data, edge_length = c(0.5, 0.5, 0.5))

Voxelization using lidR

lidR offers its own extremely versatile voxelization function, voxel_metrics(). This provides a useful alternative to voxelize(), although it is important to note that both functions utilize different algorithms and will not produce identical results (see the following section for more details).

voxel_metrics() returns a lasmetrics3d object. lacunr’s bounding_box() function can accept this as an input, but it also requires that it contain a column named N, recording the number of points in each voxel. This column can be generated by voxel_metrics() using the following:

# read in LAS point cloud file
las <- readLAS("<file.las>")
# voxelize at 1m resolution, creating a column N containing the number of points
vox <- voxel_metrics(las, ~list(N = length(Z)), res = 1)
# convert to array
box <- bounding_box(vox)

Details on voxelize() vs lidR::voxel_metrics()

voxelize() is adapted from the function voxels(), originally written by J. Antonio Guzmán Q. for the package rTLS. It is intended as a complement rather than a replacement for lidR’s more elaborate voxel_metrics(). Each function has a different underlying algorithm and will produce distinct results from the same input data. The chief advantages of voxelize() over voxel_metrics() are:

1. It allows – and in fact requires – the user to specify all three dimensions of the desired voxel resolution independently. This makes it possible to completely customize the shape of the voxels, in the rare instance that one wishes to divide up a point cloud into a non-cubic voxel grid. voxel_metrics() permits at most two dimensions.
2. The point cloud can be divided into an even number of voxel bins. For example, if you have a point cloud that spans 12 meters in the X dimension, and voxelize it at a resolution of 1 meter, the resulting data will be binned into 12 1-meter voxels along the X axis. The same point cloud will be binned into 13 voxels by voxel_metrics(). This is due to differences in how each function aligns the point cloud data within the voxel grid.