How to deal with minus values on canopy height model?

Question

I created a canopy height model (from lidar data) using lidR package and wanted to check it on Arcmap. I see there are minus values on canopy height models like -0.246219, -0.0302621. How can I deal with minus values in my canopy height model?

Answer 1

It is always advisable to filter your points prior to generating a canopy height model. The following is a processing pipeline that filters normalized points.

Pipeline Overview

1. Read point cloud data
2. Normalize point cloud so that ground = 0
3. Filter points, keeping points where Z >= 0m & Z <= 40m
4. Generate the canopy height model

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library(lidR)

indata <- '/path/to/your/lidar_data.laz'
las <- readLAS(indata)

# Normalize point cloud data
normalized_las <- lasnormalize(las, tin())

# Keep points where Z >= 0 & Z <= 40 
filtered <- lasfilter(normalized_las, Z >= 0 & Z <= 40)

# Visualize difference between filtered and unfiltered points
par(mfrow=c(2,2))
boxplot(normalized_las@data$Z, ylim = c(-10,55), ylab = "Height (m)", main = "Before Filtering")
boxplot(filtered@data$Z, ylim = c(-10,55), ylab = "Height (m)", main = "After Filtering")
hist(normalized_las@data$Z, xlim=c(-2,55), xlab = "Height (m)", main = "Before Filtering")
hist(filtered@data$Z, xlim=c(-2,55), xlab = "Height (m)", main = "After Filtering")

#Generate canopy height model
chm <- grid_canopy(filtered, 0.5, p2r(0.2))
plot(chm)