diameter_slice_pc: Diameter at certain height point cloud

In lmterryn/ITSMe: Individual Tree Structural Metrics

Diameter at certain height point cloud

Description

Returns the diameter at a certain height of a tree measured from a tree point cloud.

Usage

diameter_slice_pc(
  pc,
  slice_height = 0.1,
  slice_thickness = 0.06,
  functional = FALSE,
  concavity = 4,
  dtm = NA,
  r = 5,
  plot = FALSE,
  plotcolors = c("#000000", "#1c027a", "#08aa7c", "#fac87f")
)

Arguments

pc	The tree point cloud as a data.frame with columns X,Y,Z. Output of read_tree_pc.
slice_height	Numeric value (default = 1.3) that determines the height above the lowest point of the point cloud at which the diameter is measured.
slice_thickness	Numeric value (default = 0.6) that determines the thickness of the slice which is used to measure the diameter.
functional	Logical (default=FALSE), indicates if the functional diameter should be calculated.
concavity	Numeric value (default=4) concavity for the computation of the functional diameter using a concave hull based on concaveman.
dtm	The digital terrain model as a data.frame with columns X,Y,Z (default = NA). If the digital terrain model is in the same format as a point cloud it can also be read with read_tree_pc.
r	Numeric value (default=5) r which determines the range taken for the dtm. Should be at least the resolution of the dtm. Only relevant when a dtm is provided.
plot	Logical (default=FALSE), indicates if the optimized circle fitting is plotted.
plotcolors	list of four colors for plotting. Only relevant when plot = TRUE. The stem points, fitted circle, the concave hull and the estimated center are colored by the first, second, third and fourth element of this list respectively.

Details

The diameter is measured of the optimal circle fitted through a horizontal slice. A least squares circle fitting algorithm was applied to find the optimal fit. The height and thickness of the slice can be specified using slice_height and slice_thickness parameters. Additionally, the functional diameter is calculated. For this the area of the concave hull with (concavity 4) is determined on the slice. From this area the diameter is determined as the diameter of a circle with this area. When the bottom of the point cloud is incomplete or obstructed you can choose to add a digital terrain model as an input which is used to estimate lowest point of the point cloud in order to obtain slices at the correct height of the tree. This function is also a Support function used to determine the DBH from a tree point cloud with dbh_pc.

Value

A list with the diameter at a specified height (numeric value), the residual between circle fit and the points, the center of the circle fit, and the functional diameter calculated from the concave hull fitting. Also optionally (plot=TRUE) plots the circle fitting on the horizontal slice.

Examples

## Not run: 
# Read tree point cloud and calculate the diameter
pc_tree <- read_tree_pc(PC_path = "path/to/point_cloud.txt")
diameter <- diameter_slice_pc(pc = pc_tree)
# and plot the circle fitting
output <- diameter_slice_pc(pc = pc_tree, plot = TRUE)
diameter <- output$diameter
residual <- output$R2
center <- out$center

## End(Not run)

lmterryn/ITSMe documentation built on Feb. 4, 2025, 2:21 a.m.