dab_pc: Diameter above buttresses point cloud

In lmterryn/ITSMe: Individual Tree Structural Metrics

Diameter above buttresses point cloud

Description

Returns the diameter above buttresses (DAB) and the functional diameter above buttresses (fDAB) of a tree measured from a tree point cloud.

Usage

dab_pc(
  pc,
  thresholdbuttress = 0.001,
  maxbuttressheight = 7,
  slice_thickness = 0.06,
  functional = FALSE,
  concavity = 4,
  dtm = NA,
  r = 5,
  plot = FALSE,
  plotcolors = c("#000000", "#808080", "#1c027a", "#08aa7c", "#fac87f")
)

Arguments

pc	The tree point cloud as a data.frame with columns X,Y,Z. Output of read_tree_pc.
thresholdbuttress	Numeric value (default=0.001) that is multiplied with the radius to determine if the stem is circular or irregular at the height the slice is taken. For example with the default value 0.001: when the average residual (obtained after an initial circle fitting at 1.3 m) exceeds a value of 0.001 times the radius, indicating a non-circular (irregular) stem shape and presumably buttresses, the circle fitting process is repeated with a new slice 6 mm higher than the previous one until a slice above the buttresses is reached.
maxbuttressheight	Numeric value (default=7) that limits the height at which the diameter is measured. When this height is reached (because residuals do not become smaller than thresholdbuttress * R), the thresholdbuttress value is increased with 0.0005 and the fitting starts again at 1.3 m.
slice_thickness	Numeric value (default = 0.06) 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 optimised circle fitting is plotted.
plotcolors	list of five colors for plotting. Only relevant when plot = TRUE. The stem points above buttresses, stem points at breast height, fitted circle, the concave hull and the estimated center are colored by the first, second, third, fourth and fifth element of this list respectively.

Details

The DAB is measured as the diameter of the optimal circle fitted through a 6mm thick horizontal slice taken above the buttresses using using diameter_slice_pc. A least squares circle fitting algorithm was applied to find the optimal fit. The height at which the horizontal slice is taken, is determined iteratively. Starting at 1.27 m to 1.33 m from the lowest point of the tree point cloud. The average residual between the points and the fitted circle is calculated. When the average residual exceeds a value of "thresholdbuttress" times the radius, indicating a non-circular (irregular) stem shape and presumably buttresses, the process is repeated with a new slice 6 mm higher than the previous one until a slice above the buttresses is reached. When the "maxbuttressheight" is exceeded the iterative process is restarted with a "thresholdbuttress" increased with 0.0005. At the determined height above buttresses also the functional diameter is calculated using diameter_slice_pc. 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.

Value

List with the diameter of the stem above buttresses, the residuals on the fitting, and the functional diameter at breast height. Also optionally (plot=TRUE) plots the circle fitting on the horizontal slice which is then included in the list output.

Examples

## Not run: 
# Read tree point cloud and calculate the DAB
pc_tree <- read_tree_pc(PC_path = "path/to/point_cloud.txt")
dab <- dab_pc(pc = pc_tree)
# and plot the circle fitting
output <- dab_pc(pc = pc_tree, plot = TRUE)
dab <- output$dab
# with non-default settings
dab <- dab_pc(pc = pc_tree, thresholdbuttress = 0.002, maxbuttressheight = 5)

## End(Not run)

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