Diameter at breast height point cloud

Returns the diameter at breast height (DBH) and functional diameter at breast height (fDBH) of a tree measured from a tree point cloud. There should be only one stem at breast height.

Usage

dbh_pc(
  pc,
  thresholdR2 = 0.001,
  slice_thickness = 0.06,
  functional = FALSE,
  concavity = 4,
  dtm = NA,
  r = 5,
  how = "median",
  arc_min_length_cm = NULL,
  arc_min_angle = 18,
  arc_tolerance = 0.05,
  min_inner_buffer = 0.06,
  inner_buffer_fraction = 0.5,
  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.
thresholdR2: Numeric value (default=0.001) that is multiplied with the radius to determine if at breast height (1.3 m above the lowest point of the point cloud) the circle fit is influenced by branches. If the resulting value is exceeded, the lower trunk without branches is extracted using extract_lower_trunk_pc. Increase the thresholdR2 if your point cloud quality is low (for example, errors in co-registration of point clouds in multi-scan due to wind-effect).
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.
how: Method used to summarise point-to-centre radii when estimating DBH. Use "mean" for the original ITSMe behaviour, "median" for the median radius (default), or a numeric value such as 10 to trim 5 percent of radii on each side before taking the mean.
arc_min_length_cm: Optional numeric. Minimum arc length, in centimetres, represented by one angular sector when calculating arc coverage for the final DBH circle.
arc_min_angle: Numeric. Minimum angular sector width in degrees used to calculate arc coverage for the final DBH circle. Default is 18, corresponding to 20 sectors.
arc_tolerance: Numeric. Radial tolerance, in metres, around the fitted circle. Points within radius +/- arc_tolerance are counted as supporting the fitted circle when calculating arc coverage.
min_inner_buffer: Numeric. Minimum buffer distance, in metres, excluded from the fitted DBH radius before checking whether the inner circle is empty.
inner_buffer_fraction: Numeric. Fraction of the fitted DBH radius used as buffer before checking whether the inner circle is empty. The effective buffer is max(min_inner_buffer, inner_buffer_fraction * radius).
plot: Logical (default=FALSE), indicates if the optimised 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 and third and fourth element of this list respectively.

Value

List with the diameter of the stem at breast height, the residuals on the fitting, the estimated center of the circle fit, 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. The list also contains arc_coverage, a quality-control metric between 0 and 1 indicating the proportion of angular sectors around the fitted DBH circle that contain at least one nearby point. The list also contains inner_circle_empty, a logical quality-control metric indicating whether the checked inner part of the fitted DBH circle contains no slice points.

Details

The DBH is measured as the diameter of the optimal circle fitted through a 6mm thick horizontal slice (from 1.27 m to 1.33 m above the lowest tree point) using diameter_slice_pc. A least squares circle fitting algorithm is applied to find the optimal fit. Also the functional diameter at breast height (fDBH) is determined using diameter_slice_pc. 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. In case there are branches or foliage at this height, the lower trunk is extracted using extract_lower_trunk_pc. Whether this is the case is determined using the thresholdR2 parameter. 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.

Examples

if (FALSE) { # \dontrun{
# Read tree point cloud and calculate the DBH
pc_tree <- read_tree_pc(PC_path = "path/to/point_cloud.txt")
dbh <- dbh_pc(pc = pc_tree)
# and plot the circle fitting
output <- dbh_pc(pc = pc_tree, plot = TRUE)
dbh <- output$dbh
} # }