Diameter at certain height point cloud — diameter_slice

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,
  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,
  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 = 0.06) 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 optimized circle fitting is plotted.
how: Method used to summarise point-to-centre radii when estimating slice diameter. Use "mean" for the original ITSMe behaviour, "median" for the median radius, 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. If supplied, this is converted to degrees based on the fitted radius.
arc_min_angle: Numeric. Minimum angular sector width in degrees used to calculate arc coverage. 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 radius before checking whether the inner circle is empty.
inner_buffer_fraction: Numeric. Fraction of the fitted radius used as buffer before checking whether the inner circle is empty. The effective buffer is max(min_inner_buffer, inner_buffer_fraction * radius).
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.

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. The list also contains arc_coverage, a quality-control metric between 0 and 1 indicating the proportion of angular sectors around the fitted 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 circle contains no slice points.

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.

Examples

if (FALSE) { # \dontrun{
# 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 <- output$center
} # }