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Crown classification point cloud

Source: R/basic_metrics_pc.R
classify_crown_pc.Rd

Returns the crown points from a tree point cloud.

Usage

classify_crown_pc(
  pc,
  thresholdbranch = 1.5,
  minheight = 1,
  buttress = FALSE,
  thresholdR2 = 0.001,
  slice_thickness = 0.06,
  thresholdbuttress = 0.001,
  maxbuttressheight = 7,
  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("#08aa7c", "#fac87f")
)

Arguments

pc

The tree point cloud as a data.frame with columns X,Y,Z. Output of read_tree_pc.

thresholdbranch

Numeric value (default=1.5) that is multiplied with the diameter of the tree (calculated with dbh_pc or dab_pc when buttress =TRUE) which determines the cutt-off where a branch emerges and the crown begins.

minheight

Numeric value (default=1) with the minimum height at which the crown begins. Should be above the widest part of the buttresses for buttressed trees (value of 4 is recommended). For non-buttressed trees choose a lower value (such as 1).

buttress

Logical (default=FALSE), indicates if the trees have buttresses (higher than breast height).

thresholdR2

Numeric value (default=0.001). Parameter of the dbh_pc function used to calculate the diameter at breast height. Only relevant when buttress == FALSE.

slice_thickness

Numeric value (default = 0.06). Parameter of the dbh_pc function used to calculate the diameter at breast height. Only relevant when buttress == FALSE.

thresholdbuttress

Numeric value (default=0.001). Parameter of the dab_pc function used to calculate the diameter above buttresses. Only relevant when buttress == TRUE.

maxbuttressheight

Numeric value (default=7). Parameter of the dab_pc function used to calculate the diameter at breast height. Only relevant when buttress == TRUE.

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 with dbh_pc. 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. Only relevant when buttress == FALSE.

arc_min_length_cm

Optional numeric. Minimum arc length, in centimetres, represented by one angular sector when calculating arc coverage with dbh_pc. If supplied, this is converted to degrees based on the fitted radius. Only relevant when buttress == FALSE.

arc_min_angle

Numeric. Minimum angular sector width in degrees used to calculate arc coverage with dbh_pc. Default is 18, corresponding to 20 sectors. Only relevant when buttress == FALSE.

arc_tolerance

Numeric. Radial tolerance, in metres, around the fitted DBH circle. Points within radius +/- arc_tolerance are counted as supporting the fitted circle when calculating arc coverage with dbh_pc. Only relevant when buttress == FALSE.

min_inner_buffer

Numeric. Minimum buffer distance, in metres, excluded from the fitted DBH radius before checking whether the inner circle is empty with dbh_pc. Only relevant when buttress == FALSE.

inner_buffer_fraction

Numeric. Fraction of the fitted DBH radius used as buffer before checking whether the inner circle is empty with dbh_pc. The effective buffer is max(min_inner_buffer, inner_buffer_fraction * radius). Only relevant when buttress == FALSE.

plot

Logical (default=FALSE), indicates if the classified tree is plotted.

plotcolors

list of two colors for plotting. Only relevant when plot = TRUE. The crown and trunk are colored by the first and second element of this list respectively.

Value

List with data.frame with the crown point cloud (part of the tree above the first branch) in crownpoints and data.frame with the trunk point cloud in trunkpoints. Also optionally (plot=TRUE) plots the crown vs non-crown points and in this case returns a list with the crown point cloud as first element, trunk point clouds as a second element and the plots as the third to fifth elements.

Details

The classification is based on the increased distance between the minimum and maximum X (and Y) coordinates of the tree points within a horizontal slice when the first branch is reached with increasing height. 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 extract the crown points
pc_tree <- read_tree_pc(PC_path = "path/to/point_cloud.txt")
crown_pc <- classify_crown_pc(pc = pc_tree)
# and plot the classification results
output <- classify_crown_pc(pc = pc_tree, plot = TRUE)
crown_pc <- output$crownpoints
# with non-default settings for a buttressed tree
crown_pc <- classify_crown_pc(pc = pc_tree, minheight = 4, buttress = TRUE)
} # }