Save figures of classify_crown_pc function

Classifies the tree point clouds into crown and non crown points and saves the figures with classify_crown_pc for multiple tree point clouds in a folder. Use different values for the thresholdbranch and minheight parameter to optimise the crown classification for your tree point clouds. Mainly minheight parameter needs to be optimised, small values (e.g

1. when the trees don't have buttresses and higher values (e.g 4) for trees with buttresses. For buttressed trees, first optimise the thresholdbuttress and maxbuttressheight parameter values using plot_dab_fit_pcs and use those optimised values in this function.

Usage

plot_crown_classification_pcs(
  PCs_path,
  extension = ".txt",
  OUT_path = "./",
  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,
  plotcolors = c("#08aa7c", "#fac87f")
)

Arguments

PCs_path

A character with the path to the folder that contains the tree point clouds.

extension

A character refering to the file extension of the point cloud files (default=".txt"). Can be ".txt", ".ply" or ".las".

OUT_path

A character with the path to the folder where the figures should be saved (default = current folder).

thresholdbranch

Numeric value (default=1.5) from classify_crown_pc.

minheight

Numeric value (default=1) from classify_crown_pc. The default value is based on non-buttressed trees. Choose a higher value (e.g. 4) for buttressed trees.

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 and dab_pc functions used to calculate the diameter at breast height and above buttresses.

thresholdbuttress

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

maxbuttressheight

Numeric value (default=7). Parameter of the dab_pc function used to calculate the diameter above buttresses which is used in classify_crown_pc. 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 (default = NA), parameter of tree_height_pc.

r

Numeric value (default=5) r, parameter of tree_height_pc. Only relevant if a dtm is provided.

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

Returns a list with the plots and individual plots saved in the output folder.

Details

Uses read_tree_pc to read the point clouds and classify_crown_pc with parameter plot = TRUE to classify the tree point cloud and plot the classification.

Examples

if (FALSE) {
# Run the crown classification with default settings and save figures
plot_crown_classification_pcs(
  PCs_path = "path/to/folder/PCs/",
  extension = ".txt",
  OUT_path = "path/to/figure/folder/"
)
# Run the crown classification with non-default settings and save figures
plot_crown_classification_pcs(
  PCs_path = "path/to/folder/PCs/",
  extension = ".txt",
  OUT_path = "path/to/figure/folder/",
  thresholdbranch = 2, minheight = 4
)
# Run the crown classification with non-default settings and save figures
# for buttressed trees
plot_crown_classification_pcs(
  PCs_path = "path/to/folder/PCs/",
  extension = ".txt",
  OUT_path = "path/to/figure/folder/",
  thresholdbranch = 2, minheight = 4,
  buttress = TRUE, thresholdbuttress = 0.002,
  maxbuttressheight = 5
)
}