plot_circle_fit_pcs: Calculate and save figures of 'diameter_slice_pc' function

In lmterryn/ITSMe: Individual Tree Structural Metrics

Calculate and save figures of diameter_slice_pc function

Description

Calculates the diameter and saves the figures acquired when running diameter_slice_pc on multiple tree point clouds in a folder.

Usage

plot_circle_fit_pcs(
  PCs_path,
  extension = ".txt",
  slice_height = 1.3,
  slice_thickness = 0.06,
  functional = TRUE,
  concavity = 4,
  dtm = NA,
  r = 5,
  OUT_path = "./",
  plotcolors = c("#000000", "#1c027a", "#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".
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. Parameter of the diameter_slice_pc function used to calculate the diameter of a stem slice.
slice_thickness	Numeric value (default = 0.6) that determines the thickness of the slice which is used to measure the diameter. Parameter of the diameter_slice_pc function used to calculate the diameter of a stem slice.
functional	Logical (default=FALSE), indicates if the functional diameter should be calculated.
concavity	Numeric value (default=2) 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.
OUT_path	A character with the path to the folder where the figures should be saved (default = current folder).
plotcolors	list of three 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.

Details

Uses read_tree_pc to read the point clouds and diameter_slice_pc with parameter plot = TRUE to calculate the diameter and plot the circle fitting.

Value

A list with in the first element a numeric containing the diameter values for each tree point cloud, the second element the residuals on the circle fittings, the third element the functional diameters. In the fourth element there is the list with the plots. Figures are also saved in the output folder.

Examples

## Not run: 
# Calculate diameters at breast height (1.3m) and save circle fitting figures
diam_values <- plot_circle_fit_pcs(
  PCs_path = "path/to/folder/PCs/",
  extension = ".txt",
  OUT_path = "path/to/figure/folder/"
)
# Calculate diameters at 2.5 m with a slice of 20 cm and save the figures
diam_values <- plot_circle_fit_pcs(
  PCs_path = "path/to/folder/PCs/",
  extension = ".txt", slice_height = 2.5,
  slice_thickness = 0.2,
  OUT_path = "path/to/figure/folder/"
)

## End(Not run)

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