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Calculate tree and plot metrics from a classified LAS file

Source: R/metrics_from_las.R
metrics_from_las.Rd

Recalculates tree-level and plot-level metrics starting from a classified LAS file. Intended for use after manual correction of an automatic classification produced by Forest_seg.

Wood points (class 4) are re-clustered into individual trees using DBSCAN with fixed, permissive parameters (5 cm voxels, eps = 2, minPts = 5). These parameters are intentionally loose because the classification is already trusted; DBSCAN here only separates spatially distinct trunks.

Tree height is computed as the difference between the tree base elevation (minimum z of the wood cluster) and the maximum z of any point in the full cloud within a 0.5 m XY buffer around the tree base, consistent with the Forest_seg approach.

Crown Base Height (CBH) is calculated with the GAB (Geometrical Aggregation of Biomass) Voronoi method, identical to Forest_seg.

Output CSV files use the same column layout as Forest_seg reports.

Usage

metrics_from_las(
  las_file,
  output_path = NULL,
  filename = NULL,
  dbh_tolerance = 0.05,
  dbh_max_rmse = 5,
  dbh_min_radius = 0.025,
  dbh_max_radius = 0.8,
  calculate_cbh = TRUE,
  cbh_hex_side = 0.15,
  cbh_min_branch_length = 2,
  canopy_vox_dim = 0.15,
  canopy_min_density = 100,
  generate_reports = TRUE
)

Arguments

las_file

Character. Path to the classified LAS file.

output_path

Character. Directory for output files. Default: same directory as las_file.

filename

Character. Prefix for output file names. Default: derived from las_file (stripping _classified).

dbh_tolerance

Vertical half-width of the DBH slice in metres (default = 0.05).

dbh_max_rmse

Maximum acceptable RMSE for circle fit in cm (default = 5).

dbh_min_radius

Minimum valid stem radius in metres (default = 0.025).

dbh_max_radius

Maximum valid stem radius in metres (default = 0.8).

calculate_cbh

Logical. If TRUE, calculate Crown Base Height using the GAB method (default = TRUE). Requires crown points (class 5).

cbh_hex_side

Hexagonal cell side length in metres for GAB (default = 0.15).

cbh_min_branch_length

Minimum horizontal foliage extent in metres to consider a branch valid for CBH (default = 2.0).

canopy_vox_dim

Voxel size in metres for crown and wood voxelisation used in GAB CBH (default = 0.15).

canopy_min_density

Minimum point density in pts/m\(^3\) used to derive the minimum points per hex cell for GAB (default = 100).

generate_reports

Logical. If TRUE (default), saves <filename>_tree_report.csv and <filename>_plot_report.csv.

Value

Invisibly returns a named list:

tree_metrics

data.table with one row per detected tree.

plot_stats

data.frame with plot-level aggregate metrics.

tree_report

Path to the tree-level CSV, or NULL.

plot_report

Path to the plot-level CSV, or NULL.

LAS classification codes expected

  • 2 = Ground / forest floor (convex hull for plot area)

  • 3 = Understory

  • 4 = Wood (re-clustered into individual trees)

  • 5 = Crown / foliage (used for height buffer and CBH)

  • 6 = Non-valid trees (ignored)

  • 7 = Noise (ignored)

See also

Forest_seg, SegOne