Stem branch distance TreeQSM — stem_branch_distance

Calculates the stem branch distance from a TreeQSM.

Usage

stem_branch_distance_qsm(
  cylinder,
  treedata,
  normalisation = "no",
  pc = NA,
  buttress = FALSE,
  thresholdR2 = 0.001,
  slice_thickness = 0.06,
  thresholdbuttress = 0.001,
  maxbuttressheight = 7,
  concavity = 4,
  dtm = NA,
  r = 5
)

Arguments

cylinder: Cylinder field of a TreeQSM that is returned by read_tree_qsm.
treedata: Treedata field of a TreeQSM that is returned by read_tree_qsm.
normalisation: Can either be "dbh" or nothing. In case of "dbh" the average distance is divided by the DBH (Akerblom et al., 2017).
pc: The tree point cloud as a data.frame with columns X,Y,Z. Output of read_tree_pc. Default is NA and indicates no tree point cloud is available. Only relevant if normalisation equals "dbh".
buttress: Logical (default=FALSE), indicates if the trees have buttresses. Only relevant if pc is available and normalisation equals "dbh".
thresholdR2: Numeric value (default=0.001). Parameter of the dbh_pc function used to calculate the diameter at breast height. Only relevant if the tree point cloud is available and 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. Only relevant if the tree point cloud is available.
thresholdbuttress: Numeric value (default=0.001). Parameter of the dab_pc function used to calculate the diameter above buttresses. Only relevant if the tree point cloud is available and buttress == TRUE.
maxbuttressheight: Numeric value (default=7). Parameter of the dab_pc function used to calculate the diameter at breast height. Only relevant if the tree point cloud is available and buttress == TRUE.
concavity: Numeric value (default=4) concavity for the computation of the functional diameter using a concave hull based on concaveman. only relevant when a point cloud is provided.
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. only relevant when a point cloud is provided.
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.

Value

The stem branch distance. Unitless with normalisation, in meters without normalisation. NaN when there are no stem branches.

Details

The stem branch distance is defined as "Average distance between 1st order branches computed using a moving average with a window width 1 m. If window is empty average distance in window is set as half of window width. Can be normalised by the DBH" (Akerblom et al., 2017 & Terryn et al., 2020). When something different than "dbh" is given, no normalisation is done. Default is no normalisation. DBH is calculated with dbh.

References

Akerblom, M., Raumonen, P., Makipaa, R., & Kaasalainen, M. (2017). Automatic tree species recognition with quantitative structure models. Remote Sensing of Environment, 191, 1-12.

Terryn, L., Calders, K., Disney, M., Origo, N., Malhi, Y., Newnham, G., ... & Verbeeck, H. (2020). Tree species classification using structural features derived from terrestrial laser scanning. ISPRS Journal of Photogrammetry and Remote Sensing, 168, 170-181.

Examples

if (FALSE) {
# Read tree qsm and calculate the stem branch distance
# from Akerblom et al. (2017)
qsm <- read_tree_qsm(QSM_path = "path/to/qsm.mat")
sbd <- stem_branch_distance_qsm(
  cylinder = qsm$cylinder,
  treedata = qsm$treedata,
  normalisation = "dbh"
)
# with point cloud data for buttressed trees
pc <- read_tree_pc(PC_path = "path/to/point_cloud.txt")
sbd <- stem_branch_distance_qsm(
  cylinder = qsm$cylinder,
  treedata = qsm$treedata,
  normalisation = "dbh", pc = tree_pc,
  buttress = TRUE
)
# from Terryn et al. (2020)
sbd <- stem_branch_distance_qsm(
  cylinder = qsm$cylinder,
  treedata = qsm$treedata,
  normalisation = "no"
)
}