lidR: dalponte2016 – R documentation

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dalponte2016

Individual Tree Segmentation Algorithm

Description

This function is made to be used in segment_trees. It implements an algorithm for tree segmentation based on the Dalponte and Coomes (2016) algorithm (see reference). This is a seeds + growing region algorithm. This algorithm exists in the package itcSegment. This version has been written from the paper in C++. Consequently it is hundreds to millions times faster than the original version. Note that this algorithm strictly performs a segmentation, while the original method as implemented in itcSegment and described in the manuscript also performs pre- and post-processing tasks. Here these tasks are expected to be done by the user in separate functions.

Usage

dalponte2016(
  chm,
  treetops,
  th_tree = 2,
  th_seed = 0.45,
  th_cr = 0.55,
  max_cr = 10,
  ID = "treeID"
)

Arguments

`chm`	RasterLayer. Image of the canopy. Can be computed with grid_canopy or read from an external file.
`treetops`	`SpatialPointsDataFrame`. Can be computed with find_trees or read from an external shapefile.
`th_tree`	numeric. Threshold below which a pixel cannot be a tree. Default is 2.
`th_seed`	numeric. Growing threshold 1. See reference in Dalponte et al. 2016. A pixel is added to a region if its height is greater than the tree height multiplied by this value. It should be between 0 and 1. Default is 0.45.
`th_cr`	numeric. Growing threshold 2. See reference in Dalponte et al. 2016. A pixel is added to a region if its height is greater than the current mean height of the region multiplied by this value. It should be between 0 and 1. Default is 0.55.
`max_cr`	numeric. Maximum value of the crown diameter of a detected tree (in pixels). Default is 10.
`ID`	character. If the `SpatialPointsDataFrame` contains an attribute with the ID for each tree, the name of this attribute. This way, original IDs will be preserved. If there is no such data trees will be numbered sequentially.

Details

Because this algorithm works on a CHM only there is no actual need for a point cloud. Sometimes the user does not even have the point cloud that generated the CHM. lidR is a point cloud-oriented library, which is why this algorithm must be used in segment_trees to merge the result with the point cloud. However the user can use this as a stand-alone function like this:

chm = raster("file/to/a/chm/")
 ttops = find_trees(chm, lmf(3))
 crowns = dalponte2016(chm, ttops)()

References

Dalponte, M. and Coomes, D. A. (2016), Tree-centric mapping of forest carbon density from airborne laser scanning and hyperspectral data. Methods Ecol Evol, 7: 1236–1245. doi:10.1111/2041-210X.12575.

Examples

LASfile <- system.file("extdata", "MixedConifer.laz", package="lidR")
las <- readLAS(LASfile, select = "xyz", filter = "-drop_z_below 0")
col <- pastel.colors(200)

chm <- grid_canopy(las, 0.5, p2r(0.3))
ker <- matrix(1,3,3)
chm <- raster::focal(chm, w = ker, fun = mean, na.rm = TRUE)

ttops <- find_trees(chm, lmf(4, 2))
las   <- segment_trees(las, dalponte2016(chm, ttops))
#plot(las, color = "treeID", colorPalette = col)

lidR

Airborne LiDAR Data Manipulation and Visualization for Forestry Applications

v3.1.2

GPL-3

Authors

Jean-Romain Roussel [aut, cre, cph], David Auty [aut, ctb] (Reviews the documentation), Florian De Boissieu [ctb] (Fixed bugs and improved catalog features), Andrew Sánchez Meador [ctb] (Implemented wing2015() for segment_snags()), Bourdon Jean-François [ctb] (Contributed to Roussel2020() for track_sensor()), Gatziolis Demetrios [ctb] (Implemented Gatziolis2019() for track_sensor())

Initial release

2021-03-11