Package: CspStandSegmentation 0.2.0

Julian Frey

CspStandSegmentation: Comparative Shortest Path Forest Stand Segmentation from LiDAR Data

Functionality for segmenting individual trees from a forest stand scanned with a close-range (e.g., terrestrial or mobile) laser scanner. The complete workflow from a raw point cloud to a complete tabular forest inventory is provided. The package contains several algorithms for detecting tree bases and a graph-based algorithm to attach all remaining points to these tree bases. It builds heavily on the 'lidR' package. A description of the segmentation algorithm can be found in Larysch et al. (2025) <doi:10.1007/s10342-025-01796-z>.

Authors:Julian Frey [aut, cre], Zoe Schindler [ctb], Katja Kröner [ctb]

CspStandSegmentation_0.2.0.tar.gz
CspStandSegmentation_0.2.0.tar.gz(r-4.7-arm64)CspStandSegmentation_0.2.0.tar.gz(r-4.7-x86_64)CspStandSegmentation_0.2.0.tar.gz(r-4.6-arm64)CspStandSegmentation_0.2.0.tar.gz(r-4.6-x86_64)
CspStandSegmentation_0.2.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
CspStandSegmentation/json (API)
NEWS

# Install 'CspStandSegmentation' in R:
install.packages('CspStandSegmentation', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/julfrey/cspstandsegmentation/issues

Uses libs:
  • openblas– Optimized BLAS
  • c++– GNU Standard C++ Library v3
  • openmp– GCC OpenMP (GOMP) support library

On CRAN:

Conda:

openblascppopenmp

2.00 score 7 scripts 152 downloads 22 exports 67 dependencies

Last updated from:0326c84887. Checks:6 OK. Indexed: no.

TargetResultTimeFilesSyslog
linux-devel-arm64OK216
linux-devel-x86_64OK226
source / vignettesOK216
linux-release-arm64OK227
linux-release-x86_64OK244
wasm-releaseOK198

Exports:add_geometryadd_las_attributesadd_voxel_coordinatescomparative_shortest_pathcsp_cost_segmentationeigen_decompositionfast_unlistfast_unlist_distfdsfind_base_coordinates_geomfind_base_coordinates_rasterforest_inventoryforest_inventory_simplelas_mergep_distp_mat_distplot_inventorypoint_center_anglepoint_circle_distanceransac_circle_fitsuppress_catvoxelize_points_mean_attributes

Dependencies:abindbase64encBHbslibcachemclassclassIntclicodetoolsconicfitcpp11data.tableDBIdbscandigestdoParallele1071evaluatefastmapfontawesomeforeachfsgeigengenericsgluehighrhtmltoolshtmlwidgetsigraphiteratorsjquerylibjsonliteKernSmoothknitrlatticelazyevallidRlifecyclemagrittrMASSMatrixmemoisemimeparallellypkgconfigpracmaproxyR6rappdirsRcppRcppArmadilloRCSFrglrlangrlasrmarkdowns2sasssfstarsterratinytexunitsvctrswkxfunyaml

Readme and manuals

Help Manual

Help pageTopics
Add geometric features to a LAS objectadd_geometry
Add all las_attributes from las@data to the header of a las elementadd_las_attributes
Add voxel coordinates to a las fileadd_voxel_coordinates
helper function for csp_cost_segemntationcomparative_shortest_path
Comparative Shortest Path with cost weighting tree segmentationcsp_cost_segmentation
Fast Eigenvalues decomposition for k nearest neighbors using a C++ functioneigen_decomposition
helper function to unlist IDs generated by dbscan::frNNfast_unlist
helper function to unlist distances computed by dbscan::frNNfast_unlist_dist
Farthest Distance Sampling (Farthest Point Sampling)fds
Find stem base position using a geometric feature filtering and clustering approachfind_base_coordinates_geom
Find stem base position using a density raster approachfind_base_coordinates_raster
Function to perform a forest inventory based on a segmented las object (needs to contain TreeID)forest_inventory
Function to perform a forest inventory based on a segmented las object (needs to contain TreeID) This version is a faster but more simplistic approach than forest_inventory() for the DBH estimatesforest_inventory_simple
Makes one las-object from multiple las-objectslas_merge
Point distance functionp_dist
Point distance functionp_mat_dist
Function to plot the inventory results into a lidR 3d plot of the point cloudplot_inventory
Returns the angle between the center of the circle and a point in degreespoint_center_angle
Helper function to compute distances from a point to the circlepoint_circle_distance
RANSAC circle fitting algorithm specially adapted for tree DBH estimationransac_circle_fit
Suppress only the cat() outputsuppress_cat
helper function to voxelize a las elementvoxelize_points_mean_attributes