Package: CspStandSegmentation 0.2.0

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.zip(r-4.7)CspStandSegmentation_0.2.0.zip(r-4.6)CspStandSegmentation_0.2.0.zip(r-4.5)
CspStandSegmentation_0.2.0.tgz(r-4.6-x86_64)CspStandSegmentation_0.2.0.tgz(r-4.6-arm64)CspStandSegmentation_0.2.0.tgz(r-4.5-x86_64)CspStandSegmentation_0.2.0.tgz(r-4.5-arm64)
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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://julfrey.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

5.58 score 27 stars 6 scripts 171 downloads 24 exports 69 dependencies

Last updated from:69ac1ba9c8. Checks:13 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64OK297
linux-devel-x86_64OK285
source / vignettesOK285
linux-release-arm64OK309
linux-release-x86_64OK239
macos-release-arm64OK247
macos-release-x86_64OK326
macos-oldrel-arm64OK256
macos-oldrel-x86_64OK600
windows-develOK235
windows-releaseOK322
windows-oldrelOK237
wasm-releaseOK201

Exports:add_geometryadd_las_attributesadd_voxel_coordinatescolor_idscomparative_shortest_pathcsp_cost_segmentationeigen_decompositionfast_unlistfast_unlist_distfdsfind_base_coordinates_geomfind_base_coordinates_rasterforest_inventoryforest_inventory_simpleget_pallas_mergep_distp_mat_distplot_inventorypoint_center_anglepoint_circle_distanceransac_circle_fitsuppress_catvoxelize_points_mean_attributes

Dependencies:abindbase64encBHbslibcachemclassclassIntclicodetoolscolorspaceconicfitcpp11data.tableDBIdbscandigestdoParallele1071evaluatefastmapfontawesomeforeachfsgeigengenericsgluehighrhtmltoolshtmlwidgetsigraphiteratorsjquerylibjsonliteKernSmoothknitrlatticelazyevallidRlifecyclemagrittrMASSMatrixmemoisemimeparallellypkgconfigpracmaproxyR6RANNrappdirsRcppRcppArmadilloRCSFrglrlangrlasrmarkdowns2sasssfstarsterratinytexunitsvctrswkxfunyaml

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
Assign colours to instances in a LAS object using a graph-colouring heuristiccolor_ids
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
Return a palette-generating functionget_pal
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