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triplclust

R package providing an interface to the TriplClust algorithm for 3D point-cloud clustering.

Build & Install

From the subdirectory r-package of the repository root, build the source tarball with:

bash ./makecrandist.sh

This creates the source tarball triplclust_*.*.*.tar.gz that is installed with

R CMD INSTALL triplclust_*.*.*.tar.gz

Basic usage

The main function is triplclust that accepts an n x 3 numeric matrix and returns a triplclust object with four entries: the input points (points), the assigned clusters per point as a list labels of the same length as nrow(points), the parameters of the run (params) and the merge distances of the triplet clustering (cdist). A point may occur in multiple clusters; points absent from every cluster have an empty numeric label vector.

params is a named list of the parameters of the run. A parameter given as a multiple of dNN appears twice: under its plain name is the requested value and its _dnn flag is TRUE (for example r is 2 and r_dnn is TRUE for "2dNN"), while the same name with the suffix _real holds the absolute value that was actually used. So params$r_real is the resulting smoothing radius and params$dnn_real the characteristic length it was derived from. The _real entries are resolved during the run and are only reported for debugging and reproducibility. The meaning of every entry is documented in ?triplclust.

cdist is a numeric vector with the distance of each of the n-1 merge steps of the triplet clustering, i.e. the heights of the dendrogram in ascending order. These are the same values the command line version writes to debug_cdist.csv with -vv; plot_threshold(tc) returns that file content as a string, without writing it.

Here is an example how to apply triplclust to the included dataset attpc:

library(triplclust)
tc <- triplclust(attpc)

# visualization with rgl
colors <- label_colors(tc)
library(rgl)
plot3d(tc$points, col=colors)

# visualization with external software gnuplot
save_gnuplot(tc, "/tmp/tc.gnuplot")
system("gnuplot -persist /tmp/tc.gnuplot")

# save result as CSV file
save_csv(tc, "result.csv")

# show cluster distances during hierarchical clustering and chosen threshold
plot_threshold(tc)

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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