treeseg

Extract individual trees from lidar point clouds

Overview

treeseg has been developed to near-automatically extract tree-level point clouds from high-density larger-area lidar point clouds acquired in forested scenes. A full description of the methods can be found here: http://discovery.ucl.ac.uk/1575534/ (pp. 96-167)

Briefly, libtreeseg provides a set of generic functions that have been wrapped here into a series of executables to: i) identify individual stems in the larger-area point cloud (findstems), ii) extract each of these identified stems up to the first order of branching (segmentstem), and iii) segment each individual crown from neighbouring vegetation (segmentcrown).

Integrated into treeseg is libleafsep, a library providing methods to separate wood and leaf returns in unorganised point clouds. libleafsep is a modified translation of TLSeparation (https://github.com/TLSeparation).

Prerequisites

treeseg has been developed using:

Point Cloud Library (PCL) (http://pointclouds.org) (v1.7 or later)
Armadillo (http://arma.sourceforge.net) (v7.960 or later)

On RHEL 7, these dependencies can be installed via:

yum install cmake
yum install pcl pcl-devel pcl-tools pcl-doc
yum install armadillo armadillo-devel

On Ubuntu:

apt-get install -y git cmake
apt-get install -y libpcl-dev
apt-get install -y libproj-dev

On macOS 10.13, dependencies are perhaps most easily installed via Homebrew (https://brew.sh):

brew install cmake
brew install pcl
brew install armadillo

Installation

Install libtreeseg and the associated binaries as follows:

git clone https://github.com/apburt/treeseg.git;
cd treeseg;
mkdir build;
cd build;
cmake ../src;
make;

Also included in treeseg is rxp2pcd, for conversion of REIGL V-Line scan data to .pcd binary format. Linux-only, this requires the RiVLIB headers and libraries (downloadable from: http://www.riegl.com/index.php?id=224) to be installed in /treeseg/include/riegl/ and /treeseg/lib/ respectively.

Usage

Below is an example usage of the treeseg binaries:

plotcoords ../matrix/ > nouragesH20_coords.dat
rxp2pcd ../ nouraguesH20_coords.dat 60 15 nouraguesH20
nearestneighbour 1 4 nouraguesH20.sample.pcd > nouraguesH20_nn.dat
downsample 0.04 1 nouraguesH20_*.pcd
getdemslice 2 3 6 nouraguesH20_*.downsample.pcd
findstems 15 0.2 2 ../nouraguesH20_coords.dat ../nouraguesH20.slice.downsample.pcd
segmentstem 12.5 ../nouraguesH20.downsample.pcd ../clusters/cluster_*.pcd
getcrownvolume ../nouraguesH20.downsample.pcd ../stems/stem_*.pcd
segmentcrown [14 - 16] ../volume_*.pcd

Authors

Andrew Burt
Mathias Disney
Kim Calders
Matheus Boni Vicari

License

This project is licensed under the MIT License - see the LICENSE file for details

Acknowledgements

treeseg makes use of the Point Cloud Library (PCL) (http://pointclouds.org) and Armadillo (http://arma.sourceforge.net).
AB was supported by NERC CASE PhD NE/J016926/1 with EADS Astrium; additional funding was via the NERC National Centre for Earth Observation (NCEO), NERC funding awards NE/N00373X/1, NE/P011780/1 and NE/K002554/1; MD is also supported by the EU Horizon2020 project (BACI project funded by the EU's Horizon 2020 Research and Innovation Programme under grant agreement 640176).

philwilkes/treeseg