TreeGraph

Treegraph is a Python library for extracting structural parameters from terrestrial LiDAR point clouds of individual trees.

Usage

File structure

It is assumed the following folders have been created:

treegraph_tutorial/
├── clouds/
│   └── <individual tree point clouds in .ply format>
├── inputs/
│   └── <input parameters files for individual trees created by generate_inputs.py>
└── results/
    └── <outputs from treegraph generated by tree2qsm.py>

Generate input files

Required input args are the path for input data and outputs. More optional input args see treegraph/scripts/generate_inputs.py.

conda activate treegraph
cd treegraph_tutorial/inputs/
python /PATH/TO/treegraph/scripts/generate_inputs.py -d '/PATH/TO/clouds/*.ply' -o '/PATH/TO/results/'

Run Treegraph

Option 1: Run on a single tree

python treegraph/script/tree2qsm.py -i 'inputs/XXX.yml'

Option 2: Run all the trees one after another:

python treegraph/script/batch_tree2qsm.py -i 'inputs/*.yml'

Option 3: Batch process on HPC

Example job_script.sh for SLURM system

#!/bin/bash 
# scheduling queue
#SBATCH --partition=high-mem
# max runtime limit
#SBATCH --time=10:00:00
# job name
#SBATCH --job-name=treegraph
# job output and error output
#SBATCH --output %j.out 
#SBATCH --error %j.err
# required memory, unit MB
#SBATCH --mem=102400
# working dir 
#SBATCH -D /PATH/TO/OUTPUTS/
# Number of CPU cores
#SBTACH -n 1

# executable 
conda activate treegraph
echo "python ~/miniconda3/envs/treegraph/lib/python3.7/treegraph/scripts/tree2qsm.py -i '$tree'"
python ~/miniconda3/envs/treegraph/lib/python3.7/treegraph/scripts/tree2qsm.py -i "${tree}"