Terrestrial lidar data collected from four large tropical rainforest trees in Floresta Nacional de Caxiuanã

Title
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Terrestrial lidar data collected from four large tropical rainforest trees in Floresta Nacional de Caxiuanã

Authors
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A. Burt
M. Boni Vicari
A. C. L. da Costa
I. Coughlin
P. Meir
L. Rowland
M. Disney

Contact
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a.burt@ucl.ac.uk

License
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These data are distributed under the terms of the Creative Commons Attribution 4.0 International Public License (CC BY 4.0) - see the LICENSE file for details.

Overview
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Terrestrial lidar data were acquired from four large tropical rainforest trees prior to harvest (diameter range: 0.6-1.2m, height range: 30-46m) in a natural closed forest stand in Floresta Nacional de Caxiuanã, Pará, Brazil (approx. coordinates in the WGS-84 datum: -1.798, -51.435 degrees), during August/October 2018.
This dataset includes: i) raw lidar data, ii) tree-level point clouds, and iii) quantitative structural models.
A complete description of the four trees, these data, and the companion destructive harvest data can be found in our paper entitled: ‘New insights into large tropical tree mass and structure from direct harvest and terrestrial lidar’.

Acquisition
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Neighbouring vegetation surrounding each tree was removed before data collection.
Lidar data were acquired using a RIEGL VZ-400 terrestrial laser scanner.
A minimum of 16 scans (upright and tilt) were collected from 8 scan positions around each tree.
The angular step between sequentially fired pulses was 0.04 degrees, and the distance between scanner and tree varied.
This arrangement provided a 45 degree sampling arc around each tree, and a complete sample of the scene from each position.
The laser pulse has a wavelength of 1550nm, a beam divergence of 0.35mrad, and the diameter of the footprint at emission is 7mm.
The instrument was in ‘High Speed Mode’ (pulse repetition rate: 300kHZ), ‘Near Range Activation’ was off (minimum measurement range: 1.5m), and waveforms were not stored. 

Processing
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i) Individual scans were registered onto a common coordinate system using RIEGL RiSCAN PRO (v2.7.0, http://riegl.com).
ii) Tree-level point clouds were extracted from the larger-area point cloud using treeseg (v0.2.0, https://github.com/apburt/treeseg).
iii) Points were classified as returns from wood or leaf material using TLSeparation (v1.2.1.5, https://github.com/TLSeparation).
iv) Points from buttresses were manually removed using CloudCompare (v2.10.3, https://cloudcompare.org).
v) Quantitative structural models were constructed using TreeQSM (v2.3.2, https://github.com/InverseTampere/TreeQSM) via optqsm (v0.1.0, https://github.com/apburt/optqsm). 

File and directory naming convention
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The four trees are identified: CAX-H_T1, CAX-H_T2, CAX-H_T3 and CAX-H_T4.
The various files and directories are described as follows: 

./CAXH-H/
├───CAX-H_T1/                    (Directory: tree-level directories)
├───CAX-H_T2/
├───CAX-H_T3/
├───CAX-H_T4/
│   ├───2018-10-06.001.riproject/
│   │   ├───ScanPos001/                (Directory: individual scan directories containing raw lidar data and other auxiliary files; odd: upright, even: tilt)
│   │   ├───ScanPos.../
│   │   ├───ScanPos020/
│   │   │   ├───181006_194253.rxp            (File: measurement data stream)
│   │   │   ├───181006_194253.mon.rxp            (File: monitoring data stream) 
│   │   ├───matrix/                (Directory: contains the registration matrices)
│   │   │   ├───001.dat
│   │   │   ├───....dat
│   │   │   ├───020.dat                    (File: 3x4 matrix used to rotate and translate scan 20 into the coordinate system of scan 1)
│   │   ├───clouds/                (Directory: contains tree-level point clouds)
│   │   │   ├───CAXH_T4.txt                (File: point cloud of CAX-H_T4 as extracted by treeseg)
│   │   │   ├───CAXH_T4nb.txt                (File: CAXH_T4.txt with buttress points manually removed using CloudCompare)
│   │   │   ├───CAXH_T4w.txt                (File: CAXH_T4.txt with leafy returns removed using TLSeparation)
│   │   │   ├───CAXH_T4l.txt                (File: CAXH_T4.txt with woody returns removed using TLSeparation)
│   │   │   ├───CAXH_T4wnb.txt                (File: CAXH_T4.txt with buttress points manually removed using CloudCompare, and leafy returns removed using TLSeparation)
│   │   ├───models/                (Directory: contains quantitative structural models constructed from the tree-level point clouds)
│   │   │   ├───CAXH_T4.mat                (File: quantitative structural model of CAXH_T4.txt)
│   │   │   ├───CAXH_T4nb.mat
│   │   │   ├───CAXH_T4w.mat
│   │   │   ├───CAXH_T4wnb.mat
│   │   │   ├───CAXH_T4.models.dat            (File: reports the volume (m3) and standard deviation (m3) of the QSMs)
│   │   │   ├───intermediate/            (Directory: contains intermediate QSMs generated by optqsm)
│   │   │   │   ├───CAXH_T4/
│   │   │   │   ├───CAXH_T4nb/
│   │   │   │   ├───CAXH_T4w/
│   │   │   │   ├───CAXH_T4wnb/
│   │   │   │   │    ├───CAXH_T4wnb-1.mat
│   │   │   │   │    ├───CAXH_T4wnb-....mat
│   │   │   │   │    ├───CAXH_T4wnb-10.mat