Orange tree canopy volume estimation by manual and LiDAR-based methods

Abstract

LiDAR ( Light detection and ranging ) technology is an alternative to current manual methods of canopy geometry estimations in orange trees. The objective of this work was to compare different types of canopy volume estimations of orange trees, some inspired on manual methods and others based on a LiDAR sensor. A point cloud was generated for 25 individual trees using a laser scanning system. The convex-hull and the alpha-shape surface reconstruction algorithms were tested. LiDAR derived models are able to represent orange trees more accurately than traditional methods. However, results differ significantly from the current manual method. In addition, different 3D modeling algorithms resulted in different canopy volume estimations. Therefore, a new standard method should be developed and established.

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This document is the preprint of the full paper presented at the 11th European Conference on Precision
Agriculture – ECPA and is to be published at the journal Advances in Animal Biosciences Volume 8 Issue 2
with DOI: http://dx.doi.org/10.1017/S2040470017001133.
Orange tree canopy volume estimation by manual and LiDAR-based methods
A. F. Colaço1*; R. G. Trevisan1; J. P. Molin1, J. R. Rosell-Polo2; A. Escolà2
1. University of São Paulo, ‘Luiz de Queiroz’ College of Agriculture, Biosystems Engineering
Department, Piracicaba-SP, Brazil;
2. University of Lleida – Agrotecnio Center, School of Agrifood and Forestry Science and
Engineering, Department of Agricultural and Forest Engineering, Research Group on
AgroICT & Precision Agriculture, Lleida - Catalonia, Spain.
*andre.colaco@usp.br
Abstract
LiDAR (Light detection and ranging) technology is an alternative to current manual methods
of canopy geometry estimations in orange trees. The objective of this work was to compare
different types of canopy volume estimations of orange trees, some based on manual methods
and others based on a LiDAR sensor. A point cloud was generated for 25 individual trees using
a laser scanning system. The convex-hull and the alpha-shape surface reconstruction algorithms
were tested. LiDAR derived models are able to represent orange trees more accurately than
traditional methods. However, results differ significantly from the current manual method. In
addition, different 3D modeling algorithms resulted in different canopy volume estimations.
Therefore, a new standard method should be developed and established.
Keywords: tree crops; laser scanner; convex-hull; alpha-shape; citrus
Introduction
Canopy volume is an indicator of growth, health and yield potential in tree crops. It is also used
for estimating sparing and fertilizer requirements. The current methods for canopy volume
estimation in Brazilian orange groves are quite simplistic. One of the most used considers the
tree volume as the volume of a cube enclosing the whole tree. Each side of such a cube is
measured manually with a measuring tape. Besides its inaccuracy, the manual method is time
consuming and requires a significant number of sampled trees for an adequate representation
of the whole grove.
One alternative for the manual method is the ranging sensor (Dworak et al, 2011). Such
technology permits not only a higher accuracy on the estimation of canopy geometric
parameters but also higher amount of collected data. These data can be georeferenced and
acquired throughout the entire field in order to characterize spatial variability. Once spatial
variability of canopy volume is known, inputs can be applied in a variable-rate approach
according to the tree size variation. Such applications can be carried out at the same time as
sensor readings are acquired (i.e in “real time”) (Escolà et al. 2013). For these reasons, ranging
sensors meet the needs of precision horticulture and represent great potential to enhance
management in tree crops.
Two types of ranging sensors are mostly investigated in research, the ultrasonic and the LiDAR
(Light detection and ranging) sensors. These sensors are usually mounted facing the side of the
tree row being able to estimate the distance to the vegetation at different heights along the
canopy. LiDAR sensors are considered a better solution than ultrasonic sensors because they

This document is the preprint of the full paper presented at the 11th European Conference on Precision
Agriculture – ECPA and is to be published at the journal Advances in Animal Biosciences Volume 8 Issue 2
with DOI: http://dx.doi.org/10.1017/S2040470017001133.
are usually more accurate, more rapid, and permit distance measurements in multiple directions
from one single sensor.
In the past decade, research has developed data acquisition and processing methods based on
LiDAR technology aiming at providing 3D models of trees and retrieve canopy volume
information (Rosell and Sanz, 2012). Rosell et al. (2009) described a mobile terrestrial laser
scanner (MTLS) in which raw LiDAR sensor data was transformed into a 3D point cloud
representing the laser beam impacts on the canopy. Further works showed how to extract
geometric canopy information from 3D point clouds obtained by similar data acquisition
systems (Escolà et al., 2016). Different methods are available for computing canopy volume
from point clouds. Auat Cheein et al. (2015) classified such methods into two main approaches,
one referred as the occupancy grid, in which small regular sized objects are created inside the
point cloud structure; and another based on connecting the outer points of the point cloud in
order to reconstruct the shape of the object formed by the point cloud structure. Both approaches
were tested by the authors and were considered viable methods for estimating canopy volume.
Orange groves in Brazil cover approximately 500,000 ha of land (CONAB, 2013). Spray
applications are crucial operations in the management of the groves and might occur at least
once a month during the cropping season. Spraying prescriptions are currently based on manual
and poorly accurate measurements of canopy volume. Sensor-based estimation should greatly
improve the management of these groves.
The hypothesis of this work is that LiDAR-based methods for canopy geometry estimation
should be more accurate than manual methods. However, because different methods and
algorithms can be used for processing LiDAR data, different results might be achieved
evidencing the need for stablishing new standard methods of canopy volume estimation.
The objective of this work was to compare estimations of orange tree canopy volume by six
different methods; two based on traditional manual methods and four based on LiDAR
technology using different processing algorithms.
Material and Methods
Data acquisition
A mobile terrestrial laser scanner was developed based on a 2D LMS 200 LiDAR sensor (Sick,
Waldkirch, Germany) and an RTK (Real Time Kinematic) GR3 GNSS receiver (Topcon,
Tokyo, Japan). The system was mounted on an ATV vehicle as shown in Figure 1. The LiDAR
sensor collected distance values in 181 directions every 13.3 ms (75 Hz) at one-degree angular
steps along a vertical plane of the tree canopy. The vehicle moved along the two sides of the
tree row at 3.3 m s-1.
A commercial orange grove located in the state of São Paulo, Brazil, was scanned using the
developed system. 25 trees inside the grove were selected for this study. The variety of the trees
was “Valencia” grafted to “Swingle” rootstock. Trees were six years old at the time of data
acquisition (October of 2015).
Data processing
The first step of data processing consisted in creating a georeferenced 3D point cloud
representing the laser beam impacts over the canopy. Del-Moral-Martínez et al. (2015) give
details about this process. The following step is to exclude points that did not represent the
target tree canopy (soil and neighboring plants). This step was carried out using tools for
selecting and deleting points available in the CloudCompare 2.6.2 software. With the final point
cloud from each of the 25 selected trees, the next step was to compute the canopy volume. Two

This document is the preprint of the full paper presented at the 11th European Conference on Precision
Agriculture – ECPA and is to be published at the journal Advances in Animal Biosciences Volume 8 Issue 2
with DOI: http://dx.doi.org/10.1017/S2040470017001133.
types of surface reconstruction algorithms were applied, the convex-hull and the alpha-shape,
using the R software packages grDevices and the alphashape3d, respectively. Both algorithms
connect the outer points of the cloud in order to produce the surface of the enveloping object.
Unlike the convex-hull, the alpha-shape permits the creation of concave objects. The level of
concavity is given by setting the index α (lower index results in greater concavities). Three
indexes were tested: 0.25, 0.50 and 0.75.
Two types of canopy volume estimation based on traditional manual methods were also tested.
The first one, which is the most common among Brazilian orange growers, consisted in
measuring the volume of a cube that encloses the entire tree. This method is hereafter referred
as the cube-fit. The second, referred as the cylinder-fit, considered the canopy volume as two-
thirds the volume of a cylinder that encloses the tree. The dimensions of the cube and cylinder
were not measured manually as it would be normal. Instead, it was collected directly from the
point cloud using distance-measuring tools available in the CloudCompare 2.6.2 software.
Figure 1 LiDAR sensor and GNSS receiver mounted on an ATV vehicle (a); LiDAR sensor
(in blue) facing the side of the tree row (b)
Results and Discussion
After the LiDAR scanning and the point cloud generation, the average number of points
representing each tree was 12,100 distributed into approximately 60 perpendicular transects.
The 3D models from the proposed algorithms applied to a single tree are shown in Figure 2. It
is noticeable how the convex-hull model apparently produced a larger object, which occurs
because salient branches enlarges the hull structure. As expected, concavities of the canopy
were better represented by the alpha-shape algorithm. Because this algorithm permits the
representation of concave structures, it is reasonable to consider it a suitable model for
representing the tree canopy. However, the index α should be appropriately set (not too high
neither too low). A low index might produce disconnected structures forming holes inside the
canopy, which is not desirable (see alpha-shapes with α set to 0.25 and 0.50 in Figure 2). A
guideline for setting α is to choose a value that produces the smallest volume while keeping the
canopy as a whole. That result was obtained when α was set to 0.75.

This document is the preprint of the full paper presented at the 11th European Conference on Precision
Agriculture – ECPA and is to be published at the journal Advances in Animal Biosciences Volume 8 Issue 2
with DOI: http://dx.doi.org/10.1017/S2040470017001133.
Figure 2 3D canopy structure of a single tree modeled by different algorithms. Top: point
cloud section and selected single tree. Middle: Alpha shape models (left, α=0.25; right, α=0.75).
Bottom left: Alpha shape model, α=0.50. Bottom right: Convex-hull model.
The volumes for each of the 25 individual trees calculated by the proposed algorithms and by
the manual methods are showed in Figure 3. The plant IDs were given based on a rank from the
smallest to the largest tree according to the alpha-shape (α = 0.75) and convex-hull
computation. It is to be noticed that this ranking is roughly followed by all the other algorithms.
Generally, the manual methods produced a ranking with some disagreement with the other
algorithms, which indicated a certain level of randomness in the manual measurements. The
rough simplification of the canopy structure by the manual method based on the cube-fit
overestimated the canopy volume in relation to all the other algorithms. The measurements
from the cylinder-fit method were mainly close to the ones computed with the alpha-shape with
index of 0.50, but sometimes closer to index 0.75 and other to 0.25.

This document is the preprint of the full paper presented at the 11th European Conference on Precision
Agriculture – ECPA and is to be published at the journal Advances in Animal Biosciences Volume 8 Issue 2
with DOI: http://dx.doi.org/10.1017/S2040470017001133.
Figure 3 Canopy volume of 25 individual trees computed by different methods. Plant IDs
were given based on a rank from the smallest to the largest tree according to the alpha-shape
(α = 0.75) and convex-hull computation.
Table 1 shows the descriptive statistics of the measurements of the 25 orange trees. A noticeable
difference in all statistical parameters between different computation methods is evident. As
expected, the convex-hull model resulted in the highest mean canopy volume among the
proposed algorithms, followed by the alpha-shape with higher index α. The volume retrieved
from the alpha-shape with α set to 0.25 was significantly smaller than that of other algorithms,
due to disconnected structures formed by the model and significant voids inside the canopy, as
viewed in Figure 2. On the other end, the cube-fit method resulted in a significantly larger
volume than all evaluated methods. Regarding the cylinder-fit, because it considered only two
thirds of the cylinder, the final canopy volume is not as large as in the cube-fit method. The
cylinder-fit method got closer results to the alpha-shape with index of 0.5, which, as noticed in
Figure 1, produced voids inside the 3D model.
It is also noticeable from Table 1 that the manual methods presented lower coefficient of
variation than the 3D modeling algorithms, with exception to the alpha-shape with index 0.25.
That might occur because the cube-fit and cylinder-fit represent the tree using less complex
figures which are less variable and often do not represent the actual volume of the canopy, i. e.,
trees with different volume in reality might present similar volumes when these methods are
used.
Table 1 Descriptive statistics of canopy volume of 25 individual trees by different methods
Mean
St. Dev.
Min.
Max.
Range
Coef. Var.
------------------------------ m³ ----------------------------
%
α-shape (i=0.25)
6.43
2.26
1.65
12.28
10.63
35.11
α-shape (i=0.50)
12.66
5.44
2.12
24.15
22.03
42.98
α-shape (i=0.75)
14.92
6.64
2.22
26.89
24.68
44.48
Convex-hull
16.95
7.46
2.42
31.26
28.84
44.04
Manual (cylinder-fit)
12.15
4.59
2.35
22.31
19.96
37.80
Manual (cube-fit)
23.01
8.54
4.48
40.56
36.08
37.14

This document is the preprint of the full paper presented at the 11th European Conference on Precision
Agriculture – ECPA and is to be published at the journal Advances in Animal Biosciences Volume 8 Issue 2
with DOI: http://dx.doi.org/10.1017/S2040470017001133.
Conclusions
LiDAR-based methods provided more realistic representation of the canopies than current
manual methods and should be considered as a new standard for canopy volume estimations.
Important differences among the evaluated methods of canopy volume estimation in orange
trees were found. The average canopy volume retrieved by the cube-fit method (the current
practice in Brazilian orange groves) was approximately 150% larger than the volume from the
alpha-shape with 0.75 index. The alpha-shape modeling with α set to 0.75 might be considered
an adequate method since it permitted the representation of concave structures of the canopy
without creating disconnected objects or voids inside the canopy.
Manual inspired methods were less capable of representing tree size variability than LiDAR-
based ones.
Testing more 3D modeling options in a larger amount of sampled trees are still needed.
Nevertheless, some guidelines and promising results were presented in this study.
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