SEMANTIC LABELING OF ALS POINT CLOUDS FOR TREE SPECIES MAPPING USING THE DEEP NEURAL NETWORK POINTNET++

Abstract

Most methods for the mapping of tree species are based on the segmentation of single trees that are subsequently classified using a set of hand-crafted features and an appropriate classifier. The classification accuracy for coniferous and deciduous trees just using airborne laser scanning (ALS) data is only around 90% in case the geometric information of the point cloud is used. As deep neural networks (DNNs) have the ability to adaptively learn features from the underlying data, they have outperformed classic machine learning (ML) approaches on well-known benchmark datasets provided by the robotics, computer vision and remote sensing community. Though, tree species classification using deep learning (DL) procedures has been of minor research interest so far. Some studies have been conducted based on an extensive prior generation of images or voxels from the 3D raw data. Since innovative DNNs directly operate on irregular and unordered 3D point clouds on a large scale, the objective of this study is to exemplarily use PointNet++ for the semantic labeling of ALS point clouds to map deciduous and coniferous trees. The dataset for our experiments consists of ALS data from the Bavarian Forest National Park (366 trees/ha), only including spruces (coniferous) and beeches (deciduous). First, the training data were generated automatically using a classic feature-based Random Forest (RF) approach classifying coniferous trees (precision = 93%, recall = 80%) and deciduous trees (precision = 82%, recall = 92%). Second, PointNet++ was trained and subsequently evaluated using 80 randomly chosen test batchesàbatches`batchesà 400 m 2. The achieved per-point classification results after 163 training epochs for coniferous trees (precision = 90%, recall = 79%) and deciduous trees (precision = 81%, recall = 91%) are fairly high considering that only the geometry was included. Nevertheless, the classification results using PointNet++ are slightly lower than those of the baseline method using a RF classifier. Errors in the training data and occurring edge effects limited a better performance. Our first results demonstrate that the architecture of the 3D DNN PointNet++ can successfully be adapted to the semantic labeling of large ALS point clouds to map deciduous and coniferous trees. Future work will focus on the integration of additional features like i.e. the laser intensity, the surface normals and multispectral features into the DNN. Thus, a further improvement of the accuracy of the proposed approach is to be expected. Furthermore, the classification of numerous individual tree species based on pre-segmented single trees should be investigated.

Full text

SEMANTIC LABELING OF ALS POINT CLOUDS FOR TREE SPECIES MAPPING
USING THE DEEP NEURAL NETWORK POINTNET++
S. Briechle1, P. Krzystek1, G. Vosselman2
1Munich University of Applied Sciences, Munich, Germany - (sebastian.briechle, peter.krzystek)@hm.edu
2Faculty of Geo-Information Science and Earth Observation (ITC), University of Twente, Enschede,
the Netherlands - george.vosselman@utwente.nl
KEY WORDS: semantic labeling, ALS point clouds, tree species mapping, deep neural network, PointNet++
ABSTRACT:
Most methods for the mapping of tree species are based on the segmentation of single trees that are subsequently classified using
a set of hand-crafted features and an appropriate classifier. The classification accuracy for coniferous and deciduous trees just
using airborne laser scanning (ALS) data is only around 90% in case the geometric information of the point cloud is used. As
deep neural networks (DNNs) have the ability to adaptively learn features from the underlying data, they have outperformed classic
machine learning (ML) approaches on well-known benchmark datasets provided by the robotics, computer vision and remote
sensing community. Though, tree species classification using deep learning (DL) procedures has been of minor research interest
so far. Some studies have been conducted based on an extensive prior generation of images or voxels from the 3D raw data.
Since innovative DNNs directly operate on irregular and unordered 3D point clouds on a large scale, the objective of this study
is to exemplarily use PointNet++ for the semantic labeling of ALS point clouds to map deciduous and coniferous trees. The
dataset for our experiments consists of ALS data from the Bavarian Forest National Park (366 trees/ha), only including spruces
(coniferous) and beeches (deciduous). First, the training data were generated automatically using a classic feature-based Random
Forest (RF) approach classifying coniferous trees (precision = 93%, recall = 80%) and deciduous trees (precision = 82%, recall =
92%). Second, PointNet++ was trained and subsequently evaluated using 80 randomly chosen test batches `
a 400 m2. The achieved
per-point classification results after 163 training epochs for coniferous trees (precision = 90%, recall = 79%) and deciduous trees
(precision = 81%, recall = 91%) are fairly high considering that only the geometry was included. Nevertheless, the classification
results using PointNet++ are slightly lower than those of the baseline method using a RF classifier. Errors in the training data and
occurring edge effects limited a better performance. Our first results demonstrate that the architecture of the 3D DNN PointNet++
can successfully be adapted to the semantic labeling of large ALS point clouds to map deciduous and coniferous trees. Future work
will focus on the integration of additional features like i.e. the laser intensity, the surface normals and multispectral features into
the DNN. Thus, a further improvement of the accuracy of the proposed approach is to be expected. Furthermore, the classification
of numerous individual tree species based on pre-segmented single trees should be investigated.
1. INTRODUCTION
1.1 2D and 3D DNNs
Recently, DNNs have gained huge interest as a segmentation
and classification method for 2D and 3D data. Examples
for well-known deep convolutional neural networks (CNNs)
are VGG-16 (Simonyan et al., 2014), ResNet-50 (He et al.,
2016) and Mask R-CNN (He et al., 2017). In the past,
benchmark datasets have been published to verify and to
compare the performance of neural networks. For 2D datasets,
very popular benchmarks are the MNIST database (LeCun et
al., 1998), the CIFAR-10 dataset (Krizhevsky et al., 2009) and
the ImageNet dataset (Deng et al., 2009). In the remote sensing
community, state-of-the-art DL methods have been modified
for various use-cases: Gevaert et al. (2018) adjusted a Fully
Convolutional Network to the application of Digital Terrain
Model (DTM) extraction in challenging areas. The method
includes an automatic labeling strategy and outperformed two
reference DTM extraction algorithms. Vetrivel et al. (2018)
successfully detected severe building damages by combining
CNN features from oblique aerial images and 3D features from
dense photogrammetric point clouds. Since sensors capable
of generating 3D data (i.e. stereo camera systems, LiDAR
systems) have gained more and more attention and are now
widespread in numerous technical fields, the semantic labeling
and classification of 3D irregular and unordered point clouds
using DNNs is of major research interest. Tchapmi et al. (2017)
introduced a framework called SegCloud to obtain semantic
scene labeling on point-level using a 3D fully CNN. Based
on a voxelization of the 3D point cloud, their approach was
evaluated on indoor and outdoor datasets (i.e. KITTI (Geiger
et al., 2013)) and a performance comparable or superior to the
state-of-the-art was achieved. Zhou et al. (2018) presented the
neural network VoxelNET to detect objects (i.e. pedestrians,
cyclists) in 3D point clouds based on the encoding of point
clouds into equally spaced 3D voxels. Zhao et al. (2018)
classified ALS point clouds via deep features learned by a
multi-scale CNN. The method creates a group of multi-scale
contextual images for each 3D point and is ranked first on the
ISPRS benchmark dataset (ISPRS, 2019). All the mentioned
3D approaches transform the irregular 3D data into regular 3D
voxel grids or accumulations of 2D images to advantageously
utilize neural networks. In contrast to that, algorithms have
been developed that directly use the original dataset in a
set of sequenced layers to find a best mapping between the
input data and the target predictions. These point-based
DNNs directly operate on the point cloud without the need
for a prior rasterization or voxelization (Figure 1). Qi et al.
(2016) developed a highly efficient and effective type of neural
network (PointNet) showing i.e. a high performance on the
The International Archives of the Photogrammetry, Remote Sensing and Spatial Information Sciences, Volume XLII-2/W13, 2019
ISPRS Geospatial Week 2019, 10–14 June 2019, Enschede, The Netherlands
This contribution has been peer-reviewed.
https://doi.org/10.5194/isprs-archives-XLII-2-W13-951-2019 | © Authors 2019. CC BY 4.0 License.
951

shape classification benchmarks ShapeNet (Chang et al., 2015)
and ModelNet40 (Wu et al., 2015). The offered applications
include object classification, part segmentation and semantic
labeling. Since PointNet showed limiting ability concerning
the recognition of fine-grained patterns and the generalizability
to complex scenes, Qi et al. (2017) introduced an enhanced
version called PointNet++. This hierarchical neural network
recursively applies PointNet and learns local features from
multiple contextual scales. It enables an even more accurate
classification of single objects as well as the semantic labeling
of large-scale point clouds. PointNet++ outperforms PointNet
especially on point sets with varying densities like ScanNet
(Dai et al., 2017). For object classification, PointNet++
reaches a classification accuracy of 90.7% on the ModelNet40
dataset (40 object categories) and 84.5% on the ScanNet
dataset (20 object categories). As robotics and applications
like virtual reality and autonomous driving boost the interest
in 3D data, innovative approaches for the semantic labeling
and the classification of 3D point clouds are being published
high-frequently. Landrieu et al. (2018) proposed a DL-based
framework for the semantic segmentation of large-scale point
clouds and set a new state-of-the-art for outdoor LiDAR scans
(i.e. S3DIS (Armeni et al., 2016) and SEMANTIC3D.NET
(Hackel et al., 2017)). After efficiently pre-organizing 3D
point clouds into geometrically homogeneous elements called
superpoint graphs (SPG), a graph convolutional network
manages to learn contextual relationships between object
parts. In the same year, Li et al. (2018) presented the
neural network PointCNN for feature learning from 3D point
clouds by generalizing typical CNNs and achieved on par or
better performance on multiple challenging 2D (i.e. MNIST,
CIFAR-10) and 3D (i.e. S3DIS) benchmark datasets and tasks.
Figure 1. Basic principle of 3D DNNs like PointNet++,
operating directly on 3D point clouds without a prior
transformation into 2D images or 3D voxel grids
1.2 3D vegetation mapping
Many methods for tree species classification based on
segmented single trees use a set of hand-crafted features in
combination with an appropriate classifier like RF, Support
Vector Machine or logistic regression (Fassnacht et al., 2016).
Using only the geometric information of the ALS point cloud,
the classification accuracy for coniferous and deciduous trees
is around 90%. By extending the feature set with the laser
intensity, the accuracy increases to around 95% (Reitberger
et al., 2009). DL methods have the ability to automatically
learn features and mostly generate more accurate classification
results than classic ML approaches using hand-crafted features
(see section 1.1). Yet, tree species classification using neural
networks has been of minor research interest. Presumably,
one reason is the lack of large training datasets. Just recently,
Hamraz et al. (2018) use a CNN along with 2D images
generated from ALS point clouds to classify coniferous and
deciduous trees with 92% and 86% accuracy, respectively. So
far, the direct usage of 3D data in DNNs for 3D vegetation
mapping is more uncommon.
In this paper, we demonstrate that the architecture of
PointNet++ can successfully be adapted to the semantic
labeling of large ALS point clouds to map the two tree species
spruce and beech.
2. MATERIAL
Airborne full waveform data were acquired in June 2017
(leaf-on condition) using a Riegl LMS-Q 680i instrument which
was carried by a plane at a flying altitude of 550 m. The
resulting point density was at average 54 points/m2. The
mission area is located in the Bavarian Forest National Park
where mainly spruces and beeches are present (95%). Single
trees were segmented via the well-known normalized cut (Ncut)
segmentation (Reitberger et al., 2009) for the entire area of
the National Park (Figure 2). As a baseline method, a RF
classifier was trained with 918 manually labeled reference
trees (380 coniferous, 538 deciduous) using only geometric
features (height dependent and density dependent features,
crown shape) to classify the segments with respect to the tree
species. Next, the classifier was evaluated using a test dataset
comprising 529 trees (293 coniferous, 236 deciduous). For this
standard method, the classification results for coniferous trees
(precision = 93%, recall = 80%) and deciduous trees (precision
= 82%, recall = 92%) were as expected fairly good. Finally,
the classifier was used to predict the tree species of all single
tree segments. Compared to classic ML approaches like RF,
deep learning models require extremely large training datasets
in order to capture the essential features in a multilayer structure
(Ioannidou et al., 2017). Hence, a study area of 5270 m x
500 m (2.64 km2) was extracted from the park area comprising
approximately 97000 tree segments (48.5% coniferous, 51.5%
deciduous) with around 1500 points per tree and a tree density
of 366 trees/ha. This dataset was used to train PointNet++
containing 143.3 million points labeled by the classified tree
segments and was fully balanced with respect to the two object
categories. Potentially misclassified tree segments were not
removed by visual inspection.
Figure 2. Exemplary single tree segments resulting from
the Ncut segmentation; random color rendering
The International Archives of the Photogrammetry, Remote Sensing and Spatial Information Sciences, Volume XLII-2/W13, 2019
ISPRS Geospatial Week 2019, 10–14 June 2019, Enschede, The Netherlands
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952

3. METHODOLOGY
The neural network PointNet++ (Qi et al., 2017) operates
on unordered 3D data without initially generating images or
voxels from the point clouds and calculates per-point scores.
It includes a hierarchical feature learning technique as well as
special layers that are able to aggregate multi-scale information
according to local point densities. For our task, the decisive
hyperparameters of the semantic segmentation implementation
of PointNet++ (Qi et al., 2019) were adjusted to get a
well-performing network (Table 1). Since the dataset comprises
two class labels, the activation function of the network was
changed from ”softmax” to ”sigmoid”. Next, the training
dataset was divided into cubic blocks with an edge length
of 60 m (Figure 3). In each training epoch (batch size =
16), smaller batches of 20 m x 20 m x 60 m were extracted
and preprocessed including zero centering. Basically, zero
centering defines the origin of a local coordinate system as the
center of gravity of the selected batches by subtracting the mean
X, mean Y, and mean Z values from the absolute coordinates.
After each training epoch, the network based on the updated
weights was evaluated on randomly chosen test batches. To
estimate the performance of the network, standard metrics
(precision, recall) were calculated on a single point scale. As
graphics processing unit (GPU) we utilized a ”NVIDIA Titan
V” (NVIDIA Corporation, 2019).
Hyperparameter Value Declaration
BATCH SIZE 16 Number of batches per epoch.
NUM POINT 8192 Number of points per batch.
NUM CLASSES 2 Number of object categories.
MAX EPOCH 200 Number of training epochs.
BASE LR 0.001 Initial learning rate.
OPTIMIZER ”adam” Optimization algorithm.
MOMENTUM 0.9 Momentum value for stochastic gradient descent.
DECAY STEP 200000 Increment for the reduction of the learning rate.
DECAY RATE 0.7 Decay rate for the learning rate.
MAX DROPOUT 0.875 Maximal dropout rate.
CUBE DIM 60 Edge length of the cubic training blocks in [m].
Table 1. Hyperparameters and default / optimized values
reference
prediction
decid. conif. recall
decid. 294623 30516 0.91
conif. 68707 261514 0.79
precision 0.81 0.90
OA 0.85
kappa 0.70
Table 2. Classification result (epoch 163) for applying the
trained neural network on randomly chosen test data; OA
= overall accuracy, decid. = deciduous, conif. =
coniferous
4. RESULTS AND DISCUSSION
The neural network was trained using 8192 points per batch.
Hence, the number of training points per epoch added up
to 131072. Assuming approximately 1500 points per tree,
this equates to around 87 tree segments per training epoch.
After each epoch, the weights of the network were updated.
Subsequently, the performance of the network was evaluated
on 80 randomly chosen test batches (655360 points b=437 trees
b=1.19 ha). After 163 of 200 training epochs (21.4 million
points b=14243 trees b=38.9 ha), the classification result for
coniferous trees (precision = 90%, recall = 79%) and deciduous
trees (precision = 81%, recall = 91%) reached its maximum.
Clearly, some experiments were needed to find an optimized set
of hyperparameters. The point-based results (Table 2) are fully
comparable to the classification results provided by the standard
method based on a single tree segmentation and a tree species
classification with RF. Appropriate features were automatically
generated from the point cloud and are able to discriminate the
complex 3D tree structure of both tree species. Nevertheless, it
needs to be pointed out to the reader that the given precision
and recall values for the DL approach were calculated on a
single-point level. In contrast, the performance measures for
the RF classifier given in section 2 are per-tree scores. Figure
4 exemplarily shows the predicted class labels compared to the
reference data (”ground truth”) for an area with a size of 6.4
ha. Like the standard method, PointNet++ performed better for
coniferous trees than for deciduous trees. One reason for this
is the superior representation of the crown shape of coniferous
trees in leaf-on condition at a point density of 54 points/m2.
For the time being we just used the geometrical information
of the ALS point cloud, whereas the laser intensity has not
been included yet. We encountered misclassification effects
at the edges of the blocks, since no inter-block neighborhood
information was provided to the model. One promising
approach to solve this issue is the utilization of Superpoint
Graphs (Landrieu et al., 2018) for the semantic labeling of the
point cloud. Of course, we expected that the neural network
outperforms the RF classifier. Very likely, the errors in the
training data and the mentioned edge effects limited a better
performance.
Figure 3. Cubic blocks used for training of PointNet++;
3D points colored in dependence of the class labels
”coniferous” (blue) and ”deciduous” (red)
The International Archives of the Photogrammetry, Remote Sensing and Spatial Information Sciences, Volume XLII-2/W13, 2019
ISPRS Geospatial Week 2019, 10–14 June 2019, Enschede, The Netherlands
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953

Figure 4. Semantic labeling result (left) and reference data (right) for coniferous trees (blue) and deciduous trees (red);
area size 200 m x 320 m
5. CONCLUSION AND OUTLOOK
The conducted experiments prove that the architecture of the 3D
DNN PointNet++ can successfully be adapted to the semantic
labeling of large ALS point clouds to map the two tree species
spruce and beech. The neural network was trained using ALS
data with a point density of 54 points/m2. The training dataset
was generated automatically using a classical feature-based RF
classifier that distinguished single coniferous trees (precision
= 93%, recall = 80%) and deciduous trees (precision = 82%,
recall = 92%). Using the architecture of PointNet++, the
achieved classification results for single points belonging to
either coniferous trees (precision = 90%, recall = 79%) or
deciduous trees (precision = 81%, recall = 91%) are fairly
high considering that only the geometry was included. We
want to emphasize that - depending on the point density and
the extent of the objects - the decisive hyperparameters of
the neural network need to be adjusted in order to get a
well-performing network for the particular classification task.
Moreover, the classification of individual tree species has not
been solved yet and it is still a challenging task. For instance,
a recent study by Amiri et al. (2019) reported on an accuracy
of around 78% by fusing multispectral data from LiDAR and
optical imagery to classify four tree species (spruce, fir, beech,
dead tree). Hence, future work will focus on the mapping of
individual tree species using PointNet++ or comparable DNNs
(e.g. SPG, PointCNN). Furthermore, laser intensity values,
surface normals and multispectral features should be integrated
to further improve the accuracy of the proposed DL approach.
ACKNOWLEDGEMENTS
We would like to thank PD Dr. Marco Heurich and his team
from the Bavarian Forest National Park for the supply of the
ALS data.
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The International Archives of the Photogrammetry, Remote Sensing and Spatial Information Sciences, Volume XLII-2/W13, 2019
ISPRS Geospatial Week 2019, 10–14 June 2019, Enschede, The Netherlands
This contribution has been peer-reviewed.
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