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Hyperspectral Data Dimensionality Reduction and
the Impact of Multi-seasonal Hyperion EO-1
Imagery on Classification Accuracies of
Tropical Forest Species
Manjit Saini, Binal Christian, Nikita Joshi, Dhaval Vyas, Prashanth Marpu, and Krishnayya Nadiminti
Abstract
Synchronizing hyperspectral data acquisition with phenologi-
cal changes in a tropical forest can generate comprehensive
information for their effective management. The present
study was performed to identify a suitable dimensional-
ity reduction method for better classification and to evalu-
ate the impact of seasonality on classification accuracy of
tropical forest cover. EO-1 Hyperion images were acquired
for three different seasons (summer (April), monsoon (Oc-
tober), and winter (January)). Spectral signatures of pure
patches of Teak, Bamboo, and mixed species covers are
significantly different across the three seasons indicating
distinctive phenology of each cover. Kernel Principal Com-
ponent Analysis (k-PCA) is more suitable for dimensional-
ity reduction for these covers. The three vegetation covers
classified using images of three seasons achieved the best
classification accuracies using k-PCA with maximum likeli-
hood classifier for the monsoon season with overall accura-
cies of 83 to 100 percent for single species, 74 to 81 percent
for two species, and 72 percent for three species respectively.
Introduction
The Importance of Tropical Forests
Tropical forests constitute about half of the world’s forests
and have the intrinsic property of being extremely rich in
terms of species richness and diversity (Bradshaw et al., 2009;
Gibson et al., 2011). They store 40 to 50 percent of carbon in
terrestrial vegetation and are responsible for one third of the
global terrestrial primary productivity (Beer et al., 2010). Over
the past century tropical forests have been suffering from
exceptional rates of changes as they are destroyed by human
activities and climate change (Achard et al., 2004; Féret and
Asner, 2013; Morris, 2010). The global character of tropical
deforestation and its consequences on climate change and
biodiversity make it an important emerging global concern
that increasingly transcends individual nations and their
boundaries (Fuller, 2006). Tropical forest destruction is likely
to continue in the future, causing an extinction crisis among
Manjit Saini, Binal Christian, Nikita Joshi, Dhaval Vyas, and
Krishnayya Nadiminti with the Ecology Laboratory, Depart-
ment of Botany, Faculty of Science, The M.S. University of
Baroda, Gujarat, India (krish14@gmail.com).
Prashanth Marpu is with the Institute Center for Water and
Environment (iWATER), Masdar Institute of Science and
Technology, PO Box 54224, Abu Dhabi, United Arab Emirates.
PHOTOGRAMMETRIC ENGINEERING & REMOTE SENSING
tropical forest species (Bradshaw et al., 2009). Therefore,
comprehensive information on the spatial distribution and
composition of existing plant species is fundamental to de-
sign effective strategies for conservation and management of
increasingly fragmented tropical forests (Gillespie et al., 2008;
Rodriguez et al., 2007). Hence, strong preference has been
given to acquire updated data on vegetation cover changes
regularly or annually so as to better assess the environment
and ecosystem (Knight et al., 2006). Unfortunately, such
information cannot be obtained exclusively from traditional
survey techniques, due to logistical difficulties and the costs
involved. For a subcontinent like India, survey for mapping
vegetation and other land covers using conventional tech-
niques is too complex and demands a huge amount of human
resource and time (Roy and Joshi, 2002). Quite the opposite,
forest vegetation mapping using remotely sensed observations
is efficient and cost effective. Currently hyperspectral remote
sensing is fast emerging as a key technology for advanced and
improved understanding, classification, modeling, and moni-
toring of complex forest vegetation.
The Importance of Phenological Variation in Species Discrimination
Vegetation phenology can provide an useful signal for classi-
fying forest cover. Seasonal phenological changes are mainly
caused by inter-annual climatic variability and are reflected
through an increase or decrease in green biomass (Pettorelli
et al., 2005). Phenological changes significantly influence
spectral reflectance curves. Changes in vegetation spectral
response caused by phenology can conceal long term changes
in the landscape (Hobbs, 1989; Lambin and Ehrlich, 1996).
An understanding of vegetation phenology is prerequisite to
inter-annual studies and predictive modeling of land surface
responses to climate change (Myneni et al., 1997; Vina et al.,
2004). However, the phenology and interactions of tropical
forests with environmental, climate, and anthropogenic fac-
tors are not well perceived. Synchronizing hyperspectral data
acquisition with phenological changes in tropical trees is a
daunting task. At times, it is practically not feasible. Identi-
fying appropriate endmembers for classifying tropical trees
with diverse phenologies is an important aspect to look at.
Photogrammetric Engineering & Remote Sensing
Vol. 80, No. 5, August 2014, pp. 000–000.
0099-1112/14/8007–000
© 2014 American Society for Photogrammetry
and Remote Sensing
doi: 10.14358/PERS.80.7.000
Aug u s t 2014 33
It is equally important to verify the suitability of endmem-
ber spectra coming from one season on classifying an image
of a different season. Larger spatial heterogeneity in tropics
suggests more complex control of the phenology (Maignan
et al., 2008). Thus, attention to phenology is vital for the
characterization and mapping of forests from spaceborne
sensors. In several recent studies, phenological differences in
leaf traits (Castro-Esau et al., 2006) and canopy characteristics
(Castro-Esau and Kalacska, 2008) allowed discrimination of
vegetation at the species level based on leaf spectral signa-
tures. Extending these for configuring canopy scale studies in
tropics is to be addressed.
Merits and Demerits of Hyperspectral Sensors for Vegetation Mapping
Numerous studies (Datt et al., 2003; Wu et al., 2010) have
shown that the Hyperion imaging spectrometer onboard the
Earth Observing One (EO-1) satellite has provided signifi-
cantly enhanced data over conventional multi-spectral remote
sensing systems (Thenkabail et al., 2013). The ability of hy-
perspectral data to significantly improve the characterization,
discrimination, modeling and mapping of forested vegeta-
tion is well known (Thenkabail et al., 2011). This has led to
improved modeling and mapping of forest vegetation char-
acteristics such as biochemical-biophysical quantities (Asner
and Martin, 2008; Haboudane et al. 2008; Vyas et al., 2013)
and species discrimination (Cho et al., 2008; Cochrane, 2000;
Vaiphasa et al., 2005). Development of base line spectral data
and tools for the characterization and detection of tree species
as a function of hyperspectral characteristics was identified
as priority area of remote sensing research in tropical forests
before a decade ago (Sanchez-Azofeifa, 2003). However, the
main problem with hyperspectral image processing is the
huge amount of data involved. It is imperative that new meth-
ods and techniques are to be developed to handle these high
dimensional datasets. At the same time, it will be important
to optimize future hyperspectral sensors by identifying and
dropping redundant bands (Thenkabail et al., 2004). Optimiz-
ing hyperspectral sensors will help to reduce the volume and
dimensionality of the datasets, and makes it feasible to clas-
sify vegetation in a pertinent manner.
Dimensionality Reduction Techniques and Endmember Extraction
A simple and effective way of dealing with high dimensional
data is to reduce the number of dimensions (Benediktsson
et al., 1995; Landgrebe, 2001; Lee and Landgrebe, 1993).
Dimensionality reduction is mostly done by band selection.
Feature extraction by band selection can minimize computa-
tional time for high dimensional hyperspectral data. Efficient
statistical methods are required to reduce dimensionality
(Chan and Palinckx, 2008). Large number of linear and non-
linear dimensionality reduction methods such as Principal
Component Analysis (PCA), Minimum Noise Fraction (MNF),
Discriminant Analysis (DA), Decision Boundary Feature
Extraction (DBFE), Independent Component Analysis (ICA),
Fisher’s Linear Discriminant Analysis (LDA), Kernel Principal
Component Analysis (k-PCA), and ISOMAP have been used
for the data reduction (Bachmann et al., 2006; Chang et al.,
2002; Féret and Asner, 2013; Marpu et al., 2012; Thenkabail,
2004). Each method works differently. The PCA is an orthogo-
nal linear transformation which projects the data into a new
coordinate system, such that the greatest amount of variance
of the original data is contained in the first few principal com-
ponents (Richards, 2005). ICA identifies components which
share minimal mutual information to ensure statistical inde-
pendence of the derived components. ICA can be viewed as an
improvement over PCA as an unsupervised feature extraction
tool. PCA and ICA are linear projection methods and they work
perfectly well on the linear data. However, real world data
are often nonlinear, in which case linear techniques are not
34 Aug us t 2 014
appropriate. k-PCA (Mika et al., 1999; Schölkopf et al., 1998)
is a kernel version of standard PCA. It is a method of non-
linear feature extraction, closely related to methods applied
in Support Vector Machines (Schölkopf et al., 1999). All these
methods have been commonly employed in optimum fea-
ture extraction band identification for different applications
(Fauvel et al., 2013; Plaza et al., 2009; Tsai et al., 2007; Wang
and Chang, 2006). Similarly, endmember selection is essential
to accurately classify tree species in heterogeneous tropical
forests. It involves the identification of appropriate endmem-
bers and their corresponding spectral signatures. Reference
endmember spectra can be directly derived manually from
the image data themselves using ground truth information.
An important advantage of the manual endmember selec-
tion is the capability of deriving endmembers whose spectra
reflect some of the scene-specific processes affecting the
signal received by the sensor (Bateson and Curtiss, 1996).
Manual endmember extraction gets influenced by the propor-
tion of homogeneous occupancy of a species. A combination
of suitable endmember, appropriate dimensionality reduction
technique can improve classification accuracy of forest cover.
Forest Ecosystems and Species Mapping
A number of studies have indicated the advantages of nar-
row band data to obtain the most sensitive information on
species level discrimination using lab spectra (Castro-Esau
et al., 2006; Zhang et al., 2006), airborne spectra (Carlson
et al., 2007; Skoupý et al., 2011) and spaceborne spectra
(Christian and Krishnayya, 2009; Mitri and Gitas, 2010; Vyas
et al., 2011) by applying different classification algorithms.
In the past few years many advanced methods have been
developed and are used for species level classification such
as Maximum Likelihood (ML) Classification (Buddenbaum et
al., 2005; Clark et al., 2005; Govender et al., 2008), Spectral
Angle Mapper (SAM) (Buddenbaum et al., 2005; Christian and
Krishnayya, 2009; Clark et al., 2005) and Artificial Neural
Network (ANN) (Filippi and Jenson, 2007; Skoupý et al.,
2011). Most of these hyperspectral studies were carried out
for boreal and temperate forest ecosystems. These areas are
relatively more homogeneous as compared to tropical cov-
ers. Temperate landscapes offer a more manageable location
for such studies, with a relatively small number of habitat
types, and within each type, a greater predominance of a few,
dominant species. Phenological changes are mostly uniform
across the regions. This minimizes the complexity of studying
these covers through remote sensing. The tropics on the other
hand offers a challenge of an altogether greater magnitude,
with far greater numbers of landscapes, habitats and species,
distributed across a variety of stages of growth and succes-
sion, and with far more complex canopy structures (Kalacska
et al., 2004; Nagendra, 2001). Although there have been major
advances in remote sensing research of boreal and temperate
ecosystems, tropical remote sensing research currently is lack-
ing the fundamental scientific understanding and potential
for routine applications observed in these parts of the globe.
This knowledge gap is due in part to the complexity of tropi-
cal forest ecosystems, the underdevelopment of scientific and
engineering infrastructure in the tropics, and the tendency of
many countries to treat tools for conservation and resource
management as a low priority relative to immediate economic
needs (Sanchez-Azofeifa et al., 2003). Townsend et al. (2008)
mentioned that heterogeneity has not been well captured in
large-scale estimates of tropical ecosystem function. They
suggested that new developments in Remote Sensing can
help bridge the gap. These issues pose major hurdles in the
classification of hyperspectral data of tropics. Heterogeneity
and diverse phenological conditions of tropics augments the
complexity. The present study has been carried out to address
these issues with the following objectives:
PHOTOGRAMMETRIC ENGINEERING & REMOTE SENSING
 1. Selection of an appropriate dimensionality reduction 100 m) covered with pure patches of Teak, Bamboo and mixed
technique to improve the classification accuracy, and patches of other dry deciduous species are spread across the
2. Impact of phenological changes on classification accuracy. sanctuary (Pradeepkumar, 1993). Mixed species cover consist-
ed of species like Anogeissus latifolia (Roxb. ex DC.) Wall. ex
Bedd., Butea monosperma (Lam.) Taub., Mitragyna parvifolia
Materials and Methods (Roxb.) Korth., Garuga pinnata Roxb., Lagerstromia parvifolia
Roxb., Wrightia tinctoria R.Br., Terminalia crenulata Roth.,
Study Area
and Ficus glomerata Roxb.. Few individuals of Teak and Bam-
Tropical, dry deciduous forests of the Shoolpaneshwar Wild-
boo were also present in this mixed species cover. Phenologi-
life Sanctuary (SWS) (Gujarat, India) was selected as the study
cal cycles of the three covers were distinct. Leaf longevity was
area (Figure 1). It is located between latitude and longitude
relatively lesser in Teak as compared to Dendrocalamus cover
of 21° 29'N to 21° 52'N and 73° 29'E to 73° 54'E, respectively.
in the study area. Mixed cover showed wider variation cor-
Hilly tract of the Sanctuary bordering the Narmada River
related with the composition of species in the quadrat. A total
supports some of the deciduous forests in Gujarat and is one
of 120 quadrats were laid down across the study site (91.50
of the important, naturally protected regions nurturing a
Km2). 58 quadrats were laid down for Teak, 26 for Bamboo
sizeable biota. Annual precipitation of the area is in the range
and 36 for mixed species cover. Number of quadrats laid down
of 900 to 1,200 mm. Minimum and maximum annual mean
for each cover is proportional to its distribution in the study
temperatures are 8°C and 42°C, respectively. Topography of
site. Quadrats laid down were randomly spread across the
the study area is undulated with continuous and discontinu-
selected area. Each quadrat was of 30 m × 30 m size, match-
ous hilly tracts up to an elevation of ~800 m ASL intermingled
ing the spatial resolution of Hyperion sensor. Each quadrat
with valleys, streams, and sporadic clearings for agriculture.
of a vegetation cover was coming from a 2 × 2 or 3 × 3 pixel
The area is important for its support to wildlife, tribal popula-
window of the same cover. In all the quadrats, biophysical
tion, and as a catchment area for local water bodies (Sabnis
parameters such as Diameter Breast at Height, density, height
and Amin, 1992).
and spread of canopy (Vyas et al., 2010) were recorded. Per-
Field Data Collection centage occupancy of each vegetation cover was calculated.
An extensive field survey was done to collect information on Global positioning system (GPS) locations of all the quadrats
homogenous vegetation patches, heterogeneous covers, and were taken within ±5 m error using GPS (Magellan Explorist
signs of human disturbance. Field surveys were carried out 600) and considered as Ground Control Points (GCPs).
on all the three dates coinciding with the EO-1 Hyperion data
Image Acquisition and Preprocessing of Hyperion Data
acquisition time. This has been done to record seasonal dif-
Three narrow-band Hyperion images were acquired for the
ferences in the phenology and growth of the vegetation cover.
seasons, summer (March to June), monsoon (July to October)
Like in any tropical area, heterogeneity in species distribu-
and winter (November to February). Images were acquired on
tion is unique to the study area. The major types found in the
03 April 2006 (summer-dry season), 21 October 2006 (mon-
sanctuary include covers of Tectona grandis L. f., patches of
soon-wet season), and 22 January 2011 (winter-middle of fall
mixed deciduous trees, Dendrocalamus strictus (Roxb.) Nees,
season) (Figure 2). The spatial resolution of the sensor was 30
and dry tropical riverine forests. Large tracts of land (≈100 m ×

Figure 1. The location of the study area in western India (21.7017E, 73.735N) and the area where trees were
sampled (displayed in Google® map image with utm projections). The selected forest covers are Teak, Bamboo,
and Mixed species.

PHOTOGRAMMETRIC ENGINEERING & REMOTE SENSING Aug u s t 2014 35

m and the spectral resolution was 10 nm with a wavelength
range of 356 to 2578 nm. At the time of image acquisition, the
study area had less than 25 percent cloud cover. Characteris-
tics of three Hyperion images are given in Table 1.
The delivered USGS Hyperion product contains 242
hyperspectral narrow bands (HNBs). Out of these, bands 1
through 7 (356 to 417 nm) and bands 225 to 242 (2406 to
2578 nm) are not calibrated, bands 56 and 57, 77 and 78
fall in the overlap region of the two spectrometers (VNIR and
SWIR). Along with uncalibrated HNBs, bands 77 and 78 were
removed because they have usually been found to be noisier
than the corresponding bands (56 and 57) in the VNIR region.
Strong water vapor absorption bands falling at 1356 nm, 1366
nm, 1406 nm, 1417 nm, and between 1820 to 1931 nm were
also ignored. After the removal of all these uncalibrated,
overlapped and water absorptive HNBs, a spectral subset of
179 HNBs has been retained for further processing from each
of the three datasets. A “destreaking” routine was applied
to minimize the striping artifact present in the Hyperion
datasets. For destreaking, ENVI add-on tool “workshop” (CSIRO
Office of space science and applications, Earth Observation
Centre, Australia) was used. The Hyperion radiance values
from the 179 HNBs were converted to surface reflectance using
FLAASH (Fast Line-of-sight Atmospheric Analysis of Spec-
tral Hypercube, USA), a Modtran-4 based program to remove
atmospheric scattering and absorption effects. We estimated
the amount of aerosols and the scene average visibility (40
km) using the 2-Band (k-T) method (Kaufman et al., 1997),
which uses a dark pixel reflectance ratio approach with bands
placed around 660 and 2100 nm. Precipitable water vapor
was derived on a per pixel basis from the 1130 nm spectral
feature. A correction for adjacency effects was also applied to
the data. Model parameters included were a tropical atmo-
sphere with a rural aerosol model. The atmospherically cor-
rected images were geometrically registered using the nearest
(a)
Figure 2. The three Hyperion datasets analyzed are displayed as false color composite images (R-813 nm; G-651 nm; B-559 nm). The
three datasets are: (a) Monsoon, (b) Winter, and (c) Summer.
Table 1. Characteristics of the Three Hyperion Images
Date of Solar zenith Solar azimuth
Seasons
acquisition angle angle
Monsoon 21 Oct 2006 39.87 141.63
Summer 03 Apr 2006 30.04 119.23
Winter 22 Jan 2011 51.11 143.68
36 Aug us t 2 014
neighborhood sampling method and second order polynomial
model where resultant RMSE was ≤0.5 pixels for all three data-
sets. For the classification and analysis of the three vegetation
covers, a spatial subset of 345 × 256 pixels (91.50 km2) was
generated within the scene. GPS positions of all the quadrats
of the field study are falling in this subset. NDVI values were
calculated by utilizing bands 620 nm (Red band) and 800
nm (NIR band). Masking of the image was performed using
threshold NDVI values so as to exclude water bodies. Tempo-
ral variation of spectral characteristics of the study area was
assessed based on two hyperspectral narrow band vegetation
indices (HVIs), NDVI (Normalized Difference Vegetation Index)
and PRI (Photochemical Reflectance Index). PRI was calculated
by following the formula given by Gamon et al. (1997).
Endmember Extraction
Endmember spectra for the three identified covers were
selected manually from the hyperspectral image using ground
truth data. Quadrats with the highest ground occupancy (>80
percent) of each vegetation cover were considered as purer
ones and spectra from these quadrats were extracted for fur-
ther analysis. The underlying assumption was that the influ-
ence of other vegetation (<20 percent) on the spectral curve of
a particular vegetation cover would be negligible; 50 percent
of total quadrats of each cover were used as training sites
and the rest for testing the accuracy. The number of quadrats
used as training sites differed across vegetation covers. For
the maximum likelihood algorithm, 29 quadrats were identi-
fied as training sites for Teak, 18 for Mixed species cover and
13 quadrats were considered for Bamboo. The same quadrats
locations were used as training sites across all the seasons.
Spectra coming from these quadrats (marked as training sites)
for the three covers were considered as endmembers. The
mean of these spectra was used as endmember spectrum for
Spectral Angle Mapper (SAM) for the three seasons.
(b) (c)
Viewing Spectral Spatial Radiometric
geometry resolution resolution resolution
Nadir 10 nm 30 m 16 bit
Nadir 10 nm 30 m 16 bit
Nadir 10 nm 30 m 16 bit
PHOTOGRAMMETRIC ENGINEERING & REMOTE SENSING
Dimensionality Reduction
Hyperspectral remote sensing imagery has high correlations
among adjacent bands and provides an excessive amount
of features to explore. Hence, band selection and feature
extraction are important to overcome the problem of dimen-
sionality and computational burden. Dimensionality reduc-
tion techniques help in identifying an optimal set of spectral
bands suitable for characterizing a specific vegetation cover.
We have tested the efficacy of three different unsupervised
feature reduction methods. These are PCA, ICA, and k-PCA.
ENVI 4.6 was used to run the principal component transfor-
mation and independent component transformation. In both
cases forward transformation was applied on all 179 HNBs for
the three selected seasons. The k-PCA plug-in for ENVI was
obtained from Dr. Morton Canty (http://mcanty.homepage.t-
online.de/software.html). The implementation is discussed
in detail in Canty and Nielsen (2012). Considering 1,000 as a
sample size and 1.5 as the scale for kernel parameter, k-PCA
was performed to extract 10 kernel principal components,
which account for 99 percent of the variance, out of 179 HNBs
across the selected three seasons.
All the three reduction techniques were performed on the
spatial subset of 179 HNBs image datasets of all seasons for
feature extraction which produced the best discriminatory
model. Out of 179 components, the first 20 components for
ICA, PCA, and the first 10 components for k-PCA were selected
considering their eigenvalues. From these selected compo-
nents, spatially coherent components were extracted by care-
ful visual inspection (looking at the quality and contrast of
the image) to formulate a new feature image for classification.
Some of the components were common across the seasons.
Few others differed. Principal and independent components
from PCA, ICA, and k-PCA for three seasons could discriminate
the objects effectively. For k-PCA, 8 components were selected
for summer (1,2,3,4,5,6,7,9) and winter (1,2,3,4,5,7,8,9); and 9
for monsoon (1,2,3,4,5,6,7,8,9), thus reducing data volume by
approximately 95 percent. Selected independent components
were 8 (1,2,4,5,6,9,12,15) for monsoon and 9 for summer
(1,3,4,5,6,10,11,14,17) and winter (1,3,4,6,7,8,9,11,20) in ICA
reducing the data volume by 95 percent. Principal compo-
nents selected were 5 (1,2,7,9,14) for monsoon, 4 (1,2,5,6) for
summer, and 3 (1,2,5) for winter reducing the data volume
by 98 percent. These feature extraction techniques reduced
data dimensionality and also showed variability in the data
coming from the three seasons. Identification of these uncor-
related components help in overcoming the Hughes phe-
nomenon. These components were used for both ML and SAM
classification.
Supervised Classification Algorithms
Two different classifiers, Maximum Likelihood (ML) and
Spectral Angle Mapper (SAM) were used separately to classify
three covers for each season with the components obtained
from the feature extraction methods tested. These classifiers
were selected as they are most extensively applied in classify-
ing forest covers of Mediterranean, Temperate and Tropical
regions (Buddenbaum et al., 2005; Clark et al., 2005; Good-
enough et al., 2003; Pignatti et al., 2009; Tsai et al., 2007). ML
classification algorithm calculates variance and covariance
of each selected class (here it is the selected forest cover) as-
suming a Gaussian distribution in the classes. Each quadrat is
assigned to the class that has the highest probability (Shafri et
al., 2007). Three classification approaches namely single spe-
cies, two species (Teak-Bamboo, Teak-Mixed species, Bam-
boo-Mixed species), and three species (Teak-Bamboo - Mixed
species) were carried out. Classification was performed for
all the three seasons. Here other areas like human settlement,
agricultural land, barren land, and other kinds of vegetation
were considered in a separate class as unclassified.
PHOTOGRAMMETRIC ENGINEERING & REMOTE SENSING
SAM is a classification technique determining the similar-
ity between an endmember spectrum and a pixel spectrum
in a n-dimensional space (Boardman and Kruse, 1994). It is
insensitive to illumination and albedo effects. As compared
to ML classification, the calibration of the SAM algorithm re-
quires a relatively small amount of training spectra to provide
maximal performance. Only one classification approach was
considered to classify all the three covers (Teak-Bamboo -
Mixed species). Selected components were spatially informa-
tive. Other two approaches (single species and two species
(Teak-Bamboo, Teak - Mixed species, Bamboo - Mixed spe-
cies)) also were performed. However, SAM was overestimating
the selected covers in the output images, and hence was not
included here.
The error matrix and Kappa statistic (Congalton and Mead,
1983) has served as the standard approach in accuracy as-
sessment. We constructed the error matrix and calculated the
Kappa statistics for the classifications. The overall accuracy
is defined as the ratio of the number of validation samples
that are classified correctly to the total number of validation
samples irrespective of the class. The kappa value describes
the proportion of correctly classified validation samples after
random agreement is removed.
Results
Phenological Variation
Impact of seasonal variation (of winter, summer, and mon-
soon) was distinctly visible in the selected subset of the study
area coming from EO-1 Hyperion datasets (Figure 2). Dry
deciduous forest of SWS showed a distinct wet and dry season
with a brief transition period. Vegetation covers of the forest
showed high biophysical and corresponding biochemical
diversity. These features were distinctly reflected in the phe-
nological cycle of vegetation. Leaf emergence was a periodic
phenomenon in all these woody species. All or most of the
old leaves got abscised before the arrival of new ones, and the
tree cover was bare for a period extending up to few months.
Teak started leaf shedding from December. Leaf fall of Bamboo
started later (mid-January onwards). Leaf fall was observed as
relatively faster in Teak and in a gradual manner in Bamboo.
Species in mixed cover showed diverse temporal variation in
leaf fall. Different species of the cover had their own pheno-
logical cycle thereby giving a mosaic pattern in appearance.
Leaf sprouting was abrupt in both Teak and Bamboo. The
same was gradual in mixed cover because of the diversity. In
the month of April, few of the trees in mixed cover were leaf-
less, and many others were with new leaves of different hues.
It was observed that Teak and Bamboo showed the highest
leaf fall in the months of March and April. At the onset of the
first rains, almost all the tree species flushed with large quan-
tities of new leaves. The selected three covers had a maximum
density of crown foliage in monsoon season. This condition
was extended up to November across the study area.
Results from the HVIs (NDVI and PRI) are illustrated in Fig-
ures 3 and 4, respectively. Seasonality is distinctly seen in the
values of HVIs across the three images. Vegetation was in lush
green condition in monsoon season with NDVI values in the
range of (0.35 to 0.8). Maximum number of pixels (78 per-
cent) showed higher values (>0.5; Figure 3a). Figure 3b shows
a decline in foliage cover during winter season with NDVI
values ranging from 0.2 to 0.8. Maximum number of pixels
(72 percent) showed NDVI values <0.45 (Figure 3b). The dry
deciduous nature of the forest was apparent in the summer
season characterized by a profound drop in NDVI values (0.1 to
0.35) (Figure 3c). The maximum number of pixels (80 percent)
showed NDVI values <0.25. Mean PRI values for three vegeta-
tion covers across the seasons ranged from -0.16 to -0.02
Aug u s t 2014 37
 (a) (b) (c)
Figure 3. ndvi Images coming from (a) Monsoon, (b) Winter, and (c) Summer season datasets.

(Figure 4). All three covers exhibited a peak in PRI in monsoon

indicating higher photosynthetic efficiency in this season.
Figure 5 depicts mean reflectance spectra of three vegeta-
tion covers for the three seasons indicating strong phenologi-
cal variations. The largest change in the reflectance spectra
occurred between monsoon and summer season. There was a
considerable difference in the shape and features of spectra for
the three selected covers from visible to the Near Infrared (NIR)
spectral regions. A typical reflectance pattern of lush green
vegetation could be seen in the spectra of monsoon image.
Each cover had a distinct absorptive feature pattern and sharp
transition was observed from red (centered at 670 nm) to the
NIR wavelength region (770 to 1340 nm). Spectral features for
Teak and Bamboo in monsoon showed similarity and were sta-
tistically insignificant (t-test, p ≥0.05) in VIS-NIR (425 to 900nm)
and SWIR-II (2000 to 2395 nm) regions of the spectrum. Teak
and Mixed species showed lesser separation in the visible Figure 4. Seasonal change in the average of Photochemical
wavelength and higher in NIR and in SWIR (1477 to 1800nm) Reflectance Index values by species (n = 20).
(p ≤0.05). A similar pattern was also observed between the
spectra of Bamboo and Mixed species. In the spectra of winter
season, chlorophyll absorption features of mixed species were Discussion
stronger followed by Bamboo and Teak. In the NIR region, all
Hyperspectral Data and Phenology Monitoring
the three species were separated distinctly. Teak and Bamboo
Differences in the values of measured HVIs and leaf character-
were similar in the visible and the SWIR region, but were more
istics observed in the dry deciduous forest of SWS synchro-
different in the NIR region. The mean reflectance spectra of
nized well with the phenological cycle. Leaf fall and leaf flush
three covers in summer were characterized by weaker absorp-
patterns of SWS forests were discrete and coincided with the
tion features in the visible region. The mean spectrum of Teak
three seasons. It was reported earlier that rainfall and other
had much higher reflectance in the NIR plateau.
seasonally occurring events influence leaf fall and leaf flush-
Dimensionality Reduction and Classification Accuracy ing of forest ((Borchert, 1994; Lima and Rodal, 2010; Valdez-
Table 2 shows the OAA achieved using k-PCA-, ICA-, and PCA- Hernández et al., 2010). van Schaik et al. (1993) reported
based components through maximum likelihood algorithm that tropical forests exhibit a range of phenological behavior,
for three different approaches namely single species, two spe- episodes of ephemeral leaf bursts followed by continuous
cies (Teak-Bamboo , Teak - Mixed species, Bamboo - Mixed leafing. Field observations of present study showed that leaf
species) and three species (Teak-Bamboo - Mixed species). Er- fall of each cover were followed by leaf flushing. Teak and
ror matrices were developed using three species classification Bamboo cover showed similarity in their phenological pattern
approach and illustrated in Tables 3, 4, and 5 for k-PCA-ML, whereas mixed species cover responded different. In case of
and Tables 6, 7, and 8 for ICA-ML. Generated multi-seasonal Teak and Bamboo, leaf bursting started from the mid-April
classified maps using k-PCA-ML and ICA-ML for three selected and completed leaf expansion and maturity by the months
forest covers are illustrated in Figures 6 and 7, respectively. of October and November. Signs of leaf fall started from the
Tables and Figures of PCA-ML classification are not provided month of December. Rate of leaf fall was different in Teak and
as their classification accuracy was low. OAA acquired from Bamboo. Tree species of mixed cover showed different pattern
SAM classification for the components obtained from k-PCA for of leaf fall. Species such as A. latifolia , M. Parvifolia, and B.
the monsoon image was 50 percent: for winter 31 percent and monosperma showed leaf fall from the month of February
for summer 30 percent. Components coming from ICA gave followed by leaf flushing from the month of May. Similar to
OAA of 69 percent for monsoon, 52 percent for winter and 36 our observations, Murali and Sukumar (1993) reported that
percent for summer. Components extracted from PCA provided leaf flushing peaks in the dry season before the onset of rains
OAA of 42 percent for monsoon, 25 percent for winter, and 33 at tropical deciduous forests of India. Phenological varia-
percent for summer. Tables and Figures for SAM classifier are tions of the three covers were correlated with the NDVI values
not provided because of lower classification accuracy. of the subset. Higher NDVI values were seen in monsoon and

38 Aug us t 2 014 PHOTOGRAMMETRIC ENGINEERING & REMOTE SENSING

 (a) (b)

(c)
Figure 5. Mean (n = 20) spectral profile of three vegetation covers collected from (a) Monsoon, (b) Winter, and (c) Summer.

(a) (b) (c)

Figure 6. mlc-based classified images using k-pca extracted bands with three endmembers for (a) Monsoon, (b) Winter, and (c) Summer.

minimal during summer. Variations in the NDVI values as
reported by Silva et al. (2013) are in support of our observa-
tions. PRI values for wet and dry seasons showed a pattern
similar to the one reported by Pape et al. (2013) for tropical
cover. They were higher in wet season. Lower PRI values dur-
ing dry season reflected seasonality in phenological cycle.
It is linked to the seasonal variations in water availability.
Previous studies have shown that the changes in PRI values
could be related to the leaf development and aging (Garbulsky
et al., 2011; Penuelas et al., 2011). Variations in PRI values
correlating with leaf phenology go together with these reports.
Relatively higher PRI values seen in April image (as compared
to the ones in January) could be linked to leaf flushing specifi-
cally seen in mixed species cover. Significant variation in
the values of HVIs (NDVI, PRI) indicates the utility aspect of
temporal Hyperion data in monitoring phenological changes
of vegetation covers.
Spectral reflectance values of vegetation get strongly influ-
enced because of variations in foliar chemistry. These changes
are said to bring variability in the spectral shape (Dennison
and Roberts, 2003; Roberts et al., 1997). Spectra of the three
covers obtained in these studies evidently showed this phe-
nomenon. The greatest variation in spectral signatures across
seasons was the most pronounced in the NIR and SWIR regions.

PHOTOGRAMMETRIC ENGINEERING & REMOTE SENSING Aug u s t 2014 39

 Table 2. Overall Accuracies (oaa) Attained from Single, Two and Three Species Classification Approaches for Three Different Seasons
(T - Teak; B - Bamboo; M - Mixed species)
Single species classification
T B M T-B
Monsoon 86% 83% 100%
Winter 84% 75% 93%
Summer 82% 75% 100%
Monsoon 83% 75% 100%
Winter 76% 50% 80%
Summer 76% 75% 87%
Monsoon 76% 50% 100%
Winter 59% 25% 24%
Summer 41% 42% 76%
A gradual rise in the absorptive strength of chlorophyll has
been observed from summer to monsoon season manifest-
ing the phenological state of the vegetation at that season.
During monsoon season, individuals of selected three covers
had very high density of crown foliage. All the three covers
showed typical spectral pattern of healthy vegetation with
stronger chlorophyll absorption. Reflectance spectra obtained
for monsoon season showed consistency and displayed low
variability in the VIS region compared to that of the summer
and winter season datasets. Spectral variability in VIS region
among species is low due to strong absorption by chlorophyll
(Cochrane, 2000). Leaf fall had started in winter and because
of this there was an increase in the reflectance values at VIS
region of the spectra coming from Teak and Bamboo covers.
Similarly, Ustin et al. (2004) reported that senescent nature of
temperate vegetation in summer season has increased reflec-
tance across the VIS region and shifted the red edge towards
the shorter wavelength (termed the “blue shift”). Three covers
of this study had very low density of crown foliage in the
summer season. Spectra of this season showed lower NIR
reflectance, could be because of fewer newly formed or older
senescent leaves in the crowns of Teak, Bamboo, and Mixed
species covers. Analogous results were observed by Clark
et al. (2005). Earlier reports (Key et al., 2001, Dennison and
Roberts, 2003) indicated that seasonal variations lead to finer
levels of spectral details in hyperspectral data helping in iden-
tifying the phenology and classification of species. Chambers
et al. (2007) said that deciduousness is a key functional trait of
many tropical trees, and often provides a main axis for vegeta-
tion classification. Variation seen in the spectra of the three
covers (coming from different seasons) reflecting phenological
changes are congruent to these findings. Papeş et al. (2013)
reported that understanding seasonality of spectral charac-
teristics of tropical tree crowns has implications in spectral
based multi-seasonal species mapping and studying ecosystem
processes. Variations in the spectral reflectance characteristics
for the three forest covers of this study help in understanding
phenological changes of similar kind in tropical covers.
Dimensionality Reduction, Endmember Selection and Classifiers Tested
We noticed that linear (PCA and ICA) and nonlinear (k-PCA)
methods tested here differed from each other in computa-
tional speed and performance. Nonlinear methods are thought
to give better results with the trade-off of slower runtime.
Our results are supported by the findings of Burgers et al.
(2009) and Fong et al. (2007). A larger number of principal
components were extracted in k-PCA, eventually resulting in
the best generalization performance in comparison to that of
PCA. Cao et al. (2003) also found that k-PCA can perform better
40 Aug us t 2 014
Two species classification Three species classification
T-M B-M T-B-M
k-PCA-ML
74% 81% 77% 72%
71% 72% 71% 70%
57% 74% 68% 55%
ICA-ML
76% 77% 71% 77%
57% 62% 52% 57%
69% 66% 74% 55%
PCA-ML
62% 74% 68% 57%
48% 47% 48% 43%
40% 60% 48% 48%
compared to PCA. Images classified using k-PCA components
were much sharper (without “salt-and-pepper” effect) as
compared to the classified images based on PCA and ICA com-
ponents. It appeared very close to the actual distribution of
vegetation and other details, as seen in the study area. Among
the three dimensionality reduction methods, k-PCA fared bet-
ter followed by ICA. PCA-ML showed lower accuracies. This is
because k-PCA and ICA can explore higher order information of
the original inputs than PCA. PCA only considers second-order
statistics, and this cannot make it very effective with hyper-
spectral data, since many substances covered by very high
spectral resolution sensors cannot be characterized by second-
order statistics (Villa et al., 2009). Our results are consistent
with that of Cao et al. (2003) which showed that Support
Vector Machine forecasting by feature extraction using PCA, k-
PCA, and ICA performed best in k-PCA followed by ICA. Results
reported here are in contradiction to Burgers et al. (2009) and
Rodarmel and Shan (2002) who showed effective performance
of PCA results coming from PCA-ML of our study are in tune
with Zagajewski et al. (2005) who reported lower OAA values
using supervised classification for forests and meadows (20 to
56 percent) in a PCA-derived components. Manually selected
endmembers with highest occupied quadrats worked well
for all the dimensionality reduction methods. This reempha-
sizes the importance of occupancy of a species in extracting
endmembers for better classification. The same quadrats were
considered to obtain endmember spectrum of each vegetation
cover for testing across seasons. The accuracy levels were
appropriate (coming from Hyperion sensor) as illustrated in
Tables 3, 4, and 5 for k-PCA-ML. Results indicate that ground
truth of forest cover can be successfully utilized in the classi-
fication of remote sensing data of different dates and seasons
provided that the land-use land-cover changes due to defores-
tation, anthropogenic activities and forest fire are minimal.
Results indicate that the single cover classification showed
highest accuracy (with k-PCA-ML, ICA-ML). As the number of
vegetation covers increased (123), classification accuracy
decreased. Féret and Asner (2013) reported that increasing
species richness results in decreased classification accuracy
for all the used classifiers. Castro-Esau et al. (2006) stated that
differences in leaf optical properties appear promising when a
limited number of species are discriminated. This is because
confusion during classification, increases with species rich-
ness as probability of overlapping feature/s increases. Mixed
species cover showed higher accuracy in single species clas-
sification across all the three seasons as compare to Teak and
Bamboo. This is attributed to the diverse nature of phenologi-
cal cycles of the species which was reflected in its characteris-
tic spectral signature. Teak and Bamboo did not show similar
PHOTOGRAMMETRIC ENGINEERING & REMOTE SENSING
 (a) (b) (c)
Figure 7. mlc-based classified images using ica extracted bands with three endmembers for (a) Monsoon, (b) Winter, and (c) Summer.

Table 3. Confusion Matrix Obtained Using ml Classification with k-pca Table 6. Confusion Matrix Obtained Using ml Classification with ica
Selected Components for Monsoon Season Selected Components for Monsoon Season
Mixed User’s Mixed User’s
Teak Bamboo Unclassified Total Teak Bamboo Unclassified Total
species accuracy species accuracy
Teak 21 2 1 - 24 88% Teak 23 5 1 - 29 86%
Bamboo 3 8 2 - 13 62% Bamboo 2 7 1 - 10 70%
Mixed Mixed
3 3 14 - 20 70% - 1 16 - 17 94%
species species
Unclassified 2 - 1 - 3 Unclassified 4 - - - 4
Total 29 13 18 - 60 Total 29 13 18 - 60
Producer’s OAA = Producer’s OAA =
72% 62% 78% - 86% 54% 89% -
accuracy 72% accuracy 77%
Kappa coefficient = 0.57 Kappa coefficient = 0.64

Table 4. Confusion Matrix Obtained using ml Classification with k-pca Table 7. Confusion Matrix Obtained using ml Classification with ica Selected
Selected Components for Winter Season Components for Winter Season
Mixed User’s Mixed User’s
Teak Bamboo Unclassified Total Teak Bamboo Unclassified Total
species accuracy species accuracy
Teak 21 4 1 - 26 81% Teak 17 2 5 - 24 71%
Bamboo 2 6 1 - 9 67% Bamboo 2 6 1 - 9 67%
Mixed Mixed
5 2 15 - 22 68% 9 5 11 - 25 44%
species species
Unclassified 1 1 1 - 3 Unclassified 1 - 1 - 2
Total 29 13 18 - 60 Total 29 13 18 - 60
Producer’s OAA = Producer’s OAA =
72% 46% 83% - 59% 46% 61% -
accuracy 70% accuracy 57%
Kappa coefficient = 0.54 Kappa coefficient = 0.33

Table 5. Confusion Matrix Obtained Using ml Classification with k-pca Table 8. Confusion Matrix Obtained Using ML Classification with ica
Selected Components for Summer Season Selected Components for Summer Season
Mixed User’s Mixed User’s
Teak Bamboo Unclassified Total Teak Bamboo Unclassified Total
species accuracy species accuracy
Teak 17 - - - 17 100% Teak 16 3 4 - 23 70%
Bamboo 8 2 3 - 13 15% Bamboo 3 8 4 - 15 53%
Mixed Mixed
4 11 14 - 29 48% 8 2 9 - 19 47%
species species
Unclassified - - 1 - 1 Unclassified 2 - 1 - 3
Total 29 13 18 - 60 Total 29 13 18 - 60
Producer’s OAA = Producer’s OAA =
58% 15% 78% - 55% 62% 50% -
accuracy 55% accuracy 55%
Kappa coefficient = 0.33 Kappa coefficient = 0.32

PHOTOGRAMMETRIC ENGINEERING & REMOTE SENSING Aug u s t 2014 41

features, as there is sizeable intra-specific synchrony in the
phenological cycle. Amongst two cover classification, Teak
- Mixed species cover combination fared better with greater
OAA across the seasons. We attribute this to better uniformity
noticed in the canopy thickness of these two covers as com-
pared to Bamboo which showed a dissected canopy structure
(Christian and Krishnayya, 2009).
Extracted components of ICA and k-PCA showed a succes-
sive improvement in the classification of the three covers
from summer to winter to monsoon. Classification accuracies
and kappa values acquired show strong seasonality. Similar
feature was not seen with PCA. For PCA, information was dis-
cerned in a small number of components in contrast to k-PCA
and ICA. According to Mika et al. (1999), k-PCA can provide a
larger number of features carrying information about the clus-
tering structure in the data. This may be one of the reasons for
getting good results for all the three seasons using k-PCA-ML
classification. Phenological state of the three covers, interfer-
ence of soil reflectance could have caused inconsistency in
classification in summer season. Previously, Lee et al. (2005)
reported that in summer, spectral characteristics of vegetation
are influenced by chemical constituents of dry vegetation and
moisture conditions of soil and vegetation. Similar infer-
ences can be made for the variations seen in the classification
accuracy. Keeping in view of the data used, complexity, and
patchy distribution of vegetation at the study site, the OAA is
appropriate for species level classification of tropical forest
cover in varying phenological conditions. An analogous con-
clusion was drawn by Thenkabail et al. (2004).
The SAM classifier was not efficient regardless of the three
dimensionality reduction techniques used. Maximum OAA
of 69 percent came from ICA extracted components of mon-
soon image. Classification accuracies of other seasons were
not exceeding 50 percent. Similar range of OAA values were
also reported for discriminating rainforest species using SAM
as a classification algorithm, with no accuracy exceeding 50
percent (Clark et al., 2005). Cho et al. (2010) reported a mean
OAA of 57 percent utilizing air-borne hyperspectral data and
SAM classifier. SAM classification, working on a single distance
metric appears to be lesser effective in looking at within spec-
tral separability for the three vegetation covers.
Conclusions
In this study multi-seasonal EO-1 Hyperion data was used to
classify three distinct tropical forest covers. We explored three
unsupervised dimensionality reduction methods (k-PCA, ICA,
and PCA) to obtain the best discriminatory model across three
seasons. We draw the following conclusions from this study:
1. Identification of uncorrelated components using
unsupervised feature extraction method has helped in
overcoming the Hughes phenomenon. A 95 percent
reduction in data volume is feasible when hundreds of
HNBs are reduced to the visually selected components
for different seasons using ICA and k-PCA.
2. Multi-seasonal EO-1 Hyperion data proves its potential
application for classifying tropical deciduous forest
covers akin to the ones seen in the Shoolpaneshwar
Wildlife Sanctuary, India. The three vegetation covers
classified using images of three seasons achieved the
best classification accuracies using k-PCA through maxi-
mum likelihood classifier for the monsoon season with
overall accuracies of 83 to 100 percent for single spe-
cies, 74 to 81 percent for two species, and 72 percent
for three species.
3. Results indicate that ground truth of forest cover can
be successfully utilized in the classification of remote
42 Aug us t 2 014
sensing data of different dates and seasons provided that
the land-use land-cover changes due to deforestation,
anthropogenic activities and forest fire are minimal.
Acknowledgments
MS, NJ, NSR are thankful for the financial assistance by NRDMS,
DST, New Delhi (NRDMS/11/1669/10/Pr: 3). BC is thankful
to DST’s Women scientist program. DV is thankful to the D.S.
Kothari Post-Doctoral Fellowship Progamme (UGC). Authors are
thankful to Dr. Morton Canty for providing the kernel PCA code.
They are grateful to reviewers and the guest editor of this special
issue, Dr. Prasad S. Thenkabail, USGS, for valuable suggestions.
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