Disertasi Coffee Mapping by Gis

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Using Image Analysis and GIS for coffee Mapping
Sandra Bolanos
Department of Geography
McGill University, Montreal
April, 2007
A thesis submitted to the faculty of Graduate Studies and

Research in partial fulfillm ent of the requirements of degree of
Master of Science
Sandra Bolanos 2007
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Abstract
Currently, the system that developing countries use to map coffee crops is
expensive, tedious and inaccurate; therefore coffee maps cannot be updated
frequently and production cannot be accurately estimated. If such countries could
map coffee crops in a cost-effective way, they would have an advantage in terms of
setting the prices and getting a higher return for their product.
Here I hypothesize that coffee systems can be properly characterized and
mapped using the spectral and spatial information derived from satellite images and
topographic data. I also believe that during the spatial analysis of the data, the
additional information provided by an object-based approach (comprehensive
information about the shape and context of a particular area) provides more
information than a pixel-based one, traditionally used in the integration of Remote
Sensing and Geographic Information Systems (GIS).
I statistically analyzed spatial and spectral characteristics of different coffee
systems (monoculture, polyculture and agroforestry systems) in three study areas in
Colombia of 70km2 each. I integrated satellite images and topographic grids using
both pixel-based and object-based approaches in a hierarchical approach and the
results were compared. Following this hierarchical approach, a preliminary
classification was performed to reduce the number of classes spectrally similar to
iii
Abstract
coffee systems. Then in a second step, the classification was refined using decision
rules from the statistical analysis of objects (composed of at least 3 pixels). Finally,
using the same objects, the classification was refined further, through linear spectral
unmixing.
The results show that the rule-based classification combined with an object-based
approach can improve the overall accuracy of the classification by 3% and by 17.47%
for the coffee class when compared to the pixel-based analysis. The linear spectral
unmixing, however, does not contribute to improve the classification accuracy when
Landsat images are used to map the different types of coffee systems
iv
Resume
Actuellement, le systeme que les pays en voie de developpement emploient
pour cartographier les recoltes de cafe est cher, penible et imprecis. Ainsi, les cartes
de cafe ne peuvent etre mises a jour frequemment et la production ne peut pas etre
estimee avec exactitude. Si ces pays pouvaient cartographier les recoltes de cafe d'une
maniere plus economique, ils auraient un avantage pour fixer les prix et obtenir des
revenus plus eleves pour leur produit.
Je pose ici lhypothese que les zones de cafe peuvent etre correctement
caracterises et cartographies en utilisant l'information spectrale et spatiale derivee des
images satellites et des donnees topographiques. Je suppose egalement que pendant
l'analyse spatiale des donnees, l'information additionnelle foumie par une approche
object-basee (informations completes sur la forme et le contexte dune zone
particuliere) fournit plus d'informations que quune approche pixel-basee \
traditionnellement utilisee dans l'integration de la teledetection et des systemes
d'information geographiques (GIS).
J'ai analyse (statistiquement) les caracteristiques spatiales et spectrales des
systemes de cafe dans trois secteurs d'etude en Colombie de 70km2 chacun. J'ai
Resume
integre des images satellites et des grilles topographiques en utilisant les 2 approches
"pixel-basee et object-basee dans une approche hierarchique et les resultats ont ete
compares. Des objets ont ete formes sur la base de la similitude spectrale des bandes
2.3.4 5 et 7. Apres l'approche hierarchique, une classification preliminaire a ete
effectuee pour reduire le nombre de classes spectralement semblables aux systemes
de cafe. Alors, dans une deuxieme etape, la classification est affinee en utilisant des
regies de decision sur l'analyse statistique de plus petits objets (composes de 5 pixel
ou moins). Finalement, en utilisant les memes objets, la classification a ete de
nouveau affinee, par unmixing spectral lineaire.
Les resultats prouvent que la classification basee sur les regies a combine avec
une approche objet-basee peut ameliorer l'exactitude globale de la classification de
3% et par 17.47% pour la classe de cafe une fois comparee a l'analyse Pixel-basee. Le
unmixing spectral lineaire, cependant, ne contribue pas pour ameliorer l'exactitude de
classification quand des images de Landsat sont employees pour tracer les differents
types de systemes de cafe
vi
Acknowledgements
This research could not be achieved without the support of the J.W.
McConnell, that provided me a McConnell fellowship in environment for two years,
and without the support of both; my advisor, Dr. Raja Sengupta, at McGill University
and Dr. Thomas Oberthur, my mentor at the International Center for Tropical
Agriculture. I would like to acknowledge the German Cooperation Agency -G T Z -
for providing financial support for this research through the macro project New
Opportunities for Hillside Farmers: Matching Product Quality, Environments and
Market Demandfor High-Value Agricultural Products developed by CIAT.
Thanks are extended to the Smithsonian Tropical Research Institute for
providing a Levinson Fellowship for my studies and to Department of Geography at
McGill University, for the Warren Fellowship in GIS I got. I sincerely thank to the
professors and classmates at the Geography department for their valuable support
during my stay at McGill. I want to give special thanks to professor Jonathan
Seaquist for his technical and professional advice.
I also want to acknowledge German Escobar, Herman Usma and Natalia Uribe
for their technical support during the fieldwork. I want to give special
acknowledgments to the coffee farmers associations in Colombia, especially to
Federation Nacional de Cafeteros de Colombia FNC for providing the technical
vii
Acknowledgements
and financial support for my fieldwork. I hope this methodology can be integrated
into their information system and improve the strategic planning by providing a better
quantification of the coffee areas in Colombia.
Contents
A B S T R A C T ............................................................................................................................................................................I l l
R E S U M E ...................................................................................................................................................................................V
C O N T E N T S ...........................................................................................................................................................................IX
L IS T O F T A B L E S ................................................................................................... XI
L IS T O F F I G U R E S ..........................................................................................................................................................X I I
I N T R O D U C T I O N ................................................................................................................................................................ 1
1 .1 . R e s e a r c h O b je c t iv e s ............................................................................................. :.................................... 4
1.1.1 What are the physical features that characterize different coffee systems?...................... 4
1.1.2 What is the accuracy that can be obtained as a result o f combining spectral and
elevation data to map coffee systems?.................................................................................................. 4
S T U D Y A R E A A N D D A T A ....................................... 6
2.1 S t u d y A r e a .........................................................................................................................................................6
2 .2 G IS a n d I m a g e D a t a : ....................................................................................................................................8
2 .3 F ie l d W o r k M e t h o d o l o g y ..................................................................................................................... 10
C O N T E X T ......................................... 13
3.1 T h e U s e o f S at el l it e Im a g e r y f o r C r o p M a p p i n g ...................................................................13
3 .2 T h e U s e o f I m a g e A n a l y s is f o r C o ffe e M a p p i n g ..................................................................... 16
3 .3 T h e U s e o f O bject B a s e d Im a g e A n a l y s i s ............................................. !.....................................19
3 .4 In t e g r a t e d G e o g r a p h ic I n f o r m a t i o n S y s t e m s .............................. 20
3 .5 T h e U s e o f D ig it a l E l e v a t io n M o d e l s (D E M s ) f o r L a n d C o v e r A n a l y s i s 24
M E T H O D S .................................................................................. 25
4 .1 D E M E v a l u a t i o n .......................................................................... 25
4 .2 I m a g e P r e p r o c e s s in g ................................................................................................................................. 26
4.2.1 Radiometric Correction.........................................................................................................27
4.2.2 Terrain Illumination Correction........................................................................................... 30
4.3.4 Soil Background Influence:...................................................................................................33
4 .4 H ie r a r c h ic a l C l a s s if ic a t io n ..................................................... :......................................................33
4 .5 S e g m e n t a t io n : b u il d in g t h e u n it s f o r o bjec t - b a s e d a n a l y s i s .......................................34
4 .6 S c a l e effec ts o n im a g e s e g m e n t a t i o n .......................................................................................... 35
4 .7 S h a p e a s a d d i t io n a l fe a t u r e f o r l a n d c o v e r c h a r a c t e r i z a t i o n : .............................37
4 .8 S i g n a t u r e E v a l u a t io n : S t a t is t ic a l a n a l y s is o f s a m p l e s ..................................................3 8
4 .9 R u l e - b a s e d im a g e c l a s s if ic a t io n .......................................................................................................42
4 .1 0 th e L in e a r M ix in g M o d e l f o r S p e c t r a l U n m ix in g i n c o f f e e f ie l d s !............. 44
4 .1 1 A c c u r a c y A s s e s s m e n t ...............................................................................................................................47
R E S U L T S ................................................................................................................................................................................ 52
5 .1 D E M E v a l u a t io n .....................................................................................................................................5 2
ix
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Contents
5 .2 I m a g e P r e p r o c e s s in g : ................................................................................................................. 54
5 .3 P r e l im in a r y C l a s s if ic a t io n :.................................................................................................................54
5 .4 E x p l o r a t o r y A n a l y s is : P ixel B a s e d A n a l y s is ............................................................. 57
5.4.1 ND VI vs. percentage o f shade............................................................................................. 57
5.4.2 Spectral separation between coffee and non-coffee fields...................................... 58
5 .5 P ixel - b a s e d c l a s s if ic a t i o n ................................................................................................................... 60
5 .6 Im a g e S e g m e n t a t i o n : C h o o s i n g t h e A p p r o p r ia t e S p a t ia l U n i t s ................................ 63
5 .7 S ig n a t u r e A n a l y s is : .................................................................................................................................. 65
5 .8 R u l e d - b a s e d C l a s s if ic a t io n u s in g o b je c t s : ................................................................................68
5 .9 E v a l u a t in g L in e a r S pe c t r a l U n m i x in g T o M a p d if f e r e n t ty pe s o f c o ffe e
s y s t e m s ................................................................................................................................................................................ 73
5 .1 0 A c c u r a c y A s s e s s m e n t .............................................................................................................................. 75
D IS C U S S IO N ...................... 79
SUMMARY A N D CONCLUSIO NS.....................................................................................................86
BIBLIOGRAPHY.................................................................................. 89
ANNEXES
ETM+ CALIBRATION PARAMETERS............................................................................................ 101
D ATA DISTRIBUTION: SPECTRAL A N D TOPOGRAPHIC CHARACTERISTICS 102
BOX PLOTS FOR COFFEE SYSTEMS VS. NON-COFFEE SYSTEMS.................................... 107
NORMALITY TEST................................................................................
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List of Tables
Table 2-1: Spectral Bands in Landsat ETM+ image................................... 8
Table 5-2. Differences between coffee and non-coffee systems..................................60
Table 5-3: Features ranges used in pixel-based classification..................................... 61
Table 5-4: Accuracy statistics for per-pixel classification........................................... 61
Table 5-5 Comparison between mean objects and pixels values fo coffee..............64
Table 5-6 Comparison between mean objects and pixels values for Non-coffee ... 65
Table 5-7: Non-significant differences between coffee and non-coffee systems.
Radiometric features.............................................................................................. 67
Table 5-8: Significant differences between coffee- and non-coffee systems Shape
features.............................................................................................................................. 67
Table 5-9: Non-significant differences between coffee and non-coffee systems:
Shape Features................................................................................................................. 67
Table 5-10: Range values for object-based classification.................... 68
Table 5-11: Accuracy statistics for object based classification................................ 69
Table 5-12: Accuracy statistics after the spectral unmixing........................................ 76
Table 6-13: Comparison between different methodologies......................................... 79
xi
List of Figures
Figure 2-1: Study Area and distribution of Sampling Points......................................... 7
Figure 2-2: Structure for Field Sampling......................................................................12
Figure 3-3: Spectral Behavior of Vegetation....................... 14
Figure 3-4: Representation of polygon classification functionality.............................23
Figure 4-5: Box Plot Diagram............................................. 39
Figure 4-6: The Spectral Angle Mapping in a two-dimensional space....................... 46
Figure 4-7: Methodological Sequence...........................................................................51
Figure 5-8: DEM evaluation...........................................................................................53
Figure 5-9: Overlap between image and rivers generated from D E M ........................53
Figure 5-10: Terrain illumination correction................................................................ 54
Figure 5-11: Preliminary classification..................................................... 56
Figure 5-12: Correlation between percentage of cover and N D V I.............................58
Figure 5-13: Scatter plot in all bands for coffee and non-coffee areas....................... 59
Figure 5-14: Box Plot for both land cover classes in band 1 ........ 60
Figure 5-15: Ruled-Based classification map obtained from pixel-based analysis... 62
Figure 5-16: Omnidirectional variogram.......................................................................63
Figure 5-17: Ruled-Based classification using object-based analysis........................ 70
Figure 5-18: Spatial distribution of coffee systems in the area....................................72
Figure 5-19: Spectral separation between mean values of coffee and non-coffee areas
in bands blue and green.............................................. 73
Figure 5-20: Spectral separation between mean values of coffee systems and non
coffee areas, in bands green and red ............................................................................... 74
Figure 5-21: Classification map resulting from the linear spectral unmixing 75
Figure 5-22: Spatial distribution of the error: the RMS image.................................... 78
xii
Chapter 1
Introduction
Coffee ranks as one of the world's most important commodities, being second in
the list of income-generating products exported from developing countries after
petroleum, and represents the main source of income for 25 million families on the
hillsides of Latin America, Southeast Asia and East Africa (Gresser and Tickell, 2002).
In Colombia, coffee has traditionally been an essential part of the economy, the social
networks, and the culture in the tropical mountain forest (Garcia, 2001).
Coffees role in the economy of developing countries has always been of primary
importance: in 2000, coffee represented 79% of the exports in Burundi, 54% in Ethiopia,
43% in Uganda, 31% in Rwanda and between 7 and 24% for many other countries in
Latin America (Gresser and Tickell, 2002; Varangais et al., 2003). However, in 2002,
coffee reached its lowest historical price. Continuous global overproduction caused
coffee prices to fall below production cost for many producers (Gresser and Tickell,
2002), which led to social and economic problems such as unemployment, migration and
diminishing well being (Del Corral et al., 2002; Hoyos, 2002; Ponte, 2002; Varangais et
al, 2003; Bacon, 2005).
Introduction
Furthermore, decreases in prices lead producers to change from traditional
agroforestry systems (shade coffee) to non-shade coffee varieties with higher
productivity. This has generated environmental problems due to deforestation and the
use of agrochemicals (Evenson and Gollin, 2003, Lee, 2002; Roach, 2003; Smithsonian,
1997a; Rainforest Alliance, 2000). Considering the strong impact on the environment,
many international certification programs are using differential coffee brands to promote
the use of shade coffee (Rainforest Alliance, 2000, Smithsonian 1997b, Dietsh et al.
2004, Perfecto et al. 2005) which requires less fertilizers due to improved soil
management (i.e., leaf litter from the trees serves to fertilize the soil), thus influencing
coffee quality (DaMatta, 2004).
The increase in the participation of smaller farms provides the opportunity to
grow specialty coffee, which benefits from shade (Muschler, 2001). Shaded systems also
contribute to food security and economic income from accompanying species (e.g. fruits).
However, the inventory and monitoring of areas of shade coffee plantations is a tedious
task with the current methodologies. Therefore, is not clear to what extent areas suitable
for growing shade coffee have been sustainably utilized worldwide.
Also, not much has been done to evaluate the impacts of changes in coffee
systems on the environment in large geographical regions. Any evaluation of the impacts
will require a cost-efficient methodology to analyze land use change. Cost-efficient
methodologies for coffee mapping have yet to be developed (Croome, 1989; Moreira,
Introduction
2004) because the existing methods are expensive (e.g. use of infrared photography by
NASA, 2005 or IKONOS by Widayatti et al, 2005), inefficient (use of manual editing
after image processing), or not applicable to all types of coffee systems.
Landsat data provides an affordable means of mapping vegetation, and has been
widely used for crop mapping and monitoring. Many studies have focused on few
agricultural crops, specifically on sugar cane, wheat, maize, and rice, which have a
seasonal pattern of growth (Maas 1988, Van Niel and Me Vicar, 2004, Wall et al, 1984,
Zwiggelaar, 1998). But permanent crops, such as coffee have not yet been analyzed to
the same extent. Due to the spectral similarity with forest, shade-coffee systems have
been difficult to reliably map under different shade densities (Moreira, 2004).
In order to contribute to a better strategic planning of coffee production areas, this
research evaluated the potential of merging GIS data and Landsat imagery to characterize
diverse coffee systems using an integrated approach. The proposed approach consisted
of image and spatial data segmentation for landscape analysis. The main hypothesis is
that different coffee growing systems can be mapped using spectral information derived
from Landsat imagery and topographic features derived from DEMs. It is also
hypothesized that the additional information contained in an object-based approach will
lead to a better characterization o f th e different co ffe e system s as com pared to th e
traditional pixel-based analysis.
Introduction
1.1. Research Objectives
To determine how different coffee growing systems can be mapped and
characterized by integrating Geographic Information Systems (GIS) data and Remote
Sensing (RS) information, two specific objectives are addressed:
1.1.1 What are the physical features that characterize different coffee systems?
It is well known that coffee grows on hillsides. Therefore, it is expected that the
degree of slope can be used as complementary information for determining the existence
of coffee plantations. It is also known that quality of coffee is influenced by temperature
associated with elevation (Chapman and SuranSubhadrabandhu, 2001) and yield is
associated with the amount of solar radiation (Matoso et al, 2004). The correlations
between environmental variables, spectral information and crop characteristics such as
leaf area index (Asrar et. al., 1984), plant health (Apan, 2004) and yield (Doberman and
Ping, 2004; Hatfield, 1983; Vina et al., 2004) have been widely analyzed in the literature
(Moran et al., 1997; Moulin et al., 1998; Wiegand et al., 1991; Zwiggelaar, 1988).
Therefore, it is hypothesized that the type of coffee system (shade, non-shade) can be
identified using specific topographic (altitude, slope and aspect) and spectral signatures.
1.1.2 What is the accuracy that can be obtained as a result o f combining spectral and
elevation data to map coffee systems?
In order to analyze if the several coffee systems can be differentiated, a statistical
analysis should be done to evaluate their differences. If differences exist for some
characteristics, those characteristics can be used to map coffee systems. It is expected
Introduction
that the accuracy will be lower for shaded systems, due to the confusion with forest and
other agroforestry systems.
To answer the above questions, I combine topographic (altitude slope and aspect)
and spectral data to differentiate between the two coffee systems, from question 1 above.
By doing this, I expect to establish a cost-efficient methodology to map coffee systems.
Chapter 2
Study Area and Data

2.1 Study Area
The study area encompasses the region of coffee cultivation in the Department of
Huila in Colombia, located between 1 45 N to 237 N of latitude and from 7550 to
7650 W longitude, elevation values between 1270 to 2070 meters above sea level, and
slopes between 15 and 30 degrees. With precipitation ranges from 1200-1800 mm per
year and temperatures from 8 C to 30 C, the natural vegetation in the area consists
predominantly of coffee, secondary forest, grasslands and riparian vegetation along
streams and in lowlands. As part of the Diversification Agriculture Project Alliance -
DAP A - funded by the German Ministry for International Cooperation and Development
-B M Z - (Oberthur, 2004), a total of 240 farms in the municipalities of Oporapa, Palestina
and Timana in Huila were georeferenced by a high-precision Trimble PRO-XRS Global
Positioning System (GPS) device that provided the latitude, longitude, and elevation
value. DAPAs main objective is to help farmers to make decisions that lead to the
production and marketing of high value products (such as tropical fruits, nuts, specialty
coffees and medicinal plants) for diversification on particular farm sites not suitable to
sustain commodity coffee production. Fig.2-1 shows the location of the study area and
the distribution of sample points:
Figure 2-1: Study Area and distribution of Sampling Points
Study Area and Data
2.2 GIS and Image Data:
The data sets available for this analysis include:
A Landsat image ETM+path 09 row 059 from August 24th 2001. The image was
obtained from GLCF1 web site. The spectral information carried by this image is
shown in Table 2-1.
Nominal Spatial
Spectral Bands Colour
Resolution (m)
28.5 0.450-0.515 Blue
28.5 0.525 -0.605 Green
28.5 0.630 - 0.690 Red
28.5 0.760 - 0.900 Near IR
28.5 1.550 - 1.750 MidIR
60 10.40 -12.5 Thermal IR
28.5 2.080 - 2.35 MidIR
12.5 0.52 - 0.92 Panchromatic
T able 2-1: Spectral Bands in Landsat E' TV1+ image
A Digital Elevation Model (30 m pixel) generated by the Shuttle Radar
Topographic Mission of NASA (SRTM-NASA).
Aerial photography at a scale of 1:40000, taken in 1996 in the three municipalities
in the department of Huila, Colombia, provided by Federacion Nacional de
Cafeteros, FNC2. These photographs were georeferenced using first-grade
polynomial algorithm (Mather, 2004) and ground control points.
A total of 26,355 points that contains the geographic position of the all coffee
farms surveyed by a Garmin eTrex GPS system in the three municipalities. This
dataset belongs to the coffee information system -SICA-, built and managed by
FNC. It represents an exhaustive sampling of all coffee farms in the study area.
In addition the X,Y and Z coordinates, this data set contains the farm size, age of
the plantation, density (i.e. number of plants), variety, and illumination conditions
'GLCF: Global Land Cover Facility Project: (http://glcf.umiacs.umd.edu/index.shtml)

2 FNC is the coffee farmers association in Colombia.
Study Area and Data
A total of 240 points established in 2004 by a Trimble PRO-XRS GPS device
with OmniSTAR real-time differential correction that determined the latitude,
longitude, and elevation in the center of each farm. Those farms were located in
Huila, within the framework of the DAPA project.
44 polygons with different percentage of shade (23 in Oporapa, 6 in Palestina and
15 in Timana) surveyed as well by a Trimble PRO-XRS GPS device with
OmniSTAR real-time differential correction3 during august 2005. Each polygon
contains information about the coffee system (polycuture or agroforestry system),
the illumination conditions (percentage of cover over the coffee) and geographic
position (X, Y, Z) of selected farms in the three municipalities. Farms were
selected on the criterion that the minimum percentage of shade was 30%. The
methodology for this data collection is described in section 2.3. Due to
accessibility to most polyculture systems (coffee grown with plantain or banana)
in the study area, the sampling contains mainly agroforestry systems (coffee
grown with citric fruits and/or introduced species of secondary forest such as Inga
sp. and Erythrina sp.)
300 points randomly taken in areas that do not contain any type of coffee system
at all (called non-coffee areas, from this point forward). Those points were taken
by visual interpretation of the image, and were selected due to a) their spectral
similarity with coffee systems and b) their location: away from areas with high
density of coffee farms, determined by the SICA inventory (see above). This set
3 This term will be explained in the next section
Study Area and Data
of points was divided in two groups: 140 points for training and 140 points for
accuracy assessment.
2.3 Field Work M ethodology
The coffee systems can be extensively classified as: a) monoculture, also known
as non-shade or Sun coffee b) polyculture, which is shaded coffee, consisting of mainly
plantain over the coffee bushes and c) agroforestry systems (partially shaded coffee).
Sites were picked, in an attempt to cover as much variation as possible. In the first step, a
reconnaissance trip was done in order to test techniques for data collection in the field
and to evaluate the appropriateness of the classification system mentioned above.
The fieldwork methodology followed the guidelines provided by GLOBE (2005):
a representative4 square of 30 meters long was selected (Figure 2-2a) and georeferenced
with a Trimble Pro-XRS GPS system provided with OmniSTAR real-time differential
correction. A real-time differential correction occurs when the base station (a GPS
receiver) compares its precisely known location to the position co-ordinates as obtained
from satellite signals to estimate the errors in the satellite signal as it receives the data
(Leick, 1995). The correction is calculated by the difference between the calculated and
known coordinates and broadcasted to the roving GPS receiver via radio signal if the
source is land based, or via a satellite signal if it is satellite based. The correction is then
applied to the position the differential GPS is calculating to correct its positional estimate.
The premise underlying this concept is that the receivers will experience similar
4Representative of the coverage over coffee bushes
10
Study Area and Data
atmospheric errors. Differential correction reduces the error in location from some
meters to a few centimeters, depending on the topographic and atmospheric conditions.
Crown closure5, also called canopy closure (i.e. % of shade over coffee) was
measured by the amount of ground area the tree crowns occupies (see Fig. 2-2b).
Transects located within the polygon were used to measure canopy closure. The percent
of crown closure was determined by the presence or absence of tree crown at 2m
intervals along the transects. Each diagonal (in north East and South West directions)
was surveyed with a tubular densitometer by walking on it and stopping every two
meters, looking up and counting the number of times a tree was at the crosshairs (taken as
a positive record). The number of positives divided by the total number of readings (i.e.
the length of the diagonal divided by two) gives us the percent of tree canopy cover over
the coffee field within the sample area, which is taken as a representative of the
percentage of cover over the coffee in the whole farm. Given that our pixel is 30m
length, the minimum farm size was one hectare. Figure 2-2 shows the structure for
sampling. .
5The progressive reduction o f space between crowns as they spread laterally, increasing canopy cover.
11
Study Area and Data
j
\i
30 m
X
i1
N
/
Figure 2-2: Structure for Field Sampling: a) sampling square b) canopy closure taken
from Becker et al., 2004
12
Chapter 3
Context
3.1 The Use o f Satellite Imagery for Crop M apping
Remote sensing technology offers a broad array of opportunities for crop mapping
and monitoring (Moran, 1997). However, previous studies have focused on crops such as
wheat, com, maize, soybeans and rice, which have a seasonal pattern of growth, allowing
for the adoption of multi-seasonal approaches (Daughtry et al, 1992; Badhwar, 2001;
Lobell, and Asner, 2003; Vina et al., 2004). Some tropical crops are included in these
seasonal varieties; but permanent crops such as coffee, usually require mapping
methodologies that call for an intense process of editing after the initial image processing.
The use of image analysis for crop mapping is grounded in the physical and chemical
characteristics of the plants, which determine their spectral response to solar irradiation
(Figure 3-1). Some of these characteristics include chlorophyll absorption, leaf pigment
content, biomass and water content.
Context
Leaf
Cell
Pigments Structure Water Content Leaf
Reflectance
Water
Vegetation
Water Content
Sand
Chlorophyll
Absorption
0 ,4 0 ,6
Visible Near Infrared SWIR
Figure 3-3: Spectral Behavior of Vegetation, Sand and Water for Different Wavelengths.
Adapted from Chuvieco, (2002).
As mentioned earlier, remote sensing has primarily been used to map seasonal
crops with several combinations of the near infrared and red bands of the spectrum
(Haboudane et al, 2002; Sims, 2002; Daughtry, 1992; Zwiggelaar, 1998; Apan et al.,
2004, Vina et al., 2004). Some approaches use raw bands (especially the information in
the green, red and near infrared part of the spectrum), while others use spectral
enhancements (mathematical transformation of raw bands, such as vegetation indices) or
temporal variation in spectral response of seasonal crops for mapping and monitoring
(Wall et al., 1984; Odenweller, 1984; Badhwar, 1984; Fisher, 1994; Grignetti etal., 1997;
Ippoliti-Ramilo, 2003; Markley, 2003; Van Niel and McVicar, 2004). Combinations of
bands into vegetation indices are useful to differentiate between land cover classes as
well. The basis behind vegetation indices is the difference between the absorption by
chlorophyll in the red part of the spectrum (0.650pm) and the reflectance in Near Infrared
14
Context
-N IR - (0.79 - 0.90(Am) in healthy vegetation. The most widely used index has been the
Normalized Difference Vegetation Index (NDVI), which is the difference between NIR
and red values divided by their sum. Healthier, denser and more productive crops have
higher values of NDVI. The use of NDVI and other vegetation Indices - Plant Pigment
Ratio, Photosynthetic Vigor Ratio, and Greenness - have also been incorporated into
cost-effective systems for crop management and monitoring (Mettemicht, 2003; Sims,
2002 ).
Satellite imagery has also been widely used to tune crop growth and yield models and
improve their predictive capacity (Maas, 1988; Moulin et al, 1998). The two ways in
which remote sensing information has contributed to yield prediction/assessment have
been through the use of empirical and semiempirical models. In the former, a regression
equation between vegetation indices and measured yield in seasonal crops is found, and
this function is used to predict future yield of the same crop (Vina et al., 2004). In the
latter, semi-empirical models use other plant parameters, such as harvest index (dry
biomass/total biomass) to predict future yields but utilize remote sensing information for
calibration and parameterization. Calibration usually involves the use of Leaf Area Index
or Absorbed Photosynthetically Active Radiation (APAR) values from measurements
with satellite imagery -specifically red, near infrared and NDVI - and parameterization
involves the calculation of light use efficiency of the plant, inferred from measurements
in the visible bands. Usually semi-empirical models can be more universally applied,
requiring less calibration for application to other regions and temporal domains than the
fully empirical models.
15
Context
3.2 The Use of Image Analysis for Coffee M apping
Mapping coffee plantations have been of special interest to the remote sensing
community in Brazil (Moreira, 2004), and interest in studies of plantation dynamics has
grown in Colombia over the last decade; (Guhl, 2004). The total area used for coffee
plantations can provide an indicator of the production limits in terms of the area available
to each crop and the associated environmental conditions. Furthermore, the
quantification of the total existing and potentially developable coffee area might serve to
analyze accessibility to local markets (Southworth et al 2002), strategic planning
(Rubiano, 2004) and for the creation of special databases for precision crop management
(Moran, 1997).
As an example of the applications of image analysis in monitoring of coffee
plantations, coffee yields are being predicted using infrared photography (NASA, 2004).
In a special partnership program with the private industry, NASA6 supports Community
Coffee Inc., a company which buys coffee primarily from Guatemala and Brazil, in
monitoring coffee growth and yield trends. The project involves the use of remote
sensing data and Geographic Information System (GIS) technology as a means of
tracking coffee growth and assessing crop health. NASA provided satellite imagery of an
area in Guatemala and supplemented it with infrared aerial photography of the same area.
The resulting product was a composite colour image of the area showing the size,
National Space Aeronautics Administration
16
Context
location, health status and yields of coffee-growing areas. However, for larger areas, the
use of commercial infrared photography is extremely expensive. Only Croome (1989)
and Moreira (2004) have used Landsat images for coffee mapping. They integrated
topographic data and Landsat images together to map coffee fields.
Moreira (2004) and Croome (1989) found useful spectral band combinations to
distinguish between shade and non-shade coffee using spectral enhancements of Landsat
Thematic Mapper (TM) images. Nevertheless, they highlight the need for more research
in coffee mapping. The methodologies used by Moreira (2004) and Croome (1989)
involved intensive editing after image processing, as well as the use of masks over steep
areas which isolates the coffee without the influence of topographic shade.
Croome (1989) established a methodology to map coffee systems as heavily shaded,
lightly shaded and non-shaded. In his study, band 2 of TM (0.52 - 0.60 pm) was
determined to be the most useful channel to distinguish coffee from other vegetation
types, and also to identify spectral variations within different coffee systems (shade and
non-shade). Croome suggested that a color composition of the far infrared (TM7), green
(TM2) and infrared (TM5) will accurately identify the coffee plantations. By using an
affine transformation7 algorithm, bands TM2 (green) and TM7 (medium infrared) were
combined to identify the three coffee systems (shade, partial shade and non-shade). The
results from the TM image were evaluated with aerial photography. However, in slopes
greater than 20 degrees, the influence of shadows resulted in poor coffee discrimination.
A n affine transformation is a linear combination followed by an offset factor, which performs a multidimensional
manipulation o f the image data
17
R eproduced w ith perm ission o f the copyright owner. Further reproduction prohibited w ith o u t perm ission.
Context
Croome also used the first two components of a Principal Component Analysis (PCA) to
distinguish between shade and non-shade coffee but is not clear why this approach led to
accuracte results. Although Croome (1989) evaluated his results using aerial
photography, the accuracy assessment process was not described.
In his study, Moreira (2004) analyzed the spectral and temporal behavior of coffee
crops in Landsat Images. He found that the images acquired during the dry season were
more efficient to map coffee plantations at an early development stage and under
production. Band 4 (near infrared) of Landsat Thematic Mapper and Enhanced Thematic
Mapper (ETM+) gave the best performance for spectral differentiation between coffee
and other land cover classes during the dry season. During the rainy season, mature
coffee was mixed with pastures, forest and coffee at an early development stage.
According to the author, higher accuracies were obtained during the dry season using
band 4 of TM because the canopy structure is denser in coffee areas as compared to the
sparser surroundings. In Moreiras study, the variability within the reflectance values for
active producing coffee plantations :caused by different plant ages, development stages
and space between plants indicating a need for further field work for the identification
of coffee crop in Landsat images. For instance, the loss of leaves during the harvest
resulted in lower band 4 (NIR) values, and higher values in band 3 (Red). As with
Croome, Moreira also evaluated his results with aerial photography.
Context
3.3 The Use o f Object Based Image Analysis
The traditional approach in remote sensing imagery has been per-pixel classification
using multidimensional spectral band analysis (i.e. several spectral bands). In this
approach the objects in the image are grouped into categories using statistical analysis on
a per-pixel basis (De Jong, S. and Van der Meer, F., 2004), a process known as image
classification. Some of these algorithms for image classification, such as the well-known
maximum likehood classifier, assume normal distributions for data analysis, which is not
always the case. Frequently, the classification analysis ends with filtering in order to
eliminate noisy pixels in the final land cover map. By introducing the concepts of
neighborhood, distance and location, homogeneous pixels can be grouped into objects
through a segmentation of the image (Haralick and Shapiro, 1985; Blaschke and Strobl
2001), the main conceptual framework behind object-based remote sensing. In contrast
to traditional image processing methods, the basic processing units of object-based
analysis are image objects, not single pixels. Image objects are created through a process
called image segmentation, which is the grouping of pixels into homogeneous objects.
The overall objective of image segmentation is to define regions in an image that
correspond to homogeneous areas in the image, reducing the amount of data for analysis
and reducing uncertainty (Lucieer, 2005). It is assumed that those homogeneous areas
(called objects) have low internal variance. Image information can be represented in
different scales based on the average size of image objects. The concept of hierarchy in
image segmentation recognizes the presence of different scales in homogeneous areas in
the image (Woodcock and Harward, 1992). Using different levels, context-based
19
Context
features, such as texture features (e.g. homogeneity, compactness) can be also be used to
characterize each object.
In addition to texture, shape features and spatial distribution have been used to
characterize landscape in object-based approach, assuming the organization of landscape
patterns as a complex of homogeneous areas, called patches (Southworth et al., 2002). A
patch refers to a spatial and functional unit of the landscape and has a spatial geometric
and thematic pattern. Coffee plantations can be seen as homogeneous objects with
different levels of spectral patchiness depending on the canopy cover of the trees over the
coffee (in shaded coffee systems) and the density of the coffee bushes (in Sun or non
shaded coffee systems) (Widayati et al, 2002).
3.4 Integrated Geographic Information System s
A Geographic Information System (GIS) is a computer system that allows the
analysis and display of spatially referenced data. Through spatial analysis of topographic
information stored in digital elevation models, biophysical attributes of specific locations
on a landscape, such as elevation, slope, curvature, incident solar radiation, and
topographic indices, can be derived using GIS routines (Wilson and Gallant, 2000). It
has been demonstrated that when these biophysical attributes are combined with spectral
information from satellite imagery, the accuracy in the characterization of land cover is
improved (Wheatley et al., 2000, Walsh et al., 1998, Michalak, 1993). For instance,
Walsh et al. (1998) used data from Landsat TM, and landscape metrics to assess the
20
Context
composition and spatial organization of alpine vegetation associated with different
drainages. In another example, Janssen et al. (1990) combined objects from digitized
polygons with a per-pixel classification: Objects were assigned to the land cover class
with the highest frequency. The 12% improvement in classification accuracy obtained by
Janssen et al (1990) provides an example of the potential benefit to classification
accuracy that could be obtained from the inclusion of geometric data.
The term Integrated Geographic Information Systems (IGIS) has been used to
describe the link between an image analysis system and GIS (Hinton, 1996). GIS and
remote sensing have been widely linked for spatial data analysis, such as: image
georeferencing, supervised image classification using field data, extraction of landscape
characteristics from image interpretation (such as roads or rivers), image terrain
illumination correction and orthorectification using digital elevation models (Justice et al.
1980), generation of digital elevation models from satellite images (Bolanos, 2000), land
cover change analysis (Michalak, 1993; Muller and Zeller, 2002; Xiuwan 2002), natural
hazards research (Nagarajan et al. 1998, Walsh et al., 1998) and sustainable land
management (Skidmore et al., 1997) among others.
Traditionally, data stored in a GIS needs to be converted into raster format in order to
be integrated into the image processing chain. Raster layers generated from remote
sensing data are incorporated into a GIS database through a transformation (e.g.
classification, vectorization or re-formatting) before the data integration step. This
causes certain problems due to generalization such as loss of accuracy (when data are
21
Context
converted between formats) and constrains the full range of applications, caused by
differences between vector-based and raster-based spatial models. Once transferred to
the image analysis system, GIS functions can no longer be applied to the data (e.g.
attribute and topological queries, etc). Similarly, products derived for image analysis
(e.g. land cover maps) loose their raw radiometric data, and are generalized into a limited
number of classes.
Obviously, a full integration can optimize the extraction of information from imagery
and vector data by utilizing all of the relations and functions that GIS and image analysis
might provide in a two-way flow (Hinton, 1996, Janssen and Molenaar, 1995). For
instance, in the selection o f training areas for image classification, image and topographic
statistics might be combined to make optimum use of the full range of terrain data and
spectral information in an object-based analysis (Fig.3-2). Raster topographic
information and vector data can also be used as additional bands in image segmentation,
in which the creation of objects at different scales minimizes much of the heterogeneity
in the image (heuristic optimization). Figure 3-2 shows the conceptual framework in
image segmentation integrating topographic and imagery data using an object based
approach.
22
Context
Figure 3-4: Representation of polygon classification functionality: Attributes of objects stored in the
database table are used for image segmentation and classification. Those attributes are generated form
spectral information (e.g. mean of red) or from GIS data (e.g. soils, topography). The output classification
still contains a database table associated to the object using the polygon identifier. Adapted from Hinton
(1996).
The object-based approach is used to generate image objects or GIS statistics within
and between polygons, and then to incorporate those statistics directly into a database.
Those statistics, stored as polygon attributes, can be used for image classification or
generation of thematic maps. The result is a description of the image content by objects
with a number of attributes (e.g. mean reflectance, size, shape and neighborhood
relations). Furthermore, IGIS technology gives us an analytical framework for data
synthesis. The user can generate thematic or statistic raster products by evaluating the
occurrence of spatial and non-spatial attributes through operations such as attribute query,
and neighborhood analysis. One of the most common spatial attributes used to
characterize the environment of a specific land cover class is the elevation value, derived
from digital elevation models.
23
Context
3.5 The Use o f D igital Elevation M odels (DEMs) for Land Cover A nalysis
The use of DEMs to represent terrain conditions as a surrogate for soil information -
often unavailable- for landscape characterization is an approach that has been widely
used in the literature (Walsh et al., 1998, Franklin et al. 2000). Topographic indices such
as relative elevation, slope, wetness index, upslope length and curvature have also been
used to explain spatial variability in crop yields and biomass (Zeleke, et al 2004).
Therefore, there is a need to carefully evaluate the use of digital elevation data in
landscape characterization based upon a detailed knowledge of the methods used in their
generation and the evaluation of documentation of errors.
24
Chapter 4
Methods
4.1 DEM Evaluation
The DEM used in this research was generated by the 11-day Shuttle Radar
Topographic Mission (SRTM) of NASA and obtained from the GLCF8. The data
acquired by two antenna pairs in C and X bands, by Interferometric Synthetic Aperture
Radar (InSAR), represents the most complete high-resolution digital topographic
database of the Earth. The reported horizontal accuracy of this DEM is 3m, and 6 to
10m for the absolute and relative vertical accuracy, respectively (Rabus, 2003).
Since most applications of the DEMs depend on representations of surface shape,
absolute measures of elevation error do not provide a complete assessment of DEM
quality. For instance, sinks (i.e., local depressions) and horizontal shifts between the
images and the DEM affect subsequent procedures such as image orthorectification and
environmental characterization. Therefore, the vertical and horizontal accuracy of this
DEM were evaluated and the descriptive statistics are presented in the results section.
For the vertical accuracy, the elevation available in 240 data points obtained in the field
8GLCF is the acronym for the Global Land Cover Facility project, supported by NASA.
25
Methods
using a high precision Trimble PRO-XRS differential GPS system were used. For the
horizontal accuracy, a stream network produced from the DEM was overlaid on the
Landsat image. The stream network was produced by performing a full drainage analysis
on the DEM, as described and proposed by Jenson and Dominique (1988). In this
analysis, primary and secondary topographic attributes such as slope9, aspect, flow
direction and flow accumulation are derived from a DEM and the stream network layer is
produced using the higher flow accumulation values. The methods to derive primary
topographic attributes such as slope and aspect (i.e., orientation of the line of steepest
descent) are described in detail by Gallant and Wilson (2000).
Based on slope and aspect values, the primary flow direction determines the direction
of water moving over the land surface. Once the flow direction is established for each
cell, a value, equal to the number of cell that flow to it is assigned, resulting in a flow
accumulation data set. The flow accumulation is used to produce a raster drainage
network dataset, in which cells with a greater accumulation value of threshold are
selected. As the threshold decreases, the density of the network increases. Finally, a
raster to vector conversion is used to translate it into a vector format.
4.2 Image Preprocessing
When topography is irregular, as is normally the case with coffee fields, it is
necessary to correct localized horizontal displacements and radiometric errors created by
the viewing geometry in areas of moderate relief.
9 Slope measures the rate of change of elevation in the direction of steepest descent Slope influences the
flow of water, and hence, the soil water content
26
Methods
The geometric correction involves modeling relationships between the image and
a set of accurately measured ground coordinates (in X, Y and Z). The product is an
orthorectified image, an image that appears as if the satellite or the viewer is looking
perpendicular to the Earth at every location. The orthorectified image is geo-coded to
Earth coordinates, and is corrected to remove errors due to elevation changes (Cheng et
al., 2000). The image used in this research was orthorectified by Earth Satellite
Corporation using methods described by Tucker et al. (2004). It is expected that the
positional error of the image is less than 50m, as described by Tucker (2004). A few
GPS points were also located in roads intersections to verify this. The radiometric
correction for this image, however, deserved a more detailed analysis, as described
below.
4.2.1 Radiometric Correction
The scattering of electromagnetic energy by the atmosphere results in the clear
sky being a source of illumination. Consequently the Earth's surface is illuminated by
incoming solar radiation and diffuses radiation from the sky, or skylight. This skylight
prevents absolute darkness in shadows where direct sunlight is absent and acts as a
masking agent, reducing the clarity of images obtained from airborne or spacebome
sensors.
Therefore, satellite images need to be corrected for top-of-atmosphere reflectance
by adjusting for sensor measurements, on-ground gains and offsets, Sun angle and Earth-
Sun distance. Conversion from digital numbers to reflectance values and constants
follows the equations provided by Markham and Barker (1986) and Chavez (1996). To
27
Methods
implement this conversion to reflectance values, Irish (2002) proposed equation 4-3 to
convert digital numbers in Landsat ETM+ to spectral calibrated radiances
L=Gain*DN+Offset
Equation 4-1
Where:
2 1 1
L ; Spectral calibrated radiance, in units w m ' sr fim
DN ; Digital Number (0, 255),
(Lnax/^.n) upper and lower spectral radiance limit, units wm ~2s r ]jum~\
Offset=Lmm. Rescaled offset, in units wm ~2sr~Jfim 1,
Gain= jy"'"'
(C^max C/min/ | Rescaled gain, in units wm ^ s r 1fa n 1.
The lower and upper radiance limits are related to their correspondent minimum
(Q m m ) and maximum (Q*) digital number, equal to 0 and 255 respectively, in Landsat
images.
The reflectance values for bands 1 to 5 and 7 are calculated using the Dark Object
Subtraction (DOS) procedure described by Chavez (1996):
Vca=(x*L M *d$)
(,*cos(&))
Equation 4-2
Where:
R ea ; xhe reflectance at the Top of the Atmosphere for a given Spectral

calibrated radiance.
Lcai(A) xhe spectral calibrated radiance at the TOA.
28
Methods
E* : Solar spectral irradiance at the TOA atmospheric irradiances, units

wm '2f/m'] (for values of solar spectral irradiance in each band, see annex 1).
9s ; Solar zenith angle, degrees units.
d : The radius vector (ratio of mean to actual Sun-Earth distance) that can be
computed as:
d= 1
(1 0.016729*cos(0.9856(Z)(9]/ 4))) w here^O E is the julian day number10.
Band 6 is also converted from spectral radiance (as described above) to at-satellite
temperatures of the viewed Earth-atmosphere system under an assumption of unity
emmissivity11 and using pre-launch calibration constants (see annex 1), using the formula
provided by Irish (2002):
K2
T=
In
J
Equation 4-3
Where T = Effective at-satellite temperature in Kelvin
K2 = Calibration constant 2 (see annex 1)
K1 = Calibration constant 1 (see annex 1)
L = Spectral radiance in wm 2sr'um !
Satellite imagery data are observed from viewing angles that vary from near to far
range12 of the image, which causes differences in reflectance of the same type of
coverage depending on their position within the image. To correct for this variation, a
10 The Julian day number is a continuous count o f days that have elapsed since January 1st.
11 It means that the material absorbs all electromagnetic radiation that falls on to it
12 The width o f the track covered by a sensing system. Also called the range
29
Methods
Bidirectional Reflectance Distribution Function (BRDF) can be applied, which is based
on viewing and illumination geometry (Susaki et al., 2004). A BDRF model consists of a
set of equations that relate surface physical properties (e.g. soil reflectance, canopy
archictures, canopy reflectances) to the observed signal as a function of wavelength. To
model bi-directional reflectance, parameters such as scattering albedo13 of leaves, leaf
inclination, distribution and anisotropic properties of canopy and soil are required (Qi et
al., 2000). However, the BDRF effects mainly affect satellite images that have a wide
swath7 (e.g. NOAA-AVHRR or MODIS that have a swath of approximately 2300 km)
but have a negligible effect on images covering smaller areas. Therefore, the BDRF
effect is considered to be negligible in the image subset used for this research.
4.2.2 Terrain Illumination Correction
The area selected for this study is mountainous, as are many agricultural areas in
the tropics. In such areas, the steepness of the terrain causes the slopes of hills facing
away from the Sun to appear darker and the slopes facing towards the Sun to appear
brighter than corresponding flat areas. This differential illumination effect causes
difficulties in quantitative remote sensing procedures such as automated land cover
classification from satellite images. In order to reduce this variation, the illumination
effect is corrected for each pixel in the image by a proper simulation of illumination
determined by elevation, slope, aspect, Sun elevation and Sun azimuth (Eastman, 2001).
13 The ratio of the radiation reflected from an object to the total amount incident upon it, for a particular
portion of the spectrum
17 The width of the track covered by a sensing system. Also called the range
30
Methods
There are two different approaches to correct for the varying illumination and
reflection geometry caused by topography. The first approach employs radiative
transfer14 models to obtain a deterministic description of the correction of topographic
effects (Pons and Sugranes, 1994; Sandmeier and Klaus, 1997; Dymond, 1999). The
difficulty with this approach is that the estimation of radiances, transmittances, and
diffuse solar fluxes for each land cover in the image is necessary before this technique
can be applied (Richter, 1997; Shepherd and Dymond, 2003). The second approach is
empirical, and uses band ratios (Justice et al., 1980; Holben and Justice, 1981; Colby,
1991) or statistical transformations, such as principal component analysis or regression
techniques (Eastman 200115) to derive band-specific and scene-dependent correction.
Although, is the simplest and most used approach, the main drawback is the
differentiated diffuse radiation16 in each band. The most common of these methods is
called cosine correction which has proved to over-estimate the value of slopes close to
0 (Law and Nichol, 2004; Teillet et al., 1982; Uribe, 2005).
In this research, a scene-dependent approach, the c-correction algorithm, was used
because it leads to the appropriate correction for topographic effects of coffee fields in
Landsat ETM+ (Uribe, 2005). Teillet et al (1982) and Meyer et al. (1993) found that the
c-correction algorithm improves classification accuracy on forest environments as well.
In the c-correction algorithm, the intensity reflected by diffuse scattering is modeled as
14 A radiative transfer model is the fate of electromagnetic radiation as it is scattered, absorbed or reflected
while passing through a medium
15 Eastman (2001) proposes a topographic correction based on a linear regression between a hillshade and
the image, and uses the slope of this regression to calibrate the hillshade and subtract it from the original
image to apply the correction.
16 Diffuse radiation is the radiation scattered by particles in the atmosphere, and is wavelength dependent
31
Methods
being proportional to the cosine of the emergent angle of reflection defined with respect
to the surface normal vector (i.e. the incidence angle). The c-correction algorithm is a
semi-empirical function, that uses a c-factor, defined as c=h/m, where m represents the
slope and b the intercept of a linear regression between L, the radiance and cos the
incidence angle (see Fig. 4-1). The c-correction is defined by Teillet et al. (1982) as:
r cos# + c
L h LT
COS/+C
Equation 4-4
Where: LH - radiance observed for horizontal surface
L t = radiance observed on sloped terrain
i = incident angle with respect to surface normal
0S= Solar zenith angle (i.e. 90 - solar elevation angle. See Fig. 4-1)
c = the correction factor, as described above.
According to Smith et. al. (1980), the incidence angle can be calculated as:
cos 7 = cos 0Scos 0 + sin 0Ssin0 cos (Os - On)
Equation 4-5
Where, 0Z= Solar zenith angle
0 = Surface normal zenith angle or slope of the terrain surface
<l>s = Solar azimuth angle
On = Surface azimuth or aspect angle
Methods
Therefore, the c-correction simulates the effect of indirect illumination from sky:
the c-factor simulates the effect of path radiance17 on the terrain at given slope and aspect.
Figure 4-1: Representation of the solar zenith angle Z and the incidence angle i
4.3.4 Soil Background Influence:
Soil background also has an effect in the radiometric spectral signature of land cover
(Huete, 1988; Rondeaux, 1996). However, due to the density of the coffee bushes and
the pixel size, the effect of soil background on the signatures of coffee systems was not
considered in this research.
4.4 Hierarchical Classification: separating the more suitable areas for coffee
The classification of a satellite image in several stages is known to improve
classification results (Benz et al., 2004). A preliminary classification that separates the
areas that have higher probability to have coffee fields will help to focus the image
analysis for such areas (e.g. areas of agroforestry systems). In this stage, the minimum
distance to means classifier was used to run a preliminary classification of clouds,
17 Path radiance is the effect of the atmosphere acting as a reflector itself, adding scattered radiance to the
signal detected by the sensor (Lillesand and Kiefer, 1994)
33
Methods
pastures, water, forest, urban and agricultural areas (that include coffee systems as well as
any other type of agriculture or agroforestry systems). The algorithm uses the mean
reflectance on each band for a signature and each pixel is assigned to the class with the
mean closest to the value of that pixel (Mather, 2001). Subsequent steps with object-
based and pixel-based approach were run using only the mask of both forest and
agriculture.
4.5 Segmentation: b uilding the units for object-based analysis
The reflectance from bands 1 to 7, the at-satellite temperature (obtained from the
thermal infrared band) and the DEM can be integrated in a database to run segmentation
and classification algorithms in e-cognition software (Baatz et al, 2004). Meinel and
Neuberth (2002) evaluated different segmentation algorithms using high-resolution data
and they showed accurate shape estimates (e.g, area, diameter, shape index) using e-
cognition. The software combines neighboring pixels that show a degree of spectral
similarity, which is lower than a threshold defined by the scale parameter18. The smaller
the scale parameter, the larger the number of objects and the smaller their size. The
resulting topological network gives more characteristics that can be distinguished as
intrinsic features (e.g. color, shape), topological features (e.g. position regarding to
another object) and context features (e.g. texture, a measure of the amount of tonal
change between neighbor objects). However, context features characterize an area only if
the pixel size is much smaller than the objects of interest. Therefore, only intrinsic
features will be used in this research.
18 The segmentation results (polygons, delineating objects) can be converted into a GIS-readable vector
format.
34
Methods
4.6 Scale effects on im age segm entation
Segmentation in object-based image analysis can provide multiple solutions
(Blaschke and Strobl 2001). Therefore, the objects created through image segmentation
process must be meaningful; in order to analyze their properties and make the
correspondence between the objects (as defined) and their attributes. Statistical and
geostatistical19 models can quantitatively characterize spatial structures. As the main tool
for geostatistical analysis, the variogram is a quantitative descriptive statistic that has
been long used to characterize spatial continuity/heterogeneity (Curran, 1988; Atkinson
and Tate, 2000). A variogram analysis consists of the experimental variogram calculated
using the data and the variogram model fitted to the data. The experimental variogram is
calculated by averaging one-half the squared differences of the values over all pairs of
observations with the specified separation distance (called lag distance) and direction
(Goovaerts, 1997):
I n (h )
Yk = O /AA Z W h (*,) - dnk (X, + h ) y

2(/r) ,=I
Equation 4-6
Where n(h) is the number of pairs in lag h, dn(xi) represents the image digital
number values at location x, and (x i +^ ) and k denotes the waveband.
19 Geostatistics is a branch of statistics that deals specifically with the spatial relations indexed over
continuous space and focus on spatial variability.
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Methods
The variogram is plotted as a two-dimensional graph, with lag distance in x-axis
and semi-variance in the j-axis. Variogram analysis has also been used to characterize
the local variance in satellite images to determine optimal pixel size (Atkinson and
Curran 1997). It has been shown (Woodcock and Strahler, 1987, Woodcock et al.,
1988a, 1988b) that the variograms range (i.e. the x coordinate of the sill point of the
variogram, see fig. 4-2) is directly related to the texture and/or object size (i.e. the scale
of spatial variation), while the sill (i.e. the y coordinate) estimates the a priori variance at
certain support (i.e. pixel size). The nugget effect represents variability at distances
smaller than the pixel, and is attributed to the measurement error, caused by noise. The
magnitude of variation in spatial data is a function of the characteristics of the objects in
the ground and the sampling framework, constituted by the pixel size, the sampling
scheme and the sampling density (Atkinson, 2004)
1.0
0.8
0u)
I 0.6
i
W 0.4
0.2 Nugget
0.0
0 2000 4000 6000 8000 10000
Lag (meters)
Figure 4-2: Representation of the experimental variogram
36
with perm ission o f the copyright owner. F urther reproduction prohibited w itho ut perm ission.
Methods
Assuming that the variance is the same in all directions (i.e. isotropy) the
variogram is used in this research to estimate the size of the homogeneous areas in the
image, for the creation of objects, by analyzing coffee fields in aerial photographs.
Despite their multiples advantages, the segmentation of an image into objects will
involve the modifiable areal unit problem -M A U P- (Openshaw and Taylor, 1981). It
refers to the fact that the same pixels can be aggregated differently and that the results of
the spatial analysis depend to some extent of the aggregation strategy used. Spatial
aggregation reduces the size of data by converting raw data into spatial units that are
modifiable, and affect the statistical analysis when the information is grouped at different
levels of spatial resolution (called the scale component of the MAUP). The variability in
the statistical results obtained as a result of the different ways in which the information is
grouped at a given scale is the aggregation component of the MAUP, which also affects
the spatial analysis (Wrigley et al., 1997). In order to explore how much variation is
attributed to the aggregation system, statistics from pixels and objects are compared and
the effects of aggregation are analyzed using the differences. As described by Wong
(1996) reporting the scale-sensitivity of the results (e.g. the error due to aggregation
process) give us an indication of how variable the results can be.
4.7 Shape as additional feature for land cover characterization:
Shape features are based on the statistics of the spatial distribution of the pixels that
form each image object and have been widely used to characterize different types of land
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Methods
cover (Southworth, 2002). Some of the general shape features used for land cover
characterization are: area, ratio length/width (calculated by dividing the length by the
width of the bounding box surrounding the object), border length, shape index20
(calculated by dividing an image objects border length by four times the square root of
its area), density (calculated by dividing the area of the image object by its radius: a
square image object has the highest density), compactness (i.e., the product of its length
and width, divided by the number of pixels forming the object) and asymmetry:
expressed as the ratio of the lengths of minor and major axes of an ellipse surrounding the
object. As an alternative way to characterize the objects shape, the elliptic and
rectangular fits compare the object to an ellipse and rectangle, respectively. While 0
means no fit, 1 stands for a complete fitting object.
4.8 Signature Evaluation: Statistical analysis of samples.
The descriptive statistics (e.g. means, standard deviations, minimum and maximum
values) provide measures of central tendency21 and variability in spectral bands and
topographic data that characterize each land cover, and assist in the analysis of their
differences. A first step in using these measures is plotting the samples on a two-
dimensional feature space, in which each axis represents a spectral band, gives an idea of
the spectral separability of the samples.
20The shape index is used to describe the smoothness of the image object boundaries: the more fractal an
image object appears, the higher its shape index.
21 The tendency of the set of measurements to cluster
38
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Methods
Graphs such as the histogram, which represents the distribution (values and
frequency) of the data values, and the box plot were analyzed for each land cover class in
each band in order to evaluate the data distribution. The box plot is a graph based on
quartiles of the data set (see Figure 4-3). Quartiles are values that partition the data set
into four groups, each containing 25% of the measurements. The lower quartile contains
25% of the measurements, the middle quartile is the median and the upper contains 75%
of the data set. A box plot is drawn on the interquartile range, the distance between the
lower and upper quartile. The two lines emanating from the borders of the box (the
whiskers) extend 1.5 times the box length (i.e. 1.5 times the interquartile range) and it
contains the smallest and largest measurement. Values that are beyond the whiskers are
extreme values that represent rare occurrences. In fact, in normal distributions less than
1% of the data are expected to fall outside the whiskers. Measurements that fall beyond
three times the interquartile range are called outliers. Outliers are very extreme
measurements that stand out from the rest of the sample and may be faulty (e.g. incorrect
recorded observations).
> Chillier
> yyjusker
3rd quartile
* Median
~ -> 1st quaitile
G ro u p A G ro u p B
Figure 4-5: Box Plot Diagram
Most of the signature evaluation (divergence, transformed divergence and
Jeffries-Matusita distance) and classification algorithms (e.g. maximum likehood) are
39
Methods
based on a normal distribution of the sample data for each land cover class. Then, in
order to determine the type of test that best fits the type of data and to make inferences
about the parameters of the population, a test of normality should be carried out. The
Shapiro-Wilk test (Shapiro and Wilk, 1965) tests the hypothesis that a random sample
comes from a normally distributed population. It is recognized as the best test for
evaluating normality (Griffith, 1997, Meyers, 2006). It is based on a W statistic, which is
given by:
( )2 i
^ = , where x =~ x>
I>,-*)2
<=1
Equation 4-7
Where x,- represents the value for each observation, and a are a series of
weights generated from the means, variances and covariances of the statistics of a
sample of size rt from normal distribution.
The significance value associated with the W statistic (known as a p-value)
represents the probability of obtaining a result by chance alone. A p-value of .05, for
example, indicates that we would have only a 5% chance of drawing the sample being
tested and reject the hypothesis, when the null hypothesis was actually true. The p-value
measures consistency: a small p-value is strong evidence against the null hypothesis
while a large p-value means little or no evidence against the null hypothesis, i.e., that
there is high probability of having the wrong sample.
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Methods
P-values are compared with a , the significance level. The significance level is the
pre-chosen probability that the null hypothesis will be rejected when is true (also known
as type I error, i.e., observing a difference when in fact, there is none). Common levels
of significance are 5% and 1%, and these are chosen arbitrarily. If a test of significance
gives a p-value lower than the a level, such result are normally referred as statistically
significant and the null hypothesis (of equality) is rejected. If the chosen alpha level is
0.05 and the p-value is less than 0.05, then the null hypothesis of normality is rejected. If
the p-value is greater than 0.05, then the null hypothesis cannot be rejected. Note that in
this situation, the hypothesis being tested is accepted (or rejected) if the p-value is greater
(or lower) than a certain significance level. This is called an one-sided hypothesis.
If the samples do not follow a normal distribution, as measured by the Shapiro-
Wilk test, a non-parametric test can be used in order to evaluate their differences of
means. The Mann-Whitney test can be used to test the differences between the medians
in two groups when the data are collected using different subjects in each group (as is the
case in the sampling of remote sensing data for land cover analysis). As a non-parametric
test, the Mann-Whitney test works by looking at the differences in the ranked positions of
scores in different groups. Although it is a non-parametric test, it does assume that the
two distributions are similar in shape. In the case where the only distributional difference
is a shift in location, this can indeed be described as a difference in medians.
Theoretically, in large samples the Mann-Whitney test can detect differences in spread
even when the medians are very similar. It test the null hypothesis that the two samples
are drawn from the same population, and therefore that the medians are equal. It requires
the two samples to be independent, and the observations to be ordinal or continuous
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Methods
measurements. It is one of the best-known non-parametric tests (Field, 2000) to evaluate
differences between groups. The test involves the calculation of a statistic called U,
whose distribution under the null hypothesis is known, which is defined as the minimum
value between:
Equation 4-8
Where rti and n2 are the two samples sizes and Rj and R2 is the sum of the ranks in
sample 1 and 2, respectively. The maximun value of U is the product of the two sample
sizes. With samples above about 20, the U statistic aproximates to a normal distribution,
with mean mu: and standard deviation a u . Using the normal approximation, the z
statistic (under the null hypothesis of equal means), is calculated as:
z-(U mu ) / a u where m u = nsn2/2 and
Equation 4-9
If the chosen alpha level is 0.05 and the p-value associated with this z value is less
than 0.05, then the null hypothesis is rejected, otherwise it is accepted.
4.9 Rule-based image classification.
Traditional methods for land cover classification with satellite imagery do not
handle the use of ancillary data appropriately (Oruc et al., 2004). In the integration of
GIS and remote sensing data, the use of ruled-based (also know as knowledge-based
classifiers), neural networks and expert-knowledge has provided higher accuracies
(Goodenough et al., 1987; Fierens et al., 1994, Benediktsson et al., 1990) than statistical
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Methods
classifiers. For instance, Murai and Omatu (1997) demostrated that ruled-based methods,
when integrated to neural networks, can improve the classification by about 9%.
The ruled based classification is implemented in this research through the use of a very
simple decision tree. A decision tree is defined as a classification procedure that
recursively partitions a data set into smaller subdivisions on the basis of tests defined at
each branch in the tree (Friedl and Brodley, 1997). In this framework, a data set is
classified by subsequentially dividing it according to the decision framework defined by
the tree, and the pixel (or object) is assigned to a class according to the leaf node into
which the observation falls. As opposite to other classifiers, this method do not rely on
normality assumptions and handles numeric and categorical data in the same routine
(Quinlan, 1986) The decision rules in each node can be based solely on analyst
expertise, which is difficult to implement across different times and geographic places, or
they can be defined based on the statistical analysis of training data. The classification
system used in this research uses an univariate decision tree in which the decision rule in
each branch is defined by statistical analysis of a single feature (e.g. elevation). To
improve accuracy, the tree is pruned by removing leaf nodes until training samples are
classified correctly (Friedl and Brodley, 1997). The elimination of leaf nodes is stopped
when further removal reduces the classification accuracy with respect to the independent
group of samples (used for accuracy assessment).
Methods
4.10 R efining the classification: Using the Linear M ixing M odel for Spectral
Unm ixing in coffee fields.
In order to refine the classification results after the ruled-based classification, and
identify the specific type of coffee system, a mask can was created to delineate areas
most likely to have coffee fields, given their spectral and environmental characteristics
(topography and temperature, specifically). However, due to the small size of the
individual coffee fields in this area, this mask contains some pixels with features that are
smaller than the resolution of the sensor. For instance, the reflectance of a pixel that has
coffee in an agroforestry system (i.e. shade coffee), will contain the combined reflectance
of forest and coffee co-existing within that pixel.
The mixed pixel problem has called the attention of many scholars in remote sensing
(Foody, 2004, Foody et al. 1996, Huguenin et al. 1997, Quarmby et al.,1992, Settle and
Drake, 1993, Sohn and McCoy, 1997, Van der Meer, 1997). In order to segregate a pixel
into its components, a technique called spectral unmixing is performed. Different cover
types are discriminated with a pixel by comparing the observed spectra of the pixel with
the end-members. An end-member is the signature of a pure pixel, which only contains
one cover type.
There are several models for spectral unmixing (Ali, 2002): the linear mixture, the
probabilistic, the geometric, geometric-optical and stochastic. The linear mixture model,
also called linear unmixing model, assumes that the reflectance in each pixel is a linear
44
Methods
combination of the response of each component in it (Shimabukuro and Smith, 1991).
Because its simplicity and independence of the normality assumption, the linear mixture
model is often preferred. In equation form, the linear mixture model can be represented
as:
i'i = a n x, + a 12 + ......... + a, x n + c,
f tl7 Omi X ] ........ An i C,))
Equation 4-10
Where m represents the number of spectral bands, n represents the number of
components within the pixel, r represents the mean spectral reflectance of the pixel in
each band, x represents the proportion of the each component (or land cover class) in the
pixel, amn represents the spectral reflectance of the each component in the pixel for the
specific spectral band and e represents the error component, caused by noise. Assuming
that the sum of proportions within a pixel is one, the proportions are positive and the
number of components does not exceed the number of spectral bands, this equation can
be resolved using the constrained least-squares method described by Shimabukuro and
Smith (1991). The method estimates the proportion of each component inside the pixel
by minimizing the sum of squares of the errors.
The key factor to resolve this model relies in the selection of the end-members.
The selection o f the end-members can be achieved using a spectral library (from field or
laboratory measurements) or from the purest pixels in the image (Van der Meer, 1999).
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Methods
If a spectral library is not available for the type of cover of interest, the purest pixels in
the image can be used for end-member selection. This method has the advantage that the
spectral signatures for the end-members are collected under the same atmospheric
conditions.
The identification of the purest pixels in the image can be done using Principal
Component Analysis (PCA), Pixel Purity Index (PPI) and Spectral Angle Mapping (Ali,
2002). For its simplicity, the principle of the Spectral Angle Mapping (SAM) is preferred
to assess the selection of endmembers. The spectral angle mapping calculates the
spectral similarity between two spectra by calculating the spectral angle between them,
treating them as vectors in a space with dimensionality equal to the number of bands
(Van der Meer, 1995, 1997). Figure 4-4 shows a two dimensional example of spectral
angle mapping. This method was implemented for the selection of end-members.
Sand j
Figure 4-6: The Spectral Angle Mapping in a two-dimensional space. Taken from Ali
(2002)
Methods
4.11 Accuracy A ssessm ent
The classification accuracy can be evaluated by comparing the classified image
with ground truth data. For this research, GPS polygons representing coffee farms in
Huila, surveyed using DGPS units, were compared with the classified image. The
number of samples for accuracy assessment (as well as for training) depends on the
budget and practical issues, but it should be adequate to maintain the validity of the
proposed statistical analysis. Most of the statistical tests are based on binomial or normal
distribution of the error, for each land cover class. Therefore, the sample size should be
computed using the multinomial distribution. Usually, 30 samples are the minimum
required for the t-test to approach a normal distribution, but this number can be adjusted
according to the importance of certain category (or the complexity of the landscape for
certain category) or by the variability within each land cover signature. In any case, the
minimum number of samples must be preserved for all land cover classes. If we
calculate the number of samples required in a multinomial distribution, with 9 categories
(k=9), and a confidence level of 95% (a =5%) that the classes are in average 20% of the
map area ([X=0.20), we get approximately 47 samples per class, according to the
equation (Congalton, 1999):
_ ^ n .o no
b1
Equation 4-11
The value for /? is determined from a chi-square table with 1 degree of freedom
and (1- a/k). If the confidence interval is lower, the required sample size decreases.
47
Methods
Note, however, that the sampling scheme (simple random, systematic, stratified
random, cluster, stratified systematic unaligned) determines the distribution of samples
across the landscape. Good statistical properties result from random selection of samples,
which guarantees independence (i.e. equal and independent chance to be chosen).
However, a fully random sampling is not always possible due to accessibility in many
areas. Therefore, for this research, both training and accuracy assessment, the area is
divided up according to land cover classes, and a random sampling is carried within each
land cover (i.e. stratified random sampling). This method has been demonstrated be
adequate for classification accuracy (Stehman, 1992)
The overall error can be estimated using the error matrix and the kappa index of
agreement (Congalton, 1999). The error matrix is a square array of numbers set in rows
(the map labels or classified data) and columns (the reference data) that shows the labels
of sample units (pixels or polygons) assigned to a particular category, in the classification
relative to the labels assigned to the same point in the reference data.
The output of the error matrix is a matrix of percentages that allows the evaluation
of the number of pixels in each sample that are assigned to each class. The error matrix
will give us the errors of omission, commission, the producers and the users accuracies
as measurements of the overall accuracy. A commission error (or inclusion error) is
defined as including an area into a category when it does not belong to that category. An
omission error (or exclusion error) is defined as the exclusion of an area from the
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Methods
category in which it truly belongs. Every error is an omission of the correct and
commission to the wrong category. The overall accuracy is the sum of the major
diagonal (which is the correctly classified sample data) divided by the total number of
sample units. The users accuracy (rows) is computed by dividing the total number of
correctly classified pixels in a category by the total number of pixels classified as that
category. Producers accuracy (omission error) refers to the percentage of reference
pixels correctly identified in the map (the proportion of pixels or objects that are correctly
recognized by the classifier), while users accuracy (commission error) is the percentage
of the areas identified in the map that actually belongs to that category on the ground (the
proportion of pixels identified by the classifier that agree with the ground truth).
The kappa index is another indicator of accuracy derived from the values in the
error matrix. It indicates the probability that a pixel classified on the image corresponds
to the same category as observed on the ground, taking into account all marginal
distribution of the error matrix (Congalton, 1991). A binomial distribution would be
appropriate only to determine the accuracy of one category as right or wrong based on the
proportion of correctly classified pixels, the allowable error, and the desired level of
confidence. However it will not be related with the error matrix with n land cover
classes, in which there is one correct and (n-1) incorrect possibilities. This case is better
described by a multinomial distribution. The estimate of kappa is based on the difference
between the actual agreement (the major diagonal) and the chance agreement indicated
by the row and column totals. This value is computed for each error matrix and is a
measure o f how well the produced classification agrees with the reference data and it
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Methods
goes from -1 to +1. The higher the value of kappa, the better the classification
performance: as the values in the off-diagonal increase, the value of kappa decreases.
The estimate of kappa value is defined by:
N T ux - Z < x + #x)
= ^ ----- _i=!-------------
<=i
Equation 4-12
Where N is the total number of samples, r is the number of classes, xu is the entry ii
(the diagonal) and xi+, x +i are the marginal totals of row i and column /, respectively.
Errors in the reference data, the sensitivity of the classification scheme to
observer variability, or the inappropriateness of the data for mapping a specific land
cover class can cause differences in the error matrix. The misapplication of the
classification scheme to the map or reference data (i.e. a reference point which land cover
class is in between one or more classes in the classification scheme), the subjectiveness in
interpretation and reference sampling and land cover change, all contribute to differences
in the error matrix.
As summary, the flowchart in figure 4-5 presents the sequence of the
aforementioned steps that constitute the methodology used in this research.
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Methods
Image pre-processing DEM Evaluation
Preliminary Classification Derivation of Secondary

Topographic Attributes
Mask: Miscellaneous Class
Object segmentation Pixels

Definition of objects
Signature Evaluation size: scale analysis Signature Evaluation
Ruled Based Classification Ruled Based Classification
Mask: Coffee Accuracy Assessment (error Matrix)
Linear Spectral unmixing
Land Cover Map: Sun coffee and

Shaded Coffee
Accuracy Assessment
Error Matrix RMS Image
Evaluation of the Spatial Distribution

of Land Cover classes
Figure 4-7: Methodological Sequence
51
Chapter 5
Results
5.1 DEM Evaluation
The quality of the DEM was evaluated by comparing the 280 DGPS22 points
taken in the field and analyzing the differences between the GPS height and DEM values
for the study area. The mean error was 24.039m. The standard deviation, minimum
and maximum values of the error were 10.33, -59.6 and 2.30 meters, respectively. The
distribution of the error is shown in figure 5-1. Given the scale of the analysis and the
pixel size (28.5m) of Landsat images, this error was considered to be acceptable for the
purposes of this study. The evaluated DEM will be used for topographic illumination
correction (see section 4.3.3. and 5.2), and to generate secondary topographic attributes
(slope and aspect) that characterize the topography of coffee and non-coffee fields.
22Differential Global Positioning System DGPS -See section 4.7 for theoretical details
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Results
Error D istribution DEM SRTM
0.000
10.000
m
Urn
1 - 2 0.00 0
g - 3 0.00 0
C
1 - 4 0.0 0 0
5 0.00 0
- 60 .0 0 0
- 70 .0 0 0
Figure 5-8: DEM evaluation. Error Distribution calculated as DEM values-GPS height.
In order to evaluate the overlap in X, Y between the image and DEM, a drainage
network was created using hydrologic modeling in Arcview-SWAT23, as described in
section 4.2. The fitting between image and DEM was then analyzed by visual inspection
of the overlap between image and vectors on rivers. Figure 5-2 shows the overlap for
two areas of the image.
Figure 5-9: Overlap between image and rivers generated from DEM in two subareas.
See section 4-2 for theoretical details
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Results
5.2 Image Preprocessing:
The geometric and radiometric corrections were done following the procedure
described in section 4.3. The values for gain, offset, solar spectral irradiance, solar zenith
angle and calibration constants K1 and K2, are given in Annex 1. The terrain
illumination correction was done using the c-correction method described in section 4.3.3
by Uribe (2005). Figure 5-3 shows the image before and after the terrain illumination
correction was applied.
Figure 5-10: Subset over the study area showing the image before (left) and after (right) the
terrain illumination correction was applied. Band Combination: Blue:ETM3, Green:ETM5, Red:
ETM4
5.3 Preliminary Classification:
As described in section 4.4, a preliminary unsupervised classification was
performed in order to extract the most likely areas to have coffee fields. The
classification scheme contains seven classes: forest, pastures, clouds, shadows, urban,
water and miscellaneous. The miscellaneous category includes areas that contain all
coffee systems and non-coffee areas as well. Non-coffee areas include those land cover
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Results
classes whose spectral signature is either, similar to coffee systems or very different to
the other six classes (pastures, clouds, etc.). The overall classification accuracy obtained
was 97%, as evaluated by the kappa statistic (see section 4.11). Points for classification
training and accuracy assessment at this stage were taken by visual interpretation of the
image. Two sets of fifty points per class were randomly localized for training and
accuracy assessment, respectively (as described in section 4.11). A mask was created
using the miscellaneous class and all the subsequent analyzes on the image and GIS data
were done using this mask. Figure 5-4 shows the result of this preliminary classification.
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Results
Preliminary Classification Map
Legend
H i Forest
I | C lo uds
Shadows
1
P astures
Urban
M is c e lla n e o u s
3 0 3 6 9 12 Kilometers
Projection: UTM 18 North, Datum: WGS84
Figure 5-11: Preliminary classification
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Results
5.4 Exploratory Analysis: Pixel Based Analysis.
5.4.1 NDV1 vs. percentage o f shade
Because the Normalized Difference Vegetation Index (NDVI) has been long
related to biomass content (Baret and Guyot, 1991; Hatchfield, 1993; Lobel, 2003;
Moran, 1997, Moulin et al., 1998; Vina et. al., 2004; Zwiggelaar, 1998), the NDVI was
used to explore the capability of Landsat images to discriminate between non-shade and
shade coffee systems, which have a higher biomass content. The NDVI enhances the
differences between band 4 (reflection by the plant structure) and band 3 (absorption by
the chlorophyll):
N IR -R E D B 4 - B 3
NDVI = ---------------= -----------
NIR + RED B4+B3
Using the reflectance in these two bands, the NDVI was calculated in order to
evaluate the correlation between NDVI values and percentage of shade (overstory) over
coffee bushes, as measured by 44 points taken in the field (see section 2.3).
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Results
MPVt v& % of cover over coffee plants
0,8-i
0.80 -
S Ip 'J H #**

ft ?ft 1 ---
* * * * *
0 0,1 0.2 0J 0,4 63 m 0.7 0.8 0.0

NDVI
Figure 5-12: Correlation between percentage of cover (measured in the Field) and NDVI values
calculated using reflectances in Landsat
Although the slope of the regression line between the two variables is 0.745, i.e, it
is almost a linear relationship, the NDVI values only explains 12.33% of the outcome
variable (i.e. percentage of shade) with a significance level of 0.05. The linear
relationship, if exists, seems to be stronger at NDVI values of 0.5 to 0.8. This can be
associated to the saturation of the model at NDVI values higher than 0.8. Note also, that
at NDVI values lower than 0.1, the model does not detect any change in percentage of
shade. One possible reason for this is that changes in percentage of shade can be
occurring at short distances (i.e. less than 30m) that will not be detected by a Landsat
image, with a minimum mapping unit of 30m.
5.4.2 Spectral separation between coffee and non-coffee fields
In order to choose the bands that will separate coffee from non-coffee fields and
to analyze their representative signature, the spectral reflectance in each one of the seven
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Results
bands for all sample points (280 for coffee systems and 300 for non-coffee areas) was
mapped in a scatter plot, as shown in figure 5-5. From the figure, it is noticeable that
some combinations of bands 3, 4, 5 and 7 will provide better separation between the
coffee systems and non-coffee areas (miscellaneous), and that band 1 shows the highest
overlap between both. For this reason, band 1 was discarded for subsequent analysis.
*SjdbP
00 A3 3
0 A 3 3
/ A 3 0
p PP
0 0 P 0
0 0 P
bl to hi M
/b5 bT
Figure 5-13: Scatter plot in all bands for coffee (dark blue) and non-coffee classes (green)
Samples were also evaluated through the inspection of histograms (see Annex 2)
and box plots for coffee systems and non-coffee areas for bands 1 to 7, temperature,
elevation, slope and aspect, shown in Annex 3. The box plot for band 1 in both land
cover classes confirms the strong overlap in this band (see figure 5-7). Given that the
samples have strong deviations from normality24, the difference between both land cover
classes was analyzed with a Mann-Whitney test (see table 5-1).
24 See Annex 3 for normality test
59
Results
I !'!
0 MOM
0.12300
o mm
29... 2?
B.mmo
OJB0OH
S.QsifiOO
class
Figure 5-14: Box Plot for both land cover classes in band 1
M ann-W hitney U Z p-value

B and 1 29070 -5.83 .00
B and 2 20317 -10.30 .00
B and 3 18675 -11.13 .00
B and 4 20987 -9.94 .00
B and 5 28203 -6.26 .00
B and 7 21000 -9.94 .00
T em perature 34573 -3.02 .00
Elevation 29830 -5.72 .00
Slope 40147 -0.27 .78
A spect 38410 -1.14 .25
Tab e 5-1: Differences between coffee systems and non-coffee areas using pixel-based signatures
5.5 Pixel-based classification
As described in section 4.9, a ruled-based classification was performed on the
image using pixel-based statistics, i.e., range values of sample pixels in bands 2 to 7,
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Results
temperature, elevation, slope and aspect. The criterion used to get coffee systems is
shown in table 5-2:
Factor Range
Band 2 0.08 <b2< 0.135
Band 3 0.030 <b3 <0.10
Band 4 0.15 <b4< 0.50
Band 5 0.05 < b5 < 0.30
Band 7 0.025 <b7< 0.17
Temperature 17 < temp < 25
Elevation 1200 < elevation < 1850
Table 5-2: Features ranges used in pixel-based classification
A total of 1429 points were used to evaluate accuracy. For forest, clouds,
shadows, pastures, urban, miscellaneous and water, the points were located by visual
inspection of the image. For the coffee class, the points were selected form the SICA
database (see section 2.2 for details), using two criteria: a) the farms size was bigger than
1 hectare and b) The density was higher than 4500 plants. The overall accuracy was
71.89% and the kappa statistic25 was 0.659. The 95% Confidence Interval ranges from
69.553% to 74.219%. Table 5-3 shows the user and producers accuracy and the kappa
statistic for each class, based on the confusion matrix.
Class Name Producer's 95% Confidence Users 95% Confidence Kappa

Accuracy (%) Interval (%) Accuracy (%) Interval (%)
Clouds 99.55 (98.46 - 100.65) 97.39 (95.11 -99.67) 0.97
Shadows 78.33 (72.04 - 84.63) 96.57 (93.28 - 99.87) 0.96
Urban 87.50 (72.18- 102.82) 84.00 (67.62 - 100.37) 0.84
Water 30.19 (16.88 - 43.49) 100.00 (96.87- 103.12) 1.00
Pastures 96.72 (91.43 - 102.01) 51.75 (42.14-61.36) 0.45
Forest 97.72 (95.88 - 99.55) 81.52 (77.42 - 85.62) 0.76
Miscellaneous 23.67 (18.69-28.64) 51.45 (42.75-60.15) 0.39
Coffee 70.22 ( 65.04 - 75 .39 ) 51.85 (47.02 - 56.68) 0.38
Table 5-3: Accuracy statistics forper-pixel classification
Note that despite the overall accuracy being acceptable, the accuracy achieved for
coffee systems and non-coffee (i.e. miscellaneous) areas, is about 40%, and, according to
25 See section 4.12 for technical details
Results
the confidence interval, it goes up to 60% for the users accuracy. Likewise, note that the
omission error (as measured by the producers accuracy) is less than the commission
error. Therefore, there are more pixels classified as coffee than actually are in the
ground. Figure 5-15 shows the classification map.
Ruled-based Classification Map

(pixel-based analysis)
Legend
Forest
I I C loud s
Shadows
Pastures
Urban
W ater
12 Kilometers a
I
C of fe e S y s t e m s
I M isc e lla n e o u s
F igure 5-15: Ruled-Based classification map obtained from pixel-based analysis
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Results
5.6 Image Segmentation: Choosing the Appropriate Spatial Units
The corrected image (following the removal of geometric and radiometric errors)
was segmented using a region growing segmentation technique, where neighboring pixels
whose spectral properties (in bands 2,3,4,5 and 7) are similar enough, were aggregated,
by a region-growing scheme described in section 4.5. Two neighboring pixels were
considered to be similar enough if the absolute value of the difference between their tone
intensities was smaller than a threshold (Haralick and Shapiro, 1985). The threshold is
defined by the scale parameter in e-cognition. In order to evaluate the scale component
of the MAUP (see section 4.6) a variogram analysis was performed. It determined an
average objects diameter of 100 meters for coffee fields, which results in a scale
parameter of 10 for the segmentation. To define this scale parameter, the variogram
analysis was done on a representative coffee fields identified on aerial photographs using
the spatial dependence modeler in Idrisi software. Aerial photographs were used for
this part of the analysis, because coffee fields are easier to distinguish due to their higher
spatial resolution. Figure 5-8 shows the variogram.
distance between pairs
Figure 5-16: Left: omni-directional variogram for a coffee field in an aerial photo. Right:
segmented image
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Results
Mean value Mean value Mann-Whitney Z Significance

(object-based) (pixel - based) U (2-tailed)
B2 0.09 0.07 337 -0.61 0.22
B3 0.05 0.09 284 -1.33 0.48
B4 0.36 0.05 281 -1.69 0.09
B5 0.16 0.36 384 -0.29 0.11
B7 0.06 0.06 302 -0.18 0.07
Temp 20.52 21.49 39520 -1.65 0.09
Elevation 1469 1326 35247 -0.22 0.08
(m)
Slope (dg) 16 18 46781 -0.56 0.57
Aspect (dg) 156 168 43156 -1.26 0.21
Table 5-5 Comparison between mean objects reflectance and pixels values for Non-cofFee areas
Note that, according to the test, the differences between pixels and objects mean
value for the same point are minimal. From this comparison, I conclude that the
aggregation of pixels into objects will not modify the mean spectral signatures for the
coffee and non-coffee fields in the area. One possible reason for this, is that the objects
size were kept as small and as homogeneous as possible, in order to avoid introducing
variations in the signatures when pixels from different land cover classes are merged into
the same object (that normally occurs when the objects size is increased).
5.7 Signature Analysis:
In order to determine the appropriate statistical tools for subsequent analysis, a
normality test was applied to all signatures for coffee systems and non-coffee areas for
mean values and standard deviations in bands one to seven, elevation, slope and
curvature. Since the algorithm uses a rule-based classifier, minimum and maximum
values in each object can also be used for classification. Those were evaluated for
normality as well (see Annex 4). The general shape features described in section 4.8
were obtained from the segmented image (e.g. area, diameter) and evaluated for
65
Results
normality, because they can also be used in the decision rule. Results of the normality
tests for these features are provided in annex 4.
Given that the data had significant deviations from normality, a Mann-Whitney U
test for difference of means (see section 4.9) and a careful analysis of the box plot for
object-based features was used to choose the variables in which the coffee systems were
significantly different from non-coffee areas. Tables 5-5 through 5-8 summarize the
results of this test.
Mann-Whitney U Z Asymp. Sig. (2-tailed)

Mean B2 2764 -2.73 0.00
Mean B3 2337 -4.05 0.00
Mean B7 2226 -3.87 0.00
Mean elevation 2332 -3.39 0.00
Stdev. B2 3276 -6.27 0.00
Stdev. B3 2772 -7.36 0.00
Stdev. B4 2548 -3.72 0.00
Stdev. B5 2885 -2.88 0.00
Stdev. B7 2425 -4.11 0.00
Stdev. Aspect 1944 -4.28 0.00
Min B2 2306 -3.93 0.00
Max B2 1955 -4.82 0.00
Min B3 2712 -2.88 0.00
Max B3 2115 -4.26 0.00
Max B5 2743 -2.48 0.01
Min B7 2787 -2.48 0.01
Max B7 2427 -3.30 0.00
Min Elev 2618 -2.74 0.00
Max Elev 2812 -2.30 0.02
Min Aspect 2378 -3.30 0.00
Max Aspect 2511 -2.99 0.00
Table 5-6: Significant differences between coffee systems and non-coffee areas -radiometric and
topographic features
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Results

Mean B4 3101 -1.64 0.10
Mean B5 3305 -1.19 0.23
Mean Slope 3430 -8.93 0.37
Mean Aspect 3658 -0.37 0.70
Stdev. Temp 3039 -1.78 0.07
Stdev. Elevation 3326 -1.13 0.26
Stdev. Slope 3067 -1.72 0.08
Min B4 3363 -1.05 0.29
Max B4 3383 -1.00 0.32
Min B5 3428 -0.91 0.36
Min Temp 3193 -1.43 0.15
Max Temp 3386 -0.99 0.32
Min Slope 2983 -1.91 0.06
Max Slope 3532 -0.66 0.51
Table 5-6:>: Non-significant di Ferences between co: Fee systems and non-coffee areas -ra
and topographi c features

Area 30112 -8.01 0.00
Length 31692 -7.32 0.00
Width 33609 -6.48 0.00
Compactness 39795 -3.69 0.00
Border Length 32885 -6.79 0.00
Shape Index 40048 -3.57 0.00
Density 29972 -8.08 0.00
Perimeter 33803 -6.37 0.00
: Significant differences between coffee systems an< non-coffee areas: Shape features

Length Width 44672 -1.51 0.13
Elliptic Fit 43317 -2.14 0.03
Rectangular Fit 44332 -1.66 0.10
Asymmetry 46162 -0.84 0.40
Table 5-8: Non-
Features
<57
Results
5.8 R uled-based Classification using objects:
Features that show significant differences between all types of coffee systems and
non-coffee areas were used to create a rule-based classification. For instance, elevation
(as shown in table 5-5), presents significant differences for coffee systems and non-coffee
areas, using the sample data. Although there were significant differences between coffee
systems and non-coffee areas in many features, not all of them lead to accurate
classification results. Therefore, using the group of variables with significant differences
between coffee systems and non-coffee areas, several classifications were done, adding
one feature each time. This can be described as a trial and error process, where features
for classification were entered (or removed), as the classification accuracies were higher
(or lower). The structure of the decision rule is shown in table 5-9.
Factor Range
Mean Band 2 0.08 <b2 < 0.135
Mean Band 3 0.030 < b3 < 0.10
Mean Band 4 0.15 <b 4 < 0.50
Mean Band 5 0.05 <b 5 < 0.30
Mean Band 7 0.025 <b 7 < 0.17
Mean Temperature 17 < temp < 25
Mean Elevation 1200<elevation< 1850
Std. Dev B3 0.005<St.Dev.B3<0.01
Std. Dev. B7 0.005<St.Dev.B4<0.03
Std. Dev. B7 0.005<St.Dev.B7<0.03
Max. B2 0.06<MaxB2 <0.13
Min. Aspect Min Asp>3
Table 5-9: Range values 'or object-based classification
Note that not all features show significant differences between coffee systems and
non-coffee areas. For instance, although the slope is a feature that characterize the
topography of coffee fields, the use of a narrow range, as the one shown in Annexes 2
and 3 (see box plot for slope, object-based statistics) constrains the algorithm to select
Results
only those fields that have slopes values higher than 20, which excludes many objects of
the same area with lower values.
The corresponding classification result is shown in figure 5-9. Note, that though
the coffee systems area (shown in red) is overestimated, the classification clearly
eliminates some areas very unlikely to have any type of coffee system. As an example,
note that the area surrounding the urban center, the areas surrounding the clouds and the
piedmonts are classified as such areas.
Using the same data set described in section 5.5, the overall accuracy was
74.881% and the kappa statistic26 was 0.696. The 95% Confidence Interval ranges from
72.629% to 77.133%. Table 5-7 shows the user and producers accuracy and the kappa
statistic for each class.
Class Producer's 95% Confidence Users 95% Confidence Kappa

Name Accuracy (%) Interval (%) Accuracy (%) Interval (%)
Clouds 100.00 (99.77-100.22) 96.97 (94.54 - 99.39) 0.96
Shadows 78.77 (72.50 - 85.04) 96.92 (93.38 - 99.45) 0.95
Urban 91.30 (77.60 - 104.99) 87.50 (72.18-102.81) 0.87
Water 34.61 (20.72-48.51) 100.00 (97.22 - 102.78) 1.00
Pastures 98.33 (94.26 - 102.41) 51.30 (41.73 - 60.87) 0.49
Forest 97.71 (95.87-99.55) 81.47 (77.36 - 85.58) 0.76
Miscellan. 66.66 (61.17-72.17) 56.02 (50.73 -61.31) 0,45
Coffee 42.46 (36.93 - 47.49) 65.71 (59.06-71.37) 0.56
Table 5-10: Accuracy statistics for object based classification
Although the overall accuracy is improved only in 3% by the object-based
classification, the accuracy for the coffee class is improved by 17%. As indicated by the
69
Results
user and producers accuracy, the omission errors are still less than the commission
errors. It means that there is more likely to find that a coffee field in the map is not a
coffee field on the ground, than to find a coffee field in the ground that is not mapped as
such. I other words, the area of coffee class has been overestimated.
Ruled-based Classification Map

(object-based analysis)
Legend
m | Forest
I | C lo uds
Shadows

H
P astures
Urban
W ater
C o ffe e S y s t e m s
3 0 3 6 9 12 Kilometers

M is c e lla n e o u s
Figure 5-17: Ruled-Based classification using object-based analysis: Coffee areas are in red
70
Results
As another measure of accuracy, the SICA points, which contain an exhaustive sample of
all coffee farms in the municipalities of Pitalito, Oporapa, Palestina and Timana were
overlaid on this map, in order to evaluate the spatial distribution of the coffee systems
land cover class in the map versus the true spatial distribution of the coffee fields from
the ground truth survey (26535 points from SICA27).
27 SICA is the Spanish acronym used to denote Sistema de Informacion Cafetera
71
Results
Spatial distribution of coffee fields
w e
Legend
I i M unicipal B oundary
SICA points
m F o re s t
[ I Clouds
m S h ad o w s
P a s tu re s
12 Kilometers
I W a ter
C offee S y ste m s
M is cellan e o u s
Projection: UTM 18 North. Datum: WGS84
F igure 5-18: Spatial distribution of coffee systems in the area: the magenta points represent the
real location of all coffee farms in the area, as indicated by the SICA database.
72
Results
5.9 R efining the Classification Result: Evaluating Linear Spectral Unm ixing
To Map different types of coffee system s
A mask was created using the ruled-based classification showed in figure 5-8.
Using this mask, the image was cut and the principles of spectral angle mapping
described in section 4.11 were used to select the most useful bands that better separate
coffee systems from other coverages. Three components were identified that influenced
the spectral signature of coffee within a pixel: coffee, forest and topographic shadows
that still remain in areas of highest slopes. Pure pixels (i.e. pixels with 100% of one and
only one cover) of forest (740 points), coffee (448 points) and shadows (137 points) were
used to analyze the separation between bands, as shown in Figure 5-10 and 5-11.
0. 1 - ^ _
[
0.099
0.098
0.097
0.096
2 0.095
0.094
0.093
0.092
0.091
0.09
0.064 0.065 0.066 0.067 0.068 0.069 0.07 0.071 0.072 0.073 0.074
b1
[Forest BShadows ASuncoffee [
F igure 5-19: Spectral separation between mean values of coffee systems and non-coffee areas,
measured at the pixel level. Note that the combination of bands 1 and 2 is not optimum because
all mean values for forest, shadows and Sun coffee fall in the same line
73
Results
0.06
0.092 0.093 0.094 0.095 0.096 0.097 0.098 0.099
Forest Shadows ASun coffee
Figure 5-20: Spectral separation between mean values of coffee systems and non-coffee areas,
measured at the pixel level. The combination of bands 2 and 3 works better, because of the
existence of wider angle between coffee systems and forest
Following this approach, different combinations of all bands were evaluated and
bands 2,3,4,5 and 7 were chosen as input for the linear spectral unmixing. The mean
values calculated for each land cover in each band were input into Idrisi software and the
Linear Spectral Unmixing28 module was run. Figure 5-12 shows the final map.
For technical details see section 4.11
74
Results
Coffee systems' classification map
Legend
Fo r es t
I I Clouds
Shadows
Pastures
Urban
B 3 M is c e ll a n eo u s
I Su n Coffee
9 12 Kilometers
S h a d e d C offee
Figure 5-21: Classification map resulting from the linear spectral unmixing. Coffee systems
were divided in sun and shade coffee classes.
5.10 R efining the classification result: Accuracy A ssessm ent
The product o f the linear spectral unmixing model was evaluated using the same
set of points described in section 5.5. The overall accuracy was 70.184% and the kappa
75
Results
statistic29 was 0.646. The 95% Confidence Interval ranges from 67.810% to 72.557%.
Table 5-7 shows the user and producers accuracy and the kappa statistic for each class.
Class Producer's 95% Confidence Users 95% Confidence Kappa

Name Accuracy (%) Interval (%) Accuracy (%) Interval (%)
Clouds 100.00 (99.77 - 100.22) 96.97 (94.54 - 99.39) 0.96
Shadows 78.77 (72.50 - 85.04) 96.92 (93.38 - 99.46) 0.95
Urban 91.30 (77.61 - 104.99) 87.50 (72.18 102.81) 0.87
Water 34.65 (20.72 - 48.51) 100.00 (97.22 102.78) 1.00
Pastures 98.33 (94.26 - 102.41) 51.30 (41.73 60.87) 0.49
Forest 97.71 (95.87 - 99.55) 81.47 (77.36 85.58) 0.77
Miscellan. 67.67 (62.20-73.13) 55.46 (50.24 60.69) 0.44
Shaded 15.18 (10.26-20.10) 45.33 (33.40 57.27) 0.35
Coffee
Sun Coffee 31.68 (22.11 -41.25) 25.81 (17.70 33.91) 0.20
Table 5-1 1: Accuracy statistics after the spectral unmixing
Note, that the overall accuracy is much higher than the accuracy for shaded coffee
and miscellaneous (i.e. non-coffee areas) classes, because of the influence of other land
cover classes with higher accuracies (e.g. pastures, clouds, shadows, forest, urban and
water). Also, note the low accuracy in shaded coffee class, where omission errors are
still less than the commission errors.
The accuracy for the Sun-coffee class, as measured by the kappa statistic is very
low (20% approximately) which does not agrees with the accuracy obtained by using the
training points (i.e. the DAPA set of Sun coffee) for accuracy (that was about 75%). This
can be an indication of a) the inappropriateness of the sample to get the end-member
spectra or b) the variability of the Sun coffee areas that is not measured by the sample.
Since there were as many sun coffee areas as shaded coffee areas in the study region, this
type of coffee areas deserves further attention for future research.
76
Results
As another indicator of accuracy, the RMS error image (see figure 5-11) shows
the spatial distribution of the error component in equation 4-29. Also, the SICA points
provided by FNC (see section 2.2) were overlaid to the image and their spatial
distribution was visually compared against the spatial distribution of the coffee systems
produced by the classification map.
77
Results
Linear Spectral Unmixing: RMS image
Legend
EZ 3 - 1 - * *?
r I 1.897 - 3:794
f I -i 7 9 4
H g 5.691 . 7.58$
H l i '7 . 5 8 8 - 9.435
H P 9.485 11.382
1 11.382 - 13.279
H | 13 2 7 9 15.176
15.176 - 17.873
H i 17.073 - 18.97
0 3 9 12 K ilom eters
Projection: UTM 18 Nortti. Datum; W G S84
Figure 5-22: Spatial distribution o f the error: the RMS image shows that most o f the study area
presents less than 10% o f error within the unmixing model.
78
Chapter 6
Discussion
The results of the accuracy assessment of both, pixel-based and object-based
analysis support the hypothesis that coffee systems can be characterized using
radiometric and topographic information. Those characteristics can be used to map areas
with higher probability of having coffee fields given certain radiometric and topographic
characteristics. The table 6-1 summarizes the results for the different methodologies
compared.
Overall Overall Kappa (per class)

Method
Accuracy kappa Coffee Miscellaneous
Pixel-based 71.89 0.66 0.38 0.39
Object-Based 74.88 0.70 0.70 0.45
Table 6-12: Comparison between di Terent methodologies
Despite the kappa value per class being lower than the desired value for a land
cover classification; it is better than the existing methodologies to map coffee Crops. For
instance, Wood and You (2006) used census data to map the spatial distribution of coffee
crops in Latin America, but the overall accuracy for this map was less than 6%, as
checked through the use of the same 1469 GPS points used here for the accuracy
assessment. Furthermore, although the methodological approaches by Coome (1989) and
Moreira (2004) did not described the achieved accuracies, is expected that is their
79
Discussion
accuracies are lower, given that both authors emphasized the need for manual edition
(through photo-interpretation) of the classification results as a key final step.
As demonstrated by the similarity between the spatial distribution of the GPS
points and the coffee systems in the land cover map, and by the overall accuracy, the fact
that this methodology narrows the geographic area that is more likely to have certain type
of crop (i.e. coffee, in this case), helps to focus the efforts in field work and subsequent
mapping methodologies to smaller regions, minimizing the costs associated to the image
interpretation.
Further, the object-based analysis provides more information than a pixel-based
analysis about the local variation (e.g. minimum and maximum values of reflectance and
topography for each homogeneous area represented by an object). This can be used (e.g.
minimum aspect) during the classification and represents an enormous advantage when
characterizing land cover for thematic mapping. The variation in these characteristics
agrees with the variation in the biophysical characteristics of coffee plantations, as is
shown in annexes 2 and 3. The values in band 3, as a response to chlorophyll content
might vary due to different plant development stages. Variations in band 4 agree with the
different foliage structure that the coffee plants and accompanying introduced species of
forest might have. Variations in bands 5 and 7 can be attributed to the different moisture
conditions, closely related to the stage of growth of the plant and the microclimatic
conditions in which the plantation is located. Nevertheless, note that the similarity in
altitude, slope and aspect values between objects and pixels based box-plots (see Annex
80
Discussion
2) shows that coffee plantations are fairly homogeneous: the altitude, slope and aspect
values of all pixels within the same object is roughly the same.
It is important to highlight that to analyze this information, we should take into
consideration that the coffee systems are diverse, and the sampling values might not
follow a normal distribution. Furthermore, the presence of different plant stages,
moisture and physiology of the cover over coffee, results in variations in the signature
that might affect the spectral separation/clustering of land cover classes.
However, the separability of the signatures also relies in the statistical method used to
analyze them. The loss of information involved in substituting ranks for original values
makes the non-parametric tests less powerful than their parametric counterpart. The
difference between samples is then accounted for ranks, instead of raw values, which
does not take into consideration the magnitude of the distances between the values (Field,
2000). Further, the Mann-Whitney test is unable to detect the difference in data
distribution thought it preserves the initial ordering of the original values. The median
value used by the Mann-Whitney test is not as representative as the mean value for a
normally distributed data. To partially overcome this problem, the analysis of the box
plot and the histograms is presented as an alternative to evaluate the separation between
features values for two land cover classes30. A drawback of the Mann-Whitney test is
that regardless of the set of data values, the mean and the variance of a set of distinct
rankings is always known (the sum of n consecutive rankings is (n(n+l))/2 (Griffith,
30Although the box plot contains 75% o f the values, those are not necessarily the most common values (i.e.
the values with the higher frequency). An examination to the histogram is needed to assess this.
81
Discussion
1997): all possible samples of size n, regardless whether a population is finite, yield a
sampling distribution that can be constructed by simply enumerating all possible
permutations of n rankings. In summary, non-parametric statistics are primary
parametric statistics computed with ranked data; however, substituting ranked data into
parametric formula fails to identify the correct sampling distribution of a non-parametric
statistic. The Mann-Withney statistic is a non-parametric alternative for the t statistic
(Griffith, 1997), but its associated measures of the sampling variation do not come from
the parametric results.
While the accuracy of the results can be affected by the overlap between land cover
classes, it is also affected by the image pre-processing. It has been shown (Smith et al.,
1980) that the Lambertian assumption may be more valid when analysis is restricted to
slopes of less than 25 degrees and effective illumination angles of less than 45 degrees.
This effect can be observed in the RMS error image (see fig.5-11), in which higher values
of error are located in areas with higher slopes. Additionally, significant radiometric
errors can be introduced as a result of the calculation of diffuse radiation during the
application of the terrain illumination correction. Ideally the model should be able to
consider the effects of slopes on diffuse irradiance and path radiance and diffuse sky
illumination as well. But it has been demonstrated that this correction is difficult to
implement (Richter, 1997).
The accuracy of the results can also be affected by the definition of objects in the
object-based analysis, when using a medium-resolution image such as Landsat to map
82
Discussion
small fields. According to the literature, the different levels of segmentation must be
reduced to a few which are geometrical and semantically robust (Blaschke and Strobl
2001; Schiewe et ah, 2001). This problem focuses on meaningful objects; as often
transitions in land cover depend on scale of the defined objects of interest (Woodcock
and Harward 1992).
Hierarchical Classification helps to focus the efforts in a fewer number of objects, but
several scales need to be considered in order to describe different objects in the
landscape. To conduct a multi-level segmentation, different thresholds and the relevant
parameters should be set for different objects. At greater scales, segmentation might
create an overrepresentation of larger areas at the cost of smaller features. Also, the
value of the scale parameter, product of the scale analysis is difficult to implement in the
software for the definition of objects. Although the target objects size is defined from
the analysis of the variogram, the resulting objects size in the segmentation is achieved
by trial and error, which undermines the efforts of the scale analysis.
With the creation of objects, the particularities of each unit as well as the dissimilarity
among units are smoothed (see Annex 3, band 2, for an example). As Wong (1996)
pointed out, the magnitude of the smoothing relies not only on the spatial autocorrelation,
but also upon the cross-correlation of variables in adjacent units. This effect was not
analyzed due to the lack of appropriate high spatial resolution data to analyze the objects
size in different bands and their cross-correlation. It constitutes one important issue for
further research when high spatial resolution images are available.
83
Discussion
After the creation and evaluation of objects, the accuracy obtained with the ruled-
based classification using objects could not be improved through spectral unmixing,
which, according to the literature review, was found to be a valuable resource to map
crops and features whose spatial resolution is lower than the pixel size. The spectral
unmixing algorithm used in this case (i.e. the linear mixture model) assumes a linear
response of all coverages within the pixel. It assumes that there is no multiple scattering
and photons interact with a single material only. This is not always true: first, some
coverages might have higher reflectance values that affect the response of a neighboring
coverage (i.e. spatial autocorrelation). Secondly, the point-spread function31 of the
sensor implies that the cover in the center of the pixels contributes more to the reflectance
of that pixel, than the perimeter. Finally, as mentioned by Fisher (1997) the adequacy of
any algorithm for land cover mapping is also affected by how the pixel, as a geographic
entity is modeling the reality, and specifically, the objects of interest.
Nevertheless, despite the existence of many techniques for sub-pixel mapping, the
linear mixture model is the simplest and most used for practical reasons. Fuzzy
classifiers are also another alternative for sub-pixel mapping (Foody, 2004). They allow
for explicit recognition of the possibility that ambiguity might exist regarding the
appropriate map label for some locations; but the difficulty lies on defining the
membership functions for each land cover class (Gianneti et al., 2001).
31 The point spread function (PSF) describes the response of an imaging system to a point source or point
object. It has been analyzed in remote sensing to determine the optimum pixel size (Atkinson, 2004)
84
Discussion
The accuracy of the results however is not limited to the analysis of the error matrix.
The spatial distribution of the GPS points collected in SICA32, overlaps fairly well with
the coffee systems in the land cover map. Those points provide a holistic view of the
spatial distribution of this crop.
Finally, as noted by Lambin (2001), the integration of GIS data into the image
analysis facilitates the interpretation of remote sensing data by linking biophysical
information measured by the image (i.e. reflectance) with landscape attributes (such as
elevation) and field measurements. This fact also highlights the role of environmental
variables in the formation and development of a plant cover.
32 SICA represents an exhaustive sampling of coffee field in the area.
85
Chapter 7
Summary and Conclusions
This research has evaluated the potential of remote sensing and GIS data to map
different types of coffee systems. Topographic attributes from a DEM were evaluated
and integrated with a Landsat image corrected by terrain and atmospheric effects. First, a
preliminary unsupervised classification was performed in order to determine a mask of
areas suitable to have coffee systems due to their spectral properties. The result of this
mask was divided in two land cover classes, coffee systems and miscellaneous (i.e. areas
with similar chlorophyll and moisture content to the coffee systems). The spectral
separation between both land cover classes was evaluated by analyzing their differences
in all bands. Second, objects were created using the minimum size determined by a
variogram analysis, and a ruled-based classification using objects and pixels was
compared.
As a result, the object-based approach increased the overall accuracy by 2.99%
and, for the coffee class specifically, the accuracy increased by 17%. Also, a visual
inspection to the maps confirms that the spatial distribution of the coffee class in the
classification map resembles the spatial distribution of the coffee fields in the area.
86
Finally, in an attempt to refine the classification result to include the type of coffee
system, pure samples of coffee and forest were extracted from the image and the linear
spectral unmixing was applied. Due to the variability in moisture, chlorophyll and size of
the coffee fields and forest, the spectral unmixing did not improve the classification
result.
One of the main contributions of this methodology is the fact that it uses a
Landsat image. High-resolution data such as IKONOS or Quickbird are more
appropriate to map coffee fields and other type of crops, but given the cloudy conditions,
the long periods of revisit/programming of the satellite and the lack of funds to acquire
those images, high resolution data do not represent a feasible resource for crop mapping
in the tropics.
This research also contributes to understand the potentialities and limitation that
remote sensing data have for crop discrimination. With the use of ancillary GIS data
within the image interpretation it was possible to generate statistics within polygons and
associate those statistics to the land cover attributes and then, use them in the
classification rule.
As mentioned in the introductory paragraphs, at the present, there are no good
cost-efficient methodologies to map coffee. The present study was designed to explore a
new approach, using a low-cost image and object-based analysis to produce maps that
show areas where coffee field are expected to be, due to certain topographic and
87
radiometric conditions. The findings suggest that, in fact, topographic conditions and
spectral information can be used to get areas of coffee fields with and accuracy of 70%,
using only automatic procedures. Therefore, it is expected that this research contributes
with a methodology that can be used to find areas most likely to contain coffee fields,
without extensive manual digitizing or visual interpretation of images. Further, the
resulting mask produced after the topographic and radiometric data has been analyzed
will serve for a better planning by providing a narrower geographic area were the
technical efforts for crop management can be better distributed.
However, the evidence from this study suggests that, to map the different types of
coffee systems more research is needed. Coffee systems are extremely variable (with
respect to reflectance and topography) and their specific environmental conditions make
difficult to determine a specific signature for each one. Further research with a better
spectral sampling of the different coffee systems (i.e. using multispectral images with
higher spatial resolution or radiometric measures in the field) will clarify the specific
signature for each type, and will contribute to improve the results. Due to the cost and
the permanent cloudy conditions in areas with agroforestry and polyculture systems,
higher resolution images are difficult to obtain, and, although this became one of the
main limitations of this research, the findings provide a valuable tool to target those
areas.
88
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Annex 1
ETM+ Calibration Parameters
Landsat ETM+ calibration Parameters (Taken from Irish, R., 2002)
Solar Spectral Irradiances

Landsat ETM+
(watts/(m2* sr)
band 1 1969.00
band 2 1840.00
band 3 1551.00
band 4 1044.00
band 5 225.70
band 7 82.07
band 8 1368.00
ETM+ Thermal Constants

Constant Value Units
K1 666.09 watts/(meter squared * stereo
radian * m)
K2 1282.71 temperature degrees (Kelvin)
Annex 2
Data Distribution: Spectral and

Topographic Characteristics (N = 180)
Coffee Non-Coffee
3ITS3C 3.1 M 2 c. 2 315C3C C17S3B

l2 b2
Mean = 0.100 Mean = 0.092
Std. Dev. = 0.012 Std. Dev. = 0.005
102
Annex 2: Data Distribution
86 -

u.I
16-
I
ojraeao 9mm o.wwo o.orooo o.iwoa ft.iaooo a,p
m
Mean = 0.060 Mean = 0.048
Std. Dev. = 0.016 Std. Dev. = 0.005
Coffee Non-Coffee
a.
M m
Mean = 0.316 Mean = 0.363
Std. Dev. = 0.054 Std. Dev. = 0.048
103
6 . 1:1 4 #- t.v . 4JN i|i3S
Mean = 0.111 Mean = 0.158

Std. Dev. = 0.043 Std. Dev. = 0.023
Coffee Non-Coffee
*
48
U
oa*m mum sw9 .9 1 m ,wuw .imoc

b7
Mean = 0.080 Mean = 0.060
Std. Dev. = 0.030 Std. Dev. = 0.010
w
u.
Mean = 20.73 Mean = 20.76

Std. Dev. = 1.95 Std. Dev. = 1.97
Coffee Non-Coffee
U.
123QJDS 1403 S3 1; iom:s mzQ.it
Mean =1595 Mean = 1494

Std. Dev. = 151 Std. Dev. = 246
105
20-
C
#
3cr
i
r rr i innr
I
0-f-
I.- . . *
i }
JU JU
...
.J J
J
it
D
if 3lP*
Mean = 17 Mean = 17
Std. Dev. = 8.6 Std. Dev. = 10.7
Coffee Non-Coffee
It
HI
m

wm
c.at icyiL s u jtij jl' j o
as pac t
asp ect
Mean = 163 Mean = 160

Std. Dev. = 82.1 Std. Dev. = 102.6
106
Annex 3
Box Plots for Coffee Systems vs. Non

coffee Systems
a) Comparison between pixels and objects
Pixels Objects
2m
m
HB'JS
cots# cisisS class
107
Annex 3: Box Plots
class
108
Annex 3: Box Plots
eoffii
109
Annex 3: Box Plots
coffee Non-coffee
cjites
c la s s
lar.i ex.
RHtyt S#5
110
Annex 3: Box Plots
class
f J T- 'iff*#
Ill
Annex 3: Box Plots
b) Radiometric features that provide the best separation
112
Annex 3: Box Plots
O414
sw
l3.'5S
220D.CC
l inck.m
s
sUss ela&a
113
Annex 3: Box Plots
iCjO"'
c) Shape features that provide the best separation:
0
It' in
DO.03
els s s
114
Annex 3: Box Plots
C'^nsriy
115
Annex 4
Normality Test
a) Pixel values
Shapiro - W ilk
Feature Class Statistic Df. Sig.
Band 2 CofFee- .76 280 .00
Non-coffee .98 300 .00
B and 3 CoFfee- .87 280 .00
B and 4 CofFee- .99 280 .26
B and 5 CoFFee- .98 280 .00
Non-cofFee .99 300 .02
B and 7 CofFee- .94 280 .00
T em perature CofFee- .99 280 .03
Elevation CoFfee- .98 280 .00
Non-coFFee .95 300 .00
Slope CofFee- .97 280 .00
Non-coFfee .96 300 .00
A spect CoFfee- .98 280 .00
Non-coFfee .95 300 .00
Annex 4: Normality Test
b) Objects Values
Mean and standard deviation values:
Shapiro - W ilk
M ean B2 Coffee .80 280 .000
Non-coffee .75 300 .000
M ean B3 Coffee .84 280 .000
Non-coffee .74 300 .050
M ean B4 Coffee .98 280 .002
Non-coffee .98 300 .000
M ean B5 Coffee .96 280 .000
Non-coffee .96 300 .000
M ean B7 Coffee .89 280 .000
Non-coffee .89 300 .000
M ean Tem perature Coffee .99 280 .071
M ean Elevation Coffee .98 280 .00
M ean Slope Coffee .96 280 .00
M ean Aspect Coffee .98 280 .00
StD ev. B2 Coffee .19 280 .00
StD ev. Tem perature Coffee .96 280 .00
StD ev. Elevation Coffee .80 280 .00
StD ev. Slope Coffee .94 280 .00
StD ev. A spect Coffee .72 280 .00
Minimum and Maximum values:
Shapiro - W ilk
M in b2 Coffee .81 280 .00
M ax b2 Coffee .82 280 .00
M in b3 Coffee .80 280 .00
M ax b3 Coffee .88 280 .00
M in b4 Coffee .98 280 .00
M in b5 Coffee .95 280 .00
M ax b5 Coffee .97 280 .00
M in b7 Coffee .87 280 .00
Non-coffee .90 300 .00 .
M ax b7 Coffee .99 280 .02
M in Temp Coffee .99 280 .02
M ax Temp Coffee .99 280 .02
M in Elevation Coffee .98 280 .00
M ax Elevation Coffee .98 280 .00
M in Slope Coffee .92 280 .00
M ax Slope Coffee .98 280 .00
M in Aspect Coffee .97 280 .00
M ax Aspect Coffee .95 280 .00
118
Feature values:
Shapiro - Wilk
Area Coffee .784 280 .00
Non-coffee .861 300 .00
Length Coffee .866 280 .00
Non-coffee .936 300 .00
Width Coffee .904 280 .00
Non-coffee .909 300 .00
Length/Width Coffee .855 280 .00
Non-coffee .954 300 .00
Compactness Coffee .944 280 .00
Non-coffee .967 300 .00
Border Length Coffee .797 280 .00
Non-coffee .871 300 .00
Shape Index Coffee .882 280 .00
Non-coffee .922 300 .00
Density Coffee .982 280 .00
Non-coffee .994 300 .31
Asymmetry Coffee .968 280 .00
Non-coffee .970 300 .00
Perimeter Coffee .857 280 .00
Non-coffee .873 300 .00
119

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A thesis submitted to the faculty of Graduate Studies and

Sandra Bolanos 2007

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expensive, tedious and inaccurate; therefore coffee maps cannot be updated

frequently and production cannot be accurately estimated. If such countries could

Here I hypothesize that coffee systems can be properly characterized and

additional information provided by an object-based approach (comprehensive

information than a pixel-based one, traditionally used in the integration of Remote

Sensing and Geographic Information Systems (GIS).

I statistically analyzed spatial and spectral characteristics of different coffee

systems (monoculture, polyculture and agroforestry systems) in three study areas in

both pixel-based and object-based approaches in a hierarchical approach and the

results were compared. Following this hierarchical approach, a preliminary

classification was performed to reduce the number of classes spectrally similar to

Actuellement, le systeme que les pays en voie de developpement emploient

revenus plus eleves pour leur produit.

caracterises et cartographies en utilisant l'information spectrale et spatiale derivee des

images satellites et des donnees topographiques. Je suppose egalement que pendant

object-basee (informations completes sur la forme et le contexte dune zone

particuliere) fournit plus d'informations que quune approche pixel-basee \

traditionnellement utilisee dans l'integration de la teledetection et des systemes

d'information geographiques (GIS).

J'ai analyse (statistiquement) les caracteristiques spatiales et spectrales des

2.3.4 5 et 7. Apres l'approche hierarchique, une classification preliminaire a ete

effectuee pour reduire le nombre de classes spectralement semblables aux systemes

ou moins). Finalement, en utilisant les memes objets, la classification a ete de

nouveau affinee, par unmixing spectral lineaire.

une approche objet-basee peut ameliorer l'exactitude globale de la classification de

unmixing spectral lineaire, cependant, ne contribue pas pour ameliorer l'exactitude de

types de systemes de cafe

McConnell, that provided me a McConnell fellowship in environment for two years,

Agriculture. I would like to acknowledge the German Cooperation Agency -G T Z -

Opportunities for Hillside Farmers: Matching Product Quality, Environments and

Market Demandfor High-Value Agricultural Products developed by CIAT.

Thanks are extended to the Smithsonian Tropical Research Institute for

providing a Levinson Fellowship for my studies and to Department of Geography at

during my stay at McGill. I want to give special thanks to professor Jonathan

Seaquist for his technical and professional advice.

acknowledgments to the coffee farmers associations in Colombia, especially to

Federation Nacional de Cafeteros de Colombia FNC for providing the technical

quantification of the coffee areas in Colombia.

the list of income-generating products exported from developing countries after

al, 2003; Bacon, 2005).

Furthermore, decreases in prices lead producers to change from traditional

agroforestry systems (shade coffee) to non-shade coffee varieties with higher

coffee quality (DaMatta, 2004).

The increase in the participation of smaller farms provides the opportunity to

for growing shade coffee have been sustainably utilized worldwide.

will require a cost-efficient methodology to analyze land use change. Cost-efficient

after image processing), or not applicable to all types of coffee systems.

In order to contribute to a better strategic planning of coffee production areas, this

hypothesized that the additional information contained in an object-based approach will

lead to a better characterization o f th e different co ffe e system s as com pared to th e

traditional pixel-based analysis.

1.1. Research Objectives

To determine how different coffee growing systems can be mapped and

characterized by integrating Geographic Information Systems (GIS) data and Remote