vii
TABLE OF CONTENTS
CHAPTER
1
2
TITLE
PAGE
DECLARATION
ii
DEDICATION
iii
ACKNOWLEDGMENTS
iv
ABSTRACT
v
ABSTRAK
vi
TABLE OF CONTENTS
vii
LIST OF TABLES
x
LIST OF FIGURES
xii
LIST OF SYMBOLS
xvi
LIST OF ABBREVIATIONS
xix
LIST OF APPENDICES
xx
INTRODUCTION
1
1.1 Background
1
1.2 Problem Statement
6
1.3 Objectives
7
1.4 Scope of Study
8
1.5 Significance of Research
9
1.6 Study Area
10
LITERATURE REVIEW
12
2.1 Introduction
12
2.2 The Basic Concept for Understanding Signal and Light
13
Interference within Marine Features from Space
2.3 Techniques used to Study and Map Sea Bottom
16
viii
Distribution
3
2.3.1 Mapping Sea Bottom using Direct Observations
16
2.3.2 Mapping Sea Bottom using Indirect Methods
19
2.4 Algorithms for Sea Bottom Mapping
24
2.5 Summary
29
DATA AND METHODOLOGY
30
3.1 Introduction
30
3.2 Data Sources and Materials
30
3.2.1 Satellite Data
31
3.2.2 Ancillary Data
36
3.3 Software
45
3.4 Methodology
45
3.4.1 Pre-processing
47
3.4.1.1 Subset Image
47
3.4.1.2 Geometric Correction
47
3.4.1.3 Masking
48
3.4.1.4 Sun Glint Removal
49
3.4.1.5 Transformation of Digital Number (DN) to
50
Radiance
3.4.2 Processing
3.4.2.1 Depth Invariant Index Technique
54
3.4.2.2 Bottom Reflectance Index Technique
56
3.4.2.3 Density Slicing
60
3.4.2.4 Supervised Classification
60
3.4.3 Analyses of the Results
4
53
61
3.5 Summary
62
RESULTS, ANALYSIS AND DISCUSSION
64
4.1 Introduction
64
4.2 Pre-processing Results
65
4.2.1 Results of Subset Images
65
4.2.2 Results of Geometric Correction
67
4.2.3 Results of Image Masking
67
4.2.4 Results of Sun Glint Removal
69
ix
4.2.5 Results of Transformation of Digital Number to
73
Radiance
4.3 Results and Analysis of Sea Bottom Mapping Using
76
Depth Invariant Index Technique in Sibu Island and
Merambong Shoal
4.4 Results and Analysis of Sea Bottom Mapping Using
97
Bottom Reflectance Index Technique in Sibu Island and
Merambong Shoal
5
4.5 Discussion
115
4.6 Summary
121
CONCLUSIONS AND RECOMMENDATIONS
122
5.1 Conclusions
122
5.2 Recommendations
123
REFERENCES
125
APPENDICES
135
x
LIST OF TABLES
TABLE NO. TITLE
PAGE
1.1
Comparison between Seaweed and Seagrass
2
1.2
Habitat Requirement for Seaweeds, Seagrass and Coral Reefs
5
2.1
Summary of Techniques and Equipment
18
3.1
Characteristics of ALOS AVNIR-2, Quickbird and Landsat-5
32
TM satellite data Satellite
3.2
Description of Images Used for Sibu Island
33
3.3
Description of Image Used for Merambong Shoal
33
3.4
Summary of Equipment Used
37
3.5
Constant Value for Rescaling Gains and Biases for ALOS
51
AVNIR-2
3.6
Constant Value for Rescaling Gains and Biases for Landsat-5
52
TM
3.7
Quickbird absCalFactorBand Value
53
3.8
Quickbird effective bandwidth (Δλ)
53
3.9
Level of Agreement of Kappa Coefficient Values
61
4.1
Deep Water Radiance Value for Each Satellite Data and
76
Study Area
4.2
Value of Correlation Coefficient, R2 for Sibu Island
2
83
4.3
Value of Correlation Coefficient, R for Merambong shoal
83
4.4
Ratio of Ki/Kj
83
4.5
Error Matrix for Depth Invariant Index Using Quickbird
92
Satellite Data in Sibu Island
4.6
Error Matrix for Depth Invariant Index Using ALOS
94
AVNIR-2 Satellite Data in Sibu Island
4.7
Error Matrix for Depth Invariant Index Using ALOS
96
xi
AVNIR-2 Satellite Data in Merambong Shoal
4.8
Date and Time of Satellite Pass
97
4.9
Value of Attenuation Coefficient for band 1 (blue) and band
102
2 (green) for ALOS AVNIR-2 and Quickbird Satellite Data
4.10
Sun and Satellite Elevation Angle for ALOS AVNIR-2
103
and Quickbird Satellite Data
4.11
Geometric Factor, g Value for ALOS AVNIR-2 and
103
Quickbird Satellite Data
4.12
Error Matrix for Bottom Reflectance Index Using Quickbird
110
Satellite Data in Sibu Island
4.13
Error Matrix for Bottom Reflectance Index Using ALOS
112
AVNIR-2 Satellite Data in Sibu Island
4.14
Error Matrix for Bottom Reflectance Index Using ALOS
114
AVNIR-2 Satellite Data in Merambong Shoal
4.15
Analysis of Results for Both Techniques
119
xii
LIST OF FIGURES
FIGURE NO. TITLE
PAGE
1.1
Morphological Differences Between Seaweed and Seagrass
2
1.2
Types of Coral Reefs
3
1.3
Location Map of Sibu Island and Merambong Shoal in
11
Johor
2.1
Absorption, Scattering and Attenuation of Light in Water
14
2.2
Signal Components of Electromagnetic Radiation Between
15
Sea and Satellite Sensor
2.3
Box Classification for Seven Classes
26
3.1
Full Raw Satellite Scene for (a) ALOS AVNIR-2 (b)
35
Landsat-5 TM and (c) Quickbird of Sibu Island
3.2
Full Raw Satellite Scene of ALOS AVNIR-2 of
35
Merambong Shoal
3.3
Sea Truth Equipment
37
3.4
Side Scan Sonar Image in Sibu Island
38
3.5
Sea Truth Map of Sibu Island Obtained on 28 September
39
2011
3.6
Sea Truth Map of Merambong Shoal Obtained on 2 July
40
2010
3.7
Topographic Map of Sibu Island
41
3.8
Topographic Map of Merambong Shoal
42
3.9
Hydrographic Chart of Sibu Island and Surrounding Areas
43
3.10
Hydrographic Chart of Merambong Shoal and Surrounding
44
Areas
3.11
Flow Chart of Methodology
46
3.12
Relationship Between Visible Band and NIR Band of
Glinted Image
50
xiii
3.13
Graph of Xi Versus Xj
54
3.14
Sun and Satellite Zenith Angles on Air and Below Water
57
3.15
Satellite Zenith Angle
58
3.16
Relationship Between Radiance and Depth for Sand Where
59
 is y-Intercept,  is Horizontal Asymptote and  is
Regression Value
4.1
Subset of Satellite Images in Sibu Island
66
4.2
Subset of Satellite Images in Merambong shoal
67
4.3
Masked Images of Sibu Island
68
4.4
Masked Images of Merambong Shoal
69
4.5
Relationship of Sun Glint Digital Number Between Visible
70
Band and NIR Band
4.6
Deglinted Image for (a) Band 1 (Blue), (b) Band 2 (Green),
72
(c) Band 3 (Red) and (d) All Bands
4.7
Image Radiances for Bands 1, 2 and 3 in Sibu Island
74
4.8
Image Radiances for Bands 1, 2 and 3 in Merambong Shoal
75
4.9
Maps Derived from ALOS AVNIR-2 Imagery of Sibu
77
Island Using Density Slicing of Bands 1 and 3
4.10
Enhanced Methodology Using Maximum Likelihood
77
Supervised Classification
4.11
Scatter Plot of Sand Substrate at Various Depths Between
79
Transformed Measured Radiance, X Values from Bands 1
& 3 for Landsat-5 TM, ALOS AVNIR-2 and Quickbird
Satellite Data in Sibu Island and Merambong shoal
4.12
Scatter Plot of Sand Substrate at Various Depths Between
81
Transformed Measured Radiance, X Values from Bands 2
& 3 for Landsat-5 TM, ALOS AVNIR-2 and Quickbird
Satellite Data in Sibu Island and Merambong shoal
4.13
Depth Invariant Index Images of Sibu Island
85
4.14
Depth Invariant Index Images of Merambong Shoal
86
4.15
Sea Bottom Map Using Landsat-5 TM Satellite Data (2005)
87
in Sibu Island Over Sibu Island
4.16
Sea Bottom Map Using Quickbird Satellite Data (2007) in
88
Sibu Island
4.17
Sea Bottom Map Using ALOS AVNIR-2 Satellite Data
89
xiv
(2008) in Sibu Island
4.18
Sea Bottom Map Using ALOS AVNIR-2 Satellite Data
90
(2010) in Merambong Shoal
4.19
Qualitative Analysis of Processed Quickbird Satellite Data
91
Using Depth Invariant Index Technique for Sibu Island
4.20
Qualitative Analysis of Processed ALOS AVNIR-2
93
Satellite Data Using Depth Invariant Index Technique for
Sibu Island
4.21
Qualitative Analysis of Processed ALOS AVNIR-2
95
Satellite Data Using Depth Invariant Index Technique of
Merambong Shoal
4.22
Tidal Height During Satellite Passes in Study Areas
98
4.23
Relationship Between Radiance and Depth for Bands 1 and
99
2 for Quickbird Satellite Data in Sibu Island
4.24
Relationship Between Radiance and Depth for Bands 1 and
100
2 for ALOS AVNIR-2 Satellite Data in Sibu Island
4.25
Relationship Between Radiance and Depth for Bands 1 and
101
2 for ALOS AVNIR-2 Satellite Data in Merambong Shoal
4.26
Bottom Reflectance Index from Band 1 and Band 2 Using
104
Quickbird and ALOS AVNIR-2 Satellite Data in Sibu
Island
4.27
Bottom Reflectance Index from Band 1 and Band 2 Using
105
ALOS AVNIR-2 Satellite Data in Merambong Shoal
4.28
Sea Bottom Map from Quickbird Satellite Data (2007) in
106
Sibu Island
4.29
Sea Bottom Map from ALOS AVNIR-2 Satellite Data
107
(2008) in Sibu Island
4.30
Sea Bottom Map from ALOS AVNIR-2 Satellite Data
108
(2010) in Merambong Shoal
4.31
Qualitative Analysis of Processed Quickbird Satellite Data
109
Using Bottom Reflectance Index Technique in Sibu Island
4.32
Qualitative Analysis of Processed ALOS AVNIR-2
Satellite Data Using Bottom Reflectance Index Technique
in Sibu Island
111
xv
4.33
Qualitative Analysis of Processed ALOS AVNIR-2
113
Satellite Data Using Bottom Reflectance Index Technique
in Merambong Shoal
4.34
Coral Reefs Distribution in Sibu Island in 1997
116
4.35
Location of Pulai estuary
117
4.36
Accuracy Comparison of Sibu Island
120
4.37
Accuracy Comparison of Merambong Shoal
120
xvi
LIST OF SYMBOLS
absCalFactorBand
-
Absolute Radiometric Calibration Factor
c
-
y-intercept
Dn, DNi
-
Digital Number
FOV
-
Field of View
g
-
Geometric Factor Accounting for Path Length Through Water
h
-
Satellite Height
i
-
i-th Habitat
M
-
Number of Habitats
m
-
Slope of Graph
N
-
Total Number of Sites
qPixel,Band
-
Radiometrically Corrected Image Pixels
R
-
Earth Radius
-RB
-
Index Substrate Reflectance
SX
-
Swath Width
T
-
Tau Coefficient
X, Y
-
Coordinates on Map
x, y
-
Coordinates on Image
Z
-
Depth
ΔλBand
-
Effective Bandwidth for a Given Band
Ø
-
Satellite Zenith Angle

-
y-intercept

-
Horizontal Asymptote

-
Regression Value
Ri’
-
Deglinted Image
Ø’s
-
Sun Zenith Angle Below Water
Ø’
-
Satellite Zenith Angle Below Water
xvii
Øs
-
Sun Zenith Angle
ai
-
Wavelength Dependent Constant Accounting for Atmospheric
Effects and Water Surface Reflection
a1-a6
-
Coefficients
Brescale
-
LMINλ
b1-b6
-
Coefficients
bi
-
Regression Slope
CalCoefi
-
In-band Radiance Calibration Coefficient
Ki, Kj
-
Attenuation Coefficient for Bands i and j
Li, Lj
-
Measured Radiance in Bands i and j
Lsi, Lsj
-
Deep Water Radiance in Bands i and j
LMAXλ
-
Spectral Radiance that is Scaled to Qcal max
LMINλ
-
Spectral Radiance that is Scaled to Qcal min
Lλ
-
Spectral Radiance at the Sensors Aperture
LλPixel,Band
-
Top-of-atmosphere (TOA) Band Integrated Radiance Image
Pixels
MinNIR
-
Minimum Pixel Value in NIR Band
na
-
Air Refraction Index
ni
-
Total Row for Habitat i
nw
-
Water Refraction Index
P0
-
Overall Accuracy
Qcal
-
Digital Number
Qcal max
-
Maximum Quantized Calibrated Pixel Value (DN)
Corresponding to LMAX
Qcalmin
-
Minimum Quantized Calibrated Pixel Value (DN) Corresponding
to LMIN
Rbi
-
Bottom Reflectance
Ri
-
Pixel Value in Band i
RNIR
-
Pixel Value in NIR Band
ri, rj
-
Bottom Reflectance in Bands i and j
Xi, Xj
-
Transformed Measured Radiance in Bands i and j
X1
-
Transformed Measured Radiance for Band 1
X3
-
Transformed Measured Radiance for Band 3
xi
-
Diagonal Value for Habitat i
Yi
-
Depth Invariant Index
xviii
Yio
-
Constant for Fixed Illumination and Atmospheric Conditions
xix
LIST OF ABBREVIATIONS
ALOS
:
Advanced Land Observing Satellite
AVIRIS
:
Airborne Visible Infrared Imaging Spectrometer
AVNIR-2
:
Advanced Visible and Near Infrared Radiometer Type 2
CASI
:
Compact Airborne Spectrographic Imager
DIB
:
Depth-invariant Bottom Index
DGPS
:
Differential Global Positioning System
DN
:
Digital Numbers
EMR
:
Electromagnetic Radiation
ETM+
:
Enhanced Thematic Mapper Plus
GCP
:
Ground Control Points
GIS
:
Geographic Information System
GPS
:
Global Positioning System
IRS
:
Indian Remote Sensing
JAXA
:
Japan Aerospace Exploration Agency
LISS III
:
1C and 1D Linear Imaging Self-scanning Sensor III
MSS
:
Multispectral Scanner
NIR
:
Near Infrared
NRE
:
Ministry of Natural Resources and Environment
ROV
:
Remotely Operated Vehicle
SOS
:
Save Our Seahorses
SPOT
:
Systeme Probatoire de I’Observation de la Terre
TM
:
Thematic Mapper
TOA
:
Top-of-Atmosphere
xx
LIST OF APPENDICES
APPENDIX
TITLE
PAGE
A
Sea Truth Calibration Points for Sibu Island
135
B
Sea Truth Validation Points for Sibu Island
137
C
Sea Truth Calibration Points for Merambung Shoal
146
D
Sea Truth Validation Points for Merambong Shoal
147
E
Sea Bottom Features of Sibu Island
152
F
Sea Bottom Features of Merambong shoal
153