UNIVERSITI PUTRA MALAYSIA. DETERMINATION OF CHLOROPHYLL-a AND TOTAL SUSPENDED SEDIMENT USING AIRBORNE REMOTE SENSING DATA AKMALHISHAM BIN JASNI

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1 UNIVERSITI PUTRA MALAYSIA DETERMINATION OF CHLOROPHYLL-a AND TOTAL SUSPENDED SEDIMENT USING AIRBORNE REMOTE SENSING DATA AKMALHISHAM BIN JASNI ITMA

2 DETERMINATION OF CHLOROPHYLL-a AND TOTAL SUSPENDED SEDIMENT USING AIRBORNE REMOTE SENSING DATA By AKMALHISHAM BIN JASNI Thesis Submitted to the School of Graduate Studies, Universiti Putra Malaysia, in Fulfilment of the Requirements for the Degree of Master of Science March 2007

3 DEDICATION All praise and glory are expressed to the Almighty Lord for His blessings and graciousness that strengthen me to complete this thesis. Utmost gratitude to my parents, Jasni Ismail and Salmah Alias for their patience, faith and undying support for my success. Beloved big families in Selangor and Melaka for inspiring me all the time and Finally, to my dearest wife Mah (Siti Asmah Hj. Ahmad), my loving daughter baby umai (Siti Humaira Akmalhisham) and my loving new born baby (Muhammad Fawwaz Akmalhisham)who are always by my side, thank you for your never ending support, patience and encouragement. ii

4 Abstract of thesis presented to the Senate of Universiti Putra Malaysia in fulfilment of the requirement for the degree of Master of Science DETERMINATION OF CHLOROPHYLL-a AND TOTAL SUSPENDED SEDIMENT USING AIRBORNE REMOTE SENSING DATA By AKMALHISHAM BIN JASNI March 2007 Chairman Faculty : Professor Shattri Mansor, PhD : Institute of Advanced Technology The objective of this study are to derive the pattern of Chlorophyll-a (Chl-a) and Total Suspended Sediments (TSS) distribution as well as to built and integrate the Chl-a and TSS graphical models to a sub-system that can be utilized to generate the distribution maps of those parameters. The Chl-a and TSS modeling were generated from MASTER airborne data over the Kuala Terengganu coastal region. They were extracted by the empirical approach where the recorded reflectance of MASTER data was coincided to in situ data during the overpass. A linear coefficient of correlation R 2 gained for Chl-a was from the band ratio of 1/2 and for TSS was from the band 8. This weak interaction was resulted due to the limited sampling points and restricted sea surface region in the study area. These models were then integrated into IMAGINE image processing software through an automated processing sub-system that was created to hold on Chl-a and TSS modeling. iii

5 Abstrak tesis yang dikemukakan kepada Senat Universiti Putra Malaysia sebagai memenuhi keperluan untuk Ijazah Master Sains PENENTUAN KLOROFIL-a DAN KANDUNGAN SEDIMEN TERAMPAI MENGGUNAKAN DATA PENERBANGAN PENDERIAAN JAUH Oleh AKMALHISHAM BIN JASNI March 2007 Pengerusi Fakulti : Profesor Shattri Mansor, PhD : Institut Teknologi Maju Objektif kajian ini adalah untuk mendapatkan corak taburan Klorofil-a (Chla) dan Kandungan Sedimen Terampai (TSS) serta membina dan mengintegrasikan model grafik Chl-a dan TSS ke dalam suatu sub-sistem supaya boleh digunakan untuk menjana peta taburan parameter-parameter tersebut. Permodelan Chl-a dan TSS dijanakan daripada data MASTER di kawasan perairan Kuala Terengganu. Ia diekstrak melalui kaedah empirikal di mana pembalikan data MASTER yang direkod diseiringkan dengan data lapangan ketika laluan pesawat. Nilai pekali hubungan linear R 2 untuk Chl-a yang didapati adalah daripada nisbah jalur 1/2 dan bagi TSS adalah daripada jalur 8. Hubungan yang lemah ini terhasil disebabkan titik sampel yang terhad dan kawasan permukaan laut yang terbatas di dalam kawasan kajian. Model ini kemudiannya diintegrasikan ke dalam perisian pemprosesan imej IMAGINE melalui suatu sub-sistem pemprosesan automatik yang dibina untuk menyimpan permodelan Chl-a dan TSS. iv

6 ACKNOWLEDGEMENTS Praise to Almighty Lord for His blessings, endless love and guidance throughout the study. With a deep sense of gratitude, the author would like to acknowledge his project supervisory committee Prof. Dr. Shattri Mansor, Assoc. Prof. Dr. Zelina Zaiton Ibrahim and Dr. Helmi Zulhaidi Mohd Shafri for their invaluable guidance, constructive suggestions and encouragement throughout the duration of this project. Sincere thanks are extended to laboratory staff from Spatial and Numerical Modeling Laboratory (SNML) for their valuable guidance and support in the technical part. Thanks are also extended to the staff of the Geomatic Laboratory. Gratitude to Dr. Billa L. and other members in the lab for their encouragement and ideas. Sincere gratefulness also to Mrs. Adzuhaidah Md. Taha, Sekolah Seri Puteri, for her meaningful guidance and suggestions. Lastly, the author would like to express his sincere appreciation to his family especially to his lovely wife for their undying love, patience, encouragement and continuous supports during the course of the study. v

7 I certify that an Examination Committee met on 19 th March 2007 to conduct the final examination of Akmalhisham bin Jasni on his Master of Science thesis entitled Application of Master Imagery in Determination of Chlorophyll-a and Total Suspended Sediment in accordance with Universiti Pertanian Malaysia (Higher Degree) Act 1980 and Universiti Putra Malaysia (Higher Degree) Regulation The committee recommends that the candidate be awarded the relevant degree. Members of the Examination Committees are as follows: Ahmad Rodzi Mahmud, PhD Associate Professor Faculty of Graduate Studies Universiti Putra Malaysia (Chairman) Abdul Rashid Mohamed Shariff, PhD Associate Professor Faculty of Graduate Studies Universiti Putra Malaysia (Internal Examiner) Mohd Ibrahim Hj. Mohamed, PhD Professor Faculty of Graduate Studies Universiti Putra Malaysia (Internal Examiner) Mazlan Hashim, PhD Professor Faculty of Graduate Studies Universiti Putra Malaysia (External Examiner) HASANAH MOHD. GHAZALI, PhD Professor/Deputy Dean School of Graduate Studies Universiti Putra Malaysia Date: 21 JUNE 2007 vi

8 This thesis submitted to the Senate of Universiti Putra Malaysia and has been accepted as fulfilment of the requirement for the degree of Master of Science. The members of the Supervisory Committee are as follows: Shattri Mansor, PhD Professor Institute of Advanced Technology Universiti Putra Malaysia (Chairman) Zelina Zaiton Ibrahim, PhD Associate Professor Faculty of Environmental Sciences Universiti Putra Malaysia (Member) Helmi Zulhaidi Mohd Shafri, PhD Lecturer Faculty of Engineering Universiti Putra Malaysia (Member) AINI IDERIS, PhD Professor/Dean School of Graduate Studies Universiti Putra Malaysia Date: 17 JULY 2007 vii

9 DECLARATION I hereby declare that the thesis is based on my original work except for quotations and citations which have been duly acknowledged. I also declare that it has not been previously or concurrently submitted for any other degree at UPM or other institutions. AKMALHISHAM BIN JASNI Date: 30 MAY 2007 viii

10 TABLE OF CONTENTS DEDICATION ABSTRACT ABSTRAK ACKNOWLEDGEMENTS APPROVAL DECLARATION LIST OF TABLES LIST OF FIGURES LIST OF ABBREVIATIONS Page ii iii iv v vi viii xi xii xiv CHAPTER 1 INTRODUCTION 1.1 General 1.2 Statement of the problem 1.3 Objective 1.4 Scope of the study 1.5 Thesis structure LITERATURE REVIEW 2.1 Introduction 2.2 Approaches to Chl-a and TSS mapping using airborne remote sensing Chlorophyll-a Total Suspended Sediment 2.3 Airborne and spaceborne remote sensing Landsat 7 Enhanced Thematic Mapper Plus (ETM+) Sea-viewing Wide Field of View Sensor (SeaWiFS) Airborne Thematic Mapper (ATM) Micro Surface Acquisition System (MicroSAS) Modis-Aster (MASTER) 2.4 Digital image processing Image rectification Remote sensing reflectance Image analysis and extraction 2.5 Automated processing sub-system 2.6 Summary ix

11 3 METHODOLOGY 3.1 Introduction Study framework Description of the study area and ground truthing MASTER image processing Image rectification Remote sensing reflectance Extraction of Chl-a and TSS 3.5 Development of the sub-system 3.6 Summary RESULTS AND DISCUSSION 4.1 Introduction 4.2 Chlorophyll-a 4.3 Total Suspended Sediment 4.4 Justification of Chl-a and TSS of an airborne MASTER to spaceborne Landsat 7 ETM+ data The retrieval of Chl-a from Landsat 7 ETM+ data The re trieval of TSS from Landsat 7 ETM+ data The comparison of Chl-a and TSS concentration between MASTER, Landsat 7 ETM+ and in situ measurement 4.5 Coastal Zone Information Management Sub-system (CZ-IMS) Development of the Sub-system CZ-IMS image processing time frame 4.6 Summary CONCLUSIONS AND RECOMMENDATIONS 5.1 Conclusions 5.2 Recommendations R EFERENCES R.1 BIODATA OF THE AUTHOR B.1 x

12 LIST OF TABLES Table Page 2.1 The historical Landsat satellites information The spectral characteristics of Landsat 7 ETM Spectral characteristics of SeaWiFS Spectral characteristics of ATM Spectral characteristics of MicroSAS Modis-Aster (MASTER) sensor s specification MASTER flight line information A comparison of different types of remote sensing instruments Product survey on remote sensing image processing 2.30 software (Source: Limp, 2005) 3.1 Ground truth parameters taken from field site (Source: 3.7 NASA MACRES PACRIM 2000 field campaign) 4.1 Remote sensing reflectance (RRS) for Chlorophyll-a 4.2 obtained at sampling points 4.2 R 2 values for chlorophyll and remote sensing reflectance 4.3 in different regression modes 4.3 Comparison between measured and calculated 4.5 Chlorophyll-a concentration 4.4 Remote sensing reflectance (RRS) of sedimentation 4.8 obtained at sampling points 4.5 R 2 values for sedimentation and remote sensing 4.9 reflectance in different regression modes 4.6 Comparison between measured and calculated Total Suspended Sediment concentration xi 4.11

13 4.7 Comparison of Chl-a concentration between in situ, MASTER and Landsat 7 ETM+ measurement 4.8 Comparison of TSS concentration between in situ, MASTER and Landsat 7 ETM+ measurement 4.9 The time frame expects to be accomplished by using CZ-IMS module xii

14 LIST OF FIGURES Figure 2.1 Airborne remote sensing processes (Source: Walthall, 2006) 2.2 Figure 2.2: Spectral response of Chlorophyll-a at the sea water (Modified from: Khorram et al., 1987; Flink et al., 2001; Martin et al., 2005) 2.3 Figure 2.3: Spectral response of TSS at the sea water (Modified from: Ritchie and Cooper, 1988; Rainey et al., 2003; Wakefield et al., 2003) Page MASTER airborne instrument (Source: Hook et al., 2000) Flow chart of the research methodology The location of Kuala Terengganu coastal area, Terengganu Parameter s coordinates from field site Flow chart of the MASTER airborne digital image processing Nearest Neighborhood resampling method Geometric correction for MASTER imagery The spatial model of remote sensing reflectance Spectral signature before conversion to remote sensing reflectance 3.9 Spectral signature after conversion to remote sensing reflectance Flow chart of the CZ-IMS development Correlation between measured chlorophyll and remote sensing reflectance Chlorophyll-a modeling in IMAGINE software 4.5 xiii

15 4.3 Distribution of Chlorophyll-a concentration in Kuala Terengganu coastal area using MASTER data 4.4 Correlation between measured sedimentation and remote sensing reflectance 4.5 Total Suspended Sediment modeling in IMAGINE software 4.6 Distribution of Total Suspended Sediment in Kuala Terengganu coastal area using MASTER data The location of the study area The spatial model of conversion of radiance to reflectance and atmospheric correction of Landsat 7 ETM Chl-a concentration from Landsat 7 ETM+ satellite data TSS concentration from Landsat 7 ETM+ satellite data CZ-IMS menu has been integrated to the IMAGINE main toolbar 4.12 Chlorophyll-a and Total Suspended Sediment submenu in CZ-IMS 4.13 An example of TSS modeling interface in the CZ-IMS module xiv

16 LIST OF ABBREVIATIONS ALT ASF ASTER Altitude Ames Airborne Sensor Facility Advanced Spaceborne Thermal Emission and Reflection Radiometer ATM AVHRR AZI CASI Chl-a CZCS CZ-IMS DEG DN E d EML ESA ETM+ FOV GCPs GIS GLI Airborne Thematic Mapper Advanced Very High Resolution Radiometer Azimuth Compact Airborne Spectrographic Imager Chlorophyll-a Coastal Zone Color Scanner Coastal Zone Information Management Sub-system Degree Digital Number Total Incident Irradiance Erdas Macro Language European Space Agency Enhanced Thematic Mapper Plus Field of View Ground Control Points Geographical Information System Global Imager xv

17 GPS GUI HDF HH IFOV IRS km LAT LONG L up L w m MACRES MASTER MESSR MERIS MicroSAS MIR MM MODIS MOS MOS Global Positioning System Graphical User Interface Hierarchical Data Format Hour Instantaneous Field of View Indian Remote Sensing Satellite kilometer Latitude Longitude Upwelling Radiance Water Leaving Radiance meter Malaysian Center for Remote Sensing Modis-Aster Multispectral Electronic Self-Scanning Radiometer Medium Resolution Imaging Spectrometer Micro Surface Acquisition System Middle Infra Red Minute Moderate Resolution Imaging Spectroradiometer Marine Observation Satellite Modular Opto-electronic Sensor xvi

18 MSL MSR MSS NASA NDCI nm NOAA OCI OCTS R 2 RADAR Ref RMSE RRS SAR SeaWiFS SLAR SML SNML sol SPOT SS Mean Sea Level Microwave Scanning Radiometer Multi Spectral Scanner National Aeronautics and Space Administration Normalized Difference Chlorophyll Index nanometer National Oceanic and Atmospheric Administration Ocean Color Imager Ocean Color Thermal Sensor Coefficient of Correlation Radio Detection and Ranging Reflectance Root Mean Square Error Remote Sensing Reflectance Synthetic Aperture Radar Sea Viewing Wide Field of View Sensor Side Looking Airborne Radar Spatial Modeling Language Spatial and Numerical Modeling Laboratory Sun at Zenith Angle Satellite Pour l'observation de la Terre Second xvii

19 SWIR TIR TM TSS UPM US UTM VNIR VTIR WGS ZEN Short Wave Infra Red Thermal Infra Red Thematic Mapper Total Suspended Sediment Universiti Putra Malaysia United State Universal Transverse Mercator Visible Near Infra Red Visible and Thermal Infrared Radiometer World Geodetic System Zenith µm micrometer xviii

20 CHAPTER 1 INTRODUCTION 1.1 General The coastal zone is the most intensively used area compared to all other areas settled by humans in the world. In the next several years, more people will live in the coastal zone. For these reasons, coastal resources will continue to be, and are being placed under multiple, intensive and often competing pressures. These pressures on the coastal zone will certainly be more intensive in the future. The use of techniques which attempts to assist in managing the many conflicts in a sustainable way will therefore become increasingly important in both developed and developing countries (Kay and Alder 1999). Various approaches from conventional to recent technology have been applied to monitor and manage this critical region. One of the modern techniques that are increasingly accepted by many scientists and engineers is remote sensing. Remote sensing plays an important role in coastal area management by providing a synoptic view of the landscape. Such view is partially impossible to be obtained by conventional in situ measurements, thus remote sensing offers a way to manage it. Remotely sensed imagery has been used to map coastal areas and their components such as water quality, 1. 1

21 bathymetry, coastal dynamics, bottom features terrestrial and marine habitat and some coastal hazards. The use of this method has become more important in understanding the behavior of coastal environments because of its capacity to provide both spatial and temporal information. An example of the usage of remotely sensed image data is in the monitoring of water bodies including the monitoring of high concentrations of sea surface temperature, chlorophyll and suspended sediments in coastal waters. Moreover, the importance of remote sensing imagery and derived products for showing coastal and marine spatio-temporal trends on longer time scales are widely recognized, especially in relation to climatic variability. This applies to features on both sides of the land-sea boundary such as chlorophyll and sedimentation. Therefore, development of methods to characterize the state and interaction of coastal water to remotely sensed image particularly in monitoring of chlorophyll and sedimentation concentration patterns and estimation of their constituents are challenging topics. 1. 2

22 1.2 Statement of the Problem There is growing awareness among the Malaysian public that the environment is a vital part of our lives. It is important for Malaysian to come with consistent and comprehensive action to conserve natural resources, tackle pollution problems and phase out unsustainable practise and technologies. The country s marine ecosystem, among the world s richest in terms of biodiversity is rapidly deteriorating. For example, the coral reefs which are essential breeding and nursery areas for many types of fish, are being exploited by commercial and tourism purposes, at the same time the concentration of phytoplankton and chlorophyll that most always for fish feeding also reduced, threatened by siltation and sedimentation caused by development project. The use of conventional technique such as cruise observation certainly has limited contribution in order to solve the problem stated. For example, synoptic chlorophyll and sedimentation mapping from this particular technique has not been feasible due to the dynamic condition like as strong winds, rain, long-shore transport and else (Stabeno et al., 2004). Nevertheless, remote sensing in this application is able to manage this problem particularly in mapping of chlorophyll and sedimentation at single time scale for the entire study area. This study was focused to the use of remote sensing technique from an airborne platform in relation to retrieve Chlorophyll-a 1. 3

23 (Chl-a) and Total Suspended Sediment (TSS) pattern and distribution from the data called Modis-Aster (MASTER). In this study, the Kuala Terengganu coastal area had been chosen as a study area. It is among the most popular vacation and tourism zones in the country. In parts of its coastal zones, there are also large scale fishery activities and security-defences oriented, but other areas are supposed to be in a relative untouched status. Different ecosystems and their variability habitats are related to different tolerance and response to factors such as land reclamation activities, sediment load (turbidity), nutrient availability, currents and tides. These factors should be considered by the municipal and government for the duration of upgrading the area so that any error can be reduced or totally be avoided. 1.3 Objective The goal of this study was to gain an advantage to the use of MASTER imagery in coastal zone management which was focused to two objectives as identified below: 1. To derive the pattern of Chlorophyll-a and Total Suspended Sediments distribution. 2. To built and integrate the graphical models as a sub-system that can be utilized to generate the distribution maps of Chlorophyll-a and 1. 4

24 Total Suspended Sediments. 1.4 Scope of the Study In order to achieve the objectives, the study was focused on these specific areas. 1. An airborne sensing data called Modis-Aster (MASTER) data was used. The data was obtained from PACRIM 2000 campaign coordinated by National Aeronautics and Space Administration (NASA) and Malaysia Center for Remote Sensing (MACRES). 2. The Chlorophyll-a and Total Suspended Sediment distribution were extracted base on empirical relationship between MASTER data and field data. 3. The graphical models and sub-system developed were integrated into image processing software Imagine 8.6, running under Window Operating System. 1.5 Thesis Structure Chapter 1 (Introduction) reviewed to the introduction of coastal zone information management. The objectives and the scopes of the research were briefly described. 1. 5

25 Chapter 2 (Literature Review) presents the past-related research by scientists in coastal zone information management and oceanography using an airborne remote sensing techniques. Chapter 3 (Methodology) was contained the investigations of chlorophyll and sedimentation mapping. Methodology of the research and field data measurement was also discussed. Details about the Coastal Zone Information Management Sub-system (CZ-IMS) that had been integrated in to Imagine 8.6 were also included. The results of this study were presented in Chapter 4 (Results and Discussion). This chapter had addressed the results of oceanography parameters extraction namely Chlorophyll-a and Total Suspended Sediment. The discussion of the results of those parameters had also been included. The validation of Chl-a and TSS had also been performed which were compared to Landsat & ETM+ (Enhanced Thematic Mapper plus). Next, the result and discussion of Coastal Zone Information Management Sub-system (CZ-IMS) also had been presented here. Chapter 5 (Conclusions and Recommendations) gave the overall ending stages, which summarizes the overall results and recommendations onto this application of an airborne remote sensing for Chlorophyll-a and Total Suspended Sediment studies. 1. 6