iSAT: The Integrated Satellite and Acoustic Telemetry system for tracking marine megafauna ...

194 Pages·2014·50.74 MB·English

iSAT: The Integrated Satellite and Acoustic Telemetry system for tracking marine megafauna
Dissertation by
Pedro Roberto De La Torre Olazabal
In Partial Fulfillment of the Requirements
For the Degree of
Doctor of Philosophy
King Abdullah University of Science and Technology, Thuwal,
Kingdom of Saudi Arabia
May, 2014
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The dissertation of Pedro R De La Torre Olazabal is approved by the examination committee
Committee Chairperson: Dr. Michael Lee Berumen
Committee Member: Dr. Georgiy Stenchikov
Committee Member: Dr. Khaled N. Salama
Committee Member: Dr. Christian Claudel
External Committee Member: Kim N. Holland
King Abdullah University of Science and Technology
2014
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Copyright ©2014
Pedro Roberto De La Torre Olazabal
All Rights Reserved
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ABSTRACT
iSAT: The Integrated Satellite and Acoustic Telemetry system for tracking marine megafauna
Pedro Roberto De La Torre Olazabal
In this dissertation an innovative technology to study whale sharks, Rhincodon typus is pre-
sented. The Integrated Satellite and Acoustic Telemetry project (iSAT) combines underwater
acoustic telemetry, autonomous navigation and radio frequency communications into a stan-
dalone system. The whale shark, a resident of the Saudi Arabian Red Sea, is the target of
the study. The technology presented is designed to help close current gaps in the knowledge of
whale shark biology; these are gaps that prohibit the design of optimal conservation strategies.
Unfortunately, the various existing tracking technologies each have limitations and are unable
to solve all the unanswered questions. Whale shark populations are increasingly threatened by
anthropogenic activities such as targeted and indirect fishing pressure, creating an urgent need
for better management practices.
This dissertation addresses the current state-of-the-art of relevant technologies, including
autonomous surface vehicles (ASVs), sensors for research in the ocean and remote monitoring
of wild fauna (biotelemetry). iSAT contains components of all of these technologies, but the
primaryachievementofthisdissertationisthedevelopmentofiSAT’sAcousticTrackingSystem
(ATS). Underwater, the most efficient way of transmitting energy through long distances is
sound. An electronic tag is attached to an animal and works as its acoustic identifier. iSAT’s
hydrophonearraydetectsthepresenceanddirectionoftheacousticsignalgeneratedbythetag.
Theexpectedperformance,range,andcapacitytotellthedirectiontothetagareexplainedand
compared to the actual measured values. The first operational iSAT ATS is demonstrated.
This work represents significant advancement towards a fully autonomous iSAT system. De-
velopmentsonthepowerelectronics,navigation,renewableenergyharvesting,andothermodules
are included in this research. With the recent integration of digital acquisition systems, iSAT’s
capabilities were increased to minimize its size and allow it to communicate with other acoustic
systems. Future engineering works are still necessary to achieve a fully automated system, but
the current developments with the ATS have immediate applications.
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ACKNOWLEDGEMENTS
I would like to thank my evaluation committee, Dr. Khaled N Salama, Dr. Christian Claudel
andDr. GeorgiyStenchikovforencouragingmetodeliverresults,keepingtrackonmyprogress,
and providing their help when it was necessary.
Thanks also go to Coastal and Marine Research Core laboratory team, to Dr. Abdulaziz for
allowing me to use their space to have a more practical project development, Ramzi Jahdali for
havingreadytheboatsandpermitswhenIneededthem,FrancisMallonforthereadilyavailable
gear. Theteamoftechniciansthatrepliedtomyrequestsondemandmakinginfactmoreefficient
themanufactureprocessatKAUST:Marlon,Mayknel,Jason,Rodelio,Rico,Ezekiel. Iwouldlike
to recognize the efforts of Ihab to efficiently follow up with the job requests. Additionally, Mark
Pantalita’sandSamerMahmoud’shelpintheelectronicslabwaskeytosuccesfullyconcludinga
vast amount of experiments. In the electronics lab, Meshal AbdulKareem and Yang Liu played
a key role in time efficiency, specially material procurement for our circuits, thank you guys.
I would like to recognize the patience and effort of the Workshop Core Lab, the designers Ali
Khoder, Tayyab Ahmed, Milan Maity and Yussef for their efforts in satisfying my job requests.
Thanks go to my colleagues, Jesse Cochran, Gerrit Nanninga, Julia Spaet, Maha Khalil,
JessicaBouwmeester,AlexKattan,RemyGatinsandMayRobertsfortheirvaluablehelpinthe
field.
Special thanks go to Lloyd Smith for being an excellent guide into the marine engineering
design. ThankyouAjaySanchetiforsharingyourknowledgewithmeintheprogrammersslang
and project organization. This project was only possible by the outstanding interdisciplinary
work that we did together as a team.
I would like to thank my advisor Dr. Michael Berumen for his guidance and commitment
with the project and for finding alternatives to the challenging situations that we went through.
I dedicate this dissertation to my sister, Adriana, with love.
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TABLE OF CONTENTS
EXAMINATION COMMITTEE APPROVAL 2
COPYRIGHT 3
ABSTRACT 4
ACKNOWLEDGEMENTS 5
TABLE OF CONTENTS 8
LIST OF FIGURES 12
1 ON THE WHALE SHARK, Rhincodon typus, ECOLOGY 13
1.1 Taxonomy . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
1.2 Feeding . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
1.3 Life history and reproduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
1.4 Social behavior . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
1.5 Movement patterns: migrations and aggregations . . . . . . . . . . . . . . . . . . 16
1.6 Diving characteristics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
1.7 The human role in conservation of the species . . . . . . . . . . . . . . . . . . . . 19
2 MARINE TECHNOLOGY AND BIOTELEMETRY 22
2.1 The iSAT project . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
2.2 General purpose underwater tracking platforms . . . . . . . . . . . . . . . . . . . 25
2.3 Power considerations for autonomous surface vehicles in the Red Sea . . . . . . . 26
2.4 Using sound to study marine life . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
2.5 Biotelemetry . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
2.5.1 Satellite tracking . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
2.5.2 Electronic acoustic biotelemetry . . . . . . . . . . . . . . . . . . . . . . . 32
2.6 Localization . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
2.7 Marine technology remarks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
3 iSAT’S ACOUSTIC TRACKING SYSTEM 38
3.1 Environmental framework of the marine acoustic system. . . . . . . . . . . . . . 38
3.2 Transducer for acoustic applications . . . . . . . . . . . . . . . . . . . . . . . . . 40
3.3 Design of a marine biotelemetric tag . . . . . . . . . . . . . . . . . . . . . . . . . 43
3.4 A narrow band hydrophone . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46
3.5 Order-of-arrival-based directionality . . . . . . . . . . . . . . . . . . . . . . . . . 51
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4 EXPERIMENTAL ACOUSTIC TRACKING RESULTS 54
4.1 Transducer characterization . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54
4.2 Hydrophone noise floor level. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55
4.3 Tag performance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57
4.3.1 Waveform generation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58
4.3.2 Tag calibration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59
4.4 Hydrophone performance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60
4.4.1 Transducer selection and circuit tuning . . . . . . . . . . . . . . . . . . . 60
4.4.2 Transducer calibration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62
4.5 Acoustic range of the system . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62
4.5.1 Performance at 100m vs a passive sonar model . . . . . . . . . . . . . . . 62
4.5.2 Hydrophone’s detection delay . . . . . . . . . . . . . . . . . . . . . . . . . 64
4.5.3 Wide baseline range test . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65
4.6 Signal processing methods for detection . . . . . . . . . . . . . . . . . . . . . . . 66
4.7 The ATS and the integrated autonomous platform . . . . . . . . . . . . . . . . . 68
5 THE iSAT MODULAR EMBEDDED ARCHITECTURE 70
5.1 Intra modular communication. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70
5.2 Main12V. The master controller board . . . . . . . . . . . . . . . . . . . . . . . . 71
5.3 The human machine interface (HMI) . . . . . . . . . . . . . . . . . . . . . . . . . 71
5.4 On board battery power management module . . . . . . . . . . . . . . . . . . . . 72
6 SYNTHESIS, FUTURE WORK AND CONCLUDING REMARKS 75
6.1 Synthesis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75
6.2 Future research and design . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 78
6.2.1 Future work on iSAT’s ATS . . . . . . . . . . . . . . . . . . . . . . . . . . 78
6.2.2 Work to be done on iSAT’s ASV . . . . . . . . . . . . . . . . . . . . . . . 79
6.2.3 Further developments on iSAT’s modules . . . . . . . . . . . . . . . . . . 80
6.3 Conclusions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 80
REFERENCES 82
APPENDICES 91
A TRANSDUCER CHARACTERISTICS 92
Using a calibrated hydrophone . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 92
Transducer’s electrical characteristics . . . . . . . . . . . . . . . . . . . . . . . . . . . . 94
B iSAT ELECTRONIC CIRCUIT SCHEMATICS 95
Acoustic tag. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 96
Hydrophone . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 97
Master board . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 98
Lithium battery charger . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 99
C iSAT FIRMWARE 100
Acoustic tag code . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 101
Acoustic tag header file . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 108
Hydrophone main board code . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 111
Hydrophone header file . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 120
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Hydrophones interface code . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 122
Hydrophones interface header file . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 126
I2C master code . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 127
I2C master header file . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 132
I2C slave code . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 133
I2C slave header file . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 136
USCI UART code . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 137
Tag detection code . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 141
Tag detection header file . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 145
D MECHANICAL DRAWINGS 147
E LIST OF PUBLICATIONS 153
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LIST OF FIGURES
1.1 An aggregation of whale sharks Rhincodon typus was discovered in Al-Lith in
2009. The development of the technology described through this dissertation is
to expand the knowledge on this species. . . . . . . . . . . . . . . . . . . . . . . . 13
1.2 Visual inspection of whale shark gender. The pelvic fins protect the cloaca in
females (left). Males (right) show a pair of claspers. This individual is probably
sexually immature due to the short size of the claspers. . . . . . . . . . . . . . . 16
1.3 A compilation of the movement studies available in R. typus literature [85]. . . . 17
1.4 A recent study in the Red Sea shows the largest number of whale sharks tagged
in a single project [10]. Migrations to the north of the Red Sea and to the south
into the Indian Ocean were observed. Knowledge of these routes is important to
design better protection schemes for the species. . . . . . . . . . . . . . . . . . . 18
1.5 Whale sharks are a bycatch of other fisheries. In cooperation with the local
authorities and fishermen, KAUST scientists had the opportunity to dissect a
stranded shark in Al-Lith. Stomach contents, vertebrae, and tissue samples were
conserved . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
2.1 Al-LithisacitylocatedatthecenteroftheRedSeawithintheFarasanBanksin
Saudi Arabia. An aggregation of whale sharks has been under study since 2009
using the latest telemetry technology available. . . . . . . . . . . . . . . . . . . . 22
2.2 Telemetry tags. From left to right, a Mk10 Fastloc-equipped and a MiniPAT
pop-up archival tag with light-based geolocation. The antennas are for satellite
communication. Then, a V16 (69kHz) acoustic tag and the tag developed for the
iSAT project at KAUST. (further discussion is available in section 4.3). . . . . . 23
2.3 Thetagneedstoberecoveredinordertohaveaccesstothefulldatarecord. This
collage exemplifies the complications that scientists experience while retrieving
tags in the field. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
2.4 The iSAT project. A vessel on the surface tracks closely a whale shark. GPS
providesglobalreferenceandacousticsunderwaterlocalizetheacousticallytagged
specimen with respect to the vessel. Data from the onboard sensors is regularly
transmitted through any of the wireless networks available, including satellites.
Drawing credit: Manalle Al-Salamah . . . . . . . . . . . . . . . . . . . . . . . . . 25
2.5 Autonomoussurfacevessels(ASV).A)ASVC-enduroB)CMRSailbuoyandC)Liquid
Robotics Wave Glider SV3. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
2.6 SolarirradiationintheRedSeafromtheKAUSTmeteorologicalbuoyintheRed
Sea and tower for the year 2009. Monthly averages of daily values are displayed
This source of renewable energy is available in high concentrations at any time of
the year. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
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2.7 Acoustic tagging. (Left) First, a network of receivers needs to be installed in the
region of the study. (Middle) Then, an acoustic identifier needs to be attached to
the specimen. Finally, data needs to be downloaded regularly from each receiver
and analyzed. (Right)The shark has a satellite tag on the left side of the dorsal
fin and an acoustic tag on the right side. . . . . . . . . . . . . . . . . . . . . . . 33
2.8 iSAT’smodulararchitectureallowssimpletaskdistributionandmakesthesystem
easily expandable and capable of including new instrumentation. . . . . . . . . . 37
3.1 Characteristic temperature, salinity and sound speed profiles from measurements
performed in Al-Lith (20.1N 40.2E) in November 2013. Thanks to Ioannis Geor-
gakakis. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38
3.2 Transmission loss as a function of frequency. Variation as a function of tempera-
ture is indicated for a frequency of 51kHz. . . . . . . . . . . . . . . . . . . . . . . 39
3.3 The geometry of a hollow cylindrical transducers and encapsulation methods. A)
free flooded ring, b) air-backed transducer and c)shielded ports. . . . . . . . . . . 42
3.4 Ontop,ablockdiagramoftheprojectoranditselectricalcircuit. Thetransducer
is represented as an impedance, i.e. as a resistor in parallel to a capacitance. . . 44
3.5 Minimum detection threshold or maximum noise level for an acoustic receiver to
have a signal larger than noise. Losses due to absorption α = 11.8dB/km and
spherical spreading (r2) are considered. . . . . . . . . . . . . . . . . . . . . . . . . 46
3.6 Single-sided, normalized, amplitude spectral density of the projected signal. En-
ergy within a band increases proportionally to the duration of the pulse. The
bandwidth of the signal narrows as power increases. . . . . . . . . . . . . . . . . 47
3.7 iSAT’s acoustic tracking system. The transducers (1) transform sound into an
electrical signal that is amplified and filtered (2,3). A PLL tone decoder (4)
transforms it into a digital signal that is sent to the directionality module (5).
The main board receives this information from three or more hydrophones to
determine a bearing to the source. . . . . . . . . . . . . . . . . . . . . . . . . . . 48
3.8 RVS as a function of the internal diameter. (*) indicates the RVS of the 1mm
thick wall transducers used. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49
3.9 Hydrophone’s signal conditioning circuit. A preamplifier balances the impedance
from the transducer, two identical stages (labelled Stage 1 and 2) are band pass
filters centered on 51kHz. The bode diagram underneath shows the output of
Stage 1 in red and a higher quality output from Stage 2. . . . . . . . . . . . . . . 50
3.10 Theoretical range of the hydrophone sensor with a gain of 59dB, operating at
51kHz, considering transmission losses due to absorption and spherical spreading
3.3. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51
3.11 iSAT’s algorithm to estimate directionality to a tag. The triangular acoustic
array calculates direction to the source based on the order of arrival of the signal
to each of the hydrophones(A,B,C). The strip at the right exemplifies a signal
coming from direction 1. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53