UNIVERSITY OF HAWAI'I LIBRARY Automated Rugosity Values from High Frequency Multibeam Sonar Data for Benthic Habitat Classification A THESIS SUBMITTED TO THE GRADUATE DIVISION OF THE UNIVERSITY OF HAWAI'I IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF MASTER OF SCIENCE IN GEOLOGY AND GEOPHYSICS MAY 2007 By Erin S. Diurba Thesis Committee: Bruce Appelgate. Chairperson Paul Wessel John Rooney We certify that we have read this thesis and that, in our opinion, it is satisfactory in scope and quality as a thesis for the degree of Master of Science in Geology and Geophysics. THESIS COMMITIEE ~E&:-. ii ACKNOWLEDGEMENTS "Acknowledge yourself for how far you have come, instead of how far you think you have to go." I recited that quote every time I felt overwhelmed and thought I was going to break:. It forced me to take a deep breath, take small steps forward and realize how many great things I have already accomplished in my life. The quote also made me realize that none of this would have been possible if it wasn't for the sacrifices of my friends and family who pushed me to succeed and were there to hold me up when I believed I had failed. To Morn and Dad- Thanks for paying the phone bill and always being there. To Landon -Thank you for bringing love. friendship and Monkey into my life. To all the friends I have made along the way - Thanks for putting up with me and always giving me good advice whether or not I wanted to hear it. I would like to thank Bruce Appelgate, for funding a girl from Mars, and my committee for their support and collaboration. I am also grateful to NOAA and CRED for helping me to gain research experience, and utilize their extensive data collection for my thesis. Finally, I would like to thank all the amazing teachers I have had in the past who have shaped who I am today and who I hope are proud of me now. iii ABSTRACT Rugosity literally means wrinkled, or marked with folds and ridges. When applied to seafloor texture, rugosity is one piece of the puzzle that is necessary in order to understand benthic habitats. Traditionally, rugosity was calculated by draping a chain of known length over the seafloor and comparing the total chain length with the horizontal distance the chain covered. The equation Rugosity=IOO*(horizontallength of chainl actual length of chain) was then applied to get a percent rugosity. However, the process is subjective, time consuming, depth limited and is capable of only small scale coverage. My objective was to develop an automated algorithm that would calculate rugosity from clean, un-gridded, multibeam data using the manual rugosity method. This method rapidly produces objective, reproducible rugosity data for any multibeam data set that is comparable with manual rugosity data. The final product is an objectively derived, quantitative map that can be used for benthic habitat mapping. iv TABLE OF CONTENTS Acknowledgements ................................................................................ .iii Abstract ................................................................................................iv List of Tables ........................................................................................vii List of Figures ......................................................................................viii Chapter I: Introduction .............................................................................. 1 Chapter 2: Background ...............................................................................5 2.1 Coral Reefs .........................................................................................5 2.2 Area of Study...................................................................................... 6 2.2.1 Saipan ..................................................................................7 2.3 Tools for Habitat Mapping..................................................................... 13 2.3.1 Satellite Imagery .................................................................... 14 2.3.2 Aerial Imaging...................................................................... 17 2.3.3 Side-scan Sonar...................................................................... 18 2.3.4 Video Data............................................................................ 20 2.3.5 High Frequency Multibeam Sonar................................................ 22 2.4 Methods for Measuring Rugosity............................................................. 24 2.4.1 Manual Measurements ............................................................ 24 2.4.1.1 Chain method ..............................................................24 2.4.1.2 Proftle Gauge ..............................................................25 2.4.1.3 Complexity................................................................ 26 2.4.2 Other Seafloor Classification Techniques....................................... 27 2.4.2.1 Measuring Signal Returns ............................................... 28 2.4.2.2 Local Fourier Histograms ...............................................29 2.4.2.3 Surface Ratio Grids ...................................................... 29 Chapter 3: Data and Methods for Benthic Mapping of Garapan Anchorage. Saipan...... 32 3.1 Remote Sensing Tool Selection ...................................................................... 32 3.2 Towed Video Data...................................................................... 33 3.2.1 Video Data Analysis ........................................................33 3.3 Manual Rugosity Measurements ....................................................40 v Chapter 4: Data and Methods For Rugosity Algorithm ....................................... 45 4.1 Objectives ...............................................................................45 4.2 Multibeam Overview .................................................................. 45 4.3 How the Algorithm Works ........................................................... .48 4.3.1 Algorithm ....................................................................48 4.3.2 Presets ........................................................................52 4.3.2.1 Error Factor and Search Radius ...............................52 4.3.2.2 Minimum Sounding Requirement. ............................53 4.3.3 Choosing Bin Size .................................................................. .55 4.3.4 Slope Removal and Contoured Chain Length Calculation ............57 4.3.5 Striping Effect............................................................... 58 4.4 Understanding the Rugosity OUtput. ............................................... 61 4.4.1. Testing ....................................................................... 61 Chapter 5: Results ................................................................................... 65 5.1 Interpretation .................................................................................................... 65 5.2 Correlations with Video Classification................................................. 71 5.3 Additional Video Error.................................................................................... 76 5.4 Rugosity Data Compared With Manual Rugosity Measurements ................78 Chapter 6: Discussion .............................................................................. 82 6.1 How Useful is the Rugosity Algorithm ..................................................82 6.2 Bin Size and Sounding Requirements in Depth ........................................ 83 6.3 Conclusions ............................................................................................................ 84 Appendix A: Look Up Table of Sounding Spacing............................................. 86 Appendix B: Rugosity Algorithm.................................................................. 89 References ............................................................................................94 vi LIST OF TABLES 1. Video Classification Chart ...................................................................... 34 2. Manual Rugosity measurements ............................................................... .42 3. Look Up Table of Sounding Spacing .............................................. Appendix A vii LIST OF FIGURES Figure Page 1. Calculating Rugosity Using the Chain Method ..................................................4 2. Oceania Map .........................................................................................8 3. Saipan Harbor Map ............................................................................... 11 4. Multibearn Bathymetry Map of the Saipan Anchorage ...................................... 12 5. Remote Sensing Tools and Their Capabilities ................................................. 14 6. Pictures of Benthic Cover........................................................................ 35 7. Frame Capture from Video Survey in 2004.................................................... 36 8. Medium Visibility Frame Capture from 2004 Video Survey .................................36 9. Low Visibility Frame Capture from Video Survey.......................................... 37 10. Substrate Map ................................................................................... 38 II. Interpolated Substrate Map .....................................................................39 12. Dive Site Map ............................................................................................................