Passive Acoustic Monitoring of Cetaceans

Cover......Page 1
About......Page 3
Passive Acoustic Monitoring of Cetaceans......Page 5
©......Page 6
Dedication......Page 7
Contents......Page 9
Acknowledgements......Page 12
Introduction......Page 13
Part I: Underwater acoustics (the basics)......Page 17
1.1.1 Wave equation......Page 19
1.1.2 The solution of the wave equation......Page 23
Matlab script......Page 24
Matlab script......Page 26
1.1.4 Wavelength frequency relation......Page 27
1.1.5 Acoustic impedance......Page 28
1.1.7 Acoustic intensity......Page 29
1.1.8 Acoustic energy flux......Page 30
1.1.9 Mean acoustic intensity......Page 31
1.1.10 Total radiated acoustic energy......Page 32
1.2.1 Formal definition of the decibel scale......Page 33
1.2.3 dB arithmetic made simple......Page 34
1.3.1 Sound velocity in air......Page 35
1.3.2 Sound velocity in oceans......Page 36
Matlab script......Page 39
1.4.1 Snell’s law......Page 41
1.4.2 Reflection at a plane interface......Page 42
Sound transmission water to air......Page 44
Matlab code......Page 45
1.4.4 Sound absorption......Page 47
1.5 Signals, noise and interference......Page 48
1.5.2 Noise......Page 49
2.1 Classification of cetaceans......Page 51
2.2.1 General characteristics of echolocation signals......Page 52
2.2.2 General characteristics of communication signals......Page 53
2.3.1 Beaked whale clicks......Page 54
Matlab script......Page 56
2.3.2 Dolphin clicks......Page 57
2.3.3 Sperm whale echolocation clicks......Page 58
2.3.4 Remotely received sperm whale clicks......Page 61
2.3.5 Sperm whale coda......Page 62
2.3.7 Inter-click interval......Page 64
2.4.1 Spectral analysis......Page 65
Fourier transform......Page 66
Mathematical note......Page 0
Fast Fourier Transform......Page 67
Matlab code......Page 69
Interpolating FFT......Page 70
Matlab code......Page 71
Support function......Page 72
2.5.1 Theoretical basis......Page 73
Short Time Fourier Transform (STFT)......Page 74
Matlab code for generating Figures 2.15 and 2.16......Page 76
Power spectral density......Page 78
Matlab code to generate Figure 2.17......Page 79
2.5.2 Dolphin whistles......Page 81
Matlab codes for Figures 2.18, 2.19 and 2.21......Page 84
Script for Figure 2.20......Page 85
Empirical mode decomposition (EMD)......Page 86
Matlab code to generate Figures 2.23 – 2.26......Page 90
2.5.4 Buzzes and rapid pulse trains......Page 92
2.5.5 Call trains......Page 94
2.5.6 Whale songs......Page 97
2.6 Sound source directionality......Page 98
2.6.1 Physical acoustics of sound source......Page 99
2.7 Cetacean source levels......Page 100
2.8 Order Cetacea......Page 101
2.8.1 Suborder Mysticeti: baleen whales......Page 102
2.8.2 Suborder Odontoceti: toothed whales......Page 103
3.1 Passive sonar equations......Page 108
3.2 Apparent source level......Page 109
Broadband off-axis attenuation of Gaussian bio-sonar pulses......Page 110
Matlab code......Page 111
3.3 Sound propagation......Page 112
3.3.1 Transmission loss modelling......Page 113
Matlab code......Page 114
3.3.2 Alternative geometric spreading laws......Page 118
3.4 Noise level......Page 120
3.4.2 Noise masking effect......Page 121
3.4.4 Attenuation of surface noise with depth......Page 122
3.4.7 Thermal noise......Page 123
3.4.8 Overall ambient noise spectrum......Page 124
3.5 Array gain......Page 125
3.5.1 Array gain estimation......Page 126
3.7 Detection threshold......Page 127
Part II: Signal processing (designing the tools)......Page 129
4.1 Detection of echolocation clicks......Page 131
4.1.1 Threshold detector......Page 132
Definition of detection......Page 133
Matlab script for running the detector and plotting the results......Page 134
4.1.2 Signal amplitudes, signal power and signal envelope......Page 135
Hilbert transform......Page 136
Matlab code for estimating the complex valued analytic time series......Page 137
4.1.3 Signal extraction......Page 138
Matlab code of the refined detection algorithm for estimation of start and stop time......Page 139
Matlab code to extract the signal time series and to plot a single detection......Page 140
4.1.4 Pre-processing raw data......Page 141
4.1.5 Sequential probability ratio detector (Page test)......Page 145
Matlab code of the Page test detector......Page 146
Comments on the Matlab code......Page 147
4.1.6 Detection performance......Page 148
4.2 Data filter......Page 150
4.2.1 Noise equalization filter......Page 151
4.2.2 Bandpass filter......Page 153
Matlab code for calling the bandpass filter......Page 154
4.2.3 Filter performance......Page 155
4.3 Detection of FM signals with pulse compression (matched filter)......Page 156
4.3.1 Matched filter theory......Page 157
Constructing the replica......Page 158
Comments on the matched filter code......Page 161
4.4 Detection of dolphin whistles......Page 162
4.4.1 Spectral equalizing......Page 164
4.4.2 Local max detector......Page 166
Data association......Page 169
Matlab code of data association function......Page 171
Comment on the Matlab script......Page 172
Matlab code of tracker module......Page 173
5.1 Classification basics......Page 176
5.2 Optimal classification......Page 177
5.2.1 Detection as a two-class classification......Page 180
5.2.2 Gaussian distributed feature vectors......Page 181
5.2.3 Variance analysis......Page 183
5.2.4 Principal components......Page 184
5.2.5 Cluster analysis......Page 185
Matlab code for generation of Figure 5.1......Page 189
Matlab code for cluster analysis function......Page 190
Matlab code for F-ratio criterion function......Page 191
5.3.1 Click classification......Page 192
5.3.2 Deep diver classification......Page 196
Matlab code for double click classification......Page 198
5.3.3 Click train classification......Page 199
Improved Matlab code for multiple double-click classification......Page 202
Comment on the Matlab code......Page 203
Matlab code for click train classification......Page 204
5.3.4 Whistle classification......Page 206
6.1 Multi-hydrophone ranging......Page 210
Matlab code to test multi-hydrophone ranging......Page 214
6.2 Triangulation......Page 215
6.3 Multi-path ranging......Page 217
6.3.1 Sound source range estimation......Page 219
6.3.2 Sound source depth estimation......Page 220
6.3.3 Sound source depth estimation using angle of arrival......Page 221
6.4 Ranging by acoustic modelling......Page 222
6.5 Measurement of arrival time difference......Page 223
6.6 Direction finding......Page 224
6.7 Three-dimensional direction finding......Page 225
6.7.1 Rotation matrix......Page 227
6.8 Two-dimensional constrained direction finding......Page 228
6.9 Beam-forming......Page 230
6.10 Beam patterns......Page 231
6.10.1 Beam-forming with widely spaced arrays?......Page 235
Matlab code to generate Figure 6.12......Page 237
6.11.1 Basics of tracking......Page 238
6.11.2 Data association......Page 240
6.11.3 Data filter and state prediction......Page 241
Matlab code for example......Page 245
Part III: Passive acoustic monitoring (putting it all together)......Page 249
7.1 Abundance estimation......Page 251
Probability of detecting an animal......Page 252
Line transects......Page 255
Point transects......Page 256
7.1.2 Acoustic cue counting......Page 257
7.1.3 Acoustic dive counting......Page 258
7.1.5 Moving whales during line and point transects......Page 259
7.2 Mitigation: absence estimation......Page 262
7.3 Habitat and behaviour analysis......Page 265
Modelling covariates......Page 266
7.4 Monitoring rare and elusive species......Page 268
7.5 Logging acoustic information......Page 269
8.1 Empirical detection function......Page 271
8.3 Sonar equation-based modelling of the detection function......Page 272
8.3.1 Modelling the off-axis attenuation......Page 274
Detection of near on-axis echolocation clicks......Page 275
8.3.3 Sonar equation based detection function......Page 276
Matlab code for Figures 8.1 and 8.2......Page 280
8.4 Modelling animal behaviour......Page 281
8.4.1 Acoustic activity of cetaceans......Page 283
8.5.1 Distribution models for depth, pitch and heading......Page 284
9 Simulating sampling strategies......Page 286
9.1 Modelling a point survey detection probability......Page 287
Matlab code......Page 288
9.2.2 Simulating detections......Page 290
Matlab code for Figure 9.3......Page 291
9.3 Point survey abundance estimation......Page 292
Matlab code for Figure 9.4......Page 294
9.4 Distance distribution of echolocation clicks of randomly moving animals......Page 296
Matlab code for Figure 9.6......Page 297
Caveats......Page 298
Matlab code for Figure 9.7......Page 299
9.5.1 Distance and off-axis joint probability distribution......Page 301
9.5.2 Detection function......Page 302
Matlab code for Figure 9.10......Page 306
9.5.3 Advantage of model-based detection functions......Page 310
10.1.1 Hydrophones......Page 311
Diffraction effect......Page 312
10.1.2 Hydrophone frequency response......Page 313
Matlab code to generate Figures 10.2 and 10.3......Page 314
Thermal noise......Page 317
Electric equivalent environmental noise......Page 318
Total system noise......Page 319
Matlab code to generate Figure 10.5......Page 320
10.1.4 Analogue digital converter......Page 322
Binary notation......Page 323
Dynamic range......Page 324
Data sampling......Page 325
Equalization filter......Page 326
10.2 Software......Page 327
10.2.1 Data acquisition module......Page 328
10.2.2 Data archiving module......Page 329
10.2.3 Signal processing modules......Page 330
10.2.4 Display modules......Page 331
10.2.5 Monitoring module......Page 332
10.3.1 Lowered hydrophones......Page 333
10.3.2 Towed arrays......Page 334
10.3.3 Acoustic buoys and autonomous systems......Page 335
10.4 The future of PAM......Page 337
References and further reading......Page 338
Index......Page 366