scatmod - Open Source Acoustic Scattering Models for fisheries acoustics

Table of Contents

• About
• Licence
• Types of scattering models
• Which model to use?
  • Overview Table
    • Model Acoronyms:
    • References:
• Model Descriptions
• Multiscattering
• TO DO:
• Models in scatmod
  • Analytical
• Examples
  • Installing
• Running the tests
• Primary Authors
• License
• Acknowledgments

About

scatmod is a platform to distribute and develop acoustic scattering models, with the aim of simulating acoustic targets (e.g. fish, zooplankton, phytoplankton, crustaceans, jellyfish, bubbles, etc.).

scatmod aims to be a cross-language platform, containing models written in various languages, including Matlab, Python and R. In order to keep Scatmod consistent, documentation standards have been defined for all used languages.

scatmod is developped and maintained by members of the ICES WGFAST group originating from various institutes including NWFSC NOAA, Scripps Institute Of Oceanography, St Andrews University, NIWA and CMR

Licence

MIT License

Copyright (c) 2019 sctamod team

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

Types of scattering models

Three major categories of scattering models can be distinguished:

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• Analytic / semi-analythic models
  • Application: for simple geometric shapes (e.g. spheres, cylinders, prolate spheroids)
  • Advantages: exact, fast, not restricted in frequency/material properties
  • Disadvantages: not possible to resolve for complex, realistic targets, assumes a single scattering object

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• Numerical models
  • Models: Finite Element Methods (FEM), Boundary Element Methods (BEM), combinations of those
  • Application: Arbitrary shapes, frequencies and materials
  • Advantages:
    • allows for modelling of complex shapes and internal structures
    • includes diffraction / Fluid-Structure-Interaction (FSI)
    • can be applied to arbitrary materials and frequencies
  • Disadvantages:
    • Computationally complex and expensive

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• Approximate models
  • Models: Kirchhoff Ray Mode (KRM), Distorted Wave Born Approximation(DWBA), Deformed Cylinder Model (DCM), Resonance Scattering, etc.
  • Application: Various scattering surface and orientations for a range of frequencies (model dependent)
  • Advantages:
    • Can represent arbitrary scattering surface and orientations
    • (very) fast and relatively simple
  • Disadvantages:
    • Frequency restrictions for some models
    • Does not include diffraction effects or internal structure implicitly
    • Multibody scattering generally assumed to be linearly additive

Which model to use?

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Overview Table

Modified from Jech et al. (2015)

Model	Accuracy / Type	Range of Validity	Limitations	Examples
MSS	Exact / Analytical	Canonical shapes (currently 11 available)	Convergence issues with some shapes	Anderson (1950)
BEM	Quasi-exact / Numerical	All shapes, all frequencies, all angles	High computational demands (slightly better with Fast-Multipole BEM)	Francis et al. (1998); Francis and Foote (2003); Okumura et al. (2003)
FEM	Quasi-exact / Numerical	All shapes, all frequencies, all angles	High computational demands	Zampolli et al. (2007); Macaulay et al. (2013)
FMM	Exact / Analytical	If Axisymmetric - All shapes, all frequencies, all angles	Non-axisymmetric, convergence issues at high aspect ratios	Reeder and Stanton (2004)
KA	Approximate	High Frequencies only, near normal incidence, homogenous material	Off-normal incidence, low frequencies, no circumferential waves	Macaulay et al. (2013)
KRM	Approximate	All frequencies, homogenous material; at high frequencies: high aspect ratios; at low frequencies: near-normal incidence	Off-normal incidence, no circumferential waves, no longitudinal modes of vibration near resonance	Horne et al. (2000); Macaulay et al. (2013); Gastauer et al. (2016)
Modal series based DCM	Approximate	Near normal incidence; all frequencies; circular cross-sections; all material	off-normal incidence, low aspect ratios, irregular shapes with high local slopes	Gorska and Ona (2003); Stanton (1989)
DWBA (incl PT-DWBA,SDWBA)	Approximate	Weak scatterers (g and h < 1.005 i.e. < 5%), all shapes, all angles	Strong scatterers (g and h > 5%)	Chu and Ye (1999); Demer et al. (2003); Calise and Skaret (2011); Gastauer et al. (2019)

Model Acoronyms:

• MSS - Exact Modal Series Solutions
• BEM - Boundary Element Model
• FEM - Finite Element Model
• FMM - Fourier Matching Method
• KA - Kirchhoff Approximation
• DCM - Deformed Cylinder scattering Model
• DWBA - Distorted Wave Born Approximation

References:

• Anderson, V. C. (1950). Sound scattering from a fluid sphere. The Journal of the Acoustical Society of America, 22(4), 426-431.
• Calise, L., and Skaret, G. (2011). “Sensitivity investigation of the SDWBA Antarctic krill target strength model to fatness, material contrasts and orientation,” Ccamlr Science 18, 97–122.
• Chu, D., Foote, K. G., & Stanton, T. K. (1993). Further analysis of target strength measurements of Antarctic krill at 38 and 120 kHz: Comparison with deformed cylinder model and inference of orientation distribution. The Journal of the Acoustical Society of America, 93(5), 2985-2988.
• Chu, D., and Ye, Z. (1999). “A phase-compensated distorted wave born approximation representation of the bistatic scattering by weakly scattering objects: Application to zooplankton,” J. Acoust. Soc. Am.106, 1732–1743.
• Gauthier, S., & Horne, J. K. (2004). Acoustic characteristics of forage fish species in the Gulf of Alaska and Bering Sea based on Kirchhoff-approximation models. Canadian Journal of Fisheries and Aquatic Sciences, 61(10), 1839-1850.
• Demer, D. A., and Conti, S. G. (2003). “Reconciling theoretical versus empirical target strengths of krill: Effects of phase variability on the distorted-wave Born approximation,” ICES J. Mar. Sci. 60, 429–434.
• Francis, D. T., Foote, K. G., Alippi, A., & Cannelli, G. B. (1998). ‘Boundary-element-model predictions of acoustic scattering by swimbladder-bearing fish. In Proceedings of the Fourth European Conference on Underwater Acoustics (Vol. 1, pp. 255-260). Rome: CNR-IDAC.
• Faran Jr, J. J. (1951). Sound scattering by solid cylinders and spheres. The Journal of the acoustical society of America, 23(4), 405-418.
• Foote, K. G. (1985). Rather‐high‐frequency sound scattering by swimbladdered fish. The Journal of the Acoustical Society of America, 78(2), 688-700.
• Francis, D. T., & Foote, K. G. (2003). Depth-dependent target strengths of gadoids by the boundary-element method. The Journal of the Acoustical Society of America, 114(6), 3136-3146.
• Gastauer, S., Chu, D., & Cox, M. J. (2019). ZooScatR—An r package for modelling the scattering properties of weak scattering targets using the distorted wave Born approximation. The Journal of the Acoustical Society of America, 145(1), EL102-EL108.
• Gastauer, S., Scoulding, B., Fässler, S. M., Benden, D. P., & Parsons, M. (2016). Target strength estimates of red emperor (Lutjanus sebae) with Bayesian parameter calibration. Aquatic Living Resources, 29(3), 301.
• Gorska, N., & Ona, E. (2003). Modelling the acoustic effect of swimbladder compression in herring. ICES Journal of Marine Science, 60(3), 548-554.
• Horne, J. K., Walline, P. D., & Jech, J. M. (2000). Comparing acoustic model predictions to in situ backscatter measurements of fish with dual‐chambered swimbladders. Journal of fish Biology, 57(5), 1105-1121.
• Jech, J. M., Horne, J. K., Chu, D., Demer, D. A., Francis, D. T., Gorska, N., ... & Reeder, D. B. (2015). Comparisons among ten models of acoustic backscattering used in aquatic ecosystem research. The Journal of the Acoustical Society of America, 138(6), 3742-3764.
• Macaulay, G. J., Peña, H., Fässler, S. M., Pedersen, G., & Ona, E. (2013). Accuracy of the Kirchhoff-approximation and Kirchhoff-ray-mode fish swimbladder acoustic scattering models. PloS one, 8(5), e64055.
• Okumura, T., Masuya, T., Takao, Y., & Sawada, K. (2003). Acoustic scattering by an arbitrarily shaped body: An application of the boundary-element method. ICES Journal of Marine Science, 60(3), 563-570.
• Reeder, D. B., & Stanton, T. K. (2004). Acoustic scattering by axisymmetric finite-length bodies: An extension of a two-dimensional conformal mapping method. The Journal of the Acoustical Society of America, 116(2), 729-746.
• Stanton T.K. Sound scattering by cylinders of finite length. III. Deformed cylinders, Journal of the Acoustical Society of America, 1989, vol. 86 (pg. 691-705)
• Zampolli, M., Tesei, A., Jensen, F. B., Malm, N., & Blottman III, J. B. (2007). A computationally efficient finite element model with perfectly matched layers applied to scattering from axially symmetric objects. The Journal of the Acoustical Society of America, 122(3), 1472-1485.

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Gas bubbles or swimbladders

• Best:
  • Numerical models for complex shapes e.g. BEM, FEM
  • Analystical solutions for simple shapes
• Easier:
  • Resonance scattering: Find he resonance frequency, high frequencies for small bubbles, low frequencies for swimbladders
  • KRM: Limited to high frequencies, can be used for flesh and swimbladder if swimbladdered fish are to be modelled Examples:

BEM, FEM:

• Macaulay, G. J., Peña, H., Fässler, S. M., Pedersen, G., & Ona, E. (2013). Accuracy of the Kirchhoff-approximation and Kirchhoff-ray-mode fish swimbladder acoustic scattering models. PloS one, 8(5), e64055.
• Zampolli, M., Tesei, A., Jensen, F. B., Malm, N., & Blottman III, J. B. (2007). A computationally efficient finite element model with perfectly matched layers applied to scattering from axially symmetric objects. The Journal of the Acoustical Society of America, 122(3), 1472-1485.

Analytical Solutions:

• Anderson, V. C. (1950). Sound scattering from a fluid sphere. The Journal of the Acoustical Society of America, 22(4), 426-431.
• Gastauer, S., Chu, D., & Cox, M. J. (2019). ZooScatR—An r package for modelling the scattering properties of weak scattering targets using the distorted wave Born approximation. The Journal of the Acoustical Society of America, 145(1), EL102-EL108.

Resonance Scattering:

• Godø, O. R., Patel, R., & Pedersen, G. (2009). Diel migration and swimbladder resonance of small fish: some implications for analyses of multifrequency echo data. ICES Journal of Marine Science, 66(6), 1143-1148.
• Holliday, D. V. (1972). Resonance structure in echoes from schooled pelagic fish. The Journal of the Acoustical Society of America, 51(4B), 1322-1332.
• Love, R. H. (1978). Resonant acoustic scattering by swimbladder‐bearing fisha. The Journal of the Acoustical Society of America, 64(2), 571-580.
• McCartney, B. S., & Stubbs, A. R. (1971). Measurements of the acoustic target strengths of fish in dorsal aspect, including swimbladder resonance. Journal of Sound and Vibration, 15(3), 397-420.

KRM:

• Gastauer, S., Scoulding, B., Fässler, S. M., Benden, D. P., & Parsons, M. (2016). Target strength estimates of red emperor (Lutjanus sebae) with Bayesian parameter calibration. Aquatic Living Resources, 29(3), 301.
• Hazen, E. L., & Horne, J. K. (2004). Comparing the modelled and measured target-strength variability of walleye pollock, Theragra chalcogramma. ICES Journal of Marine Science, 61(3), 363-377.
• Horne, J. K., Walline, P. D., & Jech, J. M. (2000). Comparing acoustic model predictions to in situ backscatter measurements of fish with dual‐chambered swimbladders. Journal of fish Biology, 57(5), 1105-1121.
• Horne, J. K. (2003). The influence of ontogeny, physiology, and behaviour on the target strength of walleye pollock (Theragra chalcogramma). Ices Journal of marine science, 60(5), 1063-1074.
• Macaulay, G. J., Peña, H., Fässler, S. M., Pedersen, G., & Ona, E. (2013). Accuracy of the Kirchhoff-approximation and Kirchhoff-ray-mode fish swimbladder acoustic scattering models. PloS one, 8(5), e64055.

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Bones

• Best:
  • Numerical models for complex shapes e.g. BEM, FEM
  • Analystical solutions for simple shapes
• Easier:
  • DCM Examples:

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Fluid-like / flesh

• Best:
  • Numerical models for complex shapes e.g. BEM, FEM
  • Analystical solutions for simple shapes
• Easier:
  • DCM
  • DWBA
  • KRM Examples:

Model Descriptions

Analytical models

• Analytical fluid-like sphere

DWBA

• DWBA

Multiscattering

-> Put some content here... The idea is to talk about the different options to model multiscattering, e.g. simple linear addition, the case of bubbles, the more complex cse of reality (mention possible methods and BEM/FEM options)

TO DO:

• Write documentation standard for R, Python and Matlab

Models in scatmod

Analytical

• Sphere and finite cylinde:
  • Solid / rigid
  • Pressure release
  • Elastic
  • Shelled

Examples

Installing

A step by step series of examples that tell you how to get a development env running

Say what the step will be

Give the example

And repeat

until finished

End with an example of getting some data out of the system or using it for a little demo

Running the tests

Explain how to run the automated tests for this system

Primary Authors

• Sven Gastauer - Antarctic Climate and Ecosystem Cooperative Research Centre, University of Tasmania, Private Bag 80, Hobart, Tasmania 7001, Australia
• Dezhang Chu - Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, 2725 Montlake Boulevard East, Seattle, Washington 98112, USA
• Roland Proud - Pelagic Ecology Research Group, Gatty Marine Laboratory, Scottish Oceans Institute, University of St Andrews, St Andrews, Fife KY16 8LB, UK
• Yoann Ladroit - National Institute of Water and Atmospheric Research (NIWA) Ltd, Private Bag 14-901, Wellington 6241, New Zealand
• Geir Pedersen - * Norwegian Research Centre (NORCE), Bergen, Norway*
• Pablo Escobar - National Institute of Water and Atmospheric Research (NIWA) Ltd, Private Bag 14-901, Wellington 6241, New Zealand

See also the list of contributors who participated in this project.

License

This project is licensed under the MIT License - see the LICENSE.md file for details

Acknowledgments

• Hat tip to anyone whose code was used
• Inspiration
• etc