Efficient three-dimensional reconstruction of aquatic vegetation geometry: Estimating morphological parameters influencing hydrodynamic drag

Estuarine, Coastal and Shelf Science

Volumn 178, Issue , 2016, Pages 77-85

  Liénard, Jean ^a   Lynn, Kendra ^a   Strigul, Nikolay ^a   Norris, Benjamin K ^b   Gatziolis, Demetrios ^c   Mullarney, Julia C ^b   Bryan, Karin R ^b   Henderson, Stephen M ^a  

^a WASHINGTON STATE UNIVERSITY   (United States)

^b UNIVERSITY OF WAIKATO   (New Zealand)

^c PACIFIC NORTHWEST RESEARCH STATION   (United States)

Author keywords

Drag coefficient; Emergent vegetation; Estuaries; Mangrove; Photogrammetry; Plant morphology

Indexed keywords

ACCRETION; AQUATIC PLANT; CANOPY ARCHITECTURE; COMPUTER VISION; DRAG; DRAG COEFFICIENT; ESTUARINE ECOSYSTEM; FLOW MODELING; GEOMETRY; HYDRODYNAMICS; MANGROVE; MORPHOLOGY; RECONSTRUCTION; TRIANGULATION;

MEKONG RIVER; VIET NAM;

THORACICA;

EID: 84973441999     PISSN: 02727714     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ecss.2016.05.011     Document Type: Article

References (64)

1. Alongi D.M. Mangrove forests: resilience, protection from tsunamis, and responses to global climate change. Estuar. Coast. Shelf Sci. 2008, 76(1):1-13.
2. Arkema K.K., Guannel G., Verutes G., Wood S.A., Guerry A., Ruckelshaus M., Kareiva P., Lacayo M., Silver J.M. Coastal habitats shield people and property from sea-level rise and storms. Nat. Clim. Change 2013, 3(10):913-918.
3. Belcher S., Jerram N., Hunt J. Adjustment of a turbulent boundary layer to a canopy of roughness elements. J. Fluid Mech. 2003, 488:369-398.
4. Bouma T.J., van Duren L.A., Temmerman S., Claverie T., Blanco-Garcia A., Ysebaert T., Herman P.M.J. Spatial flow and sedimentation patterns within patches of epibenthic structures: combining field, flume and modelling experiments. Cont. Shelf Res. 2007, 27(8):1020-1045.
5. Brander L., Florax R.J., Vermaat J.E. The empirics of wetland valuation: a comprehensive summary and a meta-analysis of the literature. Environ. Resour. Econ. 2006, 33:223-250.
6. Britter R., Hanna S. Flow dispersion in urban areas. Ann. Rev. Fluid Mech. 2003, 35:469-496.
7. Brutto M., Meli P. Computer vision tools for 3d modelling in archaeology. Int. J. Herit. Digit. Era 2012, 1(Suppl. 1):1-6.
8. Calders K., Newnham G., Burt A., Murphy S., Raumonen P., Herold M., Culvenor D., Avitabile V., Disney M., Armston J., et al. Nondestructive estimates of above-ground biomass using terrestrial laser scanning. Methods Ecol. Evol. 2015, 6(2):198-208.
9. Comaniciu D., Meer P. Mean shift: a robust approach toward feature space analysis. Pattern Anal. Mach. Intell. IEEE Trans. 2002, 24(5):603-619.
10. Côté J.-F., Widlowski J.-L., Fournier R.A., Verstraete M.M. The structural and radiative consistency of three-dimensional tree reconstructions from terrestrial lidar. Remote Sens. Environ. 2009, 113(5):1067-1081.
11. Dalrymple R., Kirby J., Hwang P. Wave diffraction due to areas of energy dissipation. J. Waterw. Port, Coast. Ocean Eng. ASCE 1984, 110(1):67-79.
12. Einbeck J. Bandwidth selection for mean-shift based unsupervised learning techniques: a unified approach via self-coverage. J. Pattern Recognit. Res. 2011, 6(2):175-192.
13. Feagin R.A., Figlus J., Zinnert J.C., Sigren J., Martinez M.L., Silva R., Smith W.K., Cox D., Young D.R., Carter G. Going with the flow or against the grain? the promise of vegetation for protecting beaches, dunes, and barrier islands from erosion. Front. Ecol. Environ. 2015, 13:203-210.
14. Feagin R.A., Irish J., Möller I., Williams A., Colon-Rivera R., Mousavi M. Short communication: engineering properties of wetland plants with application to wave attenuation. Coast. Eng. 2011, 58:251-255.
15. Finnigan J. Turbulence in plant canopies. Annu. Rev. Fluid Mech. 2000, 32:519-571.
16. Furukawa K., Wolanski E., Mueller H. Currents and sediment transport in mangrove forests. Estuar. Coast. Shelf Sci. 1997, 44(3):301-310.
17. Furukawa Y., Ponce J. Accurate, dense, and robust multiview stereopsis. Pattern Anal. Mach. Intell. IEEE Trans. 2010, 32(8):1362-1376.
18. Gacia E., Duarte C. Sediment retention by a mediterranean Posidonia oceanica meadow: the balance between deposition and resuspension. Estuar. Coast. Shelf Sci. 2001, 52(4):505-514.
19. Gatziolis D., Liénard J.F., Vogs A., Strigul N.S. 3d tree dimensionality assessment using photogrammetry and small unmanned aerial vehicles. PloS One 2015, 10(9):e0137765.
20. Gatziolis D., Popescu S., Sheridan R., Ku N. Evaluation of terrestrial lidar technology for the development of local tree volume equations. Proceedings of SilviLaser 2010, 197-205.
21. Girardeau-Montaut D. Cloudcompare-open source project 2011, OpenSource Project.
22. Giri C., Ochieng E., Tieszen L.L., Zhu Z., Singh A., Loveland T., Masek J., Duke N. Status and distribution of mangrove forests of the world using earth observation satellite data. Glob. Ecol. Biogeogr. 2011, 20(1):154-159.
23. Greenberg R., Maldonado J.E., Droege S., Mcdonald M.V. Tidal marshes: a global perspective on the evolution and conservation of their terrestrial vertebrates. Bioscience 2006, 56(8):675-685.
24. Gren I.-M. The value of investing in wetlands for nitrogen abatement. Eur. Rev. Agric. Econ. 1995, 22:157-172.
25. Guannel G., Ruggiero P., Faries J., Arkema K., Pinsky M., Gelfenbaum G., Guerry A., Kim C.-K. Integrated modeling framework to quantify the coastal protection services supplied by vegetation. J. Geophys. Res. 2015, 120:324-345. 10.1002/2014JC009821.
26. Hartley R.I., Zisserman A. Multiple View Geometry in Computer Vision 2004, Cambridge University Press. second ed.
27. Jadhav R.S., Chen Q., Smith J.M. Spectral distribution of wave energy dissipation by salt marsh vegetation. Coast. Eng. 2013, 77:99-107.
28. Kaandorp J.A., Koopman E.A., Sloot P.M., Bak R.P., Vermeij M.J., Lampmann L.E. Simulation and analysis of flow patterns around the scleractinian coral Madracis mirabilis (Duchassiang and Michelotti. Philos. Trans. R. Soc. Lond. B 2003, 358:1551-1557.
29. Kirwan M.L., Murray A.B. A coupled geomorphic and ecological model of tidal marsh evolution. Proc. Natl. Acad. Sci. U. S. A. 2007, 104(15):6118-6122.
30. Lane S., James T., Crowell M. Application of digital photogrammetry to complex topography for geomorphological research. Photogramm. Record 2000, 16(95):793-821.
31. Lejot J., Delacourt C., Piegay H., Fournier T., Tremelo M.-L., Allemand P. Very high spatial resolution imagery for channel bathymetry and topography from an unmanned mapping controlled platform. Earth Surf. Process. Landf. 2007, 32(11):1705-1725.
32. Lemein T., Cox D., Albert D., Mori N. Accuracy of optical image analysis compared to conventional vegetation measurements for estimating morphological features of emergent vegetation. Estuar. Coast. Shelf Sci. 2015, 155:66-74.
33. Liénard J., Strigul N. An individual-based forest model links canopy dynamics and shade tolerances along a soil moisture gradient. R. Soc. Open Sci. 2016, 3(2).
34. Liénard J., Vogs A., Gatziolis D., Strigul N. Embedded, real-time UAV control for improved, image-based 3D scene reconstruction. Measurement 2016, 81:264-269.
35. Lightbody A.F., Avener M.E., Nepf H.M. Observations of short-circuiting flow paths within a free-surface wetland in Augusta, Georgia, USA. Limnol. Oceanogr. 2008, 53(3):1040-1053.
36. Lightbody A.F., Nepf H.M. Prediction of velocity profiles and longitudinal dispersion in emergent salt marsh vegetation. Limnol. Oceanogr. 2006, 51:218-228.
37. Lowe D.G. Distinctive image features from scale-invariant keypoints. Int. J. Comput. Vis. 2004, 60(2):91-110.
38. Mazda Y., Magi M., Ikeda Y., Kurokawa T., Asano T. Wave reduction in a mangrove forest dominated by sonneratia sp. Wetl. Ecol. Manag. 2006, 14:365-378.
39. Méndez F.J., Losada I.J., Losada M.A. Hydrodynamics induced by wind waves in a vegetation field. J. Geophys. Res. Oceans 1999, 104(C8):18383-18396.
40. Möller I. Quantifying saltmarsh vegetation and its effect on wave height dissipation: results from a UK east coast saltmarsh. Estuar. Coast. Shelf Sci. 2006, 69:337-351.
41. Mullarney J.C., Henderson S.M. Wave-forced motion of submerged single stem vegetation. J. Geophys. Res. 2010, 115. 10.1029/2010JC006448.
42. Mullarney J.C., Henderson S.M. Flows within marine vegetation canopies. Advances in Coastal Hydraulics 2016, (under revision).
43. Nepf H.M. Flow and transport in regions with aquatic vegetation. Annu. Rev. Fluid Mech. 2012, 44:123-142.
44. Neumeier U. Quantification of vertical density variations of salt-marsh vegetation. Estuar. Coast. Shelf Sci. 2005, 63(4):489-496.
45. Nicholls R., Hoozemans F., Marchand M. Increasing flood risk and wetland losses due to global sea-level rise: regional and global analyses. Glob. Environ. Change Hum. Policy Dimens. 1999, 9(Suppl. 1):S69-S87.
46. Paul M., Amos C. Spatial and seasonal variation in wave attenuation over Zostera noltii. J. Geophys. Res. Oceans 2011, 116(C8). (1978-2012). 10.1029/2010JC006797.
47. Riffe K.C., Henderson S.M., Mullarney J.C. Wave dissipation by flexible vegetation. Geophys. Res. Lett. 2011, 38. 10.1029/2011GL048773.
48. Siikamäki J., Sanchirico J.N., Jardine S.L. Global economic potential for reducing carbon dioxide emissions from mangrove loss. Proc. Natl. Acad. Sci. U. S. A. 2012, 109(36):14369-14374.
49. Small C., Nicholls R. A global analysis of human settlement in coastal zones. J. Coast. Res. 2003, 19(3):584-599.
50. Strigul N. Individual-based models and scaling methods for ecological forestry: implications of tree phenotypic plasticity. Sustainable Forest Management 2012, 359-384. InTech, Rijeka, Croatia. J. Garcia, J. Casero (Eds.).
51. Sumer B., Fredsøe J. Hydrodynamics Around Cylindrical Structures. Advanced Series in Applied Physics 1997, World Scientific.
52. Temmerman S., Bouma T., Govers G., Lauwaet D. Flow paths of water and sediment in a tidal marsh: relations with marsh developmental stage and tidal inundation height. Estuaries 2005, 28(3):338-352.
53. Temmerman S., Bouma T., Govers G., Wang Z., De Vries M., Herman P. Impact of vegetation on flow routing and sedimentation patterns: three-dimensional modeling for a tidal marsh. J. Geophys. Res. Earth Surf. 2005, 110(F4).
54. Temmerman S., Meire P., Bouma T.J., Herman P.M.J., Ysebaert T., De Vriend H.J. Ecosystem-based coastal defence in the face of global change. Nature 2013, 504(7478):79-83.
55. Thu P.M., Populus J. Status and changes of mangrove forest in Mekong Delta: case study in Tra Vinh, Vietnam. Estuar. Coast. Shelf Sci. 2007, 71(1-2):98-109.
56. Utter B.D., Denny M.W. Wave-induced forces on the giant kelp Macrocystis pyrifera (AGARDH): field test of a computational model. J. Exp. Biol. 1996, 199:2645-2654.
57. van Maanen B., Coco G., Bryan K.R. On the ecogeomorphological feedbacks that control tidal channel network evolution in a sandy mangrove setting. Proc. R. Soc. Lond. A Math. Phys. Eng. Sci. 2015, 471(2180).
58. Westoby M., Brasington J., Glasser N., Hambrey M., Reynolds J. structure-from-motion photogrammetry: a low-cost, effective tool for geoscience applications. Geomorphology 2012, 179:300-314.
59. Wu C. Siftgpu: a GPU Implementation of Scale Invariant Feature Transform (Sift) 2007.
60. Wu C. Visualsfm: a Visual Structure from Motion System. 9 2011.
61. Wu C., Agarwal S., Curless B., Seitz S.M. Multicore bundle adjustment. Computer Vision and Pattern Recognition (CVPR), 2011 IEEE Conference on 2011, 3057-3064. IEEE.
62. Yastikli N. Documentation of cultural heritage using digital photogrammetry and laser scanning. J. Cult. Herit. 2007, 8(4):423-427.
63. Zeller R.B., Weitzman J.S., Abbett M.E., Zarama F.J., Fringer O.B., Koseff J.R. Improved parameterization of seagrass blade dynamics and wave attenuation based on numerical and laboratory experiments. Limnol. Oceanogr. 2014, 59(1):251-266.
64. Zhang X., Chua V.P., Cheong H.-F. Geometrical and material properties of Sonneratia alba mangrove roots. Trees 2015, 29:285-297.