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Original Research Papers

A virtual canopy generator (V-CaGe) for modelling complex heterogeneous forest canopies at high resolution

Authors:

Gil Bohrer,

Department of Civil and Environmental Engineering, Duke University, North Carolina 27708, US
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Michael Wolosin,

Department of Biology, Duke University, North Carolina 27708, US
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Rachael Brady,

Department of Computer Science, Duke University, North Carolina 27708, US
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Roni Avissar

Department of Civil and Environmental Engineering, Duke University, North Carolina 27708, US
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Abstract

The structure of tree canopies affects turbulence in the atmospheric boundary layer, and light attenuation, reflection and emission from forested areas. Through these effects, canopy structure interacts with fluxes of heat, water, CO2, and volatile organic compounds, and affects patterns of soil moisture and ecosystem dynamics. The effects of canopy structure on the atmosphere are hard to measure and can be studied efficiently with large-eddy simulations. Remote sensing images that can be interpreted for biophysical properties are prone to errors due to effects of canopy structure, such as shading. However, the detailed 3-D canopy structure throughout a large spatial domain (up to several km2) is rarely available.

We introduce a new method, namely the virtual canopy generator (V-CaGe), to construct finely detailed, 3-D, virtual forest canopies for use in remote sensing, and atmospheric and other environmental models. These virtual canopies are based on commonly observed mean and variance of biophysical forest properties, and a map (or a remotely-sensed image) of leaf area, or canopy heights, of a canopy subdomain. The canopies are constructed by inverse 2-D Fouriertransform of the observed spatial autocorrelation function and a random phase. The resulting field is expanded to 3-D by using empirical allometric profiles. We demonstrate that the V-CaGe can generate realistic simulation domains.

How to Cite: Bohrer, G., Wolosin, M., Brady, R. and Avissar, R., 2007. A virtual canopy generator (V-CaGe) for modelling complex heterogeneous forest canopies at high resolution. Tellus B: Chemical and Physical Meteorology, 59(3), pp.566–576. DOI: http://doi.org/10.1111/j.1600-0889.2007.00253.x
  Published on 01 Jan 2007
 Accepted on 13 Nov 2006            Submitted on 28 Apr 2006

References

  1. Adcroft , A. , Hill , C. and Marshall , J. 1997. Representation of topography by shaved cells in a height coordinate ocean model. Mon. Weather Rev. 125, 2293 – 2315.  

  2. Albertson , J. D., Katul, G. G., Parlange, M. B. and Eichinger, W. E. 1998. Spectral scaling of static pressure fluctuations in the atmospheric surface layer: The interaction between large and small scales . Phys. Fluids 10 , 1725– 1732 .  

  3. Asner , G. P. , Bateson , C. A. , Privette , J. L. , El Saleous, N. and Wessman, C. A. 1998. Estimating vegetation structural effects on carbon uptake using satellite data fusion and inverse modeling. J. Geophys. Res.-Atmos. 103, 28839 – 28853.  

  4. Asner , G. P. and Warner , A. S . 2003 . Canopy shadow in IKONOS satellite observations of tropical forests and savannas . Remote Sens. Environ . 87 , 521 – 533 .  

  5. Asner , G. P. , Carlson , K. M. and Martin , R. E. 2005. Substrate age and precipitation effects on Hawaiian forest canopies from spacebome imaging spectroscopy. Remote Sens. Environ. 98, 457 – 467.  

  6. Aubinet , M. , Heinesch , B. and Yemaux , M . 2003 . Horizontal and vertical CO2 advection in a sloping forest . Bound. Layer Meteor 108 , 397 – 417 .  

  7. Avissar , R. and Schmidt , T . 1998 . An evaluation of the scale at which ground-surface heat flux patchiness affects the convective boundary layer using large-eddy simulations. J. Atmos. Sci . 55 , 2666 – 2689. Baldocchi, D., Finnigan, J., Wilson, K., Paw, U.K. T. and Falge, E. 2000. On measuring net ecosystem carbon exchange over tall vegetation on complex terrain . Bound. Layer Meteor 96 , 257 – 291 .  

  8. Bohrer , G. , Mourad , H. , Laursen , T. A , Drewry , D. , Avissar, R. and co-authors. 2005. Finite-Element Tree Crown Hydrodynamics model (FETCH) using porous media flow within branching elements - a new representation of tree hydrodynamics. Water Resour Res. 41, W11404, https://doi.org/10.11029/12005WR004181 .  

  9. Bou-Zeid , E. , Meneveau , C. and Parlange , M. B . 2004. Large-eddy simu-lation of neutral atmospheric boundary layer flow over heterogeneous surfaces: Blending height and effective surface roughness. Water Re-sour Res. 40, WR002475, https://doi.org/10.001029/002003WR002475 .  

  10. Burke , E. J. , Shuttleworth , W. J. and Houser , P. R. 2004. Impact of horizontal and vertical heterogeneities on retrievals using multiangle microwave brightness temperature data. IEEE Trans. Geosci. Remote Sensing 42, 1495 – 1501.  

  11. Chuang , Y.-L. , Oren , R. , Bertozzi , A. L , Phillips, N. and Katul, G. G. 2006. The porous media model for the hydraulic system of a conifer tree: Linking sap flux data to transpiration rate. EcoL Model. 191, 447 – 468.  

  12. Couteron , P. , Pelissier , R. , Nicolini , E. A. and Dominique , P. 2005. Pre-dicting tropical forest stand structure parameters from Fourier trans-form of very high-resolution remotely sensed canopy images. J. AppL EcoL 42, 1121 – 1128.  

  13. Falkowski , M. J. , Gessler , P. E. , Morgan , P. , Hudak , A. T and Smith, A. M. S. 2005. Characterizing and mapping forest fire fuels using ASTER imagery and gradient modeling. For. EcoL Manage. 217, 129 – 146.  

  14. Farquhar , G. D. , Caemmerer , S. V. and Berry , J. A. 1980. A biochemical model of photosynthetic CO2 assimilation in leaves of C-3 species. Planta 149, 78 – 90.  

  15. Feigenwinter , C. , Bemhofer , C. and Vogt , R . 2004 . The influence of advection on the short term CO2-budget in and above a forest canopy . Bound. Layer. Meteor 113 , 201 – 224 .  

  16. Ferraris , L. , Gabellani , S. , Parodi , U. , von Hardenberg, J. and Provenzale, A. 2003. Revisiting multifractality in rainfall fields. J. HydrometeoroL 4, 544 – 551.  

  17. Finnigan , J. 2000. Turbulence in plant canopies. Annu. Rev. Fluid Mech. 32, 519 – 571.  

  18. Finnigan , J . 2004 . The footprint concept in complex terrain . Agric. For Meteorol . 127 , 117 – 129 .  

  19. Fitzgerald , G. J. , Pinter , P. J. , Hunsaker , D. J. and Clarke , T. R. 2005. Multiple shadow fractions in spectral mixture analysis of a cotton canopy. Remote Sens. Environ. 97, 526 – 539.  

  20. Foken , T. and Leclerc , M. Y . 2004 . Methods and limitations in validation of footprint models . Agric. For Meteorol . 127 , 223 – 234 .  

  21. Gilbert , K. E. , Raspet , R. and Di , X . 1990 . Calculation of turbulence effects in an upward-refracting atmosphere . J. Acoust. Soc. Am . 87 , 2428 – 2437 .  

  22. Gong , P. , Biging , G. S. and Standiford , R . 2000 . Use of digital surface model for hardwood rangeland monitoring . J. Range Manage . 53 , 622 – 626 .  

  23. Gopalakrishnan , S. G. , Roy , S. B. and Avissar , R . 2000 . An evaluation of the scale at which topographical features affect the convective bound-ary layer using large eddy simulations . J. Atmos. Sci . 57 , 334 – 351 .  

  24. Gopalakrishnan , S. G. and Avissar , R . 2000 . An LES study of the impacts of land surface heterogeneity on dispersion in the convective boundary layer . J. Atmos. Sci . 57 , 352 – 371 .  

  25. Houser , P. R. , Shuttleworth , W. J. , Famiglietti , J. S. , Gupta , H. V. , Syed , K. H. and co-authors. 1998. Integration of soil moisture remote sensing and hydrologic modeling using data assimilation. Water Resour. Res. 34, 3405 – 3420.  

  26. Hurtt , G. C. , Dubayah , R. , Drake , J. , Moorcroft , P. R , Pacala, S. W. and co-authors. 2004. Beyond potential vegetation: combining LiDAR data and a height-structured model for carbon studies. EcoL AppL 14, 873 – 883.  

  27. Jackson , R . B., Jobbagy, E. G., Avissar, R., Baidya Roy, S., Barrett, D. J. and co-authors. 2005. Trading water for carbon with biological sequestration . Science 310 , 1944– 1947 .  

  28. Kanda , M. , Inagaki , A. , Letzel , M.O. , Raasch, S. and Watanabe, T. 2004. LES study of the energy imbalance problem with eddy covariance fluxes. Bound. Layer Meteor. 110, 381 – 404.  

  29. Karl , T. , Potosnak , M. , Guenther , A. , Clark , D. , Walker , J. and co-authors. 2004. Exchange processes of volatile organic compounds above a tropical rain forest: Implications for modeling tropospheric chem-istry above dense vegetation. J. Geophys. Res.-Atmos. 109, D18306, https://doi.org/10.11029/12004JD004738 .  

  30. Katul , G. G. , Finnigan , J. , Poggi , D. , L,euning, R. and Belcher, S. E. 2006a. The influence of hilly terrain on canopy-atmosphere carbon dioxide exchange. Bound. Layer Meteor. 118, 186 – 216.  

  31. Katul , G. G. , Williams , C. G. , Siqueira , M. , Poggi , D. , Porporato , A. and co-authors. 2006b. Spatial modelling of transgenic conifer pollen. In: Landscapes, Genomics, and Transgenic Conifers (ed. C. G. Williamss ). Springer, New York, 265  

  32. Kruijt , B. , Malhi , Y. , Lloyd , J. , Norbre , A. D. , Miranda , A. C. and co-authors. 2000. Turbulence statistics above and within two Amazon rain forest canopies. Bound. Layer Meteor 94, 297 – 331.  

  33. Kruijt , B. , Elbers , J. A. , von Randow, C., Araujo, A. C., Oliveira, P. J. and co-authors. 2004. The robustness of eddy correlation fluxes for Amazon rain forest conditions. EcoL AppL 14, S101-S113.  

  34. L,efsky, M. A., Cohen, W . B., Parker, G. G. and Harding, D. J. 2002. Lidar remote sensing for ecosystem studies. Bioscience 52, 19 – 30.  

  35. L,euning, R., Kelliher, E M., Depury, D. G. G. and Schulze, E. D . 1995 . Leaf nitrogen, photosynthesis, conductance and transpiration - scaling from leaves to canopies . Plant Cell Environ . 18 , 1183 – 1200 .  

  36. Li , B. and Avissar , R . 1994 . The impact of spatial variability of land-surface characteristics on land-surface heat fluxes. J. Clim. 7 , 527 - 537 .  

  37. McCarthy , H. R. , Oren , R. , Finzi , A. C. , Ellsworth , D. S. , Kim, H.-S. and co-authors. 2007. Temporal dynamics and spatial variability in the enhancement of canopy leaf area under elevated atmospheric CO2. Glob. Change Biol. (in press).  

  38. Moorcroft , P. R. , Hurtt , G. C. and Pacala , S. W . 2001 . A method for scal-ing vegetation dynamics: The ecosystem demography model (ED) . EcoL Monogr 71 , 557 – 585 .  

  39. Naidu , S. L. , DeLucia , E. H. and Thomas , R. B . 1998 . Contrasting pat-terns of biomass allocation in dominant and suppressed loblolly pine . Can. J. For. Res . 28 , 1116 – 1124 .  

  40. Nathan , R. and Katul , G. G . 2005 . Foliage shedding in deciduous forests lifts up long-distance seed dispersal by wind . Proc. Natl. Acad. Sci. USA . 102 , 8251 – 8256 .  

  41. Nathan , R. , Sapir , N. , Trakhtenbrot , A. , Katul , G. G. , Bohrer , G. and co-authors. 2005. Long-distance biological transport processes through the air: Can nature's complexity be unfolded in silico? Divers. Distrib. 11, 131 – 137.  

  42. Patton , E. G. , Shaw , R. H. , Judd , M. J. and Raupach , M. R. 1998. Large-eddy simulation of windbreak flow. Bound. Layer Meteor 87, 275 – 306.  

  43. Patton , E.G. , Davis , K. J. , Barth , M. C. and Sullivan , P. P. 2001. Decaying scalars emitted by a forest canopy: A numerical study. Bound. Layer Meteor. 100, 91 – 129.  

  44. Patton , E. G. , Sullivan , P. P. and Davis, K. J. 2003. The influence of a forest canopy on top-down and bottom-up diffusion in the planetary boundary layer. Q. J. R. Meteorol. Soc. 129, 1415 – 1434.  

  45. Patton , E. G. , Sullivan , P. P. and Moeng , C. H . 2005 . The influence of idealized heterogeneity on wet and dry planetary boundary layers coupled to the land surface . J. Atmos. Sci . 62 , 2078 – 2097 .  

  46. Patton , E. G. , Sullivan , P. P. and Ayotte , K. W . 2006 . Flow and transport above and within forests in complex topography. Integrated Land-Ecosystem Atmosphere Study Conference. Boulder, CO. pp. 376. Peters-Lidard, C. D., Pan, E and Wood, E. E 2001. A re-examination of modeled and measured soil moisture spatial variability and its impli-cations for land surface modeling . Adv. Water. Resour 24 , 1069 – 1083 .  

  47. Poggi , D. , Porporato , A. , Ridolfi , L. , Albertson , J. D. and Katul, G. G. 2004a. The effect of vegetation density on canopy sub-layer turbu-lence. Bound. Layer Meteor 111, 565 – 587.  

  48. Poggi , D. , Katul , G. G. and Albertson , J. D. 2004b. Momentum transfer and turbulent kinetic energy budgets within a dense model canopy. Bound. Layer. Meteor 111, 589 – 614.  

  49. Rannik , U. , Aubinet , M. , Kurbanmuradov, 0., Sabelfeld, K. K., Markka-nen, T. and co-authors. 2000. Footprint analysis for measurements over a heterogeneous forest. Bound. Layer Meteor 97, 137 – 166.  

  50. Raupach , M. R . 1989a . Applying Lagrangian fluid-mechanics to in-fer scalar source distributions from concentration profiles in plant canopies . Agric. For Meteorol . 47 , 85 – 108 .  

  51. Raupach , M. R . 1989b . A practical Lagrangian method for relating scalar concentrations to source distributions in vegetation canopies . Q. J. R. Meteorol. Soc . 115 , 609 – 632 .  

  52. Raupach , M. R . 1998 . Influences of local feedbacks on land-air ex-changes of energy and carbon . Glob. Change Biol . 4 , 477 – 494 .  

  53. Rogallo , R. S . 1981. Numerical experiments in homogeneous turbulence. Pages 1-91. NASA, Ames Research Center .  

  54. Scanlon , T. M. and Albertson , J. D . 2003 . Water availability and the spa-tial complexity of CO2, water, and energy fluxes over a heterogeneous sparse canopy . J. HydrometeoroL 4 , 798 – 809 .  

  55. Schafer , K. V. R . 2002. Effects of increased atmospheric CO2 concentra-tions on water and carbon relations of four co-occurring tree species. PhD thesis. Nicolas School of the Environment and Earth Sciences, Duke University, Durham, NC, pp 208.  

  56. Shaw , R. H. , Denhartog , G. and Neumann , H. H . 1988 . Influence of foliar density and thermal-stability on profiles of reynolds stress and turbulence intensity in a deciduous forest . Bound. Layer Meteor . 45 , 391 – 409 .  

  57. Shaw , R. H. and Patton , E. G . 2003 . Canopy element influences on resolved- and subgrid-scale energy within a large-eddy simulation . Agric. For MeteoroL 115 , 5 – 17 .  

  58. Slaymaker , D. , Schultz , H. , Hanson , A. , Riseman , E. , Holmes , C. and co-authors. 1999. Calculating forest biomass with small format aerial photography, videography and a profiling laser. ASPRS Proceedings of the 17th Biennial Workshop on Color Photography and Videography in Resource Assessment. Reno, NV. pp. 241 – 260.  

  59. Sogachev , A. , Menzhulin , G. V. , Heimann , M. and Lloyd , J . 2002 . A sim-ple three-dimensional canopy - planetary boundary layer simulation model for scalar concentrations and fluxes . Tellus 54B , 784 – 819 .  

  60. Sogachev , A. , Leclerc , M. Y. , Karipot , A. , Zhang , G. and Vesala , T . 2005 . Effect of clearcuts on footprints and flux measurements above a forest canopy . Agric. For. MeteoroL 133 , 182 – 196 .  

  61. Staebler , R. M. and Fitzjarrald , D. R . 2004 . Observing subcanopy CO2 advection . Agric. For. MeteoroL 122 , 139 – 156 .  

  62. Staebler , R. M. and Fitzjarrald , D. R . 2005 . Measuring canopy struc-ture and the kinematics of subcanopy flows in two forests . J. AppL Meteorol . 44 , 1161 – 1179 .  

  63. Stenberg , P . 1995 . Penumbra in within-shoot and between-shoot shading in conifers and its significance for photosynthesis . Ecol. Model . 77 , 215 – 231 .  

  64. Styles , J. M. , Raupach , M. R. , Farquhar , G. D. , Kolle, 0., Lawton, K. A. and co-authors. 2002. Soil and canopy CO2, '3(CO2), H20 and sensi-ble heat flux partitions in a forest canopy inferred from concentration measurements. Tellus 54B, 655 – 676.  

  65. Su , H. B. , Shaw , R. H. , Paw , U. K. T. , Moeng , C. H. and Sullivan , P. P. 1998. Turbulent statistics of neutrally stratified flow within and above a sparse forest from large-eddy simulation and field observa-tions. Bound. Layer. Meteor. 88, 363 – 397.  

  66. Toivonen , T. , Kalliola , R. , Ruokolainen , K. and Malik , R. N. 2006. Across-path DN gradient in Landsat TM imagery of Amazonian forests: A challenge for image interpretation and mosaicking. Remote Sens. Environ. 100, 550 – 562.  

  67. Venema , V. , Meyer , S. , Garcia , S. G. , Kniffka , A. , Simmer , C. and co-authors. 2006. Surrogate cloud fields generated with the itera-tive amplitude adapted Fourier transform algorithm. Tellus 58A, 104 – 120.  

  68. Venugopal , V. , Basu , S. and Foufoula-Georgiou , E . 2005 . A new metric for comparing precipitation patterns with an application to ensemble forecasts . J. Geophys. Res.-Atmos . 110 , D08111 , https://doi.org/10.01029/02004JDO05395 .  

  69. Vesala , T. , Markkanen , T. , Palva , L. , Siivola , E. , Pahnroth , S. and co-authors. 2000. Effect of variations of PAR on CO2 exchange estimation for Scots pine. Agric. For. MeteoroL 100, 337 – 347.  

  70. Vmuesa , J. E and De Arellano, J. V.-G. 2003. Fluxes and (co-)variances of reacting scalars in the convective boundary layer. Tellus 55B, 935 – 949.  

  71. Walko , R. L. , Band , L. E. , Baron , J. , Kittel , T. G E, Lammers, R. and co-authors. 2000. Coupled atmosphere-biophysics-hydrology models for environmental modeling. J. AppL MeteoroL 39, 931 – 944.  

  72. Wang , H. , Takle , E. S. and Shen , J. M. 2001. Shelterbelts and windbreaks: Mathematical modeling and computer simulations of turbulent flows. Annu. Rev. Fluid Mech. 33, 549 – 586.  

  73. Weishampel , J. E , Blair , J. B. , Knox , R. G. , Dubayah, R. and Clark, D. B. 2000. Volumetric LiDAR return patterns from an old-growth tropical rainforest canopy. Int. J. Remote Sens. 21, 409 – 415.  

  74. Wirth , R. , Weber , B. and Ryel , R. J. 2001. Spatial and temporal variability of canopy structure in a tropical moist forest. Acta Oecol.-Int. J. EcoL 22, 235 – 244.  

  75. Yang , B. , Raupach , M. , Shaw , R. H. , U , K. T. P. and Morse , A. P. 2006. Large-eddy simulation of turbulent flow across a forest edge. Part I: flow statistics. Bound. Layer Meteor 119, DOI: https://doi.org/10.1007/s10546-10006-19083-10543 .  

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