根系可视化模型及其在富营养化废水净化中的应用
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摘要
根系是植物的重要组成部分，是植物生长发育、新陈代谢的主要营养器官。而根系的结构是反映根系生长情况的因素之一，通过研究植物的根系结构了解植物的生长发育以及其它应用均具有重要意义。但由于根系生长在地下，准确取样、测定、观察存在一定困难，尤其是研究方法欠缺、采样破坏性大、工作量大，阻碍了根系研究的深入开展。
本文从研究“牧草轮种轮收富营养化废水净化系统”中牧草根系的机械滤清等效化的实际需要出发，采用模型方法来研究根系的结构特征，提出了一种基于计算机视觉、测量及模式识别的根系可视化模型，并生成了多年生黑麦草的三维根系图形；首次定义了根系的机械滤清等效过滤精度的概念，并用根系可视化模型计算了等效过滤精度与过滤效率，为“牧草轮种轮收富营养化废水净化系统”的设计研究提供了进一步的理论依据；在分析J2EE架构规范的基础上，给出了一个基于J2EE架构的原型实现，为可视化模型的分布式研究奠定了基础。具体内容如下：
(1)提出了基于计算机视觉测量与模式识别的根系可视化模型的基本原理：用L-System为主要框架，用图像模式识别的方法得到L-System生成规则，即拓扑信息，用图像测量的方法得到几何信息，并在此基础上进行了几何参数的随机性修正，最后生成了根系三维图形，并用分形维数刻划其复杂性，以此为依据来验证模型。
(2)在基于计算机视觉测量与模式识别的根系可视化模型中首先探讨了L-System的基本原理，并给出了DOL的形式化描述；然后为了描述分枝结构，引入了加括号的L-System；在L-System的规则生成中，根据根系的结构具有自相似的有限分形特征，本文从分析根系图像的结构出发，把复杂结构的图像看成是由简单的子图像(子根)所组成，又把最简单的子图像作为基元，从基元的集合出发，按照一定的文法(构图规则)去描述较复杂的图像，这些构图规则可以生成L-System的规则。在本文中经过基元选择、语法推导、基于基元的文法向L-System文法转化等步骤后，得到L-System规则。
(3)用基于计算机视觉的方法进行参数测量。在设计了图像采集系统的基础上，采集得到根系的原始图像。经过图像的低层处理(对比度增强、中值滤波、锐化处理、二值化处理)后，再把图像进行细化处理，剥离出根系的骨架。在此基础上，得到了Freeman链码字符串、根系的长度、角度、根数、侧根间距、分形维数。
(4)在生成几何参数后，由于根系的构型受到多种因素的影响，所以需要在根系测量参数中加入一定的随机性，以便更好地反映根系在实际环境中生长的情况，产生更加逼真的效果。在模型中主要采用分形布朗运动(FBM)、正态分布、均匀分布对参数进行了修正。
浙江大学硕士学位论文
根系可视化模型及其在富营养化废水净化中的应用
(5)在生成根系三维模型的过程中，考虑到xML具有合理的数据组织结
构、面向数据的描述方法和可扩展的特性，引入了基于xML的L一system表示
方法，我们称之为LSML(L一System Markup Language)，并用Java3D设计与
实现了基于LSML的三维图形引擎。
(6)提出了等效过滤精度的概念，并把其应用于表征根系在富营养化废
水净化中的机械滤清效果，然后用根系的三维可视化模型计算了根系的等效过
滤精度和过滤效率。这是在国内外首次提出的概念与方法，能用于量化根系的
机械滤清能力。用模型法计算过滤精度与实验室方法测定相比，更加高效、方
便、快捷、精确，因此具有很好的应用前景。
(7)给出了一个基于JZEE架构的原型实现。设计原型的目的是为了验证
可视化模型的算法，并为根系可视化模型提供一个可扩展的研究框架，更重要
的是，原型实现采用S以P Webservice包装后，可以通过Internet网络后
进行远程渲染，方便其它研究者或用户发现此服务，并进行查看或采用其它程
序进行调用。
Root is one of the important components of the plant and the main organ of growth and metabolism. Root architecture reflects the plant growth in a way, so it is very meaningful to understand plant growth and other applications by studying root architecture. But underground root is hard to be sampled, measured and observed accurately, especially research is a time consuming work and lacks of its method, what's more the sample is easy to be destroyed, which block the deep study of root.
In order to attain the equivalent machine filter effect based on the grazing waste-filter system, model method is used to study root's architecture feature. A root visualization model is put forward based on computer vision, measurement and pattern recognition and perennial rye-grass (Lolium perenne) root 3-dimensional graphic is generated as well. The concept of equivalent-filter precision in machine filtrate is defined; meanwhile the equivalent-filter precision and filter efficiency are computed using the root visualization model, which provide a further theoretic approach to design and research grazing waste-filter system. On the basis of analyzing the J2EE architecture specification, a prototype is carried out, that research established the foundation of distributive approach of visualization model. The detail content is listed as follows:
(1) The principle of the root visualization model based on computer vision, measurement and pattern recognitions is listed: L-System is used as the main framework, and the L-System generated rules are created by image pattern recognition method, namely the topological information. Image-based measurement is used to get geometrical information, and the geometrical parameter is random modified at random according to that, at last the 3-dimension root graphic is generated using the fractal dimension to depict the complexity of root and validate the model.
(2) In the root visualization model based on computer vision, measurement and pattern recognition, the principle of L-System is discussed firstly, and the formalization of DOL is described, then a bracket L-System is inducted to describe the branch architecture. In the generation of L-System rule, because the root architecture has the self-similar finite fractal feature, the architecture of root image is analyzed. Considering that the complicated image is composed of simple subsidiary image(subsidiary root), the simplest subsidiary image is defined as the basal elements, from the aggregate of basal elements, the complicated image is described applying the grammar(rules of generating image), L-System rules can be made from these rules. In the paper, L-System rules is generated from the step of
selecting basal element, evolving grammar, and mapping the grammar based on the basal element to L-System grammar.
(3) Measure the parameter based on the computer vision method. On the basis of image collection system design, the origin image of root is acquired. The image is thinned after the step of low layer process (contrast enhance, mid-value filter, sharpen, binary process), then the skeleton of root is derivated. After the above processes, we can get the string of Freeman chain code, root length, angle, the number of root, side-root's distance, and fractal dimension.
(4) After generating the geometrical parameter, we should add randomicity to reflect the actual growth and create more realistic effect because in the real environment root architecture is affected by many factors. The parameter is modified by FBM, normal school and uniformity distribution in the model.
(5) In the process of generating 3-dimension root model, considering the feature of reasonable data organization, data-oriented expression and extensibility in XML, a expression of L-System called LSML (L-System Markup Language) is introduced, and A 3-D graphic engine is designed and achieved.
(6) The concept of equivalent-filter precision is defined and applied to the effect of machine filtrate of root in the eutrophic water. Then equivalent-filter precision and
本文从研究“牧草轮种轮收富营养化废水净化系统”中牧草根系的机械滤清等效化的实际需要出发，采用模型方法来研究根系的结构特征，提出了一种基于计算机视觉、测量及模式识别的根系可视化模型，并生成了多年生黑麦草的三维根系图形；首次定义了根系的机械滤清等效过滤精度的概念，并用根系可视化模型计算了等效过滤精度与过滤效率，为“牧草轮种轮收富营养化废水净化系统”的设计研究提供了进一步的理论依据；在分析J2EE架构规范的基础上，给出了一个基于J2EE架构的原型实现，为可视化模型的分布式研究奠定了基础。具体内容如下：
(1)提出了基于计算机视觉测量与模式识别的根系可视化模型的基本原理：用L-System为主要框架，用图像模式识别的方法得到L-System生成规则，即拓扑信息，用图像测量的方法得到几何信息，并在此基础上进行了几何参数的随机性修正，最后生成了根系三维图形，并用分形维数刻划其复杂性，以此为依据来验证模型。
(2)在基于计算机视觉测量与模式识别的根系可视化模型中首先探讨了L-System的基本原理，并给出了DOL的形式化描述；然后为了描述分枝结构，引入了加括号的L-System；在L-System的规则生成中，根据根系的结构具有自相似的有限分形特征，本文从分析根系图像的结构出发，把复杂结构的图像看成是由简单的子图像(子根)所组成，又把最简单的子图像作为基元，从基元的集合出发，按照一定的文法(构图规则)去描述较复杂的图像，这些构图规则可以生成L-System的规则。在本文中经过基元选择、语法推导、基于基元的文法向L-System文法转化等步骤后，得到L-System规则。
(3)用基于计算机视觉的方法进行参数测量。在设计了图像采集系统的基础上，采集得到根系的原始图像。经过图像的低层处理(对比度增强、中值滤波、锐化处理、二值化处理)后，再把图像进行细化处理，剥离出根系的骨架。在此基础上，得到了Freeman链码字符串、根系的长度、角度、根数、侧根间距、分形维数。
(4)在生成几何参数后，由于根系的构型受到多种因素的影响，所以需要在根系测量参数中加入一定的随机性，以便更好地反映根系在实际环境中生长的情况，产生更加逼真的效果。在模型中主要采用分形布朗运动(FBM)、正态分布、均匀分布对参数进行了修正。
浙江大学硕士学位论文
根系可视化模型及其在富营养化废水净化中的应用
(5)在生成根系三维模型的过程中，考虑到xML具有合理的数据组织结
构、面向数据的描述方法和可扩展的特性，引入了基于xML的L一system表示
方法，我们称之为LSML(L一System Markup Language)，并用Java3D设计与
实现了基于LSML的三维图形引擎。
(6)提出了等效过滤精度的概念，并把其应用于表征根系在富营养化废
水净化中的机械滤清效果，然后用根系的三维可视化模型计算了根系的等效过
滤精度和过滤效率。这是在国内外首次提出的概念与方法，能用于量化根系的
机械滤清能力。用模型法计算过滤精度与实验室方法测定相比，更加高效、方
便、快捷、精确，因此具有很好的应用前景。
(7)给出了一个基于JZEE架构的原型实现。设计原型的目的是为了验证
可视化模型的算法，并为根系可视化模型提供一个可扩展的研究框架，更重要
的是，原型实现采用S以P Webservice包装后，可以通过Internet网络后
进行远程渲染，方便其它研究者或用户发现此服务，并进行查看或采用其它程
序进行调用。
Root is one of the important components of the plant and the main organ of growth and metabolism. Root architecture reflects the plant growth in a way, so it is very meaningful to understand plant growth and other applications by studying root architecture. But underground root is hard to be sampled, measured and observed accurately, especially research is a time consuming work and lacks of its method, what's more the sample is easy to be destroyed, which block the deep study of root.
In order to attain the equivalent machine filter effect based on the grazing waste-filter system, model method is used to study root's architecture feature. A root visualization model is put forward based on computer vision, measurement and pattern recognition and perennial rye-grass (Lolium perenne) root 3-dimensional graphic is generated as well. The concept of equivalent-filter precision in machine filtrate is defined; meanwhile the equivalent-filter precision and filter efficiency are computed using the root visualization model, which provide a further theoretic approach to design and research grazing waste-filter system. On the basis of analyzing the J2EE architecture specification, a prototype is carried out, that research established the foundation of distributive approach of visualization model. The detail content is listed as follows:
(1) The principle of the root visualization model based on computer vision, measurement and pattern recognitions is listed: L-System is used as the main framework, and the L-System generated rules are created by image pattern recognition method, namely the topological information. Image-based measurement is used to get geometrical information, and the geometrical parameter is random modified at random according to that, at last the 3-dimension root graphic is generated using the fractal dimension to depict the complexity of root and validate the model.
(2) In the root visualization model based on computer vision, measurement and pattern recognition, the principle of L-System is discussed firstly, and the formalization of DOL is described, then a bracket L-System is inducted to describe the branch architecture. In the generation of L-System rule, because the root architecture has the self-similar finite fractal feature, the architecture of root image is analyzed. Considering that the complicated image is composed of simple subsidiary image(subsidiary root), the simplest subsidiary image is defined as the basal elements, from the aggregate of basal elements, the complicated image is described applying the grammar(rules of generating image), L-System rules can be made from these rules. In the paper, L-System rules is generated from the step of
selecting basal element, evolving grammar, and mapping the grammar based on the basal element to L-System grammar.
(3) Measure the parameter based on the computer vision method. On the basis of image collection system design, the origin image of root is acquired. The image is thinned after the step of low layer process (contrast enhance, mid-value filter, sharpen, binary process), then the skeleton of root is derivated. After the above processes, we can get the string of Freeman chain code, root length, angle, the number of root, side-root's distance, and fractal dimension.
(4) After generating the geometrical parameter, we should add randomicity to reflect the actual growth and create more realistic effect because in the real environment root architecture is affected by many factors. The parameter is modified by FBM, normal school and uniformity distribution in the model.
(5) In the process of generating 3-dimension root model, considering the feature of reasonable data organization, data-oriented expression and extensibility in XML, a expression of L-System called LSML (L-System Markup Language) is introduced, and A 3-D graphic engine is designed and achieved.
(6) The concept of equivalent-filter precision is defined and applied to the effect of machine filtrate of root in the eutrophic water. Then equivalent-filter precision and
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63. P. M. Room. 'Falling apart' as a lifestyle: the rhizome architecture and population growth of Salvinia molesta. Journal of Ecology, 1983, 71:349-365.
64. W.R. Remphrey, B. R. Neal, and T. A. Steeves. The morphology and growth of Arctostaphylos uva-ursi (bearberry), parts Ⅰ and Ⅱ. Canadian Journal of Botany, 1983, 61(9): 2430-2458.
65. D. M. Raup and A. Michelson. Theoretical morphology of the coiled shell.Science, 1965, 147:1294-1295.
66. P. Prusinkiewicz, W. Remphrey, C. Davidson, and M. Hammel. Modeling the architecture of expanding Fraxinus pennsylvanica shoots using L-systems.
Canadian Journal of Botany, 1994, 72:701-714.
67. P. Prusinkiewicz, A. Lindenmayer, and J. Hanan. Developmental models of herbaceous plants for computer imagery purposes. Proceedings of SIGGRAPH'88 (Atlanta, Georgia, August 1-5, 1988), in Computer Graphics 22, 4(August 1988), ACM SIGGRAPH, New York, 1988.
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69. P. Prusinkiewicz and A. Lindenmayer. The algorithmic beauty of plants. Springer-Verlag, New York, 1990. With J. S. Hanan, E D. Fracchia, D. R.Fowler, M. J. M. de Boer, and L. Mercer.
70. P. Prusinkiewicz and L. Kari. Subapical bracketed L-systems. To appear in the Proceedings of the Fifth International Workshop on Graph Grammars and their Application to Computer Science, Williamsburg, 1994.
71. P. Prusinkiewicz, M. James, and R. Mech. Synthetic topiary. Proceedings of SIGGRAPH '94 (Orlando, Florida, July 24{29, 1994), ACM SIGGRAPH, New York, 1994.
72. P. Prusinkiewicz and J. Hanan. L-systems: From formalism to programming languages.G. Rozenberg and A. Salomaa, editors, Lindenmayer systems: Impacts on theoretical computer science, computer graphics, and developmental biology, Springer-Verlag, Berlin, 1992.
73. P. Prusinkiewicz and J. Hanan. Visualization of botanical structures and processes using parametric L-systems. D. Thalmann, editor, Scientific visualization and graphics simulation,J. Wiley & Sons, Chichester, 1990.
74. P. Prusinkiewicz and J. Hanan. Lindenmayer systems, fractals, and plants, volume 79 of Lecture Notes in Biomathematics. Springer-Verlag, Berlin, 1989.
75. P. Prusinkiewicz, M. Hammel, and E. Mjolsness. Animation of plant development.Proceedings of SIGGRAPH 93 (Anaheim, California, August 1-6, 1993).In Computer Graphics Proceedings, Annual Conference Series, 1993. ACM SIGGRAPH. New York. 1993.
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84. Zaki, M., Mahdy, Y.B., Ali, S.A., El-Reefy.K.F. Two practical systems for
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62. P. M. Room and J. S. Hanan. Virtual cotton: a new tool for research, management and training. To appear in the Proceedings of the World Cotton Research Conference, Brisbane, Australia, February 14-17, 1994.
63. P. M. Room. 'Falling apart' as a lifestyle: the rhizome architecture and population growth of Salvinia molesta. Journal of Ecology, 1983, 71:349-365.
64. W.R. Remphrey, B. R. Neal, and T. A. Steeves. The morphology and growth of Arctostaphylos uva-ursi (bearberry), parts Ⅰ and Ⅱ. Canadian Journal of Botany, 1983, 61(9): 2430-2458.
65. D. M. Raup and A. Michelson. Theoretical morphology of the coiled shell.Science, 1965, 147:1294-1295.
66. P. Prusinkiewicz, W. Remphrey, C. Davidson, and M. Hammel. Modeling the architecture of expanding Fraxinus pennsylvanica shoots using L-systems.
Canadian Journal of Botany, 1994, 72:701-714.
67. P. Prusinkiewicz, A. Lindenmayer, and J. Hanan. Developmental models of herbaceous plants for computer imagery purposes. Proceedings of SIGGRAPH'88 (Atlanta, Georgia, August 1-5, 1988), in Computer Graphics 22, 4(August 1988), ACM SIGGRAPH, New York, 1988.
68. P. Prusinkiewicz, A. Lindenmayer, and E D. Fracchia. Synthesis of space-filling curves on the square grid. H.-O. Peitgen. J. M. Henriques, and L.F.Penedo,editors, Fractals in the fundamental and applied sciences,North-Holland, Amsterdam, 1991.
69. P. Prusinkiewicz and A. Lindenmayer. The algorithmic beauty of plants. Springer-Verlag, New York, 1990. With J. S. Hanan, E D. Fracchia, D. R.Fowler, M. J. M. de Boer, and L. Mercer.
70. P. Prusinkiewicz and L. Kari. Subapical bracketed L-systems. To appear in the Proceedings of the Fifth International Workshop on Graph Grammars and their Application to Computer Science, Williamsburg, 1994.
71. P. Prusinkiewicz, M. James, and R. Mech. Synthetic topiary. Proceedings of SIGGRAPH '94 (Orlando, Florida, July 24{29, 1994), ACM SIGGRAPH, New York, 1994.
72. P. Prusinkiewicz and J. Hanan. L-systems: From formalism to programming languages.G. Rozenberg and A. Salomaa, editors, Lindenmayer systems: Impacts on theoretical computer science, computer graphics, and developmental biology, Springer-Verlag, Berlin, 1992.
73. P. Prusinkiewicz and J. Hanan. Visualization of botanical structures and processes using parametric L-systems. D. Thalmann, editor, Scientific visualization and graphics simulation,J. Wiley & Sons, Chichester, 1990.
74. P. Prusinkiewicz and J. Hanan. Lindenmayer systems, fractals, and plants, volume 79 of Lecture Notes in Biomathematics. Springer-Verlag, Berlin, 1989.
75. P. Prusinkiewicz, M. Hammel, and E. Mjolsness. Animation of plant development.Proceedings of SIGGRAPH 93 (Anaheim, California, August 1-6, 1993).In Computer Graphics Proceedings, Annual Conference Series, 1993. ACM SIGGRAPH. New York. 1993.
76．盛立东．关于有限状态文法推断的实用算法．北京邮电学院学报，1990，13(3)：84-88．
77．荆仁杰．计算机图像处理．杭州：浙江大学出版社，1991．
78．刘勇奎．Freemon链码压缩算法的研究．计算机学报，2001，24(12)：1294-1298．
79．陈士金等．基于链码的轮廓跟踪技术在二值图像中的应用．华中理工大学学报，1998，26(12)：26-28．
80．丁明．基于平均链码的曲率分割法．山东生物医学工程，2000,19(1)：17-21．
81．张小莉等．一种有限的基于Freeman链码的拐角检测法．电子测量与仪器学报，1999，13(2)：14-19．
82．史勇红等．一种基于Freemon链码描述及其应用的快速图象复原算法．昆明理工大学学报,2001，26(3)：88-92．
83. Xia, Franck. Normal vector and winding number in 2D digital images with their application for hole detection. Volume: 36, Issue: 6, June, 2003:1383-1395
84. Zaki, M., Mahdy, Y.B., Ali, S.A., El-Reefy.K.F. Two practical systems for
classification of three-dimensional objects. Journal of Systems and Software Volume: 48, Issue: 1, August 1, 1999:59-71