3D visualization and finite element mesh formation from wood anatomy samples, Part I – Theoretical approach

KOŇAS, P.: 3D visualization and fi nite element mesh formation from wood anatomy samples, Part II – Algorithm approach. Acta univ. agric. et silvic. Mendel. Brun., 2009, LVII, No. 1, pp. 79–88 Paper presents new original application WOOD3D in form of program code assembling. The work extends the previous article “Part I – Theoretical approach” in detail description of implemented C++ classes of utilized projects Visualization Toolkit (VTK), Insight Toolkit (ITK) and MIMX. Code is written in CMake style and it is available as multiplatform application. Currently GNU Linux (32/64b) and MS Windows (32/64b) platforms were released. Article discusses various fi lter classes for image fi ltering. Mainly Otsu and Binary threshold fi lters are classifi ed for anatomy wood samples thresholding. Registration of images series is emphasized for diff erence of colour spaces compensation is included. Resulted work fl ow of image analysis is new methodological approach for images processing through the composition, visualization, fi ltering, registration and fi nite element mesh formation. Application generates script in ANSYS parametric design language (APDL) which is fully compatible with ANSYS fi nite element solver and designer environment. The script includes the whole defi nition of unstructured fi nite element mesh formed by individual elements and nodes. Due to simple notation, the same script can be used for generation of geometrical entities in element positions. Such formed volumetric entities are prepared for further geometry approximation (e.g. by boolean or more advanced methods). Hexahedral and tetrahedral types of mesh elements are formed on user request with specifi ed mesh options. Hexahedral meshes are formed both with uniform element size and with anisotropic character. Modifi ed octree method for hexahedral mesh with anisotropic character was declared in application. Multicore CPUs in the application are supported for fast image analysis realization. Visualization of image series and consequent 3D image are realized in VTK format suffi ciently known and public format, visualized in GPL application Paraview. Future work based on mesh improvement through mesh error statistic, image acquisition and thresholding improvement by more sophisticated fi lters together with code optimization for fast image analysis is discussed. Also fractal characteristics classifi cation on microscopic scale level is taken into account for further work. wood, anatomy, binary image, fi nite element, mesh converter Mapping of pixels intensity values from space of fi xed image into the moving image is made by class of linear interpolator itk::LinearInterpolateImage Function, which evaluates intensity values on nongrid values of moving image, which is generally deformed according to the fi xed image. In presented program two thresholding fi lters were used. By utilization of ITK two following fi lters were included. Otsu fi lter based on itkOtsuThresholdImageFilter class and binary fi lter based on itkBinaryThresholdImageFilter were used. Both of thresholding fi lters process image according to appropriate threshold. Whereas Otsu fi lter automatically computes value of threshold, binary fi lter allows defi ning the user value for sensitive separation of structure from image background. Mean value of pixels within the selected region is computed by itk::MeanCalculator and itk::CovarianceCalculator classes.