Multi-Material Marching Cubes (Slice at a Time)

Group (Subgroup)

SurfaceMesh

Description

This filter creates a surface mesh using a MultiMaterial Marching Cubes (M3C) algorithm as implemented at Carnegie-Mellon University by Dr. Sukbin Lee in the Materials Engineering department. The implementation is based on the Wu/Sullivan algorithm**. Heavy modifications were performed by M. Groeber and M. Jackson for the DREAM3D project. The user is urged to read the original article by Wu/Sullivan in order to gain an understanding of how the algorithm works.

This version of the code meshes by looking at 2 slices of Cells at a time. The temporary data is then serialized out to disk and is then gathered into the complete shared vertex list and triangle list at the conclusion of the filter. The ramifications of this means that the working amount of RAM during the main part of the algorithm is much lower than the Volume at a Time version of the M3C algorithm but does involve potentially a large amount of disk activity. At the conclusion of the filter the entire mesh is then read into memory which means that the user's computer must still have enough RAM to hold the final mesh in memory.

This version of the code does not have any restrictions on the wrapping of the Cell volume with a ghost layer of Cells. If the user's volume does have a ghost layer then those Cells should have a value that is NEGATIVE. This is very important as the algorithm that determines if a layer needs to be added looks specifically for negative values along the outside of the volume. Other Considerations If you have created your Cell volume outside of DREAM3D and have imported it into DREAM3D then the user should take note that Feature/regions with an ID=0 are a special case inside of DREAM3D therefor the user should start their Feature numbering from 1 and be contiguous in numbers to the maximum number of Features. An effort is made to renumber Cells with a value of Zero (0) to Max + 1 during the meshing and then the Cell array is reset back to its pre-surface meshing input.

The values for the Node Type array can take one of the following values.

namespace SurfaceMesh {
  namespace NodeType {
    const int8_t Unused = -1;
    const int8_t Default = 2;
    const int8_t TriplePoint = 3;
    const int8_t QuadPoint = 4;
    const int8_t SurfaceDefault = 12;
    const int8_t SurfaceTriplePoint = 13;
    const int8_t SurfaceQuadPoint = 14;
  }
}

Example output showing a single grain on the edge of a box. Note the beveled edge of the box.

@image latex M3CSurfaceMeshOutput.png "Example output showing a single grain on the edge of a box. Note the beveled edge of the box." width=3in


Parameters

Name Type
Delete Temp Files Boolean: Should the temporary files that are generated be deleted at the end of the filter. This is mostly for debugging.

Required DataContainers

Voxel SurfaceMesh - This will create the Topology (Vertices and Triangles) of the surface mesh over writing anything that is currently in the SurfaceMeshDataContainer

Required Objects

Type Default Name Description Comment Filters Known to Create Data
Cell (Voxel) GrainIds Ids (ints) that specify to which Feature each Cell belongs. Values should be present from segmentation of experimental data or synthetic generation and cannot be determined by this filter. Not having these values will result in the filter to fail/not execute. Segment Features (Misorientation, C-Axis Misorientation, Scalar) (Reconstruction), Read Dx File (IO), Read Ph File (IO), Pack Primary Phases (SyntheticBuilding), Insert Precipitate Phases (SyntheticBuilding), Establish Matrix Phase (SyntheticBuilding)

Created Objects

Type Default Name Comment
Vertex Array SurfaceMeshNodes The shared list of nodes that make up the mesh
Triangle Array SurfaceMeshTriangles The List of triangles in the Surface Mesh
Vertex SurfaceMeshNodeType N x 1 Col of unsigned char
Face SurfaceMeshFaceLabels N x 2 Col of signed integer

Authors

**

Bibliography

Ziji Wu, John M. Sullivan Jr, 2003, "Multiple material marching cubes algorithm". International Journal for Numerical Methods in Engineering. 07/2003; 58(2):189 - 207. DOI:10.1002/nme.775 pp.189 - 207

ABSTRACT

The accurate reconstruction of three-dimensional (3D) boundary surfaces from two-dimensional (2D) medical images is a crucial procedure in most applications of computational biomedical engineering. This paper addresses an innovative system that efficiently reconstructs accurate, multiple-material, 3D surface meshes from 2D medical images. It is based on an enhanced marching cubes algorithm, the multi-material marching cubes algorithm (M3C), which extracts boundary surfaces between different materials within one sweep of the image stack in an integrated manner. The continuity and integrity of the surfaces are ensured with this robust algorithm. Surface adjustment algorithms were also revised to adapt to the multiple-material nature of the system. Copyright © 2003 John Wiley & Sons, Ltd.

Example Pipelines

Please see the description file distributed with this Plugin

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