Surface Meshing¶
Creating a surface mesh in DREAM.3D can currently be accomplished by using the Quick Surface Mesh Filter. This Filter will surface mesh a set of Features that exists on an Image Geometry. For example, you could mesh a structure created synthetically, or mesh a structure reconstructed from a serial sectioning experiment. The Quick Surface Mesh Filter is "quick" because it simply draws triangles across the voxel faces of an Image Geometry. Thus, the result of the Filter is a Triangle Geometry where the boundaries between Features are defined by connected triangles. Note that this means that any given triangle is shared by two Features.
Most Geometry objects in DREAM.3D are defined by their shared vertex list. A shared vertex list is a complete list of all the unique vertices in a Geometry, defined by their spatial coordinates. The exception to this rule is an Image Geometry, which can be defined implicitly by its dimensions, resolution, and origin. All other Geometries, including a Triangle Geometry, will also have a list of shared elements, where the elements are the primary unit element of the Geometry. For example, a Triangle Geometry has primary elements that are triangles with three vertices, so such a Geometry will have a list of triangles that are defined by referencing the three vertex Ids of which they are composed.
As explained in the data structure section, Attributes can be associated with any of the unit elements that make up a Geometry. The type of Attribute Matrix that holds these data is defined by the dimensional topology of the underlying unit element. So for a Triangle Geometry, data can lie on the Vertices, the Edges, or the Faces of the triangles. For Geometries that have a shared vertex list, understanding the winding of the Vertices is important. The winding defines the order you go around the object while labeling of the Vertices. For example, a Triangle can be wound going around clockwise or counter-clockwise. In DREAM.3D, the "right hand rule" is adopted for windings. This means that the Vertex winding goes in a counter-clockwise manner. If the user desires, it is possible to reverse the winding of a Triangle Geometry.
Geometry Connectivity¶
Consider a Triangle Geometry. The least amount of information that is needed to describe this Geometry is a shared vertex list and a shared triangle list that indexes into the vertex list. However, it is often desirable to know more about the connectivity of a given Geometry. This means knowing not just the Vertices and the Faces, but also the shared Edges. Additional connectivity information includes generating a list of triangle neighbors, or generating the reverse associations from Vertices to triangles. This sort of connectivity information can be generated within DREAM.3D. Additionally, due to the design of the Geometry objcets, all implemented Geometries can have their connectivities generated.
Generating a Surface Mesh¶
There are several Prebuilt Pipelines that showcase the steps to generate a surface mesh, using the Small IN100 data set as an example. These Pipelines include (01) SmallIN100 Quick Mesh and (02) SmallIN100 Smooth Mesh. Ultimately, generating a surface mesh is as simple as running the Quick Surface Mesh Filter on a set of Features defined on an Image Geometry. However, the resulting surface mesh is usually not satisfactory, since it will remain "blocky" from the original Image Geometry. To solve this problem, the user can smooth the surface mesh by applying the Laplacian Smoothing Filter. To understand the parameters of the Laplacian smoothing procedure, visit that Filter's documentation.
After running the Prebuilt Pipelines (01) SmallIN100 Quick Mesh and (02) SmallIN100 Smooth Mesh, a .dream3d file and a .xdmf file will be written to the Data/Output directory. Opening the .xdmf in ParaView does not yield what you may expect. First, make sure that you are only viewing the Data Container that contains your Triangle Geometry. Even when doing this, the surface mesh will still look "incorrect". To get a view of what the internal meshed surfaces look like, apply ParaView's Threshold filter on the SurfaceMeshNodeTypes array. This array is a set of Attribute data that sits on the Vertices of the surface mesh. The array defines an integer Id that indentifies what kind of node it is:
| Id Value | Node Type |
|---|---|
| 2 | Normal Vertex |
| 3 | Triple Line |
| 4 | Quadruple Point |
| 12 | Normal Vertex on the outer surface |
| 13 | Triple Line on the outer surface |
| 14 | Quadruple Point on the outer surface |
Thus, to see the internal mesh structure, simply apply the ParaView Threshold filter for the values 2 to 4 of the SurfaceMeshNodeTypes array. Additionally, to see the triangles, select the Surface With Edges rendering type.
