Completing the mesh
After drawing all subdomains, answering No when asked if you want to add another one, and either reviewing or not reviewing the SD information, you will be prompted for the mesh file base name. If you type example, the program will generate files called example.gen and example_mesh.dat. It will then draw the mesh in the axes, showing all elements, and the Mesh Complete button will appear.
The file example.gen is called a mesh generation file.
It is passed to the program mesh_3tri which actually defines the mesh (nodal point
coordinates and connectivity). The mesh generation file will look something like this:
2 3 5 5 0 0 0 0 0 0 0 0 0.00000e+00 0.00000e+00 5.00000e-01 0.00000e+00 1.00000e+00 0.00000e+00 1.00000e+00 5.00000e-01 1.00000e+00 1.00000e+00 5.00000e-01 1.00000e+00 0.00000e+00 1.00000e+00 0.00000e+00 5.00000e-01 5 8 1 2 0 0 0 0 0 0 1.00000e+00 1.00000e+00 1.00000e+00 5.00000e-01 1.00000e+00 0.00000e+00 1.50000e+00 0.00000e+00 2.00000e+00 0.00000e+00 2.00000e+00 5.00000e-01 2.00000e+00 1.00000e+00 1.50000e+00 1.00000e+00
The join array has information about how to connect the subdomains to each other.
Each subdomain has a join array with 4 pairs of numbers where each pair corresponds to one side of that
subdomain. The first number in each pair is the subdomain number to which the side is joined.
The second number is the side number on the other subdomain. Any side that is not joined to another
subdomain will have 0 0 for its pair in the join array. The join array for each subdomain
must only reference already existing subdomains. Therefore, subdomain 1 should always have 8 zeros as its
join array. For example, if you have two subdomains and the third side of the second subdomain is joined
to the fourth side of the first subdomain, the join arrays would look like this:
SD#1: 0 0 0 0 0 0 0 0
SD#2: 0 0 0 0 1 4 0 0
The meshing program mesh_3tri will use the mesh generation file to form the mesh and will write the mesh file example_mesh.dat. That mesh file is then saved to your current directory, and can be loaded into redAnTS using the Import - Mapping choice from the Mesh menu there.
After the mesh file is created, the function MappingMethod is automatically called, so the mesh is already active in the redAnTS GUI. Pressing the Mesh Complete button will close the MappingMeshTool and return you to the redAnTS GUI.