How to generate the su mesh file?

[zhang-qiang-github]

Is your feature request related to a problem? Please describe.

Currently, I can segment a aorta vessel mask. How can I convert it to the mesh file?

Describe the solution you'd like

I can generate the surface (vtkPolyData) by vtk. Is there any tool can convert vtkPolyData to su file?

Or is there any tool can convert a 3D mask to su file?

[bigfooted]

There are no publicly available tools to directly convert vtkpolydata to an su2 file, you'll have to write the connectivity and point information to a file yourself, this is easy when you are e.g. in paraview or in python. You also need to write the boundary surfaces and connectivity information as separate entities. You can also look into the capabilities of meshio, which is a very good python library with support for many mesh types.

You could also try to export your data as cgns data and read a cgns file directly in su2.

[bigfooted]

By the way, which software do you use?

[zhang-qiang-github]

I am using python.

You can also look into the capabilities of meshio

Can meshio directly save su file?

[bigfooted]

yes, meshio supports su2: https://pypi.org/project/meshio/

[zhang-qiang-github]

I have another question. If I have mask, how to generate the mesh file? Is there a GUI tool so that I can interactive modify it?

[zhang-qiang-github]

yes, meshio supports su2: https://pypi.org/project/meshio/

Unfortunately, I find that meshio failed to read SU2 file. The code to reproduce my problem is:

import meshio
mesh = meshio.read(filename='.\\su2code-TestCases-v7.4.0-0-gda71b2f\\su2code-TestCases-da71b2f\\incomp_navierstokes\\streamwise_periodic\\chtPinArray_3d\\3D_chtPinArray_coarse.su2')

mesh.write('test.ply')

And warning is reported:

Warning: meshio does not support tags of string type.
    Surface tag  fluid_bottom_interface will be replaced by 1
Warning: meshio does not support tags of string type.
    Surface tag  fluid_pin1 will be replaced by 2
Warning: meshio does not support tags of string type.
    Surface tag  fluid_pin2 will be replaced by 3
Warning: meshio does not support tags of string type.
    Surface tag  fluid_pin3 will be replaced by 4
Warning: meshio does not support tags of string type.
    Surface tag  fluid_top will be replaced by 5
Warning: meshio does not support tags of string type.
    Surface tag  fluid_inlet will be replaced by 6
Warning: meshio does not support tags of string type.
    Surface tag  fluid_outlet will be replaced by 7
Warning: meshio does not support tags of string type.
    Surface tag  fluid_sym_sides will be replaced by 8
Warning: meshio does not support tags of string type.
    Surface tag  solid_bottom_interface will be replaced by 9
Warning: meshio does not support tags of string type.
    Surface tag  solid_pin1 will be replaced by 10
Warning: meshio does not support tags of string type.
    Surface tag  solid_pin2 will be replaced by 11
Warning: meshio does not support tags of string type.
    Surface tag  solid_pin3 will be replaced by 12
Warning: meshio does not support tags of string type.
    Surface tag  solid_sym_sides will be replaced by 13
Warning: meshio does not support tags of string type.
    Surface tag  solid_pins_top will be replaced by 14
Warning: meshio does not support tags of string type.
    Surface tag  solid_bottom_heater will be replaced by 15
Warning: meshio does not support tags of string type.
    Surface tag  solid_pin3_outlet will be replaced by 16
Warning: meshio does not support tags of string type.
    Surface tag  solid_pin1_inlet will be replaced by 17
Warning: meshio does not support tags of string type.
    Surface tag  solid_block_inlet will be replaced by 18
Warning: meshio does not support tags of string type.
    Surface tag  solid_block_outlet will be replaced by 19
Warning: expected 11 ma

Then, I use vtk to visualize it:

import vtkmodules.all as vtk

reader = vtk.vtkPLYReader()
reader.SetFileName('test.ply')
reader.Update()

mapper = vtk.vtkPolyDataMapper()
mapper.SetInputData(reader.GetOutput())
actor = vtk.vtkActor()
actor.SetMapper(mapper)
render = vtk.vtkRenderer()
render.AddActor(actor)
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(render)
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindow(renWin)
iren.Initialize()
iren.Start()

The finally result is:

Is it the correct mesh?