nii_2_mesh_conversion.py

import vtk

def nii_2_mesh (filename_nii, filename_stl, label):

    """
    Read a nifti file including a binary map of a segmented organ with label id = label. 
    Convert it to a smoothed mesh of type stl.

    filename_nii     : Input nifti binary map 
    filename_stl     : Output mesh name in stl format
    label            : segmented label id 
    """

    # read the file
    reader = vtk.vtkNIFTIImageReader()
    reader.SetFileName(filename_nii)
    reader.Update()
    
    # apply marching cube surface generation
    surf = vtk.vtkDiscreteMarchingCubes()
    surf.SetInputConnection(reader.GetOutputPort())
    surf.SetValue(0, label) # use surf.GenerateValues function if more than one contour is available in the file
    surf.Update()
    
    #smoothing the mesh
    smoother= vtk.vtkWindowedSincPolyDataFilter()
    if vtk.VTK_MAJOR_VERSION <= 5:
        smoother.SetInput(surf.GetOutput())
    else:
        smoother.SetInputConnection(surf.GetOutputPort())
    smoother.SetNumberOfIterations(30) 
    smoother.NonManifoldSmoothingOn()
    smoother.NormalizeCoordinatesOn() #The positions can be translated and scaled such that they fit within a range of [-1, 1] prior to the smoothing computation
    smoother.GenerateErrorScalarsOn()
    smoother.Update()
     
    # save the output
    writer = vtk.vtkSTLWriter()
    writer.SetInputConnection(smoother.GetOutputPort())
    writer.SetFileTypeToASCII()
    writer.SetFileName(filename_stl)
    writer.Write()
if __name__ == '__main__':
    
    filename_nii =  '01.nii.gz'
    filename_stl = '01.stl'
    label = 1
    nii_2_mesh (filename_nii, filename_stl, label)