demo/src/convert.py

import nibabel as nib
from nibabel.processing import resample_to_output
from skimage.measure import marching_cubes


def nifti_to_obj(path, output="prediction.obj"):
    # load NIFTI into numpy array
    image = nib.load(path)
    resampled = resample_to_output(image, [1, 1, 1], order=1)
    data = resampled.get_fdata().astype("uint8")

    # Create a material with a red diffuse color (RGB value)
    red_material = "newmtl RedMaterial\nKd 1 0 0"  # Red diffuse color (RGB)

    # extract surface
    verts, faces, normals, values = marching_cubes(data, 0)
    faces += 1

    with open(output, "w") as thefile:
        # Write the material definition to the OBJ file
        thefile.write(red_material + "\n")

        for item in verts:
            # thefile.write('usemtl RedMaterial\n')
            thefile.write("v {0} {1} {2}\n".format(item[0], item[1], item[2]))

        for item in normals:
            thefile.write("vn {0} {1} {2}\n".format(item[0], item[1], item[2]))

        for item in faces:
            thefile.write("f {0}//{0} {1}//{1} {2}//{2}\n".format(item[0], item[1], item[2]))