Display nrrd as 3d using visvis

nrrd-3d.py

import numpy as np
import nrrd
import argparse
import os.path
from argparse import ArgumentParser

import imageio
import visvis as vv


def is_valid_file(parser, arg):
    if not os.path.exists(arg):
        parser.error("The file %s does not exist!" % arg)
    else:
        return open(arg, 'r')  # return an open file handle


parser = ArgumentParser(description='Display NRRD as 3D Volume')

parser.add_argument("-i", dest="file", required=True,
                    help="input nrrd file", metavar="string",
                    type=lambda x: is_valid_file(parser, x))

args = parser.parse_args()

nrrdInPath = args.file.name

data, header = nrrd.read(nrrdInPath)

npzOutPath = nrrdInPath + '.npz'

np.savez_compressed( npzOutPath, data )

app = vv.use()

vol = imageio.volread(npzOutPath)
vol_res = vv.volshow( vol )

app.Run()