test_mghimage.py

#!/usr/bin/env python
#
# test_mghimage.py -
#
# Author: Paul McCarthy <pauldmccarthy@gmail.com>
#


import os.path as op
import            shutil

import numpy   as np
import nibabel as nib

import fsl.utils.tempdir   as tempdir
import fsl.utils.transform as transform
import fsl.data.mghimage   as fslmgh
import fsl.data.image      as fslimage


datadir = op.join(op.abspath(op.dirname(__file__)), 'testdata')


def test_MGHImage():

    testfile = op.join(datadir, 'example.mgz')

    # Load from a file
    img      = fslmgh.MGHImage(testfile)
    nbimg    = nib.load(testfile)
    v2s      = nbimg.header.get_vox2ras_tkr()
    w2s      = transform.concat(v2s, transform.invert(nbimg.affine))

    assert np.all(np.isclose(img[:],             nbimg.get_data()))
    assert np.all(np.isclose(img.voxToWorldMat,  nbimg.affine))
    assert np.all(np.isclose(img.voxToSurfMat,   v2s))
    assert np.all(np.isclose(img.surfToVoxMat,   transform.invert(v2s)))
    assert np.all(np.isclose(img.worldToSurfMat, w2s))
    assert np.all(np.isclose(img.surfToWorldMat, transform.invert(w2s)))

    assert img.name         == op.basename(testfile)
    assert img.dataSource   == testfile
    assert img.mghImageFile == testfile

    # Load from an in-memory nibabel object
    img = fslmgh.MGHImage(nbimg)
    assert np.all(np.isclose(img[:],            nbimg.get_data()))
    assert np.all(np.isclose(img.voxToWorldMat, nbimg.affine))
    assert img.dataSource   is None
    assert img.mghImageFile is None


def test_MGHImage_save():

    testfile = op.join(datadir, 'example.mgz')

    with tempdir.tempdir():

        shutil.copy(testfile, 'example.mgz')

        testfile = 'example.mgz'

        img = fslmgh.MGHImage(testfile)

        img.save()

        expfile = op.abspath(fslimage.addExt('example', mustExist=False))

        assert img.dataSource == op.abspath(expfile)