def test_agg_data():
surf_gii_img = nib.load(test_data('gifti', 'ascii.gii'))
func_gii_img = nib.load(test_data('gifti', 'task.func.gii'))
shape_gii_img = nib.load(test_data('gifti', 'rh.shape.curv.gii'))
# add timeseries data with intent code ``none``
point_data = surf_gii_img.get_arrays_from_intent('pointset')[0].data
triangle_data = surf_gii_img.get_arrays_from_intent('triangle')[0].data
func_da = func_gii_img.get_arrays_from_intent('time series')
func_data = np.column_stack(tuple(da.data for da in func_da))
shape_data = shape_gii_img.get_arrays_from_intent('shape')[0].data
assert_equal(surf_gii_img.agg_data(), (point_data, triangle_data))
assert_array_equal(func_gii_img.agg_data(), func_data)
assert_array_equal(shape_gii_img.agg_data(), shape_data)
assert_array_equal(surf_gii_img.agg_data('pointset'), point_data)
assert_array_equal(surf_gii_img.agg_data('triangle'), triangle_data)
assert_array_equal(func_gii_img.agg_data('time series'), func_data)
assert_array_equal(shape_gii_img.agg_data('shape'), shape_data)
assert_equal(surf_gii_img.agg_data('time series'), ())
assert_equal(func_gii_img.agg_data('triangle'), ())
assert_equal(shape_gii_img.agg_data('pointset'), ())
assert_equal(surf_gii_img.agg_data(('pointset', 'triangle')),
(point_data, triangle_data))
assert_equal(surf_gii_img.agg_data(('triangle', 'pointset')),
(triangle_data, point_data))
def test_default(tmpdir):
infile = test_data(fname="anatomical.nii")
outfile = tmpdir / "output.nii.gz"
main([str(infile), str(outfile)])
assert outfile.isfile()
c = nib.load(outfile)
assert c.shape == (256, 256, 256)
assert c.header.get_zooms() == (1, 1, 1)
assert nib.orientations.aff2axcodes(c.affine) == ('R', 'A', 'S')
with pytest.raises(FileExistsError):
main([str(infile), str(outfile)])
main([str(infile), str(outfile), "--force"])
assert outfile.isfile()
def test_nondefault(tmpdir):
infile = test_data(fname="anatomical.nii")
outfile = tmpdir / "output.nii.gz"
out_shape = (100, 100, 150)
voxel_size = (1, 2, 4)
orientation = "LAS"
args = "{} {} --out-shape {} --voxel-size {} --orientation {}".format(
infile, outfile, " ".join(map(str, out_shape)),
" ".join(map(str, voxel_size)), orientation)
main(args.split())
assert outfile.isfile()
c = nib.load(outfile)
assert c.shape == out_shape
assert c.header.get_zooms() == voxel_size
assert nib.orientations.aff2axcodes(c.affine) == tuple(orientation)