def test_parrec2nii_save_load_qform_code(*args):
# Tests that after parrec2nii saves file, it has the sform and qform 'code'
# set to '1', which means 'scanner', so that other software, e.g. FSL picks
# up the qform.
parrec2nii.verbose.switch = False
opts = Mock()
opts.outdir = None
opts.scaling = 'off'
opts.minmax = [1, 1]
opts.store_header = False
opts.bvs = False
opts.vol_info = False
opts.dwell_time = False
opts.compressed = False
with InTemporaryDirectory() as pth:
opts.outdir = pth
for fname in [EG_PAR, VARY_PAR]:
parrec2nii.proc_file(fname, opts)
outfname = join(pth, basename(fname)).replace('.PAR', '.nii')
assert_true(isfile(outfname))
img = nibabel.load(outfname)
assert_almost_equal(img.affine, PAR_AFFINE, 4)
assert_array_equal(img.header['qform_code'], 1)
assert_array_equal(img.header['sform_code'], 1)
def test_parrec2nii_save_load_qform_code():
"""Tests that after parrec2nii saves file, it has the qform 'code'
set to '2', which means 'aligned', so that other software, e.g. FSL
picks up the qform.
"""
imp.reload(parrec2nii)
parrec2nii.verbose.switch = False
opts = Mock()
opts.outdir = None
opts.scaling = 'off'
opts.minmax = [1, 1]
opts.store_header = False
opts.bvs = False
opts.vol_info = False
opts.dwell_time = False
opts.compressed = False
with InTemporaryDirectory() as pth:
opts.outdir = pth
for fname in [EG_PAR, VARY_PAR]:
parrec2nii.proc_file(fname, opts)
outfname = join(pth, basename(fname)).replace('.PAR', '.nii')
assert_true(isfile(outfname))
img = nibabel.load(outfname)
assert_almost_equal(img.get_affine(), PAR_AFFINE, 4)
assert_array_equal(img.header['qform_code'], 2)
assert_array_equal(img.header['sform_code'], 2)
def test_parrec2nii_sets_qform_sform_code1(*args):
# Check that set_sform(), set_qform() are called on the new header.
parrec2nii.verbose.switch = False
parrec2nii.io_orientation.return_value = [[0, 1], [1, 1], [2, 1]] # LAS+
nimg = Mock()
nhdr = MagicMock()
nimg.header = nhdr
parrec2nii.nifti1.Nifti1Image.return_value = nimg
pr_img = Mock()
pr_hdr = Mock()
pr_hdr.get_data_scaling.return_value = (npa([]), npa([]))
pr_hdr.get_bvals_bvecs.return_value = (None, None)
pr_hdr.get_affine.return_value = AN_OLD_AFFINE
pr_img.header = pr_hdr
parrec2nii.pr.load.return_value = pr_img
opts = Mock()
opts.outdir = None
opts.scaling = 'off'
opts.minmax = [1, 1]
opts.store_header = False
opts.bvs = False
opts.vol_info = False
opts.dwell_time = False
infile = 'nonexistent.PAR'
parrec2nii.proc_file(infile, opts)
nhdr.set_qform.assert_called_with(AN_OLD_AFFINE, code=1)
nhdr.set_sform.assert_called_with(AN_OLD_AFFINE, code=1)
def test_parrec2nii_sets_qform_sform_code1(*args):
# Check that set_sform(), set_qform() are called on the new header.
parrec2nii.verbose.switch = False
parrec2nii.io_orientation.return_value = [[0, 1],[1, 1],[2, 1]] # LAS+
nimg = Mock()
nhdr = MagicMock()
nimg.header = nhdr
parrec2nii.nifti1.Nifti1Image.return_value = nimg
pr_img = Mock()
pr_hdr = Mock()
pr_hdr.get_data_scaling.return_value = (npa([]), npa([]))
pr_hdr.get_bvals_bvecs.return_value = (None, None)
pr_hdr.get_affine.return_value = AN_OLD_AFFINE
pr_img.header = pr_hdr
parrec2nii.pr.load.return_value = pr_img
opts = Mock()
opts.outdir = None
opts.scaling = 'off'
opts.minmax = [1, 1]
opts.store_header = False
opts.bvs = False
opts.vol_info = False
opts.dwell_time = False
infile = 'nonexistent.PAR'
parrec2nii.proc_file(infile, opts)
nhdr.set_qform.assert_called_with(AN_OLD_AFFINE, code=1)
nhdr.set_sform.assert_called_with(AN_OLD_AFFINE, code=1)