def twix(self, args):
""" Twix format handler."""
from mapvbvd import mapVBVD
from spec2nii.twixfunctions import process_twix, examineTwix
# Call mapvbvd to load the twix file.
twixObj = mapVBVD(args.file, quiet=args.quiet)
if args.view:
examineTwix(twixObj, op.basename(args.file), args.multiraid)
else:
if isinstance(twixObj, list):
twixObj = twixObj[args.multiraid - 1]
if not args.quiet:
print(f"Converting twix file {args.file}.")
print(f'Looking for evalinfo flag {args.evalinfo}.')
overrides = {
'dims': (args.dim5, args.dim6, args.dim7),
'tags': (args.tag5, args.tag6, args.tag7)
}
self.imageOut, self.fileoutNames = process_twix(
twixObj, args.fileout, args.file.name, args.evalinfo,
overrides, args.quiet, args.verbose)
def test_flagRemoveOS():
twixObj = mapVBVD(test_data_gre, quiet=False)
twixObj[1].image.flagRemoveOS = False
assert np.allclose(twixObj[1].image.dataSize,
[256, 16, 128, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1])
twixObj[1].image.flagRemoveOS = True
assert np.allclose(twixObj[1].image.dataSize,
[128, 16, 128, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1])
# broken file
twixObj = mapVBVD(test_data_vb_broken, quiet=False)
twixObj.image.flagRemoveOS = False
assert np.allclose(twixObj.image.dataSize,
[4096, 32, 1, 1, 1, 1, 1, 1, 1, 97, 1, 1, 1, 1, 1, 1])
twixObj.image.flagRemoveOS = True
assert np.allclose(twixObj.image.dataSize,
[2048, 32, 1, 1, 1, 1, 1, 1, 1, 97, 1, 1, 1, 1, 1, 1])
def test_vb():
twixObj = mapVBVD(test_data_vb, quiet=False)
assert np.allclose(twixObj.image.fullSize, [4096, 32, 1, 1, 1, 1, 1, 1, 2, 1, 1, 1, 1, 1, 1, 1])
assert np.allclose(twixObj.image.sqzSize, [2048, 32, 2])
keys = twixObj.search_header_for_keys(('sTXSPEC', 'asNucleusInfo'), top_lvl='MeasYaps')
assert ('sTXSPEC', 'asNucleusInfo', '0', 'tNucleus') in keys['MeasYaps']
key_value = twixObj.search_header_for_val('MeasYaps', ('sTXSPEC', 'asNucleusInfo', '0', 'tNucleus'))
assert key_value[0] == '"1H"'
def test_flagSkipToFirstLine():
twixObj = mapVBVD(test_data_epi, quiet=False)
twixObj[1].refscan.flagSkipToFirstLine = False
assert np.allclose(twixObj[1].refscan.dataSize,
[110, 16, 82, 1, 5, 1, 1, 1, 1, 1, 2, 1, 1, 1, 1, 1])
twixObj[1].refscan.flagSkipToFirstLine = True
assert np.allclose(twixObj[1].refscan.dataSize,
[110, 16, 54, 1, 5, 1, 1, 1, 1, 1, 2, 1, 1, 1, 1, 1])
def test_gre():
twixObj = mapVBVD(test_data_gre, quiet=False)
twixObj[1].image.squeeze = True
twixObj[1].image.flagRemoveOS = False
img_py = twixObj[1].image[:, :, :, 0]
twixObj[1].image.flagRemoveOS = True
img_py_os = twixObj[1].image[:, :, :, 0]
with h5py.File(test_data_gre_mat, 'r') as f:
base = f['img'][0, 0, :, :, :]
img_mat = (base['real'] + 1j * base['imag']).transpose()
base = f['img_os'][0, 0, :, :, :]
img_mat_os = (base['real'] + 1j * base['imag']).transpose()
assert np.allclose(img_py, img_mat)
assert np.allclose(img_py_os, img_mat_os)
def test_flagIgnoreSeg_flagDoAverage():
twixObj = mapVBVD(test_data_epi, quiet=False)
twixObj[1].refscanPC.flagIgnoreSeg = False
twixObj[1].refscanPC.flagDoAverage = False
assert np.allclose(twixObj[1].refscanPC.dataSize,
[110, 16, 1, 1, 5, 2, 1, 1, 1, 1, 2, 1, 1, 1, 1, 1])
twixObj[1].refscanPC.flagDoAverage = True
assert np.allclose(twixObj[1].refscanPC.dataSize,
[110, 16, 1, 1, 5, 1, 1, 1, 1, 1, 2, 1, 1, 1, 1, 1])
twixObj[1].refscanPC.flagIgnoreSeg = True
twixObj[1].refscanPC.flagDoAverage = False
assert np.allclose(twixObj[1].refscanPC.dataSize,
[110, 16, 1, 1, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1])
twixObj[1].refscanPC.flagDoAverage = True
assert np.allclose(twixObj[1].refscanPC.dataSize,
[110, 16, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1])
def test_epi():
twixObj = mapVBVD(test_data_epi, quiet=False)
twixObj[1].image.squeeze = True
twixObj[1].image.flagRampSampRegrid = False
twixObj[1].image.flagRemoveOS = False
img_py = twixObj[1].image[:, :, :, 0, 0, 0]
twixObj[1].image.flagRemoveOS = True
img_py_os = twixObj[1].image[:, :, :, 0, 0, 0]
twixObj[1].image.flagRampSampRegrid = True
img_py_os_rg = twixObj[1].image[:, :, :, 0, 0, 0]
with h5py.File(test_data_epi_mat, 'r') as f:
base = f['img'][0, 0, 0, 0, 0, 0, 0, 0, :, :, :]
img_mat = (base['real'] + 1j * base['imag']).transpose()
base = f['img_os'][0, 0, 0, 0, 0, 0, 0, 0, :, :, :]
img_mat_os = (base['real'] + 1j * base['imag']).transpose()
base = f['img_os_rg'][0, 0, 0, 0, 0, 0, 0, 0, :, :, :]
img_mat_os_rg = (base['real'] + 1j * base['imag']).transpose()
assert np.allclose(img_py, img_mat)
assert np.allclose(img_py_os, img_mat_os)
assert np.allclose(img_py_os_rg, img_mat_os_rg, atol=1e-6, rtol=1e-6)
def test_vb():
twixObj = mapVBVD(test_data_vb, quiet=False)
twixObj.image.flagRemoveOS = False
assert np.allclose(twixObj.image.fullSize,
[4096, 32, 1, 1, 1, 1, 1, 1, 2, 1, 1, 1, 1, 1, 1, 1])
assert np.allclose(twixObj.image.sqzSize, [4096, 32, 2])
twixObj.image.squeeze = True
assert twixObj.image[0:2000, 0:32:4, 0:2].shape == (2000, 8, 2)
assert twixObj.image[1000:2000, 0:32:4, 1].shape == (1000, 8)
assert twixObj.image[10, 0:32:4, 1].shape == (8, )
fulldata = twixObj.image['']
assert np.allclose(twixObj.image[1000:2000, 0:32:4, 1],
fulldata[1000:2000, 0:32:4, 1])
twixObj.image.squeeze = False
assert twixObj.image[0:2000, 0:32:4, :, :, :, :, :, :,
0:2, :].shape == (2000, 8, 1, 1, 1, 1, 1, 1, 2, 1, 1,
1, 1, 1, 1, 1)
assert np.allclose(
np.squeeze(twixObj.image[1000:2000, 0:32:4, :, :, :, :, :, :, 1, :]),
fulldata[1000:2000, 0:32:4, 1])