def test_nifti2nrrd(self):
PREFIX = pjoin(outdir, 'nifti2nhdr')
# run nifti2nrrd conversion
conversion.nhdr_write(REFERENCE_NIFTI, REFERENCE_BVAL, REFERENCE_BVEC,
PREFIX + '.nhdr')
shutil.copy(REFERENCE_NIFTI,
pjoin(outdir, os.path.basename(REFERENCE_NIFTI)))
# load converted output
converted_nrrd_data, converted_nrrd_hdr = read(PREFIX + '.nhdr')
converted_nrrd_bvals, converted_nrrd_bvecs = conversion.nrrd_bvals_bvecs(
converted_nrrd_hdr)[:2]
# load converted reference
reference_nrrd_data, reference_nrrd_hdr = read(CONVERTED_NHDR)
reference_nrrd_bvals, reference_nrrd_bvecs = conversion.nrrd_bvals_bvecs(
reference_nrrd_hdr)[:2]
# test equality
testing.assert_equal(reference_nrrd_hdr, converted_nrrd_hdr)
testing.assert_array_equal(reference_nrrd_data, converted_nrrd_data)
testing.assert_array_equal(reference_nrrd_bvals, converted_nrrd_bvals)
testing.assert_array_equal(reference_nrrd_bvecs, converted_nrrd_bvecs)
def main(self):
with TemporaryDirectory() as tmpdir:
tmpdir = local.path(tmpdir)
shortdwi = tmpdir / 'dwiShort.nii.gz'
shortmask = tmpdir / 'maskShort.nii.gz'
tmpdwi = tmpdir / 'dwi.nhdr'
tmpdwimask = tmpdir / 'dwimask.nhdr'
# TODO when UKFTractography supports float32, it should be removed
# typecast to short
short = load_nifti(self.dwi._path)
save_nifti(shortdwi._path,
short.get_data().astype('int16'), short.affine,
short.header)
short = load_nifti(self.dwimask._path)
save_nifti(shortmask._path,
short.get_data().astype('int16'), short.affine,
short.header)
# convert the dwi to NRRD
nhdr_write(shortdwi._path, self.bvalFile._path,
self.bvecFile._path, tmpdwi._path)
# convert the mask to NRRD
nhdr_write(shortmask._path, None, None, tmpdwimask._path)
key_val_pair = []
if self.givenParams:
key_val_pair = self.givenParams.split(',')
for i in range(
0,
len(ukfdefaults) - 1, 2
): # -1 to pass --recordTensors which is always a default
try:
ind = key_val_pair.index(ukfdefaults[i])
ukfdefaults[i + 1] = key_val_pair[ind + 1]
# since ukfdefault[i+1] has been already replaced by key_val_pair[ind+1]
# remove key_val_pair[ind] and [ind+1] to prevent double specification
key_val_pair[ind:ind + 2] = []
except ValueError:
pass
params = [
'--dwiFile', tmpdwi, '--maskFile', tmpdwimask, '--seedsFile',
tmpdwimask, '--tracts', self.out
] + list(ukfdefaults) + key_val_pair
logging.info('Peforming UKF tractography of {}'.format(tmpdwi))
UKFTractography[params] & FG
def main(self):
with TemporaryDirectory() as tmpdir:
tmpdir = local.path(tmpdir)
shortdwi = tmpdir / 'dwiShort.nii.gz'
shortmask = tmpdir / 'maskShort.nii.gz'
tmpdwi = tmpdir / 'dwi.nhdr'
tmpdwimask = tmpdir / 'dwimask.nhdr'
# TODO when UKFTractography supports float32, it should be removed
# typecast to short
short= load_nifti(self.dwi._path)
save_nifti(shortdwi._path, short.get_data().astype('int16'), short.affine, short.header)
short= load_nifti(self.dwimask._path)
save_nifti(shortmask._path, short.get_data().astype('int16'), short.affine, short.header)
if self.bhigh:
from conversion import grad_remove
bhigh_prefix= tmpdir / self.dwi.stem+ f'_bhigh_{self.bhigh}'
bhigh_dwi= bhigh_prefix+'.nii.gz'
grad_remove(shortdwi._path, bhigh_dwi, interval=[int(self.bhigh)+50,1e6], bvalFile=self.bvalFile, bvecFile=self.bvecFile)
shortdwi= local.path(bhigh_dwi)
self.bvalFile = local.path(bhigh_prefix + '.bval')
self.bvecFile = local.path(bhigh_prefix + '.bvec')
# preserve the filtered attributes in case the user wants to run UKFTractography separately in future
shortdwi.copy(self.dwi.dirname)
self.bvalFile.copy(self.dwi.dirname)
self.bvecFile.copy(self.dwi.dirname)
# convert the dwi to NRRD
nhdr_write(shortdwi._path, self.bvalFile._path, self.bvecFile._path, tmpdwi._path)
# convert the mask to NRRD
nhdr_write(shortmask._path, None, None, tmpdwimask._path)
key_val_pair=[]
if self.givenParams:
key_val_pair= self.givenParams.split(',')
for i in range(0,len(ukfdefaults)-1,2): # -1 to pass --recordTensors which is always a default
try:
ind= key_val_pair.index(ukfdefaults[i])
ukfdefaults[i + 1] = key_val_pair[ind + 1]
# since ukfdefault[i+1] has been already replaced by key_val_pair[ind+1]
# remove key_val_pair[ind] and [ind+1] to prevent double specification
key_val_pair[ind:ind+2]=[]
except ValueError:
pass
params = ['--dwiFile', tmpdwi, '--maskFile', tmpdwimask,
'--seedsFile', tmpdwimask, '--tracts', self.out] + list(ukfdefaults) + key_val_pair
logging.info('Peforming UKF tractography of {}'.format(tmpdwi))
UKFTractography[params] & FG