def test_nrrd2nifti(self):
PREFIX = pjoin(outdir, 'nrrd2nifti_prefix')
# run nrrd2nifti conversion
conversion.nifti_write(REFERENCE_NRRD, PREFIX)
# load converted output
converted_nifti = load(PREFIX + '.nii.gz')
converted_nifti_data = converted_nifti.get_data()
converted_nifti_affine = converted_nifti.affine
converted_nifti_bvals = conversion.read_bvals(PREFIX + '.bval')
converted_nifti_bvecs = conversion.read_bvecs(PREFIX + '.bvec')
# load converted reference
converted_nifti = load(CONVERTED_NIFTI)
reference_nifti_data = converted_nifti.get_data()
reference_nifti_affine = converted_nifti.affine
reference_nifti_bvals = conversion.read_bvals(CONVERTED_BVAL)
reference_nifti_bvecs = conversion.read_bvecs(CONVERTED_BVEC)
# test equality
testing.assert_array_equal(reference_nifti_data, converted_nifti_data)
testing.assert_array_equal(reference_nifti_affine,
converted_nifti_affine)
testing.assert_array_equal(reference_nifti_bvals,
converted_nifti_bvals)
testing.assert_array_equal(reference_nifti_bvecs,
converted_nifti_bvecs)
def nrrd2nifti(imgPath):
if imgPath.endswith('.nrrd') or imgPath.endswith('.nhdr'):
niftiImgPrefix = imgPath.split('.')[0]
nifti_write(imgPath, niftiImgPrefix)
return niftiImgPrefix + '.nii.gz'
else:
return imgPath
def pre_process(input_file, target_list, b0_threshold=50.):
from conversion import nifti_write, read_bvals
from subprocess import Popen
if path.isfile(input_file):
# convert NRRD/NHDR to NIFIT as the first step
# extract bse.py from just NIFTI later
if input_file.endswith(SUFFIX_NRRD) | input_file.endswith(SUFFIX_NHDR):
inPrefix = input_file.split('.')[0]
nifti_write(input_file)
input_file = inPrefix + '.nii.gz'
inPrefix = input_file.split('.nii')[0]
b0_nii = path.join(inPrefix + '_bse.nii.gz')
dwi = nib.load(input_file)
if len(dwi.shape) > 3:
print("Extracting b0 volume...")
bvals = np.array(read_bvals(input_file.split('.nii')[0] + '.bval'))
where_b0 = np.where(bvals <= b0_threshold)[0]
b0 = dwi.get_data()[..., where_b0].mean(-1)
else:
print("Loading b0 volume...")
b0 = dwi.get_fdata()
np.nan_to_num(b0).clip(min=0., out=b0)
nib.Nifti1Image(b0, affine=dwi.affine,
header=dwi.header).to_filename(b0_nii)
target_list.append((b0_nii))
else:
print("File not found ", input_file)
sys.exit(1)