def test_reorient_dwi():
"""
Test reorient_dwi functionality
"""
base_dir = os.path.abspath(
pkg_resources.resource_filename("pynets", "../data/examples"))
test_dir = f"{base_dir}/003/test_out/test_reorient_dwi"
# iso_eddy_corrected_data_denoised_LAS.nii.gz was the original image in
# radiological orientation. fslswapdim and fslorient manually used to
# create RAS image. This test attempts to convert RAS image back to LAS.
# Confirms by checking output array is equal to origal LAS image array.
dwi_prep_rad = f"{test_dir}/iso_eddy_corrected_data_denoised_LAS.nii.gz"
dwi_prep_neu = f"{test_dir}/iso_eddy_corrected_data_denoised_RAS.nii.gz"
bvecs_orig = f"{test_dir}/bvec.bvec"
out_dir = f"{test_dir}/output"
dwi_prep_out, bvecs_out = utils.reorient_dwi(dwi_prep_neu, bvecs_orig,
out_dir)
orig_rad = nib.load(dwi_prep_rad)
orig_rad_data = orig_rad.get_data()
reorient_rad = nib.load(dwi_prep_out)
reorient_rad_data = reorient_rad.get_data()
reorient_check = np.array_equal(orig_rad_data, reorient_rad_data)
bvec_check = np.array_equal(bvecs_orig, bvecs_out)
assert bvec_check is False
assert reorient_check is True
def check_orient_and_dims(infile,
outdir,
vox_size,
bvecs=None,
overwrite=True):
"""
An API to reorient any image to RAS+ and resample any image to a given
voxel resolution.
Parameters
----------
infile : str
File path to a Nifti1Image.
outdir : str
Path to base derivatives directory.
vox_size : str
Voxel size in mm. (e.g. 2mm).
bvecs : str
File path to corresponding bvecs file if infile is a dwi.
overwrite : bool
Boolean indicating whether to overwrite existing outputs. Default is
True.
Returns
-------
outfile : str
File path to the reoriented and/or resample Nifti1Image.
bvecs : str
File path to corresponding reoriented bvecs file if outfile is a dwi.
"""
from pynets.registration.utils import (
reorient_dwi,
reorient_img,
match_target_vox_res,
)
img = nib.load(infile)
vols = img.shape[-1]
# Check orientation
if (vols > 1) and (bvecs is not None):
# dwi case
# Check orientation
if ("reor-RAS" not in infile) or (overwrite is True):
[infile, bvecs] = reorient_dwi(infile,
bvecs,
outdir,
overwrite=overwrite)
# Check dimensions
if ("res-" not in infile) or (overwrite is True):
outfile = match_target_vox_res(infile,
vox_size,
outdir,
overwrite=overwrite)
print(outfile)
else:
outfile = infile
elif (vols > 1) and (bvecs is None):
# func case
# Check orientation
if ("reor-RAS" not in infile) or (overwrite is True):
infile = reorient_img(infile, outdir, overwrite=overwrite)
# Check dimensions
if ("res-" not in infile) or (overwrite is True):
outfile = match_target_vox_res(infile,
vox_size,
outdir,
overwrite=overwrite)
print(outfile)
else:
outfile = infile
else:
# t1w case
# Check orientation
if ("reor-RAS" not in infile) or (overwrite is True):
infile = reorient_img(infile, outdir, overwrite=overwrite)
# Check dimensions
if ("res-" not in infile) or (overwrite is True):
outfile = match_target_vox_res(infile,
vox_size,
outdir,
overwrite=overwrite)
print(outfile)
else:
outfile = infile
if bvecs is None:
return outfile
else:
return outfile, bvecs