def test_reorient_img():
"""
Test reorient_img functionality
"""
base_dir = str(Path(__file__).parent / "examples")
test_dir = f"{base_dir}/003/test_out/test_reorient_img"
# X axis increasing right to left (Radiological)
img_in_radio = f"{test_dir}/sub-003_T1w_LAS.nii.gz"
out_radio_dir = f"{test_dir}/output_LAS"
# X axis increase from left to right (Neurological)
img_in_neuro = f"{test_dir}/sub-003_T1w_RAS.nii.gz"
out_neuro_dir = f"{test_dir}/output_RAS"
# Outputs should be in neurological orientation.
LAStoRAS_img_out = reg_utils.reorient_img(img_in_radio, out_radio_dir)
RAStoRAS_img_out = reg_utils.reorient_img(img_in_neuro, out_neuro_dir)
# Original RAS data
orig_RAS_img = nib.load(img_in_neuro)
# Output from LAS input
LAStoRAS_img = nib.load(LAStoRAS_img_out)
# Output from RAS input
RAStoRAS_img = nib.load(RAStoRAS_img_out)
# Assert that arrays are equal
check_LAS_input = np.allclose(LAStoRAS_img.affine.astype('int'),
orig_RAS_img.affine.astype('int'))
check_RAS_input = np.allclose(RAStoRAS_img.affine.astype('int'),
orig_RAS_img.affine.astype('int'))
check_both_outputs = np.allclose(LAStoRAS_img.affine.astype('int'),
RAStoRAS_img.affine.astype('int'))
assert check_LAS_input is True
assert check_RAS_input is True
assert check_both_outputs is True
def check_orient_and_dims(infile, vox_size, bvecs=None):
"""
An API to reorient any image to RAS+ and resample any image to a given voxel resolution.
Parameters
----------
infile : str
File path to a dwi Nifti1Image.
vox_size : str
Voxel size in mm. (e.g. 2mm).
bvecs : str
File path to corresponding bvecs file if infile is a dwi.
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.
"""
import os
import os.path as op
from pynets.registration.reg_utils import reorient_dwi, reorient_img, match_target_vox_res
outdir = op.dirname(infile)
img = nib.load(infile)
vols = img.shape[-1]
reoriented = "%s%s%s%s" % (outdir, '/',
infile.split('/')[-1].split('.nii.gz')[0],
'_pre_reor.nii.gz')
resampled = "%s%s%s%s" % (outdir, '/',
os.path.basename(infile).split('.nii.gz')[0],
'_pre_res.nii.gz')
# Check orientation
if (vols > 1) and (bvecs is not None):
# dwi case
outdir = "%s%s" % (outdir, '/std_dmri')
if not os.path.isdir(outdir):
os.mkdir(outdir)
# Check orientation
if not os.path.isfile(reoriented):
[infile, bvecs] = reorient_dwi(infile, bvecs, outdir)
# Check dimensions
if not os.path.isfile(resampled):
outfile = match_target_vox_res(infile,
vox_size,
outdir,
sens='dwi')
elif (vols > 1) and (bvecs is None):
# func case
outdir = "%s%s" % (outdir, '/std_fmri')
if not os.path.isdir(outdir):
os.mkdir(outdir)
# Check orientation
if not os.path.isfile(reoriented):
infile = reorient_img(infile, outdir)
# Check dimensions
if not os.path.isfile(resampled):
outfile = match_target_vox_res(infile,
vox_size,
outdir,
sens='func')
else:
# t1w case
outdir = "%s%s" % (outdir, '/std_anat_')
if not os.path.isdir(outdir):
os.mkdir(outdir)
# Check orientation
if not os.path.isfile(reoriented):
infile = reorient_img(infile, outdir)
if not os.path.isfile(resampled):
# Check dimensions
outfile = match_target_vox_res(infile,
vox_size,
outdir,
sens='t1w')
print(outfile)
if bvecs is None:
return outfile
else:
return outfile, bvecs
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 dwi 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.reg_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
