def test_match_target_vox_res():
"""
Test match_target_vox_res functionality
"""
base_dir = str(Path(__file__).parent/"examples")
test_out = f"{base_dir}/003/test_out/test_match_target_vox_res"
# Orig anat input has isotropic (1x1x1mm) dimensions.
anat_img_file = f"{test_out}/sub-003_T1w_pre_res_res-2mm.nii.gz"
anat_vox_size = '2mm'
anat_out_dir = test_out
anat_img_file = reg_utils.match_target_vox_res(anat_img_file, anat_vox_size, anat_out_dir)
anat_new_img = nib.load(anat_img_file)
anat_dims = anat_new_img.header.get_zooms()
anat_success = True
for anat_dim in np.round(anat_dims[:3], 2):
if anat_dim != 2:
anat_success = False
# Orig dMRI image has anisotropic (1.75x1.75x3mm) dimensions.
dwi_img_file = f"{test_out}/sub-003_dwi_pre_res_res-1mm.nii.gz"
dwi_vox_size = '1mm'
dwi_out_dir = test_out
dwi_img_file = reg_utils.match_target_vox_res(dwi_img_file, dwi_vox_size, dwi_out_dir)
dwi_new_img = nib.load(dwi_img_file)
dwi_dims = dwi_new_img.header.get_zooms()
dwi_success = True
for dwi_dim in np.round(dwi_dims[:3], 2):
if dwi_dim != 1:
dwi_success = False
assert anat_img_file is not None
assert anat_success is True
assert dwi_img_file is not None
assert dwi_success 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