def embed_nifti(dcmfiles, niftifile, infofile, force=False):
import dcmstack as ds
import nibabel as nb
import os
stack = ds.parse_and_stack(dcmfiles, force=force).values()
if len(stack) > 1:
raise ValueError('Found multiple series')
stack = stack[0]
#Create the nifti image using the data array
if not os.path.exists(niftifile):
nifti_image = stack.to_nifti(embed_meta=True)
nifti_image.to_filename(niftifile)
return ds.NiftiWrapper(nifti_image).meta_ext.to_json()
orig_nii = nb.load(niftifile)
orig_hdr = orig_nii.get_header()
aff = orig_nii.get_affine()
ornt = nb.orientations.io_orientation(aff)
axcodes = nb.orientations.ornt2axcodes(ornt)
new_nii = stack.to_nifti(voxel_order=''.join(axcodes), embed_meta=True)
new_hdr = new_nii.get_header()
#orig_hdr.extensions = new_hdr.extensions
#orig_nii.update_header()
#orig_nii.to_filename(niftifile)
meta = ds.NiftiWrapper(new_nii).meta_ext.to_json()
with open(infofile, 'wt') as fp:
fp.writelines(meta)
return niftifile, infofile
def embed_nifti(dcmfiles, niftifile, infofile, bids_info, force, min_meta):
"""
If `niftifile` doesn't exist, it gets created out of the `dcmfiles` stack,
and json representation of its meta_ext is returned (bug since should return
both niftifile and infofile?)
if `niftifile` exists, its affine's orientation information is used while
establishing new `NiftiImage` out of dicom stack and together with `bids_info`
(if provided) is dumped into json `infofile`
Parameters
----------
dcmfiles
niftifile
infofile
bids_info
force
min_meta
Returns
-------
niftifile, infofile
"""
# imports for nipype
import nibabel as nb
import os
import os.path as op
import json
import re
if not min_meta:
import dcmstack as ds
stack = ds.parse_and_stack(dcmfiles, force=force).values()
if len(stack) > 1:
raise ValueError('Found multiple series')
stack = stack[0]
#Create the nifti image using the data array
if not op.exists(niftifile):
nifti_image = stack.to_nifti(embed_meta=True)
nifti_image.to_filename(niftifile)
return ds.NiftiWrapper(nifti_image).meta_ext.to_json()
orig_nii = nb.load(niftifile)
aff = orig_nii.affine
ornt = nb.orientations.io_orientation(aff)
axcodes = nb.orientations.ornt2axcodes(ornt)
new_nii = stack.to_nifti(voxel_order=''.join(axcodes), embed_meta=True)
meta = ds.NiftiWrapper(new_nii).meta_ext.to_json()
meta_info = None if min_meta else json.loads(meta)
if bids_info:
if min_meta:
meta_info = bids_info
else:
# make nice with python 3 - same behavior?
meta_info = meta_info.copy()
meta_info.update(bids_info)
# meta_info = dict(meta_info.items() + bids_info.items())
try:
meta_info['TaskName'] = (re.search(
'(?<=_task-)\w+',
op.basename(infofile)).group(0).split('_')[0])
except AttributeError:
pass
# write to outfile
with open(infofile, 'wt') as fp:
json.dump(meta_info, fp, indent=3, sort_keys=True)
return niftifile, infofile