def embed_dicom_and_nifti_metadata(dcmfiles, niftifile, infofile, bids_info):
"""Embed metadata from nifti (affine etc) and dicoms into infofile (json)
`niftifile` should exist. 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: dict
Additional metadata to be embedded. `infofile` is overwritten if exists,
so here you could pass some metadata which would overload (at the first
level of the dict structure, no recursive fancy updates) what is obtained
from nifti and dicoms
"""
# imports for nipype
import nibabel as nb
import os.path as op
import json
import re
from heudiconv.utils import save_json
from heudiconv.external.dcmstack import ds
stack = ds.parse_and_stack(dcmfiles, force=True).values()
if len(stack) > 1:
raise ValueError('Found multiple series')
# may be odict now - iter to be safe
stack = next(iter(stack))
if not op.exists(niftifile):
raise NotImplementedError(
"%s does not exist. "
"We are not producing new nifti files here any longer. "
"Use dcm2niix directly or .convert.nipype_convert helper ."
% niftifile
)
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_info = ds.NiftiWrapper(new_nii).meta_ext.to_json()
meta_info = json.loads(meta_info)
if bids_info:
meta_info.update(bids_info)
# write to outfile
save_json(infofile, meta_info)
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
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