def _hdr_from_mapping(hdr=None, mapping=None, endianness=native_code):
''' Fill `hdr` from mapping `mapping`, with given endianness '''
if hdr is None:
# passed a valid mapping as header? Copy and return
if isinstance(mapping, np.ndarray):
test_dtype = mapping.dtype.newbyteorder('=')
if test_dtype in (header_1_dtype, header_2_dtype):
return mapping.copy()
# otherwise make a new empty header. If no version specified,
# go for default (2)
if mapping is None:
version = 2
else:
version = mapping.get('version', 2)
hdr = empty_header(endianness, version)
if mapping is None:
return hdr
if isinstance(mapping, np.ndarray):
mapping = rec2dict(mapping)
for key, value in mapping.items():
hdr[key] = value
# check header values
if np.asscalar(hdr['id_string'])[:5] != asbytes('TRACK'):
raise HeaderError('Expecting TRACK as first '
'5 characaters of id_string')
if hdr['version'] not in (1, 2):
raise HeaderError('Reader only supports version 1')
if hdr['hdr_size'] != 1000:
raise HeaderError('hdr_size should be 1000')
return hdr
def _hdr_from_mapping(hdr=None, mapping=None, endianness=native_code):
''' Fill `hdr` from mapping `mapping`, with given endianness '''
if hdr is None:
# passed a valid mapping as header? Copy and return
if isinstance(mapping, np.ndarray):
test_dtype = mapping.dtype.newbyteorder('=')
if test_dtype in (header_1_dtype, header_2_dtype):
return mapping.copy()
# otherwise make a new empty header. If no version specified,
# go for default (2)
if mapping is None:
version = 2
else:
version = mapping.get('version', 2)
hdr = empty_header(endianness, version)
if mapping is None:
return hdr
if isinstance(mapping, np.ndarray):
mapping = rec2dict(mapping)
for key, value in mapping.items():
hdr[key] = value
# check header values
if np.asscalar(hdr['id_string'])[:5] != asbytes('TRACK'):
raise HeaderError('Expecting TRACK as first '
'5 characaters of id_string')
if hdr['version'] not in (1, 2):
raise HeaderError('Reader only supports version 1')
if hdr['hdr_size'] != 1000:
raise HeaderError('hdr_size should be 1000')
return hdr
def transform_to_trackvis_voxmm(streams, header):
from nibabel.volumeutils import rec2dict
from nibabel.streamlines.trk import get_affine_rasmm_to_trackvis
from dipy.tracking.utils import move_streamlines
header = rec2dict(header)
header['voxel_sizes'] = header['voxel_size']
header['voxel_to_rasmm'] = header['vox_to_ras']
header['dimensions'] = header['dim']
affine = get_affine_rasmm_to_trackvis(header)
streams = move_streamlines(streams, affine)
return streams
def transform_to_trackvis_voxmm(streams, header):
from nibabel.volumeutils import rec2dict
from nibabel.streamlines.trk import get_affine_rasmm_to_trackvis
from dipy.tracking.utils import move_streamlines
header = rec2dict(header)
header['voxel_sizes'] = header['voxel_size']
header['voxel_to_rasmm'] = header['vox_to_ras']
header['dimensions'] = header['dim']
affine = get_affine_rasmm_to_trackvis(header)
streams = move_streamlines(streams, affine)
return streams
