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FIX: Set TRK byte order to little-endian before filling values #782

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Merged
merged 3 commits into from
Aug 2, 2019
Merged

FIX: Set TRK byte order to little-endian before filling values #782

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71f29d3
FIX: Set TRK byte order to < before filling values
effigies Jul 30, 2019
2434adb
DOCTEST: Display system endianness-neutral representation of <i2
effigies Jul 30, 2019
927b6ce
ENH: Pass endianness as parameter to TrkFile._default_structarr
effigies Jul 31, 2019
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4 changes: 2 additions & 2 deletions nibabel/brikhead.py
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Original file line number Diff line number Diff line change
Expand Up @@ -295,8 +295,8 @@ def __init__(self, info):
--------
>>> fname = os.path.join(datadir, 'example4d+orig.HEAD')
>>> header = AFNIHeader(parse_AFNI_header(fname))
>>> header.get_data_dtype()
dtype('int16')
>>> header.get_data_dtype().str
'<i2'
>>> header.get_zooms()
(3.0, 3.0, 3.0, 3.0)
>>> header.get_data_shape()
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16 changes: 10 additions & 6 deletions nibabel/streamlines/trk.py
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Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@

from nibabel.openers import Opener
from nibabel.py3k import asstr
from nibabel.volumeutils import (native_code, swapped_code)
from nibabel.volumeutils import (native_code, swapped_code, endian_codes)
from nibabel.orientations import (aff2axcodes, axcodes2ornt)

from .array_sequence import create_arraysequences_from_generator
Expand Down Expand Up @@ -266,10 +266,14 @@ def is_correct_format(cls, fileobj):
return magic_number == cls.MAGIC_NUMBER

@classmethod
def _default_structarr(cls):
def _default_structarr(cls, endianness=None):
""" Return an empty compliant TRK header as numpy structured array
"""
st_arr = np.zeros((), dtype=header_2_dtype)
dt = header_2_dtype
if endianness is not None:
endianness = endian_codes[endianness]
dt = dt.newbyteorder(endianness)
st_arr = np.zeros((), dtype=dt)

# Default values
st_arr[Field.MAGIC_NUMBER] = cls.MAGIC_NUMBER
Expand All @@ -283,10 +287,10 @@ def _default_structarr(cls):
return st_arr

@classmethod
def create_empty_header(cls):
def create_empty_header(cls, endianness=None):
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I added this in passing, since it's the only other place _default_structarr is being called.

""" Return an empty compliant TRK header as dict
"""
st_arr = cls._default_structarr()
st_arr = cls._default_structarr(endianness)
return dict(zip(st_arr.dtype.names, st_arr.tolist()))

@classmethod
Expand Down Expand Up @@ -396,7 +400,7 @@ def save(self, fileobj):
of the TRK header data).
"""
# Enforce little-endian byte order for header
header = self._default_structarr().newbyteorder('<')
header = self._default_structarr(endianness='little')

# Override hdr's fields by those contained in `header`.
for k, v in self.header.items():
Expand Down