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ENH: Update NIfTI header dimensions for CIFTI-2 compliance #929

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ENH: Update NIfTI header dimensions for CIFTI-2 compliance #929

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7 changes: 7 additions & 0 deletions nibabel/cifti2/cifti2.py
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Original file line number Diff line number Diff line change
Expand Up @@ -19,6 +19,7 @@
import re
from collections.abc import MutableSequence, MutableMapping, Iterable
from collections import OrderedDict
import numpy as np
from .. import xmlutils as xml
from ..filebasedimages import FileBasedHeader
from ..dataobj_images import DataobjImage
Expand Down Expand Up @@ -1484,8 +1485,14 @@ def update_headers(self):
>>> img.update_headers()
>>> img.nifti_header.get_data_shape() == (2, 3, 4)
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Suggested change
>>> img.nifti_header.get_data_shape() == (2, 3, 4)
>>> img.nifti_header.get_data_shape() == (1, 1, 1, 1, 2, 3, 4)

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this breaks the current API, is that fine?

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In what sense? Does it change img.shape? If so, we should divorce Cifti2Image.shape from Cifti2Image.nifti_header.get_data_shape().

True
>>> np.array_equal(img.nifti_header['dim'], [7, 1, 1, 1, 1, 2, 3, 4])
True
"""
self._nifti_header.set_data_shape(self._dataobj.shape)
_dims = np.ones((8), dtype=int)
_dims[0] = 7 if len(self._dataobj.shape) == 3 else 6
_dims[5:8] = (self._dataobj.shape + (1,))[:3]
self._nifti_header['dim'] = _dims
Comment on lines 1491 to +1495
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Updating the input to set_data_shape() ought to do the trick.

Suggested change
self._nifti_header.set_data_shape(self._dataobj.shape)
_dims = np.ones((8), dtype=int)
_dims[0] = 7 if len(self._dataobj.shape) == 3 else 6
_dims[5:8] = (self._dataobj.shape + (1,))[:3]
self._nifti_header['dim'] = _dims
self._nifti_header.set_data_shape((1, 1, 1, 1) + self._dataobj.shape)

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this isn't equivalent though? dim[0] should be either 6 or 7

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dim0 indicates the length of dim[1:8]. This wlll be determined by this tuple.


def get_data_dtype(self):
return self._nifti_header.get_data_dtype()
Expand Down