Commit e4acefd6 authored by Paul McCarthy's avatar Paul McCarthy 🚵
Browse files

ENH: New Nifti.adjust method for adjusting a header shape/pixdim

parent 127e2dfd
......@@ -839,6 +839,69 @@ class Nifti(notifier.Notifier, meta.Meta):
return code
def adjust(self, pixdim=None, shape=None, origin=None):
"""Return a new ``Nifti`` object with the specified ``pixdim``
or ``shape``. The affine is of the new ``Nifti`` is adjusted
Only one of ``pixdim`` or ``shape`` can be specified.
The default behaviour of the ``origin`` argument (``'centre'``) causes
the corner voxel of the output to have the same centre as the corner
voxel of the input. If the origin is ``'corner'``, an offset is
applied which effectively causes the origin corners of the voxel grids
of the input and output to be aligned.
:arg pixdim: New voxel dimensions
:arg shape: New image shape
:arg origin: Voxel grid alignment - either ``'centre'`` (the default)
or ``'corner'``
:returns: A new ``Nifti`` object based on this one, with adjusted
pixdims, shape and affine.
if ((pixdim is not None) and (shape is not None)) or \
((pixdim is None) and (shape is None)):
raise ValueError('Exactly one of pixdim or '
'shape must be specified')
newShape = shape
newPixdim = pixdim
# if pixdims were specified,
# convert them into a shape
if newPixdim is not None:
npixdim = len(newPixdim)
newPixdim = np.array(newPixdim)
oldShape = np.array(self.shape[ :npixdim])
oldPixdim = np.array(self.pixdim[:npixdim])
newShape = oldShape * (oldPixdim / newPixdim)
# pad shape to full dimensions
if len(newShape) != 3:
raise ValueError('Three dimensions must be specified')
# Rescale the voxel-to-world affine
xform = affine.rescale(oldShape, newShape, origin)
xform = affine.concat(self.getAffine('voxel', 'world'), xform)
# Now that we've got our spatial
# scaling/offset matrix, pad the
# new shape/pixdims with those
# from any non-spatial dimensions
newShape = list(newShape) + list(self.shape[ 3:])
newPixdim = list(newPixdim) + list(self.pixdim[3:])
# And create the new header
# and we're away
header = self.header.copy()
header.set_zooms( newPixdim)
header.set_sform( xform)
header.set_qform( xform)
return Nifti(header)
class Image(Nifti):
"""Class which represents a NIFTI image. Internally, the image is
loaded/stored using a :mod:`nibabel.nifti1.Nifti1Image` or
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