def setQForm(self, m, code='scanner'):
"""Sets the qform matrix.
The supplied value has to be a 4x4 matrix. The matrix will be converted
to float.
The inverse qform matrix and the quaternion representation will be
automatically recalculated.
:Parameters:
m: 4x4 ndarray
The qform matrix.
code: str | `NIFTI_XFORM_CODE` | int (0..4)
The type of the coordinate system the qform matrix is describing.
By default this coordinate system is assumed to be the scanner
space. Please refer to the
:meth:`~nifti.format.NiftiFormat.setXFormCode` method for a
full list of possible codes and their meaning.
.. seealso::
:meth:`~nifti.format.NiftiFormat.getQForm`,
:meth:`~nifti.format.NiftiFormat.setQFormCode`,
:meth:`~nifti.format.NiftiFormat.getQFormCode`,
:meth:`~nifti.format.NiftiFormat.getQuaternion`,
:meth:`~nifti.format.NiftiFormat.getQOffset`,
:meth:`~nifti.format.NiftiFormat.setQuaternion`,
:meth:`~nifti.format.NiftiFormat.setQOffset`,
:meth:`~nifti.format.NiftiFormat.setQFac`,
:attr:`~nifti.format.NiftiFormat.qform`,
:attr:`~nifti.format.NiftiFormat.qform_inv`,
:attr:`~nifti.format.NiftiFormat.qform_code`,
:attr:`~nifti.format.NiftiFormat.quatern`,
:attr:`~nifti.format.NiftiFormat.qoffset`,
:attr:`~nifti.format.NiftiFormat.qfac`
"""
if m.shape != (4, 4):
raise ValueError, "QForm matrix has to be of size 4x4."
# make sure it is float
m = m.astype('float')
ncl.set_mat44( self.__nimg.qto_xyz,
m[0,0], m[0,1], m[0,2], m[0,3],
m[1,0], m[1,1], m[1,2], m[1,3],
m[2,0], m[2,1], m[2,2], m[2,3],
m[3,0], m[3,1], m[3,2], m[3,3] )
# recalculate inverse
self.__nimg.qto_ijk = \
ncl.nifti_mat44_inverse( self.__nimg.qto_xyz )
# update quaternions
( self.__nimg.quatern_b, self.__nimg.quatern_c, self.__nimg.quatern_d,
self.__nimg.qoffset_x, self.__nimg.qoffset_y, self.__nimg.qoffset_z,
self.__nimg.dx, self.__nimg.dy, self.__nimg.dz,
self.__nimg.qfac ) = \
ncl.nifti_mat44_to_quatern( self.__nimg.qto_xyz )
# set qform code, which decides how the qform matrix is interpreted
self.setXFormCode('qform', code)
def setSForm(self, m, code='mni152'):
"""Sets the sform matrix.
The supplied value has to be a 4x4 matrix. The matrix elements will be
converted to floats. By definition the last row of the sform matrix has
to be (0,0,0,1). However, different values can be assigned, but will
not be stored when the NIfTI image is saved to a file.
The inverse sform matrix will be automatically recalculated.
:Parameters:
m: 4x4 ndarray
The sform matrix.
code: str | `NIFTI_XFORM_CODE` | int (0..4)
The type of the coordinate system the sform matrix is describing.
By default this coordinate system is assumed to be the MNI152
space. Please refer to the
:meth:`~nifti.format.NiftiFormat.setXFormCode` method for a
full list of possible codes and their meaning.
.. seealso::
:meth:`~nifti.format.NiftiFormat.getSForm`,
:meth:`~nifti.format.NiftiFormat.setSFormCode`,
:meth:`~nifti.format.NiftiFormat.getSFormCode`,
:attr:`~nifti.format.NiftiFormat.sform`,
:attr:`~nifti.format.NiftiFormat.sform_code`
"""
if m.shape != (4, 4):
raise ValueError, "SForm matrix has to be of size 4x4."
# make sure it is float
m = m.astype('float')
ncl.set_mat44( self.__nimg.sto_xyz,
m[0,0], m[0,1], m[0,2], m[0,3],
m[1,0], m[1,1], m[1,2], m[1,3],
m[2,0], m[2,1], m[2,2], m[2,3],
m[3,0], m[3,1], m[3,2], m[3,3] )
# recalculate inverse
self.__nimg.sto_ijk = \
ncl.nifti_mat44_inverse( self.__nimg.sto_xyz )
# set sform code, which decides how the sform matrix is interpreted
self.setXFormCode('sform', code)
def __updateQFormFromQuaternion(self):
"""Recalculates the qform matrix (and the inverse) from the quaternion
representation.
.. warning::
This is an internal method. Neither its availability nor its API is
guarenteed.
"""
# recalculate qform
self.__nimg.qto_xyz = ncl.nifti_quatern_to_mat44 (
self.__nimg.quatern_b, self.__nimg.quatern_c, self.__nimg.quatern_d,
self.__nimg.qoffset_x, self.__nimg.qoffset_y, self.__nimg.qoffset_z,
self.__nimg.dx, self.__nimg.dy, self.__nimg.dz,
self.__nimg.qfac )
# recalculate inverse
self.__nimg.qto_ijk = \
ncl.nifti_mat44_inverse( self.__nimg.qto_xyz )