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nibabel.spm99analyze.Spm99AnalyzeHeader

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class nibabel.spm99analyze.Spm99AnalyzeHeader(binaryblock=None, endianness=None, check=True)

Adds origin functionality to base SPM header

Initialize header from binary data block

Parameters :

binaryblock : {None, string} optional

binary block to set into header. By default, None, in which case we insert the default empty header block

endianness : {None, ‘<’,’>’, other endian code} string, optional

endianness of the binaryblock. If None, guess endianness from the data.

check : bool, optional

Whether to check content of header in initialization. Default is True.

Examples

>>> hdr1 = AnalyzeHeader() # an empty header
>>> hdr1.endianness == native_code
True
>>> hdr1.get_data_shape()
(0,)
>>> hdr1.set_data_shape((1,2,3)) # now with some content
>>> hdr1.get_data_shape()
(1, 2, 3)

We can set the binary block directly via this initialization. Here we get it from the header we have just made

>>> binblock2 = hdr1.binaryblock
>>> hdr2 = AnalyzeHeader(binblock2)
>>> hdr2.get_data_shape()
(1, 2, 3)

Empty headers are native endian by default

>>> hdr2.endianness == native_code
True

You can pass valid opposite endian headers with the endianness parameter. Even empty headers can have endianness

>>> hdr3 = AnalyzeHeader(endianness=swapped_code)
>>> hdr3.endianness == swapped_code
True

If you do not pass an endianness, and you pass some data, we will try to guess from the passed data.

>>> binblock3 = hdr3.binaryblock
>>> hdr4 = AnalyzeHeader(binblock3)
>>> hdr4.endianness == swapped_code
True
get_best_affine()

Get affine from header, using SPM origin field if sensible

The default translations are got from the origin field, if set, or from the center of the image otherwise.

Examples

>>> hdr = Spm99AnalyzeHeader()
>>> hdr.set_data_shape((3, 5, 7))
>>> hdr.set_zooms((3, 2, 1))
>>> hdr.default_x_flip
True
>>> hdr.get_origin_affine() # from center of image
array([[-3.,  0.,  0.,  3.],
       [ 0.,  2.,  0., -4.],
       [ 0.,  0.,  1., -3.],
       [ 0.,  0.,  0.,  1.]])
>>> hdr['origin'][:3] = [3,4,5]
>>> hdr.get_origin_affine() # using origin
array([[-3.,  0.,  0.,  6.],
       [ 0.,  2.,  0., -6.],
       [ 0.,  0.,  1., -4.],
       [ 0.,  0.,  0.,  1.]])
>>> hdr['origin'] = 0 # unset origin
>>> hdr.set_data_shape((3, 5, 7))
>>> hdr.get_origin_affine() # from center of image
array([[-3.,  0.,  0.,  3.],
       [ 0.,  2.,  0., -4.],
       [ 0.,  0.,  1., -3.],
       [ 0.,  0.,  0.,  1.]])
get_origin_affine()

Get affine from header, using SPM origin field if sensible

The default translations are got from the origin field, if set, or from the center of the image otherwise.

Examples

>>> hdr = Spm99AnalyzeHeader()
>>> hdr.set_data_shape((3, 5, 7))
>>> hdr.set_zooms((3, 2, 1))
>>> hdr.default_x_flip
True
>>> hdr.get_origin_affine() # from center of image
array([[-3.,  0.,  0.,  3.],
       [ 0.,  2.,  0., -4.],
       [ 0.,  0.,  1., -3.],
       [ 0.,  0.,  0.,  1.]])
>>> hdr['origin'][:3] = [3,4,5]
>>> hdr.get_origin_affine() # using origin
array([[-3.,  0.,  0.,  6.],
       [ 0.,  2.,  0., -6.],
       [ 0.,  0.,  1., -4.],
       [ 0.,  0.,  0.,  1.]])
>>> hdr['origin'] = 0 # unset origin
>>> hdr.set_data_shape((3, 5, 7))
>>> hdr.get_origin_affine() # from center of image
array([[-3.,  0.,  0.,  3.],
       [ 0.,  2.,  0., -4.],
       [ 0.,  0.,  1., -3.],
       [ 0.,  0.,  0.,  1.]])
set_origin_from_affine(affine)

Set SPM origin to header from affine matrix.

The origin field was read but not written by SPM99 and 2. It was used for storing a central voxel coordinate, that could be used in aligning the image to some standard position - a proxy for a full translation vector that was usually stored in a separate matlab .mat file.

Nifti uses the space occupied by the SPM origin field for important other information (the transform codes), so writing the origin will make the header a confusing Nifti file. If you work with both Analyze and Nifti, you should probably avoid doing this.

Parameters :

affine : array-like, shape (4,4)

Affine matrix to set

Returns :

None :

Examples

>>> hdr = Spm99AnalyzeHeader()
>>> hdr.set_data_shape((3, 5, 7))
>>> hdr.set_zooms((3,2,1))
>>> hdr.get_origin_affine()
array([[-3.,  0.,  0.,  3.],
       [ 0.,  2.,  0., -4.],
       [ 0.,  0.,  1., -3.],
       [ 0.,  0.,  0.,  1.]])
>>> affine = np.diag([3,2,1,1])
>>> affine[:3,3] = [-6, -6, -4]
>>> hdr.set_origin_from_affine(affine)
>>> np.all(hdr['origin'][:3] == [3,4,5])
True
>>> hdr.get_origin_affine()
array([[-3.,  0.,  0.,  6.],
       [ 0.,  2.,  0., -6.],
       [ 0.,  0.,  1., -4.],
       [ 0.,  0.,  0.,  1.]])