Neuroimaging in Python — NiBabel 5.4.0.dev1+g3b1c7b37 documentation (original) (raw)

nifti2¶

Read / write access to NIfTI2 image format

Format described here:

Nifti2Image¶

class nibabel.nifti2.Nifti2Image(dataobj, affine, header=None, extra=None, file_map=None, dtype=None)¶

Bases: Nifti1Image

Class for single file NIfTI2 format image

Initialize image

The image is a combination of (array-like, affine matrix, header), with optional metadata in extra, and filename / file-like objects contained in the file_map mapping.

Parameters:

dataobjobject

Object containing image data. It should be some object that returns an array from np.asanyarray. It should have a shape attribute or property

affineNone or (4,4) array-like

homogeneous affine giving relationship between voxel coordinates and world coordinates. Affine can also be None. In this case,obj.affine also returns None, and the affine as written to disk will depend on the file format.

headerNone or mapping or header instance, optional

metadata for this image format

extraNone or mapping, optional

metadata to associate with image that cannot be stored in the metadata of this image type

file_mapmapping, optional

mapping giving file information for this image format

Notes

If both a header and an affine are specified, and the affine does not match the affine that is in the header, the affine will be used, but the sform_code and qform_code fields in the header will be re-initialised to their default values. This is performed on the basis that, if you are changing the affine, you are likely to be changing the space to which the affine is pointing. The set_sform() andset_qform() methods can be used to update the codes after an image has been created - see those methods, and the manual for more details.

__init__(dataobj, affine, header=None, extra=None, file_map=None, dtype=None)¶

Initialize image

The image is a combination of (array-like, affine matrix, header), with optional metadata in extra, and filename / file-like objects contained in the file_map mapping.

Parameters:

dataobjobject

Object containing image data. It should be some object that returns an array from np.asanyarray. It should have a shape attribute or property

affineNone or (4,4) array-like

homogeneous affine giving relationship between voxel coordinates and world coordinates. Affine can also be None. In this case,obj.affine also returns None, and the affine as written to disk will depend on the file format.

headerNone or mapping or header instance, optional

metadata for this image format

extraNone or mapping, optional

metadata to associate with image that cannot be stored in the metadata of this image type

file_mapmapping, optional

mapping giving file information for this image format

Notes

If both a header and an affine are specified, and the affine does not match the affine that is in the header, the affine will be used, but the sform_code and qform_code fields in the header will be re-initialised to their default values. This is performed on the basis that, if you are changing the affine, you are likely to be changing the space to which the affine is pointing. The set_sform() andset_qform() methods can be used to update the codes after an image has been created - see those methods, and the manual for more details.

alias of Nifti2Header

Nifti2Pair¶

class nibabel.nifti2.Nifti2Pair(dataobj, affine, header=None, extra=None, file_map=None, dtype=None)¶

Bases: Nifti1Pair

Class for NIfTI2 format image, header pair

Initialize image

The image is a combination of (array-like, affine matrix, header), with optional metadata in extra, and filename / file-like objects contained in the file_map mapping.

Parameters:

dataobjobject

Object containing image data. It should be some object that returns an array from np.asanyarray. It should have a shape attribute or property

affineNone or (4,4) array-like

homogeneous affine giving relationship between voxel coordinates and world coordinates. Affine can also be None. In this case,obj.affine also returns None, and the affine as written to disk will depend on the file format.

headerNone or mapping or header instance, optional

metadata for this image format

extraNone or mapping, optional

metadata to associate with image that cannot be stored in the metadata of this image type

file_mapmapping, optional

mapping giving file information for this image format

Notes

If both a header and an affine are specified, and the affine does not match the affine that is in the header, the affine will be used, but the sform_code and qform_code fields in the header will be re-initialised to their default values. This is performed on the basis that, if you are changing the affine, you are likely to be changing the space to which the affine is pointing. The set_sform() andset_qform() methods can be used to update the codes after an image has been created - see those methods, and the manual for more details.

__init__(dataobj, affine, header=None, extra=None, file_map=None, dtype=None)¶

Initialize image

The image is a combination of (array-like, affine matrix, header), with optional metadata in extra, and filename / file-like objects contained in the file_map mapping.

Parameters:

dataobjobject

Object containing image data. It should be some object that returns an array from np.asanyarray. It should have a shape attribute or property

affineNone or (4,4) array-like

homogeneous affine giving relationship between voxel coordinates and world coordinates. Affine can also be None. In this case,obj.affine also returns None, and the affine as written to disk will depend on the file format.

headerNone or mapping or header instance, optional

metadata for this image format

extraNone or mapping, optional

metadata to associate with image that cannot be stored in the metadata of this image type

file_mapmapping, optional

mapping giving file information for this image format

Notes

If both a header and an affine are specified, and the affine does not match the affine that is in the header, the affine will be used, but the sform_code and qform_code fields in the header will be re-initialised to their default values. This is performed on the basis that, if you are changing the affine, you are likely to be changing the space to which the affine is pointing. The set_sform() andset_qform() methods can be used to update the codes after an image has been created - see those methods, and the manual for more details.

alias of Nifti2PairHeader

load¶

nibabel.nifti2.load(filename)¶

Load NIfTI2 single or pair image from filename

Parameters:

filenamestr

filename of image to be loaded

Returns:

imgNifti2Image or Nifti2Pair

nifti2 single or pair image instance

Raises:

ImageFileError

if filename doesn’t look like nifti2;

OSError

if filename does not exist.

save¶

nibabel.nifti2.save(img, filename)¶

Save NIfTI2 single or pair to filename

Parameters:

filenamestr

filename to which to save image