nibabel.spatialimages

A simple spatial image class

The image class maintains the association between a 3D (or greater) array, and an affine transform that maps voxel coordinates to some world space. It also has a header - some standard set of meta-data that is specific to the image format, and extra - a dictionary container for any other metadata.

It has attributes:

  • extra

methods:

  • .get_fdata()

  • .get_data() (deprecated, use get_fdata() instead)

  • .get_affine() (deprecated, use affine property instead)

  • .get_header() (deprecated, use header property instead)

  • .to_filename(fname) - writes data to filename(s) derived from fname, where the derivation may differ between formats.

  • to_file_map() - save image to files with which the image is already associated.

  • .get_shape() (deprecated)

properties:

  • shape

  • affine

  • header

  • dataobj

classmethods:

  • from_filename(fname) - make instance by loading from filename

  • from_file_map(fmap) - make instance from file map

  • instance_to_filename(img, fname) - save img instance to filename fname.

You cannot slice an image, and trying to slice an image generates an informative TypeError.

There are several ways of writing data.

There is the usual way, which is the default:

img.to_filename(fname)

and that is, to take the data encapsulated by the image and cast it to the datatype the header expects, setting any available header scaling into the header to help the data match.

You can load the data into an image from file with:

img.from_filename(fname)

The image stores its associated files in its file_map attribute. In order to just save an image, for which you know there is an associated filename, or other storage, you can do:

img.to_file_map()

You can get the data out again with:

img.get_fdata()

Less commonly, for some image types that support it, you might want to fetch out the unscaled array via the object containing the data:

unscaled_data = img.dataoobj.get_unscaled()

Analyze-type images (including nifti) support this, but others may not (MINC, for example).

Sometimes you might to avoid any loss of precision by making the data type the same as the input:

hdr = img.header
hdr.set_data_dtype(data.dtype)
img.to_filename(fname)

Files interface

The image has an attribute file_map. This is a mapping, that has keys corresponding to the file types that an image needs for storage. For example, the Analyze data format needs an image and a header file type for storage:

>>> import nibabel as nib
>>> data = np.arange(24, dtype='f4').reshape((2,3,4))
>>> img = nib.AnalyzeImage(data, np.eye(4))
>>> sorted(img.file_map)
['header', 'image']

The values of file_map are not in fact files but objects with attributes filename, fileobj and pos.

The reason for this interface, is that the contents of files has to contain enough information so that an existing image instance can save itself back to the files pointed to in file_map. When a file holder holds active file-like objects, then these may be affected by the initial file read; in this case, the contains file-like objects need to carry the position at which a write (with to_files) should place the data. The file_map contents should therefore be such, that this will work:

>>> # write an image to files
>>> from io import BytesIO
>>> import nibabel as nib
>>> file_map = nib.AnalyzeImage.make_file_map()
>>> file_map['image'].fileobj = BytesIO()
>>> file_map['header'].fileobj = BytesIO()
>>> img = nib.AnalyzeImage(data, np.eye(4))
>>> img.file_map = file_map
>>> img.to_file_map()
>>> # read it back again from the written files
>>> img2 = nib.AnalyzeImage.from_file_map(file_map)
>>> np.all(img2.get_fdata(dtype=np.float32) == data)
True
>>> # write, read it again
>>> img2.to_file_map()
>>> img3 = nib.AnalyzeImage.from_file_map(file_map)
>>> np.all(img3.get_fdata(dtype=np.float32) == data)
True

Functions

supported_np_types(obj)

Numpy data types that instance obj supports

Classes

Header(*args, **kwargs)

Alias for SpatialHeader; kept for backwards compatibility.

SpatialFirstSlicer(img)

Slicing interface that returns a new image with an updated affine

SpatialHeader([data_dtype, shape, zooms])

Template class to implement header protocol

SpatialImage(dataobj, affine[, header, ...])

Template class for volumetric (3D/4D) images

Exceptions

HeaderDataError

Class to indicate error in getting or setting header data

HeaderTypeError

Class to indicate error in parameters into header functions

ImageDataError