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ToOrientation

ToOrientation

Bases: SpatialTransform

Reorient the data to a specified orientation.

This transform reorders the voxels and modifies the affine matrix to match the specified orientation code. The image intensity values are not modified, and the sample locations in the scanner space are preserved.

Common orientation codes include:

  • 'RAS' (neurological convention):
    • The first axis goes from Left to Right (R).
    • The second axis goes from Posterior to Anterior (A).
    • The third axis goes from Inferior to Superior (S).
  • 'LAS' (radiological convention):
    • The first axis goes from Right to Left (L).
    • The second axis goes from Posterior to Anterior (A).
    • The third axis goes from Inferior to Superior (S).

See NiBabel docs about image orientation for more information.

Parameters:

Name Type Description Default
orientation str

A three-letter orientation code. Examples: 'RAS', 'LAS', 'LPS', 'PLS', 'SLP'. The code must contain one character for each axis direction: R or L, A or P, and S or I.

 'RAS'
**kwargs

See Transform for additional keyword arguments.

 {}

__call__(data)

Transform data and return a result of the same type.

Parameters:

Name Type Description Default
data InputType

Instance of torchio.Subject, 4D torch.Tensor or numpy.ndarray with dimensions \((C, W, H, D)\), where \(C\) is the number of channels and \(W, H, D\) are the spatial dimensions. If the input is a tensor, the affine matrix will be set to identity. Other valid input types are a SimpleITK image, a torchio.Image, a NiBabel Nifti1 image or a dict. The output type is the same as the input type.

 required

get_base_args()

Provides easy access to the arguments used to instantiate the base class (Transform) of any transform.

This method is particularly useful when a new transform can be represented as a variant of an existing transform (e.g. all random transforms), allowing for seamless instantiation of the existing transform with the same arguments as the new transform during apply_transform.

Note

The p argument (probability of applying the transform) is excluded to avoid multiplying the probability of both existing and new transform.

add_base_args(arguments, overwrite_on_existing=False)

Add the init args to existing arguments

validate_keys_sequence(keys, name) staticmethod

Ensure that the input is not a string but a sequence of strings.

to_hydra_config()

Return a dictionary representation of the transform for Hydra instantiation.