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Mask

Mask

Bases: IntensityTransform

Set voxels outside of mask to a constant value.

Parameters:

Name Type Description Default
masking_method TypeMaskingMethod

See NormalizationTransform.

 required
outside_value float

Value to set for all voxels outside of the mask.

 0
labels Sequence[int] | None

If a label map is used to generate the mask, sequence of labels to consider. If None, all values larger than zero will be used for the mask.

 None
**kwargs

See Transform for additional keyword arguments.

 {}

Raises:

Type Description
RuntimeWarning

If a 4D image is masked with a 3D mask, the mask will be expanded along the channels (first) dimension, and a warning will be raised.

Examples:

>>> import torchio as tio
>>> subject = tio.datasets.Colin27()
>>> subject
Colin27(Keys: ('t1', 'head', 'brain'); images: 3)
>>> mask = tio.Mask(masking_method='brain')  # Use "brain" image to mask
>>> transformed = mask(subject)  # Set voxels outside of the brain to 0

__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.

arguments_are_dict()

Check if main arguments are dict.

Return True if the type of all attributes specified in the args_names have dict type.

plot

Source code 
import torchio as tio
subject = tio.datasets.Colin27()
subject.remove_image('head')
mask = tio.Mask('brain')
masked = mask(subject)
subject.add_image(masked.t1, 'Masked')
subject.plot()