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RemoveLabels

RemoveLabels

Bases: RemapLabels

Remove labels from a label map.

The removed labels are remapped to the background label.

This transformation is not invertible .

Parameters:

Name Type Description Default
labels Sequence[int]

A sequence of label integers that will be removed.

 required
background_label int

integer that specifies which label is considered to be background (typically, 0).

 0
masking_method TypeMaskingMethod

See RemapLabels.

 None
**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.

plot

Source code 
import torchio as tio
colin = tio.datasets.Colin27(2008)
label_map = colin.cls
colin.remove_image('t2')
colin.remove_image('pd')
names_to_remove = (
    'Fat',
    'Muscles',
    'Skin and Muscles',
    'Skull',
    'Fat 2',
    'Dura',
    'Marrow'
)
labels = [colin.NAME_TO_LABEL[name] for name in names_to_remove]
skull_stripping = tio.RemoveLabels(labels)
only_brain = skull_stripping(label_map)
colin.add_image(only_brain, 'brain')
colors = {
    0: (0, 0, 0),
    1: (127, 255, 212),
    2: (96, 204, 96),
    3: (240, 230, 140),
    4: (176, 48, 96),
    5: (48, 176, 96),
    6: (220, 247, 164),
    7: (103, 255, 255),
    9: (205, 62, 78),
    10: (238, 186, 243),
    11: (119, 159, 176),
    12: (220, 216, 20),
}
colin.plot(cmap_dict={'cls': colors, 'brain': colors})