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KeepLargestComponent

Bases: Transform

Keep only the largest connected component of each label.

For each specified label value, connected-component analysis is performed and all but the largest component are removed (set to the background value). This is useful for cleaning up noisy segmentation predictions.

Only single-channel LabelMap images are affected.

Parameters:

Name Type Description Default
labels Sequence[int] | None

Label values to filter. None means all non-zero labels found in the data.

 None
background_label int

Value used for removed components.

 0
fully_connected bool

If True, use 26-connectivity (voxels sharing a corner are connected). If False, use 6-connectivity (face-connected only).

 True
**kwargs Any

See Transform.

 {}

Raises:

Type Description
RuntimeError

If a label map has more than one channel.

Examples:

>>> import torchio as tio
>>> transform = tio.KeepLargestComponent()
>>> transform = tio.KeepLargestComponent(labels=[1, 2])
Source code in src/torchio/transforms/label/keep_largest.py 
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class KeepLargestComponent(Transform):
    r"""Keep only the largest connected component of each label.

    For each specified label value, connected-component analysis is
    performed and all but the largest component are removed (set to
    the background value).  This is useful for cleaning up noisy
    segmentation predictions.

    Only single-channel [`LabelMap`][torchio.LabelMap] images are
    affected.

    Args:
        labels: Label values to filter.  `None` means all non-zero
            labels found in the data.
        background_label: Value used for removed components.
        fully_connected: If `True`, use 26-connectivity (voxels
            sharing a corner are connected).  If `False`, use
            6-connectivity (face-connected only).
        **kwargs: See [`Transform`][torchio.Transform].

    Raises:
        RuntimeError: If a label map has more than one channel.

    Examples:
        >>> import torchio as tio
        >>> transform = tio.KeepLargestComponent()
        >>> transform = tio.KeepLargestComponent(labels=[1, 2])
    """

    def __init__(
        self,
        labels: Sequence[int] | None = None,
        *,
        background_label: int = 0,
        fully_connected: bool = True,
        **kwargs: Any,
    ) -> None:
        super().__init__(**kwargs)
        self.labels = list(labels) if labels is not None else None
        self.background_label = background_label
        self.fully_connected = fully_connected

    def make_params(self, batch: SubjectsBatch) -> dict[str, Any]:
        """No random parameters."""
        return {}

    def apply_transform(
        self,
        batch: SubjectsBatch,
        params: dict[str, Any],
    ) -> SubjectsBatch:
        """Keep only the largest connected component per label."""
        for _name, img_batch in batch.images.items():
            if not issubclass(img_batch._image_class, LabelMap):
                continue
            b, c = img_batch.data.shape[:2]
            if c != 1:
                msg = (
                    "KeepLargestComponent requires single-channel"
                    f" label maps, got {c} channels"
                )
                raise RuntimeError(msg)
            for i in range(b):
                img_batch.data[i, 0] = _keep_largest_per_label(
                    img_batch.data[i, 0],
                    labels=self.labels,
                    background_label=self.background_label,
                    fully_connected=self.fully_connected,
                )
        return batch

invertible property

Whether this transform can be inverted.

forward(data) 

forward(data: Subject) -> Subject

forward(data: Image) -> Image

forward(data: Tensor) -> Tensor

forward(data: np.ndarray) -> np.ndarray

forward(data: sitk.Image) -> sitk.Image

forward(data: nib.Nifti1Image) -> nib.Nifti1Image

forward(data: dict) -> dict

forward(data: ImagesBatch) -> ImagesBatch

forward(data: SubjectsBatch) -> SubjectsBatch

Apply the transform.

The output type always matches the input type.

Parameters:

Name Type Description Default
data Any

Input data to transform.

 required
Source code in src/torchio/transforms/transform.py 
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def forward(self, data: Any) -> Any:
    """Apply the transform.

    The output type always matches the input type.

    Args:
        data: Input data to transform.
    """
    if self.copy:
        data = _copy.deepcopy(data)
    batch, unwrap = self._wrap(data)
    if torch.rand(1).item() > self.p:
        return unwrap(batch)
    params = self.make_params(batch)
    batch = self.apply_transform(batch, params)
    # Record history on the batch
    trace = AppliedTransform(name=type(self).__name__, params=params)
    if not hasattr(batch, "applied_transforms"):
        batch.applied_transforms = []
    batch.applied_transforms.append(trace)
    result = unwrap(batch)
    # Propagate history to outputs that can carry it
    if (
        hasattr(batch, "applied_transforms")
        and not isinstance(result, (SubjectsBatch, Tensor, np.ndarray))
        and not isinstance(result, dict)
    ):
        with contextlib.suppress(AttributeError):
            result.applied_transforms = list(batch.applied_transforms)
    return result

inverse(params)

Return a transform that undoes this one.

Override in invertible subclasses. The returned transform, when applied, reverses the effect of the forward pass with the given parameters.

Parameters:

Name Type Description Default
params dict[str, Any]

The parameters recorded in the forward pass.

 required

Returns:

Type Description
Transform

A new Transform instance that inverts this one.
Source code in src/torchio/transforms/transform.py 
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def inverse(self, params: dict[str, Any]) -> Transform:
    """Return a transform that undoes this one.

    Override in invertible subclasses. The returned transform,
    when applied, reverses the effect of the forward pass with
    the given parameters.

    Args:
        params: The parameters recorded in the forward pass.

    Returns:
        A new `Transform` instance that inverts this one.
    """
    msg = f"{type(self).__name__} is not invertible"
    raise NotImplementedError(msg)

to_hydra()

Export as a Hydra-compatible config dict.

Returns a dict with _target_ set to the fully qualified class name and only non-default field values included.

Returns:

Type Description
dict[str, Any]

Dict suitable for hydra.utils.instantiate().
Source code in src/torchio/transforms/transform.py 
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def to_hydra(self) -> dict[str, Any]:
    """Export as a Hydra-compatible config dict.

    Returns a dict with `_target_` set to the fully qualified
    class name and only non-default field values included.

    Returns:
        Dict suitable for `hydra.utils.instantiate()`.
    """
    from .parameter_range import _ParameterRange

    cls = type(self)
    target = f"torchio.{cls.__qualname__}"
    cfg: dict[str, Any] = {"_target_": target}

    for name, default in _collect_init_params(cls).items():
        value = getattr(self, name, default)
        if isinstance(value, _ParameterRange):
            if value._original == default:
                continue
            value = _hydra_value(value._original)
        elif value == default:
            continue
        else:
            value = _hydra_value(value)
        cfg[name] = value
    return cfg

make_params(batch)

No random parameters.

Source code in src/torchio/transforms/label/keep_largest.py 
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def make_params(self, batch: SubjectsBatch) -> dict[str, Any]:
    """No random parameters."""
    return {}

apply_transform(batch, params)

Keep only the largest connected component per label.

Source code in src/torchio/transforms/label/keep_largest.py 
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def apply_transform(
    self,
    batch: SubjectsBatch,
    params: dict[str, Any],
) -> SubjectsBatch:
    """Keep only the largest connected component per label."""
    for _name, img_batch in batch.images.items():
        if not issubclass(img_batch._image_class, LabelMap):
            continue
        b, c = img_batch.data.shape[:2]
        if c != 1:
            msg = (
                "KeepLargestComponent requires single-channel"
                f" label maps, got {c} channels"
            )
            raise RuntimeError(msg)
        for i in range(b):
            img_batch.data[i, 0] = _keep_largest_per_label(
                img_batch.data[i, 0],
                labels=self.labels,
                background_label=self.background_label,
                fully_connected=self.fully_connected,
            )
    return batch