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Blur

Bases: IntensityTransform

Blur an image using a Gaussian filter.

The standard deviations \((\sigma_1, \sigma_2, \sigma_3)\) of the Gaussian kernel along each spatial axis are independently sampled from the given range. Sigmas are specified in mm and internally converted to voxels using the image spacing.

Parameters:

Name Type Description Default
std float | tuple[float, float]

Standard deviation of the Gaussian kernel in mm. A scalar \(x\) means \(\sigma_i = x\) for every axis (deterministic). A 2-tuple \((a, b)\) means \(\sigma_i \sim \mathcal{U}(a, b)\). A 6-tuple \((a_1, b_1, a_2, b_2, a_3, b_3)\) means \(\sigma_i \sim \mathcal{U}(a_i, b_i)\) independently. A Choice or Distribution may also be passed. The default std=0 is a no-op (and warns).

0.0
**kwargs Any

See Transform.

{}

Examples:

>>> import torchio as tio
>>> transform = tio.Blur(std=2.0)
>>> transform = tio.Blur(std=(0, 4))
Source code in src/torchio/transforms/intensity/blur.py
class Blur(IntensityTransform):
    r"""Blur an image using a Gaussian filter.

    The standard deviations $(\sigma_1, \sigma_2, \sigma_3)$ of the
    Gaussian kernel along each spatial axis are independently sampled
    from the given range.  Sigmas are specified in mm and internally
    converted to voxels using the image spacing.

    Args:
        std: Standard deviation of the Gaussian kernel in mm.
            A scalar $x$ means $\sigma_i = x$ for every axis
            (deterministic).
            A 2-tuple $(a, b)$ means
            $\sigma_i \sim \mathcal{U}(a, b)$.
            A 6-tuple $(a_1, b_1, a_2, b_2, a_3, b_3)$ means
            $\sigma_i \sim \mathcal{U}(a_i, b_i)$ independently.
            A `Choice` or `Distribution` may also be passed.
            The default `std=0` is a no-op (and warns).
        **kwargs: See [`Transform`][torchio.Transform].

    Examples:
        >>> import torchio as tio
        >>> transform = tio.Blur(std=2.0)
        >>> transform = tio.Blur(std=(0, 4))
    """

    def __init__(
        self,
        *,
        std: float | tuple[float, float] = 0.0,
        **kwargs: Any,
    ) -> None:
        super().__init__(**kwargs)
        self.std = to_nonneg_range(std)
        self._warn_if_noop(is_noop=self.std.is_constant(0.0), hint="std=(0, 2)")

    def make_params(self, batch: SubjectsBatch) -> dict[str, Any]:
        """Sample per-axis standard deviations (per element when batched)."""
        n = self._resolve_n(batch)
        if n is None:
            return {"std": self.std.sample()}
        keep = self._keep_mask(batch, n)
        std = self.std.sample(n)
        if keep is not None:
            std[~keep] = 0.0
        params = {"std": self._serialize_param(std)}
        self._tag_batched(params, batch, n, keep, ["std"])
        return params

    @property
    def supports_per_instance_params(self) -> bool:
        return True

    @property
    def supports_per_instance_p(self) -> bool:
        return True

    def apply_transform(
        self,
        batch: SubjectsBatch,
        params: dict[str, Any],
    ) -> SubjectsBatch:
        """Apply Gaussian smoothing to each selected image."""
        per_instance = self._is_per_instance_params(params)
        for _name, img_batch in self._get_images(batch).items():
            if per_instance:
                img_batch.data = _blur_per_element(img_batch, params["std"])
            else:
                spacing = np.asarray(img_batch.affines[0].spacing, dtype=np.float64)
                sigmas_vox = _sigmas_mm_to_voxels(params["std"], spacing)
                img_batch.data = _gaussian_smooth(img_batch.data, sigmas_vox)
        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
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)
    # When per-element gating is active, the transform handles the
    # probability itself (masked-out elements get identity params),
    # so skip the batch-wide coin flip here. Apply iff rand < p, so
    # p=0 is always a no-op and p=1 always applies.
    if not self._per_instance_p_active(batch) and 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, unless every element was gated out by
    # per-element probability: that is an exact no-op, and recording it
    # would let history replay (e.g. an invertible spatial transform)
    # trigger an unnecessary identity resample.
    if not _all_elements_gated_out(params):
        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
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
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)

Sample per-axis standard deviations (per element when batched).

Source code in src/torchio/transforms/intensity/blur.py
def make_params(self, batch: SubjectsBatch) -> dict[str, Any]:
    """Sample per-axis standard deviations (per element when batched)."""
    n = self._resolve_n(batch)
    if n is None:
        return {"std": self.std.sample()}
    keep = self._keep_mask(batch, n)
    std = self.std.sample(n)
    if keep is not None:
        std[~keep] = 0.0
    params = {"std": self._serialize_param(std)}
    self._tag_batched(params, batch, n, keep, ["std"])
    return params

apply_transform(batch, params)

Apply Gaussian smoothing to each selected image.

Source code in src/torchio/transforms/intensity/blur.py
def apply_transform(
    self,
    batch: SubjectsBatch,
    params: dict[str, Any],
) -> SubjectsBatch:
    """Apply Gaussian smoothing to each selected image."""
    per_instance = self._is_per_instance_params(params)
    for _name, img_batch in self._get_images(batch).items():
        if per_instance:
            img_batch.data = _blur_per_element(img_batch, params["std"])
        else:
            spacing = np.asarray(img_batch.affines[0].spacing, dtype=np.float64)
            sigmas_vox = _sigmas_mm_to_voxels(params["std"], spacing)
            img_batch.data = _gaussian_smooth(img_batch.data, sigmas_vox)
    return batch