Class RemoveSmallObjects

monai/transforms/post/array.py:365–450

Use `skimage.morphology.remove_small_objects` to remove small objects from images. See: https://scikit-image.org/docs/dev/api/skimage.morphology.html#remove-small-objects. Data should be one-hotted. Args: min_size: objects smaller than this size (in number of voxels; or su

class RemoveSmallObjects(Transform):
    """
    Use `skimage.morphology.remove_small_objects` to remove small objects from images.
    See: https://scikit-image.org/docs/dev/api/skimage.morphology.html#remove-small-objects.

    Data should be one-hotted.

    Args:
        min_size: objects smaller than this size (in number of voxels; or surface area/volume value
            in whatever units your image is if by_measure is True) are removed.
        connectivity: Maximum number of orthogonal hops to consider a pixel/voxel as a neighbor.
            Accepted values are ranging from  1 to input.ndim. If ``None``, a full
            connectivity of ``input.ndim`` is used. For more details refer to linked scikit-image
            documentation.
        independent_channels: Whether or not to consider channels as independent. If true, then
            conjoining islands from different labels will be removed if they are below the threshold.
            If false, the overall size islands made from all non-background voxels will be used.
        by_measure: Whether the specified min_size is in number of voxels. if this is True then min_size
            represents a surface area or volume value of whatever units your image is in (mm^3, cm^2, etc.)
            default is False. e.g. if min_size is 3, by_measure is True and the units of your data is mm,
            objects smaller than 3mm^3 are removed.
        pixdim: the pixdim of the input image. if a single number, this is used for all axes.
            If a sequence of numbers, the length of the sequence must be equal to the image dimensions.

    Example::

        .. code-block:: python

            from monai.transforms import RemoveSmallObjects, Spacing, Compose
            from monai.data import MetaTensor

            data1 = torch.tensor([[[0, 0, 0, 0, 0], [0, 1, 1, 0, 1], [0, 0, 0, 1, 1]]])
            affine = torch.as_tensor([[2,0,0,0],
                                      [0,1,0,0],
                                      [0,0,1,0],
                                      [0,0,0,1]], dtype=torch.float64)
            data2 = MetaTensor(data1, affine=affine)

            # remove objects smaller than 3mm^3, input is MetaTensor
            trans = RemoveSmallObjects(min_size=3, by_measure=True)
            out = trans(data2)
            # remove objects smaller than 3mm^3, input is not MetaTensor
            trans = RemoveSmallObjects(min_size=3, by_measure=True, pixdim=(2, 1, 1))
            out = trans(data1)

            # remove objects smaller than 3 (in pixel)
            trans = RemoveSmallObjects(min_size=3)
            out = trans(data2)

            # If the affine of the data is not identity, you can also add Spacing before.
            trans = Compose([
                Spacing(pixdim=(1, 1, 1)),
                RemoveSmallObjects(min_size=3)
            ])

    """

    backend = [TransformBackends.NUMPY]