Implementation of intensity clipping transform: bot hard and soft approaches

docs/source/transforms.rst

@@ -309,6 +309,12 @@ Intensity
     :members:
     :special-members: __call__
 
+`ClipIntensityPercentiles`
+""""""""""""""""""""""""""
+.. autoclass:: ClipIntensityPercentiles
+    :members:
+    :special-members: __call__
+
 `RandScaleIntensity`
 """"""""""""""""""""
 .. image:: https://raw.githubusercontent.com/Project-MONAI/DocImages/main/transforms/RandScaleIntensity.png
@@ -1405,6 +1411,12 @@ Intensity (Dict)
     :members:
     :special-members: __call__
 
+`ClipIntensityPercentilesd`
+"""""""""""""""""""""""""""
+.. autoclass:: ClipIntensityPercentilesd
+    :members:
+    :special-members: __call__
+
 `RandScaleIntensityd`
 """""""""""""""""""""
 .. image:: https://raw.githubusercontent.com/Project-MONAI/DocImages/main/transforms/RandScaleIntensityd.png

monai/transforms/__init__.py

@@ -92,6 +92,7 @@
 from .croppad.functional import crop_func, crop_or_pad_nd, pad_func, pad_nd
 from .intensity.array import (
     AdjustContrast,
+    ClipIntensityPercentiles,
     ComputeHoVerMaps,
     DetectEnvelope,
     ForegroundMask,
@@ -135,6 +136,9 @@
     AdjustContrastd,
     AdjustContrastD,
     AdjustContrastDict,
+    ClipIntensityPercentilesd,
+    ClipIntensityPercentilesD,
+    ClipIntensityPercentilesDict,
     ComputeHoVerMapsd,
     ComputeHoVerMapsD,
     ComputeHoVerMapsDict,

monai/transforms/intensity/array.py

@@ -30,7 +30,7 @@
 from monai.data.utils import get_random_patch, get_valid_patch_size
 from monai.networks.layers import GaussianFilter, HilbertTransform, MedianFilter, SavitzkyGolayFilter
 from monai.transforms.transform import RandomizableTransform, Transform
-from monai.transforms.utils import Fourier, equalize_hist, is_positive, rescale_array
+from monai.transforms.utils import Fourier, equalize_hist, is_positive, rescale_array, soft_clip
 from monai.transforms.utils_pytorch_numpy_unification import clip, percentile, where
 from monai.utils.enums import TransformBackends
 from monai.utils.misc import ensure_tuple, ensure_tuple_rep, ensure_tuple_size, fall_back_tuple
@@ -54,6 +54,7 @@
     "NormalizeIntensity",
     "ThresholdIntensity",
     "ScaleIntensityRange",
+    "ClipIntensityPercentiles",
     "AdjustContrast",
     "RandAdjustContrast",
     "ScaleIntensityRangePercentiles",
@@ -1007,6 +1008,151 @@ def __call__(self, img: NdarrayOrTensor) -> NdarrayOrTensor:
         return ret
 
 
+class ClipIntensityPercentiles(Transform):
+    """
+    Apply clip based on the intensity distribution of input image.
+    If `sharpness_factor` is provided, the intensity values will be soft clipped according to
+    f(x) = x + (1/sharpness_factor)*softplus(- c(x - minv)) - (1/sharpness_factor)*softplus(c(x - maxv))
+    From https://medium.com/life-at-hopper/clip-it-clip-it-good-1f1bf711b291
+
+    Soft clipping preserves the order of the values and maintains the gradient everywhere.
+    For example:
+
+    .. code-block:: python
+        :emphasize-lines: 11, 22
+
+        image = torch.Tensor(
+            [[[1, 2, 3, 4, 5],
+              [1, 2, 3, 4, 5],
+              [1, 2, 3, 4, 5],
+              [1, 2, 3, 4, 5],
+              [1, 2, 3, 4, 5],
+              [1, 2, 3, 4, 5]]])
+
+        # Hard clipping from lower and upper image intensity percentiles
+        hard_clipper = ClipIntensityPercentiles(30, 70)
+        print(hard_clipper(image))
+        metatensor([[[2., 2., 3., 4., 4.],
+                [2., 2., 3., 4., 4.],
+                [2., 2., 3., 4., 4.],
+                [2., 2., 3., 4., 4.],
+                [2., 2., 3., 4., 4.],
+                [2., 2., 3., 4., 4.]]])
+
+
+        # Soft clipping from lower and upper image intensity percentiles
+        soft_clipper = ClipIntensityPercentiles(30, 70, 10.)
+        print(soft_clipper(image))
+        metatensor([[[2.0000, 2.0693, 3.0000, 3.9307, 4.0000],
+         [2.0000, 2.0693, 3.0000, 3.9307, 4.0000],
+         [2.0000, 2.0693, 3.0000, 3.9307, 4.0000],
+         [2.0000, 2.0693, 3.0000, 3.9307, 4.0000],
+         [2.0000, 2.0693, 3.0000, 3.9307, 4.0000],
+         [2.0000, 2.0693, 3.0000, 3.9307, 4.0000]]])
+
+    See Also:
+
+        - :py:class:`monai.transforms.ScaleIntensityRangePercentiles`
+    """
+
+    backend = [TransformBackends.TORCH, TransformBackends.NUMPY]
+
+    def __init__(
+        self,
+        lower: float | None,
+        upper: float | None,
+        sharpness_factor: float | None = None,
+        channel_wise: bool = False,
+        return_clipping_values: bool = False,
+        dtype: DtypeLike = np.float32,
+    ) -> None:
+        """
+        Args:
+            lower: lower intensity percentile. In the case of hard clipping, None will have the same effect as 0 by
+                not clipping the lowest input values. However, in the case of soft clipping, None and zero will have
+                two different effects: None will not apply clipping to low values, whereas zero will still transform
+                the lower values according to the soft clipping transformation. Please check for more details:
+                https://medium.com/life-at-hopper/clip-it-clip-it-good-1f1bf711b291.
+            upper: upper intensity percentile.  The same as for lower, but this time with the highest values. If we
+                are looking to perform soft clipping, if None then there will be no effect on this side whereas if set
+                to 100, the values will be passed via the corresponding clipping equation.
+            sharpness_factor: if not None, the intensity values will be soft clipped according to
+                f(x) = x + (1/sharpness_factor)*softplus(- c(x - minv)) - (1/sharpness_factor)*softplus(c(x - maxv)).
+                defaults to None.
+            channel_wise: if True, compute intensity percentile and normalize every channel separately.
+                default to False.
+            return_clipping_values: whether to return the calculated percentiles in tensor meta information.
+                If soft clipping and requested percentile is None, return None as the corresponding clipping
+                values in meta information. Clipping values are stored in a list with each element corresponding
+                to a channel if channel_wise is set to True. defaults to False.
+            dtype: output data type, if None, same as input image. defaults to float32.
+        """
+        if lower is None and upper is None:
+            raise ValueError("lower or upper percentiles must be provided")
+        if lower is not None and (lower < 0.0 or lower > 100.0):
+            raise ValueError("Percentiles must be in the range [0, 100]")
+        if upper is not None and (upper < 0.0 or upper > 100.0):
+            raise ValueError("Percentiles must be in the range [0, 100]")
+        if upper is not None and lower is not None and upper < lower:
+            raise ValueError("upper must be greater than or equal to lower")
+        if sharpness_factor is not None and sharpness_factor <= 0:
+            raise ValueError("sharpness_factor must be greater than 0")
+
+        self.lower = lower
+        self.upper = upper
+        self.sharpness_factor = sharpness_factor
+        self.channel_wise = channel_wise
+        if return_clipping_values:
+            self.clipping_values: list[tuple[float | None, float | None]] = []
+        self.return_clipping_values = return_clipping_values
+        self.dtype = dtype
+
+    def _clip(self, img: NdarrayOrTensor) -> NdarrayOrTensor:
+        if self.sharpness_factor is not None:
+            lower_percentile = percentile(img, self.lower) if self.lower is not None else None
+            upper_percentile = percentile(img, self.upper) if self.upper is not None else None
+            img = soft_clip(img, self.sharpness_factor, lower_percentile, upper_percentile, self.dtype)
+        else:
+            lower_percentile = percentile(img, self.lower) if self.lower is not None else percentile(img, 0)
+            upper_percentile = percentile(img, self.upper) if self.upper is not None else percentile(img, 100)
+            img = clip(img, lower_percentile, upper_percentile)
+
+        if self.return_clipping_values:
+            self.clipping_values.append(
+                (
+                    (
+                        lower_percentile
+                        if lower_percentile is None
+                        else lower_percentile.item() if hasattr(lower_percentile, "item") else lower_percentile
+                    ),
+                    (
+                        upper_percentile
+                        if upper_percentile is None
+                        else upper_percentile.item() if hasattr(upper_percentile, "item") else upper_percentile
+                    ),
+                )
+            )
+        img = convert_to_tensor(img, track_meta=False)
+        return img
+
+    def __call__(self, img: NdarrayOrTensor) -> NdarrayOrTensor:
+        """
+        Apply the transform to `img`.
+        """
+        img = convert_to_tensor(img, track_meta=get_track_meta())
+        img_t = convert_to_tensor(img, track_meta=False)
+        if self.channel_wise:
+            img_t = torch.stack([self._clip(img=d) for d in img_t])  # type: ignore
+        else:
+            img_t = self._clip(img=img_t)
+
+        img = convert_to_dst_type(img_t, dst=img)[0]
+        if self.return_clipping_values:
+            img.meta["clipping_values"] = self.clipping_values  # type: ignore
+
+        return img
+
+
 class AdjustContrast(Transform):
     """
     Changes image intensity with gamma transform. Each pixel/voxel intensity is updated as::

monai/transforms/intensity/dictionary.py

@@ -26,6 +26,7 @@
 from monai.data.meta_obj import get_track_meta
 from monai.transforms.intensity.array import (
     AdjustContrast,
+    ClipIntensityPercentiles,
     ComputeHoVerMaps,
     ForegroundMask,
     GaussianSharpen,
@@ -77,6 +78,7 @@
     "NormalizeIntensityd",
     "ThresholdIntensityd",
     "ScaleIntensityRanged",
+    "ClipIntensityPercentilesd",
     "AdjustContrastd",
     "RandAdjustContrastd",
     "ScaleIntensityRangePercentilesd",
@@ -122,6 +124,8 @@
     "ThresholdIntensityDict",
     "ScaleIntensityRangeD",
     "ScaleIntensityRangeDict",
+    "ClipIntensityPercentilesD",
+    "ClipIntensityPercentilesDict",
     "AdjustContrastD",
     "AdjustContrastDict",
     "RandAdjustContrastD",
@@ -886,6 +890,36 @@ def __call__(self, data: Mapping[Hashable, NdarrayOrTensor]) -> dict[Hashable, N
         return d
 
 
+class ClipIntensityPercentilesd(MapTransform):
+    """
+    Dictionary-based wrapper of :py:class:`monai.transforms.ClipIntensityPercentiles`.
+    Clip the intensity values of input image to a specific range based on the intensity distribution of the input.
+    If `sharpness_factor` is provided, the intensity values will be soft clipped according to
+    f(x) = x + (1/sharpness_factor) * softplus(- c(x - minv)) - (1/sharpness_factor)*softplus(c(x - maxv))
+    """
+
+    def __init__(
+        self,
+        keys: KeysCollection,
+        lower: float | None,
+        upper: float | None,
+        sharpness_factor: float | None = None,
+        channel_wise: bool = False,
+        dtype: DtypeLike = np.float32,
+        allow_missing_keys: bool = False,
+    ) -> None:
+        super().__init__(keys, allow_missing_keys)
+        self.scaler = ClipIntensityPercentiles(
+            lower=lower, upper=upper, sharpness_factor=sharpness_factor, channel_wise=channel_wise, dtype=dtype
+        )
+
+    def __call__(self, data: dict) -> dict:
+        d = dict(data)
+        for key in self.key_iterator(d):
+            d[key] = self.scaler(d[key])
+        return d
+
+
 class AdjustContrastd(MapTransform):
     """
     Dictionary-based wrapper of :py:class:`monai.transforms.AdjustContrast`.
@@ -1929,6 +1963,7 @@ def __call__(self, data: Mapping[Hashable, NdarrayOrTensor]) -> dict[Hashable, N
 NormalizeIntensityD = NormalizeIntensityDict = NormalizeIntensityd
 ThresholdIntensityD = ThresholdIntensityDict = ThresholdIntensityd
 ScaleIntensityRangeD = ScaleIntensityRangeDict = ScaleIntensityRanged
+ClipIntensityPercentilesD = ClipIntensityPercentilesDict = ClipIntensityPercentilesd
 AdjustContrastD = AdjustContrastDict = AdjustContrastd
 RandAdjustContrastD = RandAdjustContrastDict = RandAdjustContrastd
 ScaleIntensityRangePercentilesD = ScaleIntensityRangePercentilesDict = ScaleIntensityRangePercentilesd

monai/transforms/utils.py

@@ -38,6 +38,7 @@
     nonzero,
     ravel,
     searchsorted,
+    softplus,
     unique,
     unravel_index,
     where,
@@ -131,9 +132,45 @@
     "resolves_modes",
     "has_status_keys",
     "distance_transform_edt",
+    "soft_clip",
 ]
 
 
+def soft_clip(
+    arr: NdarrayOrTensor,
+    sharpness_factor: float = 1.0,
+    minv: NdarrayOrTensor | float | int | None = None,
+    maxv: NdarrayOrTensor | float | int | None = None,
+    dtype: DtypeLike | torch.dtype = np.float32,
+) -> NdarrayOrTensor:
+    """
+    Apply soft clip to the input array or tensor.
+    The intensity values will be soft clipped according to
+    f(x) = x + (1/sharpness_factor)*softplus(- c(x - minv)) - (1/sharpness_factor)*softplus(c(x - maxv))
+    From https://medium.com/life-at-hopper/clip-it-clip-it-good-1f1bf711b291
+
+    To perform one-sided clipping, set either minv or maxv to None.
+    Args:
+        arr: input array to clip.
+        sharpness_factor: the sharpness of the soft clip function, default to 1.
+        minv: minimum value of target clipped array.
+        maxv: maximum value of target clipped array.
+        dtype: if not None, convert input array to dtype before computation.
+
+    """
+
+    if dtype is not None:
+        arr, *_ = convert_data_type(arr, dtype=dtype)
+
+    v = arr
+    if minv is not None:
+        v = v + softplus(-sharpness_factor * (arr - minv)) / sharpness_factor
+    if maxv is not None:
+        v = v - softplus(sharpness_factor * (arr - maxv)) / sharpness_factor
+
+    return v
+
+
 def rand_choice(prob: float = 0.5) -> bool:
     """
     Returns True if a randomly chosen number is less than or equal to `prob`, by default this is a 50/50 chance.

monai/transforms/utils_pytorch_numpy_unification.py

@@ -52,9 +52,24 @@
     "median",
     "mean",
     "std",
+    "softplus",
 ]
 
 
+def softplus(x: NdarrayOrTensor) -> NdarrayOrTensor:
+    """stable softplus through `np.logaddexp` with equivalent implementation for torch.
+
+    Args:
+        x: array/tensor.
+
+    Returns:
+        Softplus of the input.
+    """
+    if isinstance(x, np.ndarray):
+        return np.logaddexp(np.zeros_like(x), x)
+    return torch.logaddexp(torch.zeros_like(x), x)
+
+
 def allclose(a: NdarrayTensor, b: NdarrayOrTensor, rtol=1e-5, atol=1e-8, equal_nan=False) -> bool:
     """`np.allclose` with equivalent implementation for torch."""
     b, *_ = convert_to_dst_type(b, a, wrap_sequence=True)