feat: Add RandNonCentralChiNoise transform

.gitignore

@@ -165,3 +165,5 @@ runs
 *.pth
 
 *zarr/*
+
+monai-dev/

CHANGELOG.md

@@ -4,6 +4,8 @@ All notable changes to MONAI are documented in this file.
 The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/).
 
 ## [Unreleased]
+### Added
+* Added `RandNonCentralChiNoise` and `RandNonCentralChiNoised` for generalized Rician noise simulation in MRI.
 
 ## [1.5.1] - 2025-09-22
 

monai/transforms/__init__.py

@@ -117,6 +117,7 @@
     RandHistogramShift,
     RandIntensityRemap,
     RandKSpaceSpikeNoise,
+    RandNonCentralChiNoise,
     RandRicianNoise,
     RandScaleIntensity,
     RandScaleIntensityFixedMean,
@@ -202,6 +203,9 @@
     RandRicianNoised,
     RandRicianNoiseD,
     RandRicianNoiseDict,
+    RandNonCentralChiNoised,
+    RandNonCentralChiNoiseD,
+    RandNonCentralChiNoiseDict,
     RandScaleIntensityd,
     RandScaleIntensityD,
     RandScaleIntensityDict,

monai/transforms/intensity/array.py

@@ -41,6 +41,7 @@
 
 __all__ = [
     "RandGaussianNoise",
+    "RandNonCentralChiNoise",
     "RandRicianNoise",
     "ShiftIntensity",
     "RandShiftIntensity",
@@ -140,6 +141,110 @@ def __call__(self, img: NdarrayOrTensor, mean: float | None = None, randomize: b
         return img + noise
 
 
+class RandNonCentralChiNoise(RandomizableTransform):
+    """
+    Add non-central chi noise to an image.
+    This distribution is the square root of the sum of squares of k independent
+    Gaussian random variables, where one of the variables has a non-zero mean
+    (the signal).
+    This is a generalization of Rician noise. `degrees_of_freedom=2` is Rician noise.
+    See: https://en.wikipedia.org/wiki/Noncentral_chi_distribution and https://archive.ismrm.org/2024/3123_NZkvJdQat.html
+
+    Args:
+        prob: Probability to add noise.
+        mean: Mean or "centre" of the Gaussian noise distributions.
+        std: Standard deviation (spread) of the Gaussian noise distributions.
+        degrees_of_freedom: Number of Gaussian distributions (degrees of freedom).
+            `degrees_of_freedom=2` is Rician noise.
+        channel_wise: If True, treats each channel of the image separately.
+        relative: If True, the spread of the sampled Gaussian distributions will
+            be std times the standard deviation of the image or channel's intensity
+            histogram.
+        sample_std: If True, sample the spread of the Gaussian distributions
+            uniformly from 0 to std.
+        dtype: output data type, if None, same as input image. defaults to float32.
+
+    """
+
+    backend = [TransformBackends.TORCH, TransformBackends.NUMPY]
+
+    def __init__(
+        self,
+        prob: float = 0.1,
+        mean: Sequence[float] | float = 0.0,
+        std: Sequence[float] | float = 1.0,
+        degrees_of_freedom: int = 64, #64 default because typical modern brain MRI is 32 quadrature coils
+        channel_wise: bool = False,
+        relative: bool = False,
+        sample_std: bool = True,
+        dtype: DtypeLike = np.float32,
+    ) -> None:
+        RandomizableTransform.__init__(self, prob)
+        self.prob = prob
+        self.mean = mean
+        self.std = std
+        if not isinstance(degrees_of_freedom, int) or degrees_of_freedom < 1:
+            raise ValueError("degrees_of_freedom must be an integer >= 1.")
+        self.degrees_of_freedom = degrees_of_freedom
+        self.channel_wise = channel_wise
+        self.relative = relative
+        self.sample_std = sample_std
+        self.dtype = dtype
+
+    def _add_noise(self, img: NdarrayOrTensor, mean: float, std: float, k: int):
+        dtype_np = get_equivalent_dtype(img.dtype, np.ndarray)
+        im_shape = img.shape
+        _std = self.R.uniform(0, std) if self.sample_std else std
+
+        # Create a stack of k noise arrays
+        noise_shape = (k, *im_shape)
+        all_noises_np = self.R.normal(mean, _std, size=noise_shape).astype(dtype_np, copy=False)
+
+        if isinstance(img, torch.Tensor):
+            all_noises = torch.tensor(all_noises_np, device=img.device)
+            all_noises[0] = all_noises[0] + img
+            sum_sq = torch.sum(all_noises**2, dim=0)
+            return torch.sqrt(sum_sq)
+
+
+        all_noises_np[0] = all_noises_np[0] + img
+        sum_sq = np.sum(all_noises_np**2, axis=0)
+        return np.sqrt(sum_sq)
+
+    def __call__(self, img: NdarrayOrTensor, randomize: bool = True) -> NdarrayOrTensor:
+        """
+        Apply the transform to `img`.
+        """
+        img = convert_to_tensor(img, track_meta=get_track_meta(), dtype=self.dtype)
+        if randomize:
+            super().randomize(None)
+
+        if not self._do_transform:
+            return img
+
+        if self.channel_wise:
+            _mean = ensure_tuple_rep(self.mean, len(img))
+            _std = ensure_tuple_rep(self.std, len(img))
+            for i, d in enumerate(img):
+                img[i] = self._add_noise(
+                    d,
+                    mean=_mean[i],
+                    std=_std[i] * d.std() if self.relative else _std[i],
+                    k=self.degrees_of_freedom,
+                )
+        else:
+            if not isinstance(self.mean, (int, float)):
+                raise RuntimeError(f"If channel_wise is False, mean must be a float or int, got {type(self.mean)}.")
+            if not isinstance(self.std, (int, float)):
+                raise RuntimeError(f"If channel_wise is False, std must be a float or int, got {type(self.std)}.")
+            std = self.std * img.std().item() if self.relative else self.std
+            if not isinstance(std, (int, float)):
+                raise RuntimeError(f"std must be a float or int number, got {type(std)}.")
+            img = self._add_noise(img, mean=self.mean, std=std, k=self.degrees_of_freedom)
+        return img
+
+
+
 class RandRicianNoise(RandomizableTransform):
     """
     Add Rician noise to image.

monai/transforms/intensity/dictionary.py

@@ -48,6 +48,7 @@
     RandGibbsNoise,
     RandHistogramShift,
     RandKSpaceSpikeNoise,
+    RandNonCentralChiNoise,
     RandRicianNoise,
     RandScaleIntensity,
     RandScaleIntensityFixedMean,
@@ -69,6 +70,7 @@
 __all__ = [
     "RandGaussianNoised",
     "RandRicianNoised",
+    "RandNonCentralChiNoised",
     "ShiftIntensityd",
     "RandShiftIntensityd",
     "ScaleIntensityd",
@@ -236,6 +238,80 @@ def __call__(self, data: Mapping[Hashable, NdarrayOrTensor]) -> dict[Hashable, N
         return d
 
 
+class RandNonCentralChiNoised(RandomizableTransform, MapTransform):
+    """
+    Dictionary-based version :py:class:`monai.transforms.RandNonCentralChiNoise`.
+    Add non-central chi noise to image. This transform assumes all the expected fields have same shape, if want to add
+    different noise for every field, please use this transform separately.
+    This is a generalization of Rician noise. `degrees_of_freedom=2` is Rician noise.
+
+    Args:
+        keys: Keys of the corresponding items to be transformed.
+            See also: :py:class:`monai.transforms.compose.MapTransform`
+        prob: Probability to add non-central chi noise to the dictionary.
+        mean: Mean or "centre" of the Gaussian distributions sampled to make up
+            the noise.
+        std: Standard deviation (spread) of the Gaussian distributions sampled
+            to make up the noise.
+        degrees_of_freedom: Number of Gaussian distributions (degrees of freedom).
+            `degrees_of_freedom=2` is Rician noise.
+        channel_wise: If True, treats each channel of the image separately.
+        relative: If True, the spread of the sampled Gaussian distributions will
+            be std times the standard deviation of the image or channel's intensity
+            histogram.
+        sample_std: If True, sample the spread of the Gaussian distributions
+            uniformly from 0 to std.
+        dtype: output data type, if None, same as input image. defaults to float32.
+        allow_missing_keys: Don't raise exception if key is missing.
+    """
+
+    backend = RandNonCentralChiNoise.backend
+
+    def __init__(
+        self,
+        keys: KeysCollection,
+        prob: float = 0.1,
+        mean: Sequence[float] | float = 0.0,
+        std: Sequence[float] | float = 1.0,
+        degrees_of_freedom: int = 64,
+        channel_wise: bool = False,
+        relative: bool = False,
+        sample_std: bool = True,
+        dtype: DtypeLike = np.float32,
+        allow_missing_keys: bool = False,
+    ) -> None:
+        MapTransform.__init__(self, keys, allow_missing_keys)
+        RandomizableTransform.__init__(self, prob)
+        self.rand_non_central_chi_noise = RandNonCentralChiNoise(
+            prob=1.0,
+            mean=mean,
+            std=std,
+            degrees_of_freedom=degrees_of_freedom,
+            channel_wise=channel_wise,
+            relative=relative,
+            sample_std=sample_std,
+            dtype=dtype,
+        )
+
+    def set_random_state(
+        self, seed: int | None = None, state: np.random.RandomState | None = None
+    ) -> RandNonCentralChiNoised:
+        super().set_random_state(seed, state)
+        self.rand_non_central_chi_noise.set_random_state(seed, state)
+        return self
+
+    def __call__(self, data: Mapping[Hashable, NdarrayOrTensor]) -> dict[Hashable, NdarrayOrTensor]:
+        d = dict(data)
+        self.randomize(None)
+        if not self._do_transform:
+            for key in self.key_iterator(d):
+                d[key] = convert_to_tensor(d[key], track_meta=get_track_meta())
+            return d
+
+        for key in self.key_iterator(d):
+            d[key] = self.rand_non_central_chi_noise(d[key], randomize=True)
+        return d
+
 class RandRicianNoised(RandomizableTransform, MapTransform):
     """
     Dictionary-based version :py:class:`monai.transforms.RandRicianNoise`.
@@ -1953,6 +2029,7 @@ def __call__(self, data: Mapping[Hashable, NdarrayOrTensor]) -> dict[Hashable, N
 
 RandGaussianNoiseD = RandGaussianNoiseDict = RandGaussianNoised
 RandRicianNoiseD = RandRicianNoiseDict = RandRicianNoised
+RandNonCentralChiNoiseD = RandNonCentralChiNoiseDict = RandNonCentralChiNoised
 ShiftIntensityD = ShiftIntensityDict = ShiftIntensityd
 RandShiftIntensityD = RandShiftIntensityDict = RandShiftIntensityd
 StdShiftIntensityD = StdShiftIntensityDict = StdShiftIntensityd

tests/transforms/test_rand_noncentralchi_noise.py

@@ -0,0 +1,83 @@
+# Copyright (c) MONAI Consortium
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#     http://www.apache.org/licenses/LICENSE-2.0
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+from __future__ import annotations
+
+import unittest
+
+import numpy as np
+import torch
+from parameterized import parameterized
+
+from monai.transforms import RandNonCentralChiNoise
+from tests.test_utils import TEST_NDARRAYS, NumpyImageTestCase2D
+
+TESTS = []
+for p in TEST_NDARRAYS:
+    TESTS.append(("test_zero_mean", p, 0, 0.1))
+    TESTS.append(("test_non_zero_mean", p, 1, 0.5))
+
+
+class TestRandNonCentralChiNoise(NumpyImageTestCase2D):
+    @parameterized.expand(TESTS)
+    def test_correct_results(self, _, in_type, mean, std):
+        seed = 0
+        degrees_of_freedom = 64  #64 is common due to 32 channel head coil
+        noise_fn = RandNonCentralChiNoise(prob=1.0, mean=mean, std=std, degrees_of_freedom=degrees_of_freedom)
+        noise_fn.set_random_state(seed)
+        im = in_type(self.imt)
+        noised = noise_fn(im)
+        if isinstance(im, torch.Tensor):
+            self.assertEqual(im.dtype, noised.dtype)
+        np.random.seed(seed)
+        np.random.random()
+        _std = np.random.uniform(0, std)
+
+        noise_shape = (degrees_of_freedom, *self.imt.shape)
+        all_noises = np.random.normal(mean, _std, size=noise_shape).astype(np.float32)
+        all_noises[0] += self.imt
+        sum_sq = np.sum(all_noises**2, axis=0)
+        expected = np.sqrt(sum_sq)
+
+        if isinstance(noised, torch.Tensor):
+            noised = noised.cpu()
+        np.testing.assert_allclose(expected, noised, atol=1e-5)
+
+    @parameterized.expand(TESTS)
+    def test_correct_results_dof2(self, _, in_type, mean, std):
+        """
+        Test with k=2 (the Rician case)
+        """
+        seed = 0
+        degrees_of_freedom = 2
+        noise_fn = RandNonCentralChiNoise(prob=1.0, mean=mean, std=std, degrees_of_freedom=degrees_of_freedom)
+        noise_fn.set_random_state(seed)
+        im = in_type(self.imt)
+        noised = noise_fn(im)
+        if isinstance(im, torch.Tensor):
+            self.assertEqual(im.dtype, noised.dtype)
+
+        np.random.seed(seed)
+        np.random.random()  # for prob
+        _std = np.random.uniform(0, std)  # for sample_std
+        noise_shape = (degrees_of_freedom, *self.imt.shape)
+        all_noises = np.random.normal(mean, _std, size=noise_shape).astype(np.float32)
+        all_noises[0] += self.imt
+        sum_sq = np.sum(all_noises**2, axis=0)
+        expected = np.sqrt(sum_sq)
+
+        if isinstance(noised, torch.Tensor):
+            noised = noised.cpu()
+        np.testing.assert_allclose(expected, noised, atol=1e-5, rtol=1e-5)
+
+
+if __name__ == "__main__":
+    unittest.main()