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| """ |
| A collection of dictionary-based wrappers around the "vanilla" transforms for intensity adjustment |
| defined in :py:class:`monai.transforms.intensity.array`. |
| |
| Class names are ended with 'd' to denote dictionary-based transforms. |
| """ |
|
|
| from __future__ import annotations |
|
|
| from typing import Callable, Hashable, Mapping, Sequence |
|
|
| import numpy as np |
|
|
| from monai.config import DtypeLike, KeysCollection |
| from monai.config.type_definitions import NdarrayOrTensor |
| from monai.data.meta_obj import get_track_meta |
| from monai.transforms.intensity.array import ( |
| AdjustContrast, |
| ClipIntensityPercentiles, |
| ComputeHoVerMaps, |
| ForegroundMask, |
| GaussianSharpen, |
| GaussianSmooth, |
| GibbsNoise, |
| HistogramNormalize, |
| KSpaceSpikeNoise, |
| MaskIntensity, |
| MedianSmooth, |
| NormalizeIntensity, |
| RandAdjustContrast, |
| RandBiasField, |
| RandCoarseDropout, |
| RandCoarseShuffle, |
| RandGaussianNoise, |
| RandGaussianSharpen, |
| RandGaussianSmooth, |
| RandGibbsNoise, |
| RandHistogramShift, |
| RandKSpaceSpikeNoise, |
| RandRicianNoise, |
| RandScaleIntensity, |
| RandScaleIntensityFixedMean, |
| RandShiftIntensity, |
| RandStdShiftIntensity, |
| SavitzkyGolaySmooth, |
| ScaleIntensity, |
| ScaleIntensityRange, |
| ScaleIntensityRangePercentiles, |
| ShiftIntensity, |
| StdShiftIntensity, |
| ThresholdIntensity, |
| ) |
| from monai.transforms.transform import MapTransform, RandomizableTransform |
| from monai.transforms.utils import is_positive |
| from monai.utils import convert_to_tensor, ensure_tuple, ensure_tuple_rep |
| from monai.utils.enums import PostFix |
|
|
| __all__ = [ |
| "RandGaussianNoised", |
| "RandRicianNoised", |
| "ShiftIntensityd", |
| "RandShiftIntensityd", |
| "ScaleIntensityd", |
| "RandScaleIntensityd", |
| "StdShiftIntensityd", |
| "RandStdShiftIntensityd", |
| "RandBiasFieldd", |
| "NormalizeIntensityd", |
| "ThresholdIntensityd", |
| "ScaleIntensityRanged", |
| "ClipIntensityPercentilesd", |
| "AdjustContrastd", |
| "RandAdjustContrastd", |
| "ScaleIntensityRangePercentilesd", |
| "MaskIntensityd", |
| "SavitzkyGolaySmoothd", |
| "MedianSmoothd", |
| "GaussianSmoothd", |
| "RandGaussianSmoothd", |
| "GaussianSharpend", |
| "RandGaussianSharpend", |
| "GibbsNoised", |
| "RandGibbsNoised", |
| "KSpaceSpikeNoised", |
| "RandKSpaceSpikeNoised", |
| "RandHistogramShiftd", |
| "RandCoarseDropoutd", |
| "RandCoarseShuffled", |
| "HistogramNormalized", |
| "ForegroundMaskd", |
| "ComputeHoVerMapsd", |
| "RandGaussianNoiseD", |
| "RandGaussianNoiseDict", |
| "ShiftIntensityD", |
| "ShiftIntensityDict", |
| "RandShiftIntensityD", |
| "RandShiftIntensityDict", |
| "ScaleIntensityD", |
| "ScaleIntensityDict", |
| "StdShiftIntensityD", |
| "StdShiftIntensityDict", |
| "RandScaleIntensityD", |
| "RandScaleIntensityDict", |
| "RandScaleIntensityFixedMeand", |
| "RandScaleIntensityFixedMeanDict", |
| "RandScaleIntensityFixedMeanD", |
| "RandStdShiftIntensityD", |
| "RandStdShiftIntensityDict", |
| "RandBiasFieldD", |
| "RandBiasFieldDict", |
| "NormalizeIntensityD", |
| "NormalizeIntensityDict", |
| "ThresholdIntensityD", |
| "ThresholdIntensityDict", |
| "ScaleIntensityRangeD", |
| "ScaleIntensityRangeDict", |
| "ClipIntensityPercentilesD", |
| "ClipIntensityPercentilesDict", |
| "AdjustContrastD", |
| "AdjustContrastDict", |
| "RandAdjustContrastD", |
| "RandAdjustContrastDict", |
| "ScaleIntensityRangePercentilesD", |
| "ScaleIntensityRangePercentilesDict", |
| "MaskIntensityD", |
| "MaskIntensityDict", |
| "SavitzkyGolaySmoothD", |
| "SavitzkyGolaySmoothDict", |
| "MedianSmoothD", |
| "MedianSmoothDict", |
| "GaussianSmoothD", |
| "GaussianSmoothDict", |
| "RandGaussianSmoothD", |
| "RandGaussianSmoothDict", |
| "GaussianSharpenD", |
| "GaussianSharpenDict", |
| "RandGaussianSharpenD", |
| "RandGaussianSharpenDict", |
| "GibbsNoiseD", |
| "GibbsNoiseDict", |
| "RandGibbsNoiseD", |
| "RandGibbsNoiseDict", |
| "KSpaceSpikeNoiseD", |
| "KSpaceSpikeNoiseDict", |
| "RandHistogramShiftD", |
| "RandHistogramShiftDict", |
| "RandRicianNoiseD", |
| "RandRicianNoiseDict", |
| "RandCoarseDropoutD", |
| "RandCoarseDropoutDict", |
| "RandCoarseShuffleD", |
| "RandCoarseShuffleDict", |
| "HistogramNormalizeD", |
| "HistogramNormalizeDict", |
| "RandKSpaceSpikeNoiseD", |
| "RandKSpaceSpikeNoiseDict", |
| "ForegroundMaskD", |
| "ForegroundMaskDict", |
| "ComputeHoVerMapsD", |
| "ComputeHoVerMapsDict", |
| ] |
|
|
| DEFAULT_POST_FIX = PostFix.meta() |
|
|
|
|
| class RandGaussianNoised(RandomizableTransform, MapTransform): |
| """ |
| Dictionary-based version :py:class:`monai.transforms.RandGaussianNoise`. |
| Add Gaussian noise to image. This transform assumes all the expected fields have same shape, if you want to add |
| different noise for every field, please use this transform separately. |
| |
| Args: |
| keys: keys of the corresponding items to be transformed. |
| See also: :py:class:`monai.transforms.compose.MapTransform` |
| prob: Probability to add Gaussian noise. |
| mean: Mean or “centre” of the distribution. |
| std: Standard deviation (spread) of distribution. |
| dtype: output data type, if None, same as input image. defaults to float32. |
| allow_missing_keys: don't raise exception if key is missing. |
| sample_std: If True, sample the spread of the Gaussian distribution uniformly from 0 to std. |
| """ |
|
|
| backend = RandGaussianNoise.backend |
|
|
| def __init__( |
| self, |
| keys: KeysCollection, |
| prob: float = 0.1, |
| mean: float = 0.0, |
| std: float = 0.1, |
| dtype: DtypeLike = np.float32, |
| allow_missing_keys: bool = False, |
| sample_std: bool = True, |
| ) -> None: |
| MapTransform.__init__(self, keys, allow_missing_keys) |
| RandomizableTransform.__init__(self, prob) |
| self.rand_gaussian_noise = RandGaussianNoise(mean=mean, std=std, prob=1.0, dtype=dtype, sample_std=sample_std) |
|
|
| def set_random_state( |
| self, seed: int | None = None, state: np.random.RandomState | None = None |
| ) -> RandGaussianNoised: |
| super().set_random_state(seed, state) |
| self.rand_gaussian_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 |
|
|
| |
| first_key: Hashable = self.first_key(d) |
| if first_key == (): |
| for key in self.key_iterator(d): |
| d[key] = convert_to_tensor(d[key], track_meta=get_track_meta()) |
| return d |
|
|
| self.rand_gaussian_noise.randomize(d[first_key]) |
|
|
| for key in self.key_iterator(d): |
| d[key] = self.rand_gaussian_noise(img=d[key], randomize=False) |
| return d |
|
|
|
|
| class RandRicianNoised(RandomizableTransform, MapTransform): |
| """ |
| Dictionary-based version :py:class:`monai.transforms.RandRicianNoise`. |
| Add Rician 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. |
| |
| Args: |
| keys: Keys of the corresponding items to be transformed. |
| See also: :py:class:`monai.transforms.compose.MapTransform` |
| prob: Probability to add Rician noise to the dictionary. |
| mean: Mean or "centre" of the Gaussian distributions sampled to make up |
| the Rician noise. |
| std: Standard deviation (spread) of the Gaussian distributions sampled |
| to make up the 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 = RandRicianNoise.backend |
|
|
| def __init__( |
| self, |
| keys: KeysCollection, |
| prob: float = 0.1, |
| mean: Sequence[float] | float = 0.0, |
| std: Sequence[float] | float = 1.0, |
| 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_rician_noise = RandRicianNoise( |
| prob=1.0, |
| mean=mean, |
| std=std, |
| 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) -> RandRicianNoised: |
| super().set_random_state(seed, state) |
| self.rand_rician_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_rician_noise(d[key], randomize=True) |
| return d |
|
|
|
|
| class ShiftIntensityd(MapTransform): |
| """ |
| Dictionary-based wrapper of :py:class:`monai.transforms.ShiftIntensity`. |
| """ |
|
|
| backend = ShiftIntensity.backend |
|
|
| def __init__( |
| self, |
| keys: KeysCollection, |
| offset: float, |
| safe: bool = False, |
| factor_key: str | None = None, |
| meta_keys: KeysCollection | None = None, |
| meta_key_postfix: str = DEFAULT_POST_FIX, |
| allow_missing_keys: bool = False, |
| ) -> None: |
| """ |
| Args: |
| keys: keys of the corresponding items to be transformed. |
| See also: :py:class:`monai.transforms.compose.MapTransform` |
| offset: offset value to shift the intensity of image. |
| safe: if `True`, then do safe dtype convert when intensity overflow. default to `False`. |
| E.g., `[256, -12]` -> `[array(0), array(244)]`. If `True`, then `[256, -12]` -> `[array(255), array(0)]`. |
| factor_key: if not None, use it as the key to extract a value from the corresponding |
| metadata dictionary of `key` at runtime, and multiply the `offset` to shift intensity. |
| Usually, `IntensityStatsd` transform can pre-compute statistics of intensity values |
| and store in the metadata. |
| it also can be a sequence of strings, map to `keys`. |
| meta_keys: explicitly indicate the key of the corresponding metadata dictionary. |
| used to extract the factor value is `factor_key` is not None. |
| for example, for data with key `image`, the metadata by default is in `image_meta_dict`. |
| the metadata is a dictionary object which contains: filename, original_shape, etc. |
| it can be a sequence of string, map to the `keys`. |
| if None, will try to construct meta_keys by `key_{meta_key_postfix}`. |
| meta_key_postfix: if meta_keys is None, use `key_{postfix}` to fetch the metadata according |
| to the key data, default is `meta_dict`, the metadata is a dictionary object. |
| used to extract the factor value is `factor_key` is not None. |
| allow_missing_keys: don't raise exception if key is missing. |
| """ |
| super().__init__(keys, allow_missing_keys) |
| self.factor_key = ensure_tuple_rep(factor_key, len(self.keys)) |
| self.meta_keys = ensure_tuple_rep(None, len(self.keys)) if meta_keys is None else ensure_tuple(meta_keys) |
| if len(self.keys) != len(self.meta_keys): |
| raise ValueError("meta_keys should have the same length as keys.") |
| self.meta_key_postfix = ensure_tuple_rep(meta_key_postfix, len(self.keys)) |
| self.shifter = ShiftIntensity(offset, safe) |
|
|
| def __call__(self, data) -> dict[Hashable, NdarrayOrTensor]: |
| d = dict(data) |
| for key, factor_key, meta_key, meta_key_postfix in self.key_iterator( |
| d, self.factor_key, self.meta_keys, self.meta_key_postfix |
| ): |
| meta_key = meta_key or f"{key}_{meta_key_postfix}" |
| factor: float | None = d[meta_key].get(factor_key) if meta_key in d else None |
| offset = None if factor is None else self.shifter.offset * factor |
| d[key] = self.shifter(d[key], offset=offset) |
| return d |
|
|
|
|
| class RandShiftIntensityd(RandomizableTransform, MapTransform): |
| """ |
| Dictionary-based version :py:class:`monai.transforms.RandShiftIntensity`. |
| """ |
|
|
| backend = RandShiftIntensity.backend |
|
|
| def __init__( |
| self, |
| keys: KeysCollection, |
| offsets: tuple[float, float] | float, |
| safe: bool = False, |
| factor_key: str | None = None, |
| meta_keys: KeysCollection | None = None, |
| meta_key_postfix: str = DEFAULT_POST_FIX, |
| prob: float = 0.1, |
| channel_wise: bool = False, |
| allow_missing_keys: bool = False, |
| ) -> None: |
| """ |
| Args: |
| keys: keys of the corresponding items to be transformed. |
| See also: :py:class:`monai.transforms.compose.MapTransform` |
| offsets: offset range to randomly shift. |
| if single number, offset value is picked from (-offsets, offsets). |
| safe: if `True`, then do safe dtype convert when intensity overflow. default to `False`. |
| E.g., `[256, -12]` -> `[array(0), array(244)]`. If `True`, then `[256, -12]` -> `[array(255), array(0)]`. |
| factor_key: if not None, use it as the key to extract a value from the corresponding |
| metadata dictionary of `key` at runtime, and multiply the random `offset` to shift intensity. |
| Usually, `IntensityStatsd` transform can pre-compute statistics of intensity values |
| and store in the metadata. |
| it also can be a sequence of strings, map to `keys`. |
| meta_keys: explicitly indicate the key of the corresponding metadata dictionary. |
| used to extract the factor value is `factor_key` is not None. |
| for example, for data with key `image`, the metadata by default is in `image_meta_dict`. |
| the metadata is a dictionary object which contains: filename, original_shape, etc. |
| it can be a sequence of string, map to the `keys`. |
| if None, will try to construct meta_keys by `key_{meta_key_postfix}`. |
| meta_key_postfix: if meta_keys is None, use `key_{postfix}` to fetch the metadata according |
| to the key data, default is `meta_dict`, the metadata is a dictionary object. |
| used to extract the factor value is `factor_key` is not None. |
| prob: probability of shift. |
| (Default 0.1, with 10% probability it returns an array shifted intensity.) |
| channel_wise: if True, shift intensity on each channel separately. For each channel, a random offset will be chosen. |
| Please ensure that the first dimension represents the channel of the image if True. |
| allow_missing_keys: don't raise exception if key is missing. |
| """ |
| MapTransform.__init__(self, keys, allow_missing_keys) |
| RandomizableTransform.__init__(self, prob) |
|
|
| self.factor_key = ensure_tuple_rep(factor_key, len(self.keys)) |
| self.meta_keys = ensure_tuple_rep(None, len(self.keys)) if meta_keys is None else ensure_tuple(meta_keys) |
| if len(self.keys) != len(self.meta_keys): |
| raise ValueError("meta_keys should have the same length as keys.") |
| self.meta_key_postfix = ensure_tuple_rep(meta_key_postfix, len(self.keys)) |
| self.shifter = RandShiftIntensity(offsets=offsets, safe=safe, prob=1.0, channel_wise=channel_wise) |
|
|
| def set_random_state( |
| self, seed: int | None = None, state: np.random.RandomState | None = None |
| ) -> RandShiftIntensityd: |
| super().set_random_state(seed, state) |
| self.shifter.set_random_state(seed, state) |
| return self |
|
|
| def __call__(self, data) -> 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 |
|
|
| |
| first_key: Hashable = self.first_key(d) |
| if first_key == (): |
| for key in self.key_iterator(d): |
| d[key] = convert_to_tensor(d[key], track_meta=get_track_meta()) |
| return d |
|
|
| |
| self.shifter.randomize(d[first_key]) |
| for key, factor_key, meta_key, meta_key_postfix in self.key_iterator( |
| d, self.factor_key, self.meta_keys, self.meta_key_postfix |
| ): |
| meta_key = meta_key or f"{key}_{meta_key_postfix}" |
| factor: float | None = d[meta_key].get(factor_key) if meta_key in d else None |
| d[key] = self.shifter(d[key], factor=factor, randomize=False) |
| return d |
|
|
|
|
| class StdShiftIntensityd(MapTransform): |
| """ |
| Dictionary-based wrapper of :py:class:`monai.transforms.StdShiftIntensity`. |
| """ |
|
|
| backend = StdShiftIntensity.backend |
|
|
| def __init__( |
| self, |
| keys: KeysCollection, |
| factor: float, |
| nonzero: bool = False, |
| channel_wise: bool = False, |
| dtype: DtypeLike = np.float32, |
| allow_missing_keys: bool = False, |
| ) -> None: |
| """ |
| Args: |
| keys: keys of the corresponding items to be transformed. |
| See also: :py:class:`monai.transforms.compose.MapTransform` |
| factor: factor shift by ``v = v + factor * std(v)``. |
| nonzero: whether only count non-zero values. |
| channel_wise: if True, calculate on each channel separately. Please ensure |
| that the first dimension represents the channel of the image if True. |
| dtype: output data type, if None, same as input image. defaults to float32. |
| allow_missing_keys: don't raise exception if key is missing. |
| """ |
| super().__init__(keys, allow_missing_keys) |
| self.shifter = StdShiftIntensity(factor, nonzero, channel_wise, dtype) |
|
|
| def __call__(self, data: Mapping[Hashable, NdarrayOrTensor]) -> dict[Hashable, NdarrayOrTensor]: |
| d = dict(data) |
| for key in self.key_iterator(d): |
| d[key] = self.shifter(d[key]) |
| return d |
|
|
|
|
| class RandStdShiftIntensityd(RandomizableTransform, MapTransform): |
| """ |
| Dictionary-based version :py:class:`monai.transforms.RandStdShiftIntensity`. |
| """ |
|
|
| backend = RandStdShiftIntensity.backend |
|
|
| def __init__( |
| self, |
| keys: KeysCollection, |
| factors: tuple[float, float] | float, |
| prob: float = 0.1, |
| nonzero: bool = False, |
| channel_wise: bool = False, |
| dtype: DtypeLike = np.float32, |
| allow_missing_keys: bool = False, |
| ) -> None: |
| """ |
| Args: |
| keys: keys of the corresponding items to be transformed. |
| See also: :py:class:`monai.transforms.compose.MapTransform` |
| factors: if tuple, the randomly picked range is (min(factors), max(factors)). |
| If single number, the range is (-factors, factors). |
| prob: probability of std shift. |
| nonzero: whether only count non-zero values. |
| channel_wise: if True, calculate on each channel separately. |
| dtype: output data type, if None, same as input image. defaults to float32. |
| allow_missing_keys: don't raise exception if key is missing. |
| """ |
| MapTransform.__init__(self, keys, allow_missing_keys) |
| RandomizableTransform.__init__(self, prob) |
| self.shifter = RandStdShiftIntensity( |
| factors=factors, nonzero=nonzero, channel_wise=channel_wise, dtype=dtype, prob=1.0 |
| ) |
|
|
| def set_random_state( |
| self, seed: int | None = None, state: np.random.RandomState | None = None |
| ) -> RandStdShiftIntensityd: |
| super().set_random_state(seed, state) |
| self.shifter.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 |
|
|
| |
| self.shifter.randomize(None) |
| for key in self.key_iterator(d): |
| d[key] = self.shifter(d[key], randomize=False) |
| return d |
|
|
|
|
| class ScaleIntensityd(MapTransform): |
| """ |
| Dictionary-based wrapper of :py:class:`monai.transforms.ScaleIntensity`. |
| Scale the intensity of input image to the given value range (minv, maxv). |
| If `minv` and `maxv` not provided, use `factor` to scale image by ``v = v * (1 + factor)``. |
| """ |
|
|
| backend = ScaleIntensity.backend |
|
|
| def __init__( |
| self, |
| keys: KeysCollection, |
| minv: float | None = 0.0, |
| maxv: float | None = 1.0, |
| factor: float | None = None, |
| channel_wise: bool = False, |
| dtype: DtypeLike = np.float32, |
| allow_missing_keys: bool = False, |
| ) -> None: |
| """ |
| Args: |
| keys: keys of the corresponding items to be transformed. |
| See also: :py:class:`monai.transforms.compose.MapTransform` |
| minv: minimum value of output data. |
| maxv: maximum value of output data. |
| factor: factor scale by ``v = v * (1 + factor)``. In order to use |
| this parameter, please set both `minv` and `maxv` into None. |
| channel_wise: if True, scale on each channel separately. Please ensure |
| that the first dimension represents the channel of the image if True. |
| dtype: output data type, if None, same as input image. defaults to float32. |
| allow_missing_keys: don't raise exception if key is missing. |
| |
| """ |
| super().__init__(keys, allow_missing_keys) |
| self.scaler = ScaleIntensity(minv, maxv, factor, channel_wise, dtype) |
|
|
| def __call__(self, data: Mapping[Hashable, NdarrayOrTensor]) -> dict[Hashable, NdarrayOrTensor]: |
| d = dict(data) |
| for key in self.key_iterator(d): |
| d[key] = self.scaler(d[key]) |
| return d |
|
|
|
|
| class RandScaleIntensityd(RandomizableTransform, MapTransform): |
| """ |
| Dictionary-based version :py:class:`monai.transforms.RandScaleIntensity`. |
| """ |
|
|
| backend = RandScaleIntensity.backend |
|
|
| def __init__( |
| self, |
| keys: KeysCollection, |
| factors: tuple[float, float] | float, |
| prob: float = 0.1, |
| channel_wise: bool = False, |
| dtype: DtypeLike = np.float32, |
| allow_missing_keys: bool = False, |
| ) -> None: |
| """ |
| Args: |
| keys: keys of the corresponding items to be transformed. |
| See also: :py:class:`monai.transforms.compose.MapTransform` |
| factors: factor range to randomly scale by ``v = v * (1 + factor)``. |
| if single number, factor value is picked from (-factors, factors). |
| prob: probability of scale. |
| (Default 0.1, with 10% probability it returns a scaled array.) |
| channel_wise: if True, scale on each channel separately. Please ensure |
| that the first dimension represents the channel of the image if True. |
| dtype: output data type, if None, same as input image. defaults to float32. |
| allow_missing_keys: don't raise exception if key is missing. |
| |
| """ |
| MapTransform.__init__(self, keys, allow_missing_keys) |
| RandomizableTransform.__init__(self, prob) |
| self.scaler = RandScaleIntensity(factors=factors, dtype=dtype, prob=1.0, channel_wise=channel_wise) |
|
|
| def set_random_state( |
| self, seed: int | None = None, state: np.random.RandomState | None = None |
| ) -> RandScaleIntensityd: |
| super().set_random_state(seed, state) |
| self.scaler.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 |
|
|
| |
| first_key: Hashable = self.first_key(d) |
| if first_key == (): |
| for key in self.key_iterator(d): |
| d[key] = convert_to_tensor(d[key], track_meta=get_track_meta()) |
| return d |
|
|
| |
| self.scaler.randomize(d[first_key]) |
| for key in self.key_iterator(d): |
| d[key] = self.scaler(d[key], randomize=False) |
| return d |
|
|
|
|
| class RandScaleIntensityFixedMeand(RandomizableTransform, MapTransform): |
| """ |
| Dictionary-based version :py:class:`monai.transforms.RandScaleIntensity`. |
| Subtract the mean intensity before scaling with `factor`, then add the same value after scaling |
| to ensure that the output has the same mean as the input. |
| """ |
|
|
| backend = RandScaleIntensityFixedMean.backend |
|
|
| def __init__( |
| self, |
| keys: KeysCollection, |
| factors: Sequence[float] | float, |
| fixed_mean: bool = True, |
| preserve_range: bool = False, |
| prob: float = 0.1, |
| dtype: DtypeLike = np.float32, |
| allow_missing_keys: bool = False, |
| ) -> None: |
| """ |
| Args: |
| keys: keys of the corresponding items to be transformed. |
| See also: :py:class:`monai.transforms.compose.MapTransform` |
| factors: factor range to randomly scale by ``v = v * (1 + factor)``. |
| if single number, factor value is picked from (-factors, factors). |
| preserve_range: clips the output array/tensor to the range of the input array/tensor |
| fixed_mean: subtract the mean intensity before scaling with `factor`, then add the same value after scaling |
| to ensure that the output has the same mean as the input. |
| channel_wise: if True, scale on each channel separately. `preserve_range` and `fixed_mean` are also applied |
| on each channel separately if `channel_wise` is True. Please ensure that the first dimension represents the |
| channel of the image if True. |
| dtype: output data type, if None, same as input image. defaults to float32. |
| allow_missing_keys: don't raise exception if key is missing. |
| |
| """ |
| MapTransform.__init__(self, keys, allow_missing_keys) |
| RandomizableTransform.__init__(self, prob) |
| self.fixed_mean = fixed_mean |
| self.preserve_range = preserve_range |
| self.scaler = RandScaleIntensityFixedMean( |
| factors=factors, fixed_mean=self.fixed_mean, preserve_range=preserve_range, dtype=dtype, prob=1.0 |
| ) |
|
|
| def set_random_state( |
| self, seed: int | None = None, state: np.random.RandomState | None = None |
| ) -> RandScaleIntensityFixedMeand: |
| super().set_random_state(seed, state) |
| self.scaler.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 |
|
|
| |
| self.scaler.randomize(None) |
| for key in self.key_iterator(d): |
| d[key] = self.scaler(d[key], randomize=False) |
| return d |
|
|
|
|
| class RandBiasFieldd(RandomizableTransform, MapTransform): |
| """ |
| Dictionary-based version :py:class:`monai.transforms.RandBiasField`. |
| """ |
|
|
| backend = RandBiasField.backend |
|
|
| def __init__( |
| self, |
| keys: KeysCollection, |
| degree: int = 3, |
| coeff_range: tuple[float, float] = (0.0, 0.1), |
| dtype: DtypeLike = np.float32, |
| prob: float = 0.1, |
| allow_missing_keys: bool = False, |
| ) -> None: |
| """ |
| Args: |
| keys: keys of the corresponding items to be transformed. |
| See also: :py:class:`monai.transforms.compose.MapTransform` |
| degree: degree of freedom of the polynomials. The value should be no less than 1. |
| Defaults to 3. |
| coeff_range: range of the random coefficients. Defaults to (0.0, 0.1). |
| dtype: output data type, if None, same as input image. defaults to float32. |
| prob: probability to do random bias field. |
| allow_missing_keys: don't raise exception if key is missing. |
| |
| """ |
| MapTransform.__init__(self, keys, allow_missing_keys) |
| RandomizableTransform.__init__(self, prob) |
|
|
| self.rand_bias_field = RandBiasField(degree=degree, coeff_range=coeff_range, dtype=dtype, prob=1.0) |
|
|
| def set_random_state(self, seed: int | None = None, state: np.random.RandomState | None = None) -> RandBiasFieldd: |
| super().set_random_state(seed, state) |
| self.rand_bias_field.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 |
|
|
| |
| first_key: Hashable = self.first_key(d) |
| if first_key == (): |
| for key in self.key_iterator(d): |
| d[key] = convert_to_tensor(d[key], track_meta=get_track_meta()) |
| return d |
|
|
| self.rand_bias_field.randomize(img_size=d[first_key].shape[1:]) |
|
|
| for key in self.key_iterator(d): |
| d[key] = self.rand_bias_field(d[key], randomize=False) |
| return d |
|
|
|
|
| class NormalizeIntensityd(MapTransform): |
| """ |
| Dictionary-based wrapper of :py:class:`monai.transforms.NormalizeIntensity`. |
| This transform can normalize only non-zero values or entire image, and can also calculate |
| mean and std on each channel separately. |
| |
| Args: |
| keys: keys of the corresponding items to be transformed. |
| See also: monai.transforms.MapTransform |
| subtrahend: the amount to subtract by (usually the mean) |
| divisor: the amount to divide by (usually the standard deviation) |
| nonzero: whether only normalize non-zero values. |
| channel_wise: if True, calculate on each channel separately, otherwise, calculate on |
| the entire image directly. default to False. |
| 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 = NormalizeIntensity.backend |
|
|
| def __init__( |
| self, |
| keys: KeysCollection, |
| subtrahend: NdarrayOrTensor | None = None, |
| divisor: NdarrayOrTensor | None = None, |
| nonzero: bool = False, |
| channel_wise: bool = False, |
| dtype: DtypeLike = np.float32, |
| allow_missing_keys: bool = False, |
| ) -> None: |
| super().__init__(keys, allow_missing_keys) |
| self.normalizer = NormalizeIntensity(subtrahend, divisor, nonzero, channel_wise, dtype) |
|
|
| def __call__(self, data: Mapping[Hashable, NdarrayOrTensor]) -> dict[Hashable, NdarrayOrTensor]: |
| d = dict(data) |
| for key in self.key_iterator(d): |
| d[key] = self.normalizer(d[key]) |
| return d |
|
|
|
|
| class ThresholdIntensityd(MapTransform): |
| """ |
| Dictionary-based wrapper of :py:class:`monai.transforms.ThresholdIntensity`. |
| |
| Args: |
| keys: keys of the corresponding items to be transformed. |
| See also: monai.transforms.MapTransform |
| threshold: the threshold to filter intensity values. |
| above: filter values above the threshold or below the threshold, default is True. |
| cval: value to fill the remaining parts of the image, default is 0. |
| allow_missing_keys: don't raise exception if key is missing. |
| """ |
|
|
| backend = ThresholdIntensity.backend |
|
|
| def __init__( |
| self, |
| keys: KeysCollection, |
| threshold: float, |
| above: bool = True, |
| cval: float = 0.0, |
| allow_missing_keys: bool = False, |
| ) -> None: |
| super().__init__(keys, allow_missing_keys) |
| self.filter = ThresholdIntensity(threshold, above, cval) |
|
|
| def __call__(self, data: Mapping[Hashable, NdarrayOrTensor]) -> dict[Hashable, NdarrayOrTensor]: |
| d = dict(data) |
| for key in self.key_iterator(d): |
| d[key] = self.filter(d[key]) |
| return d |
|
|
|
|
| class ScaleIntensityRanged(MapTransform): |
| """ |
| Dictionary-based wrapper of :py:class:`monai.transforms.ScaleIntensityRange`. |
| |
| Args: |
| keys: keys of the corresponding items to be transformed. |
| See also: monai.transforms.MapTransform |
| a_min: intensity original range min. |
| a_max: intensity original range max. |
| b_min: intensity target range min. |
| b_max: intensity target range max. |
| clip: whether to perform clip after scaling. |
| 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 = ScaleIntensityRange.backend |
|
|
| def __init__( |
| self, |
| keys: KeysCollection, |
| a_min: float, |
| a_max: float, |
| b_min: float | None = None, |
| b_max: float | None = None, |
| clip: bool = False, |
| dtype: DtypeLike = np.float32, |
| allow_missing_keys: bool = False, |
| ) -> None: |
| super().__init__(keys, allow_missing_keys) |
| self.scaler = ScaleIntensityRange(a_min, a_max, b_min, b_max, clip, dtype) |
|
|
| def __call__(self, data: Mapping[Hashable, NdarrayOrTensor]) -> dict[Hashable, NdarrayOrTensor]: |
| d = dict(data) |
| for key in self.key_iterator(d): |
| d[key] = self.scaler(d[key]) |
| 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`. |
| Changes image intensity with gamma transform. Each pixel/voxel intensity is updated as: |
| |
| `x = ((x - min) / intensity_range) ^ gamma * intensity_range + min` |
| |
| Args: |
| keys: keys of the corresponding items to be transformed. |
| See also: monai.transforms.MapTransform |
| gamma: gamma value to adjust the contrast as function. |
| invert_image: whether to invert the image before applying gamma augmentation. If True, multiply all intensity |
| values with -1 before the gamma transform and again after the gamma transform. This behaviour is mimicked |
| from `nnU-Net <https://www.nature.com/articles/s41592-020-01008-z>`_, specifically `this |
| <https://github.com/MIC-DKFZ/batchgenerators/blob/7fb802b28b045b21346b197735d64f12fbb070aa/batchgenerators/augmentations/color_augmentations.py#L107>`_ |
| function. |
| retain_stats: if True, applies a scaling factor and an offset to all intensity values after gamma transform to |
| ensure that the output intensity distribution has the same mean and standard deviation as the intensity |
| distribution of the input. This behaviour is mimicked from `nnU-Net |
| <https://www.nature.com/articles/s41592-020-01008-z>`_, specifically `this |
| <https://github.com/MIC-DKFZ/batchgenerators/blob/7fb802b28b045b21346b197735d64f12fbb070aa/batchgenerators/augmentations/color_augmentations.py#L107>`_ |
| function. |
| allow_missing_keys: don't raise exception if key is missing. |
| """ |
|
|
| backend = AdjustContrast.backend |
|
|
| def __init__( |
| self, |
| keys: KeysCollection, |
| gamma: float, |
| invert_image: bool = False, |
| retain_stats: bool = False, |
| allow_missing_keys: bool = False, |
| ) -> None: |
| super().__init__(keys, allow_missing_keys) |
| self.adjuster = AdjustContrast(gamma, invert_image, retain_stats) |
|
|
| def __call__(self, data: Mapping[Hashable, NdarrayOrTensor]) -> dict[Hashable, NdarrayOrTensor]: |
| d = dict(data) |
| for key in self.key_iterator(d): |
| d[key] = self.adjuster(d[key]) |
| return d |
|
|
|
|
| class RandAdjustContrastd(RandomizableTransform, MapTransform): |
| """ |
| Dictionary-based version :py:class:`monai.transforms.RandAdjustContrast`. |
| Randomly changes image intensity with gamma transform. Each pixel/voxel intensity is updated as: |
| |
| `x = ((x - min) / intensity_range) ^ gamma * intensity_range + min` |
| |
| Args: |
| keys: keys of the corresponding items to be transformed. |
| See also: monai.transforms.MapTransform |
| prob: Probability of adjustment. |
| gamma: Range of gamma values. |
| If single number, value is picked from (0.5, gamma), default is (0.5, 4.5). |
| invert_image: whether to invert the image before applying gamma augmentation. If True, multiply all intensity |
| values with -1 before the gamma transform and again after the gamma transform. This behaviour is mimicked |
| from `nnU-Net <https://www.nature.com/articles/s41592-020-01008-z>`_, specifically `this |
| <https://github.com/MIC-DKFZ/batchgenerators/blob/7fb802b28b045b21346b197735d64f12fbb070aa/batchgenerators/augmentations/color_augmentations.py#L107>`_ |
| function. |
| retain_stats: if True, applies a scaling factor and an offset to all intensity values after gamma transform to |
| ensure that the output intensity distribution has the same mean and standard deviation as the intensity |
| distribution of the input. This behaviour is mimicked from `nnU-Net |
| <https://www.nature.com/articles/s41592-020-01008-z>`_, specifically `this |
| <https://github.com/MIC-DKFZ/batchgenerators/blob/7fb802b28b045b21346b197735d64f12fbb070aa/batchgenerators/augmentations/color_augmentations.py#L107>`_ |
| function. |
| allow_missing_keys: don't raise exception if key is missing. |
| """ |
|
|
| backend = RandAdjustContrast.backend |
|
|
| def __init__( |
| self, |
| keys: KeysCollection, |
| prob: float = 0.1, |
| gamma: tuple[float, float] | float = (0.5, 4.5), |
| invert_image: bool = False, |
| retain_stats: bool = False, |
| allow_missing_keys: bool = False, |
| ) -> None: |
| MapTransform.__init__(self, keys, allow_missing_keys) |
| RandomizableTransform.__init__(self, prob) |
| self.adjuster = RandAdjustContrast(gamma=gamma, prob=1.0, invert_image=invert_image, retain_stats=retain_stats) |
| self.invert_image = invert_image |
|
|
| def set_random_state( |
| self, seed: int | None = None, state: np.random.RandomState | None = None |
| ) -> RandAdjustContrastd: |
| super().set_random_state(seed, state) |
| self.adjuster.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 |
|
|
| |
| self.adjuster.randomize(None) |
| for key in self.key_iterator(d): |
| d[key] = self.adjuster(d[key], randomize=False) |
| return d |
|
|
|
|
| class ScaleIntensityRangePercentilesd(MapTransform): |
| """ |
| Dictionary-based wrapper of :py:class:`monai.transforms.ScaleIntensityRangePercentiles`. |
| |
| Args: |
| keys: keys of the corresponding items to be transformed. |
| See also: monai.transforms.MapTransform |
| lower: lower percentile. |
| upper: upper percentile. |
| b_min: intensity target range min. |
| b_max: intensity target range max. |
| clip: whether to perform clip after scaling. |
| relative: whether to scale to the corresponding percentiles of [b_min, b_max] |
| channel_wise: if True, compute intensity percentile and normalize every channel separately. |
| default to False. |
| 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 = ScaleIntensityRangePercentiles.backend |
|
|
| def __init__( |
| self, |
| keys: KeysCollection, |
| lower: float, |
| upper: float, |
| b_min: float | None, |
| b_max: float | None, |
| clip: bool = False, |
| relative: bool = False, |
| channel_wise: bool = False, |
| dtype: DtypeLike = np.float32, |
| allow_missing_keys: bool = False, |
| ) -> None: |
| super().__init__(keys, allow_missing_keys) |
| self.scaler = ScaleIntensityRangePercentiles(lower, upper, b_min, b_max, clip, relative, channel_wise, dtype) |
|
|
| def __call__(self, data: Mapping[Hashable, NdarrayOrTensor]) -> dict[Hashable, NdarrayOrTensor]: |
| d = dict(data) |
| for key in self.key_iterator(d): |
| d[key] = self.scaler(d[key]) |
| return d |
|
|
|
|
| class MaskIntensityd(MapTransform): |
| """ |
| Dictionary-based wrapper of :py:class:`monai.transforms.MaskIntensity`. |
| |
| Args: |
| keys: keys of the corresponding items to be transformed. |
| See also: :py:class:`monai.transforms.compose.MapTransform` |
| mask_data: if mask data is single channel, apply to every channel |
| of input image. if multiple channels, the channel number must |
| match input data. the intensity values of input image corresponding |
| to the selected values in the mask data will keep the original value, |
| others will be set to `0`. if None, will extract the mask data from |
| input data based on `mask_key`. |
| mask_key: the key to extract mask data from input dictionary, only works |
| when `mask_data` is None. |
| select_fn: function to select valid values of the `mask_data`, default is |
| to select `values > 0`. |
| allow_missing_keys: don't raise exception if key is missing. |
| |
| """ |
|
|
| backend = MaskIntensity.backend |
|
|
| def __init__( |
| self, |
| keys: KeysCollection, |
| mask_data: NdarrayOrTensor | None = None, |
| mask_key: str | None = None, |
| select_fn: Callable = is_positive, |
| allow_missing_keys: bool = False, |
| ) -> None: |
| super().__init__(keys, allow_missing_keys) |
| self.converter = MaskIntensity(mask_data=mask_data, select_fn=select_fn) |
| self.mask_key = mask_key if mask_data is None else None |
|
|
| def __call__(self, data: Mapping[Hashable, NdarrayOrTensor]) -> dict[Hashable, NdarrayOrTensor]: |
| d = dict(data) |
| for key in self.key_iterator(d): |
| d[key] = self.converter(d[key], d[self.mask_key]) if self.mask_key is not None else self.converter(d[key]) |
| return d |
|
|
|
|
| class SavitzkyGolaySmoothd(MapTransform): |
| """ |
| Dictionary-based wrapper of :py:class:`monai.transforms.SavitzkyGolaySmooth`. |
| |
| Args: |
| keys: keys of the corresponding items to be transformed. |
| See also: :py:class:`monai.transforms.compose.MapTransform` |
| window_length: length of the filter window, must be a positive odd integer. |
| order: order of the polynomial to fit to each window, must be less than ``window_length``. |
| axis: optional axis along which to apply the filter kernel. Default 1 (first spatial dimension). |
| mode: optional padding mode, passed to convolution class. ``'zeros'``, ``'reflect'``, ``'replicate'`` |
| or ``'circular'``. default: ``'zeros'``. See ``torch.nn.Conv1d()`` for more information. |
| allow_missing_keys: don't raise exception if key is missing. |
| |
| """ |
|
|
| backend = SavitzkyGolaySmooth.backend |
|
|
| def __init__( |
| self, |
| keys: KeysCollection, |
| window_length: int, |
| order: int, |
| axis: int = 1, |
| mode: str = "zeros", |
| allow_missing_keys: bool = False, |
| ) -> None: |
| super().__init__(keys, allow_missing_keys) |
| self.converter = SavitzkyGolaySmooth(window_length=window_length, order=order, axis=axis, mode=mode) |
|
|
| def __call__(self, data: Mapping[Hashable, NdarrayOrTensor]) -> dict[Hashable, NdarrayOrTensor]: |
| d = dict(data) |
| for key in self.key_iterator(d): |
| d[key] = self.converter(d[key]) |
| return d |
|
|
|
|
| class MedianSmoothd(MapTransform): |
| """ |
| Dictionary-based wrapper of :py:class:`monai.transforms.MedianSmooth`. |
| |
| Args: |
| keys: keys of the corresponding items to be transformed. |
| See also: :py:class:`monai.transforms.compose.MapTransform` |
| radius: if a list of values, must match the count of spatial dimensions of input data, |
| and apply every value in the list to 1 spatial dimension. if only 1 value provided, |
| use it for all spatial dimensions. |
| allow_missing_keys: don't raise exception if key is missing. |
| |
| """ |
|
|
| backend = MedianSmooth.backend |
|
|
| def __init__(self, keys: KeysCollection, radius: Sequence[int] | int, allow_missing_keys: bool = False) -> None: |
| super().__init__(keys, allow_missing_keys) |
| self.converter = MedianSmooth(radius) |
|
|
| def __call__(self, data: Mapping[Hashable, NdarrayOrTensor]) -> dict[Hashable, NdarrayOrTensor]: |
| d = dict(data) |
| for key in self.key_iterator(d): |
| d[key] = self.converter(d[key]) |
| return d |
|
|
|
|
| class GaussianSmoothd(MapTransform): |
| """ |
| Dictionary-based wrapper of :py:class:`monai.transforms.GaussianSmooth`. |
| |
| Args: |
| keys: keys of the corresponding items to be transformed. |
| See also: :py:class:`monai.transforms.compose.MapTransform` |
| sigma: if a list of values, must match the count of spatial dimensions of input data, |
| and apply every value in the list to 1 spatial dimension. if only 1 value provided, |
| use it for all spatial dimensions. |
| approx: discrete Gaussian kernel type, available options are "erf", "sampled", and "scalespace". |
| see also :py:meth:`monai.networks.layers.GaussianFilter`. |
| allow_missing_keys: don't raise exception if key is missing. |
| |
| """ |
|
|
| backend = GaussianSmooth.backend |
|
|
| def __init__( |
| self, |
| keys: KeysCollection, |
| sigma: Sequence[float] | float, |
| approx: str = "erf", |
| allow_missing_keys: bool = False, |
| ) -> None: |
| super().__init__(keys, allow_missing_keys) |
| self.converter = GaussianSmooth(sigma, approx=approx) |
|
|
| def __call__(self, data: Mapping[Hashable, NdarrayOrTensor]) -> dict[Hashable, NdarrayOrTensor]: |
| d = dict(data) |
| for key in self.key_iterator(d): |
| d[key] = self.converter(d[key]) |
| return d |
|
|
|
|
| class RandGaussianSmoothd(RandomizableTransform, MapTransform): |
| """ |
| Dictionary-based wrapper of :py:class:`monai.transforms.GaussianSmooth`. |
| |
| Args: |
| keys: keys of the corresponding items to be transformed. |
| See also: :py:class:`monai.transforms.compose.MapTransform` |
| sigma_x: randomly select sigma value for the first spatial dimension. |
| sigma_y: randomly select sigma value for the second spatial dimension if have. |
| sigma_z: randomly select sigma value for the third spatial dimension if have. |
| approx: discrete Gaussian kernel type, available options are "erf", "sampled", and "scalespace". |
| see also :py:meth:`monai.networks.layers.GaussianFilter`. |
| prob: probability of Gaussian smooth. |
| allow_missing_keys: don't raise exception if key is missing. |
| |
| """ |
|
|
| backend = RandGaussianSmooth.backend |
|
|
| def __init__( |
| self, |
| keys: KeysCollection, |
| sigma_x: tuple[float, float] = (0.25, 1.5), |
| sigma_y: tuple[float, float] = (0.25, 1.5), |
| sigma_z: tuple[float, float] = (0.25, 1.5), |
| approx: str = "erf", |
| prob: float = 0.1, |
| allow_missing_keys: bool = False, |
| ) -> None: |
| MapTransform.__init__(self, keys, allow_missing_keys) |
| RandomizableTransform.__init__(self, prob) |
| self.rand_smooth = RandGaussianSmooth( |
| sigma_x=sigma_x, sigma_y=sigma_y, sigma_z=sigma_z, approx=approx, prob=1.0 |
| ) |
|
|
| def set_random_state( |
| self, seed: int | None = None, state: np.random.RandomState | None = None |
| ) -> RandGaussianSmoothd: |
| super().set_random_state(seed, state) |
| self.rand_smooth.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 |
|
|
| |
| self.rand_smooth.randomize(None) |
| for key in self.key_iterator(d): |
| d[key] = self.rand_smooth(d[key], randomize=False) |
| return d |
|
|
|
|
| class GaussianSharpend(MapTransform): |
| """ |
| Dictionary-based wrapper of :py:class:`monai.transforms.GaussianSharpen`. |
| |
| Args: |
| keys: keys of the corresponding items to be transformed. |
| See also: :py:class:`monai.transforms.compose.MapTransform` |
| sigma1: sigma parameter for the first gaussian kernel. if a list of values, must match the count |
| of spatial dimensions of input data, and apply every value in the list to 1 spatial dimension. |
| if only 1 value provided, use it for all spatial dimensions. |
| sigma2: sigma parameter for the second gaussian kernel. if a list of values, must match the count |
| of spatial dimensions of input data, and apply every value in the list to 1 spatial dimension. |
| if only 1 value provided, use it for all spatial dimensions. |
| alpha: weight parameter to compute the final result. |
| approx: discrete Gaussian kernel type, available options are "erf", "sampled", and "scalespace". |
| see also :py:meth:`monai.networks.layers.GaussianFilter`. |
| allow_missing_keys: don't raise exception if key is missing. |
| |
| """ |
|
|
| backend = GaussianSharpen.backend |
|
|
| def __init__( |
| self, |
| keys: KeysCollection, |
| sigma1: Sequence[float] | float = 3.0, |
| sigma2: Sequence[float] | float = 1.0, |
| alpha: float = 30.0, |
| approx: str = "erf", |
| allow_missing_keys: bool = False, |
| ) -> None: |
| super().__init__(keys, allow_missing_keys) |
| self.converter = GaussianSharpen(sigma1, sigma2, alpha, approx=approx) |
|
|
| def __call__(self, data: Mapping[Hashable, NdarrayOrTensor]) -> dict[Hashable, NdarrayOrTensor]: |
| d = dict(data) |
| for key in self.key_iterator(d): |
| d[key] = self.converter(d[key]) |
| return d |
|
|
|
|
| class RandGaussianSharpend(RandomizableTransform, MapTransform): |
| """ |
| Dictionary-based wrapper of :py:class:`monai.transforms.GaussianSharpen`. |
| |
| Args: |
| keys: keys of the corresponding items to be transformed. |
| See also: :py:class:`monai.transforms.compose.MapTransform` |
| sigma1_x: randomly select sigma value for the first spatial dimension of first gaussian kernel. |
| sigma1_y: randomly select sigma value for the second spatial dimension(if have) of first gaussian kernel. |
| sigma1_z: randomly select sigma value for the third spatial dimension(if have) of first gaussian kernel. |
| sigma2_x: randomly select sigma value for the first spatial dimension of second gaussian kernel. |
| if only 1 value `X` provided, it must be smaller than `sigma1_x` and randomly select from [X, sigma1_x]. |
| sigma2_y: randomly select sigma value for the second spatial dimension(if have) of second gaussian kernel. |
| if only 1 value `Y` provided, it must be smaller than `sigma1_y` and randomly select from [Y, sigma1_y]. |
| sigma2_z: randomly select sigma value for the third spatial dimension(if have) of second gaussian kernel. |
| if only 1 value `Z` provided, it must be smaller than `sigma1_z` and randomly select from [Z, sigma1_z]. |
| alpha: randomly select weight parameter to compute the final result. |
| approx: discrete Gaussian kernel type, available options are "erf", "sampled", and "scalespace". |
| see also :py:meth:`monai.networks.layers.GaussianFilter`. |
| prob: probability of Gaussian sharpen. |
| allow_missing_keys: don't raise exception if key is missing. |
| |
| """ |
|
|
| backend = RandGaussianSharpen.backend |
|
|
| def __init__( |
| self, |
| keys: KeysCollection, |
| sigma1_x: tuple[float, float] = (0.5, 1.0), |
| sigma1_y: tuple[float, float] = (0.5, 1.0), |
| sigma1_z: tuple[float, float] = (0.5, 1.0), |
| sigma2_x: tuple[float, float] | float = 0.5, |
| sigma2_y: tuple[float, float] | float = 0.5, |
| sigma2_z: tuple[float, float] | float = 0.5, |
| alpha: tuple[float, float] = (10.0, 30.0), |
| approx: str = "erf", |
| prob: float = 0.1, |
| allow_missing_keys: bool = False, |
| ): |
| MapTransform.__init__(self, keys, allow_missing_keys) |
| RandomizableTransform.__init__(self, prob) |
| self.rand_sharpen = RandGaussianSharpen( |
| sigma1_x=sigma1_x, |
| sigma1_y=sigma1_y, |
| sigma1_z=sigma1_z, |
| sigma2_x=sigma2_x, |
| sigma2_y=sigma2_y, |
| sigma2_z=sigma2_z, |
| alpha=alpha, |
| approx=approx, |
| prob=1.0, |
| ) |
|
|
| def set_random_state( |
| self, seed: int | None = None, state: np.random.RandomState | None = None |
| ) -> RandGaussianSharpend: |
| super().set_random_state(seed, state) |
| self.rand_sharpen.set_random_state(seed, state) |
| return self |
|
|
| def __call__(self, data: dict[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 |
|
|
| |
| self.rand_sharpen.randomize(None) |
| for key in self.key_iterator(d): |
| d[key] = self.rand_sharpen(d[key], randomize=False) |
| return d |
|
|
|
|
| class RandHistogramShiftd(RandomizableTransform, MapTransform): |
| """ |
| Dictionary-based version :py:class:`monai.transforms.RandHistogramShift`. |
| Apply random nonlinear transform the image's intensity histogram. |
| |
| Args: |
| keys: keys of the corresponding items to be transformed. |
| See also: monai.transforms.MapTransform |
| num_control_points: number of control points governing the nonlinear intensity mapping. |
| a smaller number of control points allows for larger intensity shifts. if two values provided, number of |
| control points selecting from range (min_value, max_value). |
| prob: probability of histogram shift. |
| allow_missing_keys: don't raise exception if key is missing. |
| """ |
|
|
| backend = RandHistogramShift.backend |
|
|
| def __init__( |
| self, |
| keys: KeysCollection, |
| num_control_points: tuple[int, int] | int = 10, |
| prob: float = 0.1, |
| allow_missing_keys: bool = False, |
| ) -> None: |
| MapTransform.__init__(self, keys, allow_missing_keys) |
| RandomizableTransform.__init__(self, prob) |
| self.shifter = RandHistogramShift(num_control_points=num_control_points, prob=1.0) |
|
|
| def set_random_state( |
| self, seed: int | None = None, state: np.random.RandomState | None = None |
| ) -> RandHistogramShiftd: |
| super().set_random_state(seed, state) |
| self.shifter.set_random_state(seed, state) |
| return self |
|
|
| def __call__(self, data: dict[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 |
|
|
| |
| self.shifter.randomize(None) |
| for key in self.key_iterator(d): |
| d[key] = self.shifter(d[key], randomize=False) |
| return d |
|
|
|
|
| class RandGibbsNoised(RandomizableTransform, MapTransform): |
| """ |
| Dictionary-based version of RandGibbsNoise. |
| |
| Naturalistic image augmentation via Gibbs artifacts. The transform |
| randomly applies Gibbs noise to 2D/3D MRI images. Gibbs artifacts |
| are one of the common type of type artifacts appearing in MRI scans. |
| |
| The transform is applied to all the channels in the data. |
| |
| For general information on Gibbs artifacts, please refer to: |
| https://pubs.rsna.org/doi/full/10.1148/rg.313105115 |
| https://pubs.rsna.org/doi/full/10.1148/radiographics.22.4.g02jl14949 |
| |
| Args: |
| keys: 'image', 'label', or ['image', 'label'] depending on which data |
| you need to transform. |
| prob (float): probability of applying the transform. |
| alpha (float, Sequence[float]): Parametrizes the intensity of the Gibbs noise filter applied. Takes |
| values in the interval [0,1] with alpha = 0 acting as the identity mapping. |
| If a length-2 list is given as [a,b] then the value of alpha will be sampled |
| uniformly from the interval [a,b]. |
| If a float is given, then the value of alpha will be sampled uniformly from the interval [0, alpha]. |
| allow_missing_keys: do not raise exception if key is missing. |
| """ |
|
|
| backend = RandGibbsNoise.backend |
|
|
| def __init__( |
| self, |
| keys: KeysCollection, |
| prob: float = 0.1, |
| alpha: float | Sequence[float] = (0.0, 1.0), |
| allow_missing_keys: bool = False, |
| ) -> None: |
| MapTransform.__init__(self, keys, allow_missing_keys) |
| RandomizableTransform.__init__(self, prob=prob) |
| self.rand_gibbs_noise = RandGibbsNoise(alpha=alpha, prob=1.0) |
|
|
| def set_random_state(self, seed: int | None = None, state: np.random.RandomState | None = None) -> RandGibbsNoised: |
| super().set_random_state(seed, state) |
| self.rand_gibbs_noise.set_random_state(seed, state) |
| return self |
|
|
| def __call__(self, data: dict[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 |
|
|
| |
| self.rand_gibbs_noise.randomize(None) |
| for key in self.key_iterator(d): |
| d[key] = self.rand_gibbs_noise(d[key], randomize=False) |
| return d |
|
|
|
|
| class GibbsNoised(MapTransform): |
| """ |
| Dictionary-based version of GibbsNoise. |
| |
| The transform applies Gibbs noise to 2D/3D MRI images. Gibbs artifacts |
| are one of the common type of type artifacts appearing in MRI scans. |
| |
| For general information on Gibbs artifacts, please refer to: |
| https://pubs.rsna.org/doi/full/10.1148/rg.313105115 |
| https://pubs.rsna.org/doi/full/10.1148/radiographics.22.4.g02jl14949 |
| |
| Args: |
| keys: 'image', 'label', or ['image', 'label'] depending on which data |
| you need to transform. |
| alpha (float): Parametrizes the intensity of the Gibbs noise filter applied. Takes |
| values in the interval [0,1] with alpha = 0 acting as the identity mapping. |
| allow_missing_keys: do not raise exception if key is missing. |
| """ |
|
|
| backend = GibbsNoise.backend |
|
|
| def __init__(self, keys: KeysCollection, alpha: float = 0.5, allow_missing_keys: bool = False) -> None: |
| MapTransform.__init__(self, keys, allow_missing_keys) |
| self.transform = GibbsNoise(alpha) |
|
|
| def __call__(self, data: Mapping[Hashable, NdarrayOrTensor]) -> dict[Hashable, NdarrayOrTensor]: |
| d = dict(data) |
| for key in self.key_iterator(d): |
| d[key] = self.transform(d[key]) |
| return d |
|
|
|
|
| class KSpaceSpikeNoised(MapTransform): |
| """ |
| Dictionary-based wrapper of :py:class:`monai.transforms.KSpaceSpikeNoise`. |
| |
| Applies localized spikes in `k`-space at the given locations and intensities. |
| Spike (Herringbone) artifact is a type of data acquisition artifact which |
| may occur during MRI scans. |
| |
| For general information on spike artifacts, please refer to: |
| |
| `AAPM/RSNA physics tutorial for residents: fundamental physics of MR imaging |
| <https://pubmed.ncbi.nlm.nih.gov/16009826>`_. |
| |
| `Body MRI artifacts in clinical practice: A physicist's and radiologist's |
| perspective <https://doi.org/10.1002/jmri.24288>`_. |
| |
| Args: |
| keys: "image", "label", or ["image", "label"] depending |
| on which data you need to transform. |
| loc: spatial location for the spikes. For |
| images with 3D spatial dimensions, the user can provide (C, X, Y, Z) |
| to fix which channel C is affected, or (X, Y, Z) to place the same |
| spike in all channels. For 2D cases, the user can provide (C, X, Y) |
| or (X, Y). |
| k_intensity: value for the log-intensity of the |
| `k`-space version of the image. If one location is passed to ``loc`` or the |
| channel is not specified, then this argument should receive a float. If |
| ``loc`` is given a sequence of locations, then this argument should |
| receive a sequence of intensities. This value should be tested as it is |
| data-dependent. The default values are the 2.5 the mean of the |
| log-intensity for each channel. |
| allow_missing_keys: do not raise exception if key is missing. |
| |
| Example: |
| When working with 4D data, |
| ``KSpaceSpikeNoised("image", loc = ((3,60,64,32), (64,60,32)), k_intensity = (13,14))`` |
| will place a spike at `[3, 60, 64, 32]` with `log-intensity = 13`, and |
| one spike per channel located respectively at `[: , 64, 60, 32]` |
| with `log-intensity = 14`. |
| """ |
|
|
| backend = KSpaceSpikeNoise.backend |
|
|
| def __init__( |
| self, |
| keys: KeysCollection, |
| loc: tuple | Sequence[tuple], |
| k_intensity: Sequence[float] | float | None = None, |
| allow_missing_keys: bool = False, |
| ) -> None: |
| super().__init__(keys, allow_missing_keys) |
| self.transform = KSpaceSpikeNoise(loc, k_intensity) |
|
|
| def __call__(self, data: Mapping[Hashable, NdarrayOrTensor]) -> dict[Hashable, NdarrayOrTensor]: |
| """ |
| Args: |
| data: Expects image/label to have dimensions (C, H, W) or |
| (C, H, W, D), where C is the channel. |
| """ |
| d = dict(data) |
| for key in self.key_iterator(d): |
| d[key] = self.transform(d[key]) |
| return d |
|
|
|
|
| class RandKSpaceSpikeNoised(RandomizableTransform, MapTransform): |
| """ |
| Dictionary-based version of :py:class:`monai.transforms.RandKSpaceSpikeNoise`. |
| |
| Naturalistic data augmentation via spike artifacts. The transform applies |
| localized spikes in `k`-space. |
| |
| For general information on spike artifacts, please refer to: |
| |
| `AAPM/RSNA physics tutorial for residents: fundamental physics of MR imaging |
| <https://pubmed.ncbi.nlm.nih.gov/16009826>`_. |
| |
| `Body MRI artifacts in clinical practice: A physicist's and radiologist's |
| perspective <https://doi.org/10.1002/jmri.24288>`_. |
| |
| Args: |
| keys: "image", "label", or ["image", "label"] depending |
| on which data you need to transform. |
| prob: probability to add spike artifact to each item in the |
| dictionary provided it is realized that the noise will be applied |
| to the dictionary. |
| intensity_range: pass a tuple (a, b) to sample the log-intensity from the interval (a, b) |
| uniformly for all channels. Or pass sequence of intervals |
| ((a0, b0), (a1, b1), ...) to sample for each respective channel. |
| In the second case, the number of 2-tuples must match the number of channels. |
| Default ranges is `(0.95x, 1.10x)` where `x` is the mean |
| log-intensity for each channel. |
| channel_wise: treat each channel independently. True by default. |
| allow_missing_keys: do not raise exception if key is missing. |
| |
| Example: |
| To apply `k`-space spikes randomly on the image only, with probability |
| 0.5, and log-intensity sampled from the interval [13, 15] for each |
| channel independently, one uses |
| ``RandKSpaceSpikeNoised("image", prob=0.5, intensity_ranges=(13, 15), channel_wise=True)``. |
| """ |
|
|
| backend = RandKSpaceSpikeNoise.backend |
|
|
| def __init__( |
| self, |
| keys: KeysCollection, |
| prob: float = 0.1, |
| intensity_range: Sequence[Sequence[float] | float] | None = None, |
| channel_wise: bool = True, |
| allow_missing_keys: bool = False, |
| ): |
| MapTransform.__init__(self, keys, allow_missing_keys) |
| RandomizableTransform.__init__(self, prob=prob) |
| self.rand_noise = RandKSpaceSpikeNoise(prob=1.0, intensity_range=intensity_range, channel_wise=channel_wise) |
|
|
| def set_random_state( |
| self, seed: int | None = None, state: np.random.RandomState | None = None |
| ) -> RandKSpaceSpikeNoised: |
| super().set_random_state(seed, state) |
| self.rand_noise.set_random_state(seed, state) |
| return self |
|
|
| def __call__(self, data: dict[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_noise(d[key], randomize=True) |
| return d |
|
|
|
|
| class RandCoarseDropoutd(RandomizableTransform, MapTransform): |
| """ |
| Dictionary-based wrapper of :py:class:`monai.transforms.RandCoarseDropout`. |
| Expect all the data specified by `keys` have same spatial shape and will randomly dropout the same regions |
| for every key, if want to dropout differently for every key, please use this transform separately. |
| |
| Args: |
| keys: keys of the corresponding items to be transformed. |
| See also: :py:class:`monai.transforms.compose.MapTransform` |
| holes: number of regions to dropout, if `max_holes` is not None, use this arg as the minimum number to |
| randomly select the expected number of regions. |
| spatial_size: spatial size of the regions to dropout, if `max_spatial_size` is not None, use this arg |
| as the minimum spatial size to randomly select size for every region. |
| if some components of the `spatial_size` are non-positive values, the transform will use the |
| corresponding components of input img size. For example, `spatial_size=(32, -1)` will be adapted |
| to `(32, 64)` if the second spatial dimension size of img is `64`. |
| dropout_holes: if `True`, dropout the regions of holes and fill value, if `False`, keep the holes and |
| dropout the outside and fill value. default to `True`. |
| fill_value: target value to fill the dropout regions, if providing a number, will use it as constant |
| value to fill all the regions. if providing a tuple for the `min` and `max`, will randomly select |
| value for every pixel / voxel from the range `[min, max)`. if None, will compute the `min` and `max` |
| value of input image then randomly select value to fill, default to None. |
| max_holes: if not None, define the maximum number to randomly select the expected number of regions. |
| max_spatial_size: if not None, define the maximum spatial size to randomly select size for every region. |
| if some components of the `max_spatial_size` are non-positive values, the transform will use the |
| corresponding components of input img size. For example, `max_spatial_size=(32, -1)` will be adapted |
| to `(32, 64)` if the second spatial dimension size of img is `64`. |
| prob: probability of applying the transform. |
| allow_missing_keys: don't raise exception if key is missing. |
| |
| """ |
|
|
| backend = RandCoarseDropout.backend |
|
|
| def __init__( |
| self, |
| keys: KeysCollection, |
| holes: int, |
| spatial_size: Sequence[int] | int, |
| dropout_holes: bool = True, |
| fill_value: tuple[float, float] | float | None = None, |
| max_holes: int | None = None, |
| max_spatial_size: Sequence[int] | int | None = None, |
| prob: float = 0.1, |
| allow_missing_keys: bool = False, |
| ): |
| MapTransform.__init__(self, keys, allow_missing_keys) |
| RandomizableTransform.__init__(self, prob=prob) |
| self.dropper = RandCoarseDropout( |
| holes=holes, |
| spatial_size=spatial_size, |
| dropout_holes=dropout_holes, |
| fill_value=fill_value, |
| max_holes=max_holes, |
| max_spatial_size=max_spatial_size, |
| prob=1.0, |
| ) |
|
|
| def set_random_state( |
| self, seed: int | None = None, state: np.random.RandomState | None = None |
| ) -> RandCoarseDropoutd: |
| super().set_random_state(seed, state) |
| self.dropper.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 |
|
|
| |
| first_key: Hashable = self.first_key(d) |
| if first_key == (): |
| for key in self.key_iterator(d): |
| d[key] = convert_to_tensor(d[key], track_meta=get_track_meta()) |
| return d |
|
|
| self.dropper.randomize(d[first_key].shape[1:]) |
| for key in self.key_iterator(d): |
| d[key] = self.dropper(img=d[key], randomize=False) |
|
|
| return d |
|
|
|
|
| class RandCoarseShuffled(RandomizableTransform, MapTransform): |
| """ |
| Dictionary-based wrapper of :py:class:`monai.transforms.RandCoarseShuffle`. |
| Expect all the data specified by `keys` have same spatial shape and will randomly dropout the same regions |
| for every key, if want to shuffle different regions for every key, please use this transform separately. |
| |
| Args: |
| keys: keys of the corresponding items to be transformed. |
| See also: :py:class:`monai.transforms.compose.MapTransform` |
| holes: number of regions to dropout, if `max_holes` is not None, use this arg as the minimum number to |
| randomly select the expected number of regions. |
| spatial_size: spatial size of the regions to dropout, if `max_spatial_size` is not None, use this arg |
| as the minimum spatial size to randomly select size for every region. |
| if some components of the `spatial_size` are non-positive values, the transform will use the |
| corresponding components of input img size. For example, `spatial_size=(32, -1)` will be adapted |
| to `(32, 64)` if the second spatial dimension size of img is `64`. |
| max_holes: if not None, define the maximum number to randomly select the expected number of regions. |
| max_spatial_size: if not None, define the maximum spatial size to randomly select size for every region. |
| if some components of the `max_spatial_size` are non-positive values, the transform will use the |
| corresponding components of input img size. For example, `max_spatial_size=(32, -1)` will be adapted |
| to `(32, 64)` if the second spatial dimension size of img is `64`. |
| prob: probability of applying the transform. |
| allow_missing_keys: don't raise exception if key is missing. |
| |
| """ |
|
|
| backend = RandCoarseShuffle.backend |
|
|
| def __init__( |
| self, |
| keys: KeysCollection, |
| holes: int, |
| spatial_size: Sequence[int] | int, |
| max_holes: int | None = None, |
| max_spatial_size: Sequence[int] | int | None = None, |
| prob: float = 0.1, |
| allow_missing_keys: bool = False, |
| ): |
| MapTransform.__init__(self, keys, allow_missing_keys) |
| RandomizableTransform.__init__(self, prob=prob) |
| self.shuffle = RandCoarseShuffle( |
| holes=holes, spatial_size=spatial_size, max_holes=max_holes, max_spatial_size=max_spatial_size, prob=1.0 |
| ) |
|
|
| def set_random_state( |
| self, seed: int | None = None, state: np.random.RandomState | None = None |
| ) -> RandCoarseShuffled: |
| super().set_random_state(seed, state) |
| self.shuffle.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 |
|
|
| |
| first_key: Hashable = self.first_key(d) |
| if first_key == (): |
| for key in self.key_iterator(d): |
| d[key] = convert_to_tensor(d[key], track_meta=get_track_meta()) |
| return d |
|
|
| self.shuffle.randomize(d[first_key].shape[1:]) |
| for key in self.key_iterator(d): |
| d[key] = self.shuffle(img=d[key], randomize=False) |
|
|
| return d |
|
|
|
|
| class HistogramNormalized(MapTransform): |
| """ |
| Dictionary-based wrapper of :py:class:`monai.transforms.HistogramNormalize`. |
| |
| Args: |
| keys: keys of the corresponding items to be transformed. |
| See also: :py:class:`monai.transforms.compose.MapTransform` |
| num_bins: number of the bins to use in histogram, default to `256`. for more details: |
| https://numpy.org/doc/stable/reference/generated/numpy.histogram.html. |
| min: the min value to normalize input image, default to `255`. |
| max: the max value to normalize input image, default to `255`. |
| mask: if provided, must be ndarray of bools or 0s and 1s, and same shape as `image`. |
| only points at which `mask==True` are used for the equalization. |
| can also provide the mask by `mask_key` at runtime. |
| mask_key: if mask is None, will try to get the mask with `mask_key`. |
| dtype: output data type, if None, same as input image. defaults to float32. |
| allow_missing_keys: do not raise exception if key is missing. |
| |
| """ |
|
|
| backend = HistogramNormalize.backend |
|
|
| def __init__( |
| self, |
| keys: KeysCollection, |
| num_bins: int = 256, |
| min: int = 0, |
| max: int = 255, |
| mask: NdarrayOrTensor | None = None, |
| mask_key: str | None = None, |
| dtype: DtypeLike = np.float32, |
| allow_missing_keys: bool = False, |
| ) -> None: |
| super().__init__(keys, allow_missing_keys) |
| self.transform = HistogramNormalize(num_bins=num_bins, min=min, max=max, mask=mask, dtype=dtype) |
| self.mask_key = mask_key if mask is None else None |
|
|
| def __call__(self, data: Mapping[Hashable, NdarrayOrTensor]) -> dict[Hashable, NdarrayOrTensor]: |
| d = dict(data) |
| for key in self.key_iterator(d): |
| d[key] = self.transform(d[key], d[self.mask_key]) if self.mask_key is not None else self.transform(d[key]) |
|
|
| return d |
|
|
|
|
| class ForegroundMaskd(MapTransform): |
| """ |
| Creates a binary mask that defines the foreground based on thresholds in RGB or HSV color space. |
| This transform receives an RGB (or grayscale) image where by default it is assumed that the foreground has |
| low values (dark) while the background is white. |
| |
| Args: |
| keys: keys of the corresponding items to be transformed. |
| threshold: an int or a float number that defines the threshold that values less than that are foreground. |
| It also can be a callable that receives each dimension of the image and calculate the threshold, |
| or a string that defines such callable from `skimage.filter.threshold_...`. For the list of available |
| threshold functions, please refer to https://scikit-image.org/docs/stable/api/skimage.filters.html |
| Moreover, a dictionary can be passed that defines such thresholds for each channel, like |
| {"R": 100, "G": "otsu", "B": skimage.filter.threshold_mean} |
| hsv_threshold: similar to threshold but HSV color space ("H", "S", and "V"). |
| Unlike RBG, in HSV, value greater than `hsv_threshold` are considered foreground. |
| invert: invert the intensity range of the input image, so that the dtype maximum is now the dtype minimum, |
| and vice-versa. |
| new_key_prefix: this prefix be prepended to the key to create a new key for the output and keep the value of |
| key intact. By default not prefix is set and the corresponding array to the key will be replaced. |
| allow_missing_keys: do not raise exception if key is missing. |
| |
| """ |
|
|
| def __init__( |
| self, |
| keys: KeysCollection, |
| threshold: dict | Callable | str | float = "otsu", |
| hsv_threshold: dict | Callable | str | float | int | None = None, |
| invert: bool = False, |
| new_key_prefix: str | None = None, |
| allow_missing_keys: bool = False, |
| ) -> None: |
| super().__init__(keys, allow_missing_keys) |
| self.transform = ForegroundMask(threshold=threshold, hsv_threshold=hsv_threshold, invert=invert) |
| self.new_key_prefix = new_key_prefix |
|
|
| def __call__(self, data: Mapping[Hashable, NdarrayOrTensor]) -> dict[Hashable, NdarrayOrTensor]: |
| d = dict(data) |
| for key in self.key_iterator(d): |
| new_key = key if self.new_key_prefix is None else self.new_key_prefix + key |
| d[new_key] = self.transform(d[key]) |
|
|
| return d |
|
|
|
|
| class ComputeHoVerMapsd(MapTransform): |
| """Compute horizontal and vertical maps from an instance mask |
| It generates normalized horizontal and vertical distances to the center of mass of each region. |
| |
| Args: |
| keys: keys of the corresponding items to be transformed. |
| dtype: the type of output Tensor. Defaults to `"float32"`. |
| new_key_prefix: this prefix be prepended to the key to create a new key for the output and keep the value of |
| key intact. Defaults to '"_hover", so if the input key is "mask" the output will be "hover_mask". |
| allow_missing_keys: do not raise exception if key is missing. |
| |
| """ |
|
|
| def __init__( |
| self, |
| keys: KeysCollection, |
| dtype: DtypeLike = "float32", |
| new_key_prefix: str = "hover_", |
| allow_missing_keys: bool = False, |
| ) -> None: |
| super().__init__(keys, allow_missing_keys) |
| self.transform = ComputeHoVerMaps(dtype=dtype) |
| self.new_key_prefix = new_key_prefix |
|
|
| def __call__(self, data: Mapping[Hashable, NdarrayOrTensor]) -> dict[Hashable, NdarrayOrTensor]: |
| d = dict(data) |
| for key in self.key_iterator(d): |
| new_key = key if self.new_key_prefix is None else self.new_key_prefix + key |
| d[new_key] = self.transform(d[key]) |
|
|
| return d |
|
|
|
|
| RandGaussianNoiseD = RandGaussianNoiseDict = RandGaussianNoised |
| RandRicianNoiseD = RandRicianNoiseDict = RandRicianNoised |
| ShiftIntensityD = ShiftIntensityDict = ShiftIntensityd |
| RandShiftIntensityD = RandShiftIntensityDict = RandShiftIntensityd |
| StdShiftIntensityD = StdShiftIntensityDict = StdShiftIntensityd |
| RandStdShiftIntensityD = RandStdShiftIntensityDict = RandStdShiftIntensityd |
| RandBiasFieldD = RandBiasFieldDict = RandBiasFieldd |
| ScaleIntensityD = ScaleIntensityDict = ScaleIntensityd |
| RandScaleIntensityD = RandScaleIntensityDict = RandScaleIntensityd |
| RandScaleIntensityFixedMeanD = RandScaleIntensityFixedMeanDict = RandScaleIntensityFixedMeand |
| NormalizeIntensityD = NormalizeIntensityDict = NormalizeIntensityd |
| ThresholdIntensityD = ThresholdIntensityDict = ThresholdIntensityd |
| ScaleIntensityRangeD = ScaleIntensityRangeDict = ScaleIntensityRanged |
| ClipIntensityPercentilesD = ClipIntensityPercentilesDict = ClipIntensityPercentilesd |
| AdjustContrastD = AdjustContrastDict = AdjustContrastd |
| RandAdjustContrastD = RandAdjustContrastDict = RandAdjustContrastd |
| ScaleIntensityRangePercentilesD = ScaleIntensityRangePercentilesDict = ScaleIntensityRangePercentilesd |
| MaskIntensityD = MaskIntensityDict = MaskIntensityd |
| SavitzkyGolaySmoothD = SavitzkyGolaySmoothDict = SavitzkyGolaySmoothd |
| MedianSmoothD = MedianSmoothDict = MedianSmoothd |
| GaussianSmoothD = GaussianSmoothDict = GaussianSmoothd |
| RandGaussianSmoothD = RandGaussianSmoothDict = RandGaussianSmoothd |
| GaussianSharpenD = GaussianSharpenDict = GaussianSharpend |
| RandGaussianSharpenD = RandGaussianSharpenDict = RandGaussianSharpend |
| RandHistogramShiftD = RandHistogramShiftDict = RandHistogramShiftd |
| RandGibbsNoiseD = RandGibbsNoiseDict = RandGibbsNoised |
| GibbsNoiseD = GibbsNoiseDict = GibbsNoised |
| KSpaceSpikeNoiseD = KSpaceSpikeNoiseDict = KSpaceSpikeNoised |
| RandKSpaceSpikeNoiseD = RandKSpaceSpikeNoiseDict = RandKSpaceSpikeNoised |
| RandCoarseDropoutD = RandCoarseDropoutDict = RandCoarseDropoutd |
| HistogramNormalizeD = HistogramNormalizeDict = HistogramNormalized |
| RandCoarseShuffleD = RandCoarseShuffleDict = RandCoarseShuffled |
| ForegroundMaskD = ForegroundMaskDict = ForegroundMaskd |
| ComputeHoVerMapsD = ComputeHoVerMapsDict = ComputeHoVerMapsd |
|
|