| | |
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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 |
| |
|