Source code for torchio.transforms.augmentation.intensity.random_motion

from collections import defaultdict
from typing import Dict
from typing import List
from typing import Sequence
from typing import Tuple
from typing import Union

import numpy as np
import SimpleITK as sitk
import torch

from .. import RandomTransform
from ... import FourierTransform
from ... import IntensityTransform
from import nib_to_sitk
from import Subject
from ....typing import TypeTripletFloat

[docs]class RandomMotion(RandomTransform, IntensityTransform, FourierTransform): r"""Add random MRI motion artifact. Magnetic resonance images suffer from motion artifacts when the subject moves during image acquisition. This transform follows `Shaw et al., 2019 <>`_ to simulate motion artifacts for data augmentation. Args: degrees: Tuple :math:`(a, b)` defining the rotation range in degrees of the simulated movements. The rotation angles around each axis are :math:`(\theta_1, \theta_2, \theta_3)`, where :math:`\theta_i \sim \mathcal{U}(a, b)`. If only one value :math:`d` is provided, :math:`\theta_i \sim \mathcal{U}(-d, d)`. Larger values generate more distorted images. translation: Tuple :math:`(a, b)` defining the translation in mm of the simulated movements. The translations along each axis are :math:`(t_1, t_2, t_3)`, where :math:`t_i \sim \mathcal{U}(a, b)`. If only one value :math:`t` is provided, :math:`t_i \sim \mathcal{U}(-t, t)`. Larger values generate more distorted images. num_transforms: Number of simulated movements. Larger values generate more distorted images. image_interpolation: See :ref:`Interpolation`. **kwargs: See :class:`~torchio.transforms.Transform` for additional keyword arguments. .. warning:: Large numbers of movements lead to longer execution times for 3D images. """ def __init__( self, degrees: float = 10, translation: float = 10, # in mm num_transforms: int = 2, image_interpolation: str = 'linear', **kwargs ): super().__init__(**kwargs) self.degrees_range = self.parse_degrees(degrees) self.translation_range = self.parse_translation(translation) if num_transforms < 1 or not isinstance(num_transforms, int): message = ( 'Number of transforms must be a strictly positive natural' f'number, not {num_transforms}' ) raise ValueError(message) self.num_transforms = num_transforms self.image_interpolation = self.parse_interpolation( image_interpolation, ) def apply_transform(self, subject: Subject) -> Subject: arguments: Dict[str, dict] = defaultdict(dict) for name, image in self.get_images_dict(subject).items(): params = self.get_params( self.degrees_range, self.translation_range, self.num_transforms, is_2d=image.is_2d(), ) times_params, degrees_params, translation_params = params arguments['times'][name] = times_params arguments['degrees'][name] = degrees_params arguments['translation'][name] = translation_params arguments['image_interpolation'][name] = self.image_interpolation transform = Motion(**self.add_include_exclude(arguments)) transformed = transform(subject) assert isinstance(transformed, Subject) return transformed def get_params( self, degrees_range: Tuple[float, float], translation_range: Tuple[float, float], num_transforms: int, perturbation: float = 0.3, is_2d: bool = False, ) -> Tuple[np.ndarray, np.ndarray, np.ndarray]: # If perturbation is 0, time intervals between movements are constant degrees_params = self.get_params_array( degrees_range, num_transforms, ) translation_params = self.get_params_array( translation_range, num_transforms, ) if is_2d: # imagine sagittal (1, A, S) degrees_params[:, :-1] = 0 # rotate around Z axis only translation_params[:, 2] = 0 # translate in XY plane only step = 1 / (num_transforms + 1) times = torch.arange(0, 1, step)[1:] noise = torch.FloatTensor(num_transforms) noise.uniform_(-step * perturbation, step * perturbation) times += noise times_params = times.numpy() return times_params, degrees_params, translation_params @staticmethod def get_params_array(nums_range: Tuple[float, float], num_transforms: int): tensor = torch.FloatTensor(num_transforms, 3).uniform_(*nums_range) return tensor.numpy()
class Motion(IntensityTransform, FourierTransform): r"""Add MRI motion artifact. Magnetic resonance images suffer from motion artifacts when the subject moves during image acquisition. This transform follows `Shaw et al., 2019 <>`_ to simulate motion artifacts for data augmentation. Args: degrees: Sequence of rotations :math:`(\theta_1, \theta_2, \theta_3)`. translation: Sequence of translations :math:`(t_1, t_2, t_3)` in mm. times: Sequence of times from 0 to 1 at which the motions happen. image_interpolation: See :ref:`Interpolation`. **kwargs: See :class:`~torchio.transforms.Transform` for additional keyword arguments. """ def __init__( self, degrees: Union[TypeTripletFloat, Dict[str, TypeTripletFloat]], translation: Union[TypeTripletFloat, Dict[str, TypeTripletFloat]], times: Union[Sequence[float], Dict[str, Sequence[float]]], image_interpolation: Union[Sequence[str], Dict[str, Sequence[str]]], # noqa: E501 **kwargs ): super().__init__(**kwargs) self.degrees = degrees self.translation = translation self.times = times self.image_interpolation = image_interpolation self.args_names = [ 'degrees', 'translation', 'times', 'image_interpolation', ] def apply_transform(self, subject: Subject) -> Subject: degrees = self.degrees translation = self.translation times = self.times image_interpolation = self.image_interpolation for image_name, image in self.get_images_dict(subject).items(): if self.arguments_are_dict(): assert isinstance(self.degrees, dict) assert isinstance(self.translation, dict) assert isinstance(self.times, dict) assert isinstance(self.image_interpolation, dict) degrees = self.degrees[image_name] translation = self.translation[image_name] times = self.times[image_name] image_interpolation = self.image_interpolation[image_name] result_arrays = [] for channel in sitk_image = nib_to_sitk( channel[np.newaxis], image.affine, force_3d=True, ) transforms = self.get_rigid_transforms( np.asarray(degrees), np.asarray(translation), sitk_image, ) assert isinstance(image_interpolation, str) transformed_channel = self.add_artifact( sitk_image, transforms, np.asarray(times), image_interpolation, ) result_arrays.append(transformed_channel) result = np.stack(result_arrays) image.set_data(torch.as_tensor(result)) return subject def get_rigid_transforms( self, degrees_params: np.ndarray, translation_params: np.ndarray, image: sitk.Image, ) -> List[sitk.Euler3DTransform]: center_ijk = np.array(image.GetSize()) / 2 center_lps = image.TransformContinuousIndexToPhysicalPoint(center_ijk) identity = np.eye(4) matrices = [identity] for degrees, translation in zip(degrees_params, translation_params): radians = np.radians(degrees).tolist() motion = sitk.Euler3DTransform() motion.SetCenter(center_lps) motion.SetRotation(*radians) motion.SetTranslation(translation.tolist()) motion_matrix = self.transform_to_matrix(motion) matrices.append(motion_matrix) transforms = [self.matrix_to_transform(m) for m in matrices] return transforms @staticmethod def transform_to_matrix(transform: sitk.Euler3DTransform) -> np.ndarray: matrix = np.eye(4) rotation = np.array(transform.GetMatrix()).reshape(3, 3) matrix[:3, :3] = rotation matrix[:3, 3] = transform.GetTranslation() return matrix @staticmethod def matrix_to_transform(matrix: np.ndarray) -> sitk.Euler3DTransform: transform = sitk.Euler3DTransform() rotation = matrix[:3, :3].flatten().tolist() transform.SetMatrix(rotation) transform.SetTranslation(matrix[:3, 3]) return transform def resample_images( self, image: sitk.Image, transforms: Sequence[sitk.Euler3DTransform], interpolation: str, ) -> List[sitk.Image]: floating = reference = image default_value = np.float64(sitk.GetArrayViewFromImage(image).min()) transforms = transforms[1:] # first is identity images = [image] # first is identity for transform in transforms: interpolator = self.get_sitk_interpolator(interpolation) resampler = sitk.ResampleImageFilter() resampler.SetInterpolator(interpolator) resampler.SetReferenceImage(reference) resampler.SetOutputPixelType(sitk.sitkFloat32) resampler.SetDefaultPixelValue(default_value) resampler.SetTransform(transform) resampled = resampler.Execute(floating) images.append(resampled) return images @staticmethod def sort_spectra(spectra: List[torch.Tensor], times: np.ndarray): """Use original spectrum to fill the center of k-space""" num_spectra = len(spectra) if np.any(times > 0.5): index = np.where(times > 0.5)[0].min() else: index = num_spectra - 1 spectra[0], spectra[index] = spectra[index], spectra[0] def add_artifact( self, image: sitk.Image, transforms: Sequence[sitk.Euler3DTransform], times: np.ndarray, interpolation: str, ): images = self.resample_images(image, transforms, interpolation) spectra = [] for image in images: array = sitk.GetArrayFromImage(image).transpose() # sitk to np spectrum = self.fourier_transform(torch.from_numpy(array)) spectra.append(spectrum) self.sort_spectra(spectra, times) result_spectrum = torch.empty_like(spectra[0]) last_index = result_spectrum.shape[2] indices = (last_index * times).astype(int).tolist() indices.append(last_index) ini = 0 for spectrum, fin in zip(spectra, indices): result_spectrum[..., ini:fin] = spectrum[..., ini:fin] ini = fin result_image = self.inv_fourier_transform(result_spectrum).real.float() return result_image