Source code for torchio.transforms.preprocessing.intensity.z_normalization

from typing import Optional

import torch

from ....data.subject import Subject
from .normalization_transform import NormalizationTransform
from .normalization_transform import TypeMaskingMethod




class ZNormalization(NormalizationTransform):
    """Subtract mean and divide by standard deviation.

    Args:
        masking_method: See
            :class:`~torchio.transforms.preprocessing.intensity.NormalizationTransform`.
        **kwargs: See :class:`~torchio.transforms.Transform` for additional
            keyword arguments.
    """

    def __init__(self, masking_method: TypeMaskingMethod = None, **kwargs):
        super().__init__(masking_method=masking_method, **kwargs)
        self.args_names = ['masking_method']

    def apply_normalization(
        self,
        subject: Subject,
        image_name: str,
        mask: torch.Tensor,
    ) -> None:
        image = subject[image_name]
        standardized = self.znorm(
            image.data,
            mask,
        )
        if standardized is None:
            message = (
                'Standard deviation is 0 for masked values'
                f' in image "{image_name}" ({image.path})'
            )
            raise RuntimeError(message)
        image.set_data(standardized)

    @staticmethod
    def znorm(
        tensor: torch.Tensor,
        mask: torch.Tensor,
    ) -> Optional[torch.Tensor]:
        tensor = tensor.clone().float()
        values = tensor[mask]
        mean, std = values.mean(), values.std()
        if std == 0:
            return None
        tensor -= mean
        tensor /= std
        return tensor