torchio.data.image

Complexity

Total Complexity

90

Size/Duplication

Total Lines	542
Duplicated Lines	0 %

Importance

Changes

0

36 Methods

Rating	Name	Duplication	Size	Complexity
A	Image.parse_affine()	0	9	4
A	Image.get_center()	0	15	2
A	Image.set_check_nans()	0	2	1
A	Image.numpy()	0	3	1
A	Image.is_2d()	0	2	1
A	Image.as_sitk()	0	3	1
A	Image.spatial_shape()	0	3	1
A	Image.__array__()	0	2	1
A	Image._parse_single_path()	0	21	5
B	Image.flip_axis()	0	12	7
B	Image.parse_tensor()	0	12	7
A	Image.get_bounds()	0	9	1
A	Image.data()	0	3	1
A	Image.save()	0	13	1
A	LabelMap.__init__()	0	5	3
A	Image.memory()	0	3	1
A	Image.__repr__()	0	15	2
A	Image.type()	0	3	1
A	Image.__copy__()	0	11	3
A	Image.crop()	0	17	3
A	Image._parse_path()	0	10	3
C	Image.__init__()	0	42	9
C	Image.load()	0	53	10
A	Image.check_is_2d()	0	4	2
A	Image.shape()	0	3	1
A	Image.__getitem__()	0	5	3
A	Image.orientation()	0	3	1
A	Image.width()	0	4	1
A	Image.tensor()	0	3	1
A	Image.parse_tensor_shape()	0	6	1
A	Image.spacing()	0	4	1
A	Image.get_spacing_string()	0	4	1
A	ScalarImage.__init__()	0	5	3
A	Image.axis_name_to_index()	0	36	4
A	Image.height()	0	4	1
A	Image.affine()	0	3	1

import warnings
from pathlib import Path
from typing import Any, Dict, Tuple, Optional, Union, Sequence, List

import torch
import humanize
import numpy as np
import nibabel as nib
import SimpleITK as sitk

from ..utils import (
    nib_to_sitk,
    get_rotation_and_spacing_from_affine,
    get_stem,
    ensure_4d,
)
from ..torchio import (
    TypeData,
    TypePath,
    TypeTripletInt,
    TypeTripletFloat,
    DATA,
    TYPE,
    AFFINE,
    PATH,
    STEM,
    INTENSITY,
    LABEL,
)
from .io import read_image, write_image


PROTECTED_KEYS = DATA, AFFINE, TYPE, PATH, STEM


class Image(dict):
    r"""TorchIO image.

    For information about medical image orientation, check out `NiBabel docs`_,
    the `3D Slicer wiki`_, `Graham Wideman's website`_, `FSL docs`_ or
    `SimpleITK docs`_.

    Args:
        path: Path to a file or sequence of paths to files that can be read by
            :mod:`SimpleITK` or :mod:`nibabel`, or to a directory containing
            DICOM files. If :py:attr:`tensor` is given, the data in
            :py:attr:`path` will not be read. The data is expected to be 2D or
            3D, and may have multiple channels (see :attr:`num_spatial_dims`).
            If a sequence of paths is given, data
            will be concatenated on the channel dimension so spatial
            dimensions must match. If the read tensor is not 4D,
            TorchIO will try to guess the dimensions meanings.
            If 2D, the shape will be interpreted as
            :math:`(W, H)`. If 3D, the number of spatial dimensions should be
            determined in :attr:`num_spatial_dims`. If :attr:`num_spatial_dims`
            is not given and the shape is 3 along the first or last dimensions,
            it will be interpreted as a multichannel 2D image. Otherwise, it
            be interpreted as a 3D image with a single channel.
        type: Type of image, such as :attr:`torchio.INTENSITY` or
            :attr:`torchio.LABEL`. This will be used by the transforms to
            decide whether to apply an operation, or which interpolation to use
            when resampling. For example, `preprocessing`_ and `augmentation`_
            intensity transforms will only be applied to images with type
            :attr:`torchio.INTENSITY`. Spatial transforms will be applied to
            all types, and nearest neighbor interpolation is always used to
            resample images with type :attr:`torchio.LABEL`.
            The type :attr:`torchio.SAMPLING_MAP` may be used with instances of
            :py:class:`~torchio.data.sampler.weighted.WeightedSampler`.
        tensor: If :py:attr:`path` is not given, :attr:`tensor` must be a 4D
            :py:class:`torch.Tensor` or NumPy array with dimensions
            :math:`(C, W, H, D)`.
        affine: If :attr:`path` is not given, :attr:`affine` must be a
            :math:`4 \times 4` NumPy array. If ``None``, :attr:`affine` is an
            identity matrix.
        check_nans: If ``True``, issues a warning if NaNs are found
            in the image. If ``False``, images will not be checked for the
            presence of NaNs.
        num_spatial_dims: If ``2`` and the input tensor has 3 dimensions, it
            will be interpreted as a multichannel 2D image. If ``3`` and the
            input has 3 dimensions, it will be interpreted as a
            single-channel 3D volume.
        **kwargs: Items that will be added to the image dictionary, e.g.
            acquisition parameters.

    TorchIO images are `lazy loaders`_, i.e. the data is only loaded from disk
    when needed.

    Example:
        >>> import torchio
        >>> image = torchio.ScalarImage('t1.nii.gz')  # subclass of Image
        >>> image  # not loaded yet
        ScalarImage(path: t1.nii.gz; type: intensity)
        >>> times_two = 2 * image.data  # data is loaded and cached here
        >>> image
        ScalarImage(shape: (1, 256, 256, 176); spacing: (1.00, 1.00, 1.00); orientation: PIR+; memory: 44.0 MiB; type: intensity)
        >>> image.save('doubled_image.nii.gz')

    .. _lazy loaders: https://en.wikipedia.org/wiki/Lazy_loading
    .. _preprocessing: https://torchio.readthedocs.io/transforms/preprocessing.html#intensity
    .. _augmentation: https://torchio.readthedocs.io/transforms/augmentation.html#intensity
    .. _NiBabel docs: https://nipy.org/nibabel/image_orientation.html
    .. _3D Slicer wiki: https://www.slicer.org/wiki/Coordinate_systems
    .. _FSL docs: https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Orientation%20Explained
    .. _SimpleITK docs: https://simpleitk.readthedocs.io/en/master/fundamentalConcepts.html
    .. _Graham Wideman's website: http://www.grahamwideman.com/gw/brain/orientation/orientterms.htm
    """
    def __init__(
            self,
            path: Union[TypePath, Sequence[TypePath], None] = None,
            type: str = None,
            tensor: Optional[TypeData] = None,
            affine: Optional[TypeData] = None,
            check_nans: bool = True,
            num_spatial_dims: Optional[int] = None,
            **kwargs: Dict[str, Any],
            ):
        self.check_nans = check_nans
        self.num_spatial_dims = num_spatial_dims

        if type is None:
            warnings.warn(
                'Not specifying the image type is deprecated and will be'
                ' mandatory in the future. You can probably use ScalarImage or'
                ' LabelMap instead'
            )
            type = INTENSITY

        if path is None and tensor is None:
            raise ValueError('A value for path or tensor must be given')
        self._loaded = False

        tensor = self.parse_tensor(tensor)
        affine = self.parse_affine(affine)
        if tensor is not None:
            self[DATA] = tensor
            self[AFFINE] = affine
            self._loaded = True
        for key in PROTECTED_KEYS:
            if key in kwargs:
                message = f'Key "{key}" is reserved. Use a different one'
                raise ValueError(message)

        super().__init__(**kwargs)
        self.path = self._parse_path(path)

        self[PATH] = '' if self.path is None else str(self.path)
        self[STEM] = '' if self.path is None else get_stem(self.path)
        self[TYPE] = type

    def __repr__(self):
        properties = []
        if self._loaded:
            properties.extend([
                f'shape: {self.shape}',
                f'spacing: {self.get_spacing_string()}',
                f'orientation: {"".join(self.orientation)}+',
                f'memory: {humanize.naturalsize(self.memory, binary=True)}',
            ])
        else:
            properties.append(f'path: "{self.path}"')
        properties.append(f'type: {self.type}')
        properties = '; '.join(properties)
        string = f'{self.__class__.__name__}({properties})'
        return string

    def __getitem__(self, item):
        if item in (DATA, AFFINE):
            if item not in self:
                self.load()
        return super().__getitem__(item)

    def __array__(self):
        return self[DATA].numpy()

    def __copy__(self):
        kwargs = dict(
            tensor=self.data,
            affine=self.affine,
            type=self.type,
            path=self.path,
        )
        for key, value in self.items():
            if key in PROTECTED_KEYS: continue
            kwargs[key] = value  # should I copy? deepcopy?
        return self.__class__(**kwargs)

    @property
    def data(self):
        return self[DATA]

    @property
    def tensor(self):
        return self.data

    @property
    def affine(self):
        return self[AFFINE]

    @property
    def type(self):
        return self[TYPE]

    @property
    def shape(self) -> Tuple[int, int, int, int]:
        return tuple(self.data.shape)

    @property
    def spatial_shape(self) -> TypeTripletInt:
        return self.shape[1:]

    def check_is_2d(self):
        if not self.is_2d():
            message = f'Image is not 2D. Spatial shape: {self.spatial_shape}'
            raise RuntimeError(message)

    @property
    def height(self) -> int:
        self.check_is_2d()
        return self.spatial_shape[1]

    @property
    def width(self) -> int:
        self.check_is_2d()
        return self.spatial_shape[0]

    @property
    def orientation(self):
        return nib.aff2axcodes(self.affine)

    @property
    def spacing(self):
        _, spacing = get_rotation_and_spacing_from_affine(self.affine)
        return tuple(spacing)

    @property
    def memory(self):
        return np.prod(self.shape) * 4  # float32, i.e. 4 bytes per voxel

    def axis_name_to_index(self, axis: str):
        """Convert an axis name to an axis index.

        Args:
            axis: Possible inputs are ``'Left'``, ``'Right'``, ``'Anterior'``,
            ``'Posterior'``, ``'Inferior'``, ``'Superior'``. Lower-case versions
            and first letters are also valid, as only the first letter will be
            used.

        .. note:: If you are working with animals, you should probably use
            ``'Superior'``, ``'Inferior'``, ``'Anterior'`` and ``'Posterior'``
            for ``'Dorsal'``, ``'Ventral'``, ``'Rostral'`` and ``'Caudal'``,
            respectively.

        .. note:: If your images are 2D, you can use ``'Top'``, ``'Bottom'``,
            ``'Left'`` and ``'Right'``.
        """
        # Top and bottom are used for the vertical 2D axis as the use of
        # Height vs Horizontal might be ambiguous

        if not isinstance(axis, str):
            raise ValueError('Axis must be a string')
        axis = axis[0].upper()

        # Generally, TorchIO tensors are (C, W, H, D)
        if axis in 'TB':  # Top, Bottom
            return -2
        else:
            try:
                index = self.orientation.index(axis)
            except ValueError:
                index = self.orientation.index(self.flip_axis(axis))
            # Return negative indices so that it does not matter whether we
            # refer to spatial dimensions or not
            index = -3 + index
            return index

    # flake8: noqa: E701
    @staticmethod
    def flip_axis(axis):
        if axis == 'R': return 'L'
        elif axis == 'L': return 'R'
        elif axis == 'A': return 'P'
        elif axis == 'P': return 'A'
        elif axis == 'I': return 'S'
        elif axis == 'S': return 'I'
        else:
            values = ', '.join('LRPAISTB')
            message = f'Axis not understood. Please use one of: {values}'
            raise ValueError(message)

    def get_spacing_string(self):
        strings = [f'{n:.2f}' for n in self.spacing]
        string = f'({", ".join(strings)})'
        return string

    def get_bounds(self):
        """Get image bounds in mm."""
        first_index = 3 * (-0.5,)
        last_index = np.array(self.spatial_shape) - 0.5
        first_point = nib.affines.apply_affine(self.affine, first_index)
        last_point = nib.affines.apply_affine(self.affine, last_index)
        array = np.array((first_point, last_point))
        bounds_x, bounds_y, bounds_z = array.T.tolist()
        return bounds_x, bounds_y, bounds_z

    @staticmethod
    def _parse_single_path(
            path: TypePath
            ) -> Path:
        try:
            path = Path(path).expanduser()
        except TypeError:
            message = (
                f'Expected type str or Path but found {path} with '
                f'{type(path)} instead'
            )
            raise TypeError(message)
        except RuntimeError:
            message = (
                f'Conversion to path not possible for variable: {path}'
            )
            raise RuntimeError(message)

        if not (path.is_file() or path.is_dir()):   # might be a dir with DICOM
            raise FileNotFoundError(f'File not found: {path}')
        return path

    def _parse_path(
            self,
            path: Union[TypePath, Sequence[TypePath]]
            ) -> Union[Path, List[Path]]:
        if path is None:
            return None
        if isinstance(path, (str, Path)):
            return self._parse_single_path(path)
        else:
            return [self._parse_single_path(p) for p in path]

    def parse_tensor(self, tensor: TypeData) -> torch.Tensor:
        if tensor is None:
            return None
        if isinstance(tensor, np.ndarray):
            tensor = torch.from_numpy(tensor.astype(np.float32))
        elif isinstance(tensor, torch.Tensor):
            tensor = tensor.float()
        if tensor.ndim != 4:
            raise ValueError('Input tensor must be 4D')
        if self.check_nans and torch.isnan(tensor).any():
            warnings.warn(f'NaNs found in tensor')
        return tensor

    def parse_tensor_shape(
            self,
            tensor: torch.Tensor,
            num_spatial_dims: int,
            ) -> torch.Tensor:
        return ensure_4d(tensor, num_spatial_dims)

    @staticmethod
    def parse_affine(affine: np.ndarray) -> np.ndarray:
        if affine is None:
            return np.eye(4)
        if not isinstance(affine, np.ndarray):
            raise TypeError(f'Affine must be a NumPy array, not {type(affine)}')
        if affine.shape != (4, 4):
            raise ValueError(f'Affine shape must be (4, 4), not {affine.shape}')
        return affine

    def load(self) -> None:
        r"""Load the image from disk.

        Returns:
            Tuple containing a 4D tensor of size :math:`(C, W, H, D)` and a 2D
            :math:`4 \times 4` affine matrix to convert voxel indices to world
            coordinates.
        """
        if self._loaded:
            return

        paths = self.path if isinstance(self.path, list) else [self.path]
        tensor, affine = read_image(paths[0])
        tensor = self.parse_tensor_shape(tensor, self.num_spatial_dims)

        if self.check_nans and torch.isnan(tensor).any():
            warnings.warn(f'NaNs found in file "{paths[0]}"')

        tensors = [tensor]
        for path in paths[1:]:
            new_tensor, new_affine = read_image(path)
            new_tensor = self.parse_tensor_shape(
                new_tensor,
                self.num_spatial_dims,
            )

            if self.check_nans and torch.isnan(tensor).any():
                warnings.warn(f'NaNs found in file "{path}"')

            if not np.array_equal(affine, new_affine):
                message = (
                    'Files have different affine matrices.'
                    f'\nMatrix of {paths[0]}:'
                    f'\n{affine}'
                    f'\nMatrix of {path}:'
                    f'\n{new_affine}'
                )
                warnings.warn(message, RuntimeWarning)

            if not tensor.shape[1:] == new_tensor.shape[1:]:
                message = (
                    f'Files shape do not match, found {tensor.shape}'
                    f'and {new_tensor.shape}'
                )
                RuntimeError(message)

            tensors.append(new_tensor)

        tensor = torch.cat(tensors)

        self[DATA] = tensor
        self[AFFINE] = affine
        self._loaded = True

    def save(self, path, squeeze=True):
        """Save image to disk.

        Args:
            path: String or instance of :py:class:`pathlib.Path`.
            squeeze: If ``True``, the singleton dimensions will be removed
                before saving.
        """
        write_image(
            self[DATA],
            self[AFFINE],
            path,
            squeeze=squeeze,
        )

    def is_2d(self) -> bool:
        return self.shape[-1] == 1

    def numpy(self) -> np.ndarray:
        """Get a NumPy array containing the image data."""
        return np.asarray(self)

    def as_sitk(self, **kwargs) -> sitk.Image:
        """Get the image as an instance of :py:class:`sitk.Image`."""
        return nib_to_sitk(self[DATA], self[AFFINE], **kwargs)

    def get_center(self, lps: bool = False) -> TypeTripletFloat:
        """Get image center in RAS+ or LPS+ coordinates.

        Args:
            lps: If ``True``, the coordinates will be in LPS+ orientation, i.e.
                the first dimension grows towards the left, etc. Otherwise, the
                coordinates will be in RAS+ orientation.
        """
        size = np.array(self.spatial_shape)
        center_index = (size - 1) / 2
        r, a, s = nib.affines.apply_affine(self.affine, center_index)
        if lps:
            return (-r, -a, s)
        else:
            return (r, a, s)

    def set_check_nans(self, check_nans: bool):
        self.check_nans = check_nans

    def crop(self, index_ini: TypeTripletInt, index_fin: TypeTripletInt):
        new_origin = nib.affines.apply_affine(self.affine, index_ini)
        new_affine = self.affine.copy()
        new_affine[:3, 3] = new_origin
        i0, j0, k0 = index_ini
        i1, j1, k1 = index_fin
        patch = self.data[:, i0:i1, j0:j1, k0:k1].clone()
        kwargs = dict(
            tensor=patch,
            affine=new_affine,
            type=self.type,
            path=self.path,
        )
        for key, value in self.items():
            if key in PROTECTED_KEYS: continue
            kwargs[key] = value  # should I copy? deepcopy?
        return self.__class__(**kwargs)


class ScalarImage(Image):
    """Alias for :py:class:`~torchio.Image` of type :py:attr:`torchio.INTENSITY`.

    Example:
        >>> import torch
        >>> import torchio
        >>> # Loading from a file
        >>> t1_image = torchio.ScalarImage('t1.nii.gz')
        >>> dmri = torchio.ScalarImage(tensor=torch.rand(32, 128, 128, 88))
        >>> image = torchio.ScalarImage('safe_image.nrrd', check_nans=False)
        >>> data, affine = image.data, image.affine
        >>> affine.shape
        (4, 4)
        >>> image.data is image[torchio.DATA]
        True
        >>> image.data is image.tensor
        True
        >>> type(image.data)
        torch.Tensor

    See :py:class:`~torchio.Image` for more information.

    Raises:
        ValueError: A :py:attr:`type` is used for instantiation.
    """
    def __init__(self, *args, **kwargs):
        if 'type' in kwargs and kwargs['type'] != INTENSITY:
            raise ValueError('Type of ScalarImage is always torchio.INTENSITY')
        kwargs.update({'type': INTENSITY})
        super().__init__(*args, **kwargs)


class LabelMap(Image):
    """Alias for :py:class:`~torchio.Image` of type :py:attr:`torchio.LABEL`.

    Example:
        >>> import torch
        >>> import torchio
        >>> labels = torchio.LabelMap(tensor=torch.rand(128, 128, 68) > 0.5)
        >>> labels = torchio.LabelMap('t1_seg.nii.gz')  # loading from a file
        >>> tpm = torchio.LabelMap(                     # loading from files
        ...     'gray_matter.nii.gz',
        ...     'white_matter.nii.gz',
        ...     'csf.nii.gz',
        ... )

    See :py:class:`~torchio.data.image.Image` for more information.

    Raises:
        ValueError: If a value for :py:attr:`type` is given.
    """
    def __init__(self, *args, **kwargs):
        if 'type' in kwargs and kwargs['type'] != LABEL:
            raise ValueError('Type of LabelMap is always torchio.LABEL')
        kwargs.update({'type': LABEL})
        super().__init__(*args, **kwargs)