torchio.data.image.Image.__init__() - Code Metrics - Inspection of "Fix 4D I/O incompatibility with ITK (#286)" - fepegar/torchio - Measure and Improve Code Quality continuously with Scrutinizer

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Push — master ( 85bce8...47d3da )

by Fernando

created 2020-08-19 19:16 UTC

torchio.data.image.Image.init() C

↳ Parent: torchio.data.image

Complexity

Conditions

Size

Total Lines	42
Code Lines	33

Duplication

Lines	0
Ratio	0 %

Importance

Changes

Metric	Value
cc	9
eloc	33
nop	8
dl	0
loc	42
rs	6.6666
c	0
b	0
f	0

How to fix Many Parameters

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.
            If a sequence of paths is given, data
            will be concatenated on the channel dimension so spatial
            dimensions must match.
        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.
        **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 = False,  # removed by ITK by default
            channels_last: bool = False,
            **kwargs: Dict[str, Any],
            ):
        self.check_nans = check_nans
        self.channels_last = channels_last

        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) -> torch.Tensor:
        return ensure_4d(tensor)

    @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 = self.read_and_check(paths[0])
        tensors = [tensor]
        for path in paths[1:]:
            new_tensor, new_affine = self.read_and_check(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 read_and_check(self, path):
        tensor, affine = read_image(path)
        tensor = self.parse_tensor_shape(tensor)
        if self.channels_last:
            tensor = tensor.permute(3, 0, 1, 2)
        if self.check_nans and torch.isnan(tensor).any():
            warnings.warn(f'NaNs found in file "{path}"')
        return tensor, affine

    def save(self, path: TypePath, squeeze: bool = 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)


1			import warnings
2			from pathlib import Path
3			from typing import Any, Dict, Tuple, Optional, Union, Sequence, List
4
5			import torch
6			import humanize
7			import numpy as np
8			import nibabel as nib
9			import SimpleITK as sitk
10
11			from ..utils import (
12			nib_to_sitk,
13			get_rotation_and_spacing_from_affine,
14			get_stem,
15			ensure_4d,
16			)
17			from ..torchio import (
18			TypeData,
19			TypePath,
20			TypeTripletInt,
21			TypeTripletFloat,
22			DATA,
23			TYPE,
24			AFFINE,
25			PATH,
26			STEM,
27			INTENSITY,
28			LABEL,
29			)
30			from .io import read_image, write_image
31
32
33			PROTECTED_KEYS = DATA, AFFINE, TYPE, PATH, STEM
34
35
36			class Image(dict):
37			r"""TorchIO image.
38
39			For information about medical image orientation, check out `NiBabel docs`_,
40			the `3D Slicer wiki`_, `Graham Wideman's website`_, `FSL docs`_ or
41			`SimpleITK docs`_.
42
43			Args:
44			path: Path to a file or sequence of paths to files that can be read by
45			:mod:`SimpleITK` or :mod:`nibabel`, or to a directory containing
46			DICOM files. If :py:attr:`tensor` is given, the data in
47			:py:attr:`path` will not be read.
48			If a sequence of paths is given, data
49			will be concatenated on the channel dimension so spatial
50			dimensions must match.
51			type: Type of image, such as :attr:`torchio.INTENSITY` or
52			:attr:`torchio.LABEL`. This will be used by the transforms to
53			decide whether to apply an operation, or which interpolation to use
54			when resampling. For example, `preprocessing`_ and `augmentation`_
55			intensity transforms will only be applied to images with type
56			:attr:`torchio.INTENSITY`. Spatial transforms will be applied to
57			all types, and nearest neighbor interpolation is always used to
58			resample images with type :attr:`torchio.LABEL`.
59			The type :attr:`torchio.SAMPLING_MAP` may be used with instances of
60			:py:class:`~torchio.data.sampler.weighted.WeightedSampler`.
61			tensor: If :py:attr:`path` is not given, :attr:`tensor` must be a 4D
62			:py:class:`torch.Tensor` or NumPy array with dimensions
63			:math:`(C, W, H, D)`.
64			affine: If :attr:`path` is not given, :attr:`affine` must be a
65			:math:`4 \times 4` NumPy array. If ``None``, :attr:`affine` is an
66			identity matrix.
67			check_nans: If ``True``, issues a warning if NaNs are found
68			in the image. If ``False``, images will not be checked for the
69			presence of NaNs.
70			**kwargs: Items that will be added to the image dictionary, e.g.
71			acquisition parameters.
72
73			TorchIO images are `lazy loaders`_, i.e. the data is only loaded from disk
74			when needed.
75
76			Example:
77			>>> import torchio
78			>>> image = torchio.ScalarImage('t1.nii.gz') # subclass of Image
79			>>> image # not loaded yet
80			ScalarImage(path: t1.nii.gz; type: intensity)
81			>>> times_two = 2 * image.data # data is loaded and cached here
82			>>> image
83			ScalarImage(shape: (1, 256, 256, 176); spacing: (1.00, 1.00, 1.00); orientation: PIR+; memory: 44.0 MiB; type: intensity)
84			>>> image.save('doubled_image.nii.gz')
85
86			.. _lazy loaders: https://en.wikipedia.org/wiki/Lazy_loading
87			.. _preprocessing: https://torchio.readthedocs.io/transforms/preprocessing.html#intensity
88			.. _augmentation: https://torchio.readthedocs.io/transforms/augmentation.html#intensity
89			.. _NiBabel docs: https://nipy.org/nibabel/image_orientation.html
90			.. _3D Slicer wiki: https://www.slicer.org/wiki/Coordinate_systems
91			.. _FSL docs: https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Orientation%20Explained
92			.. _SimpleITK docs: https://simpleitk.readthedocs.io/en/master/fundamentalConcepts.html
93			.. _Graham Wideman's website: http://www.grahamwideman.com/gw/brain/orientation/orientterms.htm
94			"""
95			def __init__(
96			self,
97			path: Union[TypePath, Sequence[TypePath], None] = None,
98			type: str = None,
99			tensor: Optional[TypeData] = None,
100			affine: Optional[TypeData] = None,
101			check_nans: bool = False, # removed by ITK by default
102			channels_last: bool = False,
103			**kwargs: Dict[str, Any],
104			):
105			self.check_nans = check_nans
106			self.channels_last = channels_last
107
108			if type is None:
109			warnings.warn(
110			'Not specifying the image type is deprecated and will be'
111			' mandatory in the future. You can probably use ScalarImage or'
112			' LabelMap instead'
113			)
114			type = INTENSITY
115
116			if path is None and tensor is None:
117			raise ValueError('A value for path or tensor must be given')
118			self._loaded = False
119
120			tensor = self.parse_tensor(tensor)
121			affine = self.parse_affine(affine)
122			if tensor is not None:
123			self[DATA] = tensor
124			self[AFFINE] = affine
125			self._loaded = True
126			for key in PROTECTED_KEYS:
127			if key in kwargs:
128			message = f'Key "{key}" is reserved. Use a different one'
129			raise ValueError(message)
130
131			super().__init__(**kwargs)
132			self.path = self._parse_path(path)
133
134			self[PATH] = '' if self.path is None else str(self.path)
135			self[STEM] = '' if self.path is None else get_stem(self.path)
136			self[TYPE] = type
137
138			def __repr__(self):
139			properties = []
140			if self._loaded:
141			properties.extend([
142			f'shape: {self.shape}',
143			f'spacing: {self.get_spacing_string()}',
144			f'orientation: {"".join(self.orientation)}+',
145			f'memory: {humanize.naturalsize(self.memory, binary=True)}',
146			])
147			else:
148			properties.append(f'path: "{self.path}"')
149			properties.append(f'type: {self.type}')
150			properties = '; '.join(properties)
151			string = f'{self.__class__.__name__}({properties})'
152			return string
153
154			def __getitem__(self, item):
155			if item in (DATA, AFFINE):
156			if item not in self:
157			self.load()
158			return super().__getitem__(item)
159
160			def __array__(self):
161			return self[DATA].numpy()
162
163			def __copy__(self):
164			kwargs = dict(
165			tensor=self.data,
166			affine=self.affine,
167			type=self.type,
168			path=self.path,
169			)
170			for key, value in self.items():
171			if key in PROTECTED_KEYS: continue
172			kwargs[key] = value # should I copy? deepcopy?
173			return self.__class__(**kwargs)
174
175			@property
176			def data(self):
177			return self[DATA]
178
179			@property
180			def tensor(self):
181			return self.data
182
183			@property
184			def affine(self):
185			return self[AFFINE]
186
187			@property
188			def type(self):
189			return self[TYPE]
190
191			@property
192			def shape(self) -> Tuple[int, int, int, int]:
193			return tuple(self.data.shape)
194
195			@property
196			def spatial_shape(self) -> TypeTripletInt:
197			return self.shape[1:]
198
199			def check_is_2d(self):
200			if not self.is_2d():
201			message = f'Image is not 2D. Spatial shape: {self.spatial_shape}'
202			raise RuntimeError(message)
203
204			@property
205			def height(self) -> int:
206			self.check_is_2d()
207			return self.spatial_shape[1]
208
209			@property
210			def width(self) -> int:
211			self.check_is_2d()
212			return self.spatial_shape[0]
213
214			@property
215			def orientation(self):
216			return nib.aff2axcodes(self.affine)
217
218			@property
219			def spacing(self):
220			_, spacing = get_rotation_and_spacing_from_affine(self.affine)
221			return tuple(spacing)
222
223			@property
224			def memory(self):
225			return np.prod(self.shape) * 4 # float32, i.e. 4 bytes per voxel
226
227			def axis_name_to_index(self, axis: str):
228			"""Convert an axis name to an axis index.
229
230			Args:
231			axis: Possible inputs are ``'Left'``, ``'Right'``, ``'Anterior'``,
232			``'Posterior'``, ``'Inferior'``, ``'Superior'``. Lower-case versions
233			and first letters are also valid, as only the first letter will be
234			used.
235
236			.. note:: If you are working with animals, you should probably use
237			``'Superior'``, ``'Inferior'``, ``'Anterior'`` and ``'Posterior'``
238			for ``'Dorsal'``, ``'Ventral'``, ``'Rostral'`` and ``'Caudal'``,
239			respectively.
240
241			.. note:: If your images are 2D, you can use ``'Top'``, ``'Bottom'``,
242			``'Left'`` and ``'Right'``.
243			"""
244			# Top and bottom are used for the vertical 2D axis as the use of
245			# Height vs Horizontal might be ambiguous
246
247			if not isinstance(axis, str):
248			raise ValueError('Axis must be a string')
249			axis = axis[0].upper()
250
251			# Generally, TorchIO tensors are (C, W, H, D)
252			if axis in 'TB': # Top, Bottom
253			return -2
254			else:
255			try:
256			index = self.orientation.index(axis)
257			except ValueError:
258			index = self.orientation.index(self.flip_axis(axis))
259			# Return negative indices so that it does not matter whether we
260			# refer to spatial dimensions or not
261			index = -3 + index
262			return index
263
264			# flake8: noqa: E701
265			@staticmethod
266			def flip_axis(axis):
267			if axis == 'R': return 'L'
268			elif axis == 'L': return 'R'
269			elif axis == 'A': return 'P'
270			elif axis == 'P': return 'A'
271			elif axis == 'I': return 'S'
272			elif axis == 'S': return 'I'
273			else:
274			values = ', '.join('LRPAISTB')
275			message = f'Axis not understood. Please use one of: {values}'
276			raise ValueError(message)
277
278			def get_spacing_string(self):
279			strings = [f'{n:.2f}' for n in self.spacing]
280			string = f'({", ".join(strings)})'
281			return string
282
283			def get_bounds(self):
284			"""Get image bounds in mm."""
285			first_index = 3 * (-0.5,)
286			last_index = np.array(self.spatial_shape) - 0.5
287			first_point = nib.affines.apply_affine(self.affine, first_index)
288			last_point = nib.affines.apply_affine(self.affine, last_index)
289			array = np.array((first_point, last_point))
290			bounds_x, bounds_y, bounds_z = array.T.tolist()
291			return bounds_x, bounds_y, bounds_z
292
293			@staticmethod
294			def _parse_single_path(
295			path: TypePath
296			) -> Path:
297			try:
298			path = Path(path).expanduser()
299			except TypeError:
300			message = (
301			f'Expected type str or Path but found {path} with '
302			f'{type(path)} instead'
303			)
304			raise TypeError(message)
305			except RuntimeError:
306			message = (
307			f'Conversion to path not possible for variable: {path}'
308			)
309			raise RuntimeError(message)
310
311			if not (path.is_file() or path.is_dir()): # might be a dir with DICOM
312			raise FileNotFoundError(f'File not found: {path}')
313			return path
314
315			def _parse_path(
316			self,
317			path: Union[TypePath, Sequence[TypePath]]
318			) -> Union[Path, List[Path]]:
319			if path is None:
320			return None
321			if isinstance(path, (str, Path)):
322			return self._parse_single_path(path)
323			else:
324			return [self._parse_single_path(p) for p in path]
325
326			def parse_tensor(self, tensor: TypeData) -> torch.Tensor:
327			if tensor is None:
328			return None
329			if isinstance(tensor, np.ndarray):
330			tensor = torch.from_numpy(tensor.astype(np.float32))
331			elif isinstance(tensor, torch.Tensor):
332			tensor = tensor.float()
333			if tensor.ndim != 4:
334			raise ValueError('Input tensor must be 4D')
335			if self.check_nans and torch.isnan(tensor).any():
336			warnings.warn(f'NaNs found in tensor')
337			return tensor
338
339			def parse_tensor_shape(self, tensor: torch.Tensor) -> torch.Tensor:
340			return ensure_4d(tensor)
341
342			@staticmethod
343			def parse_affine(affine: np.ndarray) -> np.ndarray:
344			if affine is None:
345			return np.eye(4)
346			if not isinstance(affine, np.ndarray):
347			raise TypeError(f'Affine must be a NumPy array, not {type(affine)}')
348			if affine.shape != (4, 4):
349			raise ValueError(f'Affine shape must be (4, 4), not {affine.shape}')
350			return affine
351
352			def load(self) -> None:
353			r"""Load the image from disk.
354
355			Returns:
356			Tuple containing a 4D tensor of size :math:`(C, W, H, D)` and a 2D
357			:math:`4 \times 4` affine matrix to convert voxel indices to world
358			coordinates.
359			"""
360			if self._loaded:
361			return
362			paths = self.path if isinstance(self.path, list) else [self.path]
363			tensor, affine = self.read_and_check(paths[0])
364			tensors = [tensor]
365			for path in paths[1:]:
366			new_tensor, new_affine = self.read_and_check(path)
367			if not np.array_equal(affine, new_affine):
368			message = (
369			'Files have different affine matrices.'
370			f'\nMatrix of {paths[0]}:'
371			f'\n{affine}'
372			f'\nMatrix of {path}:'
373			f'\n{new_affine}'
374			)
375			warnings.warn(message, RuntimeWarning)
376			if not tensor.shape[1:] == new_tensor.shape[1:]:
377			message = (
378			f'Files shape do not match, found {tensor.shape}'
379			f'and {new_tensor.shape}'
380			)
381			RuntimeError(message)
382			tensors.append(new_tensor)
383			tensor = torch.cat(tensors)
384			self[DATA] = tensor
385			self[AFFINE] = affine
386			self._loaded = True
387
388			def read_and_check(self, path):
389			tensor, affine = read_image(path)
390			tensor = self.parse_tensor_shape(tensor)
391			if self.channels_last:
392			tensor = tensor.permute(3, 0, 1, 2)
393			if self.check_nans and torch.isnan(tensor).any():
394			warnings.warn(f'NaNs found in file "{path}"')
395			return tensor, affine
396
397			def save(self, path: TypePath, squeeze: bool = True):
398			"""Save image to disk.
399
400			Args:
401			path: String or instance of :py:class:`pathlib.Path`.
402			squeeze: If ``True``, the singleton dimensions will be removed
403			before saving.
404			"""
405			write_image(
406			self[DATA],
407			self[AFFINE],
408			path,
409			squeeze=squeeze,
410			)
411
412			def is_2d(self) -> bool:
413			return self.shape[-1] == 1
414
415			def numpy(self) -> np.ndarray:
416			"""Get a NumPy array containing the image data."""
417			return np.asarray(self)
418
419			def as_sitk(self, **kwargs) -> sitk.Image:
420			"""Get the image as an instance of :py:class:`sitk.Image`."""
421			return nib_to_sitk(self[DATA], self[AFFINE], **kwargs)
422
423			def get_center(self, lps: bool = False) -> TypeTripletFloat:
424			"""Get image center in RAS+ or LPS+ coordinates.
425
426			Args:
427			lps: If ``True``, the coordinates will be in LPS+ orientation, i.e.
428			the first dimension grows towards the left, etc. Otherwise, the
429			coordinates will be in RAS+ orientation.
430			"""
431			size = np.array(self.spatial_shape)
432			center_index = (size - 1) / 2
433			r, a, s = nib.affines.apply_affine(self.affine, center_index)
434			if lps:
435			return (-r, -a, s)
436			else:
437			return (r, a, s)
438
439			def set_check_nans(self, check_nans: bool):
440			self.check_nans = check_nans
441
442			def crop(self, index_ini: TypeTripletInt, index_fin: TypeTripletInt):
443			new_origin = nib.affines.apply_affine(self.affine, index_ini)
444			new_affine = self.affine.copy()
445			new_affine[:3, 3] = new_origin
446			i0, j0, k0 = index_ini
447			i1, j1, k1 = index_fin
448			patch = self.data[:, i0:i1, j0:j1, k0:k1].clone()
449			kwargs = dict(
450			tensor=patch,
451			affine=new_affine,
452			type=self.type,
453			path=self.path,
454			)
455			for key, value in self.items():
456			if key in PROTECTED_KEYS: continue
457			kwargs[key] = value # should I copy? deepcopy?
458			return self.__class__(**kwargs)
459
460
461			class ScalarImage(Image):
462			"""Alias for :py:class:`~torchio.Image` of type :py:attr:`torchio.INTENSITY`.
463
464			Example:
465			>>> import torch
466			>>> import torchio
467			>>> # Loading from a file
468			>>> t1_image = torchio.ScalarImage('t1.nii.gz')
469			>>> dmri = torchio.ScalarImage(tensor=torch.rand(32, 128, 128, 88))
470			>>> image = torchio.ScalarImage('safe_image.nrrd', check_nans=False)
471			>>> data, affine = image.data, image.affine
472			>>> affine.shape
473			(4, 4)
474			>>> image.data is image[torchio.DATA]
475			True
476			>>> image.data is image.tensor
477			True
478			>>> type(image.data)
479			torch.Tensor
480
481			See :py:class:`~torchio.Image` for more information.
482
483			Raises:
484			ValueError: A :py:attr:`type` is used for instantiation.
485			"""
486			def __init__(self, args, *kwargs):
487			if 'type' in kwargs and kwargs['type'] != INTENSITY:
488			raise ValueError('Type of ScalarImage is always torchio.INTENSITY')
489			kwargs.update({'type': INTENSITY})
490			super().__init__(args, *kwargs)
491
492
493			class LabelMap(Image):
494			"""Alias for :py:class:`~torchio.Image` of type :py:attr:`torchio.LABEL`.
495
496			Example:
497			>>> import torch
498			>>> import torchio
499			>>> labels = torchio.LabelMap(tensor=torch.rand(128, 128, 68) > 0.5)
500			>>> labels = torchio.LabelMap('t1_seg.nii.gz') # loading from a file
501			>>> tpm = torchio.LabelMap( # loading from files
502			... 'gray_matter.nii.gz',
503			... 'white_matter.nii.gz',
504			... 'csf.nii.gz',
505			... )
506
507			See :py:class:`~torchio.data.image.Image` for more information.
508
509			Raises:
510			ValueError: If a value for :py:attr:`type` is given.
511			"""
512			def __init__(self, args, *kwargs):
513			if 'type' in kwargs and kwargs['type'] != LABEL:
514			raise ValueError('Type of LabelMap is always torchio.LABEL')
515			kwargs.update({'type': LABEL})
516			super().__init__(args, *kwargs)
517

fepegar / torchio

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torchio.data.image.Image.__init__() C

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