torchio.data.image.Image.__init__() - Code Metrics - Inspection of "Visualization" - fepegar/torchio - Measure and Improve Code Quality continuously with Scrutinizer

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Pull Request — master (#332)

by Fernando

created 2020-10-15 09:42 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) -> torch.Tensor:
        return self[DATA]

    @property
    def tensor(self) -> torch.Tensor:
        return self.data

    @property
    def affine(self) -> np.ndarray:
        return self[AFFINE]

    @property
    def type(self) -> str:
        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) -> None:
        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) -> Tuple[str, str, str]:
        return nib.aff2axcodes(self.affine)

    @property
    def spacing(self) -> Tuple[float, float, float]:
        _, spacing = get_rotation_and_spacing_from_affine(self.affine)
        return tuple(spacing)

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

    @property
    def bounds(self) -> np.ndarray:
        ini = 0, 0, 0
        fin = np.array(self.spatial_shape) - 1
        point_ini = nib.affines.apply_affine(self.affine, ini)
        point_fin = nib.affines.apply_affine(self.affine, fin)
        return np.array((point_ini, point_fin))

    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 plot(self, **kwargs) -> None:
        from ..visualization import plot_image  # avoid circular import
        plot_image(self, **kwargs)

    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) -> torch.Tensor:
177			return self[DATA]
178
179			@property
180			def tensor(self) -> torch.Tensor:
181			return self.data
182
183			@property
184			def affine(self) -> np.ndarray:
185			return self[AFFINE]
186
187			@property
188			def type(self) -> str:
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) -> None:
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) -> Tuple[str, str, str]:
216			return nib.aff2axcodes(self.affine)
217
218			@property
219			def spacing(self) -> Tuple[float, float, float]:
220			_, spacing = get_rotation_and_spacing_from_affine(self.affine)
221			return tuple(spacing)
222
223			@property
224			def memory(self) -> float:
225			return np.prod(self.shape) * 4 # float32, i.e. 4 bytes per voxel
226
227			@property
228			def bounds(self) -> np.ndarray:
229			ini = 0, 0, 0
230			fin = np.array(self.spatial_shape) - 1
231			point_ini = nib.affines.apply_affine(self.affine, ini)
232			point_fin = nib.affines.apply_affine(self.affine, fin)
233			return np.array((point_ini, point_fin))
234
235			def axis_name_to_index(self, axis: str):
236			"""Convert an axis name to an axis index.
237
238			Args:
239			axis: Possible inputs are ``'Left'``, ``'Right'``, ``'Anterior'``,
240			``'Posterior'``, ``'Inferior'``, ``'Superior'``. Lower-case versions
241			and first letters are also valid, as only the first letter will be
242			used.
243
244			.. note:: If you are working with animals, you should probably use
245			``'Superior'``, ``'Inferior'``, ``'Anterior'`` and ``'Posterior'``
246			for ``'Dorsal'``, ``'Ventral'``, ``'Rostral'`` and ``'Caudal'``,
247			respectively.
248
249			.. note:: If your images are 2D, you can use ``'Top'``, ``'Bottom'``,
250			``'Left'`` and ``'Right'``.
251			"""
252			# Top and bottom are used for the vertical 2D axis as the use of
253			# Height vs Horizontal might be ambiguous
254
255			if not isinstance(axis, str):
256			raise ValueError('Axis must be a string')
257			axis = axis[0].upper()
258
259			# Generally, TorchIO tensors are (C, W, H, D)
260			if axis in 'TB': # Top, Bottom
261			return -2
262			else:
263			try:
264			index = self.orientation.index(axis)
265			except ValueError:
266			index = self.orientation.index(self.flip_axis(axis))
267			# Return negative indices so that it does not matter whether we
268			# refer to spatial dimensions or not
269			index = -3 + index
270			return index
271
272			# flake8: noqa: E701
273			@staticmethod
274			def flip_axis(axis):
275			if axis == 'R': return 'L'
276			elif axis == 'L': return 'R'
277			elif axis == 'A': return 'P'
278			elif axis == 'P': return 'A'
279			elif axis == 'I': return 'S'
280			elif axis == 'S': return 'I'
281			else:
282			values = ', '.join('LRPAISTB')
283			message = f'Axis not understood. Please use one of: {values}'
284			raise ValueError(message)
285
286			def get_spacing_string(self):
287			strings = [f'{n:.2f}' for n in self.spacing]
288			string = f'({", ".join(strings)})'
289			return string
290
291			def get_bounds(self):
292			"""Get image bounds in mm."""
293			first_index = 3 * (-0.5,)
294			last_index = np.array(self.spatial_shape) - 0.5
295			first_point = nib.affines.apply_affine(self.affine, first_index)
296			last_point = nib.affines.apply_affine(self.affine, last_index)
297			array = np.array((first_point, last_point))
298			bounds_x, bounds_y, bounds_z = array.T.tolist()
299			return bounds_x, bounds_y, bounds_z
300
301			@staticmethod
302			def _parse_single_path(
303			path: TypePath
304			) -> Path:
305			try:
306			path = Path(path).expanduser()
307			except TypeError:
308			message = (
309			f'Expected type str or Path but found {path} with '
310			f'{type(path)} instead'
311			)
312			raise TypeError(message)
313			except RuntimeError:
314			message = (
315			f'Conversion to path not possible for variable: {path}'
316			)
317			raise RuntimeError(message)
318
319			if not (path.is_file() or path.is_dir()): # might be a dir with DICOM
320			raise FileNotFoundError(f'File not found: "{path}"')
321			return path
322
323			def _parse_path(
324			self,
325			path: Union[TypePath, Sequence[TypePath]]
326			) -> Union[Path, List[Path]]:
327			if path is None:
328			return None
329			if isinstance(path, (str, Path)):
330			return self._parse_single_path(path)
331			else:
332			return [self._parse_single_path(p) for p in path]
333
334			def parse_tensor(self, tensor: TypeData) -> torch.Tensor:
335			if tensor is None:
336			return None
337			if isinstance(tensor, np.ndarray):
338			tensor = torch.from_numpy(tensor.astype(np.float32))
339			elif isinstance(tensor, torch.Tensor):
340			tensor = tensor.float()
341			if tensor.ndim != 4:
342			raise ValueError('Input tensor must be 4D')
343			if self.check_nans and torch.isnan(tensor).any():
344			warnings.warn(f'NaNs found in tensor')
345			return tensor
346
347			def parse_tensor_shape(self, tensor: torch.Tensor) -> torch.Tensor:
348			return ensure_4d(tensor)
349
350			@staticmethod
351			def parse_affine(affine: np.ndarray) -> np.ndarray:
352			if affine is None:
353			return np.eye(4)
354			if not isinstance(affine, np.ndarray):
355			raise TypeError(f'Affine must be a NumPy array, not {type(affine)}')
356			if affine.shape != (4, 4):
357			raise ValueError(f'Affine shape must be (4, 4), not {affine.shape}')
358			return affine
359
360			def load(self) -> None:
361			r"""Load the image from disk.
362
363			Returns:
364			Tuple containing a 4D tensor of size :math:`(C, W, H, D)` and a 2D
365			:math:`4 \times 4` affine matrix to convert voxel indices to world
366			coordinates.
367			"""
368			if self._loaded:
369			return
370			paths = self.path if isinstance(self.path, list) else [self.path]
371			tensor, affine = self.read_and_check(paths[0])
372			tensors = [tensor]
373			for path in paths[1:]:
374			new_tensor, new_affine = self.read_and_check(path)
375			if not np.array_equal(affine, new_affine):
376			message = (
377			'Files have different affine matrices.'
378			f'\nMatrix of {paths[0]}:'
379			f'\n{affine}'
380			f'\nMatrix of {path}:'
381			f'\n{new_affine}'
382			)
383			warnings.warn(message, RuntimeWarning)
384			if not tensor.shape[1:] == new_tensor.shape[1:]:
385			message = (
386			f'Files shape do not match, found {tensor.shape}'
387			f'and {new_tensor.shape}'
388			)
389			RuntimeError(message)
390			tensors.append(new_tensor)
391			tensor = torch.cat(tensors)
392			self[DATA] = tensor
393			self[AFFINE] = affine
394			self._loaded = True
395
396			def read_and_check(self, path):
397			tensor, affine = read_image(path)
398			tensor = self.parse_tensor_shape(tensor)
399			if self.channels_last:
400			tensor = tensor.permute(3, 0, 1, 2)
401			if self.check_nans and torch.isnan(tensor).any():
402			warnings.warn(f'NaNs found in file "{path}"')
403			return tensor, affine
404
405			def save(self, path: TypePath, squeeze: bool = True):
406			"""Save image to disk.
407
408			Args:
409			path: String or instance of :py:class:`pathlib.Path`.
410			squeeze: If ``True``, the singleton dimensions will be removed
411			before saving.
412			"""
413			write_image(
414			self[DATA],
415			self[AFFINE],
416			path,
417			squeeze=squeeze,
418			)
419
420			def is_2d(self) -> bool:
421			return self.shape[-1] == 1
422
423			def numpy(self) -> np.ndarray:
424			"""Get a NumPy array containing the image data."""
425			return np.asarray(self)
426
427			def as_sitk(self, **kwargs) -> sitk.Image:
428			"""Get the image as an instance of :py:class:`sitk.Image`."""
429			return nib_to_sitk(self[DATA], self[AFFINE], **kwargs)
430
431			def get_center(self, lps: bool = False) -> TypeTripletFloat:
432			"""Get image center in RAS+ or LPS+ coordinates.
433
434			Args:
435			lps: If ``True``, the coordinates will be in LPS+ orientation, i.e.
436			the first dimension grows towards the left, etc. Otherwise, the
437			coordinates will be in RAS+ orientation.
438			"""
439			size = np.array(self.spatial_shape)
440			center_index = (size - 1) / 2
441			r, a, s = nib.affines.apply_affine(self.affine, center_index)
442			if lps:
443			return (-r, -a, s)
444			else:
445			return (r, a, s)
446
447			def set_check_nans(self, check_nans: bool):
448			self.check_nans = check_nans
449
450			def plot(self, **kwargs) -> None:
451			from ..visualization import plot_image # avoid circular import
452			plot_image(self, **kwargs)
453
454			def crop(self, index_ini: TypeTripletInt, index_fin: TypeTripletInt):
455			new_origin = nib.affines.apply_affine(self.affine, index_ini)
456			new_affine = self.affine.copy()
457			new_affine[:3, 3] = new_origin
458			i0, j0, k0 = index_ini
459			i1, j1, k1 = index_fin
460			patch = self.data[:, i0:i1, j0:j1, k0:k1].clone()
461			kwargs = dict(
462			tensor=patch,
463			affine=new_affine,
464			type=self.type,
465			path=self.path,
466			)
467			for key, value in self.items():
468			if key in PROTECTED_KEYS: continue
469			kwargs[key] = value # should I copy? deepcopy?
470			return self.__class__(**kwargs)
471
472
473			class ScalarImage(Image):
474			"""Alias for :py:class:`~torchio.Image` of type :py:attr:`torchio.INTENSITY`.
475
476			Example:
477			>>> import torch
478			>>> import torchio
479			>>> # Loading from a file
480			>>> t1_image = torchio.ScalarImage('t1.nii.gz')
481			>>> dmri = torchio.ScalarImage(tensor=torch.rand(32, 128, 128, 88))
482			>>> image = torchio.ScalarImage('safe_image.nrrd', check_nans=False)
483			>>> data, affine = image.data, image.affine
484			>>> affine.shape
485			(4, 4)
486			>>> image.data is image[torchio.DATA]
487			True
488			>>> image.data is image.tensor
489			True
490			>>> type(image.data)
491			torch.Tensor
492
493			See :py:class:`~torchio.Image` for more information.
494
495			Raises:
496			ValueError: A :py:attr:`type` is used for instantiation.
497			"""
498			def __init__(self, args, *kwargs):
499			if 'type' in kwargs and kwargs['type'] != INTENSITY:
500			raise ValueError('Type of ScalarImage is always torchio.INTENSITY')
501			kwargs.update({'type': INTENSITY})
502			super().__init__(args, *kwargs)
503
504
505			class LabelMap(Image):
506			"""Alias for :py:class:`~torchio.Image` of type :py:attr:`torchio.LABEL`.
507
508			Example:
509			>>> import torch
510			>>> import torchio
511			>>> labels = torchio.LabelMap(tensor=torch.rand(128, 128, 68) > 0.5)
512			>>> labels = torchio.LabelMap('t1_seg.nii.gz') # loading from a file
513			>>> tpm = torchio.LabelMap( # loading from files
514			... 'gray_matter.nii.gz',
515			... 'white_matter.nii.gz',
516			... 'csf.nii.gz',
517			... )
518
519			See :py:class:`~torchio.data.image.Image` for more information.
520
521			Raises:
522			ValueError: If a value for :py:attr:`type` is given.
523			"""
524			def __init__(self, args, *kwargs):
525			if 'type' in kwargs and kwargs['type'] != LABEL:
526			raise ValueError('Type of LabelMap is always torchio.LABEL')
527			kwargs.update({'type': LABEL})
528			super().__init__(args, *kwargs)
529

fepegar / torchio

Pull Request — master (#332)

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

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