torchio.transforms.transform.Transform.parse_subject() - Code Metrics - Inspection of "Add some deterministic transforms" - fepegar/torchio - Measure and Improve Code Quality continuously with Scrutinizer

Passed

Pull Request — master (#353)

by Fernando

created 2020-11-17 02:13 UTC

Transform.parse_subject() A

↳ Parent: torchio.transforms.transform

Complexity

Conditions

Size

Total Lines	8
Code Lines	6

Duplication

Lines	0
Ratio	0 %

Importance

Changes

Metric	Value
cc	2
eloc	6
nop	1
dl	0
loc	8
rs	10
c	0
b	0
f	0

import copy
import numbers
import warnings
from abc import ABC, abstractmethod
from typing import Optional, Union, Tuple, List

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

from .. import TypeData, DATA, AFFINE, TypeNumber
from ..data.subject import Subject
from ..data.image import Image, ScalarImage
from ..utils import nib_to_sitk, sitk_to_nib, to_tuple
from .interpolation import Interpolation


TypeTransformInput = Union[
    Subject,
    Image,
    torch.Tensor,
    np.ndarray,
    sitk.Image,
    dict,
]


class Transform(ABC):
    """Abstract class for all TorchIO transforms.

    All subclasses should overwrite
    :py:meth:`torchio.tranforms.Transform.apply_transform`,
    which takes data, applies some transformation and returns the result.

    The input can be an instance of
    :py:class:`torchio.Subject`,
    :py:class:`torchio.Image`,
    :py:class:`numpy.ndarray`,
    :py:class:`torch.Tensor`,
    :py:class:`SimpleITK.image`,
    or a Python dictionary.

    Args:
        p: Probability that this transform will be applied.
        copy: Make a shallow copy of the input before applying the transform.
        keys: Mandatory if the input is a Python dictionary. The transform will
            be applied only to the data in each key.
    """
    def __init__(
            self,
            p: float = 1,
            copy: bool = True,
            keys: Optional[List[str]] = None,
            ):
        self.probability = self.parse_probability(p)
        self.copy = copy
        self.keys = keys
        self.default_image_name = 'default_image_name'

    def __call__(
            self,
            data: TypeTransformInput,
            ) -> TypeTransformInput:
        """Transform data and return a result of the same type.

        Args:
            data: Instance of :py:class:`~torchio.Subject`, 4D
                :py:class:`torch.Tensor` or 4D NumPy array with dimensions
                :math:`(C, W, H, D)`, where :math:`C` is the number of channels
                and :math:`W, H, D` are the spatial dimensions. If the input is
                a tensor, the affine matrix is an identity and a tensor will be
                also returned.
        """
        if torch.rand(1).item() > self.probability:
            return data

        is_tensor = is_array = is_dict = is_image = is_sitk = is_nib = False

        if isinstance(data, nib.Nifti1Image):
            tensor = data.get_fdata(dtype=np.float32)
            data = ScalarImage(tensor=tensor, affine=data.affine)
            subject = self._get_subject_from_image(data)
            is_nib = True
        elif isinstance(data, (np.ndarray, torch.Tensor)):
            subject = self.parse_tensor(data)
            is_array = isinstance(data, np.ndarray)
            is_tensor = True
        elif isinstance(data, Image):
            subject = self._get_subject_from_image(data)
            is_image = True
        elif isinstance(data, Subject):
            subject = data
        elif isinstance(data, sitk.Image):
            subject = self._get_subject_from_sitk_image(data)
            is_sitk = True
        elif isinstance(data, dict):  # e.g. Eisen or MONAI dicts
            if self.keys is None:
                message = (
                    'If input is a dictionary, a value for "keys" must be'
                    ' specified when instantiating the transform'
                )
                raise RuntimeError(message)
            subject = self._get_subject_from_dict(data, self.keys)
            is_dict = True
        else:
            raise ValueError(f'Input type not recognized: {type(data)}')
        self.parse_subject(subject)

        if self.copy:
            subject = copy.copy(subject)

        with np.errstate(all='raise'):
            transformed = self.apply_transform(subject)
            from .augmentation import RandomTransform
            if not isinstance(self, RandomTransform):
                transformed.add_transform(self, self.get_arguments())

        for image in transformed.get_images(intensity_only=False):
            ndim = image[DATA].ndim
            assert ndim == 4, f'Output of {self.name} is {ndim}D'

        if is_tensor or is_sitk:
            image = transformed[self.default_image_name]
            transformed = image[DATA]
            if is_array:
                transformed = transformed.numpy()
            elif is_sitk:
                transformed = nib_to_sitk(image[DATA], image[AFFINE])
        elif is_image:
            transformed = transformed[self.default_image_name]
        elif is_dict:
            transformed = dict(transformed)
            for key, value in transformed.items():
                if isinstance(value, Image):
                    transformed[key] = value.data
        elif is_nib:
            image = transformed[self.default_image_name]
            data = image[DATA]
            if len(data) > 1:
                message = (
                    'Multichannel images not supported for input of type'
                    ' nibabel.nifti.Nifti1Image'
                )
                raise RuntimeError(message)
            transformed = nib.Nifti1Image(data[0].numpy(), image[AFFINE])

        return transformed

    @abstractmethod
    def apply_transform(self, subject: Subject):
        raise NotImplementedError

    @staticmethod
    def to_range(n, around):
        if around is None:
            return 0, n
        else:
            return around - n, around + n

    def parse_params(self, params, around, name, make_ranges=True, **kwargs):
        params = to_tuple(params)
        if len(params) == 1 or (len(params) == 2 and make_ranges):  # d or (a, b)
            params *= 3  # (d, d, d) or (a, b, a, b, a, b)
        if len(params) == 3 and make_ranges:  # (a, b, c)
            items = [self.to_range(n, around) for n in params]
            # (-a, a, -b, b, -c, c) or (1-a, 1+a, 1-b, 1+b, 1-c, 1+c)
            params = [n for prange in items for n in prange]
        if make_ranges and len(params) != 6:
            if len(params) != 6:
                message = (
                    f'If "{name}" is a sequence, it must have length 2, 3 or 6,'
                    f' not {len(params)}'
                )
                raise ValueError(message)
            for param_range in zip(params[::2], params[1::2]):
                self.parse_range(param_range, name, **kwargs)
        return tuple(params)

    @staticmethod
    def parse_range(
            nums_range: Union[TypeNumber, Tuple[TypeNumber, TypeNumber]],
            name: str,
            min_constraint: TypeNumber = None,
            max_constraint: TypeNumber = None,
            type_constraint: type = None,
            ) -> Tuple[TypeNumber, TypeNumber]:
        r"""Adapted from ``torchvision.transforms.RandomRotation``.

        Args:
            nums_range: Tuple of two numbers :math:`(n_{min}, n_{max})`,
                where :math:`n_{min} \leq n_{max}`.
                If a single positive number :math:`n` is provided,
                :math:`n_{min} = -n` and :math:`n_{max} = n`.
            name: Name of the parameter, so that an informative error message
                can be printed.
            min_constraint: Minimal value that :math:`n_{min}` can take,
                default is None, i.e. there is no minimal value.
            max_constraint: Maximal value that :math:`n_{max}` can take,
                default is None, i.e. there is no maximal value.
            type_constraint: Precise type that :math:`n_{max}` and
                :math:`n_{min}` must take.

        Returns:
            A tuple of two numbers :math:`(n_{min}, n_{max})`.

        Raises:
            ValueError: if :attr:`nums_range` is negative
            ValueError: if :math:`n_{max}` or :math:`n_{min}` is not a number
            ValueError: if :math:`n_{max} \lt n_{min}`
            ValueError: if :attr:`min_constraint` is not None and
                :math:`n_{min}` is smaller than :attr:`min_constraint`
            ValueError: if :attr:`max_constraint` is not None and
                :math:`n_{max}` is greater than :attr:`max_constraint`
            ValueError: if :attr:`type_constraint` is not None and
                :math:`n_{max}` and :math:`n_{max}` are not of type
                :attr:`type_constraint`.
        """
        if isinstance(nums_range, numbers.Number):  # single number given
            if nums_range < 0:
                raise ValueError(
                    f'If {name} is a single number,'
                    f' it must be positive, not {nums_range}')
            if min_constraint is not None and nums_range < min_constraint:
                raise ValueError(
                    f'If {name} is a single number, it must be greater'
                    f' than {min_constraint}, not {nums_range}'
                )
            if max_constraint is not None and nums_range > max_constraint:
                raise ValueError(
                    f'If {name} is a single number, it must be smaller'
                    f' than {max_constraint}, not {nums_range}'
                )
            if type_constraint is not None:
                if not isinstance(nums_range, type_constraint):
                    raise ValueError(
                        f'If {name} is a single number, it must be of'
                        f' type {type_constraint}, not {nums_range}'
                    )
            min_range = -nums_range if min_constraint is None else nums_range
            return (min_range, nums_range)

        try:
            min_value, max_value = nums_range
        except (TypeError, ValueError):
            raise ValueError(
                f'If {name} is not a single number, it must be'
                f' a sequence of len 2, not {nums_range}'
            )

        min_is_number = isinstance(min_value, numbers.Number)
        max_is_number = isinstance(max_value, numbers.Number)
        if not min_is_number or not max_is_number:
            message = (
                f'{name} values must be numbers, not {nums_range}')
            raise ValueError(message)

        if min_value > max_value:
            raise ValueError(
                f'If {name} is a sequence, the second value must be'
                f' equal or greater than the first, but it is {nums_range}')

        if min_constraint is not None and min_value < min_constraint:
            raise ValueError(
                f'If {name} is a sequence, the first value must be greater'
                f' than {min_constraint}, but it is {min_value}'
            )

        if max_constraint is not None and max_value > max_constraint:
            raise ValueError(
                f'If {name} is a sequence, the second value must be smaller'
                f' than {max_constraint}, but it is {max_value}'
            )

        if type_constraint is not None:
            min_type_ok = isinstance(min_value, type_constraint)
            max_type_ok = isinstance(max_value, type_constraint)
            if not min_type_ok or not max_type_ok:
                raise ValueError(
                    f'If "{name}" is a sequence, its values must be of'
                    f' type "{type_constraint}", not "{type(nums_range)}"'
                )
        return nums_range

    @staticmethod
    def parse_probability(probability: float) -> float:
        is_number = isinstance(probability, numbers.Number)
        if not (is_number and 0 <= probability <= 1):
            message = (
                'Probability must be a number in [0, 1],'
                f' not {probability}'
            )
            raise ValueError(message)
        return probability

    @staticmethod
    def parse_subject(subject: Subject) -> None:
        if not isinstance(subject, Subject):
            message = (
                'Input to a transform must be a tensor or an instance'
                f' of torchio.Subject, not "{type(subject)}"'
            )
            raise RuntimeError(message)

    def parse_tensor(self, data: TypeData) -> Subject:
        if data.ndim != 4:
            message = (
                'The input must be a 4D tensor with dimensions'
                f' (channels, x, y, z) but it has shape {tuple(data.shape)}'
            )
            raise ValueError(message)
        return self._get_subject_from_tensor(data)

    @staticmethod
    def parse_interpolation(interpolation: str) -> Interpolation:
        if isinstance(interpolation, Interpolation):
            message = (
                'Interpolation of type torchio.Interpolation'
                ' is deprecated, please use a string instead'
            )
            warnings.warn(message, FutureWarning)
        elif isinstance(interpolation, str):
            interpolation = interpolation.lower()
            supported_values = [key.name.lower() for key in Interpolation]
            if interpolation in supported_values:
                interpolation = getattr(Interpolation, interpolation.upper())
            else:
                message = (
                    f'Interpolation "{interpolation}" is not among'
                    f' the supported values: {supported_values}'
                )
                raise AttributeError(message)
        else:
            message = (
                'image_interpolation must be a string,'
                f' not {type(interpolation)}'
            )
            raise TypeError(message)
        return interpolation

    def _get_subject_from_tensor(self, tensor: torch.Tensor) -> Subject:
        image = ScalarImage(tensor=tensor)
        return self._get_subject_from_image(image)

    def _get_subject_from_image(self, image: Image) -> Subject:
        subject = Subject({self.default_image_name: image})
        return subject

    @staticmethod
    def _get_subject_from_dict(
            data: dict,
            image_keys: List[str],
            ) -> Subject:
        subject_dict = {}
        for key, value in data.items():
            if key in image_keys:
                value = ScalarImage(tensor=value)
            subject_dict[key] = value
        return Subject(subject_dict)

    def _get_subject_from_sitk_image(self, image):
        tensor, affine = sitk_to_nib(image)
        image = ScalarImage(tensor=tensor, affine=affine)
        return self._get_subject_from_image(image)

    @staticmethod
    def nib_to_sitk(data: TypeData, affine: TypeData) -> sitk.Image:
        return nib_to_sitk(data, affine)

    @staticmethod
    def sitk_to_nib(image: sitk.Image) -> Tuple[torch.Tensor, np.ndarray]:
        return sitk_to_nib(image)

    @property
    def name(self):
        return self.__class__.__name__

    def is_invertible(self):
        return hasattr(self, 'invert_transform')

    def inverse(self):
        if not self.is_invertible():
            raise RuntimeError(f'{self.name} is not invertible')
        new = copy.deepcopy(self)
        new.invert_transform = not self.invert_transform
        return new


1			import copy
2			import numbers
3			import warnings
4			from abc import ABC, abstractmethod
5			from typing import Optional, Union, Tuple, List
6
7			import torch
8			import numpy as np
9			import nibabel as nib
10			import SimpleITK as sitk
11
12			from .. import TypeData, DATA, AFFINE, TypeNumber
13			from ..data.subject import Subject
14			from ..data.image import Image, ScalarImage
15			from ..utils import nib_to_sitk, sitk_to_nib, to_tuple
16			from .interpolation import Interpolation
17
18
19			TypeTransformInput = Union[
20			Subject,
21			Image,
22			torch.Tensor,
23			np.ndarray,
24			sitk.Image,
25			dict,
26			]
27
28
29			class Transform(ABC):
30			"""Abstract class for all TorchIO transforms.
31
32			All subclasses should overwrite
33			:py:meth:`torchio.tranforms.Transform.apply_transform`,
34			which takes data, applies some transformation and returns the result.
35
36			The input can be an instance of
37			:py:class:`torchio.Subject`,
38			:py:class:`torchio.Image`,
39			:py:class:`numpy.ndarray`,
40			:py:class:`torch.Tensor`,
41			:py:class:`SimpleITK.image`,
42			or a Python dictionary.
43
44			Args:
45			p: Probability that this transform will be applied.
46			copy: Make a shallow copy of the input before applying the transform.
47			keys: Mandatory if the input is a Python dictionary. The transform will
48			be applied only to the data in each key.
49			"""
50			def __init__(
51			self,
52			p: float = 1,
53			copy: bool = True,
54			keys: Optional[List[str]] = None,
55			):
56			self.probability = self.parse_probability(p)
57			self.copy = copy
58			self.keys = keys
59			self.default_image_name = 'default_image_name'
60
61			def __call__(
62			self,
63			data: TypeTransformInput,
64			) -> TypeTransformInput:
65			"""Transform data and return a result of the same type.
66
67			Args:
68			data: Instance of :py:class:`~torchio.Subject`, 4D
69			:py:class:`torch.Tensor` or 4D NumPy array with dimensions
70			:math:`(C, W, H, D)`, where :math:`C` is the number of channels
71			and :math:`W, H, D` are the spatial dimensions. If the input is
72			a tensor, the affine matrix is an identity and a tensor will be
73			also returned.
74			"""
75			if torch.rand(1).item() > self.probability:
76			return data
77
78			is_tensor = is_array = is_dict = is_image = is_sitk = is_nib = False
79
80			if isinstance(data, nib.Nifti1Image):
81			tensor = data.get_fdata(dtype=np.float32)
82			data = ScalarImage(tensor=tensor, affine=data.affine)
83			subject = self._get_subject_from_image(data)
84			is_nib = True
85			elif isinstance(data, (np.ndarray, torch.Tensor)):
86			subject = self.parse_tensor(data)
87			is_array = isinstance(data, np.ndarray)
88			is_tensor = True
89			elif isinstance(data, Image):
90			subject = self._get_subject_from_image(data)
91			is_image = True
92			elif isinstance(data, Subject):
93			subject = data
94			elif isinstance(data, sitk.Image):
95			subject = self._get_subject_from_sitk_image(data)
96			is_sitk = True
97			elif isinstance(data, dict): # e.g. Eisen or MONAI dicts
98			if self.keys is None:
99			message = (
100			'If input is a dictionary, a value for "keys" must be'
101			' specified when instantiating the transform'
102			)
103			raise RuntimeError(message)
104			subject = self._get_subject_from_dict(data, self.keys)
105			is_dict = True
106			else:
107			raise ValueError(f'Input type not recognized: {type(data)}')
108			self.parse_subject(subject)
109
110			if self.copy:
111			subject = copy.copy(subject)
112
113			with np.errstate(all='raise'):
114			transformed = self.apply_transform(subject)
115			from .augmentation import RandomTransform
116			if not isinstance(self, RandomTransform):
117			transformed.add_transform(self, self.get_arguments())
118
119			for image in transformed.get_images(intensity_only=False):
120			ndim = image[DATA].ndim
121			assert ndim == 4, f'Output of {self.name} is {ndim}D'
122
123			if is_tensor or is_sitk:
124			image = transformed[self.default_image_name]
125			transformed = image[DATA]
126			if is_array:
127			transformed = transformed.numpy()
128			elif is_sitk:
129			transformed = nib_to_sitk(image[DATA], image[AFFINE])
130			elif is_image:
131			transformed = transformed[self.default_image_name]
132			elif is_dict:
133			transformed = dict(transformed)
134			for key, value in transformed.items():
135			if isinstance(value, Image):
136			transformed[key] = value.data
137			elif is_nib:
138			image = transformed[self.default_image_name]
139			data = image[DATA]
140			if len(data) > 1:
141			message = (
142			'Multichannel images not supported for input of type'
143			' nibabel.nifti.Nifti1Image'
144			)
145			raise RuntimeError(message)
146			transformed = nib.Nifti1Image(data[0].numpy(), image[AFFINE])
147
148			return transformed
149
150			@abstractmethod
151			def apply_transform(self, subject: Subject):
152			raise NotImplementedError
153
154			@staticmethod
155			def to_range(n, around):
156			if around is None:
157			return 0, n
158			else:
159			return around - n, around + n
160
161			def parse_params(self, params, around, name, make_ranges=True, **kwargs):
162			params = to_tuple(params)
163			if len(params) == 1 or (len(params) == 2 and make_ranges): # d or (a, b)
164			params *= 3 # (d, d, d) or (a, b, a, b, a, b)
165			if len(params) == 3 and make_ranges: # (a, b, c)
166			items = [self.to_range(n, around) for n in params]
167			# (-a, a, -b, b, -c, c) or (1-a, 1+a, 1-b, 1+b, 1-c, 1+c)
168			params = [n for prange in items for n in prange]
169			if make_ranges and len(params) != 6:
170			if len(params) != 6:
171			message = (
172			f'If "{name}" is a sequence, it must have length 2, 3 or 6,'
173			f' not {len(params)}'
174			)
175			raise ValueError(message)
176			for param_range in zip(params[::2], params[1::2]):
177			self.parse_range(param_range, name, **kwargs)
178			return tuple(params)
179
180			@staticmethod
181			def parse_range(
182			nums_range: Union[TypeNumber, Tuple[TypeNumber, TypeNumber]],
183			name: str,
184			min_constraint: TypeNumber = None,
185			max_constraint: TypeNumber = None,
186			type_constraint: type = None,
187			) -> Tuple[TypeNumber, TypeNumber]:
188			r"""Adapted from ``torchvision.transforms.RandomRotation``.
189
190			Args:
191			nums_range: Tuple of two numbers :math:`(n_{min}, n_{max})`,
192			where :math:`n_{min} \leq n_{max}`.
193			If a single positive number :math:`n` is provided,
194			:math:`n_{min} = -n` and :math:`n_{max} = n`.
195			name: Name of the parameter, so that an informative error message
196			can be printed.
197			min_constraint: Minimal value that :math:`n_{min}` can take,
198			default is None, i.e. there is no minimal value.
199			max_constraint: Maximal value that :math:`n_{max}` can take,
200			default is None, i.e. there is no maximal value.
201			type_constraint: Precise type that :math:`n_{max}` and
202			:math:`n_{min}` must take.
203
204			Returns:
205			A tuple of two numbers :math:`(n_{min}, n_{max})`.
206
207			Raises:
208			ValueError: if :attr:`nums_range` is negative
209			ValueError: if :math:`n_{max}` or :math:`n_{min}` is not a number
210			ValueError: if :math:`n_{max} \lt n_{min}`
211			ValueError: if :attr:`min_constraint` is not None and
212			:math:`n_{min}` is smaller than :attr:`min_constraint`
213			ValueError: if :attr:`max_constraint` is not None and
214			:math:`n_{max}` is greater than :attr:`max_constraint`
215			ValueError: if :attr:`type_constraint` is not None and
216			:math:`n_{max}` and :math:`n_{max}` are not of type
217			:attr:`type_constraint`.
218			"""
219			if isinstance(nums_range, numbers.Number): # single number given
220			if nums_range < 0:
221			raise ValueError(
222			f'If {name} is a single number,'
223			f' it must be positive, not {nums_range}')
224			if min_constraint is not None and nums_range < min_constraint:
225			raise ValueError(
226			f'If {name} is a single number, it must be greater'
227			f' than {min_constraint}, not {nums_range}'
228			)
229			if max_constraint is not None and nums_range > max_constraint:
230			raise ValueError(
231			f'If {name} is a single number, it must be smaller'
232			f' than {max_constraint}, not {nums_range}'
233			)
234			if type_constraint is not None:
235			if not isinstance(nums_range, type_constraint):
236			raise ValueError(
237			f'If {name} is a single number, it must be of'
238			f' type {type_constraint}, not {nums_range}'
239			)
240			min_range = -nums_range if min_constraint is None else nums_range
241			return (min_range, nums_range)
242
243			try:
244			min_value, max_value = nums_range
245			except (TypeError, ValueError):
246			raise ValueError(
247			f'If {name} is not a single number, it must be'
248			f' a sequence of len 2, not {nums_range}'
249			)
250
251			min_is_number = isinstance(min_value, numbers.Number)
252			max_is_number = isinstance(max_value, numbers.Number)
253			if not min_is_number or not max_is_number:
254			message = (
255			f'{name} values must be numbers, not {nums_range}')
256			raise ValueError(message)
257
258			if min_value > max_value:
259			raise ValueError(
260			f'If {name} is a sequence, the second value must be'
261			f' equal or greater than the first, but it is {nums_range}')
262
263			if min_constraint is not None and min_value < min_constraint:
264			raise ValueError(
265			f'If {name} is a sequence, the first value must be greater'
266			f' than {min_constraint}, but it is {min_value}'
267			)
268
269			if max_constraint is not None and max_value > max_constraint:
270			raise ValueError(
271			f'If {name} is a sequence, the second value must be smaller'
272			f' than {max_constraint}, but it is {max_value}'
273			)
274
275			if type_constraint is not None:
276			min_type_ok = isinstance(min_value, type_constraint)
277			max_type_ok = isinstance(max_value, type_constraint)
278			if not min_type_ok or not max_type_ok:
279			raise ValueError(
280			f'If "{name}" is a sequence, its values must be of'
281			f' type "{type_constraint}", not "{type(nums_range)}"'
282			)
283			return nums_range
284
285			@staticmethod
286			def parse_probability(probability: float) -> float:
287			is_number = isinstance(probability, numbers.Number)
288			if not (is_number and 0 <= probability <= 1):
289			message = (
290			'Probability must be a number in [0, 1],'
291			f' not {probability}'
292			)
293			raise ValueError(message)
294			return probability
295
296			@staticmethod
297			def parse_subject(subject: Subject) -> None:
298			if not isinstance(subject, Subject):
299			message = (
300			'Input to a transform must be a tensor or an instance'
301			f' of torchio.Subject, not "{type(subject)}"'
302			)
303			raise RuntimeError(message)
304
305			def parse_tensor(self, data: TypeData) -> Subject:
306			if data.ndim != 4:
307			message = (
308			'The input must be a 4D tensor with dimensions'
309			f' (channels, x, y, z) but it has shape {tuple(data.shape)}'
310			)
311			raise ValueError(message)
312			return self._get_subject_from_tensor(data)
313
314			@staticmethod
315			def parse_interpolation(interpolation: str) -> Interpolation:
316			if isinstance(interpolation, Interpolation):
317			message = (
318			'Interpolation of type torchio.Interpolation'
319			' is deprecated, please use a string instead'
320			)
321			warnings.warn(message, FutureWarning)
322			elif isinstance(interpolation, str):
323			interpolation = interpolation.lower()
324			supported_values = [key.name.lower() for key in Interpolation]
325			if interpolation in supported_values:
326			interpolation = getattr(Interpolation, interpolation.upper())
327			else:
328			message = (
329			f'Interpolation "{interpolation}" is not among'
330			f' the supported values: {supported_values}'
331			)
332			raise AttributeError(message)
333			else:
334			message = (
335			'image_interpolation must be a string,'
336			f' not {type(interpolation)}'
337			)
338			raise TypeError(message)
339			return interpolation
340
341			def _get_subject_from_tensor(self, tensor: torch.Tensor) -> Subject:
342			image = ScalarImage(tensor=tensor)
343			return self._get_subject_from_image(image)
344
345			def _get_subject_from_image(self, image: Image) -> Subject:
346			subject = Subject({self.default_image_name: image})
347			return subject
348
349			@staticmethod
350			def _get_subject_from_dict(
351			data: dict,
352			image_keys: List[str],
353			) -> Subject:
354			subject_dict = {}
355			for key, value in data.items():
356			if key in image_keys:
357			value = ScalarImage(tensor=value)
358			subject_dict[key] = value
359			return Subject(subject_dict)
360
361			def _get_subject_from_sitk_image(self, image):
362			tensor, affine = sitk_to_nib(image)
363			image = ScalarImage(tensor=tensor, affine=affine)
364			return self._get_subject_from_image(image)
365
366			@staticmethod
367			def nib_to_sitk(data: TypeData, affine: TypeData) -> sitk.Image:
368			return nib_to_sitk(data, affine)
369
370			@staticmethod
371			def sitk_to_nib(image: sitk.Image) -> Tuple[torch.Tensor, np.ndarray]:
372			return sitk_to_nib(image)
373
374			@property
375			def name(self):
376			return self.__class__.__name__
377
378			def is_invertible(self):
379			return hasattr(self, 'invert_transform')
380
381			def inverse(self):
382			if not self.is_invertible():
383			raise RuntimeError(f'{self.name} is not invertible')
384			new = copy.deepcopy(self)
385			new.invert_transform = not self.invert_transform
386			return new
387

fepegar / torchio

Pull Request — master (#353)

Transform.parse_subject() A

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