torchio.transforms.transform.Transform.parse_range() - Code Metrics - Inspection of "Add support to take a dict as transform input" - fepegar/torchio - Measure and Improve Code Quality continuously with Scrutinizer

Passed

Pull Request — master (#252)

by Fernando

created 2020-08-05 11:34 UTC

Transform.parse_range() F

↳ Parent: torchio.transforms.transform

Complexity

Conditions

Size

Total Lines	102
Code Lines	48

Duplication

Lines	0
Ratio	0 %

Importance

Changes

Metric	Value
cc	21
eloc	48
nop	5
dl	0
loc	102
rs	0
c	0
b	0
f	0

How to fix Long Method Complexity

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 SimpleITK as sitk

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


IMAGE_NAME = 'image'


class Transform(ABC):
    image_name = 'image'
    """Abstract class for all TorchIO transforms.

    All classes used to transform a sample from an
    :py:class:`~torchio.ImagesDataset` should subclass it.
    All subclasses should overwrite
    :py:meth:`torchio.tranforms.Transform.apply_transform`,
    which takes a sample, applies some transformation and returns the result.

    Args:
        p: Probability that this transform will be applied.
        copy: Make a deep copy of the input before applying the transform.
        keys: If the input is a dictionary, the corresponding values will be
            converted to :py:class:`torchio.ScalarImage` so that the transform
            is applied to them only.
    """
    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

    def __call__(self, data: Union[Subject, torch.Tensor, np.ndarray]):
        """Transform a sample and return the result.

        Args:
            data: Instance of :py:class:`~torchio.Subject`, 4D
                :py:class:`torch.Tensor` or 4D NumPy array with dimensions
                :math:`(C, D, H, W)`, where :math:`C` is the number of channels
                and :math:`D, H, W` 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_dict = False
        if isinstance(data, (np.ndarray, torch.Tensor)):
            is_array = isinstance(data, np.ndarray)
            is_tensor = True
            is_image = False
            sample = self.parse_tensor(data)
        elif isinstance(data, Image):
            sample = self._get_subject_from_image(data)
            is_tensor = is_array = False
            is_image = True
        elif isinstance(data, Subject):
            is_tensor = is_array = is_image = False
            sample = data
        elif isinstance(data, dict):  # e.g. Eisen dict
            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)
            sample = self._get_subject_from_dict(data, self.keys)
            is_tensor = is_array = is_image = False
            is_dict = True
        self.parse_sample(sample)


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

        with np.errstate(all='raise'):
            transformed = self.apply_transform(sample)

        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:

            transformed = transformed[self.image_name][DATA]
        if is_array:

            transformed = transformed.numpy()
        if is_image:

            transformed = transformed[IMAGE_NAME]
        if is_dict:
            transformed = dict(transformed)
            for key, value in transformed.items():
                if isinstance(value, Image):
                    transformed[key] = value.data
        return transformed

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

    @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):
            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 and \
                    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_degree, max_degree = nums_range
        except (TypeError, ValueError):
            raise ValueError(
                f'If {name} is not a single number, it muste be'
                f'a sequence of len 2, not {nums_range}'
            )

        if not isinstance(min_degree, numbers.Number) or \
                not isinstance(max_degree, numbers.Number):
            message = (
                f'{name} values must be numbers, not {nums_range}')
            raise ValueError(message)

        if min_degree > max_degree:
            raise ValueError(
                f'If {name} is a sequence, the second value must be'
                f' equal or greater than the first, not {nums_range}')

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

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

        if type_constraint is not None:
            if not isinstance(min_degree, type_constraint) or \
                    not isinstance(max_degree, type_constraint):
                raise ValueError(
                    f'If {name} is a sequence, its values must be of'
                    f'type {type_constraint}, not {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_sample(sample: Subject) -> None:
        if not isinstance(sample, Subject):
            message = (
                'Input to a transform must be a tensor or an instance'
                f' of torchio.Subject, not "{type(sample)}"'
            )
            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, channels_last=False)
        return Subject({self.image_name: image})

    @staticmethod
    def _get_subject_from_image(image: Image) -> Subject:
        subject = Subject({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)

    @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__


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 SimpleITK as sitk
10
11			from .. import TypeData, DATA, TypeNumber
12			from ..data.subject import Subject
13			from ..data.image import Image, ScalarImage
14			from ..data.dataset import ImagesDataset
15			from ..utils import nib_to_sitk, sitk_to_nib
16			from .interpolation import Interpolation
17
18
19			IMAGE_NAME = 'image'
20
21
22			class Transform(ABC):
23			image_name = 'image'
24			"""Abstract class for all TorchIO transforms.
25
26			All classes used to transform a sample from an
27			:py:class:`~torchio.ImagesDataset` should subclass it.
28			All subclasses should overwrite
29			:py:meth:`torchio.tranforms.Transform.apply_transform`,
30			which takes a sample, applies some transformation and returns the result.
31
32			Args:
33			p: Probability that this transform will be applied.
34			copy: Make a deep copy of the input before applying the transform.
35			keys: If the input is a dictionary, the corresponding values will be
36			converted to :py:class:`torchio.ScalarImage` so that the transform
37			is applied to them only.
38			"""
39			def __init__(
40			self,
41			p: float = 1,
42			copy: bool = True,
43			keys: Optional[List[str]] = None,
44			):
45			self.probability = self.parse_probability(p)
46			self.copy = copy
47			self.keys = keys
48
49			def __call__(self, data: Union[Subject, torch.Tensor, np.ndarray]):
50			"""Transform a sample and return the result.
51
52			Args:
53			data: Instance of :py:class:`~torchio.Subject`, 4D
54			:py:class:`torch.Tensor` or 4D NumPy array with dimensions
55			:math:`(C, D, H, W)`, where :math:`C` is the number of channels
56			and :math:`D, H, W` are the spatial dimensions. If the input is
57			a tensor, the affine matrix is an identity and a tensor will be
58			also returned.
59			"""
60			if torch.rand(1).item() > self.probability:
61			return data
62
63			is_dict = False
64			if isinstance(data, (np.ndarray, torch.Tensor)):
65			is_array = isinstance(data, np.ndarray)
66			is_tensor = True
67			is_image = False
68			sample = self.parse_tensor(data)
69			elif isinstance(data, Image):
70			sample = self._get_subject_from_image(data)
71			is_tensor = is_array = False
72			is_image = True
73			elif isinstance(data, Subject):
74			is_tensor = is_array = is_image = False
75			sample = data
76			elif isinstance(data, dict): # e.g. Eisen dict
77			if self.keys is None:
78			message = (
79			'If input is a dictionary, a value for "keys" must be'
80			' specified when instantiating the transform'
81			)
82			raise RuntimeError(message)
83			sample = self._get_subject_from_dict(data, self.keys)
84			is_tensor = is_array = is_image = False
85			is_dict = True
86			self.parse_sample(sample)
			0 ignored issues – show introduced 2020-08-05 11:35 UTC by Report Bug Copy Issue Report The variable `sample` does not seem to be defined for all execution paths. Loading history...
87
88			if self.copy:
89			sample = copy.copy(sample)
90
91			with np.errstate(all='raise'):
92			transformed = self.apply_transform(sample)
93
94			for image in transformed.get_images(intensity_only=False):
95			ndim = image[DATA].ndim
96			assert ndim == 4, f'Output of {self.name} is {ndim}D'
97
98			if is_tensor:
			0 ignored issues – show introduced 2020-08-05 11:35 UTC by Report Bug Copy Issue Report The variable `is_tensor` does not seem to be defined for all execution paths. Loading history...
99			transformed = transformed[self.image_name][DATA]
100			if is_array:
			0 ignored issues – show introduced 2020-08-05 11:35 UTC by Report Bug Copy Issue Report The variable `is_array` does not seem to be defined for all execution paths. Loading history...
101			transformed = transformed.numpy()
102			if is_image:
			0 ignored issues – show introduced 2020-08-05 11:35 UTC by Report Bug Copy Issue Report The variable `is_image` does not seem to be defined for all execution paths. Loading history...
103			transformed = transformed[IMAGE_NAME]
104			if is_dict:
105			transformed = dict(transformed)
106			for key, value in transformed.items():
107			if isinstance(value, Image):
108			transformed[key] = value.data
109			return transformed
110
111			@abstractmethod
112			def apply_transform(self, sample: Subject):
113			raise NotImplementedError
114
115			@staticmethod
116			def parse_range(
117			nums_range: Union[TypeNumber, Tuple[TypeNumber, TypeNumber]],
118			name: str,
119			min_constraint: TypeNumber = None,
120			max_constraint: TypeNumber = None,
121			type_constraint: type = None,
122			) -> Tuple[TypeNumber, TypeNumber]:
123			r"""Adapted from ``torchvision.transforms.RandomRotation``.
124
125			Args:
126			nums_range: Tuple of two numbers :math:`(n_{min}, n_{max})`,
127			where :math:`n_{min} \leq n_{max}`.
128			If a single positive number :math:`n` is provided,
129			:math:`n_{min} = -n` and :math:`n_{max} = n`.
130			name: Name of the parameter, so that an informative error message
131			can be printed.
132			min_constraint: Minimal value that :math:`n_{min}` can take,
133			default is None, i.e. there is no minimal value.
134			max_constraint: Maximal value that :math:`n_{max}` can take,
135			default is None, i.e. there is no maximal value.
136			type_constraint: Precise type that :math:`n_{max}` and
137			:math:`n_{min}` must take.
138
139			Returns:
140			A tuple of two numbers :math:`(n_{min}, n_{max})`.
141
142			Raises:
143			ValueError: if :attr:`nums_range` is negative
144			ValueError: if :math:`n_{max}` or :math:`n_{min}` is not a number
145			ValueError: if :math:`n_{max} \lt n_{min}`
146			ValueError: if :attr:`min_constraint` is not None and
147			:math:`n_{min}` is smaller than :attr:`min_constraint`
148			ValueError: if :attr:`max_constraint` is not None and
149			:math:`n_{max}` is greater than :attr:`max_constraint`
150			ValueError: if :attr:`type_constraint` is not None and
151			:math:`n_{max}` and :math:`n_{max}` are not of type
152			:attr:`type_constraint`.
153			"""
154			if isinstance(nums_range, numbers.Number):
155			if nums_range < 0:
156			raise ValueError(
157			f'If {name} is a single number,'
158			f' it must be positive, not {nums_range}')
159			if min_constraint is not None and nums_range < min_constraint:
160			raise ValueError(
161			f'If {name} is a single number, it must be greater'
162			f'than {min_constraint}, not {nums_range}'
163			)
164			if max_constraint is not None and nums_range > max_constraint:
165			raise ValueError(
166			f'If {name} is a single number, it must be smaller'
167			f'than {max_constraint}, not {nums_range}'
168			)
169			if type_constraint is not None and \
170			not isinstance(nums_range, type_constraint):
171			raise ValueError(
172			f'If {name} is a single number, it must be of'
173			f'type {type_constraint}, not {nums_range}'
174			)
175			min_range = -nums_range if min_constraint is None else nums_range
176			return (min_range, nums_range)
177
178			try:
179			min_degree, max_degree = nums_range
180			except (TypeError, ValueError):
181			raise ValueError(
182			f'If {name} is not a single number, it muste be'
183			f'a sequence of len 2, not {nums_range}'
184			)
185
186			if not isinstance(min_degree, numbers.Number) or \
187			not isinstance(max_degree, numbers.Number):
188			message = (
189			f'{name} values must be numbers, not {nums_range}')
190			raise ValueError(message)
191
192			if min_degree > max_degree:
193			raise ValueError(
194			f'If {name} is a sequence, the second value must be'
195			f' equal or greater than the first, not {nums_range}')
196
197			if min_constraint is not None and min_degree < min_constraint:
198			raise ValueError(
199			f'If {name} is a sequence, the first value must be greater'
200			f'than {min_constraint}, not {min_degree}'
201			)
202
203			if max_constraint is not None and max_degree > max_constraint:
204			raise ValueError(
205			f'If {name} is a sequence, the second value must be smaller'
206			f'than {max_constraint}, not {max_degree}'
207			)
208
209			if type_constraint is not None:
210			if not isinstance(min_degree, type_constraint) or \
211			not isinstance(max_degree, type_constraint):
212			raise ValueError(
213			f'If {name} is a sequence, its values must be of'
214			f'type {type_constraint}, not {nums_range}'
215			)
216			return nums_range
217
218			@staticmethod
219			def parse_probability(probability: float) -> float:
220			is_number = isinstance(probability, numbers.Number)
221			if not (is_number and 0 <= probability <= 1):
222			message = (
223			'Probability must be a number in [0, 1],'
224			f' not {probability}'
225			)
226			raise ValueError(message)
227			return probability
228
229			@staticmethod
230			def parse_sample(sample: Subject) -> None:
231			if not isinstance(sample, Subject):
232			message = (
233			'Input to a transform must be a tensor or an instance'
234			f' of torchio.Subject, not "{type(sample)}"'
235			)
236			raise RuntimeError(message)
237
238			def parse_tensor(self, data: TypeData) -> Subject:
239			if data.ndim != 4:
240			message = (
241			'The input must be a 4D tensor with dimensions'
242			f' (channels, x, y, z) but it has shape {tuple(data.shape)}'
243			)
244			raise ValueError(message)
245			return self._get_subject_from_tensor(data)
246
247			@staticmethod
248			def parse_interpolation(interpolation: str) -> Interpolation:
249			if isinstance(interpolation, Interpolation):
250			message = (
251			'Interpolation of type torchio.Interpolation'
252			' is deprecated, please use a string instead'
253			)
254			warnings.warn(message, FutureWarning)
255			elif isinstance(interpolation, str):
256			interpolation = interpolation.lower()
257			supported_values = [key.name.lower() for key in Interpolation]
258			if interpolation in supported_values:
259			interpolation = getattr(Interpolation, interpolation.upper())
260			else:
261			message = (
262			f'Interpolation "{interpolation}" is not among'
263			f' the supported values: {supported_values}'
264			)
265			raise AttributeError(message)
266			else:
267			message = (
268			'image_interpolation must be a string,'
269			f' not {type(interpolation)}'
270			)
271			raise TypeError(message)
272			return interpolation
273
274			def _get_subject_from_tensor(self, tensor: torch.Tensor) -> Subject:
275			image = ScalarImage(tensor=tensor, channels_last=False)
276			return Subject({self.image_name: image})
277
278			@staticmethod
279			def _get_subject_from_image(image: Image) -> Subject:
280			subject = Subject({IMAGE_NAME: image})
281			return subject
282
283			@staticmethod
284			def _get_subject_from_dict(
285			data: dict,
286			image_keys: List[str],
287			) -> Subject:
288			subject_dict = {}
289			for key, value in data.items():
290			if key in image_keys:
291			value = ScalarImage(tensor=value)
292			subject_dict[key] = value
293			return Subject(subject_dict)
294
295			@staticmethod
296			def nib_to_sitk(data: TypeData, affine: TypeData) -> sitk.Image:
297			return nib_to_sitk(data, affine)
298
299			@staticmethod
300			def sitk_to_nib(image: sitk.Image) -> Tuple[torch.Tensor, np.ndarray]:
301			return sitk_to_nib(image)
302
303			@property
304			def name(self):
305			return self.__class__.__name__
306

fepegar / torchio

Pull Request — master (#252)

Transform.parse_range() F

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