torchio.data.subject.Subject.get_applied_transforms() - Code Metrics - Inspection of "Add option to ignore intensity transforms when inv..." - fepegar/torchio - Measure and Improve Code Quality continuously with Scrutinizer

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Pull Request — master (#417)

by Fernando

created 2021-01-11 15:29 UTC

Subject.get_applied_transforms() A

↳ Parent: torchio.data.subject

Complexity

Conditions

Size

Total Lines	17
Code Lines	15

Duplication

Lines	0
Ratio	0 %

Importance

Changes

Metric	Value
cc	4
eloc	15
nop	2
dl	0
loc	17
rs	9.65
c	0
b	0
f	0

import copy
import pprint
from typing import Any, Dict, List, Tuple, Optional, Sequence, TYPE_CHECKING

import numpy as np

from ..constants import TYPE, INTENSITY
from .image import Image
from ..utils import get_subclasses

if TYPE_CHECKING:
    from ..transforms import Transform, Compose


class Subject(dict):
    """Class to store information about the images corresponding to a subject.

    Args:
        *args: If provided, a dictionary of items.
        **kwargs: Items that will be added to the subject sample.

    Example:

        >>> import torchio as tio
        >>> # One way:
        >>> subject = tio.Subject(
        ...     one_image=tio.ScalarImage('path_to_image.nii.gz'),
        ...     a_segmentation=tio.LabelMap('path_to_seg.nii.gz'),
        ...     age=45,
        ...     name='John Doe',
        ...     hospital='Hospital Juan Negrín',
        ... )
        >>> # If you want to create the mapping before, or have spaces in the keys:
        >>> subject_dict = {
        ...     'one image': tio.ScalarImage('path_to_image.nii.gz'),
        ...     'a segmentation': tio.LabelMap('path_to_seg.nii.gz'),
        ...     'age': 45,
        ...     'name': 'John Doe',
        ...     'hospital': 'Hospital Juan Negrín',
        ... }
        >>> subject = tio.Subject(subject_dict)

    """

    def __init__(self, *args, **kwargs: Dict[str, Any]):
        if args:
            if len(args) == 1 and isinstance(args[0], dict):
                kwargs.update(args[0])
            else:
                message = (
                    'Only one dictionary as positional argument is allowed')
                raise ValueError(message)
        super().__init__(**kwargs)
        self._parse_images(self.get_images(intensity_only=False))
        self.update_attributes()  # this allows me to do e.g. subject.t1
        self.applied_transforms = []

    def __repr__(self):
        num_images = len(self.get_images(intensity_only=False))
        string = (
            f'{self.__class__.__name__}'
            f'(Keys: {tuple(self.keys())}; images: {num_images})'
        )
        return string

    def __copy__(self):
        result_dict = {}
        for key, value in self.items():
            if isinstance(value, Image):
                value = copy.copy(value)
            else:
                value = copy.deepcopy(value)
            result_dict[key] = value
        new = Subject(result_dict)
        new.applied_transforms = self.applied_transforms[:]
        return new

    def __len__(self):
        return len(self.get_images(intensity_only=False))

    @staticmethod
    def _parse_images(images: List[Tuple[str, Image]]) -> None:
        # Check that it's not empty
        if not images:
            raise ValueError('A subject without images cannot be created')

    @property
    def shape(self):
        """Return shape of first image in subject.

        Consistency of shapes across images in the subject is checked first.
        """
        self.check_consistent_attribute('shape')
        return self.get_first_image().shape

    @property
    def spatial_shape(self):
        """Return spatial shape of first image in subject.

        Consistency of spatial shapes across images in the subject is checked
        first.
        """
        self.check_consistent_spatial_shape()
        return self.get_first_image().spatial_shape

    @property
    def spacing(self):
        """Return spacing of first image in subject.

        Consistency of spacings across images in the subject is checked first.
        """
        self.check_consistent_attribute('spacing')
        return self.get_first_image().spacing

    @property
    def history(self):
        # Kept for backwards compatibility
        return self.get_applied_transforms()

    def get_applied_transforms(
            self,
            ignore_intensity: bool = False,
            ) -> List['Transform']:
        from ..transforms.transform import Transform
        from ..transforms.intensity_transform import IntensityTransform
        name_to_transform = {
            cls.__name__: cls
            for cls in get_subclasses(Transform)
        }
        transforms_list = []
        for transform_name, arguments in self.applied_transforms:
            transform = name_to_transform[transform_name](**arguments)
            if ignore_intensity and isinstance(transform, IntensityTransform):
                continue
            transforms_list.append(transform)
        return transforms_list

    def get_composed_history(
            self,
            ignore_intensity: bool = False,
            ) -> 'Compose':
        from ..transforms.augmentation.composition import Compose
        transforms = self.get_applied_transforms(
            ignore_intensity=ignore_intensity)
        return Compose(transforms)

    def get_inverse_transform(
            self,
            warn: bool = True,
            ignore_intensity: bool = True,
            ) ->  'Compose':
        """Get a reversed list of the inverses of the applied transforms.

        Args:
            warn: Issue a warning if some transforms are not invertible.
            ignore_intensity: If ``True``, all instances of
                :class:`~torchio.transforms.intensity_transform.IntensityTransform`
                will be ignored.
        """
        history_transform = self.get_composed_history(
            ignore_intensity=ignore_intensity)
        inverse_transform = history_transform.inverse(warn=warn)
        return inverse_transform

    def apply_inverse_transform(self, **kwargs) -> 'Subject':
        """Try to apply the inverse of all applied transforms, in reverse order.

        Args:
            **kwargs: Keyword arguments passed on to
                :meth:`~torchio.data.subject.Subject.get_inverse_transform`.
        """
        inverse_transform = self.get_inverse_transform(**kwargs)
        transformed = inverse_transform(self)
        transformed.clear_history()
        return transformed

    def clear_history(self) -> None:
        self.applied_transforms = []

    def check_consistent_attribute(self, attribute: str) -> None:
        values_dict = {}
        iterable = self.get_images_dict(intensity_only=False).items()
        for image_name, image in iterable:
            values_dict[image_name] = getattr(image, attribute)
        num_unique_values = len(set(values_dict.values()))
        if num_unique_values > 1:
            message = (
                f'More than one {attribute} found in subject images:'
                f'\n{pprint.pformat(values_dict)}'
            )
            raise RuntimeError(message)

    def check_consistent_spatial_shape(self) -> None:
        self.check_consistent_attribute('spatial_shape')

    def check_consistent_orientation(self) -> None:
        self.check_consistent_attribute('orientation')

    def check_consistent_affine(self):
        # https://github.com/fepegar/torchio/issues/354
        affine = None
        first_image = None
        iterable = self.get_images_dict(intensity_only=False).items()
        for image_name, image in iterable:
            if affine is None:
                affine = image.affine
                first_image = image_name
            elif not np.allclose(affine, image.affine, rtol=1e-6, atol=1e-6):
                message = (
                    f'Images "{first_image}" and "{image_name}" do not occupy'
                    ' the same physical space.'
                    f'\nAffine of "{first_image}":'
                    f'\n{pprint.pformat(affine)}'
                    f'\nAffine of "{image_name}":'
                    f'\n{pprint.pformat(image.affine)}'
                )
                raise RuntimeError(message)

    def check_consistent_space(self):
        self.check_consistent_spatial_shape()
        self.check_consistent_affine()

    def get_images_dict(
            self,
            intensity_only=True,
            include: Optional[Sequence[str]] = None,
            exclude: Optional[Sequence[str]] = None,
            ) -> Dict[str, Image]:
        images = {}
        for image_name, image in self.items():
            if not isinstance(image, Image):
                continue
            if intensity_only and not image[TYPE] == INTENSITY:
                continue
            if include is not None and image_name not in include:
                continue
            if exclude is not None and image_name in exclude:
                continue
            images[image_name] = image
        return images

    def get_images(
            self,
            intensity_only=True,
            include: Optional[Sequence[str]] = None,
            exclude: Optional[Sequence[str]] = None,
            ) -> List[Image]:
        images_dict = self.get_images_dict(intensity_only=intensity_only, include=include, exclude=exclude)
        return list(images_dict.values())

    def get_first_image(self) -> Image:
        return self.get_images(intensity_only=False)[0]

    # flake8: noqa: F821
    def add_transform(
            self,
            transform: 'Transform',
            parameters_dict: dict,
            ) -> None:
        self.applied_transforms.append((transform.name, parameters_dict))

    def load(self) -> None:
        """Load images in subject."""
        for image in self.get_images(intensity_only=False):
            image.load()

    def update_attributes(self) -> None:
        # This allows to get images using attribute notation, e.g. subject.t1
        self.__dict__.update(self)

    def add_image(self, image: Image, image_name: str) -> None:
        """Add an image."""
        self[image_name] = image
        self.update_attributes()

    def remove_image(self, image_name: str) -> None:
        """Remove an image."""
        del self[image_name]

    def plot(self, **kwargs) -> None:
        """Plot images."""
        from ..visualization import plot_subject  # avoid circular import
        plot_subject(self, **kwargs)


1			import copy
2			import pprint
3			from typing import Any, Dict, List, Tuple, Optional, Sequence, TYPE_CHECKING
4
5			import numpy as np
6
7			from ..constants import TYPE, INTENSITY
8			from .image import Image
9			from ..utils import get_subclasses
10
11			if TYPE_CHECKING:
12			from ..transforms import Transform, Compose
13
14
15			class Subject(dict):
16			"""Class to store information about the images corresponding to a subject.
17
18			Args:
19			*args: If provided, a dictionary of items.
20			**kwargs: Items that will be added to the subject sample.
21
22			Example:
23
24			>>> import torchio as tio
25			>>> # One way:
26			>>> subject = tio.Subject(
27			... one_image=tio.ScalarImage('path_to_image.nii.gz'),
28			... a_segmentation=tio.LabelMap('path_to_seg.nii.gz'),
29			... age=45,
30			... name='John Doe',
31			... hospital='Hospital Juan Negrín',
32			... )
33			>>> # If you want to create the mapping before, or have spaces in the keys:
34			>>> subject_dict = {
35			... 'one image': tio.ScalarImage('path_to_image.nii.gz'),
36			... 'a segmentation': tio.LabelMap('path_to_seg.nii.gz'),
37			... 'age': 45,
38			... 'name': 'John Doe',
39			... 'hospital': 'Hospital Juan Negrín',
40			... }
41			>>> subject = tio.Subject(subject_dict)
42
43			"""
44
45			def __init__(self, args, *kwargs: Dict[str, Any]):
46			if args:
47			if len(args) == 1 and isinstance(args[0], dict):
48			kwargs.update(args[0])
49			else:
50			message = (
51			'Only one dictionary as positional argument is allowed')
52			raise ValueError(message)
53			super().__init__(**kwargs)
54			self._parse_images(self.get_images(intensity_only=False))
55			self.update_attributes() # this allows me to do e.g. subject.t1
56			self.applied_transforms = []
57
58			def __repr__(self):
59			num_images = len(self.get_images(intensity_only=False))
60			string = (
61			f'{self.__class__.__name__}'
62			f'(Keys: {tuple(self.keys())}; images: {num_images})'
63			)
64			return string
65
66			def __copy__(self):
67			result_dict = {}
68			for key, value in self.items():
69			if isinstance(value, Image):
70			value = copy.copy(value)
71			else:
72			value = copy.deepcopy(value)
73			result_dict[key] = value
74			new = Subject(result_dict)
75			new.applied_transforms = self.applied_transforms[:]
76			return new
77
78			def __len__(self):
79			return len(self.get_images(intensity_only=False))
80
81			@staticmethod
82			def _parse_images(images: List[Tuple[str, Image]]) -> None:
83			# Check that it's not empty
84			if not images:
85			raise ValueError('A subject without images cannot be created')
86
87			@property
88			def shape(self):
89			"""Return shape of first image in subject.
90
91			Consistency of shapes across images in the subject is checked first.
92			"""
93			self.check_consistent_attribute('shape')
94			return self.get_first_image().shape
95
96			@property
97			def spatial_shape(self):
98			"""Return spatial shape of first image in subject.
99
100			Consistency of spatial shapes across images in the subject is checked
101			first.
102			"""
103			self.check_consistent_spatial_shape()
104			return self.get_first_image().spatial_shape
105
106			@property
107			def spacing(self):
108			"""Return spacing of first image in subject.
109
110			Consistency of spacings across images in the subject is checked first.
111			"""
112			self.check_consistent_attribute('spacing')
113			return self.get_first_image().spacing
114
115			@property
116			def history(self):
117			# Kept for backwards compatibility
118			return self.get_applied_transforms()
119
120			def get_applied_transforms(
121			self,
122			ignore_intensity: bool = False,
123			) -> List['Transform']:
124			from ..transforms.transform import Transform
125			from ..transforms.intensity_transform import IntensityTransform
126			name_to_transform = {
127			cls.__name__: cls
128			for cls in get_subclasses(Transform)
129			}
130			transforms_list = []
131			for transform_name, arguments in self.applied_transforms:
132			transform = name_to_transform[transform_name](**arguments)
133			if ignore_intensity and isinstance(transform, IntensityTransform):
134			continue
135			transforms_list.append(transform)
136			return transforms_list
137
138			def get_composed_history(
139			self,
140			ignore_intensity: bool = False,
141			) -> 'Compose':
142			from ..transforms.augmentation.composition import Compose
143			transforms = self.get_applied_transforms(
144			ignore_intensity=ignore_intensity)
145			return Compose(transforms)
146
147			def get_inverse_transform(
148			self,
149			warn: bool = True,
150			ignore_intensity: bool = True,
151			) -> 'Compose':
152			"""Get a reversed list of the inverses of the applied transforms.
153
154			Args:
155			warn: Issue a warning if some transforms are not invertible.
156			ignore_intensity: If ``True``, all instances of
157			:class:`~torchio.transforms.intensity_transform.IntensityTransform`
158			will be ignored.
159			"""
160			history_transform = self.get_composed_history(
161			ignore_intensity=ignore_intensity)
162			inverse_transform = history_transform.inverse(warn=warn)
163			return inverse_transform
164
165			def apply_inverse_transform(self, **kwargs) -> 'Subject':
166			"""Try to apply the inverse of all applied transforms, in reverse order.
167
168			Args:
169			**kwargs: Keyword arguments passed on to
170			:meth:`~torchio.data.subject.Subject.get_inverse_transform`.
171			"""
172			inverse_transform = self.get_inverse_transform(**kwargs)
173			transformed = inverse_transform(self)
174			transformed.clear_history()
175			return transformed
176
177			def clear_history(self) -> None:
178			self.applied_transforms = []
179
180			def check_consistent_attribute(self, attribute: str) -> None:
181			values_dict = {}
182			iterable = self.get_images_dict(intensity_only=False).items()
183			for image_name, image in iterable:
184			values_dict[image_name] = getattr(image, attribute)
185			num_unique_values = len(set(values_dict.values()))
186			if num_unique_values > 1:
187			message = (
188			f'More than one {attribute} found in subject images:'
189			f'\n{pprint.pformat(values_dict)}'
190			)
191			raise RuntimeError(message)
192
193			def check_consistent_spatial_shape(self) -> None:
194			self.check_consistent_attribute('spatial_shape')
195
196			def check_consistent_orientation(self) -> None:
197			self.check_consistent_attribute('orientation')
198
199			def check_consistent_affine(self):
200			# https://github.com/fepegar/torchio/issues/354
201			affine = None
202			first_image = None
203			iterable = self.get_images_dict(intensity_only=False).items()
204			for image_name, image in iterable:
205			if affine is None:
206			affine = image.affine
207			first_image = image_name
208			elif not np.allclose(affine, image.affine, rtol=1e-6, atol=1e-6):
209			message = (
210			f'Images "{first_image}" and "{image_name}" do not occupy'
211			' the same physical space.'
212			f'\nAffine of "{first_image}":'
213			f'\n{pprint.pformat(affine)}'
214			f'\nAffine of "{image_name}":'
215			f'\n{pprint.pformat(image.affine)}'
216			)
217			raise RuntimeError(message)
218
219			def check_consistent_space(self):
220			self.check_consistent_spatial_shape()
221			self.check_consistent_affine()
222
223			def get_images_dict(
224			self,
225			intensity_only=True,
226			include: Optional[Sequence[str]] = None,
227			exclude: Optional[Sequence[str]] = None,
228			) -> Dict[str, Image]:
229			images = {}
230			for image_name, image in self.items():
231			if not isinstance(image, Image):
232			continue
233			if intensity_only and not image[TYPE] == INTENSITY:
234			continue
235			if include is not None and image_name not in include:
236			continue
237			if exclude is not None and image_name in exclude:
238			continue
239			images[image_name] = image
240			return images
241
242			def get_images(
243			self,
244			intensity_only=True,
245			include: Optional[Sequence[str]] = None,
246			exclude: Optional[Sequence[str]] = None,
247			) -> List[Image]:
248			images_dict = self.get_images_dict(intensity_only=intensity_only, include=include, exclude=exclude)
249			return list(images_dict.values())
250
251			def get_first_image(self) -> Image:
252			return self.get_images(intensity_only=False)[0]
253
254			# flake8: noqa: F821
255			def add_transform(
256			self,
257			transform: 'Transform',
258			parameters_dict: dict,
259			) -> None:
260			self.applied_transforms.append((transform.name, parameters_dict))
261
262			def load(self) -> None:
263			"""Load images in subject."""
264			for image in self.get_images(intensity_only=False):
265			image.load()
266
267			def update_attributes(self) -> None:
268			# This allows to get images using attribute notation, e.g. subject.t1
269			self.__dict__.update(self)
270
271			def add_image(self, image: Image, image_name: str) -> None:
272			"""Add an image."""
273			self[image_name] = image
274			self.update_attributes()
275
276			def remove_image(self, image_name: str) -> None:
277			"""Remove an image."""
278			del self[image_name]
279
280			def plot(self, **kwargs) -> None:
281			"""Plot images."""
282			from ..visualization import plot_subject # avoid circular import
283			plot_subject(self, **kwargs)
284

fepegar / torchio

Pull Request — master (#417)

Subject.get_applied_transforms() A

Complexity

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Duplication

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