torchio.transforms.augmentation.spatial.random_affine.RandomAffine.__init__() - Code Metrics - Inspection of "Add some deterministic transforms" - fepegar/torchio - Measure and Improve Code Quality continuously with Scrutinizer

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Pull Request — master (#353)

by Fernando

created 2020-11-16 23:08 UTC

RandomAffine.init() A

↳ Parent: torchio.transforms.augmentation.spatial.random_affine

Complexity

Conditions

Size

Total Lines	27
Code Lines	24

Duplication

Lines	0
Ratio	0 %

Importance

Changes

Metric	Value
cc	2
eloc	24
nop	10
dl	0
loc	27
rs	9.304
c	0
b	0
f	0

How to fix Many Parameters

import copy
from numbers import Number
from typing import Tuple, Optional, List, Union

import torch
import numpy as np
import SimpleITK as sitk

from ....data.subject import Subject
from ....utils import nib_to_sitk, get_major_sitk_version, to_tuple
from ....torchio import (
    INTENSITY,
    DATA,
    AFFINE,
    TYPE,
    TypeRangeFloat,
    TypeSextetFloat,
    TypeTripletFloat,
)
from ... import SpatialTransform
from .. import Interpolation, get_sitk_interpolator
from .. import RandomTransform


TypeOneToSixFloat = Union[TypeRangeFloat, TypeTripletFloat, TypeSextetFloat]


class RandomAffine(RandomTransform, SpatialTransform):
    r"""Random affine transformation.

    Args:
        scales: Tuple :math:`(a_1, b_1, a_2, b_2, a_3, b_3)` defining the
            scaling ranges.
            The scaling values along each dimension are :math:`(s_1, s_2, s_3)`,
            where :math:`s_i \sim \mathcal{U}(a_i, b_i)`.
            If two values :math:`(a, b)` are provided,
            then :math:`s_i \sim \mathcal{U}(a, b)`.
            If only one value :math:`x` is provided,
            then :math:`s_i \sim \mathcal{U}(1 - x, 1 + x)`.
            If three values :math:`(x_1, x_2, x_3)` are provided,
            then :math:`s_i \sim \mathcal{U}(1 - x_i, 1 + x_i)`.
            For example, using ``scales=(0.5, 0.5)`` will zoom out the image,
            making the objects inside look twice as small while preserving
            the physical size and position of the image bounds.
        degrees: Tuple :math:`(a_1, b_1, a_2, b_2, a_3, b_3)` defining the
            rotation ranges in degrees.
            Rotation angles around each axis are
            :math:`(\theta_1, \theta_2, \theta_3)`,
            where :math:`\theta_i \sim \mathcal{U}(a_i, b_i)`.
            If two values :math:`(a, b)` are provided,
            then :math:`\theta_i \sim \mathcal{U}(a, b)`.
            If only one value :math:`x` is provided,
            then :math:`\theta_i \sim \mathcal{U}(-x, x)`.
            If three values :math:`(x_1, x_2, x_3)` are provided,
            then :math:`\theta_i \sim \mathcal{U}(-x_i, x_i)`.
        translation: Tuple :math:`(a_1, b_1, a_2, b_2, a_3, b_3)` defining the
            translation ranges in mm.
            Translation along each axis is :math:`(t_1, t_2, t_3)`,
            where :math:`t_i \sim \mathcal{U}(a_i, b_i)`.
            If two values :math:`(a, b)` are provided,
            then :math:`t_i \sim \mathcal{U}(a, b)`.
            If only one value :math:`x` is provided,
            then :math:`t_i \sim \mathcal{U}(-x, x)`.
            If three values :math:`(x_1, x_2, x_3)` are provided,
            then :math:`t_i \sim \mathcal{U}(-x_i, x_i)`.
        isotropic: If ``True``, the scaling factor along all dimensions is the
            same, i.e. :math:`s_1 = s_2 = s_3`.
        center: If ``'image'``, rotations and scaling will be performed around
            the image center. If ``'origin'``, rotations and scaling will be
            performed around the origin in world coordinates.
        default_pad_value: As the image is rotated, some values near the
            borders will be undefined.
            If ``'minimum'``, the fill value will be the image minimum.
            If ``'mean'``, the fill value is the mean of the border values.
            If ``'otsu'``, the fill value is the mean of the values at the
            border that lie under an
            `Otsu threshold <https://ieeexplore.ieee.org/document/4310076>`_.
            If it is a number, that value will be used.
        image_interpolation: See :ref:`Interpolation`.
        p: Probability that this transform will be applied.
        seed: See :py:class:`~torchio.transforms.augmentation.RandomTransform`.
        keys: See :py:class:`~torchio.transforms.Transform`.

    Example:
        >>> import torchio as tio
        >>> subject = tio.datasets.Colin27()
        >>> transform = tio.RandomAffine(
        ...     scales=(0.9, 1.2),
        ...     degrees=(10),
        ...     isotropic=False,
        ...     default_pad_value='otsu',
        ...     image_interpolation='bspline',
        ... )
        >>> transformed = transform(subject)

    From the command line::

        $ torchio-transform t1.nii.gz RandomAffine --kwargs "degrees=30 default_pad_value=minimum" --seed 42 affine_min.nii.gz

    """
    def __init__(
            self,
            scales: TypeOneToSixFloat = 0.1,
            degrees: TypeOneToSixFloat = 10,
            translation: TypeOneToSixFloat = 0,
            isotropic: bool = False,
            center: str = 'image',
            default_pad_value: Union[str, float] = 'otsu',
            image_interpolation: str = 'linear',
            p: float = 1,
            keys: Optional[List[str]] = None,
            ):
        super().__init__(p=p, keys=keys)
        self.isotropic = isotropic
        _parse_scales_isotropic(scales, isotropic)
        self.scales = self.parse_params(scales, 1, 'scales', min_constraint=0)
        self.degrees = self.parse_params(degrees, 0, 'degrees')
        self.translation = self.parse_params(translation, 0, 'translation')
        if center not in ('image', 'origin'):
            message = (
                'Center argument must be "image" or "origin",'
                f' not "{center}"'
            )
            raise ValueError(message)
        self.center = center
        self.default_pad_value = _parse_default_value(default_pad_value)
        self.interpolation = self.parse_interpolation(image_interpolation)

    def get_params(
            self,
            scales: TypeSextetFloat,
            degrees: TypeSextetFloat,
            translation: TypeSextetFloat,
            isotropic: bool,
            ) -> Tuple[torch.Tensor, torch.Tensor, torch.Tensor]:
        scaling_params = self.sample_uniform_sextet(scales)
        if isotropic:
            scaling_params.fill_(scaling_params[0])
        rotation_params = self.sample_uniform_sextet(degrees)
        translation_params = self.sample_uniform_sextet(translation)
        return scaling_params, rotation_params, translation_params

    def apply_transform(self, subject: Subject) -> Subject:
        subject.check_consistent_spatial_shape()
        scaling_params, rotation_params, translation_params = self.get_params(
            self.scales,
            self.degrees,
            self.translation,
            self.isotropic,
        )
        arguments = dict(
            scales=scaling_params.tolist(),
            degrees=rotation_params.tolist(),
            translation=translation_params.tolist(),
            center=self.center,
            default_pad_value=self.default_pad_value,
            image_interpolation=self.interpolation,
        )
        transform = Affine(**arguments)
        transformed = transform(subject)
        transformed.add_transform(transform, arguments)
        return transformed


class Affine(SpatialTransform):
    r"""Apply affine transformation.

    Args:
        scales: Tuple :math:`(s_1, s_2, s_3)` defining the
            scaling values along each dimension.
        degrees: Tuple :math:`(\theta_1, \theta_2, \theta_3)` defining the
            rotation around each axis.
        translation: Tuple :math:`(t_1, t_2, t_3)` defining the
            translation in mm along each axis.
        center: If ``'image'``, rotations and scaling will be performed around
            the image center. If ``'origin'``, rotations and scaling will be
            performed around the origin in world coordinates.
        default_pad_value: As the image is rotated, some values near the
            borders will be undefined.
            If ``'minimum'``, the fill value will be the image minimum.
            If ``'mean'``, the fill value is the mean of the border values.
            If ``'otsu'``, the fill value is the mean of the values at the
            border that lie under an
            `Otsu threshold <https://ieeexplore.ieee.org/document/4310076>`_.
            If it is a number, that value will be used.
        image_interpolation: See :ref:`Interpolation`.
        keys: See :py:class:`~torchio.transforms.Transform`.
    """
    def __init__(
            self,
            scales: TypeTripletFloat,
            degrees: TypeTripletFloat,
            translation: TypeTripletFloat,
            center: str = 'image',
            default_pad_value: Union[str, float] = 'otsu',
            image_interpolation: str = 'linear',
            keys: Optional[List[str]] = None,
            ):
        super().__init__(keys=keys)
        self.scales = self.parse_params(
            scales,
            None,
            'scales',
            make_ranges=False,
            min_constraint=0,
        )
        self.degrees = self.parse_params(
            degrees,
            None,
            'degrees',
            make_ranges=False,
        )
        self.translation = self.parse_params(translation, 0, 'translation', make_ranges=False,)
        if center not in ('image', 'origin'):
            message = (
                'Center argument must be "image" or "origin",'
                f' not "{center}"'
            )
            raise ValueError(message)
        self.use_image_center = center == 'image'
        self.default_pad_value = _parse_default_value(default_pad_value)
        self.interpolation = self.parse_interpolation(image_interpolation)
        self.invert_transform = False

    @staticmethod
    def get_scaling_transform(
            scaling_params: List[float],
            center_lps: Optional[TypeTripletFloat] = None,
            ) -> sitk.ScaleTransform:
        # scaling_params are inverted so that they are more intuitive
        # For example, 1.5 means the objects look 1.5 times larger
        transform = sitk.ScaleTransform(3)
        scaling_params = 1 / np.array(scaling_params)
        transform.SetScale(scaling_params)
        if center_lps is not None:
            transform.SetCenter(center_lps)
        return transform

    @staticmethod
    def get_rotation_transform(
            degrees: List[float],
            translation: List[float],
            center_lps: Optional[TypeTripletFloat] = None,
            ) -> sitk.Euler3DTransform:
        transform = sitk.Euler3DTransform()
        radians = np.radians(degrees)
        transform.SetRotation(*radians)
        transform.SetTranslation(translation)
        if center_lps is not None:
            transform.SetCenter(center_lps)
        return transform

    def apply_transform(self, subject: Subject) -> Subject:
        scaling_params = np.array(self.scales).copy()
        rotation_params = np.array(self.degrees).copy()
        translation_params = np.array(self.translation).copy()
        subject.check_consistent_spatial_shape()
        for image in self.get_images(subject):
            if image[TYPE] != INTENSITY:
                interpolation = Interpolation.NEAREST
            else:
                interpolation = self.interpolation

            if image.is_2d():
                scaling_params[2] = 1
                rotation_params[:-1] = 0

            if self.use_image_center:
                center = image.get_center(lps=True)
            else:
                center = None

            transformed_tensors = []
            for tensor in image[DATA]:

                transformed_tensor = self.apply_affine_transform(
                    tensor,
                    image[AFFINE],
                    scaling_params.tolist(),
                    rotation_params.tolist(),
                    translation_params.tolist(),
                    interpolation,
                    center_lps=center,
                )
                transformed_tensors.append(transformed_tensor)
            image[DATA] = torch.stack(transformed_tensors)
        return subject

    def apply_affine_transform(
            self,
            tensor: torch.Tensor,
            affine: np.ndarray,
            scaling_params: List[float],
            rotation_params: List[float],
            translation_params: List[float],
            interpolation: Interpolation,
            center_lps: Optional[TypeTripletFloat] = None,
            ) -> torch.Tensor:
        assert tensor.ndim == 3

        image = nib_to_sitk(tensor[np.newaxis], affine, force_3d=True)
        floating = reference = image

        scaling_transform = self.get_scaling_transform(
            scaling_params,
            center_lps=center_lps,
        )
        rotation_transform = self.get_rotation_transform(
            rotation_params,
            translation_params,
            center_lps=center_lps,
        )

        sitk_major_version = get_major_sitk_version()
        if sitk_major_version == 1:
            transform = sitk.Transform(3, sitk.sitkComposite)
            transform.AddTransform(scaling_transform)
            transform.AddTransform(rotation_transform)
        elif sitk_major_version == 2:
            transforms = [scaling_transform, rotation_transform]
            transform = sitk.CompositeTransform(transforms)

        if self.invert_transform:
            transform = transform.GetInverse()


        if self.default_pad_value == 'minimum':
            default_value = tensor.min().item()
        elif self.default_pad_value == 'mean':
            default_value = get_borders_mean(image, filter_otsu=False)
        elif self.default_pad_value == 'otsu':
            default_value = get_borders_mean(image, filter_otsu=True)
        else:
            default_value = self.default_pad_value

        resampler = sitk.ResampleImageFilter()
        resampler.SetInterpolator(get_sitk_interpolator(interpolation))
        resampler.SetReferenceImage(reference)
        resampler.SetDefaultPixelValue(float(default_value))
        resampler.SetOutputPixelType(sitk.sitkFloat32)
        resampler.SetTransform(transform)
        resampled = resampler.Execute(floating)

        np_array = sitk.GetArrayFromImage(resampled)
        np_array = np_array.transpose()  # ITK to NumPy
        tensor = torch.from_numpy(np_array)
        return tensor

    def inverse(self):
        new = copy.deepcopy(self)
        new.invert_transform = not self.invert_transform
        return new


# flake8: noqa: E201, E203, E243
def get_borders_mean(image, filter_otsu=True):
    # pylint: disable=bad-whitespace
    array = sitk.GetArrayViewFromImage(image)
    borders_tuple = (
        array[ 0,  :,  :],
        array[-1,  :,  :],
        array[ :,  0,  :],
        array[ :, -1,  :],
        array[ :,  :,  0],
        array[ :,  :, -1],
    )
    borders_flat = np.hstack([border.ravel() for border in borders_tuple])
    if not filter_otsu:
        return borders_flat.mean()
    borders_reshaped = borders_flat.reshape(1, 1, -1)
    borders_image = sitk.GetImageFromArray(borders_reshaped)
    otsu = sitk.OtsuThresholdImageFilter()
    otsu.Execute(borders_image)
    threshold = otsu.GetThreshold()
    values = borders_flat[borders_flat < threshold]
    if values.any():
        default_value = values.mean()
    else:
        default_value = borders_flat.mean()
    return default_value

def _parse_scales_isotropic(scales, isotropic):
    params = to_tuple(scales)
    if isotropic and len(scales) in (3, 6):
        message = (
            'If "isotropic" is True, the value for "scales" must have'
            f' length 1 or 2, but "{scales}" was passed'
        )
        raise ValueError(message)

def _parse_default_value(value: Union[str, float]) -> Union[str, float]:
    if isinstance(value, Number) or value in ('minimum', 'otsu', 'mean'):
        return value
    message = (
        'Value for default_pad_value must be "minimum", "otsu", "mean"'
        ' or a number'
    )
    raise ValueError(message)


1			import copy
2			from numbers import Number
3			from typing import Tuple, Optional, List, Union
4
5			import torch
6			import numpy as np
7			import SimpleITK as sitk
8
9			from ....data.subject import Subject
10			from ....utils import nib_to_sitk, get_major_sitk_version, to_tuple
11			from ....torchio import (
12			INTENSITY,
13			DATA,
14			AFFINE,
15			TYPE,
16			TypeRangeFloat,
17			TypeSextetFloat,
18			TypeTripletFloat,
19			)
20			from ... import SpatialTransform
21			from .. import Interpolation, get_sitk_interpolator
22			from .. import RandomTransform
23
24
25			TypeOneToSixFloat = Union[TypeRangeFloat, TypeTripletFloat, TypeSextetFloat]
26
27
28			class RandomAffine(RandomTransform, SpatialTransform):
29			r"""Random affine transformation.
30
31			Args:
32			scales: Tuple :math:`(a_1, b_1, a_2, b_2, a_3, b_3)` defining the
33			scaling ranges.
34			The scaling values along each dimension are :math:`(s_1, s_2, s_3)`,
35			where :math:`s_i \sim \mathcal{U}(a_i, b_i)`.
36			If two values :math:`(a, b)` are provided,
37			then :math:`s_i \sim \mathcal{U}(a, b)`.
38			If only one value :math:`x` is provided,
39			then :math:`s_i \sim \mathcal{U}(1 - x, 1 + x)`.
40			If three values :math:`(x_1, x_2, x_3)` are provided,
41			then :math:`s_i \sim \mathcal{U}(1 - x_i, 1 + x_i)`.
42			For example, using ``scales=(0.5, 0.5)`` will zoom out the image,
43			making the objects inside look twice as small while preserving
44			the physical size and position of the image bounds.
45			degrees: Tuple :math:`(a_1, b_1, a_2, b_2, a_3, b_3)` defining the
46			rotation ranges in degrees.
47			Rotation angles around each axis are
48			:math:`(\theta_1, \theta_2, \theta_3)`,
49			where :math:`\theta_i \sim \mathcal{U}(a_i, b_i)`.
50			If two values :math:`(a, b)` are provided,
51			then :math:`\theta_i \sim \mathcal{U}(a, b)`.
52			If only one value :math:`x` is provided,
53			then :math:`\theta_i \sim \mathcal{U}(-x, x)`.
54			If three values :math:`(x_1, x_2, x_3)` are provided,
55			then :math:`\theta_i \sim \mathcal{U}(-x_i, x_i)`.
56			translation: Tuple :math:`(a_1, b_1, a_2, b_2, a_3, b_3)` defining the
57			translation ranges in mm.
58			Translation along each axis is :math:`(t_1, t_2, t_3)`,
59			where :math:`t_i \sim \mathcal{U}(a_i, b_i)`.
60			If two values :math:`(a, b)` are provided,
61			then :math:`t_i \sim \mathcal{U}(a, b)`.
62			If only one value :math:`x` is provided,
63			then :math:`t_i \sim \mathcal{U}(-x, x)`.
64			If three values :math:`(x_1, x_2, x_3)` are provided,
65			then :math:`t_i \sim \mathcal{U}(-x_i, x_i)`.
66			isotropic: If ``True``, the scaling factor along all dimensions is the
67			same, i.e. :math:`s_1 = s_2 = s_3`.
68			center: If ``'image'``, rotations and scaling will be performed around
69			the image center. If ``'origin'``, rotations and scaling will be
70			performed around the origin in world coordinates.
71			default_pad_value: As the image is rotated, some values near the
72			borders will be undefined.
73			If ``'minimum'``, the fill value will be the image minimum.
74			If ``'mean'``, the fill value is the mean of the border values.
75			If ``'otsu'``, the fill value is the mean of the values at the
76			border that lie under an
77			`Otsu threshold <https://ieeexplore.ieee.org/document/4310076>`_.
78			If it is a number, that value will be used.
79			image_interpolation: See :ref:`Interpolation`.
80			p: Probability that this transform will be applied.
81			seed: See :py:class:`~torchio.transforms.augmentation.RandomTransform`.
82			keys: See :py:class:`~torchio.transforms.Transform`.
83
84			Example:
85			>>> import torchio as tio
86			>>> subject = tio.datasets.Colin27()
87			>>> transform = tio.RandomAffine(
88			... scales=(0.9, 1.2),
89			... degrees=(10),
90			... isotropic=False,
91			... default_pad_value='otsu',
92			... image_interpolation='bspline',
93			... )
94			>>> transformed = transform(subject)
95
96			From the command line::
97
98			$ torchio-transform t1.nii.gz RandomAffine --kwargs "degrees=30 default_pad_value=minimum" --seed 42 affine_min.nii.gz
99
100			"""
101			def __init__(
102			self,
103			scales: TypeOneToSixFloat = 0.1,
104			degrees: TypeOneToSixFloat = 10,
105			translation: TypeOneToSixFloat = 0,
106			isotropic: bool = False,
107			center: str = 'image',
108			default_pad_value: Union[str, float] = 'otsu',
109			image_interpolation: str = 'linear',
110			p: float = 1,
111			keys: Optional[List[str]] = None,
112			):
113			super().__init__(p=p, keys=keys)
114			self.isotropic = isotropic
115			_parse_scales_isotropic(scales, isotropic)
116			self.scales = self.parse_params(scales, 1, 'scales', min_constraint=0)
117			self.degrees = self.parse_params(degrees, 0, 'degrees')
118			self.translation = self.parse_params(translation, 0, 'translation')
119			if center not in ('image', 'origin'):
120			message = (
121			'Center argument must be "image" or "origin",'
122			f' not "{center}"'
123			)
124			raise ValueError(message)
125			self.center = center
126			self.default_pad_value = _parse_default_value(default_pad_value)
127			self.interpolation = self.parse_interpolation(image_interpolation)
128
129			def get_params(
130			self,
131			scales: TypeSextetFloat,
132			degrees: TypeSextetFloat,
133			translation: TypeSextetFloat,
134			isotropic: bool,
135			) -> Tuple[torch.Tensor, torch.Tensor, torch.Tensor]:
136			scaling_params = self.sample_uniform_sextet(scales)
137			if isotropic:
138			scaling_params.fill_(scaling_params[0])
139			rotation_params = self.sample_uniform_sextet(degrees)
140			translation_params = self.sample_uniform_sextet(translation)
141			return scaling_params, rotation_params, translation_params
142
143			def apply_transform(self, subject: Subject) -> Subject:
144			subject.check_consistent_spatial_shape()
145			scaling_params, rotation_params, translation_params = self.get_params(
146			self.scales,
147			self.degrees,
148			self.translation,
149			self.isotropic,
150			)
151			arguments = dict(
152			scales=scaling_params.tolist(),
153			degrees=rotation_params.tolist(),
154			translation=translation_params.tolist(),
155			center=self.center,
156			default_pad_value=self.default_pad_value,
157			image_interpolation=self.interpolation,
158			)
159			transform = Affine(**arguments)
160			transformed = transform(subject)
161			transformed.add_transform(transform, arguments)
162			return transformed
163
164
165			class Affine(SpatialTransform):
166			r"""Apply affine transformation.
167
168			Args:
169			scales: Tuple :math:`(s_1, s_2, s_3)` defining the
170			scaling values along each dimension.
171			degrees: Tuple :math:`(\theta_1, \theta_2, \theta_3)` defining the
172			rotation around each axis.
173			translation: Tuple :math:`(t_1, t_2, t_3)` defining the
174			translation in mm along each axis.
175			center: If ``'image'``, rotations and scaling will be performed around
176			the image center. If ``'origin'``, rotations and scaling will be
177			performed around the origin in world coordinates.
178			default_pad_value: As the image is rotated, some values near the
179			borders will be undefined.
180			If ``'minimum'``, the fill value will be the image minimum.
181			If ``'mean'``, the fill value is the mean of the border values.
182			If ``'otsu'``, the fill value is the mean of the values at the
183			border that lie under an
184			`Otsu threshold <https://ieeexplore.ieee.org/document/4310076>`_.
185			If it is a number, that value will be used.
186			image_interpolation: See :ref:`Interpolation`.
187			keys: See :py:class:`~torchio.transforms.Transform`.
188			"""
189			def __init__(
190			self,
191			scales: TypeTripletFloat,
192			degrees: TypeTripletFloat,
193			translation: TypeTripletFloat,
194			center: str = 'image',
195			default_pad_value: Union[str, float] = 'otsu',
196			image_interpolation: str = 'linear',
197			keys: Optional[List[str]] = None,
198			):
199			super().__init__(keys=keys)
200			self.scales = self.parse_params(
201			scales,
202			None,
203			'scales',
204			make_ranges=False,
205			min_constraint=0,
206			)
207			self.degrees = self.parse_params(
208			degrees,
209			None,
210			'degrees',
211			make_ranges=False,
212			)
213			self.translation = self.parse_params(translation, 0, 'translation', make_ranges=False,)
214			if center not in ('image', 'origin'):
215			message = (
216			'Center argument must be "image" or "origin",'
217			f' not "{center}"'
218			)
219			raise ValueError(message)
220			self.use_image_center = center == 'image'
221			self.default_pad_value = _parse_default_value(default_pad_value)
222			self.interpolation = self.parse_interpolation(image_interpolation)
223			self.invert_transform = False
224
225			@staticmethod
226			def get_scaling_transform(
227			scaling_params: List[float],
228			center_lps: Optional[TypeTripletFloat] = None,
229			) -> sitk.ScaleTransform:
230			# scaling_params are inverted so that they are more intuitive
231			# For example, 1.5 means the objects look 1.5 times larger
232			transform = sitk.ScaleTransform(3)
233			scaling_params = 1 / np.array(scaling_params)
234			transform.SetScale(scaling_params)
235			if center_lps is not None:
236			transform.SetCenter(center_lps)
237			return transform
238
239			@staticmethod
240			def get_rotation_transform(
241			degrees: List[float],
242			translation: List[float],
243			center_lps: Optional[TypeTripletFloat] = None,
244			) -> sitk.Euler3DTransform:
245			transform = sitk.Euler3DTransform()
246			radians = np.radians(degrees)
247			transform.SetRotation(*radians)
248			transform.SetTranslation(translation)
249			if center_lps is not None:
250			transform.SetCenter(center_lps)
251			return transform
252
253			def apply_transform(self, subject: Subject) -> Subject:
254			scaling_params = np.array(self.scales).copy()
255			rotation_params = np.array(self.degrees).copy()
256			translation_params = np.array(self.translation).copy()
257			subject.check_consistent_spatial_shape()
258			for image in self.get_images(subject):
259			if image[TYPE] != INTENSITY:
260			interpolation = Interpolation.NEAREST
261			else:
262			interpolation = self.interpolation
263
264			if image.is_2d():
265			scaling_params[2] = 1
266			rotation_params[:-1] = 0
267
268			if self.use_image_center:
269			center = image.get_center(lps=True)
270			else:
271			center = None
272
273			transformed_tensors = []
274			for tensor in image[DATA]:
			0 ignored issues – show Comprehensibility Best Practice introduced 2020-08-02 14:22 UTC by Report Bug Copy Issue Report The variable `DATA` does not seem to be defined. Loading history...
275			transformed_tensor = self.apply_affine_transform(
276			tensor,
277			image[AFFINE],
278			scaling_params.tolist(),
279			rotation_params.tolist(),
280			translation_params.tolist(),
281			interpolation,
282			center_lps=center,
283			)
284			transformed_tensors.append(transformed_tensor)
285			image[DATA] = torch.stack(transformed_tensors)
286			return subject
287
288			def apply_affine_transform(
289			self,
290			tensor: torch.Tensor,
291			affine: np.ndarray,
292			scaling_params: List[float],
293			rotation_params: List[float],
294			translation_params: List[float],
295			interpolation: Interpolation,
296			center_lps: Optional[TypeTripletFloat] = None,
297			) -> torch.Tensor:
298			assert tensor.ndim == 3
299
300			image = nib_to_sitk(tensor[np.newaxis], affine, force_3d=True)
301			floating = reference = image
302
303			scaling_transform = self.get_scaling_transform(
304			scaling_params,
305			center_lps=center_lps,
306			)
307			rotation_transform = self.get_rotation_transform(
308			rotation_params,
309			translation_params,
310			center_lps=center_lps,
311			)
312
313			sitk_major_version = get_major_sitk_version()
314			if sitk_major_version == 1:
315			transform = sitk.Transform(3, sitk.sitkComposite)
316			transform.AddTransform(scaling_transform)
317			transform.AddTransform(rotation_transform)
318			elif sitk_major_version == 2:
319			transforms = [scaling_transform, rotation_transform]
320			transform = sitk.CompositeTransform(transforms)
321
322			if self.invert_transform:
323			transform = transform.GetInverse()
			0 ignored issues – show introduced 2020-11-16 23:09 UTC by Report Bug Copy Issue Report The variable `transform` does not seem to be defined for all execution paths. Loading history...
324
325			if self.default_pad_value == 'minimum':
326			default_value = tensor.min().item()
327			elif self.default_pad_value == 'mean':
328			default_value = get_borders_mean(image, filter_otsu=False)
329			elif self.default_pad_value == 'otsu':
330			default_value = get_borders_mean(image, filter_otsu=True)
331			else:
332			default_value = self.default_pad_value
333
334			resampler = sitk.ResampleImageFilter()
335			resampler.SetInterpolator(get_sitk_interpolator(interpolation))
336			resampler.SetReferenceImage(reference)
337			resampler.SetDefaultPixelValue(float(default_value))
338			resampler.SetOutputPixelType(sitk.sitkFloat32)
339			resampler.SetTransform(transform)
340			resampled = resampler.Execute(floating)
341
342			np_array = sitk.GetArrayFromImage(resampled)
343			np_array = np_array.transpose() # ITK to NumPy
344			tensor = torch.from_numpy(np_array)
345			return tensor
346
347			def inverse(self):
348			new = copy.deepcopy(self)
349			new.invert_transform = not self.invert_transform
350			return new
351
352
353			# flake8: noqa: E201, E203, E243
354			def get_borders_mean(image, filter_otsu=True):
355			# pylint: disable=bad-whitespace
356			array = sitk.GetArrayViewFromImage(image)
357			borders_tuple = (
358			array[ 0, :, :],
359			array[-1, :, :],
360			array[ :, 0, :],
361			array[ :, -1, :],
362			array[ :, :, 0],
363			array[ :, :, -1],
364			)
365			borders_flat = np.hstack([border.ravel() for border in borders_tuple])
366			if not filter_otsu:
367			return borders_flat.mean()
368			borders_reshaped = borders_flat.reshape(1, 1, -1)
369			borders_image = sitk.GetImageFromArray(borders_reshaped)
370			otsu = sitk.OtsuThresholdImageFilter()
371			otsu.Execute(borders_image)
372			threshold = otsu.GetThreshold()
373			values = borders_flat[borders_flat < threshold]
374			if values.any():
375			default_value = values.mean()
376			else:
377			default_value = borders_flat.mean()
378			return default_value
379
380			def _parse_scales_isotropic(scales, isotropic):
381			params = to_tuple(scales)
382			if isotropic and len(scales) in (3, 6):
383			message = (
384			'If "isotropic" is True, the value for "scales" must have'
385			f' length 1 or 2, but "{scales}" was passed'
386			)
387			raise ValueError(message)
388
389			def _parse_default_value(value: Union[str, float]) -> Union[str, float]:
390			if isinstance(value, Number) or value in ('minimum', 'otsu', 'mean'):
391			return value
392			message = (
393			'Value for default_pad_value must be "minimum", "otsu", "mean"'
394			' or a number'
395			)
396			raise ValueError(message)
397

fepegar / torchio

Pull Request — master (#353)

RandomAffine.__init__() A

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RandomAffine.init() A