Function _write_sitk has 5 arguments (exceeds 4 allowed). Consider refactoring.

Open

def _write_sitk(

Function __init__ has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.

Open

    def __init__(self, years, symmetric=False):
        self.url_dir = 'http://www.bic.mni.mcgill.ca/~vfonov/nihpd/obj1/'
        sym_string = 'sym' if symmetric else 'asym'
        if not isinstance(years, tuple) or years not in SUPPORTED_YEARS:
            message = f'Years must be a tuple in {SUPPORTED_YEARS}'

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Function apply_transform has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.

Open

    def apply_transform(self, subject: Subject) -> Subject:
        self._guess_label_key(subject)

        arguments = {
            'label_key': self.label_key,

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Function _get_subject_from_dict has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.

Open

    def _get_subject_from_dict(
        data: dict,
        image_keys: Sequence[str],
        label_keys: Optional[Sequence[str]] = None,
    ) -> Subject:

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Function get_probability_map_image has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.

Open

    def get_probability_map_image(self, subject: Subject) -> Image:
        if self.probability_map_name is None:
            for image in subject.get_images(intensity_only=False):
                if image[TYPE] == LABEL:
                    label_map = image

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Function guess_type has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.

Open

def guess_type(string: str) -> Any:
    # Adapted from
    # https://www.reddit.com/r/learnpython/comments/4599hl/module_to_guess_type_from_a_string/czw3f5s
    string = string.replace(' ', '')
    result_type: Any

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Function _stack has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.

Open

def _stack(x):
    """Determine the type of the input and stack it accordingly.

    Args:
        x: List of elements to stack.

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Function apply_transform has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.

Open

    def apply_transform(self, subject: Subject) -> Subject:
        assert self.bounds_parameters is not None
        low = self.bounds_parameters[::2]
        for image in self.get_images(subject):
            if isinstance(image, LabelMap) and self.padding_mode == 'mean':

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Function __init__ has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.

Open

    def __init__(self):
        self.name = 'NIFTI_ovine_05mm'
        self.url_dir = urllib.parse.urljoin(self.url_base, 'sheep/')
        self.filename = f'{self.name}.zip'
        self.url = urllib.parse.urljoin(self.url_dir, self.filename)

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Function __init__ has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.

Open

    def __init__(
        self,
        num_ghosts: Union[int, Tuple[int, int]] = (4, 10),
        axes: Union[int, Tuple[int, ...]] = (0, 1, 2),
        intensity: Union[float, Tuple[float, float]] = (0.5, 1),

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Function __init__ has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.

Open

    def __init__(self, version=1998):
        if version not in (1998, 2008):
            raise ValueError(f'Version must be 1998 or 2008, not "{version}"')
        self.version = version
        self.name = f'mni_colin27_{version}_nifti'

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Function _guess_label_key has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.

Open

    def _guess_label_key(self, subject: Subject) -> None:
        if self.label_key is None:
            iterable = subject.get_images_dict(intensity_only=False).items()
            for name, image in iterable:
                if isinstance(image, LabelMap):

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Function make_gif has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.

Open

def make_gif(
    tensor: torch.Tensor,
    axis: int,
    duration: float,  # of full gif
    output_path: TypePath,

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Function _write_nibabel has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.

Open

def _write_nibabel(
    tensor: torch.Tensor,
    affine: TypeData,
    path: TypePath,
) -> None:

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Avoid too many return statements within this function.

Open

            return Path(slicer_which)

Avoid too many return statements within this function.

Open

            return Path(itk_snap_which)

Avoid too many return statements within this function.

Open

                return slicer_path

Avoid too many return statements within this function.

Open

    return None  # for mypy

Function get_affine_transform has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.

Open

    def get_affine_transform(self, image):
        scaling = np.asarray(self.scales).copy()
        rotation = np.asarray(self.degrees).copy()
        translation = np.asarray(self.translation).copy()

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Function _glob_subjects has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.

Open

    def _glob_subjects(self, string):
        subjects = []
        for subject in self._subjects:
            for image_name in subject:
                if string in image_name:

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