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fepegar/torchio

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Function __init__ has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring.
Open

    def __init__(
        self,
        path: Union[TypePath, Sequence[TypePath], None] = None,
        type: Optional[str] = None,  # noqa: A002
        tensor: Optional[TypeData] = None,
Severity: Minor
Found in src/torchio/data/image.py - About 1 hr to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Function train has 8 arguments (exceeds 4 allowed). Consider refactoring.
Open

    def train(
Severity: Major
Found in src/torchio/transforms/preprocessing/intensity/histogram_standardization.py - About 1 hr to fix

    Function __init__ has 8 arguments (exceeds 4 allowed). Consider refactoring.
    Open

        def __init__(
    Severity: Major
    Found in src/torchio/transforms/transform.py - About 1 hr to fix

      Function apply_transform has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.
      Open

          def apply_transform(self, subject: Subject) -> Subject:
        gamma = self.gamma
        for name, image in self.get_images_dict(subject).items():
            if self.arguments_are_dict():
                assert isinstance(self.gamma, dict)
      Severity: Minor
      Found in src/torchio/transforms/augmentation/intensity/random_gamma.py - About 55 mins to fix

      Cognitive Complexity

      Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

      A method's cognitive complexity is based on a few simple rules:

      • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
      • Code is considered more complex for each "break in the linear flow of the code"
      • Code is considered more complex when "flow breaking structures are nested"

      Further reading

      Function generate_bias_field has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.
      Open

          def generate_bias_field(
        data: TypeData,
        order: int,
        coefficients: TypeData,
    ) -> np.ndarray:
      Severity: Minor
      Found in src/torchio/transforms/augmentation/intensity/random_bias_field.py - About 55 mins to fix

      Cognitive Complexity

      Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

      A method's cognitive complexity is based on a few simple rules:

      • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
      • Code is considered more complex for each "break in the linear flow of the code"
      • Code is considered more complex when "flow breaking structures are nested"

      Further reading

      Function apply_transform has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.
      Open

          def apply_transform(self, subject: Subject) -> Subject:
        images = subject.get_images(
            intensity_only=False,
            include=self.include,
            exclude=self.exclude,
      Severity: Minor
      Found in src/torchio/transforms/lambda_transform.py - About 55 mins to fix

      Cognitive Complexity

      Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

      A method's cognitive complexity is based on a few simple rules:

      • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
      • Code is considered more complex for each "break in the linear flow of the code"
      • Code is considered more complex when "flow breaking structures are nested"

      Further reading

      Function extract_archive has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.
      Open

      def extract_archive(from_path, to_path=None, remove_finished=False):
    if to_path is None:
        to_path = os.path.dirname(from_path)

    if _is_tar(from_path):
      Severity: Minor
      Found in src/torchio/download.py - About 55 mins to fix

      Cognitive Complexity

      Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

      A method's cognitive complexity is based on a few simple rules:

      • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
      • Code is considered more complex for each "break in the linear flow of the code"
      • Code is considered more complex when "flow breaking structures are nested"

      Further reading

      Function plot_subject has 7 arguments (exceeds 4 allowed). Consider refactoring.
      Open

      def plot_subject(
      Severity: Major
      Found in src/torchio/visualization.py - About 50 mins to fix

        Function apply_transform_to_file has 6 arguments (exceeds 4 allowed). Consider refactoring.
        Open

        def apply_transform_to_file(
        Severity: Minor
        Found in src/torchio/utils.py - About 45 mins to fix

          Function __init__ has 6 arguments (exceeds 4 allowed). Consider refactoring.
          Open

              def __init__(
          Severity: Minor
          Found in src/torchio/transforms/preprocessing/spatial/resample.py - About 45 mins to fix

            Function __init__ has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.
            Open

                def __init__(
        self,
        target_shape: Union[int, TypeTripletInt, None] = None,
        padding_mode: Union[str, float] = 0,
        mask_name: Optional[str] = None,
            Severity: Minor
            Found in src/torchio/transforms/preprocessing/spatial/crop_or_pad.py - About 45 mins to fix

            Cognitive Complexity

            Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

            A method's cognitive complexity is based on a few simple rules:

            • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
            • Code is considered more complex for each "break in the linear flow of the code"
            • Code is considered more complex when "flow breaking structures are nested"

            Further reading

            Function add_artifact has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.
            Open

                def add_artifact(
        self,
        tensor: torch.Tensor,
        num_ghosts: int,
        axis: int,
            Severity: Minor
            Found in src/torchio/transforms/augmentation/intensity/random_ghosting.py - About 45 mins to fix

            Cognitive Complexity

            Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

            A method's cognitive complexity is based on a few simple rules:

            • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
            • Code is considered more complex for each "break in the linear flow of the code"
            • Code is considered more complex when "flow breaking structures are nested"

            Further reading

            Function get_params has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.
            Open

                def get_params(
        tensor: torch.Tensor,
        patch_size: np.ndarray,
        num_iterations: int,
    ) -> List[Tuple[TypeTripletInt, TypeTripletInt]]:
            Severity: Minor
            Found in src/torchio/transforms/augmentation/intensity/random_swap.py - About 45 mins to fix

            Cognitive Complexity

            Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

            A method's cognitive complexity is based on a few simple rules:

            • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
            • Code is considered more complex for each "break in the linear flow of the code"
            • Code is considered more complex when "flow breaking structures are nested"

            Further reading

            Function _get_subjects has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.
            Open

                def _get_subjects(
        self,
        add_segmentations: bool,
        add_bounding_boxes: bool,
    ) -> List[Subject]:
            Severity: Minor
            Found in src/torchio/datasets/rsna_spine_fracture.py - About 45 mins to fix

            Cognitive Complexity

            Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

            A method's cognitive complexity is based on a few simple rules:

            • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
            • Code is considered more complex for each "break in the linear flow of the code"
            • Code is considered more complex when "flow breaking structures are nested"

            Further reading

            Function download_and_extract_archive has 6 arguments (exceeds 4 allowed). Consider refactoring.
            Open

            def download_and_extract_archive(
            Severity: Minor
            Found in src/torchio/download.py - About 45 mins to fix

              Function parse_params has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.
              Open

                  def parse_params(self, params, around, name, make_ranges=True, **kwargs):
        params = to_tuple(params)
        # d or (a, b)
        if len(params) == 1 or (len(params) == 2 and make_ranges):
            params *= 3  # (d, d, d) or (a, b, a, b, a, b)
              Severity: Minor
              Found in src/torchio/transforms/transform.py - About 45 mins to fix

              Cognitive Complexity

              Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

              A method's cognitive complexity is based on a few simple rules:

              • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
              • Code is considered more complex for each "break in the linear flow of the code"
              • Code is considered more complex when "flow breaking structures are nested"

              Further reading

              Function _fill has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.
              Open

                  def _fill(self) -> None:
        assert self.sampler is not None

        if self._incomplete_subject is not None:
            subject = self._incomplete_subject
              Severity: Minor
              Found in src/torchio/data/queue.py - About 45 mins to fix

              Cognitive Complexity

              Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

              A method's cognitive complexity is based on a few simple rules:

              • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
              • Code is considered more complex for each "break in the linear flow of the code"
              • Code is considered more complex when "flow breaking structures are nested"

              Further reading

              Function __init__ has 6 arguments (exceeds 4 allowed). Consider refactoring.
              Open

                  def __init__(
              Severity: Minor
              Found in src/torchio/transforms/augmentation/intensity/random_motion.py - About 45 mins to fix

                Function create_dummy_dataset has 6 arguments (exceeds 4 allowed). Consider refactoring.
                Open

                def create_dummy_dataset(
                Severity: Minor
                Found in src/torchio/utils.py - About 45 mins to fix

                  Function __init__ has 6 arguments (exceeds 4 allowed). Consider refactoring.
                  Open

                      def __init__(
                  Severity: Minor
                  Found in src/torchio/transforms/augmentation/intensity/random_motion.py - About 45 mins to fix
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