fepegar/torchio

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File image.py has 784 lines of code (exceeds 250 allowed). Consider refactoring.
Open

import warnings
from collections import Counter
from pathlib import Path
from typing import Any
from typing import Callable
Severity: Major
Found in src/torchio/data/image.py - About 1 day to fix

    File transform.py has 510 lines of code (exceeds 250 allowed). Consider refactoring.
    Open

    import copy
    import numbers
    import warnings
    from abc import ABC
    from abc import abstractmethod
    Severity: Major
    Found in src/torchio/transforms/transform.py - About 1 day to fix

      File random_labels_to_image.py has 418 lines of code (exceeds 250 allowed). Consider refactoring.
      Open

      from typing import List
      from typing import Optional
      from typing import Sequence
      from typing import Tuple
      
      

        File random_affine.py has 415 lines of code (exceeds 250 allowed). Consider refactoring.
        Open

        from numbers import Number
        from typing import Optional
        from typing import Sequence
        from typing import Tuple
        from typing import Union
        Severity: Minor
        Found in src/torchio/transforms/augmentation/spatial/random_affine.py - About 5 hrs to fix

          File io.py has 382 lines of code (exceeds 250 allowed). Consider refactoring.
          Open

          import warnings
          from pathlib import Path
          from typing import Optional
          from typing import Tuple
          from typing import Union
          Severity: Minor
          Found in src/torchio/data/io.py - About 5 hrs to fix

            File subject.py has 381 lines of code (exceeds 250 allowed). Consider refactoring.
            Open

            from __future__ import annotations
            
            import copy
            import pprint
            from typing import Any
            Severity: Minor
            Found in src/torchio/data/subject.py - About 5 hrs to fix

              File queue.py has 347 lines of code (exceeds 250 allowed). Consider refactoring.
              Open

              from itertools import islice
              from typing import Iterator
              from typing import List
              from typing import Optional
              
              
              Severity: Minor
              Found in src/torchio/data/queue.py - About 4 hrs to fix

                File utils.py has 338 lines of code (exceeds 250 allowed). Consider refactoring.
                Open

                from __future__ import annotations
                
                import ast
                import gzip
                import os
                Severity: Minor
                Found in src/torchio/utils.py - About 4 hrs to fix

                  Image has 30 functions (exceeds 20 allowed). Consider refactoring.
                  Open

                  class Image(dict):
                      r"""TorchIO image.
                  
                      For information about medical image orientation, check out `NiBabel docs`_,
                      the `3D Slicer wiki`_, `Graham Wideman's website`_, `FSL docs`_ or
                  Severity: Minor
                  Found in src/torchio/data/image.py - About 3 hrs to fix

                    Function apply_transform has a Cognitive Complexity of 24 (exceeds 5 allowed). Consider refactoring.
                    Open

                        def apply_transform(self, subject: Subject) -> Subject:
                            original_image = subject.get(self.image_key)
                    
                            label_map_image = subject[self.label_key]
                            label_map = label_map_image.data

                    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

                    File random_elastic_deformation.py has 302 lines of code (exceeds 250 allowed). Consider refactoring.
                    Open

                    import warnings
                    from numbers import Number
                    from typing import Sequence
                    from typing import Tuple
                    from typing import Union

                      Function guess_external_viewer has a Cognitive Complexity of 22 (exceeds 5 allowed). Consider refactoring.
                      Open

                      def guess_external_viewer() -> Optional[Path]:
                          """Guess the path to an executable that could be used to visualize images.
                      
                          Currently, it looks for 1) ITK-SNAP and 2) 3D Slicer. Implemented
                          for macOS and Windows.
                      Severity: Minor
                      Found in src/torchio/utils.py - About 3 hrs 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 ensure_4d has a Cognitive Complexity of 20 (exceeds 5 allowed). Consider refactoring.
                      Open

                      def ensure_4d(tensor: TypeData, num_spatial_dims=None) -> torch.Tensor:
                          # I wish named tensors were properly supported in PyTorch
                          tensor = torch.as_tensor(tensor)
                          num_dimensions = tensor.ndim
                          if num_dimensions == 4:
                      Severity: Minor
                      Found in src/torchio/data/io.py - About 2 hrs 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

                      File resample.py has 274 lines of code (exceeds 250 allowed). Consider refactoring.
                      Open

                      from collections.abc import Iterable
                      from numbers import Number
                      from pathlib import Path
                      from typing import Optional
                      from typing import Sized
                      Severity: Minor
                      Found in src/torchio/transforms/preprocessing/spatial/resample.py - About 2 hrs to fix

                        File random_motion.py has 274 lines of code (exceeds 250 allowed). Consider refactoring.
                        Open

                        from collections import defaultdict
                        from typing import Dict
                        from typing import List
                        from typing import Sequence
                        from typing import Tuple
                        Severity: Minor
                        Found in src/torchio/transforms/augmentation/intensity/random_motion.py - About 2 hrs to fix

                          Function plot_volume has a Cognitive Complexity of 18 (exceeds 5 allowed). Consider refactoring.
                          Open

                          def plot_volume(
                              image: Image,
                              radiological=True,
                              channel=-1,  # default to foreground for binary maps
                              axes=None,
                          Severity: Minor
                          Found in src/torchio/visualization.py - About 2 hrs 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 17 (exceeds 5 allowed). Consider refactoring.
                          Open

                              def _get_subjects(
                                  self,
                                  root_dir: Path,
                                  train: bool,
                                  ignore_empty: bool,
                          Severity: Minor
                          Found in src/torchio/datasets/rsna_miccai.py - About 2 hrs 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

                          File histogram_standardization.py has 257 lines of code (exceeds 250 allowed). Consider refactoring.
                          Open

                          from pathlib import Path
                          from typing import Callable
                          from typing import Dict
                          from typing import Optional
                          from typing import Sequence

                            Function get_subjects_from_batch has a Cognitive Complexity of 16 (exceeds 5 allowed). Consider refactoring.
                            Open

                            def get_subjects_from_batch(batch: Dict) -> List:
                                """Get list of subjects from collated batch.
                            
                                Args:
                                    batch: Dictionary generated by a :class:`torch.utils.data.DataLoader`
                            Severity: Minor
                            Found in src/torchio/utils.py - About 2 hrs 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 a Cognitive Complexity of 15 (exceeds 5 allowed). Consider refactoring.
                            Open

                            def plot_subject(
                                subject: Subject,
                                cmap_dict=None,
                                show=True,
                                output_path=None,
                            Severity: Minor
                            Found in src/torchio/visualization.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

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