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Showing 113 of 113 total issues

Function predict has 11 arguments (exceeds 4 allowed). Consider refactoring.
Open

def predict(
Severity: Major
Found in deepreg/predict.py - About 1 hr to fix

    Function __init__ has 9 arguments (exceeds 4 allowed). Consider refactoring.
    Open

        def __init__(
    Severity: Major
    Found in deepreg/dataset/loader/grouped_loader.py - About 1 hr to fix

      Function call has 28 lines of code (exceeds 25 allowed). Consider refactoring.
      Open

          def call(self, y_true: tf.Tensor, y_pred: tf.Tensor) -> tf.Tensor:
        """
        Return loss for a batch.

        :param y_true: shape = (batch, dim1, dim2, dim3)
      Severity: Minor
      Found in deepreg/loss/image.py - About 1 hr to fix

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

        def tile_slices(img_paths, save_path="", fname=None, slice_inds=None, col_titles=None):
    """
    Generate a tiled plot of multiple images for multiple slices in the image.
    Rows are different slices, columns are different images.
        Severity: Minor
        Found in deepreg/vis.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 deepreg/train.py - About 1 hr to fix

          Identical blocks of code found in 2 locations. Consider refactoring.
          Open

          filenames_all = [fn for fn in zf.namelist() if fn.split(".")[-1] == "gz"]
          Severity: Minor
          Found in demos/grouped_mr_heart/demo_data.py and 1 other location - About 55 mins to fix
          demos/unpaired_ct_abdomen/demo_data.py on lines 20..20

          Duplicated Code

          Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

          Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

          When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

          Tuning

          This issue has a mass of 37.

          We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

          The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

          If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

          See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

          Refactorings

          Further Reading

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

              def call(self, inputs: tf.Tensor, **kwargs) -> tf.Tensor:
        """
        Perform two fold resize.

        :param inputs: shape = (batch, dim1, dim2, dim3, channels)
          Severity: Minor
          Found in deepreg/model/layer.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

          Identical blocks of code found in 2 locations. Consider refactoring.
          Open

          filenames_all = [fn for fn in zf.namelist() if fn.split(".")[-1] == "gz"]
          Severity: Minor
          Found in demos/unpaired_ct_abdomen/demo_data.py and 1 other location - About 55 mins to fix
          demos/grouped_mr_heart/demo_data.py on lines 21..21

          Duplicated Code

          Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

          Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

          When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

          Tuning

          This issue has a mass of 37.

          We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

          The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

          If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

          See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

          Refactorings

          Further Reading

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

              def __init__(
          Severity: Major
          Found in examples/custom_backbone.py - About 50 mins to fix

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

                def __init__(
            Severity: Major
            Found in deepreg/model/network.py - About 50 mins to fix

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

              def save_array(
              Severity: Major
              Found in deepreg/util.py - About 50 mins to fix

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

                    def build_encode_layers(
                Severity: Major
                Found in deepreg/model/backbone/u_net.py - About 50 mins to fix

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

                      def __init__(
                  Severity: Major
                  Found in deepreg/loss/label.py - About 50 mins to fix

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

                        def __init__(
                    Severity: Major
                    Found in deepreg/model/backbone/local_net.py - About 50 mins to fix

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

                          def __init__(
                      Severity: Major
                      Found in deepreg/dataset/preprocess.py - About 50 mins to fix

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

                            def __init__(
                        Severity: Major
                        Found in deepreg/model/backbone/interface.py - About 50 mins to fix

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

                              def __init__(
                          Severity: Major
                          Found in deepreg/dataset/loader/paired_loader.py - About 50 mins to fix

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

                                def sample_image_label(
                            Severity: Minor
                            Found in deepreg/dataset/loader/interface.py - About 45 mins to fix

                              Avoid deeply nested control flow statements.
                              Open

                                              if np.sum((values - values_init) ** 2) > 0:
                    break
                              Severity: Major
                              Found in demos/unpaired_mr_brain/demo_data.py - About 45 mins to fix

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

                                    def get_dataset_and_preprocess(
        self,
        training: bool,
        batch_size: int,
        repeat: bool,
                                Severity: Minor
                                Found in deepreg/dataset/loader/interface.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

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