tomopy/tomopy

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source/tomopy/misc/corr.py

Summary

Maintainability
F
3 days
Test Coverage

File corr.py has 649 lines of code (exceeds 250 allowed). Consider refactoring.
Open

#!/usr/bin/env python
# -*- coding: utf-8 -*-

# #########################################################################
# Copyright (c) 2015-2019, UChicago Argonne, LLC. All rights reserved.    #
Severity: Major
Found in source/tomopy/misc/corr.py - About 1 day to fix

    Function remove_ring has 12 arguments (exceeds 4 allowed). Consider refactoring.
    Open

    def remove_ring(rec,
    Severity: Major
    Found in source/tomopy/misc/corr.py - About 1 hr to fix

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

      def remove_ring(rec,
                      center_x=None,
                      center_y=None,
                      thresh=300.0,
                      thresh_max=300.0,
      Severity: Minor
      Found in source/tomopy/misc/corr.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 remove_outlier1d has 6 arguments (exceeds 4 allowed). Consider refactoring.
      Open

      def remove_outlier1d(arr, dif, size=3, axis=0, ncore=None, out=None):
      Severity: Minor
      Found in source/tomopy/misc/corr.py - About 45 mins to fix

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

        def median_filter_cuda(arr, size=3, axis=0):
            """
            Apply median filter to 3D array along 0 axis with GPU support.
            The winAllow is for A6000, Tian X support 3 to 8
        
        
        Severity: Minor
        Found in source/tomopy/misc/corr.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 remove_outlier_cuda has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.
        Open

        def remove_outlier_cuda(arr, dif, size=3, axis=0):
            """
            Remove high intensity bright spots from a 3D array along axis 0
            dimension using GPU.
        
        
        Severity: Minor
        Found in source/tomopy/misc/corr.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 remove_outlier has 6 arguments (exceeds 4 allowed). Consider refactoring.
        Open

        def remove_outlier(arr, dif, size=3, axis=0, ncore=None, out=None):
        Severity: Minor
        Found in source/tomopy/misc/corr.py - About 45 mins to fix

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

          def circ_mask(arr, axis, ratio=1, val=0., ncore=None):
          Severity: Minor
          Found in source/tomopy/misc/corr.py - About 35 mins to fix

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

            def gaussian_filter(arr, sigma=3, order=0, axis=0, ncore=None):
            Severity: Minor
            Found in source/tomopy/misc/corr.py - About 35 mins to fix

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

              def median_filter_nonfinite(arr, size=3, callback=None):
                  """
                  Remove nonfinite values from a 3D array using an in-place 2D median filter.
              
                  The 2D selective median filter is applied along the last two axes of
              Severity: Minor
              Found in source/tomopy/misc/corr.py - About 35 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

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

              def remove_nan(arr, val=0., ncore=None):
                  """
                  Replace NaN values in array with a given value.
              
                  Parameters
              Severity: Major
              Found in source/tomopy/misc/corr.py and 1 other location - About 3 hrs to fix
              source/tomopy/misc/corr.py on lines 408..431

              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 62.

              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

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

              def remove_neg(arr, val=0., ncore=None):
                  """
                  Replace negative values in array with a given value.
              
                  Parameters
              Severity: Major
              Found in source/tomopy/misc/corr.py and 1 other location - About 3 hrs to fix
              source/tomopy/misc/corr.py on lines 381..405

              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 62.

              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

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

                          y_higher = min(arr.shape[2], y_idx + (size // 2) + 1)
              Severity: Minor
              Found in source/tomopy/misc/corr.py and 1 other location - About 50 mins to fix
              source/tomopy/misc/corr.py on lines 325..325

              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 36.

              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

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

                          x_higher = min(arr.shape[1], x_idx + (size // 2) + 1)
              Severity: Minor
              Found in source/tomopy/misc/corr.py and 1 other location - About 50 mins to fix
              source/tomopy/misc/corr.py on lines 327..327

              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 36.

              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

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