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source/tomopy/misc/corr.py

Summary

Maintainability
F
6 days
Test Coverage

File corr.py has 910 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 2 days to fix

    Function inpainter_morph has a Cognitive Complexity of 36 (exceeds 5 allowed). Consider refactoring.
    Open

    def inpainter_morph(
    arr,
    mask,
    size=5,
    iterations=2,
    Severity: Minor
    Found in source/tomopy/misc/corr.py - About 5 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 remove_ring has 12 arguments (exceeds 4 allowed). Consider refactoring.
    Open

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

      Function remove_outlier3d has a Cognitive Complexity of 11 (exceeds 5 allowed). Consider refactoring.
      Open

      def remove_outlier3d(arr, dif, size=3, ncore=None):
    """
    Selectively applies 3D median filter to a 3D array to remove outliers. Also
    called a dezinger.
      Severity: Minor
      Found in source/tomopy/misc/corr.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 median_filter3d has a Cognitive Complexity of 11 (exceeds 5 allowed). Consider refactoring.
      Open

      def median_filter3d(arr, size=3, ncore=None):
    """
    Apply 3D median filter to a 3D array.

    .. versionadded:: 1.13
      Severity: Minor
      Found in source/tomopy/misc/corr.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 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,
      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 inpainter_morph has 7 arguments (exceeds 4 allowed). Consider refactoring.
      Open

      def inpainter_morph(
      Severity: Major
      Found in source/tomopy/misc/corr.py - About 50 mins to fix

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

            def circ_mask(arr, axis, ratio=1, val=0.0, 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

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

                    if arr.ndim == 3:
        dz, dy, dx = arr.shape
        if (dz == 0) or (dy == 0) or (dx == 0):
            raise ValueError("The length of one of dimensions is equal to zero")
    else:
                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 457..462

                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 66.

                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

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

                    if arr.ndim == 3:
        dz, dy, dx = arr.shape
        if (dz == 0) or (dy == 0) or (dx == 0):
            raise ValueError("The length of one of dimensions is equal to zero")
    else:
                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 396..401

                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 66.

                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=0.0, 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 508..532

                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_nan(arr, val=0.0, 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 535..558

                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

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

                    if input_type == "float32":
        extern.c_median_filt3d_float32(
            np.ascontiguousarray(arr), out, kernel_half_size, dif, ncore, dx, dy, dz
        )
    else:
                Severity: Major
                Found in source/tomopy/misc/corr.py and 1 other location - About 2 hrs to fix
                source/tomopy/misc/corr.py on lines 465..471

                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 55.

                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

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

                    if input_type == "float32":
        extern.c_median_filt3d_float32(
            np.ascontiguousarray(arr), out, kernel_half_size, dif, ncore, dx, dy, dz
        )
    else:
                Severity: Major
                Found in source/tomopy/misc/corr.py and 1 other location - About 2 hrs to fix
                source/tomopy/misc/corr.py on lines 404..410

                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 55.

                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 332..332

                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 334..334

                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

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

                    if (input_type != "float32") and (input_type != "uint16"):
        arr = dtype.as_float32(arr)  # silent convertion to float32 data type
                Severity: Minor
                Found in source/tomopy/misc/corr.py and 1 other location - About 30 mins to fix
                source/tomopy/misc/corr.py on lines 388..389

                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 32.

                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

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

                    if (input_type != "float32") and (input_type != "uint16"):
        arr = dtype.as_float32(arr)  # silent convertion to float32 data type
                Severity: Minor
                Found in source/tomopy/misc/corr.py and 1 other location - About 30 mins to fix
                source/tomopy/misc/corr.py on lines 450..451

                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 32.

                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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