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neuropsychology/NeuroKit.py

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neurokit/signal/complexity.py

Summary

Maintainability
F
3 days
Test Coverage

File complexity.py has 524 lines of code (exceeds 250 allowed). Consider refactoring.
Open

# -*- coding: utf-8 -*-
import nolds
import numpy as np

# ==============================================================================
Severity: Major
Found in neurokit/signal/complexity.py - About 1 day to fix

    Function complexity has a Cognitive Complexity of 42 (exceeds 5 allowed). Consider refactoring.
    Open

    def complexity(signal, sampling_rate=1000, shannon=True, sampen=True, multiscale=True, spectral=True, svd=True, correlation=True, higushi=True, petrosian=True, fisher=True, hurst=True, dfa=True, lyap_r=False, lyap_e=False, emb_dim=2, tolerance="default", k_max=8, bands=None, tau=1):
    """
    Computes several chaos/complexity indices of a signal (including entropy, fractal dimensions, Hurst and Lyapunov exponent etc.).

    Parameters
    Severity: Minor
    Found in neurokit/signal/complexity.py - About 6 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 complexity has 20 arguments (exceeds 4 allowed). Consider refactoring.
    Open

    def complexity(signal, sampling_rate=1000, shannon=True, sampen=True, multiscale=True, spectral=True, svd=True, correlation=True, higushi=True, petrosian=True, fisher=True, hurst=True, dfa=True, lyap_r=False, lyap_e=False, emb_dim=2, tolerance="default", k_max=8, bands=None, tau=1):
    Severity: Major
    Found in neurokit/signal/complexity.py - About 2 hrs to fix

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

      def complexity_entropy_shannon(signal):
    """
    Computes the shannon entropy. Copied from the `pyEntropy <https://github.com/nikdon/pyEntropy>`_ repo by tjugo.

    Parameters
      Severity: Minor
      Found in neurokit/signal/complexity.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 complexity_entropy_multiscale has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
      Open

      def complexity_entropy_multiscale(signal, max_scale_factor=20, m=2, r="default"):
    """
    Computes the Multiscale Entropy. Uses sample entropy with 'chebychev' distance.

    Parameters
      Severity: Minor
      Found in neurokit/signal/complexity.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 3 locations. Consider refactoring.
      Open

          if spectral is True:
        try:
            complexity["Entropy_Spectral"] = complexity_entropy_spectral(signal, sampling_rate=sampling_rate, bands=bands)
        except:
            print("NeuroKit warning: complexity(): Failed to compute Spectral Entropy.")
      Severity: Major
      Found in neurokit/signal/complexity.py and 2 other locations - About 2 hrs to fix
      neurokit/signal/complexity.py on lines 168..173
      neurokit/signal/complexity.py on lines 203..208

      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 53.

      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 3 locations. Consider refactoring.
      Open

          if svd is True:
        try:
            complexity["Entropy_SVD"] = complexity_entropy_svd(signal, tau=tau, emb_dim=emb_dim)
        except:
            print("NeuroKit warning: complexity(): Failed to compute SVD Entropy.")
      Severity: Major
      Found in neurokit/signal/complexity.py and 2 other locations - About 2 hrs to fix
      neurokit/signal/complexity.py on lines 160..165
      neurokit/signal/complexity.py on lines 203..208

      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 53.

      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 3 locations. Consider refactoring.
      Open

          if fisher is True:
        try:
            complexity["Fisher_Information"] = complexity_fisher_info(signal, tau=tau, emb_dim=emb_dim)
        except:
            print("NeuroKit warning: complexity(): Failed to compute Fisher Information.")
      Severity: Major
      Found in neurokit/signal/complexity.py and 2 other locations - About 2 hrs to fix
      neurokit/signal/complexity.py on lines 160..165
      neurokit/signal/complexity.py on lines 168..173

      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 53.

      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

          if shannon is True:
        try:
            complexity["Entropy_Shannon"] = complexity_entropy_shannon(signal)
        except:
            print("NeuroKit warning: complexity(): Failed to compute Shannon entropy.")
      Severity: Major
      Found in neurokit/signal/complexity.py and 1 other location - About 1 hr to fix
      neurokit/signal/complexity.py on lines 193..198

      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 46.

      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

          if petrosian is True:
        try:
            complexity["Fractal_Dimension_Petrosian"] = complexity_fd_petrosian(signal)
        except:
            print("NeuroKit warning: complexity(): Failed to compute petrosian.")
      Severity: Major
      Found in neurokit/signal/complexity.py and 1 other location - About 1 hr to fix
      neurokit/signal/complexity.py on lines 135..140

      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 46.

      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

              power_per_band = [np.sum(psd[np.bitwise_and(freqs >= low, freqs<up)])
      Severity: Minor
      Found in neurokit/signal/complexity.py and 1 other location - About 30 mins to fix
      neurokit/bio/bio_ecg.py on lines 235..236

      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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