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neuropsychology/NeuroKit.py

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neurokit/bio/bio_eda.py

Summary

Maintainability
D
2 days
Test Coverage

File bio_eda.py has 392 lines of code (exceeds 250 allowed). Consider refactoring.
Open

# -*- coding: utf-8 -*-
from __future__ import division
import pandas as pd
import numpy as np
import biosppy
Severity: Minor
Found in neurokit/bio/bio_eda.py - About 5 hrs to fix

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

    def eda_EventRelated(epoch, event_length, window_post=4):
    """
    Extract event-related EDA and Skin Conductance Response (SCR).

    Parameters
    Severity: Minor
    Found in neurokit/bio/bio_eda.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 cvxEDA has 41 lines of code (exceeds 25 allowed). Consider refactoring.
    Open

    def cvxEDA(eda, sampling_rate=1000, tau0=2., tau1=0.7, delta_knot=10., alpha=8e-4, gamma=1e-2, solver=None, verbose=False, options={'reltol':1e-9}):
    """
    A convex optimization approach to electrodermal activity processing (CVXEDA).

    This function implements the cvxEDA algorithm described in "cvxEDA: a
    Severity: Minor
    Found in neurokit/bio/bio_eda.py - About 1 hr to fix

      Function eda_scr has a Cognitive Complexity of 13 (exceeds 5 allowed). Consider refactoring.
      Open

      def eda_scr(signal, sampling_rate=1000, treshold=0.1, method="fast"):
    """
    Skin-Conductance Responses extraction algorithm.

    Parameters
      Severity: Minor
      Found in neurokit/bio/bio_eda.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 eda_process has a Cognitive Complexity of 12 (exceeds 5 allowed). Consider refactoring.
      Open

      def eda_process(eda, sampling_rate=1000, alpha=8e-4, gamma=1e-2, filter_type = "butter", scr_method="makowski", scr_treshold=0.1):
    """
    Automated processing of EDA signal using convex optimization (CVXEDA; Greco et al., 2015).

    Parameters
      Severity: Minor
      Found in neurokit/bio/bio_eda.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 cvxEDA has 10 arguments (exceeds 4 allowed). Consider refactoring.
      Open

      def cvxEDA(eda, sampling_rate=1000, tau0=2., tau1=0.7, delta_knot=10., alpha=8e-4, gamma=1e-2, solver=None, verbose=False, options={'reltol':1e-9}):
      Severity: Major
      Found in neurokit/bio/bio_eda.py - About 1 hr to fix

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

        def eda_process(eda, sampling_rate=1000, alpha=8e-4, gamma=1e-2, filter_type = "butter", scr_method="makowski", scr_treshold=0.1):
        Severity: Major
        Found in neurokit/bio/bio_eda.py - About 50 mins to fix

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

              A = cv.spmatrix(np.tile(ar, (n-2,1)), np.c_[i,i,i], np.c_[i,i-1,i-2], (n,n))
          Severity: Major
          Found in neurokit/bio/bio_eda.py and 1 other location - About 3 hrs to fix
          neurokit/bio/bio_eda.py on lines 260..260

          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 69.

          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

              M = cv.spmatrix(np.tile(ma, (n-2,1)), np.c_[i,i,i], np.c_[i,i-1,i-2], (n,n))
          Severity: Major
          Found in neurokit/bio/bio_eda.py and 1 other location - About 3 hrs to fix
          neurokit/bio/bio_eda.py on lines 259..259

          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 69.

          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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