Sign upLogin

neuropsychology/NeuroKit.py

View on GitHub
Star

Showing 176 of 176 total issues

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

Function eeg_microstates_features has a Cognitive Complexity of 16 (exceeds 5 allowed). Consider refactoring.
Open

def eeg_microstates_features(results, method, ecg=True, nonlinearity=True, verbose=True):
    """
    Compute statistics and features for/of the microstates.
    """
Severity: Minor
Found in examples/UnderDev/eeg/eeg_microstates.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 emg_process has a Cognitive Complexity of 16 (exceeds 5 allowed). Consider refactoring.
Open

def emg_process(emg, sampling_rate=1000, emg_names=None, envelope_freqs=[10, 400], envelope_lfreq=4, activation_treshold="default", activation_n_above=0.25, activation_n_below=1):
    """
    Automated processing of EMG signal.

    Parameters
Severity: Minor
Found in neurokit/bio/bio_emg.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 plot_eeg_erp has 16 arguments (exceeds 4 allowed). Consider refactoring.
Open

def plot_eeg_erp(all_epochs, conditions=None, times=None, include="all", exclude=None, hemisphere="both", central=True, name=None, colors=None, gfp=False, ci=0.95, ci_alpha=0.333, invert_y=False, linewidth=1, linestyle="-", filter_hfreq=None):
Severity: Major
Found in neurokit/eeg/eeg_erp.py - About 2 hrs to fix

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

        b = 1/2-((fa_rate-hit_rate)*(1+fa_rate-hit_rate) / (4*fa_rate*(1-hit_rate)))
    Severity: Major
    Found in neurokit/statistics/routines.py and 1 other location - About 1 hr to fix
    neurokit/statistics/routines.py on lines 102..102

    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 49.

    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

        a = 1/2+((hit_rate-fa_rate)*(1+hit_rate-fa_rate) / (4*hit_rate*(1-fa_rate)))
    Severity: Major
    Found in neurokit/statistics/routines.py and 1 other location - About 1 hr to fix
    neurokit/statistics/routines.py on lines 103..103

    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 49.

    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 eeg_gfp has a Cognitive Complexity of 14 (exceeds 5 allowed). Consider refactoring.
    Open

    def eeg_gfp(raws, gflp_method="GFPL1", scale=True, normalize=True, smoothing=None):
    """
    Run the GFP analysis.
    """
    Severity: Minor
    Found in examples/UnderDev/eeg/eeg_microstates.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

    Similar blocks of code found in 3 locations. Consider refactoring.
    Open

            response[prefix + "_MeanDiff"] = response[prefix + "_Mean"] - response[prefix + "_Baseline"]
    Severity: Major
    Found in neurokit/bio/bio_ecg.py and 2 other locations - About 1 hr to fix
    neurokit/bio/bio_ecg.py on lines 858..858
    neurokit/bio/bio_ecg.py on lines 861..861

    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 47.

    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

            response[prefix + "_MinDiff"] = response[prefix + "_Min"] - response[prefix + "_Baseline"]
    Severity: Major
    Found in neurokit/bio/bio_ecg.py and 2 other locations - About 1 hr to fix
    neurokit/bio/bio_ecg.py on lines 861..861
    neurokit/bio/bio_ecg.py on lines 864..864

    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 47.

    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 eeg_gfp_peaks has a Cognitive Complexity of 14 (exceeds 5 allowed). Consider refactoring.
    Open

    def eeg_gfp_peaks(data, gflp_method='GFPL1', smoothing=False, smoothing_window=100, peak_method="wavelet", normalize=False):
    """
    The Global Field Power (GFP) is a scalar measure of the strength of the scalp potential field and is calculated as the standard deviation of all electrodes at a given time point (Lehmann and Skrandies, 1980; Michel et al., 1993; Murray et al., 2008; Brunet et al., 2011). Between two GFP troughs, the strength of the potential field varies but the topography remains generally stable. The local maxima of the GFP are thus the best representative of a given microstate in terms of signal-to-noise ratio (Pascual-Marqui et al., 1995), corresponding to moments of high global neuronal synchronization (Skrandies, 2007).

    Parameters
    Severity: Minor
    Found in examples/UnderDev/eeg/eeg_microstates.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 ecg_rsa has a Cognitive Complexity of 14 (exceeds 5 allowed). Consider refactoring.
    Open

    def ecg_rsa(rpeaks, rsp, sampling_rate=1000):
    """
    Returns Respiratory Sinus Arrhythmia (RSA) features. Only the Peak-to-trough (P2T) algorithm is currently implemented (see details).

    Parameters
    Severity: Minor
    Found in neurokit/bio/bio_ecg.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 eeg_power_per_epoch has a Cognitive Complexity of 14 (exceeds 5 allowed). Consider refactoring.
    Open

    def eeg_power_per_epoch(epochs, include="all", exclude=None, hemisphere="both", include_central=True, frequency_bands="all", time_start=0, time_end="max", fill_bads="NA", print_progression=True):
    """
    """
    Severity: Minor
    Found in examples/UnderDev/eeg/eeg_time_frequency.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

    Similar blocks of code found in 3 locations. Consider refactoring.
    Open

            response[prefix + "_MaxDiff"] = response[prefix + "_Max"] - response[prefix + "_Baseline"]
    Severity: Major
    Found in neurokit/bio/bio_ecg.py and 2 other locations - About 1 hr to fix
    neurokit/bio/bio_ecg.py on lines 858..858
    neurokit/bio/bio_ecg.py on lines 864..864

    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 47.

    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

        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

    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 eeg_microstates has 13 arguments (exceeds 4 allowed). Consider refactoring.
      Open

      def eeg_microstates(gfp, n_microstates=4, clustering_method="kmeans", n_jobs=1, n_init=25, occurence_rejection_treshold=0.05, max_refitting=5, clustering_metrics=True, good_fit_treshold=0, feature_reduction_method="PCA", n_features=32, nonlinearity=True, verbose=True):
      Severity: Major
      Found in examples/UnderDev/eeg/eeg_microstates.py - About 1 hr to fix

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

        def ecg_hrv_assessment(hrv, age=None, sex=None, position=None):
    """
    Correct HRV features based on normative data from Voss et al. (2015).

    Parameters
        Severity: Minor
        Found in neurokit/bio/bio_ecg.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

        Similar blocks of code found in 3 locations. Consider refactoring.
        Open

                    before_times = list(np.array(events["onsets_time"])[events["onsets_time"]<before])[:number]
        Severity: Major
        Found in neurokit/signal/events.py and 2 other locations - About 1 hr to fix
        neurokit/signal/events.py on lines 217..217
        neurokit/signal/events.py on lines 219..219

        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 45.

        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

        Severity
        Category
        Status
        Source
        Language