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neuropsychology/NeuroKit.py

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Function plot_eeg_erp has a Cognitive Complexity of 25 (exceeds 5 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):
    """
    DOCS INCOMPLETE :(
    """
    # Preserve original
Severity: Minor
Found in neurokit/eeg/eeg_erp.py - About 3 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 eeg_erp has a Cognitive Complexity of 24 (exceeds 5 allowed). Consider refactoring.
Open

def eeg_erp(eeg, times=None, index=None, include="all", exclude=None, hemisphere="both", central=True, verbose=True, names="ERP", method="mean"):
    """
    DOCS INCOMPLETE :(
    """
    erp = {}
Severity: Minor
Found in neurokit/eeg/eeg_erp.py - About 3 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 eeg_create_frequency_bands has a Cognitive Complexity of 24 (exceeds 5 allowed). Consider refactoring.
Open

def eeg_create_frequency_bands(bands="all", step=1):
    """
    Delta: 1-3Hz
    Theta: 4-7Hz
    Alpha1: 8-9Hz
Severity: Minor
Found in examples/UnderDev/eeg/eeg_time_frequency.py - About 3 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 bio_process has 25 arguments (exceeds 4 allowed). Consider refactoring.
Open

def bio_process(ecg=None, rsp=None, eda=None, emg=None, add=None, sampling_rate=1000, age=None, sex=None, position=None, ecg_filter_type="FIR", ecg_filter_band="bandpass", ecg_filter_frequency=[3, 45], ecg_segmenter="hamilton", ecg_quality_model="default", ecg_hrv_features=["time", "frequency"], eda_alpha=8e-4, eda_gamma=1e-2, scr_method="makowski", scr_treshold=0.1, emg_names=None, emg_envelope_freqs=[10, 400], emg_envelope_lfreq=4, emg_activation_treshold="default", emg_activation_n_above=0.25, emg_activation_n_below=1):
Severity: Major
Found in neurokit/bio/bio_meta.py - About 3 hrs to fix

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

                if events["onsets_time"] == []:
                events["onsets_time"] = np.array(events["onsets"])
            else:
                events["onsets_time"] = np.array(events["onsets_time"])
    Severity: Major
    Found in neurokit/signal/events.py and 1 other location - About 3 hrs to fix
    neurokit/signal/events.py on lines 213..216

    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 63.

    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 events["onsets_time"] == []:
                events["onsets_time"] = np.array(events["onsets"])
            else:
                events["onsets_time"] = np.array(events["onsets_time"])
    Severity: Major
    Found in neurokit/signal/events.py and 1 other location - About 3 hrs to fix
    neurokit/signal/events.py on lines 205..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 63.

    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

    File eeg_data.py has 290 lines of code (exceeds 250 allowed). Consider refactoring.
    Open

    """
Loading data and events submodule.
"""
from ..signal import find_events
    Severity: Minor
    Found in neurokit/eeg/eeg_data.py - About 2 hrs to fix

      Function plot_events_in_signal has a Cognitive Complexity of 21 (exceeds 5 allowed). Consider refactoring.
      Open

      def plot_events_in_signal(signal, events_onsets, color="red", marker=None):
    """
    Plot events in signal.

    Parameters
      Severity: Minor
      Found in neurokit/signal/events.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_polarbar has a Cognitive Complexity of 21 (exceeds 5 allowed). Consider refactoring.
      Open

      def plot_polarbar(scores, labels=None, labels_size=15, colors="default", distribution_means=None, distribution_sds=None, treshold=1.28, fig_size=(15, 15)):
    """
    Polar bar chart.

    Parameters
      Severity: Minor
      Found in neurokit/statistics/plot.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 eeg_complexity has 23 arguments (exceeds 4 allowed). Consider refactoring.
      Open

      def eeg_complexity(eeg, sampling_rate, times=None, index=None, include="all", exclude=None, hemisphere="both", central=True, verbose=True, 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, names="Complexity"):
      Severity: Major
      Found in neurokit/eeg/eeg_complexity.py - About 2 hrs to fix

        Function eeg_microstates_clustering has a Cognitive Complexity of 19 (exceeds 5 allowed). Consider refactoring.
        Open

        def eeg_microstates_clustering(data, n_microstates=4, clustering_method="kmeans", n_jobs=1, n_init=25, occurence_rejection_treshold=0.05, max_refitting=5, verbose=True):
    """
    Fit the clustering algorithm.
    """
    # Create training set
        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 eeg_microstates has a Cognitive Complexity of 19 (exceeds 5 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):
    """
    Run the full microstates analysis.

    Parameters
        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 rsp_find_cycles has a Cognitive Complexity of 19 (exceeds 5 allowed). Consider refactoring.
        Open

        def rsp_find_cycles(signal):
    """
    Find Respiratory cycles onsets, durations and phases.

    Parameters
        Severity: Minor
        Found in neurokit/bio/bio_rsp.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 find_events has a Cognitive Complexity of 19 (exceeds 5 allowed). Consider refactoring.
        Open

        def find_events(events_channel, treshold="auto", cut="higher", time_index=None, number="all", after=0, before=None, min_duration=1):
    """
    Find and select events based on a continuous signal.

    Parameters
        Severity: Minor
        Found in neurokit/signal/events.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

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

            if isinstance(duration, list) or isinstance(duration, np.ndarray):
        duration = np.array(duration)
    else:
        duration = np.array([duration]*len(events_onsets))
        Severity: Major
        Found in neurokit/signal/epochs.py and 1 other location - About 2 hrs to fix
        neurokit/signal/epochs.py on lines 59..62

        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 56.

        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 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

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

              if isinstance(onset, list) or isinstance(onset, np.ndarray):
        onset = np.array(onset)
    else:
        onset = np.array([onset]*len(events_onsets))
          Severity: Major
          Found in neurokit/signal/epochs.py and 1 other location - About 2 hrs to fix
          neurokit/signal/epochs.py on lines 54..57

          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 56.

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

          def eeg_microstates_plot(method, path="", extension=".png", show_sensors_position=False, show_sensors_name=False, plot=True, save=True, dpi=150, contours=0, colorbar=False, separate=False):
    """
    Plot the microstates.
    """
    # Generate and store figures
          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 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

          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

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