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

        hrv["HFn"] = hrv["HF"]/(hrv["LF"]+hrv["HF"])
Severity: Major
Found in neurokit/bio/bio_ecg.py and 1 other location - About 1 hr to fix
neurokit/bio/bio_ecg.py on lines 644..644

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 41.

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_add_events has 10 arguments (exceeds 4 allowed). Consider refactoring.
Open

def eeg_add_events(raw, events_channel, conditions=None, treshold="auto", cut="higher", time_index=None, number="all", after=0, before=None, min_duration=1):
Severity: Major
Found in neurokit/eeg/eeg_data.py - About 1 hr to fix

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

        for participant, epochs in all_evokeds.items():
        for cond, epoch in epochs.items():
            data[cond].append(epoch)
    Severity: Major
    Found in neurokit/eeg/eeg_erp.py and 1 other location - About 1 hr to fix
    neurokit/eeg/eeg_erp.py on lines 106..108

    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 41.

    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_erp has 10 arguments (exceeds 4 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"):
    Severity: Major
    Found in neurokit/eeg/eeg_erp.py - About 1 hr to fix

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

          for participant, epochs in all_evokeds.items():
        for condition, epoch in epochs.items():
            data[condition].append(epoch)
      Severity: Major
      Found in neurokit/eeg/eeg_erp.py and 1 other location - About 1 hr to fix
      neurokit/eeg/eeg_erp.py on lines 179..181

      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 41.

      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 ecg_rsa has 31 lines of code (exceeds 25 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

        Function segmenter_pekkanen has 28 lines of code (exceeds 25 allowed). Consider refactoring.
        Open

        def segmenter_pekkanen(ecg, sampling_rate, window_size=5.0, lfreq=5.0, hfreq=15.0):
    """
    ECG R peak detection based on `Kathirvel et al. (2001) <http://link.springer.com/article/10.1007/s13239-011-0065-3/fulltext.html>`_ with some tweaks (mainly robust estimation of the rectified signal cutoff threshold).

    Parameters
        Severity: Minor
        Found in neurokit/bio/bio_ecg_preprocessing.py - About 1 hr to fix

          Function bio_process has a Cognitive Complexity of 10 (exceeds 5 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):
    """
    Automated processing of bio signals. Wrapper for other bio processing functions.

    Parameters
          Severity: Minor
          Found in neurokit/bio/bio_meta.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 2 locations. Consider refactoring.
          Open

                      power =  np.trapz(y=power[(freq >= band[0]) & (freq < band[1])], x=freq[(freq >= band[0]) & (freq < band[1])])
          Severity: Major
          Found in neurokit/bio/bio_ecg.py and 1 other location - About 1 hr to fix
          neurokit/bio/bio_ecg.py on lines 633..633

          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 39.

          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 ecg_preprocess has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring.
          Open

          def ecg_preprocess(ecg, sampling_rate=1000, filter_type="FIR", filter_band="bandpass", filter_frequency=[3, 45], filter_order=0.3, segmenter="hamilton"):
    """
    ECG signal preprocessing.

    Parameters
          Severity: Minor
          Found in neurokit/bio/bio_ecg_preprocessing.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 2 locations. Consider refactoring.
          Open

                  b, a = scipy.signal.butter(2, np.array(freqs)/(sampling_rate/2.), btype = 'bandpass')
          Severity: Major
          Found in neurokit/bio/bio_emg.py and 1 other location - About 1 hr to fix
          neurokit/bio/bio_emg.py on lines 231..231

          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 39.

          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

                  b, a = scipy.signal.butter(2, np.array(lfreq)/(sampling_rate/2.), btype = 'low')
          Severity: Major
          Found in neurokit/bio/bio_emg.py and 1 other location - About 1 hr to fix
          neurokit/bio/bio_emg.py on lines 225..225

          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 39.

          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 emg_process has 8 arguments (exceeds 4 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):
          Severity: Major
          Found in neurokit/bio/bio_emg.py - About 1 hr to fix

            Function eeg_microstates_clustering has 8 arguments (exceeds 4 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):
            Severity: Major
            Found in examples/UnderDev/eeg/eeg_microstates.py - About 1 hr to fix

              Function plot_polarbar has 8 arguments (exceeds 4 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)):
              Severity: Major
              Found in neurokit/statistics/plot.py - About 1 hr to fix

                Function find_events has 8 arguments (exceeds 4 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):
                Severity: Major
                Found in neurokit/signal/events.py - About 1 hr to fix

                  Function eeg_to_all_evokeds has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.
                  Open

                  def eeg_to_all_evokeds(all_epochs, conditions=None):
    """
    Convert all_epochs to all_evokeds.

    DOCS INCOMPLETE :(
                  Severity: Minor
                  Found in neurokit/eeg/eeg_data.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 ecg_wave_detector has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.
                  Open

                  def ecg_wave_detector(ecg, rpeaks):
    """
    Returns the localization of the P, Q, T waves. This function needs massive help!

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

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

                      for participant, epochs in all_evokeds.items():
        for cond, epoch in epochs.items():
            data[cond] = []
                  Severity: Minor
                  Found in neurokit/eeg/eeg_erp.py and 1 other location - About 55 mins to fix
                  neurokit/eeg/eeg_erp.py on lines 103..105

                  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 37.

                  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

                              index_run += [run] * len(results[participant][run]["data"])
                  Severity: Minor
                  Found in examples/UnderDev/eeg/eeg_microstates.py and 1 other location - About 55 mins to fix
                  examples/UnderDev/eeg/eeg_microstates.py on lines 457..457

                  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 37.

                  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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