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examples/UnderDev/eeg/eeg_microstates.py

Summary

Maintainability
F
3 days
Test Coverage

File eeg_microstates.py has 342 lines of code (exceeds 250 allowed). Consider refactoring.
Open

"""
Microstates submodule.
"""
from ..signal import complexity
from ..miscellaneous import find_following_duplicates
Severity: Minor
Found in examples/UnderDev/eeg/eeg_microstates.py - About 4 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 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 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 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

    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 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 eeg_microstates_plot has 11 arguments (exceeds 4 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):
      Severity: Major
      Found in examples/UnderDev/eeg/eeg_microstates.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 eeg_gfp_peaks has 6 arguments (exceeds 4 allowed). Consider refactoring.
          Open

          def eeg_gfp_peaks(data, gflp_method='GFPL1', smoothing=False, smoothing_window=100, peak_method="wavelet", normalize=False):
          Severity: Minor
          Found in examples/UnderDev/eeg/eeg_microstates.py - About 45 mins to fix

            Function eeg_microstates_features has 5 arguments (exceeds 4 allowed). Consider refactoring.
            Open

            def eeg_microstates_features(results, method, ecg=True, nonlinearity=True, verbose=True):
            Severity: Minor
            Found in examples/UnderDev/eeg/eeg_microstates.py - About 35 mins to fix

              Function eeg_gfp has 5 arguments (exceeds 4 allowed). Consider refactoring.
              Open

              def eeg_gfp(raws, gflp_method="GFPL1", scale=True, normalize=True, smoothing=None):
              Severity: Minor
              Found in examples/UnderDev/eeg/eeg_microstates.py - About 35 mins to fix

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

                        for x in np.arange(0, len(set(microstates))/2*int(X), int(X)):
                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 530..530

                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

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

                            for y in np.arange(0, len(set(microstates))/2*int(Y), int(Y)):
                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 529..529

                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_participant += [participant] * 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 458..458

                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

                                    uniques_ms = results[participant][run]["microstates"][np.where(uniques)]
                Severity: Minor
                Found in examples/UnderDev/eeg/eeg_microstates.py and 1 other location - About 45 mins to fix
                examples/UnderDev/eeg/eeg_microstates.py on lines 295..295

                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 35.

                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

                                    results[participant][run]["parameters"][microstate]["occurence"] = 0
                Severity: Minor
                Found in examples/UnderDev/eeg/eeg_microstates.py and 1 other location - About 45 mins to fix
                examples/UnderDev/eeg/eeg_microstates.py on lines 305..305

                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 35.

                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

                                    uniques_times = results[participant][run]["microstates_times"][np.where(uniques)]
                Severity: Minor
                Found in examples/UnderDev/eeg/eeg_microstates.py and 1 other location - About 45 mins to fix
                examples/UnderDev/eeg/eeg_microstates.py on lines 296..296

                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 35.

                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

                                    results[participant][run]["parameters"][microstate]["coverage"] = 0
                Severity: Minor
                Found in examples/UnderDev/eeg/eeg_microstates.py and 1 other location - About 45 mins to fix
                examples/UnderDev/eeg/eeg_microstates.py on lines 307..307

                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 35.

                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

                    try:
        # Fit clustering aglorithm
        algorithm = eeg_microstates_clustering(data=data_processed,
                Severity: Minor
                Found in examples/UnderDev/eeg/eeg_microstates.py and 1 other location - About 30 mins to fix
                neurokit/bio/bio_meta.py on lines 145..145

                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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