neuropsychology/NeuroKit

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neurokit2/rsp/rsp_analyze.py

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# -*- coding: utf-8 -*-
import pandas as pd

from .rsp_eventrelated import rsp_eventrelated
from .rsp_intervalrelated import rsp_intervalrelated


def rsp_analyze(data, sampling_rate=1000, method="auto"):
    """**RSP Analysis**

    Performs RSP analysis on either epochs (event-related analysis) or on longer periods of data such as resting-state data.

    Parameters
    ----------
    data : dict or DataFrame
        A dictionary of epochs, containing one DataFrame per epoch, usually obtained via
        :func:`.epochs_create`, or a DataFrame containing all epochs, usually obtained via
        :func:`.epochs_to_df`. Can also take a DataFrame of processed signals from a longer period
        of data, typically generated by :func:`.rsp_process` or :func:`.bio_process`. Can also take
        a dict containing sets of separate periods of data.
    sampling_rate : int
        The sampling frequency of the signal (in Hz, i.e., samples/second). Defaults to 1000Hz.
    method : str
        Can be one of ``"event-related"`` for event-related analysis on epochs, or
        ``"interval-related"`` for analysis on longer periods of data. Defaults to ``"auto"`` where
        the right method will be chosen based on the mean duration of the data (``"event-related"``
        for duration under 10s).

    Returns
    -------
    DataFrame
        A dataframe containing the analyzed RSP features. If event-related analysis is conducted,
        each epoch is indicated by the `Label` column. See :func:`.rsp_eventrelated` and
        :func:`.rsp_intervalrelated` docstrings for details.

    See Also
    --------
    bio_process, rsp_process, epochs_create, rsp_eventrelated, rsp_intervalrelated

    Examples
    ----------
    .. ipython:: python

      import neurokit2 as nk

      # Example 1: Download the data for event-related analysis
      data = nk.data("bio_eventrelated_100hz")

      # Process the data for event-related analysis
      df, info = nk.bio_process(rsp=data["RSP"], sampling_rate=100)
      events = nk.events_find(data["Photosensor"], threshold_keep='below',
                             event_conditions=["Negative", "Neutral", "Neutral", "Negative"])
      epochs = nk.epochs_create(df, events, sampling_rate=100, epochs_start=-0.1, epochs_end=1.9)

      # Analyze
      nk.rsp_analyze(epochs, sampling_rate=100)

      # Example 2: Download the resting-state data
      data = nk.data("bio_resting_5min_100hz")

      # Process the data
      df, info = nk.rsp_process(data["RSP"], sampling_rate=100)

      # Analyze
      nk.rsp_analyze(df, sampling_rate=100)

    """
    method = method.lower()

    # Event-related analysis
    if method in ["event-related", "event", "epoch"]:
        # Sanity checks
        if isinstance(data, dict):
            for i in data:
                colnames = data[i].columns.values
        elif isinstance(data, pd.DataFrame):
            colnames = data.columns.values

        if len([i for i in colnames if "Label" in i]) == 0:
            raise ValueError(
                "NeuroKit error: rsp_analyze(): Wrong input or method, we couldn't extract extract epochs features."
            )
        else:
            features = rsp_eventrelated(data)

    # Interval-related analysis
    elif method in ["interval-related", "interval", "resting-state"]:
        features = rsp_intervalrelated(data, sampling_rate)

    # Auto
    elif method in ["auto"]:

        if isinstance(data, dict):
            for i in data:
                duration = len(data[i]) / sampling_rate
            if duration >= 10:
                features = rsp_intervalrelated(data, sampling_rate)
            else:
                features = rsp_eventrelated(data)

        if isinstance(data, pd.DataFrame):
            if "Label" in data.columns:
                epoch_len = data["Label"].value_counts()[0]
                duration = epoch_len / sampling_rate
            else:
                duration = len(data) / sampling_rate
            if duration >= 10:
                features = rsp_intervalrelated(data, sampling_rate)
            else:
                features = rsp_eventrelated(data)

    return features