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Time index

pynapple.core.time_index

Similar to pandas.Index, TsIndex holds the timestamps associated with the data of a time series. This class deals with conversion between different time units for all pynapple objects as well as making sure that timestamps are property sorted before initializing any objects.

- `us`: microseconds
- `ms`: milliseconds
- `s`: seconds  (overall default)

TsIndex

Bases: ndarray

Holder for timestamps. Similar to pandas.Index. Subclass numpy.ndarray

Source code in pynapple/core/time_index.py 
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class TsIndex(np.ndarray):
    """
    Holder for timestamps. Similar to pandas.Index. Subclass numpy.ndarray
    """

    @staticmethod
    def format_timestamps(t, units="s"):
        """
        Converts time index in pynapple in a default format

        Parameters
        ----------
        t : numpy.ndarray
            a vector of times
        units
            the units in which times are given

        Returns
        -------
        t : np.ndarray
            times in standard pynapple format

        Raises
        ------
        ValueError
            Description
        """
        if units == "s":
            t = np.around(t, nap_config.time_index_precision)
        elif units == "ms":
            t = np.around(t / 1.0e3, nap_config.time_index_precision)
        elif units == "us":
            t = np.around(t / 1.0e6, nap_config.time_index_precision)
        else:
            raise ValueError("unrecognized time units type")

        return t

    @staticmethod
    def return_timestamps(t, units="s"):
        """
        Converts time index in pynapple in a particular format

        Parameters
        ----------
        t : numpy.ndarray
            a vector (or scalar) of times
        units
            the units in which times are given

        Returns
        -------
        t : numpy.ndarray
            times in standard pynapple format

        Raises
        ------
        ValueError
            IF units is not in ['s', 'ms', 'us']
        """
        if units == "s":
            t = np.around(t, nap_config.time_index_precision)
        elif units == "ms":
            t = np.around(t * 1.0e3, nap_config.time_index_precision)
        elif units == "us":
            t = np.around(t * 1.0e6, nap_config.time_index_precision)
        else:
            raise ValueError("unrecognized time units type")

        return t

    @staticmethod
    def sort_timestamps(t, give_warning=True):
        """
        Raise warning if timestamps are not sorted

        Parameters
        ----------
        t : numpy.ndarray
            a vector of times
        give_warning : bool, optional
            If timestamps are not sorted

        Returns
        -------
        numpy.ndarray
            Description
        """
        if not (np.diff(t) >= 0).all():
            if give_warning and not nap_config.suppress_time_index_sorting_warnings:
                warn("timestamps are not sorted", UserWarning)
            t = np.sort(t)
        return t

    def __new__(cls, t, time_units="s"):
        assert t.ndim == 1, "t should be 1 dimensional"
        t = t.astype(np.float64)
        t = TsIndex.format_timestamps(t, time_units)
        t = TsIndex.sort_timestamps(t)
        obj = np.asarray(t).view(cls)
        return obj

    @property
    def values(self):
        """Returns the index as a ndarray

        Returns
        -------
        numpy.ndarray
            The timestamps in seconds
        """
        return np.asarray(self)

    def __setitem__(self, *args, **kwargs):
        raise RuntimeError("TsIndex object is not mutable.")

    def to_numpy(self):
        """Return the index as a ndarray. Useful for matplotlib.

        Returns
        -------
        numpy.ndarray
            The timestamps in seconds
        """
        return self.values

    def in_units(self, time_units="s"):
        """Return the index as a ndarray in the desired units

        Returns
        -------
        numpy.ndarray
            The timestamps in seconds
        """
        return TsIndex.return_timestamps(self.values, time_units)

values property 

values

Returns the index as a ndarray

Returns:

Type Description
ndarray

The timestamps in seconds

format_timestamps staticmethod 

format_timestamps(t, units='s')

Converts time index in pynapple in a default format

Parameters:

Name Type Description Default
t ndarray

a vector of times

 required
units

the units in which times are given

 's'

Returns:

Name Type Description
t ndarray

times in standard pynapple format

Raises:

Type Description
ValueError

Description
Source code in pynapple/core/time_index.py 
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@staticmethod
def format_timestamps(t, units="s"):
    """
    Converts time index in pynapple in a default format

    Parameters
    ----------
    t : numpy.ndarray
        a vector of times
    units
        the units in which times are given

    Returns
    -------
    t : np.ndarray
        times in standard pynapple format

    Raises
    ------
    ValueError
        Description
    """
    if units == "s":
        t = np.around(t, nap_config.time_index_precision)
    elif units == "ms":
        t = np.around(t / 1.0e3, nap_config.time_index_precision)
    elif units == "us":
        t = np.around(t / 1.0e6, nap_config.time_index_precision)
    else:
        raise ValueError("unrecognized time units type")

    return t

return_timestamps staticmethod 

return_timestamps(t, units='s')

Converts time index in pynapple in a particular format

Parameters:

Name Type Description Default
t ndarray

a vector (or scalar) of times

 required
units

the units in which times are given

 's'

Returns:

Name Type Description
t ndarray

times in standard pynapple format

Raises:

Type Description
ValueError

IF units is not in ['s', 'ms', 'us']
Source code in pynapple/core/time_index.py 
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@staticmethod
def return_timestamps(t, units="s"):
    """
    Converts time index in pynapple in a particular format

    Parameters
    ----------
    t : numpy.ndarray
        a vector (or scalar) of times
    units
        the units in which times are given

    Returns
    -------
    t : numpy.ndarray
        times in standard pynapple format

    Raises
    ------
    ValueError
        IF units is not in ['s', 'ms', 'us']
    """
    if units == "s":
        t = np.around(t, nap_config.time_index_precision)
    elif units == "ms":
        t = np.around(t * 1.0e3, nap_config.time_index_precision)
    elif units == "us":
        t = np.around(t * 1.0e6, nap_config.time_index_precision)
    else:
        raise ValueError("unrecognized time units type")

    return t

sort_timestamps staticmethod 

sort_timestamps(t, give_warning=True)

Raise warning if timestamps are not sorted

Parameters:

Name Type Description Default
t ndarray

a vector of times

 required
give_warning bool

If timestamps are not sorted

 True

Returns:

Type Description
ndarray

Description
Source code in pynapple/core/time_index.py 
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@staticmethod
def sort_timestamps(t, give_warning=True):
    """
    Raise warning if timestamps are not sorted

    Parameters
    ----------
    t : numpy.ndarray
        a vector of times
    give_warning : bool, optional
        If timestamps are not sorted

    Returns
    -------
    numpy.ndarray
        Description
    """
    if not (np.diff(t) >= 0).all():
        if give_warning and not nap_config.suppress_time_index_sorting_warnings:
            warn("timestamps are not sorted", UserWarning)
        t = np.sort(t)
    return t

to_numpy 

to_numpy()

Return the index as a ndarray. Useful for matplotlib.

Returns:

Type Description
ndarray

The timestamps in seconds
Source code in pynapple/core/time_index.py 
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def to_numpy(self):
    """Return the index as a ndarray. Useful for matplotlib.

    Returns
    -------
    numpy.ndarray
        The timestamps in seconds
    """
    return self.values

in_units 

in_units(time_units='s')

Return the index as a ndarray in the desired units

Returns:

Type Description
ndarray

The timestamps in seconds
Source code in pynapple/core/time_index.py 
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def in_units(self, time_units="s"):
    """Return the index as a ndarray in the desired units

    Returns
    -------
    numpy.ndarray
        The timestamps in seconds
    """
    return TsIndex.return_timestamps(self.values, time_units)