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Loader

pynapple.io.loader

BaseLoader is the general class for loading session with pynapple.

@author: Guillaume Viejo

BaseLoader

Bases: object

General loader for epochs and tracking data

Source code in pynapple/io/loader.py 
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class BaseLoader(object):
    """
    General loader for epochs and tracking data
    """

    def __init__(self, path=None):
        self.path = path

        file_found = False
        # Check if a pynapplenwb folder exist
        if self.path is not None:
            nwb_path = os.path.join(self.path, "pynapplenwb")
            if os.path.exists(nwb_path):
                files = os.listdir(nwb_path)
                if len([f for f in files if f.endswith(".nwb")]):
                    file_found = True
                    self.load_data(path)

        # Starting the GUI
        if not file_found:
            raise RuntimeError(get_error_text(path))

    def load_data(self, path):
        """
        Load NWB data saved with pynapple in the pynapplenwb folder

        Parameters
        ----------
        path : str
            Path to the session folder
        """
        self.nwb_path = os.path.join(path, "pynapplenwb")
        if not os.path.exists(self.nwb_path):
            raise RuntimeError("Path {} does not exist.".format(self.nwb_path))
        self.nwbfilename = [f for f in os.listdir(self.nwb_path) if "nwb" in f][0]
        self.nwbfilepath = os.path.join(self.nwb_path, self.nwbfilename)

        io = NWBHDF5IO(self.nwbfilepath, "r+")
        nwbfile = io.read()

        position = {}
        acq_keys = nwbfile.acquisition.keys()
        if "CompassDirection" in acq_keys:
            compass = nwbfile.acquisition["CompassDirection"]
            for k in compass.spatial_series.keys():
                position[k] = pd.Series(
                    index=compass.get_spatial_series(k).timestamps[:],
                    data=compass.get_spatial_series(k).data[:],
                )
        if "Position" in acq_keys:
            tracking = nwbfile.acquisition["Position"]
            for k in tracking.spatial_series.keys():
                position[k] = pd.Series(
                    index=tracking.get_spatial_series(k).timestamps[:],
                    data=tracking.get_spatial_series(k).data[:],
                )
        if len(position):
            position = pd.DataFrame.from_dict(position)

            # retrieveing time support position if in epochs
            if "position_time_support" in nwbfile.intervals.keys():
                epochs = nwbfile.intervals["position_time_support"].to_dataframe()
                time_support = nap.IntervalSet(
                    start=epochs["start_time"], end=epochs["stop_time"], time_units="s"
                )

            self.position = nap.TsdFrame(
                position, time_units="s", time_support=time_support
            )

        if nwbfile.epochs is not None:
            epochs = nwbfile.epochs.to_dataframe()
            # NWB is dumb and cannot take a single string for labels
            epochs["label"] = [epochs.loc[i, "tags"][0] for i in epochs.index]
            epochs = epochs.drop(labels="tags", axis=1)
            epochs = epochs.rename(columns={"start_time": "start", "stop_time": "end"})
            self.epochs = self._make_epochs(epochs)

            self.time_support = self._join_epochs(epochs, "s")

        io.close()

        return

    def _make_epochs(self, epochs, time_units="s"):
        """
        Split GUI epochs into dict of epochs
        """
        labels = epochs.groupby("label").groups
        isets = {}
        for lbs in labels.keys():
            tmp = epochs.loc[labels[lbs]]
            isets[lbs] = nap.IntervalSet(
                start=tmp["start"], end=tmp["end"], time_units=time_units
            )
        return isets

    def _join_epochs(self, epochs, time_units="s"):
        """
        To create the global time support of the data
        """
        with warnings.catch_warnings():
            warnings.simplefilter("ignore")
            isets = nap.IntervalSet(
                start=epochs["start"].sort_values(),
                end=epochs["end"].sort_values(),
                time_units=time_units,
            )
            iset = isets.merge_close_intervals(1, time_units="us")
        if len(iset):
            return iset
        else:
            return None

    def save_nwb_intervals(self, iset, name, description=""):
        """
        Add epochs to the NWB file (e.g. ripples epochs)
        See pynwb.epoch.TimeIntervals

        Parameters
        ----------
        iset : IntervalSet
            The intervalSet to save
        name : str
            The name in the nwb file
        """
        io = NWBHDF5IO(self.nwbfilepath, "r+")
        nwbfile = io.read()

        epochs = iset.as_units("s")
        time_intervals = TimeIntervals(name=name, description=description)
        for i in epochs.index:
            time_intervals.add_interval(
                start_time=epochs.loc[i, "start"],
                stop_time=epochs.loc[i, "end"],
                tags=str(i),
            )

        nwbfile.add_time_intervals(time_intervals)
        io.write(nwbfile)
        io.close()

        return

    def save_nwb_timeseries(self, tsd, name, description=""):
        """
        Save timestamps in the NWB file (e.g. ripples time) with the time support.
        See pynwb.base.TimeSeries


        Parameters
        ----------
        tsd : TsdFrame
            _
        name : str
            _
        description : str, optional
            _
        """
        io = NWBHDF5IO(self.nwbfilepath, "r+")
        nwbfile = io.read()

        ts = TimeSeries(
            name=name,
            unit="s",
            data=tsd.values,
            timestamps=tsd.as_units("s").index.values,
        )

        time_support = TimeIntervals(
            name=name + "_timesupport", description="The time support of the object"
        )

        epochs = tsd.time_support.as_units("s")
        for i in epochs.index:
            time_support.add_interval(
                start_time=epochs.loc[i, "start"],
                stop_time=epochs.loc[i, "end"],
                tags=str(i),
            )
        nwbfile.add_time_intervals(time_support)
        nwbfile.add_acquisition(ts)
        io.write(nwbfile)
        io.close()

        return

    def load_nwb_intervals(self, name):
        """
        Load epochs from the NWB file (e.g. 'ripples')

        Parameters
        ----------
        name : str
            The name in the nwb file
        """
        io = NWBHDF5IO(self.nwbfilepath, "r")
        nwbfile = io.read()

        if name in nwbfile.intervals.keys():
            epochs = nwbfile.intervals[name].to_dataframe()
            isets = nap.IntervalSet(
                start=epochs["start_time"], end=epochs["stop_time"], time_units="s"
            )
            io.close()
            return isets
        else:
            io.close()
        return

    def load_nwb_timeseries(self, name):
        """
        Load timestamps in the NWB file (e.g. ripples time)

        Parameters
        ----------
        name : str
            _

        Returns
        -------
        Tsd
            _
        """
        io = NWBHDF5IO(self.nwbfilepath, "r")
        nwbfile = io.read()

        ts = nwbfile.acquisition[name]

        time_support = self.load_nwb_intervals(name + "_timesupport")

        tsd = nap.Tsd(
            t=ts.timestamps[:], d=ts.data[:], time_units="s", time_support=time_support
        )

        io.close()

        return tsd

load_data 

load_data(path)

Load NWB data saved with pynapple in the pynapplenwb folder

Parameters:

Name Type Description Default
path str

Path to the session folder

 required
Source code in pynapple/io/loader.py 
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def load_data(self, path):
    """
    Load NWB data saved with pynapple in the pynapplenwb folder

    Parameters
    ----------
    path : str
        Path to the session folder
    """
    self.nwb_path = os.path.join(path, "pynapplenwb")
    if not os.path.exists(self.nwb_path):
        raise RuntimeError("Path {} does not exist.".format(self.nwb_path))
    self.nwbfilename = [f for f in os.listdir(self.nwb_path) if "nwb" in f][0]
    self.nwbfilepath = os.path.join(self.nwb_path, self.nwbfilename)

    io = NWBHDF5IO(self.nwbfilepath, "r+")
    nwbfile = io.read()

    position = {}
    acq_keys = nwbfile.acquisition.keys()
    if "CompassDirection" in acq_keys:
        compass = nwbfile.acquisition["CompassDirection"]
        for k in compass.spatial_series.keys():
            position[k] = pd.Series(
                index=compass.get_spatial_series(k).timestamps[:],
                data=compass.get_spatial_series(k).data[:],
            )
    if "Position" in acq_keys:
        tracking = nwbfile.acquisition["Position"]
        for k in tracking.spatial_series.keys():
            position[k] = pd.Series(
                index=tracking.get_spatial_series(k).timestamps[:],
                data=tracking.get_spatial_series(k).data[:],
            )
    if len(position):
        position = pd.DataFrame.from_dict(position)

        # retrieveing time support position if in epochs
        if "position_time_support" in nwbfile.intervals.keys():
            epochs = nwbfile.intervals["position_time_support"].to_dataframe()
            time_support = nap.IntervalSet(
                start=epochs["start_time"], end=epochs["stop_time"], time_units="s"
            )

        self.position = nap.TsdFrame(
            position, time_units="s", time_support=time_support
        )

    if nwbfile.epochs is not None:
        epochs = nwbfile.epochs.to_dataframe()
        # NWB is dumb and cannot take a single string for labels
        epochs["label"] = [epochs.loc[i, "tags"][0] for i in epochs.index]
        epochs = epochs.drop(labels="tags", axis=1)
        epochs = epochs.rename(columns={"start_time": "start", "stop_time": "end"})
        self.epochs = self._make_epochs(epochs)

        self.time_support = self._join_epochs(epochs, "s")

    io.close()

    return

save_nwb_intervals 

save_nwb_intervals(iset, name, description='')

Add epochs to the NWB file (e.g. ripples epochs) See pynwb.epoch.TimeIntervals

Parameters:

Name Type Description Default
iset IntervalSet

The intervalSet to save

 required
name str

The name in the nwb file

 required
Source code in pynapple/io/loader.py 
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def save_nwb_intervals(self, iset, name, description=""):
    """
    Add epochs to the NWB file (e.g. ripples epochs)
    See pynwb.epoch.TimeIntervals

    Parameters
    ----------
    iset : IntervalSet
        The intervalSet to save
    name : str
        The name in the nwb file
    """
    io = NWBHDF5IO(self.nwbfilepath, "r+")
    nwbfile = io.read()

    epochs = iset.as_units("s")
    time_intervals = TimeIntervals(name=name, description=description)
    for i in epochs.index:
        time_intervals.add_interval(
            start_time=epochs.loc[i, "start"],
            stop_time=epochs.loc[i, "end"],
            tags=str(i),
        )

    nwbfile.add_time_intervals(time_intervals)
    io.write(nwbfile)
    io.close()

    return

save_nwb_timeseries 

save_nwb_timeseries(tsd, name, description='')

Save timestamps in the NWB file (e.g. ripples time) with the time support. See pynwb.base.TimeSeries

Parameters:

Name Type Description Default
tsd TsdFrame

_

 required
name str

_

 required
description str

_

 ''
Source code in pynapple/io/loader.py 
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def save_nwb_timeseries(self, tsd, name, description=""):
    """
    Save timestamps in the NWB file (e.g. ripples time) with the time support.
    See pynwb.base.TimeSeries


    Parameters
    ----------
    tsd : TsdFrame
        _
    name : str
        _
    description : str, optional
        _
    """
    io = NWBHDF5IO(self.nwbfilepath, "r+")
    nwbfile = io.read()

    ts = TimeSeries(
        name=name,
        unit="s",
        data=tsd.values,
        timestamps=tsd.as_units("s").index.values,
    )

    time_support = TimeIntervals(
        name=name + "_timesupport", description="The time support of the object"
    )

    epochs = tsd.time_support.as_units("s")
    for i in epochs.index:
        time_support.add_interval(
            start_time=epochs.loc[i, "start"],
            stop_time=epochs.loc[i, "end"],
            tags=str(i),
        )
    nwbfile.add_time_intervals(time_support)
    nwbfile.add_acquisition(ts)
    io.write(nwbfile)
    io.close()

    return

load_nwb_intervals 

load_nwb_intervals(name)

Load epochs from the NWB file (e.g. 'ripples')

Parameters:

Name Type Description Default
name str

The name in the nwb file

 required
Source code in pynapple/io/loader.py 
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def load_nwb_intervals(self, name):
    """
    Load epochs from the NWB file (e.g. 'ripples')

    Parameters
    ----------
    name : str
        The name in the nwb file
    """
    io = NWBHDF5IO(self.nwbfilepath, "r")
    nwbfile = io.read()

    if name in nwbfile.intervals.keys():
        epochs = nwbfile.intervals[name].to_dataframe()
        isets = nap.IntervalSet(
            start=epochs["start_time"], end=epochs["stop_time"], time_units="s"
        )
        io.close()
        return isets
    else:
        io.close()
    return

load_nwb_timeseries 

load_nwb_timeseries(name)

Load timestamps in the NWB file (e.g. ripples time)

Parameters:

Name Type Description Default
name str

_

 required

Returns:

Type Description
Tsd

_
Source code in pynapple/io/loader.py 
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def load_nwb_timeseries(self, name):
    """
    Load timestamps in the NWB file (e.g. ripples time)

    Parameters
    ----------
    name : str
        _

    Returns
    -------
    Tsd
        _
    """
    io = NWBHDF5IO(self.nwbfilepath, "r")
    nwbfile = io.read()

    ts = nwbfile.acquisition[name]

    time_support = self.load_nwb_intervals(name + "_timesupport")

    tsd = nap.Tsd(
        t=ts.timestamps[:], d=ts.data[:], time_units="s", time_support=time_support
    )

    io.close()

    return tsd