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Misc

pynapple.io.misc

Various io functions

load_file

load_file(path)

Load file. Current format supported is (npz,nwb,)

.npz -> If the file is compatible with a pynapple format, the function will return a pynapple object. Otherwise, the function will return the output of numpy.load

.nwb -> Return the pynapple.io.NWBFile class wrapping the NWBFile

Parameters:

Name Type Description Default
path str

Path to the file

required

Returns:

Type Description
(Tsd, TsdFrame, Ts, IntervalSet, TsGroup, NWBFile)

One of the 5 pynapple objects or pynapple.io.NWBFile

Raises:

Type Description
FileNotFoundError

If file is missing

Source code in pynapple/io/misc.py
def load_file(path):
    """Load file. Current format supported is (npz,nwb,)

    .npz -> If the file is compatible with a pynapple format, the function will return a pynapple object.
    Otherwise, the function will return the output of numpy.load

    .nwb -> Return the pynapple.io.NWBFile class wrapping the NWBFile

    Parameters
    ----------
    path : str
        Path to the file

    Returns
    -------
    (Tsd, TsdFrame, Ts, IntervalSet, TsGroup, pynapple.io.NWBFile)
        One of the 5 pynapple objects or pynapple.io.NWBFile

    Raises
    ------
    FileNotFoundError
        If file is missing
    """
    if os.path.isfile(path):
        if path.endswith(".npz"):
            return NPZFile(path).load()
        elif path.endswith(".nwb"):
            return NWBFile(path)
        else:
            raise RuntimeError("File format not supported")
    else:
        raise FileNotFoundError("File {} does not exist".format(path))

load_folder

load_folder(path)

Load folder containing files or other folder. Pynapple will walk throught the subfolders to detect compatible npz files or nwb files.

Parameters:

Name Type Description Default
path str

Path to the folder

required

Returns:

Type Description
Folder

A dictionary-like class containing all the sub-folders and compatible files (i.e. npz, nwb)

Raises:

Type Description
RuntimeError

If folder is missing

Source code in pynapple/io/misc.py
def load_folder(path):
    """Load folder containing files or other folder.
    Pynapple will walk throught the subfolders to detect compatible npz files
    or nwb files.

    Parameters
    ----------
    path : str
        Path to the folder

    Returns
    -------
    Folder
        A dictionary-like class containing all the sub-folders and compatible files (i.e. npz, nwb)

    Raises
    ------
    RuntimeError
        If folder is missing
    """
    if os.path.isdir(path):
        return Folder(path)
    else:
        raise RuntimeError("Folder {} does not exist".format(path))

load_session

load_session(path=None, session_type=None)

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % WARNING : THIS FUNCTION IS DEPRECATED % %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% General Loader for

  • Neurosuite

  • Phy

  • Minian

  • Inscopix-cnmfe

  • Matlab-cnmfe

  • Suite2p

  • None for default session.

Parameters:

Name Type Description Default
path str

The path to load the data

None
session_type str

Can be 'neurosuite', 'phy', 'minian', 'inscopix-cnmfe', 'cnmfe-matlab', 'suite2p' or None for default loader.

None

Returns:

Type Description
Session

A class holding all the data from the session.

Source code in pynapple/io/misc.py
def load_session(path=None, session_type=None):
    """
    %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
    % WARNING : THIS FUNCTION IS DEPRECATED %
    %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
    General Loader for

    - Neurosuite\n
    - Phy\n
    - Minian\n
    - Inscopix-cnmfe\n
    - Matlab-cnmfe\n
    - Suite2p
    - None for default session.

    Parameters
    ----------
    path : str, optional
        The path to load the data
    session_type : str, optional
        Can be 'neurosuite', 'phy',
        'minian', 'inscopix-cnmfe', 'cnmfe-matlab',
        'suite2p' or None for default loader.

    Returns
    -------
    Session
        A class holding all the data from the session.

    """
    if path:
        if not os.path.isdir(path):
            raise RuntimeError("Path {} is not found.".format(path))

    if isinstance(session_type, str):
        session_type = session_type.lower()

    if session_type == "neurosuite":
        return NeuroSuite(path)

    elif session_type == "phy":
        return Phy(path)

    elif session_type == "inscopix-cnmfe":
        return InscopixCNMFE(path)

    elif session_type == "minian":
        return Minian(path)

    elif session_type == "cnmfe-matlab":
        return CNMF_E(path)

    elif session_type == "suite2p":
        return Suite2P(path)

    else:
        return BaseLoader(path)

load_eeg

load_eeg(
    filepath,
    channel=None,
    n_channels=None,
    frequency=None,
    precision="int16",
    bytes_size=2,
)

Standalone function to load eeg/lfp/dat file in binary format.

Parameters:

Name Type Description Default
filepath str

The path to the eeg file

required
channel int or list of int

The channel(s) to load. If None return a memory map of the dat file to avoid memory error

None
n_channels int

Number of channels

None
frequency float

Sampling rate of the file

None
precision str

The precision of the binary file

'int16'
bytes_size int

Bytes size of the binary file

2

Raises:

Type Description
RuntimeError

If can't find the lfp/eeg/dat file

Returns:

Type Description
Tsd or TsdFrame

The lfp in a time series format

Deleted Parameters

extension : str, optional The file extenstion (.eeg, .dat, .lfp). Make sure the frequency match

Source code in pynapple/io/misc.py
def load_eeg(
    filepath,
    channel=None,
    n_channels=None,
    frequency=None,
    precision="int16",
    bytes_size=2,
):
    """
    Standalone function to load eeg/lfp/dat file in binary format.

    Parameters
    ----------
    filepath : str
        The path to the eeg file
    channel : int or list of int, optional
        The channel(s) to load. If None return a memory map of the dat file to avoid memory error
    n_channels : int, optional
        Number of channels
    frequency : float, optional
        Sampling rate of the file
    precision : str, optional
        The precision of the binary file
    bytes_size : int, optional
        Bytes size of the binary file

    Raises
    ------
    RuntimeError
        If can't find the lfp/eeg/dat file

    Returns
    -------
    Tsd or TsdFrame
        The lfp in a time series format

    Deleted Parameters
    ------------------
    extension : str, optional
        The file extenstion (.eeg, .dat, .lfp). Make sure the frequency match

    """
    # Need to check if a xml file exists
    path = os.path.dirname(filepath)
    basename = os.path.basename(filepath).split(".")[0]
    listdir = os.listdir(path)

    if frequency is None or n_channels is None:
        if basename + ".xml" in listdir:
            xmlpath = os.path.join(path, basename + ".xml")
            xmldoc = minidom.parse(xmlpath)
        else:
            raise RuntimeError(
                "Can't find xml file; please specify sampling frequency or number of channels"
            )

        if frequency is None:
            if filepath.endswith(".dat"):
                fs_dat = int(
                    xmldoc.getElementsByTagName("acquisitionSystem")[0]
                    .getElementsByTagName("samplingRate")[0]
                    .firstChild.data
                )
                frequency = fs_dat
            elif filepath.endswith((".lfp", ".eeg")):
                fs_eeg = int(
                    xmldoc.getElementsByTagName("fieldPotentials")[0]
                    .getElementsByTagName("lfpSamplingRate")[0]
                    .firstChild.data
                )
                frequency = fs_eeg

        if n_channels is None:
            n_channels = int(
                xmldoc.getElementsByTagName("acquisitionSystem")[0]
                .getElementsByTagName("nChannels")[0]
                .firstChild.data
            )

    f = open(filepath, "rb")
    startoffile = f.seek(0, 0)
    endoffile = f.seek(0, 2)
    bytes_size = 2
    n_samples = int((endoffile - startoffile) / n_channels / bytes_size)
    duration = n_samples / frequency
    f.close()
    fp = np.memmap(filepath, np.int16, "r", shape=(n_samples, n_channels))
    timestep = np.arange(0, n_samples) / frequency

    time_support = nap.IntervalSet(start=0, end=duration, time_units="s")

    if channel is None:
        return fp
    elif type(channel) is int:
        return nap.Tsd(
            t=timestep, d=fp[:, channel], time_units="s", time_support=time_support
        )
    elif type(channel) is list:
        return nap.TsdFrame(
            t=timestep,
            d=fp[:, channel],
            time_units="s",
            time_support=time_support,
            columns=channel,
        )

append_NWB_LFP

append_NWB_LFP(path, lfp, channel=None)

Standalone function for adding lfp/eeg to already existing nwb files.

Parameters:

Name Type Description Default
path str

The path to the data. The function will looks for a nwb file in path or in path/pynapplenwb.

required
lfp Tsd or TsdFrame

Description

required
channel None

channel number in int ff lfp is a Tsd

None

Raises:

Type Description
RuntimeError

If can't find the nwb file

If no channel is specify when passing a Tsd

Source code in pynapple/io/misc.py
def append_NWB_LFP(path, lfp, channel=None):
    """Standalone function for adding lfp/eeg to already existing nwb files.

    Parameters
    ----------
    path : str
        The path to the data. The function will looks for a nwb file in path
        or in path/pynapplenwb.
    lfp : Tsd or TsdFrame
        Description
    channel : None, optional
        channel number in int ff lfp is a Tsd

    Raises
    ------
    RuntimeError
        If can't find the nwb file \n
        If no channel is specify when passing a Tsd

    """
    new_path = os.path.join(path, "pynapplenwb")
    nwb_path = ""
    if os.path.exists(new_path):
        nwbfilename = [f for f in os.listdir(new_path) if f.endswith(".nwb")]
        if len(nwbfilename):
            nwb_path = os.path.join(path, "pynapplenwb", nwbfilename[0])
    else:
        nwbfilename = [f for f in os.listdir(path) if f.endswith(".nwb")]
        if len(nwbfilename):
            nwb_path = os.path.join(path, "pynapplenwb", nwbfilename[0])

    if len(nwb_path) == 0:
        raise RuntimeError("Can't find nwb file in {}".format(path))

    if isinstance(lfp, nap.TsdFrame):
        channels = lfp.columns.values
    elif isinstance(lfp, nap.Tsd):
        if isinstance(channel, int):
            channels = [channel]
        else:
            raise RuntimeError("Please specify which channel it is.")

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

    all_table_region = nwbfile.create_electrode_table_region(
        region=channels, description="", name="electrodes"
    )

    lfp_electrical_series = ElectricalSeries(
        name="ElectricalSeries",
        data=lfp.values,
        timestamps=lfp.index.values,
        electrodes=all_table_region,
    )

    lfp = LFP(electrical_series=lfp_electrical_series)

    ecephys_module = nwbfile.create_processing_module(
        name="ecephys", description="processed extracellular electrophysiology data"
    )
    ecephys_module.add(lfp)

    io.write(nwbfile)
    io.close()

    return