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N/A N/A Conversion tool from SQD to FIF

RawKIT class is adapted from Denis Engemann et al.'s mne_bti2fiff.py

 os SEEK_CUR path op struct unpack N/A time N/A numpy np scipy linalg pick pick_types coreg fit_matched_points _decimate_points utils verbose logger warn transforms apply_trans als_ras_trans als_ras_trans_mm get_ras_to_neuromag_trans Transform base _BaseRaw utils _mult_cal_one epochs _BaseEpochs constants FIFF meas_info _empty_info _read_dig_points _make_dig_points constants KIT KIT_CONSTANTS SYSNAMES coreg read_mrk externals.six string_types event read_events RawKIT N/A _BaseRaw N/A N/A Raw object from KIT SQD file

    Parameters
    ----------
    input_fname : str
        Path to the sqd file.
    mrk : None | str | array_like, shape (5, 3) | list of str or array_like
        Marker points representing the location of the marker coils with
        respect to the MEG Sensors, or path to a marker file.
        If list, all of the markers will be averaged together.
    elp : None | str | array_like, shape (8, 3)
        Digitizer points representing the location of the fiducials and the
        marker coils with respect to the digitized head shape, or path to a
        file containing these points.
    hsp : None | str | array, shape (n_points, 3)
        Digitizer head shape points, or path to head shape file. If more than
        10,000 points are in the head shape, they are automatically decimated.
    stim : list of int | '<' | '>'
        Channel-value correspondence when converting KIT trigger channels to a
        Neuromag-style stim channel. For '<', the largest values are assigned
        to the first channel (default). For '>', the largest values are
        assigned to the last channel. Can also be specified as a list of
        trigger channel indexes.
    slope : '+' | '-'
        How to interpret values on KIT trigger channels when synthesizing a
        Neuromag-style stim channel. With '+', a positive slope (low-to-high)
        is interpreted as an event. With '-', a negative slope (high-to-low)
        is interpreted as an event.
    stimthresh : float
        The threshold level for accepting voltage changes in KIT trigger
        channels as a trigger event. If None, stim must also be set to None.
    preload : bool or str (default False)
        Preload data into memory for data manipulation and faster indexing.
        If True, the data will be preloaded into memory (fast, requires
        large amount of memory). If preload is a string, preload is the
        file name of a memory-mapped file which is used to store the data
        on the hard drive (slower, requires less memory).
    stim_code : 'binary' | 'channel'
        How to decode trigger values from stim channels. 'binary' read stim
        channel events as binary code, 'channel' encodes channel number.
    verbose : bool, str, int, or None
        If not None, override default verbose level (see mne.verbose).

    Notes
    -----
    ``elp`` and ``hsp`` are usually the exported text files (*.txt) from the
    Polhemus FastScan system. hsp refers to the headshape surface points. elp
    refers to the points in head-space that corresponds to the HPI points.
    Currently, '*.elp' and '*.hsp' files are NOT supported.

    See Also
    --------
    mne.io.Raw : Documentation of attribute and methods.
     __init__ N/A N/A self input_fname mrk elp hsp stim slope stimthresh preload stim_code verbose N/A None None None > - 1 False binary None N/A N/A N/A N/A logger info N/A Extracting SQD Parameters from %s... input_fname N/A input_fname N/A N/A op abspath input_fname N/A N/A self preload False N/A N/A N/A logger info Creating Raw.info structure... N/A N/A info kit_info N/A get_kit_info input_fname N/A N/A kit_info N/A slope slope N/A N/A kit_info N/A stimthresh stimthresh N/A N/A N/A kit_info N/A acq_type 1 N/A N/A err SQD file contains epochs, not raw data. Wrong reader. N/A N/A TypeError err N/A N/A N/A logger info Creating Info structure... N/A last_samps N/A N/A N/A kit_info N/A n_samples 1 N/A N/A self _raw_extras N/A kit_info N/A N/A N/A self _set_stimchannels info stim stim_code N/A N/A N/A N/A super RawKIT self __init__ info preload last_samps last_samps filenames N/A input_fname raw_extras N/A self _raw_extras verbose verbose N/A N/A isinstance mrk list N/A N/A mrk N/A N/A N/A isinstance marker string_types N/A read_mrk marker marker N/A marker mrk N/A mrk N/A N/A np mean mrk axis 0 N/A N/A N/A mrk None N/A elp None N/A hsp None N/A N/A N/A dig_points dev_head_t N/A _set_dig_kit mrk elp hsp N/A N/A N/A self info N/A dig dig_points N/A N/A N/A self info N/A dev_head_t dev_head_t N/A N/A N/A N/A mrk None N/A elp None N/A hsp None N/A N/A N/A ValueError mrk, elp and hsp need to be provided as a group (all or none) N/A N/A N/A logger info Ready. N/A verbose read_stim_ch N/A N/A self buffer_size N/A 100000.0 N/A N/A Read events from data

        Parameter
        ---------
        buffer_size : int
            The size of chunk to by which the data are scanned.

        Returns
        -------
        events : array, [samples]
           The event vector (1 x samples).
         N/A buffer_size N/A int buffer_size N/A start N/A int N/A self first_samp N/A stop N/A int N/A N/A self last_samp 1 N/A pick N/A pick_types N/A self info meg False ref_meg False stim True exclude N/A N/A stim_ch N/A N/A np empty N/A 1 stop dtype N/A np int N/A b_start N/A range start stop buffer_size N/A N/A b_stop N/A b_start buffer_size N/A x N/A N/A self N/A N/A pick N/A b_start b_stop N/A 0 N/A N/A stim_ch N/A N/A N/A b_start N/A b_start N/A N/A x shape N/A 1 x N/A stim_ch N/A _set_stimchannels N/A N/A self info stim stim_code N/A N/A N/A Specify how the trigger channel is synthesized from analog channels.

        Has to be done before loading data. For a RawKIT instance that has been
        created with preload=True, this method will raise a
        NotImplementedError.

        Parameters
        ----------
        info : instance of MeasInfo
            The measurement info.
        stim : list of int | '<' | '>'
            Can be submitted as list of trigger channels.
            If a list is not specified, the default triggers extracted from
            misc channels will be used with specified directionality.
            '<' means that largest values assigned to the first channel
            in sequence.
            '>' means the largest trigger assigned to the last channel
            in sequence.
        stim_code : 'binary' | 'channel'
            How to decode trigger values from stim channels. 'binary' read stim
            channel events as binary code, 'channel' encodes channel number.
         N/A N/A stim_code N/A binary channel N/A N/A N/A ValueError N/A stim_code=%r, needs to be 'binary' or 'channel' stim_code N/A N/A stim None N/A N/A N/A isinstance stim str N/A N/A picks N/A N/A pick_types info meg False ref_meg False misc True exclude N/A N/A 8 N/A N/A stim < N/A N/A stim N/A picks N/A -1 N/A N/A N/A stim > N/A N/A stim picks N/A N/A N/A ValueError N/A stim needs to be list of int, '>' or '<', not %r N/A str stim N/A N/A N/A N/A N/A np max stim N/A N/A N/A self _raw_extras N/A 0 N/A nchan N/A N/A N/A ValueError N/A Tried to set stim channel %i, but sqd file only has %i channels N/A N/A N/A np max stim N/A N/A N/A self _raw_extras N/A 0 N/A nchan N/A nchan N/A N/A N/A N/A self _raw_extras N/A 0 N/A nchan 1 N/A ch_name STI 014 N/A chan_info N/A N/A N/A chan_info N/A cal N/A KIT CALIB_FACTOR N/A N/A chan_info N/A logno nchan N/A N/A chan_info N/A scanno nchan N/A N/A chan_info N/A range 1.0 N/A N/A chan_info N/A unit N/A FIFF FIFF_UNIT_NONE N/A N/A chan_info N/A unit_mul 0 N/A N/A chan_info N/A ch_name ch_name N/A N/A chan_info N/A coil_type N/A FIFF FIFFV_COIL_NONE N/A N/A chan_info N/A loc N/A N/A np zeros 12 N/A N/A chan_info N/A kind N/A FIFF FIFFV_STIM_CH N/A N/A N/A N/A info N/A chs append chan_info N/A N/A N/A info _update_redundant N/A N/A self preload N/A N/A err Can't change stim channel after preloading data N/A N/A NotImplementedError err N/A N/A N/A N/A self _raw_extras N/A 0 N/A stim stim N/A N/A N/A N/A self _raw_extras N/A 0 N/A stim_code stim_code N/A _read_segment_file N/A N/A self data idx fi start stop cals mult N/A N/A N/A Read a chunk of raw data N/A nchan N/A N/A N/A self _raw_extras N/A fi N/A nchan N/A data_left N/A N/A stop start nchan N/A n_sens N/A N/A N/A self _raw_extras N/A fi N/A n_sens N/A sensor_gain N/A N/A N/A N/A N/A self _raw_extras N/A fi N/A sensor_gain copy N/A N/A sensor_gain N/A n_sens N/A N/A sensor_gain N/A n_sens N/A N/A N/A self _raw_extras N/A fi N/A amp_gain N/A conv_factor N/A N/A np array N/A N/A N/A KIT VOLTAGE_RANGE N/A N/A N/A self _raw_extras N/A fi N/A DYNAMIC_RANGE sensor_gain N/A n_bytes 2 N/A blk_size N/A min data_left N/A N/A N/A 100000000 n_bytes nchan nchan N/A N/A open N/A N/A self _filenames N/A fi rb buffering 0 fid N/A N/A data_offset N/A KIT RAW_OFFSET N/A N/A N/A fid seek data_offset N/A data_offset N/A N/A unpack i N/A N/A fid read N/A KIT INT N/A 0 N/A pointer N/A N/A start nchan N/A KIT SHORT N/A N/A N/A fid seek N/A data_offset pointer N/A blk_start N/A N/A N/A np arange 0 data_left blk_size nchan N/A N/A blk_size N/A min blk_size N/A data_left N/A blk_start nchan N/A block N/A N/A np fromfile fid dtype h count blk_size N/A block N/A N/A N/A N/A block reshape nchan -1 order F astype float N/A blk_stop N/A blk_start N/A N/A block shape N/A 1 N/A data_view N/A data N/A N/A N/A blk_start blk_stop N/A block N/A conv_factor N/A N/A N/A N/A np newaxis N/A N/A N/A N/A N/A self _raw_extras N/A fi N/A stim None N/A N/A trig_chs N/A block N/A N/A N/A N/A N/A self _raw_extras N/A fi N/A stim N/A N/A N/A N/A N/A N/A self _raw_extras N/A fi N/A slope + N/A N/A trig_chs N/A trig_chs N/A N/A N/A self _raw_extras N/A 0 N/A stimthresh N/A N/A N/A N/A N/A N/A self _raw_extras N/A fi N/A slope - N/A N/A trig_chs N/A trig_chs N/A N/A N/A self _raw_extras N/A 0 N/A stimthresh N/A N/A N/A ValueError slope needs to be '+' or '-' N/A N/A N/A N/A N/A self _raw_extras N/A 0 N/A stim_code binary N/A N/A ntrigchan N/A len N/A N/A N/A self _raw_extras N/A 0 N/A stim N/A trig_vals N/A N/A N/A np array N/A 2 N/A N/A np arange ntrigchan ndmin 2 T N/A N/A trig_vals N/A N/A np reshape N/A N/A N/A self _raw_extras N/A 0 N/A stim N/A -1 1 N/A trig_chs N/A trig_chs trig_vals N/A stim_ch N/A N/A np array N/A N/A trig_chs sum axis 0 ndmin 2 N/A block N/A N/A np vstack N/A block stim_ch N/A N/A _mult_cal_one data_view block idx None mult N/A verbose N/A EpochsKIT N/A _BaseEpochs N/A N/A Epochs Array object from KIT SQD file

    Parameters
    ----------
    input_fname : str
        Path to the sqd file.
    events : str | array, shape (n_events, 3)
        Path to events file. If array, it is the events typically returned
        by the read_events function. If some events don't match the events
        of interest as specified by event_id,they will be marked as 'IGNORED'
        in the drop log.
    event_id : int | list of int | dict | None
        The id of the event to consider. If dict,
        the keys can later be used to access associated events. Example:
        dict(auditory=1, visual=3). If int, a dict will be created with
        the id as string. If a list, all events with the IDs specified
        in the list are used. If None, all events will be used with
        and a dict is created with string integer names corresponding
        to the event id integers.
    tmin : float
        Start time before event.
    baseline : None or tuple of length 2 (default (None, 0))
        The time interval to apply baseline correction.
        If None do not apply it. If baseline is (a, b)
        the interval is between "a (s)" and "b (s)".
        If a is None the beginning of the data is used
        and if b is None then b is set to the end of the interval.
        If baseline is equal to (None, None) all the time
        interval is used.
        The baseline (a, b) includes both endpoints, i.e. all
        timepoints t such that a <= t <= b.
    reject : dict | None
        Rejection parameters based on peak-to-peak amplitude.
        Valid keys are 'grad' | 'mag' | 'eeg' | 'eog' | 'ecg'.
        If reject is None then no rejection is done. Example::

            reject = dict(grad=4000e-13, # T / m (gradiometers)
                          mag=4e-12, # T (magnetometers)
                          eeg=40e-6, # V (EEG channels)
                          eog=250e-6 # V (EOG channels)
                          )
    flat : dict | None
        Rejection parameters based on flatness of signal.
        Valid keys are 'grad' | 'mag' | 'eeg' | 'eog' | 'ecg', and values
        are floats that set the minimum acceptable peak-to-peak amplitude.
        If flat is None then no rejection is done.
    reject_tmin : scalar | None
        Start of the time window used to reject epochs (with the default None,
        the window will start with tmin).
    reject_tmax : scalar | None
        End of the time window used to reject epochs (with the default None,
        the window will end with tmax).
    mrk : None | str | array_like, shape = (5, 3) | list of str or array_like
        Marker points representing the location of the marker coils with
        respect to the MEG Sensors, or path to a marker file.
        If list, all of the markers will be averaged together.
    elp : None | str | array_like, shape = (8, 3)
        Digitizer points representing the location of the fiducials and the
        marker coils with respect to the digitized head shape, or path to a
        file containing these points.
    hsp : None | str | array, shape = (n_points, 3)
        Digitizer head shape points, or path to head shape file. If more than
        10`000 points are in the head shape, they are automatically decimated.
    verbose : bool, str, int, or None
        If not None, override default verbose level (see mne.verbose).

    Notes
    -----
    ``elp`` and ``hsp`` are usually the exported text files (*.txt) from the
    Polhemus FastScan system. hsp refers to the headshape surface points. elp
    refers to the points in head-space that corresponds to the HPI points.
    Currently, '*.elp' and '*.hsp' files are NOT supported.

    See Also
    --------
    mne.Epochs : Documentation of attribute and methods.
     __init__ N/A N/A self input_fname events event_id tmin baseline reject flat reject_tmin reject_tmax mrk elp hsp verbose N/A None 0 None None None None None None None None None N/A N/A N/A isinstance events string_types N/A N/A events N/A read_events events N/A N/A isinstance mrk list N/A N/A mrk N/A N/A N/A isinstance marker string_types N/A read_mrk marker marker N/A marker mrk N/A mrk N/A N/A np mean mrk axis 0 N/A N/A N/A mrk None N/A elp None N/A hsp None N/A N/A N/A dig_points dev_head_t N/A _set_dig_kit mrk elp hsp N/A N/A N/A self info N/A dig dig_points N/A N/A N/A self info N/A dev_head_t dev_head_t N/A N/A N/A N/A mrk None N/A elp None N/A hsp None N/A N/A err mrk, elp and hsp need to be provided as a group (all or none) N/A N/A ValueError err N/A N/A N/A logger info N/A Extracting KIT Parameters from %s... input_fname N/A input_fname N/A N/A op abspath input_fname N/A N/A N/A self info kit_info N/A get_kit_info input_fname N/A N/A self _raw_extras N/A kit_info N/A N/A N/A len events N/A N/A N/A self _raw_extras N/A 0 N/A n_epochs N/A N/A N/A ValueError Event list does not match number of epochs. N/A N/A N/A N/A N/A self _raw_extras N/A 0 N/A acq_type 3 N/A N/A N/A N/A N/A self _raw_extras N/A 0 N/A data_offset N/A KIT RAW_OFFSET N/A N/A N/A N/A self _raw_extras N/A 0 N/A data_length N/A KIT INT N/A N/A N/A N/A self _raw_extras N/A 0 N/A dtype h N/A N/A err SQD file contains raw data, not epochs or average. Wrong reader. N/A N/A TypeError err N/A N/A event_id None N/A N/A event_id N/A dict N/A N/A N/A str e N/A int e N/A e N/A N/A np unique N/A events N/A N/A N/A 2 N/A N/A key val N/A N/A event_id items N/A N/A N/A val N/A events N/A N/A N/A 2 N/A N/A N/A ValueError N/A No matching events found for %s (event id %i) N/A key val N/A N/A self _filename input_fname N/A data N/A N/A self _read_kit_data N/A N/A N/A data shape N/A N/A N/A N/A self _raw_extras N/A 0 N/A n_epochs N/A N/A self info N/A nchan N/A N/A N/A self _raw_extras N/A 0 N/A frame_length N/A tmax N/A N/A N/A N/A N/A data shape N/A 2 1 N/A N/A self info N/A sfreq tmin N/A N/A N/A N/A super EpochsKIT self __init__ N/A self info data events event_id tmin tmax baseline reject reject flat flat reject_tmin reject_tmin reject_tmax reject_tmax verbose verbose N/A N/A N/A logger info Ready. N/A verbose _read_kit_data N/A N/A self N/A N/A N/A Read epochs data

        Returns
        -------
        data : array, [channels x samples]
           the data matrix (channels x samples).
        times : array, [samples]
            returns the time values corresponding to the samples.
         N/A epoch_length N/A N/A N/A self _raw_extras N/A 0 N/A frame_length N/A n_epochs N/A N/A N/A self _raw_extras N/A 0 N/A n_epochs N/A n_samples N/A N/A N/A self _raw_extras N/A 0 N/A n_samples N/A N/A open N/A self _filename rb buffering 0 fid N/A N/A data_offset N/A N/A N/A self _raw_extras N/A 0 N/A data_offset N/A dtype N/A N/A N/A self _raw_extras N/A 0 N/A dtype N/A N/A N/A fid seek data_offset N/A data_offset N/A N/A unpack i N/A N/A fid read N/A KIT INT N/A 0 N/A nchan N/A N/A N/A self _raw_extras N/A 0 N/A nchan N/A count N/A n_samples nchan N/A N/A N/A fid seek data_offset N/A data N/A N/A np fromfile fid dtype dtype count count N/A data N/A N/A data reshape N/A n_samples nchan N/A n_sens N/A N/A N/A self _raw_extras N/A 0 N/A n_sens N/A sensor_gain N/A N/A np copy N/A N/A N/A self _raw_extras N/A 0 N/A sensor_gain N/A N/A sensor_gain N/A n_sens N/A N/A sensor_gain N/A n_sens N/A N/A N/A self _raw_extras N/A 0 N/A amp_gain N/A conv_factor N/A N/A np array N/A N/A N/A KIT VOLTAGE_RANGE N/A N/A N/A self _raw_extras N/A 0 N/A DYNAMIC_RANGE sensor_gain ndmin 2 N/A data N/A conv_factor data N/A data N/A data T N/A data N/A N/A data reshape N/A nchan n_epochs epoch_length N/A data N/A N/A data transpose N/A 1 0 2 N/A data N/A N/A _set_dig_kit N/A N/A mrk elp hsp N/A N/A N/A Add landmark points and head shape data to the KIT instance

    Digitizer data (elp and hsp) are represented in [mm] in the Polhemus
    ALS coordinate system.

    Parameters
    ----------
    mrk : None | str | array_like, shape = (5, 3)
        Marker points representing the location of the marker coils with
        respect to the MEG Sensors, or path to a marker file.
    elp : None | str | array_like, shape = (8, 3)
        Digitizer points representing the location of the fiducials and the
        marker coils with respect to the digitized head shape, or path to a
        file containing these points.
    hsp : None | str | array, shape = (n_points, 3)
        Digitizer head shape points, or path to head shape file. If more
        than 10`000 points are in the head shape, they are automatically
        decimated.

    Returns
    -------
    dig_points : list
        List of digitizer points for info['dig'].
    dev_head_t : dict
        A dictionary describe the device-head transformation.
     N/A N/A isinstance hsp string_types N/A N/A hsp N/A _read_dig_points hsp N/A n_pts N/A len hsp N/A N/A n_pts N/A KIT DIG_POINTS N/A N/A hsp N/A _decimate_points hsp res 5 N/A n_new N/A len hsp N/A N/A warn N/A N/A The selected head shape contained {n_in} points, which is more than recommended ({n_rec}), and was automatically downsampled to {n_new} points. The preferred way to downsample is using FastScan. format n_in n_pts n_rec N/A KIT DIG_POINTS n_new n_new N/A N/A isinstance elp string_types N/A N/A elp_points N/A _read_dig_points elp N/A N/A N/A len elp_points 8 N/A N/A N/A ValueError N/A File %r should contain 8 points; got shape %s. N/A elp N/A elp_points shape N/A elp elp_points N/A N/A N/A N/A len elp 8 N/A N/A N/A ValueError N/A ELP should contain 8 points; got shape %s. N/A N/A elp shape N/A N/A isinstance mrk string_types N/A N/A mrk N/A read_mrk mrk N/A hsp N/A apply_trans als_ras_trans_mm hsp N/A elp N/A apply_trans als_ras_trans_mm elp N/A mrk N/A apply_trans als_ras_trans mrk N/A N/A nasion lpa rpa N/A elp N/A 3 N/A nmtrans N/A get_ras_to_neuromag_trans nasion lpa rpa N/A elp N/A apply_trans nmtrans elp N/A hsp N/A apply_trans nmtrans hsp N/A trans N/A fit_matched_points tgt_pts N/A elp N/A 3 src_pts mrk out trans N/A N/A nasion lpa rpa N/A elp N/A 3 N/A elp N/A elp N/A 3 N/A dig_points N/A _make_dig_points nasion lpa rpa elp hsp N/A dev_head_t N/A Transform meg head trans N/A N/A dig_points dev_head_t N/A get_kit_info N/A N/A rawfile N/A N/A N/A Extracts all the information from the sqd file.

    Parameters
    ----------
    rawfile : str
        KIT file to be read.

    Returns
    -------
    info : instance of Info
        An Info for the instance.
    sqd : dict
        A dict containing all the sqd parameter settings.
     N/A sqd N/A dict N/A N/A sqd N/A rawfile rawfile N/A N/A open rawfile rb buffering 0 fid N/A N/A N/A N/A fid seek N/A KIT BASIC_INFO N/A basic_offset N/A N/A unpack i N/A N/A fid read N/A KIT INT N/A 0 N/A N/A N/A fid seek basic_offset N/A N/A N/A fid seek N/A N/A KIT INT 2 SEEK_CUR N/A sysid N/A N/A unpack i N/A N/A fid read N/A KIT INT N/A 0 N/A sysname N/A unpack 128s N/A N/A fid read N/A KIT STRING N/A sysname N/A N/A N/A N/A N/A N/A sysname N/A 0 decode split N/A 0 N/A N/A sysid KIT_CONSTANTS N/A N/A N/A NotImplementedError N/A Data from the KIT system %s (ID %s) can not currently be read, please contact the MNE-Python developers. N/A sysname sysid N/A KIT_SYS N/A KIT_CONSTANTS N/A sysid N/A N/A sysid SYSNAMES N/A N/A N/A sysname N/A SYSNAMES N/A sysid N/A N/A N/A warn N/A KIT file %s has system-name %r, expected %r N/A rawfile sysname N/A SYSNAMES N/A sysid N/A N/A N/A fid seek N/A KIT STRING SEEK_CUR N/A N/A sqd N/A nchan N/A N/A unpack i N/A N/A fid read N/A KIT INT N/A 0 N/A N/A N/A fid seek N/A KIT_SYS CHAN_LOC_OFFSET N/A chan_offset N/A N/A unpack i N/A N/A fid read N/A KIT INT N/A 0 N/A chan_size N/A N/A unpack i N/A N/A fid read N/A KIT INT N/A 0 N/A N/A N/A fid seek chan_offset N/A sensors N/A N/A i N/A range N/A KIT_SYS N_SENS N/A N/A N/A N/A fid seek N/A chan_offset N/A chan_size i N/A sens_type N/A N/A unpack i N/A N/A fid read N/A KIT INT N/A 0 N/A N/A sens_type 1 N/A N/A N/A N/A sensors append N/A N/A np fromfile fid dtype d count 6 N/A N/A N/A sens_type 2 N/A N/A N/A N/A sensors append N/A N/A np fromfile fid dtype d count 7 N/A N/A N/A sens_type 3 N/A N/A N/A N/A sensors append N/A N/A np fromfile fid dtype d count 9 N/A N/A N/A sens_type 257 N/A N/A N/A N/A sensors append N/A N/A np zeros 7 N/A N/A sqd N/A i sens_type N/A N/A sqd N/A sensor_locs N/A N/A np array sensors N/A N/A N/A fid seek N/A KIT_SYS AMPLIFIER_INFO N/A amp_offset N/A N/A unpack i N/A N/A fid read N/A KIT_SYS INT N/A 0 N/A N/A N/A fid seek amp_offset N/A amp_data N/A N/A unpack i N/A N/A fid read N/A KIT_SYS INT N/A 0 N/A gain1 N/A N/A KIT_SYS GAINS N/A N/A N/A N/A KIT_SYS GAIN1_MASK amp_data N/A KIT_SYS GAIN1_BIT N/A gain2 N/A N/A KIT_SYS GAINS N/A N/A N/A N/A KIT_SYS GAIN2_MASK amp_data N/A KIT_SYS GAIN2_BIT N/A N/A KIT_SYS GAIN3_BIT N/A N/A gain3 N/A N/A KIT_SYS GAINS N/A N/A N/A N/A KIT_SYS GAIN3_MASK amp_data N/A KIT_SYS GAIN3_BIT N/A N/A sqd N/A amp_gain N/A N/A gain1 gain2 gain3 N/A N/A N/A sqd N/A amp_gain N/A gain1 gain2 N/A N/A sqd N/A lowpass N/A N/A KIT_SYS LPFS N/A N/A N/A N/A KIT_SYS LPF_MASK amp_data N/A KIT_SYS LPF_BIT N/A N/A sqd N/A highpass N/A N/A KIT_SYS HPFS N/A N/A N/A N/A KIT_SYS HPF_MASK amp_data N/A KIT_SYS HPF_BIT N/A N/A sqd N/A notch N/A N/A KIT_SYS BEFS N/A N/A N/A N/A KIT_SYS BEF_MASK amp_data N/A KIT_SYS BEF_BIT N/A N/A N/A fid seek N/A KIT_SYS CHAN_SENS N/A sens_offset N/A N/A unpack i N/A N/A fid read N/A KIT_SYS INT N/A 0 N/A N/A N/A fid seek sens_offset N/A sens N/A N/A np fromfile fid dtype d count N/A N/A sqd N/A nchan 2 N/A N/A sens shape N/A N/A sqd N/A nchan 2 N/A N/A sqd N/A sensor_gain N/A N/A np ones N/A KIT_SYS NCHAN N/A N/A N/A sqd N/A sensor_gain N/A N/A KIT_SYS N_SENS N/A sens N/A N/A N/A KIT_SYS N_SENS N/A 1 N/A N/A N/A fid seek N/A KIT_SYS SAMPLE_INFO N/A acqcond_offset N/A N/A unpack i N/A N/A fid read N/A KIT_SYS INT N/A 0 N/A N/A N/A fid seek acqcond_offset N/A acq_type N/A N/A unpack i N/A N/A fid read N/A KIT_SYS INT N/A 0 N/A N/A sqd N/A sfreq N/A N/A unpack d N/A N/A fid read N/A KIT_SYS DOUBLE N/A 0 N/A N/A acq_type 1 N/A N/A N/A N/A fid read N/A KIT_SYS INT N/A N/A sqd N/A n_samples N/A N/A unpack i N/A N/A fid read N/A KIT_SYS INT N/A 0 N/A N/A N/A N/A acq_type 2 N/A acq_type 3 N/A N/A N/A sqd N/A frame_length N/A N/A unpack i N/A N/A fid read N/A KIT_SYS INT N/A 0 N/A N/A sqd N/A pretrigger_length N/A N/A unpack i N/A N/A fid read N/A KIT_SYS INT N/A 0 N/A N/A sqd N/A average_count N/A N/A unpack i N/A N/A fid read N/A KIT_SYS INT N/A 0 N/A N/A sqd N/A n_epochs N/A N/A unpack i N/A N/A fid read N/A KIT_SYS INT N/A 0 N/A N/A sqd N/A n_samples N/A N/A sqd N/A frame_length N/A sqd N/A n_epochs N/A N/A err Your file is neither continuous nor epoched data. What type of file is it?! N/A N/A TypeError err N/A N/A sqd N/A n_sens N/A KIT_SYS N_SENS N/A N/A sqd N/A nmegchan N/A KIT_SYS NMEGCHAN N/A N/A sqd N/A nmiscchan N/A KIT_SYS NMISCCHAN N/A N/A sqd N/A DYNAMIC_RANGE N/A KIT_SYS DYNAMIC_RANGE N/A N/A sqd N/A acq_type acq_type N/A info N/A _empty_info N/A float N/A sqd N/A sfreq N/A N/A N/A info update meas_date N/A int N/A N/A time time lowpass N/A sqd N/A lowpass highpass N/A sqd N/A highpass filename rawfile buffer_size_sec 1.0 N/A N/A N/A logger info Setting channel info structure... N/A ch_names N/A N/A N/A ch_names N/A MEG N/A N/A MEG %03d ch N/A ch N/A range 1 N/A N/A sqd N/A n_sens 1 N/A N/A ch_names N/A MISC N/A N/A MISC %03d ch N/A ch N/A range 1 N/A N/A sqd N/A nmiscchan 1 N/A locs N/A sqd N/A sensor_locs N/A chan_locs N/A apply_trans als_ras_trans N/A locs N/A N/A N/A 3 N/A chan_angles N/A locs N/A N/A N/A 3 N/A N/A info N/A chs N/A N/A N/A idx ch_info N/A enumerate N/A zip N/A ch_names N/A MEG chan_locs chan_angles 1 N/A N/A N/A ch_name ch_loc ch_angles ch_info N/A chan_info N/A N/A N/A chan_info N/A cal N/A KIT CALIB_FACTOR N/A N/A chan_info N/A logno idx N/A N/A chan_info N/A scanno idx N/A N/A chan_info N/A range N/A KIT RANGE N/A N/A chan_info N/A unit_mul N/A KIT UNIT_MUL N/A N/A chan_info N/A ch_name ch_name N/A N/A chan_info N/A unit N/A FIFF FIFF_UNIT_T N/A N/A chan_info N/A coord_frame N/A FIFF FIFFV_COORD_DEVICE N/A N/A idx N/A sqd N/A nmegchan N/A N/A N/A chan_info N/A coil_type N/A FIFF FIFFV_COIL_KIT_GRAD N/A N/A chan_info N/A kind N/A FIFF FIFFV_MEG_CH N/A N/A N/A chan_info N/A coil_type N/A FIFF FIFFV_COIL_KIT_REF_MAG N/A N/A chan_info N/A kind N/A FIFF FIFFV_REF_MEG_CH N/A ch_angles N/A N/A np radians ch_angles N/A x N/A N/A N/A np sin N/A ch_angles N/A 0 N/A N/A np cos N/A ch_angles N/A 1 N/A y N/A N/A N/A np sin N/A ch_angles N/A 0 N/A N/A np sin N/A ch_angles N/A 1 N/A z N/A N/A np cos N/A ch_angles N/A 0 N/A vec_z N/A N/A np array N/A x y z N/A length N/A N/A linalg norm vec_z N/A vec_z length N/A vec_x N/A N/A np zeros N/A vec_z size dtype N/A np float N/A N/A N/A vec_z N/A 1 N/A vec_z N/A 2 N/A N/A N/A N/A vec_z N/A 0 N/A vec_z N/A 1 N/A N/A N/A vec_x N/A 0 1.0 N/A N/A N/A vec_x N/A 1 1.0 N/A N/A N/A N/A vec_z N/A 0 N/A vec_z N/A 2 N/A N/A N/A vec_x N/A 0 1.0 N/A N/A N/A vec_x N/A 2 1.0 N/A vec_x N/A N/A N/A np sum N/A vec_x vec_z vec_z N/A length N/A N/A linalg norm vec_x N/A vec_x length N/A vec_y N/A N/A np cross vec_z vec_x N/A vecs N/A N/A np vstack N/A vec_x vec_y vec_z N/A vecs N/A apply_trans als_ras_trans vecs N/A N/A chan_info N/A loc N/A N/A N/A N/A np vstack N/A ch_loc vecs ravel N/A N/A N/A N/A info N/A chs append chan_info N/A N/A idy ch_name N/A enumerate N/A ch_names N/A MISC N/A N/A sqd N/A n_sens 1 N/A N/A chan_info N/A N/A N/A chan_info N/A cal N/A KIT CALIB_FACTOR N/A N/A chan_info N/A logno idy N/A N/A chan_info N/A scanno idy N/A N/A chan_info N/A range 1.0 N/A N/A chan_info N/A unit N/A FIFF FIFF_UNIT_V N/A N/A chan_info N/A unit_mul 0 N/A N/A chan_info N/A ch_name ch_name N/A N/A chan_info N/A coil_type N/A FIFF FIFFV_COIL_NONE N/A N/A chan_info N/A loc N/A N/A np zeros 12 N/A N/A chan_info N/A kind N/A FIFF FIFFV_MISC_CH N/A N/A N/A N/A info N/A chs append chan_info N/A N/A N/A info _update_redundant N/A N/A info sqd N/A read_raw_kit N/A N/A input_fname mrk elp hsp stim slope stimthresh preload stim_code verbose N/A None None None > - 1 False binary None N/A N/A Reader function for KIT conversion to FIF

    Parameters
    ----------
    input_fname : str
        Path to the sqd file.
    mrk : None | str | array_like, shape (5, 3) | list of str or array_like
        Marker points representing the location of the marker coils with
        respect to the MEG Sensors, or path to a marker file.
        If list, all of the markers will be averaged together.
    elp : None | str | array_like, shape (8, 3)
        Digitizer points representing the location of the fiducials and the
        marker coils with respect to the digitized head shape, or path to a
        file containing these points.
    hsp : None | str | array, shape (n_points, 3)
        Digitizer head shape points, or path to head shape file. If more than
        10,000 points are in the head shape, they are automatically decimated.
    stim : list of int | '<' | '>'
        Channel-value correspondence when converting KIT trigger channels to a
        Neuromag-style stim channel. For '<', the largest values are assigned
        to the first channel (default). For '>', the largest values are
        assigned to the last channel. Can also be specified as a list of
        trigger channel indexes.
    slope : '+' | '-'
        How to interpret values on KIT trigger channels when synthesizing a
        Neuromag-style stim channel. With '+', a positive slope (low-to-high)
        is interpreted as an event. With '-', a negative slope (high-to-low)
        is interpreted as an event.
    stimthresh : float
        The threshold level for accepting voltage changes in KIT trigger
        channels as a trigger event.
    preload : bool
        If True, all data are loaded at initialization.
        If False, data are not read until save.
    stim_code : 'binary' | 'channel'
        How to decode trigger values from stim channels. 'binary' read stim
        channel events as binary code, 'channel' encodes channel number.
    verbose : bool, str, int, or None
        If not None, override default verbose level (see mne.verbose).

    Returns
    -------
    raw : Instance of RawKIT
        A Raw object containing KIT data.

    See Also
    --------
    mne.io.Raw : Documentation of attribute and methods.
     N/A N/A RawKIT input_fname input_fname mrk mrk elp elp hsp hsp stim stim slope slope stimthresh stimthresh preload preload stim_code stim_code verbose verbose N/A read_epochs_kit N/A N/A input_fname events event_id mrk elp hsp verbose N/A None None None None None N/A N/A Reader function for KIT epochs files

    Parameters
    ----------
    input_fname : str
        Path to the sqd file.
    events : array, shape (n_events, 3)
        The events typically returned by the read_events function.
        If some events don't match the events of interest as specified
        by event_id, they will be marked as 'IGNORED' in the drop log.
    event_id : int | list of int | dict | None
        The id of the event to consider. If dict,
        the keys can later be used to access associated events. Example:
        dict(auditory=1, visual=3). If int, a dict will be created with
        the id as string. If a list, all events with the IDs specified
        in the list are used. If None, all events will be used with
        and a dict is created with string integer names corresponding
        to the event id integers.
    mrk : None | str | array_like, shape (5, 3) | list of str or array_like
        Marker points representing the location of the marker coils with
        respect to the MEG Sensors, or path to a marker file.
        If list, all of the markers will be averaged together.
    elp : None | str | array_like, shape (8, 3)
        Digitizer points representing the location of the fiducials and the
        marker coils with respect to the digitized head shape, or path to a
        file containing these points.
    hsp : None | str | array, shape (n_points, 3)
        Digitizer head shape points, or path to head shape file. If more than
        10,000 points are in the head shape, they are automatically decimated.
    verbose : bool, str, int, or None
        If not None, override default verbose level (see mne.verbose).

    Returns
    -------
    epochs : instance of Epochs
        The epochs.

    Notes
    -----
    .. versionadded:: 0.9.0
     N/A epochs N/A EpochsKIT input_fname input_fname events events event_id event_id mrk mrk elp elp hsp hsp verbose verbose N/A epochs N/A