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FiffRawData

Namespace: FIFFLIB  ·  Library: FIFF Library

Python equivalent

mne.io.Raw in MNE-Python.

#include <fiff/fiff_raw_data.h>

class FiffRawData

Public Methods​

FiffRawData()​

Default constructor.

FiffRawData(p_FiffRawData)​

Copy constructor.

Parameters:

  • p_FiffRawData : const FiffRawData & FIFF raw measurement which should be copied.

FiffRawData(p_IODevice)​

Constructs fiff raw data, by reading from a IO device.

Parameters:

  • p_IODevice : QIODevice & IO device to read the raw data from .

FiffRawData(p_IODevice, b_littleEndian)​

Constructs fiff raw data, by reading from a IO device with specified endianness.

Parameters:

  • p_IODevice : QIODevice & IO device to read the raw data from.

  • b_littleEndian : bool If true, read data as little-endian.

~FiffRawData()​

Destroys the FiffInfo.

clear()​

Initializes the fiff raw measurement data.

isEmpty()​

True if fiff raw data are empty.

Returns:

  • bool — true if fiff raw data are empty.

read_raw_segment(data, times, from, to, sel, do_debug)​

Read a specific raw data segment.

Parameters:

  • data : Eigen::MatrixXd & returns the data matrix (channels x samples).

  • times : Eigen::MatrixXd & returns the time values corresponding to the samples.

  • from : fiff_int_t first sample to include. If omitted, defaults to the first sample in data (optional).

  • to : fiff_int_t last sample to include. If omitted, defaults to the last sample in data (optional).

  • sel : const Eigen::RowVectorXi & channel selection vector (optional).

Returns:

  • bool — true if succeeded, false otherwise.

read_raw_segment(data, times, multSegment, from, to, sel, do_debug)​

Read a specific raw data segment.

Parameters:

  • data : Eigen::MatrixXd & returns the data matrix (channels x samples).

  • times : Eigen::MatrixXd & returns the time values corresponding to the samples.

  • multSegment : Eigen::SparseMatrix< double > & used multiplication matrix (compensator,projection,calibration).

  • from : fiff_int_t first sample to include. If omitted, defaults to the first sample in data (optional).

  • to : fiff_int_t last sample to include. If omitted, defaults to the last sample in data (optional).

  • sel : const Eigen::RowVectorXi & channel selection vector (optional).

Returns:

  • bool — true if succeeded, false otherwise.

read_raw_segment_times(data, times, from, to, sel)​

Read a specific raw data segment.

Parameters:

  • data : Eigen::MatrixXd & returns the data matrix (channels x samples).

  • times : Eigen::MatrixXd & returns the time values corresponding to the samples.

  • from : float starting time of the segment in seconds.

  • to : float end time of the segment in seconds.

  • sel : const Eigen::RowVectorXi & optional channel selection vector.

Returns:

  • bool — true if succeeded, false otherwise.

save(p_IODevice, picks, decim, from, to)​

Save raw data to a FIFF file, optionally with decimation and channel picking.

Ported from save.c (MNE-C).

Parameters:

  • p_IODevice : QIODevice & Output device to write to.

  • picks : const Eigen::RowVectorXi & Channel indices to include (empty = all channels).

  • decim : int Decimation factor (1 = no decimation).

  • from : int First sample to save (-1 = from start of raw data).

  • to : int Last sample to save (-1 = to end of raw data).

Returns:

  • bool — true on success.

Example​

Source: src/examples/ex_read_raw/main.cpp

#include <iostream>
#include <vector>
#include <math.h>

#include <fiff/fiff.h>
#include <mne/mne.h>
#include <utils/generics/mne_logger.h>

//=============================================================================================================
// QT INCLUDES
//=============================================================================================================

#include <QtCore/QCoreApplication>
#include <QCommandLineParser>
#include <QFile>

//=============================================================================================================
// USED NAMESPACES
//=============================================================================================================

using namespace FIFFLIB;
using namespace MNELIB;
using namespace UTILSLIB;
using namespace Eigen;

//=============================================================================================================
// MAIN
//=============================================================================================================

//=============================================================================================================

/**
 * The function main marks the entry point of the program.
 * By default, main has the storage class extern.
 *
 * @param[in] argc (argument count) is an integer that indicates how many arguments were entered on the command line when the program was started.
 * @param[in] argv (argument vector) is an array of pointers to arrays of character objects. The array objects are null-terminated strings, representing the arguments that were entered on the command line when the program was started.
 * @return the value that was set to exit() (which is 0 if exit() is called via quit()).
 */
int main(int argc, char *argv[])
{
    qInstallMessageHandler(MNELogger::customLogWriter);
    QCoreApplication app(argc, argv);

    // Command Line Parser
    QCommandLineParser parser;
    parser.setApplicationDescription("Read Raw Example");
    parser.addHelpOption();

    QCommandLineOption inputOption("fileIn", "The input file <in>.", "in", QCoreApplication::applicationDirPath() + "/../resources/data/MNE-sample-data/MEG/sample/sample_audvis_raw.fif");
    QCommandLineOption fromOption("from", "Read data from <from> (in seconds).", "from", "42.956");
    QCommandLineOption toOption("to", "Read data from <to> (in seconds).", "to", "320.670");
    QCommandLineOption inSamplesOption("inSamples", "Timing is set in samples.", "inSamples", "false");
    QCommandLineOption keepCompOption("keepComp", "Keep compensators.", "keepComp", "false");

    parser.addOption(inputOption);
    parser.addOption(fromOption);
    parser.addOption(toOption);
    parser.addOption(inSamplesOption);
    parser.addOption(keepCompOption);

    parser.process(app);

    QFile t_fileRaw(parser.value(inputOption));

    float from = parser.value(fromOption).toFloat();
    float to = parser.value(toOption).toFloat();

    bool in_samples = false;
    if(parser.value(inSamplesOption) == "false" || parser.value(inSamplesOption) == "0") {
        in_samples = false;
    } else if(parser.value(inSamplesOption) == "true" || parser.value(inSamplesOption) == "1") {
        in_samples = true;
    }

    bool keep_comp = false;
    if(parser.value(keepCompOption) == "false" || parser.value(keepCompOption) == "0") {
        keep_comp = false;
    } else if(parser.value(keepCompOption) == "true" || parser.value(keepCompOption) == "1") {
        keep_comp = true;
    }

    //
    //   Setup for reading the raw data
    //
    FiffRawData raw(t_fileRaw);

    //
    //   Set up pick list: MEG + STI 014 - bad channels
    //
    //
    QStringList include;
    include << "STI 014";
    bool want_meg   = true;
    bool want_eeg   = false;
    bool want_stim  = false;

    RowVectorXi picks = raw.info.pick_types(want_meg, want_eeg, want_stim, include, raw.info.bads);

    //
    //   Set up projection
    //
    qint32 k = 0;
    if (raw.info.projs.size() == 0)
        qInfo("No projector specified for these data\n");
    else
    {
        //
        //   Activate the projection items
        //
        for (k = 0; k < raw.info.projs.size(); ++k)
            raw.info.projs[k].active = true;

        qInfo("%lld projection items activated\n",
              static_cast<long long>(raw.info.projs.size()));
        //
        //   Create the projector
        //
        fiff_int_t nproj = raw.info.make_projector(raw.proj);

        if (nproj == 0)
            qWarning("The projection vectors do not apply to these channels\n");
        else
            qInfo("Created an SSP operator (subspace dimension = %d)\n",nproj);
    }

    //
    //   Set up the CTF compensator
    //
    qint32 current_comp = raw.info.get_current_comp();
    qint32 dest_comp = 0;

    if (current_comp > 0)
        qInfo("Current compensation grade : %d\n",current_comp);

    if (keep_comp)
        dest_comp = current_comp;

    if (current_comp != dest_comp)
    {
        if(MNE::make_compensator(raw.info, current_comp, dest_comp, raw.comp))
        {
            raw.info.set_current_comp(dest_comp);
            qInfo("Appropriate compensator added to change to grade %d.\n",dest_comp);
        }
        else
        {
            qWarning("Could not make the compensator\n");
            return -1;
        }
    }
    //
    //   Read a data segment
    //   times output argument is optional
    //
    bool readSuccessful = false;
    MatrixXd data;
    MatrixXd times;
    if (in_samples)
        readSuccessful = raw.read_raw_segment(data, times, (qint32)from, (qint32)to, picks);
    else
        readSuccessful = raw.read_raw_segment_times(data, times, from, to, picks);

    if (!readSuccessful)
    {
        qWarning("Could not read raw segment.\n");
        return -1;
    }

    qInfo("Read %d samples.\n",(qint32)data.cols());

    std::cout << data.block(0,0,10,10) << std::endl;

    return app.exec();
}

//=============================================================================================================
// STATIC DEFINITIONS
//=============================================================================================================

Authors of this file​