mri_cor_fif_io.cpp

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//=============================================================================================================
 
//=============================================================================================================
// INCLUDES
//=============================================================================================================
 
#include "mri_cor_fif_io.h"
 
#include <fiff/fiff_stream.h>
#include <fiff/fiff_tag.h>
#include <fiff/fiff_coord_trans.h>
#include <fiff/fiff_file.h>
#include <fiff/fiff_constants.h>
 
//=============================================================================================================
// QT INCLUDES
//=============================================================================================================
 
#include <QFile>
#include <QDebug>
 
//=============================================================================================================
// EIGEN INCLUDES
//=============================================================================================================
 
#include <Eigen/Core>
 
//=============================================================================================================
// USED NAMESPACES
//=============================================================================================================
 
using namespace MRILIB;
using namespace FIFFLIB;
using namespace Eigen;
 
//=============================================================================================================
// DEFINE MEMBER METHODS
//=============================================================================================================
 
bool MriCorFifIO::write(const QString& fileName,
                        const QVector<MriSlice>& slices,
                        const QVector<FiffCoordTrans>& additionalTrans)
{
    //
    // File structure (ported from save_slices() / write_slice() in write_mri_set.c):
    //
    //   FIFFB_MRI
    //     FIFF_BLOCK_ID
    //     FIFFB_MRI_SET
    //       HEAD -> MRI identity transform
    //       Additional transforms (Talairach etc.)
    //       For each slice:
    //         FIFFB_MRI_SLICE
    //           FIFF_MRI_WIDTH
    //           FIFF_MRI_WIDTH_M
    //           FIFF_MRI_HEIGHT
    //           FIFF_MRI_HEIGHT_M
    //           CoordTrans (slice -> MRI)
    //           FIFF_MRI_PIXEL_ENCODING
    //           FIFF_MRI_PIXEL_DATA
    //         /FIFFB_MRI_SLICE
    //     /FIFFB_MRI_SET
    //   /FIFFB_MRI
    //
 
    QFile file(fileName);
    FiffStream::SPtr stream = FiffStream::start_file(file);
 
    if (!stream) {
        qCritical() << "MriCorFifIO::write - Could not open file for writing:" << fileName;
        return false;
    }
 
    // Start MRI block
    stream->start_block(FIFFB_MRI);
    stream->write_id(FIFF_BLOCK_ID);
 
    // Start MRI set block
    stream->start_block(FIFFB_MRI_SET);
 
    // Write identity HEAD -> MRI transform
    // Ported from write_mri_set.c: identity rotation, zero translation
    Matrix3f identityRot = Matrix3f::Identity();
    Vector3f zeroMove = Vector3f::Zero();
    FiffCoordTrans headMriT(
        FIFFV_COORD_HEAD, FIFFV_COORD_MRI, identityRot, zeroMove);
    stream->write_coord_trans(headMriT);
 
    // Write additional transforms (Talairach etc.)
    for (const FiffCoordTrans& t : additionalTrans) {
        stream->write_coord_trans(t);
    }
 
    // Write each slice
    for (int k = 0; k < slices.size(); ++k) {
        const MriSlice& slice = slices[k];
 
        stream->start_block(FIFFB_MRI_SLICE);
 
        // Width and height in pixels
        fiff_int_t w = slice.width;
        fiff_int_t h = slice.height;
        stream->write_int(FIFF_MRI_WIDTH, &w);
 
        float wm = static_cast<float>(slice.width) * slice.dimx;
        stream->write_float(FIFF_MRI_WIDTH_M, &wm);
 
        stream->write_int(FIFF_MRI_HEIGHT, &h);
 
        float hm = static_cast<float>(slice.height) * slice.dimy;
        stream->write_float(FIFF_MRI_HEIGHT_M, &hm);
 
        // Coordinate transform
        stream->write_coord_trans(slice.trans);
 
        // Pixel encoding
        fiff_int_t encoding = slice.pixelFormat;
        stream->write_int(FIFF_MRI_PIXEL_ENCODING, &encoding);
 
        // Pixel data
        auto pixelTag = std::make_unique<FiffTag>();
        pixelTag->kind = FIFF_MRI_PIXEL_DATA;
 
        int nPixels = slice.width * slice.height;
        switch (slice.pixelFormat) {
            case FIFFV_MRI_PIXEL_BYTE: {
                pixelTag->type = FIFFT_BYTE;
                pixelTag->resize(nPixels);
                memcpy(pixelTag->data(), slice.pixels.constData(), nPixels);
                break;
            }
            case FIFFV_MRI_PIXEL_WORD: {
                pixelTag->type = FIFFT_USHORT;
                pixelTag->resize(nPixels * 2);
                memcpy(pixelTag->data(), slice.pixelsWord.constData(), nPixels * 2);
                break;
            }
            case FIFFV_MRI_PIXEL_FLOAT: {
                pixelTag->type = FIFFT_FLOAT;
                pixelTag->resize(nPixels * 4);
                memcpy(pixelTag->data(), slice.pixelsFloat.constData(), nPixels * 4);
                break;
            }
        }
 
        stream->write_tag(pixelTag);
 
        stream->end_block(FIFFB_MRI_SLICE);
    }
 
    // End blocks
    stream->end_block(FIFFB_MRI_SET);
    stream->end_block(FIFFB_MRI);
    stream->end_file();
 
    return true;
}