mri_cor_io.cpp

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//=============================================================================================================
 
//=============================================================================================================
// INCLUDES
//=============================================================================================================
 
#include "mri_cor_io.h"
 
#include <fiff/fiff_coord_trans.h>
#include <fiff/fiff_constants.h>
#include <fiff/fiff_file.h>
 
//=============================================================================================================
// QT INCLUDES
//=============================================================================================================
 
#include <QDir>
#include <QFile>
#include <QDebug>
 
//=============================================================================================================
// EIGEN INCLUDES
//=============================================================================================================
 
#include <Eigen/Core>
 
//=============================================================================================================
// USED NAMESPACES
//=============================================================================================================
 
using namespace MRILIB;
using namespace FIFFLIB;
using namespace Eigen;
 
//=============================================================================================================
// DEFINE MEMBER METHODS
//=============================================================================================================
 
bool MriCorIO::read(const QString& dir,
                    QVector<MriSlice>& slices,
                    bool verbose)
{
    //
    // COR files contain 256 coronal slices of 256×256 unsigned chars (1mm isotropic).
    //
    // The coordinate system is:
    //   - Coronal orientation
    //   - 1mm pixel spacing
    //   - Origin offset: (0.128, -0.128, 0.128) meters
    //   - Rotation: x -> -x, y -> z, z -> y (coronal to MRI surface RAS)
    //
    // Ported from make_cor_set() in mne_make_cor_set/make_cor_set.c
    //
 
    int nPixels = COR_WIDTH * COR_HEIGHT;
 
    slices.resize(COR_NSLICE);
 
    for (int k = 0; k < COR_NSLICE; ++k) {
        QString fileName = QString("%1/COR-%2").arg(dir).arg(k + 1, 3, 10, QChar('0'));
        QFile file(fileName);
 
        if (!file.open(QIODevice::ReadOnly)) {
            qCritical() << "MriCorIO::read - Could not open COR file" << fileName;
            return false;
        }
 
        QByteArray data = file.readAll();
        file.close();
 
        if (data.size() < nPixels) {
            qCritical() << "MriCorIO::read - COR file" << fileName << "is too small:"
                         << data.size() << "bytes (expected" << nPixels << ")";
            return false;
        }
 
        MriSlice& slice = slices[k];
        slice.fileName = fileName;
        slice.width = COR_WIDTH;
        slice.height = COR_HEIGHT;
        slice.dimx = COR_PIXEL_SIZE;
        slice.dimy = COR_PIXEL_SIZE;
        slice.scale = 1.0f;
        slice.pixelFormat = FIFFV_MRI_PIXEL_BYTE;
 
        // Copy pixel data
        slice.pixels.resize(nPixels);
        memcpy(slice.pixels.data(), data.constData(), nPixels);
 
        // Build the coordinate transformation: slice -> MRI (surface RAS)
        // Ported from the original C code in make_cor_set.c:
        //   move[X] = 0.128; move[Y] = -0.128 + k/1000.0; move[Z] = 0.128;
        //   rot = {{-1,0,0},{0,0,1},{0,1,0}};
        Matrix3f rot;
        rot << -1.0f,  0.0f,  0.0f,
                0.0f,  0.0f,  1.0f,
                0.0f,  1.0f,  0.0f;
 
        Eigen::Vector3f move;
        move << 0.128f, -0.128f + static_cast<float>(k) / 1000.0f, 0.128f;
 
        slice.trans = FiffCoordTrans(FIFFV_COORD_MRI_SLICE, FIFFV_COORD_MRI, rot, move);
    }
 
    if (verbose) {
        printf("Read %d COR slices from %s\n", COR_NSLICE, qPrintable(dir));
    }
 
    return true;
}