IMU.h

class IMU {
public:
    // Scaled readings
    virtual vector readMag() = 0;  // In body coords, scaled to -1..1 range
    virtual vector readAcc() = 0;  // In body coords, with units = g
    virtual vector readGyro() = 0; // In body coords, with units = rad/sec
    void read(){ readAcc(); readMag(); readGyro(); }

    virtual void measureOffsets() = 0;
    virtual void enable() = 0;
    virtual void loadCalibration() = 0;

    vector gyro_offset;
    matrix calMatrix;
    vector calOffset;

    int_vector raw_m, raw_a, raw_g;
};

MinIMU9.cpp

void MinIMU9::loadCalibration()
{
    wordexp_t expansion_result;
    wordexp("~/.ahrs-cal", &expansion_result, 0);

    std::ifstream file(expansion_result.we_wordv[0]);
    if (file.fail())
    {
        throw posix_error("Failed to open calibration file ~/.ahrs-cal.");
    }

    file >> calMatrix(0,0) >> calMatrix(0,1) >> calMatrix(0,2);
    file >> calMatrix(1,0) >> calMatrix(1,1) >> calMatrix(1,2);
    file >> calMatrix(2,0) >> calMatrix(2,1) >> calMatrix(2,2);

    file >> calOffset(0) >> calOffset(1) >> calOffset(2);

    if (file.fail() || file.bad())
    {
        throw std::runtime_error("Failed to parse calibration file ~/.minimu9-ahrs-cal.");
    }

}

vector MinIMU9::readMag()
{
    compass.readMag();
    IMU::raw_m = int_vector_from_ints(&compass.m);

    vector v;
    v = IMU::raw_m.cast<float>() - calOffset;
    v = calMatrix * v;

    return v;
}

Wait... Just figured it out: you posted your alterations to David's code. Now I get it... Sorry.