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namespaces míght help:

// myfreak.h

#include "opencv/features2d/features2d.hpp"

namespace my {
    struct FREAK {
         ...
    };
}

// myfreak.cpp

#include "opencv/highgui/highgui.hpp"
#include "freak.h"
namespace my {
    // FREAK impl
}

// main.cpp

#include "opencv/highgui/highgui.hpp"
#include "freak.h"

int main() {
   my::FREAK;
   cv::SURF;
}