How to replace SURF with FREAK in Features2D + Homography example??

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FREAK will only extract descriptors. You need to detect features points first, for instance using FAST. Here is a small sample of what you could do:

cv::FastFeatureDetector detector(50);
cv::FREAK extractor;

std::vector<cv::KeyPoint> keypoints;
cv::Mat descriptors;

detector.detect(img, keypoints);
extractor.compute(img, keypoints, descriptors);

Notice that FREAK extracts binary descriptors, which is different than SURF.

Hope it helps.