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imho, you're calculating something different, than compare() / countNonzero().

try:

uchar s1 = mat1.at<uchar>(y,x);
uchar s2 = mat2.at<uchar>(y,x);
score += (s1 == s2);

imho, you're calculating something different, than compare() / countNonzero().

try:

uchar s1 = mat1.at<uchar>(y,x);
uchar s2 = mat2.at<uchar>(y,x);
score += (s1 == s2);

score += (s1.val[0]/255)*(s2.val[0]/255);