For those of you wondering about the paper, it's:
Rectangle Detection based on a Windowed Hough Transform by Cláudio Rosito Jung and Rodrigo Schramm.
Now according to the paper, the intersection points are expressed as polar coordinates, obviously you implementation may be different (the only way to tell is to show us your code).
Assuming you are being consistent with his notation, your peaks should be expressed as:
You must then perform peak paring given by equation (3) in section 4.3 or
where represents the angular threshold corresponding to parallel lines
and is the normalized threshold corresponding to lines of similar length.
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