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zeros(int ndims, const int* sz, int type) is the old api, referred to as the C-api to create the zeros array.
zeros(Size size, int type) is the new api preferred since openCV2.0, referring to the C++ implementation where pointers are not the way to go anymore :) It's made easier for you so I suggest using the C++ interface, since this is the direction new developments are going also.
