Your question is really badly explained but I think I've understood what you want.
My understanding is that you have a J matrix where the odd rows are labeled 1 and even rows labeled 2. For each column, you want to sum the sorted odd rows over a non-overlapping sliding window of length K and divide that by the corresponding sum over the sorted even rows.
If so:
%J: a matrix whose number of rows is a multiple of 2*K.
%K: an integer, the window size
assert(mod(size(J, 1) / 2, K) == 0, 'Height of J is not a multiple of 2*K')
result = zeros(size(J, 1) / 2 / K, size(J, 2)); %preallocate result
for col = 1:size(J, 2) %loop over the columns. You can't do this without a loop due to the requirement to sort each columns separately
result(:, col) = sum(reshape(sort(J(1:2:end, col)), K, []), 1) ./ sum(reshape(sort(J(2:2:end, col)), K, []), 1); %sort even/odd rows, reshape each into a Kx? matrix, sum across rows and divide the two sums
end
