xcorr question - better align two signals

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I tried to align two signal better using the below code. The s1 and s2 is in the attached txt file. However, td I got is -24482. I am wondering if there is a way to improve this function. Please help!!
function [td,ny]=align_signal(s1,s2)
ny=ones(size(s1))*NaN;
[C21,lag21] = xcorr(s2,s1);
C21 = C21/nanmax(C21);
[M21,I21] = nanmax(C21);
t21 = lag21(I21);
if t21<0
ny(-t21:end) = s1(-t21:end);
else
ny(t21:end)=s1(t21:end);
end
td=abs(t21);

Accepted Answer

Jordan Ross
Jordan Ross on 10 Jan 2017
Hello Fan,
Unfortunately, the MATLAB functions that compute the sample cross-correlation from two provided sequences (such as "xcorr" in the Signal Processing Toolbox) cannot deal with incomplete data.
One possible solution is to find the NaN value's in the signals and to ignore the measurements (at that time value) for both sequences. The following code shows how you can remove those NaN's:
% Remove NaNs
s2NanLoc = find(isnan(s2));
s1NanLoc = find(isnan(s1));
nanLocs = unique([s1NanLoc; s2NanLoc]);
s1(nanLocs) = [];
s2(nanLocs) = [];
When I do this with your dataset I am able to get a "td" of 4.

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