How can I match time series data to times in a different, smaller matrix?

This is not homework, I am doing genuine research. So I have two files, one with data in half hour increments and one with sunrise and sunset times for each day. Basically, I want to be able to say "if its night time, do a certain calculation, if it's day time, do a different calculation" for each day in the 1st data set by referencing the second one based off the date Any help would be appreciated (could be a simple for loop), thanks! below is my code thus far (I know its not pretty):

    %Hudson River Water Quality 1995-2000
    data=xlsread('Hudson_test1.xlsx');
    tm=data(:,1)+datenum(1904,1,1);
    [yr,mo,day,hr,min]=datevec(tm);
    DO_p=data(:,5);
    DO=data(:,6);
    z=data(:,7);

    dif_DO=DO(2:end)-DO(1:end-1);
    air_sea=(1-((DO_p(1:end-1)+DO_p(2:end))/200))*0.5*0.5;
    O_flux=(dif_DO.*z(2:end))-air_sea;

    sun=xlsread('rise_set_test.xls');
    tm_sun=sun(:,1)+datenum(1904,1,1);
    [yr_s,mo_s,day_s]=datevec(tm_sun); 
    rise=(sun(:,2));
    set=sun(:,3);

    %put sunrise and sunset into proper matlab date format
    srh=floor(rise/100);
    srm=rise-100*srh;
    sr=(srh+srm/60)/24;
    sr_tm=sr+tm_sun; %puts in date format

    ssh=floor(set/100);
    ssm=set-100*ssh;
    ss=(ssh+ssm/60)/24 ;
    ss_tm=ss+tm_sun;

    r_s=[sr_tm,ss_tm]; %creates array of rise and set times