%% NCOM download 
Count=1;
for Day = 2:10
    for t=[45 48 51 54 57 60]
        url =['https://ecowatch.ncddc.noaa.gov/thredds/fileServer/us_east/ncom_relo_useast_u_201909' ...
            num2str(Day,'%02d') '00_t0' num2str(t,'%02d') '.nc'];
        websave(['D:\Alexander\NCOM\201909' ...
            num2str(Day,'%02d') '00_t0' num2str(t,'%02d') '.nc'],url)
        disp(['201909' num2str(Day,'%02d') '00_t0' num2str(t,'%02d')])
    end
end

%%
NCOM.Lat = ncread('https://ecowatch.ncddc.noaa.gov/thredds/dodsC/ncom_us_east_agg/US_East_Apr_05_2013_to_Current_best.ncd',...
    'lat',[331],[240]);
NCOM.Lon = ncread('https://ecowatch.ncddc.noaa.gov/thredds/dodsC/ncom_us_east_agg/US_East_Apr_05_2013_to_Current_best.ncd',...
    'lon',91,180);
NCOM.depth = ncread('https://ecowatch.ncddc.noaa.gov/thredds/dodsC/ncom_us_east_agg/US_East_Apr_05_2013_to_Current_best.ncd',...
    'depth');
NCOM.time = ncread('https://ecowatch.ncddc.noaa.gov/thredds/dodsC/ncom_us_east_agg/US_East_Apr_05_2013_to_Current_best.ncd',...
    'time',[9825],[624]);
NCOM.time_run = ncread('https://ecowatch.ncddc.noaa.gov/thredds/dodsC/ncom_us_east_agg/US_East_Apr_05_2013_to_Current_best.ncd',...
    'time_run',[9825],[624]);
%[17775],[64]
for missStep = 1:length(MISSING)
    tStep = MISSING(missStep)-1
    noData=1
    while noData==1
        NCOM.water_u(:,:,:,tStep+1) = ncread('https://ecowatch.ncddc.noaa.gov/thredds/dodsC/ncom_us_east_agg/US_East_Apr_05_2013_to_Current_best.ncd',...
            'water_u',[91 331 1 9825+tStep],[180 240 inf 1],[1 1 1 1]);
        NCOM.water_v(:,:,:,tStep+1) = ncread('https://ecowatch.ncddc.noaa.gov/thredds/dodsC/ncom_us_east_agg/US_East_Apr_05_2013_to_Current_best.ncd',...
            'water_v',[91 331 1 9825+tStep],[180 240 inf 1],[1 1 1 1]);
        NCOM.surf_el(:,:,tStep+1) = ncread('https://ecowatch.ncddc.noaa.gov/thredds/dodsC/ncom_us_east_agg/US_East_Apr_05_2013_to_Current_best.ncd',...
            'surf_el',[91 331 9825+tStep],[180 240 1],[1 1 1]);
        NCOM.salinity(:,:,:,tStep+1) = ncread('https://ecowatch.ncddc.noaa.gov/thredds/dodsC/ncom_us_east_agg/US_East_Apr_05_2013_to_Current_best.ncd',...
            'salinity',[91 331 1 9825+tStep],[180 240 inf 1],[1 1 1 1]);
        if (squeeze(NCOM.water_v(100,100,1,tStep+1))==0|squeeze(NCOM.water_u(100,100,1,tStep+1))==0|squeeze(NCOM.surf_el(100,100,tStep+1))==0|squeeze(NCOM.salinity(100,100,1,tStep+1))==0)==1
        	noData=1
        else
            noData=0
        end
    end
disp(missStep)
    
end
save('NCOM_2016_V4.mat','-v7.3','NCOM')
% https://ecowatch.ncddc.noaa.gov/thredds/dodsC/ncom_us_east_agg/US_East_Apr_05_2013_to_Current_best.ncd?lon[0:1:543],lat[0:1:663],depth[0:1:39],time[17774:1:17838],time_run[17774:1:17838],water_u[17774:1:17838][0:1:39][0:1:663][0:1:543],water_v[17774:1:17838][0:1:39][0:1:663][0:1:543],water_temp[17774:1:17838][0:1:39][0:1:663][0:1:543],salinity[17774:1:17838][0:1:39][0:1:663][0:1:543]


%%


NCOM.mag = vecmag(NCOM.water_u,NCOM.water_v);
depthWeight = [diff(NCOM.depth)' 0];

for Layer = 1:40
    DAVfac(:,:,Layer,:) = ones(180,240,1,64).*depthWeight(Layer);
end
    DAVtrue = DAVfac;
    DAVtrue(isnan(NCOM.mag)==1) = 0;
    DAVfac(isnan(NCOM.mag)==1) = nan;
    DAVFac2 = sum(DAVtrue,3);
    clear DAVtrue
    NCOM.dav  = nansum(DAVfac.*NCOM.mag,3)./DAVFac2;
    NCOM.davX = nansum(DAVfac.*NCOM.water_u,3)./DAVFac2;
    NCOM.davY = nansum(DAVfac.*NCOM.water_v,3)./DAVFac2;
    
save('NCOM2016Final.mat','NCOM')