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extractGPIdailyVars_Bootstrapped.m
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extractGPIdailyVars_Bootstrapped.m
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% Adapted from extractDataForKerry to extract daily variables needed for
% computing GPI.
%
% Meg D. Fowler, 2017-10-27
%
%% Set path to variable files and read in dimensions
%load('/Volumes/MyPassport/Data/TCs/SavedMatlabData/MJOindex&time_monthPhase'); % MJOindex_monthPhase, MJOtime_monthPhase - RMM
% % ---------- Commented out below when computing climatology -------------
load('/Volumes/MyPassport/Data/TCs/SavedMatlabData/MJOindex&time_monthPhase-OMI'); % MJOindex_monthPhase, MJOtime_monthPhase
% % -----------------------------------------------------------------------
%
SLPfiles = '/Volumes/MyPassport/Data/TCs/obs/DailySLP/slp_';
%
rootPath = '/Users/meganfowler/gp_fuse/TC/MJO_obs/ECMWF_ERA-Interim/2.5x2.5/'; %Path to Greenplanet ECMWF obs
%
Ufile = [rootPath, 'dailyAvg/globalU_1983-2013_dailyAvg.nc'];
Vfile = [rootPath, 'dailyAvg/globalV_1983-2013_dailyAvg.nc'];
SSTfile = [rootPath, 'dailyAvg/globalSST_1983-2013_dailyAvg.nc'];
Tfile = [rootPath, 'dailyAvg/globalT_1983-2013_dailyAvg.nc'];
Qfile = [rootPath, 'dailyAvg/globalQ_1983-2013_dailyAvg.nc'];
%Read in time for all variables
timeRaw = ncread(Ufile,'time'); %Time is the same in U,V,Q,T, and SST files (confirmed)
startTime = datenum([1900 01 01 0 0 0 ]);
ERAtime = startTime + (timeRaw/24.0); %Units of hours since 1900, but matlab operates on days
lon = ncread(SSTfile,'longitude');
lat = ncread(SSTfile,'latitude');
levU = ncread(Ufile, 'level');
levT = ncread(Tfile, 'level');
%SET DOMAIN
ilon = find(lon>=60 & lon<=200);
ilat = find(lat>-5 & lat<40);
%Try reading in all arrays at once, but only for selected domain....
start = [ilon(1) ilat(1) 1 1];
stride = [1 1 1 1];
countU = [length(ilon) length(ilat) length(levU) length(ERAtime)];
countT = [length(ilon) length(ilat) length(levT) length(ERAtime)];
%Read in variables for selected domain
U_allDays = ncread(Ufile,'u',start,countU,stride); %[m/s]
fprintf('Loaded U file...\n')
V_allDays = ncread(Vfile,'v',start,countU,stride); %[m/s]
fprintf('Loaded V file...\n')
SST_allDays = ncread(SSTfile,'sst',[ilon(1) ilat(1) 1],[length(ilon) length(ilat) length(ERAtime)],[1 1 1]); %[K]
fprintf('Loaded SST file...\n')
Q_allDays = ncread(Qfile,'q',start,countT,stride); %[K]
fprintf('Loaded Q file...\n')
T_allDays = ncread(Tfile,'t',start,countT,stride); %[kg/kg]
fprintf('Loaded T file...\n')
%% Save individual bootstrap files
retPhases = 8; %Phases to retrieve
retMonths = 1:12; %Months to retrieve
daysInMonth = [31,28,31,30,31,30,31,31,30,31,30,31]; %Days in each month
getTimes_Save = nan(100,12,31);
for iBoot=40:42
for iPhase = 1:numel(retPhases)
%for iPhase = 1:1
%Pre-define arrays to save output in
dailySST = NaN(365,numel(ilon),numel(ilat));
dailyT = NaN(365,numel(ilon),numel(ilat),numel(levT));
dailyQ = NaN(365,numel(ilon),numel(ilat),numel(levT));
dailyU = NaN(365,numel(ilon),numel(ilat),numel(levU));
dailyV = NaN(365,numel(ilon),numel(ilat),numel(levU));
dailySLP = NaN(365,numel(ilon),numel(ilat));
dates = NaN(365);
dayYr = 1.0; %Day of the year
for iMon = 1:numel(retMonths)
%Choose random samples to fill in particulat months (bootstrap)
% Max value for randi call = number of events
rng('shuffle'); %So that random numbers are based on current time, not on number of times it's run
selectTime = MJOtime_monthPhase{iMon,iPhase}; %Number of observations in month/phase
getTimeIndex = randi(length(MJOtime_monthPhase{iMon,iPhase}),[1,daysInMonth(iMon)]); %Indices to pick out from month/phase
getTimes = selectTime(getTimeIndex); %Times of specified MJO events
getTimes_Save(iBoot,iMon,1:daysInMonth(iMon))=getTimes;
%Use function to select which days to match with in obs record
%[getTimes]=selectLargeMJOevents(MJOindex_monthPhase,MJOtime_monthPhase,retMonths(iMon),retPhases(iPhase));
ndays = daysInMonth(iMon); %Number of days in month
for it = 1:numel(getTimes)
retDate = find(ERAtime == getTimes(it)); %Date to retain
% ---- For SLP
vec = datevec(double(ERAtime(retDate)));
yr = vec(1);
mon = vec(2);
day = vec(3);
if mon<10
slpFileName = [SLPfiles,'0',num2str(mon),'_',num2str(yr),'.nc'];
else
slpFileName = [SLPfiles,num2str(mon),'_',num2str(yr),'.nc'];
end
%Read in variables for selected date
SLP = ncread(slpFileName,'msl'); %[Pa]
SLPday(:,:,it) = SLP(ilon,ilat,day);
%Replacing missing values with NaNs before averaging
SLPday(SLPday<=-32767) = NaN;
% ---- For all other variables
start = [ilon(1) ilat(1) 1 retDate];
stride = [1 1 1 1];
countU = [length(ilon) length(ilat) length(levU) length(retDate)];
countT = [length(ilon) length(ilat) length(levT) length(retDate)];
%Read in variables for selected date
Uday(it,:,:,:) = U_allDays(:,:,:,retDate); %[m/s]
Vday(it,:,:,:) = V_allDays(:,:,:,retDate); %[m/s]
SSTday(:,:,it) = SST_allDays(:,:,retDate); %[K]
Qday(:,:,:,it) = Q_allDays(:,:,:,retDate); %[K]
Tday(:,:,:,it) = T_allDays(:,:,:,retDate); %[kg/kg]
%Replacing missing values with NaNs before averaging
Tday(Tday<=-32767) = NaN;
Qday(Qday<=-32767) = NaN;
SSTday(SSTday<=-32767) = NaN;
Uday(Uday<=-32767) = NaN;
Vday(Vday<=-32767) = NaN;
end
%Daily U and V values
dailyU(dayYr:dayYr+(ndays-1),:,:,:) = Uday; %[ time lat lon lev]
dailyV(dayYr:dayYr+(ndays-1),:,:,:) = Vday;
%Re-arrange others so dimension order is same
SSTday = permute(SSTday,[3 1 2]);
Qday = permute(Qday,[4 1 2 3]);
Tday = permute(Tday,[4 1 2 3]);
SLPday = permute(SLPday,[3 1 2]);
dailySST(dayYr:dayYr+(ndays-1),:,:) = SSTday;
dailyQ(dayYr:dayYr+(ndays-1),:,:,:) = Qday;
dailyT(dayYr:dayYr+(ndays-1),:,:,:) = Tday;
dailySLP(dayYr:dayYr+(ndays-1),:,:) = SLPday;
%Dates used in the averages and for U/V records
dates(dayYr:dayYr+(ndays-1)) = getTimes;
%Increment day of year to begin on the first of the next month
dayYr = dayYr+ndays;
%Clearing variables necessary to avoid size errors on pre-existing arrays
clearvars Uday Vday SSTday Qday Tday SLPday
%If verbose option is enabled, print status at end of each loop
verbose=1;
if verbose==1
fprintf('Stored data for Phase %d month %d \n',retPhases(iPhase),iMon);
end
end
% Create netCDF files for phase
% Set missing values appropriately, rather than keeping as NaNs
dailyU(isnan(dailyU)) = -32767;
dailyV(isnan(dailyV)) = -32767;
dailyT(isnan(dailyT)) = -32767;
dailyQ(isnan(dailyQ)) = -32767;
dailySST(isnan(dailySST)) = -32767;
dailySLP(isnan(dailySLP)) = -32767;
numPhase = num2str(retPhases(iPhase));
%filename = ['/Users/meganfowler/gp_fuse/TC/GPI_daily/Bootstrap_DailyGPIvariables-RMM/DailyGPIvars_MJOphase_',numPhase,'-RMM_iBoot',num2str(iBoot),'.nc'];
%filename = ['/Volumes/MyPassport/Data/TCs/GPI/Bootstrap_ERAI/DailyGPIvars_MJOphase_',numPhase,'-OMI_iBoot',num2str(iBoot),'.nc'];
filename = ['/Users/meganfowler/gp_fuse/TC/GPI_daily/Bootstrap_DailyGPIvariables/DailyGPIvars_MJOphase_',numPhase,'-OMI_iBoot',num2str(iBoot),'.nc'];
nccreate(filename, 'lon',...
'Dimensions',{'lon',numel(ilon)});
ncwrite(filename,'lon',lon(ilon));
ncwriteatt(filename,'lon','long_name','degrees_east');
fprintf('Wrote lon \n')
nccreate(filename,'lat',...
'Dimensions',{'lat',numel(ilat)});
ncwrite(filename,'lat',lat(ilat));
ncwriteatt(filename,'lat','long_name','degrees_north');
fprintf('Wrote lat\n')
nccreate(filename,'levT',...
'Dimensions',{'levT',numel(levT)});
ncwrite(filename,'levT',levT);
ncwriteatt(filename,'levT','long_name','Vertical pressure levels for T and Q');
fprintf('Wrote levT \n')
nccreate(filename,'levU',...
'Dimensions',{'levU',numel(levU)});
ncwrite(filename,'levU',levU);
ncwriteatt(filename,'levU','long_name','Pressure levels for U and V');
fprintf('Wrote levU \n');
nccreate(filename,'T',...
'Dimensions',{'day',365,'lon',numel(ilon),'lat',numel(ilat),'levT',numel(levT)});
ncwrite(filename,'T',dailyT);
ncwriteatt(filename,'T','units','K');
ncwriteatt(filename,'T','long_name','Temperature');
ncwriteatt(filename,'T','FillValue', -32767);
ncwriteatt(filename,'T','missing_value',-32767);
fprintf('Wrote T \n');
nccreate(filename,'Q',...
'Dimensions',{'day',365,'lon',numel(ilon),'lat',numel(ilat),'levT',numel(levT)});
ncwrite(filename,'Q',dailyQ);
ncwriteatt(filename,'Q','units','kg/kg');
ncwriteatt(filename,'Q','long_name','Specific humidity');
ncwriteatt(filename,'Q','FillValue', -32767);
ncwriteatt(filename,'Q','missing_value',-32767);
fprintf('Wrote Q \n')
nccreate(filename,'SST',...
'Dimensions',{'day',365,'lon',numel(ilon),'lat',numel(ilat)});
ncwrite(filename,'SST',dailySST);
ncwriteatt(filename,'SST','units','K');
ncwriteatt(filename,'SST','long_name','Sea surface temperature');
ncwriteatt(filename,'SST','FillValue',-32767);
ncwriteatt(filename,'SST','missing_value',-32767);
fprintf('Wrote SST \n');
nccreate(filename,'SLP',...
'Dimensions',{'day',365,'lon',numel(ilon),'lat',numel(ilat)});
ncwrite(filename,'SLP',dailySLP);
ncwriteatt(filename,'SLP','units','Pa');
ncwriteatt(filename,'SLP','long_name','Sea surface pressure');
ncwriteatt(filename,'SLP','FillValue',-32767);
ncwriteatt(filename,'SLP','missing_value',-32767);
fprintf('Wrote SLP \n');
nccreate(filename,'U',...
'Dimensions',{'day',365,'lon',numel(ilon),'lat',numel(ilat),'levU',numel(levU)});
ncwrite(filename,'U',dailyU);
ncwriteatt(filename,'U','units','m/s');
ncwriteatt(filename,'U','long_name','U component of wind');
ncwriteatt(filename,'U','FillValue',-32767);
ncwriteatt(filename,'U','missing_value',-32767);
fprintf('Wrote U \n');
nccreate(filename,'V',...
'Dimensions',{'day',365,'lon',numel(ilon),'lat',numel(ilat),'levU',numel(levU)});
ncwrite(filename,'V',dailyV);
ncwriteatt(filename,'V','units','m/s');
ncwriteatt(filename,'V','long_name','U component of wind');
ncwriteatt(filename,'V','FillValue',-32767);
ncwriteatt(filename,'V','missing_value',-32767);
fprintf('Wrote V \n')
if verbose==1
fprintf('File successfully created for phase of the MJO, for bootstrap number %i \n',iBoot);
end
end
end
%% Determine dates/phases to retreive
% retPhases = 1:8; %Phases to retrieve
% retMonths = 1:12; %Months to retrieve
% daysInMonth = [31,28,31,30,31,30,31,31,30,31,30,31]; %Days in each month
%
% for iBoot=4:4
% %for iPhase = 1:numel(retPhases)
% for iPhase = 3:3
% %Pre-define arrays to save output in
% dailySST = NaN(365,numel(ilon),numel(ilat));
% dailyT = NaN(365,numel(ilon),numel(ilat),numel(levT));
% dailyQ = NaN(365,numel(ilon),numel(ilat),numel(levT));
% dailyU = NaN(365,numel(ilon),numel(ilat),numel(levU));
% dailyV = NaN(365,numel(ilon),numel(ilat),numel(levU));
% dailySLP = NaN(365,numel(ilon),numel(ilat));
% dates = NaN(365);
%
% dayYr = 1.0; %Day of the year
%
% for iMon = 1:numel(retMonths)
% %Choose random samples to fill in particulat months (bootstrap)
% % Max value for randi call = number of events
% rng('shuffle'); %So that random numbers are based on current time, not on number of times it's run
% selectTime = MJOtime_monthPhase{iMon,iPhase}; %Number of observations in month/phase
% getTimeIndex = randi(length(MJOtime_monthPhase{iMon,iPhase}),[1,daysInMonth(iMon)]); %Indices to pick out from month/phase
% getTimes = selectTime(getTimeIndex); %Times of specified MJO events
%
% %Use function to select which days to match with in obs record
% %[getTimes]=selectLargeMJOevents(MJOindex_monthPhase,MJOtime_monthPhase,retMonths(iMon),retPhases(iPhase));
%
% ndays = daysInMonth(iMon); %Number of days in month
% for it = 1:numel(getTimes)
% retDate = find(ERAtime == getTimes(it)); %Date to retain
%
% % ---- For SLP
% vec = datevec(double(ERAtime(retDate)));
% yr = vec(1);
% mon = vec(2);
% day = vec(3);
%
% if mon<10
% slpFileName = [SLPfiles,'0',num2str(mon),'_',num2str(yr),'.nc'];
% else
% slpFileName = [SLPfiles,num2str(mon),'_',num2str(yr),'.nc'];
% end
%
% %Read in variables for selected date
% SLP = ncread(slpFileName,'msl'); %[Pa]
% SLPday(:,:,it) = SLP(ilon,ilat,day);
%
% %Replacing missing values with NaNs before averaging
% SLPday(SLPday<=-32767) = NaN;
%
% % ---- For all other variables
% start = [ilon(1) ilat(1) 1 retDate];
% stride = [1 1 1 1];
% countU = [length(ilon) length(ilat) length(levU) length(retDate)];
% countT = [length(ilon) length(ilat) length(levT) length(retDate)];
%
% %Read in variables for selected date
% Uday(it,:,:,:) = ncread(Ufile,'u',start,countU,stride); %[m/s]
% Vday(it,:,:,:) = ncread(Vfile,'v',start,countU,stride); %[m/s]
% SSTday(:,:,it) = ncread(SSTfile,'sst',[1 1 retDate],[length(ilon) length(ilat) length(retDate)],[1 1 1]); %[K]
% Qday(:,:,:,it) = ncread(Qfile,'q',start,countT,stride); %[K]
% Tday(:,:,:,it) = ncread(Tfile,'t',start,countT,stride); %[kg/kg]
%
% %Replacing missing values with NaNs before averaging
% Tday(Tday<=-32767) = NaN;
% Qday(Qday<=-32767) = NaN;
% SSTday(SSTday<=-32767) = NaN;
% Uday(Uday<=-32767) = NaN;
% Vday(Vday<=-32767) = NaN;
%
% end
%
% %Daily U and V values
% dailyU(dayYr:dayYr+(ndays-1),:,:,:) = Uday; %[ time lat lon lev]
% dailyV(dayYr:dayYr+(ndays-1),:,:,:) = Vday;
% %Re-arrange others so dimension order is same
% SSTday = permute(SSTday,[3 1 2]);
% Qday = permute(Qday,[4 1 2 3]);
% Tday = permute(Tday,[4 1 2 3]);
% SLPday = permute(SLPday,[3 1 2]);
%
% dailySST(dayYr:dayYr+(ndays-1),:,:) = SSTday;
% dailyQ(dayYr:dayYr+(ndays-1),:,:,:) = Qday;
% dailyT(dayYr:dayYr+(ndays-1),:,:,:) = Tday;
% dailySLP(dayYr:dayYr+(ndays-1),:,:) = SLPday;
%
% %Dates used in the averages and for U/V records
% dates(dayYr:dayYr+(ndays-1)) = getTimes;
%
% %Increment day of year to begin on the first of the next month
% dayYr = dayYr+ndays;
%
% %Clearing variables necessary to avoid size errors on pre-existing arrays
% clearvars Uday Vday SSTday Qday Tday SLPday
%
% %If verbose option is enabled, print status at end of each loop
% verbose=1;
% if verbose==1
% fprintf('Stored data for Phase %d month %d \n',retPhases(iPhase),iMon);
% end
% end
% % Create netCDF files for phase
%
% % Set missing values appropriately, rather than keeping as NaNs
% dailyU(isnan(dailyU)) = -32767;
% dailyV(isnan(dailyV)) = -32767;
% dailyT(isnan(dailyT)) = -32767;
% dailyQ(isnan(dailyQ)) = -32767;
% dailySST(isnan(dailySST)) = -32767;
% dailySLP(isnan(dailySLP)) = -32767;
%
% numPhase = num2str(retPhases(iPhase));
%
% filename = ['/Users/meganfowler/gp_fuse/TC/GPI_daily/Bootstrap_DailyGPIvariables/DailyGPIvars_MJOphase_',numPhase,'-OMI_iBoot',num2str(iBoot),'--TEST1.nc'];
%
% nccreate(filename, 'lon',...
% 'Dimensions',{'lon',numel(ilon)});
% ncwrite(filename,'lon',lon(ilon));
% ncwriteatt(filename,'lon','long_name','degrees_east');
%
% nccreate(filename,'lat',...
% 'Dimensions',{'lat',numel(ilat)});
% ncwrite(filename,'lat',lat(ilat));
% ncwriteatt(filename,'lat','long_name','degrees_north');
%
% nccreate(filename,'levT',...
% 'Dimensions',{'levT',numel(levT)});
% ncwrite(filename,'levT',levT);
% ncwriteatt(filename,'levT','long_name','Vertical pressure levels for T and Q');
%
% nccreate(filename,'levU',...
% 'Dimensions',{'levU',numel(levU)});
% ncwrite(filename,'levU',levU);
% ncwriteatt(filename,'levU','long_name','Pressure levels for U and V');
%
% nccreate(filename,'T',...
% 'Dimensions',{'day',365,'lon',numel(lon),'lat',numel(lat),'levT',numel(levT)});
% ncwrite(filename,'T',dailyT);
% ncwriteatt(filename,'T','units','K');
% ncwriteatt(filename,'T','long_name','Temperature');
% ncwriteatt(filename,'T','FillValue', -32767);
% ncwriteatt(filename,'T','missing_value',-32767);
%
% nccreate(filename,'Q',...
% 'Dimensions',{'day',365,'lon',numel(lon),'lat',numel(lat),'levT',numel(levT)});
% ncwrite(filename,'Q',dailyQ);
% ncwriteatt(filename,'Q','units','kg/kg');
% ncwriteatt(filename,'Q','long_name','Specific humidity');
% ncwriteatt(filename,'Q','FillValue', -32767);
% ncwriteatt(filename,'Q','missing_value',-32767);
%
% nccreate(filename,'SST',...
% 'Dimensions',{'day',365,'lon',numel(lon),'lat',numel(lat)});
% ncwrite(filename,'SST',dailySST);
% ncwriteatt(filename,'SST','units','K');
% ncwriteatt(filename,'SST','long_name','Sea surface temperature');
% ncwriteatt(filename,'SST','FillValue',-32767);
% ncwriteatt(filename,'SST','missing_value',-32767);
%
% nccreate(filename,'SLP',...
% 'Dimensions',{'day',365,'lon',numel(lon),'lat',numel(lat)});
% ncwrite(filename,'SLP',dailySLP);
% ncwriteatt(filename,'SLP','units','Pa');
% ncwriteatt(filename,'SLP','long_name','Sea surface pressure');
% ncwriteatt(filename,'SLP','FillValue',-32767);
% ncwriteatt(filename,'SLP','missing_value',-32767);
%
% nccreate(filename,'U',...
% 'Dimensions',{'day',365,'lon',numel(lon),'lat',numel(lat),'levU',numel(levU)});
% ncwrite(filename,'U',dailyU);
% ncwriteatt(filename,'U','units','m/s');
% ncwriteatt(filename,'U','long_name','U component of wind');
% ncwriteatt(filename,'U','FillValue',-32767);
% ncwriteatt(filename,'U','missing_value',-32767);
%
% nccreate(filename,'V',...
% 'Dimensions',{'day',365,'lon',numel(lon),'lat',numel(lat),'levU',numel(levU)});
% ncwrite(filename,'V',dailyV);
% ncwriteatt(filename,'V','units','m/s');
% ncwriteatt(filename,'V','long_name','U component of wind');
% ncwriteatt(filename,'V','FillValue',-32767);
% ncwriteatt(filename,'V','missing_value',-32767);
%
% if verbose==1
% fprintf('File successfully created for phase of the MJO, for bootstrap number %i \n',iBoot);
% end
%
% end
% end
%Save matlab variables in case I ever want to access them again, not in
% netCDF format...
%save('separatedObs_phases125','monthlySST','monthlyT','monthlyQ','dailyU','dailyV','dates');