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2024/02/27
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Clim Package
Doxy_convert.m
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@treynaud
treynaud committed Feb 27, 2024
1 parent 005db4f commit 41b9915
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187 changes: 187 additions & 0 deletions Additional_Packages/Package_PSAL_CLIM/DOXY_PSAL_clim_A3D_replace_apply.m
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% DOXY_PSAL_clim_replace_apply replaces float PSAL values by climatological ones.
%
% SYNTAX
% [[DATA]=DOXY_PSAL_clim_replace_apply(ptype,DATA,Work,timeclim, depthclim, latclim, lonclim,psalclim,cycle_beg,cycle_end)
%
% DESCRIPTION
% DOXY_PSAL_clim_replace replaces float PSAL values by climatological ones
% from cycle_beg to cycle_end
%
% INPUT
% timeclim climatology: time (days) relative to the current year: 15,45, .....
% depthclim climatology: depth (m)
% latclim: climatology: latitude (degrees) -90 to 90
% lonclim: climatology: longitude (degrees) 0 to 360
% psalclim: climatology field: 4D variables [time,vertical, latitude,longitude]]
% ptype profil type 'primary','nearsurf','seconday', ...
% cycle_beg replacement occures from cycle_beg
% cycle_end and ends at cycle_end
% DATA (structure) argo float "multiprofile" structure gathering the
% three kind of vertical sampling scheme. Subfields
% are argo (the data) and Dim (the dimension).
% Example :
% DATA =
% primary: [1x1 struct]
% nearsurf: [1x1 struct]
% secondary: [1x1 struct]
% other: [1x1 struct]
%
% DATA.primary =
% argo: [1x1 struct]
% Dim: [1x1 struct]
%
% DATA.primary.argo =
% dimorder: 'C'
% data_type: [1x1 struct]
% ...
% pres: [1x1 struct]
% doxy: [1x1 struct]
% doxy_qc: [1x1 struct]
% doxy_adjusted: [1x1 struct]
% doxy_adjusted_qc: [1x1 struct]
% doxy_adjusted_error: [1x1 struct]
% ...
% Work (structure) Doxy correction working structure, issued and
% computed from argo float data.
% Example:
% Work =
% readme: [1x1 struct]
% unit: 'mumol/kg'
% wmo: 1901205
% DOXY_RAW: [85x120 single]
% CAPTEUR: {'Optode'}
% DOXY_QC: [85x120 char]
% OUTPUT
% DATA
% out_std structures containing float climatological STD
% interpolated values for PSAL and TEMP.
% HISTORY
% $created: 14/12/2023 $author: Thierry Reynaud
% $Revision: version $Date: $author:
% v1.0 12/12/2023 Thierry Reynaud, LOPS
% initial
%
% v2.0 18/01/2024 Thierry Reynaud, LOPS
% adding figures details and std values

function [DATA,out_std]=DOXY_PSAL_clim_A3D_replace_apply(ptype,DATA,Work,CLIM,cycle_beg,cycle_end)


% Float P,T,S values
eval(['pres_float=DATA.',ptype,'.argo.pres.data;']);
eval(['psal_float=DATA.',ptype,'.argo.psal.data;']);
eval(['psal_float=DATA.',ptype,'.argo.psal.data;']);
eval(['psal_adjusted_float=DATA.',ptype,'.argo.psal_adjusted.data;']);
eval(['temp_float=DATA.',ptype,'.argo.temp.data;']);
eval(['cycle_float=DATA.',ptype,'.argo.cycle_number.data;']);
eval(['qc_psal_adjusted_float=DATA.',ptype,'.argo.psal_adjusted_qc.data;']);
eval(['qc_psal_float=DATA.',ptype,'.argo.psal_qc.data;']);


pres_float=double(pres_float);
psal_float=double(psal_float);
temp_float=double(temp_float);

if exist('std_psalclim','var')
std_clim_psal_float=nan*zeros(size(psal_float));
end

if exist('std_tempclim','var')
std_clim_temp_float=nan*zeros(size(temp_float));
end

% Float Positions
eval(['lon_float = DATA.',ptype,'.argo.longitude.data;']);
eval(['lat_float = DATA.',ptype,'.argo.latitude.data;']);

% Float Julian Days
eval(['tmp=DATA.',ptype,'.argo.reference_date_time.data;']);
jref=datenum(str2num(tmp(1:4)),str2num(tmp(5:6)),str2num(tmp(7:8)),str2num(tmp(9:10)),str2num(tmp(11:12)),str2num(tmp(13:14)));
eval(['juld_float = DATA.',ptype,'.argo.juld.data + jref;']);

tabyear = datestr(juld_float,10);
running_day_float= juld_float - datenum(str2num(tabyear),1,1)+1;

idx=find(lon_float<0);
lon_float_tmp = lon_float;
lon_float_tmp(idx) = lon_float(idx) + 360;

for ilat=1:length(lat_float)
if cycle_float(ilat)>=cycle_beg && cycle_float(ilat)<= cycle_end

display(num2str(ilat));
depth_float = sw_dpth(pres_float(ilat,:),lat_float(ilat));

if sum(~isnan(depth_float))
% Interpolation clim.
% interpolation on Z levels:
[out]=gen_A3D_files(juld_float(ilat),lat_float(ilat),lon_float(ilat));

% INTERPOLATION: ARMOR-3D PSAL
tmp=interp_A3D(lon_float(ilat),lat_float(ilat),depth_float,juld_float(ilat),out.dir,out.file_PSAL);
dz=diff(tmp);
idz=find(dz==0);
tmp(idz)=NaN;
tmp2=interp1(depth_float(~isnan(tmp)),tmp(~isnan(tmp)),depth_float,'linear');
ilast=find(isnan(tmp)==1,1,'first')-1;
tmp2(ilast+1:end)=tmp2(ilast);

if Work.PSAL_REPLACE_plot
fig=figure(99);
%Plot PSAL
subplot(1,3,1);
h1=plot(tmp2,-pres_float(ilat,:),'+r');
hold on;
h2=plot(psal_float(ilat,:),-pres_float(ilat,:),'+g');
xlabel('Salinity (PSU)');
ylabel('Pressure (Db)');
hleg=legend([h1,h2],'Clim','Float','Location','SouthEast');
%psal_float (:,ilat)= squeeze(tmp);
end

psal_float(ilat,:)=tmp2;
psal_adjusted_float(ilat,:)=tmp2;
idx=find(~isnan(tmp2));
qc_psal_adjusted_float(ilat,idx)=1;%Switch QCs
qc_psal_float(ilat,idx)=1;%Switch QCs

% INTERPOLATION: ARMOR-3D TEMP
tmp=interp_A3D(lon_float(ilat),lat_float(ilat),depth_float,juld_float(ilat),out.dir,out.file_TEMP);
dz=diff(tmp);
idz=find(dz==0);
tmp(idz)=NaN;
tmp2=interp1(depth_float(~isnan(tmp)),tmp(~isnan(tmp)),depth_float,'linear');
ilast=find(isnan(tmp)==1,1,'first')-1;
tmp2(ilast+1:end)=tmp2(ilast);

if Work.PSAL_REPLACE_plot
fig=figure(99);
%Plot TEMP
subplot(1,3,2);
h1=plot(tmp2,-pres_float(ilat,:),'+r');
hold on;
h2=plot(temp_float(ilat,:),-pres_float(ilat,:),'+g');
xlabel('Temperature (PSU)');
ylabel('Pressure (Db)');
hleg=legend([h1,h2],'Clim','Float','Location','SouthEast');
%psal_float (:,ilat)= squeeze(tmp);
if Work.PSAL_REPLACE_plot_close
close(fig);
end
end

end

end
end

out_std=[];

eval(['DATA.',ptype,'.argo.psal.data=psal_float;']);
eval(['DATA.',ptype,'.argo.psal_adjusted.data=psal_adjusted_float;']);
eval(['DATA.',ptype,'.argo.psal_adjusted_qc.data=qc_psal_adjusted_float;']);
eval(['DATA.',ptype,'.argo.psal_qc.data=qc_psal_float;']);


return
end
77 changes: 77 additions & 0 deletions Additional_Packages/Package_PSAL_CLIM/DOXY_PSAL_clim_A3D_replace_main.m
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% DOXY_PSAL_clim_replace_main replaces float PSAL values by climatological ones.
%
% SYNTAX
% [DATA]=DOXY_PSAL_clim_replace(DATA,WOA,WORK)
%
% DESCRIPTION
% DOXY_PSAL_clim_replace replaces float PSAL values by climatological ones.
%
% INPUT
% DATA (structure) argo float "multiprofile" structure gathering the
% three kind of vertical sampling scheme. Subfields
% are argo (the data) and Dim (the dimension).
% Example :
% DATA =
% primary: [1x1 struct]
% nearsurf: [1x1 struct]
% secondary: [1x1 struct]
% other: [1x1 struct]
%
% DATA.primary =
% argo: [1x1 struct]
% Dim: [1x1 struct]
%
% DATA.primary.argo =
% dimorder: 'C'
% data_type: [1x1 struct]
% ...
% pres: [1x1 struct]
% doxy: [1x1 struct]
% doxy_qc: [1x1 struct]
% doxy_adjusted: [1x1 struct]
% doxy_adjusted_qc: [1x1 struct]
% doxy_adjusted_error: [1x1 struct]
% WOA (struct) Climatology WOA structure.
% Example:
% WOA =
% init: [1x1 struct]
% interp: [1x1 struct]
% WOA.init
% dimorder: 'C'
% latitude: [1x1 struct]
% longitude: [1x1 struct]
% depth: [1x1 struct]
% time: [1x1 struct]
% doxywoa: [1x1 struct]
% ...
% Work (structure) Doxy correction working structure, issued and
% computed from argo float data.
% Example:
% Work =
% readme: [1x1 struct]
% unit: 'mumol/kg'
% wmo: 1901205
% DOXY_RAW: [85x120 single]
% CAPTEUR: {'Optode'}
% DOXY_QC: [85x120 char]
% HISTORY
% $created: 12/12/2023 $author: Thierry Reynaud
% $Revision: version $Date: $author:
% v1.0 7/2/2024 Thierry Reynaud, LOPS
% initial
%

function [DATA, out_std,CLIM]=DOXY_PSAL_clim_A3D_replace_main(ptype,DATA,WOA,Work,CLIM)
%

% Replacing Float PSAL values by ARMOR-3D climatological values

%ptype='primary';% Select profile type
[DATA, out_std]=DOXY_PSAL_clim_A3D_replace_apply(ptype,DATA,Work,CLIM,Work.PSAL_REPLACE_cycle_beg,Work.PSAL_REPLACE_cycle_end);

% ptype='nearsurf';% Select profile type
% [DATA, outstd]=DOXY_PSAL_clim_replace_apply(ptype,DATA,Work,timeclim, depthclim, latclim, lonclim,psalclim,Work.PSAL_REPLACE_cycle_beg,Work.PSAL_REPLACE_cycle_end);


return
end
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