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function []=process2nctiles(dirModel,fileModel,fldModel); |
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%process2nctiles(dirModel); |
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%object : convert MITgcm binary output to netcdf files (tiled) |
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%inputs : dirModel is the MITgcm run directory |
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% It is expected to contain binaries in |
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% 'diags/STATE/', 'diags/TRSP/', etc. as well |
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% as the 'available_diagnostics.log' text file. |
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% fileModel the file name base e.g. 'state_2d_set1' |
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% By default : all variables in e.g. 'state_2d_set1*' |
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% files will be processed, and writen individually to |
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% nctiles (tiled netcdf) that will be located in 'nctiles/' |
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% fldModel (optional) can be specifiec as e.g. 'ETAN' |
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%output : (netcdf files) |
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|
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gcmfaces_global; |
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|
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fprintf('to do list : embed README in global attributes\n'); |
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fprintf('to do list : create tim variable\n'); |
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|
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%directory names |
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listDirs={'STATE/','TRSP/'}; |
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filAvailDiag=[dirModel 'available_diagnostics.log']; |
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dirOut=[dirModel 'nctiles/']; |
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if ~isdir(dirOut); mkdir(dirOut); end; |
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|
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%seacrh in subdirectories |
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subDir=[]; |
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for ff=1:length(listDirs); |
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tmp1=dir([dirModel 'diags/' listDirs{ff} fileModel '*']); |
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if ~isempty(tmp1); subDir=listDirs{ff}; end; |
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end; |
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|
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if isempty(subDir); |
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error(['file ' fileModel ' was not found']); |
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else; |
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dirIn=[dirModel 'diags/' subDir]; |
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nn=length(dir([dirIn fileModel '*data'])); |
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fprintf('%s (%d files) was found in \n %s \n',fileModel,nn,dirIn); |
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end; |
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|
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%set list of variables to process |
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if ~isempty(who('fldModel')); |
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if ischar(fldModel); listFlds={fldModel}; |
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else; listFlds=fldModel; |
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end; |
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else; |
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meta=read_meta([dirIn fileModel '*']); |
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listFlds=meta.fldList; |
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end; |
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|
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%now do the actual processing |
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for vv=1:length(listFlds); |
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nameDiag=deblank(listFlds{vv}) |
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|
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%get meta information |
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meta=read_meta([dirIn fileModel '*']); |
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irec=find(strcmp(deblank(meta.fldList),nameDiag)); |
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if length(irec)~=1; error('field not in file\n'); end; |
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|
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%read time series |
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myDiag=rdmds2gcmfaces([dirIn fileModel '*'],NaN,'rec',irec); |
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|
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%ancilliary fields for netcdf file |
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tim=[1:size(myDiag{1},3)]; |
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timName='month index'; |
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descr=nameDiag; |
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|
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%get units and long name from available_diagnostics.log |
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[avail_diag]=read_avail_diag(filAvailDiag,nameDiag); |
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|
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%convert to MITgcm format (90x1170 array) |
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myFile=[dirOut nameDiag]; |
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|
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%get grid params |
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[grid_diag]=set_grid_diag(avail_diag); |
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|
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%create netcdf file using write2nctiles (works only with old matlab, thus far ...) |
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doCreate=1; |
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dimOut=write2nctiles(myFile,myDiag,doCreate,... |
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{'fldName',nameDiag},{'longName',avail_diag.longNameDiag},... |
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{'units',avail_diag.units},{'descr',descr}); |
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|
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%prepare to add fields |
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doCreate=0; |
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|
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%determine relevant dimensions (note the reverse order) |
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for ff=1:mygrid.nFaces; |
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dim2d{ff}={dimOut{ff}{end-1:end}}; |
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if avail_diag.nr~=1; |
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dimmsk{ff}={dimOut{ff}{end-2:end}}; |
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dimdep{ff}={dimOut{ff}{end-2}}; |
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else; |
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dimmsk{ff}=dim2d{ff}; |
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dimdep{ff}=[]; |
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end; |
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end; |
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|
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%now add fields |
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write2nctiles(myFile,grid_diag.lon,doCreate,... |
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{'fldName','longitude'},{'units',''},{'dimIn',dim2d}); |
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write2nctiles(myFile,grid_diag.lat,doCreate,... |
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{'fldName','latitude'},{'units',''},{'dimIn',dim2d}); |
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write2nctiles(myFile,grid_diag.msk,doCreate,... |
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{'fldName','landmask'},{'units',''},... |
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{'longName','land mask'},{'dimIn',dimmsk}); |
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write2nctiles(myFile,grid_diag.RAC,doCreate,... |
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{'fldName','cellarea'},{'units','m^2'},... |
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{'longName','grid cell area'},{'dimIn',dim2d}); |
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if isfield(grid_diag,'dep'); |
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write2nctiles(myFile,grid_diag.dep,doCreate,... |
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{'fldName','depth'},{'units','m'},{'dimIn',dimdep}); |
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write2nctiles(myFile,grid_diag.dz,doCreate,... |
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{'fldName','cellthick'},{'units','m'},{'dimIn',dimdep}); |
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end; |
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|
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end;%for vv=1:length(listFlds); |
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|
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function [meta]=read_meta(fileName); |
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|
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%read meta file |
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tmp1=dir([fileName '*.meta']); tmp1=tmp1(1).name; |
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tmp2=strfind(fileName,'/'); |
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if ~isempty(tmp2); tmp2=tmp2(end); else; tmp2=0; end; |
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tmp1=[fileName(1:tmp2) tmp1]; fid=fopen(tmp1); |
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while 1; |
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tline = fgetl(fid); |
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if ~ischar(tline), break, end |
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if isempty(whos('tmp3')); tmp3=tline; else; tmp3=[tmp3 ' ' tline]; end; |
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end |
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fclose(fid); |
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|
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%add meta variables to workspace |
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eval(tmp3); |
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|
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%reformat to meta structure |
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meta.dataprec=dataprec; |
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meta.nDims=nDims; |
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meta.nFlds=nFlds; |
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meta.nrecords=nrecords; |
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meta.fldList=fldList; |
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meta.dimList=dimList; |
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if ~isempty(who('timeInterval')); meta.timeInterval=timeInterval; end; |
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if ~isempty(who('timeStepNumber')); meta.timeStepNumber=timeStepNumber; end; |
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|
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%% |
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|
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function [avail_diag]=read_avail_diag(filAvailDiag,nameDiag); |
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|
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gcmfaces_global; |
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|
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avail_diag=[]; |
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|
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fid=fopen(filAvailDiag,'rt'); |
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while ~feof(fid); |
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tline = fgetl(fid); |
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tmp1=8-length(nameDiag); tmp1=repmat(' ',[1 tmp1]); |
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tname = ['|' sprintf('%s',nameDiag) tmp1 '|']; |
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if ~isempty(strfind(tline,tname)); |
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%e.g. tline=' 235 |SIatmQnt| 1 | |SM U1|W/m^2 |Net atmospheric heat flux, >0 decreases theta'; |
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% |
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tmp1=strfind(tline,'|'); tmp1=tmp1(end-1:end); |
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avail_diag.units=strtrim(tline(tmp1(1)+1:tmp1(2)-1)); |
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avail_diag.longNameDiag=tline(tmp1(2)+1:end); |
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% |
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tmp1=strfind(tline,'|'); tmp1=tmp1(4:5); |
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pars=tline(tmp1(1)+1:tmp1(2)-1); |
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% |
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if strcmp(pars(2),'M'); avail_diag.loc_h='C'; |
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elseif strcmp(pars(2),'U'); avail_diag.loc_h='W'; |
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elseif strcmp(pars(2),'V'); avail_diag.loc_h='S'; |
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end; |
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% |
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avail_diag.loc_z=pars(9); |
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% |
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if strcmp(pars(10),'1'); avail_diag.nr=1; |
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else; avail_diag.nr=length(mygrid.RC); |
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end; |
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end; |
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end; |
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fclose(fid); |
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|
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%% |
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|
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function [grid_diag]=set_grid_diag(avail_diag); |
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|
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gcmfaces_global; |
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|
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%switch for non-tracer point values |
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if strcmp(avail_diag.loc_h,'C'); |
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grid_diag.lon=mygrid.XC; |
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grid_diag.lat=mygrid.YC; |
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grid_diag.msk=mygrid.mskC(:,:,1:avail_diag.nr); |
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elseif strcmp(avail_diag.loc_h,'W'); |
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grid_diag.lon=mygrid.XG; |
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grid_diag.lat=mygrid.YC; |
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grid_diag.msk=mygrid.mskW(:,:,1:avail_diag.nr); |
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elseif strcmp(avail_diag.loc_h,'S'); |
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grid_diag.lon=mygrid.XC; |
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grid_diag.lat=mygrid.YG; |
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grid_diag.msk=mygrid.mskS(:,:,1:avail_diag.nr); |
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end; |
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grid_diag.RAC=mygrid.RAC; |
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|
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%vertical grid |
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if avail_diag.nr~=1; |
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if strcmp(avail_diag.loc_z,'M'); |
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grid_diag.dep=-mygrid.RC; |
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grid_diag.dz=mygrid.DRF; |
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elseif strcmp(avail_diag.loc_z,'L'); |
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grid_diag.dep=-mygrid.RF(2:end); |
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grid_diag.dz=[mygrid.DRC(2:end) ; 228.25];%quick fix |
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else; |
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error('unknown vertical grid'); |
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end; |
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grid_diag.dep=reshape(grid_diag.dep,[1 1 avail_diag.nr]); |
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grid_diag.dz=reshape(grid_diag.dz,[1 1 avail_diag.nr]); |
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end; |
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