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function []=process2nctiles(dirModel,fileModel,fldModel,tileSize); |
| 2 |
%process2nctiles(dirModel); |
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%object : convert MITgcm binary output to netcdf files (tiled) |
| 4 |
%inputs : dirModel is the MITgcm run directory |
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% It is expected to contain binaries in |
| 6 |
% 'diags/STATE/', 'diags/TRSP/', etc. as well |
| 7 |
% 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 (by default []) can be specified (as e.g. 'ETAN') |
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% when fldModel is empty, all fields are processed |
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% tileSize (optional) is e.g. [90 90] (by default tiles=faces) |
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%output : (netcdf files) |
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|
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gcmfaces_global; |
| 18 |
|
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%listFiles={'state_2d_set1','state_2d_set2','state_3d_set1','state_3d_set2'}; |
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%listFiles={'trsp_3d_set1','trsp_3d_set2','trsp_3d_set3'}; |
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%for ff=1:length(listFiles); process2nctiles('iter12/',listFiles{ff},[],[90 90]); end; |
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|
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%replace time series with monthly climatology? |
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doClim=0; |
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|
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%directory names |
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listDirs={'STATE/','TRSP/'};%BUDG? |
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filAvailDiag=[dirModel 'available_diagnostics.log']; |
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filReadme=[dirModel 'README']; |
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dirOut=[dirModel 'nctiles_tmp/']; |
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%dirOut=[dirModel 'nctiles_post_tmp/']; |
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if ~isdir(dirOut); mkdir(dirOut); end; |
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|
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%search in subdirectories |
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subDir=[]; |
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diagsDir='diags/'; |
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%diagsDir='diags_post/'; |
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%diagsDir='diags_interp/'; |
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for ff=1:length(listDirs); |
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tmp1=dir([dirModel diagsDir 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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tmp1=dir([dirModel diagsDir fileModel '/' fileModel '*']); |
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if ~isempty(tmp1); subDir=[fileModel '/']; 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 diagsDir 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(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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%determine map of tile indices (by default tiles=faces) |
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if isempty(whos('tileSize')); |
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tileNo=mygrid.XC; |
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for ff=1:mygrid.nFaces; tileNo{ff}(:)=ff; end; |
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else; |
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tileNo=gcmfaces_loc_tile(tileSize(1),tileSize(2)); |
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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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%replace time series with monthly climatology |
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if doClim; myDiag=compClim(myDiag); end; |
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|
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%set ancilliary time variable |
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nn=length(size(myDiag{1})); |
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nn=size(myDiag{1},nn); |
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%tim=[1:nn]; |
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tim=[1992*ones(nn,1) [1:nn]' 15*ones(nn,1)]; |
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tim=datenum(tim)-datenum([1992 1 0]); |
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timUnits='days since 1992-1-1 0:0:0'; |
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|
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%get time step axis |
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[listTimes]=diags_list_times({dirIn},{fileModel}); |
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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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%get description of estimate from README |
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[rdm]=read_readme(filReadme); |
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disp(rdm'); |
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|
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%set output directory/file name |
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myFile=[dirOut nameDiag];%first instance is for subdirectory name |
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if ~isdir(myFile); mkdir(myFile); end; |
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myFile=[myFile filesep nameDiag];%second instance is for file name base |
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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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%apply mask, and convert to land mask |
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if ~isempty(mygrid.RAC); |
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msk=grid_diag.msk; |
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if length(size(myDiag{1}))==3; |
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msk=repmat(msk(:,:,1),[1 1 size(myDiag{1},3)]); |
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else; |
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msk=repmat(msk,[1 1 1 size(myDiag{1},4)]); |
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end; |
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myDiag=myDiag.*msk; |
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clear msk; |
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% |
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land=isnan(grid_diag.msk); |
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end; |
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|
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%set 'coord' attribute |
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if avail_diag.nr~=1; |
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coord='lon lat dep tim'; |
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else; |
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coord='lon lat tim'; |
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end; |
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|
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%replace time series with monthly climatology |
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if doClim; |
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listTimes=listTimes(1:12); |
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timUnits='days since year-1-1 0:0:0'; |
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avail_diag.longNameDiag=[avail_diag.longNameDiag ' (climatology) ']; |
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end; |
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|
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%create netcdf file using write2nctiles |
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doCreate=1; |
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dimlist=write2nctiles(myFile,myDiag,doCreate,{'tileNo',tileNo},... |
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{'fldName',nameDiag},{'longName',avail_diag.longNameDiag},... |
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{'units',avail_diag.units},{'descr',nameDiag},{'coord',coord},{'rdm',rdm}); |
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|
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%determine relevant dimensions |
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for ff=1:length(dimlist); |
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dim.tim{ff}={dimlist{ff}{1}}; |
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dim.twoD{ff}={dimlist{ff}{end-1:end}}; |
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if avail_diag.nr~=1; |
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dim.threeD{ff}={dimlist{ff}{end-2:end}}; |
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dim.dep{ff}={dimlist{ff}{end-2}}; |
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else; |
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dim.threeD{ff}=dim.twoD{ff}; |
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dim.dep{ff}=[]; |
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end; |
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end; |
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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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%now add fields |
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write2nctiles(myFile,grid_diag.lon,doCreate,{'tileNo',tileNo},... |
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{'fldName','lon'},{'units','degrees_east'},{'dimIn',dim.twoD}); |
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write2nctiles(myFile,grid_diag.lat,doCreate,{'tileNo',tileNo},... |
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{'fldName','lat'},{'units','degrees_north'},{'dimIn',dim.twoD}); |
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if isfield(grid_diag,'dep'); |
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write2nctiles(myFile,grid_diag.dep,doCreate,{'tileNo',tileNo},... |
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{'fldName','dep'},{'units','m'},{'dimIn',dim.dep}); |
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end; |
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write2nctiles(myFile,tim,doCreate,{'tileNo',tileNo},... |
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{'fldName','tim'},{'longName','time'},... |
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{'units',timUnits},{'dimIn',dim.tim}); |
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if ~isempty(mygrid.RAC); |
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write2nctiles(myFile,listTimes,doCreate,{'tileNo',tileNo},... |
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{'fldName','timstep'},{'longName','final time step number'},... |
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{'units','1'},{'dimIn',dim.tim}); |
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write2nctiles(myFile,grid_diag.msk,doCreate,{'tileNo',tileNo},... |
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{'fldName','land'},{'units','1'},{'longName','land mask'},{'dimIn',dim.threeD}); |
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write2nctiles(myFile,grid_diag.RAC,doCreate,{'tileNo',tileNo},... |
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{'fldName','area'},{'units','m^2'},{'longName','grid cell area'},{'dimIn',dim.twoD}); |
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if isfield(grid_diag,'dz'); |
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write2nctiles(myFile,grid_diag.dz,doCreate,{'tileNo',tileNo},... |
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{'fldName','thic'},{'units','m'},{'dimIn',dim.dep}); |
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end; |
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end; |
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|
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clear myDiag; |
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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,filesep); |
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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 [rdm]=read_readme(filReadme); |
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|
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gcmfaces_global; |
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|
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rdm=[]; |
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|
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fid=fopen(filReadme,'rt'); |
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while ~feof(fid); |
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nn=length(rdm); |
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rdm{nn+1} = fgetl(fid); |
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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 [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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%% |
| 276 |
|
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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; |
| 288 |
grid_diag.lat=mygrid.YC; |
| 289 |
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; |
| 292 |
grid_diag.lat=mygrid.YG; |
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grid_diag.msk=mygrid.mskS(:,:,1:avail_diag.nr); |
| 294 |
end; |
| 295 |
grid_diag.RAC=mygrid.RAC; |
| 296 |
|
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%vertical grid |
| 298 |
if avail_diag.nr~=1; |
| 299 |
if strcmp(avail_diag.loc_z,'M'); |
| 300 |
grid_diag.dep=-mygrid.RC; |
| 301 |
grid_diag.dz=mygrid.DRF; |
| 302 |
elseif strcmp(avail_diag.loc_z,'L'); |
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grid_diag.dep=-mygrid.RF(2:end); |
| 304 |
grid_diag.dz=[mygrid.DRC(2:end) ; 228.25];%quick fix |
| 305 |
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]); |
| 309 |
grid_diag.dz=reshape(grid_diag.dz,[1 1 avail_diag.nr]); |
| 310 |
end; |
| 311 |
|
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%%replace time series with monthly climatology |
| 313 |
function [FLD]=compClim(fld); |
| 314 |
|
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gcmfaces_global; |
| 316 |
|
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ndim=length(size(fld{1})); |
| 318 |
nyear=size(fld{1},ndim)/12; |
| 319 |
|
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if ndim==3; FLD=NaN*fld(:,:,1:12); end; |
| 321 |
if ndim==4; FLD=NaN*fld(:,:,:,1:12); end; |
| 322 |
|
| 323 |
for mm=1:12; |
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if ndim==3; FLD(:,:,mm)=mean(fld(:,:,mm:12:12*nyear),ndim); end; |
| 325 |
if ndim==4; FLD(:,:,:,mm)=mean(fld(:,:,:,mm:12:12*nyear),ndim); end; |
| 326 |
end; |
| 327 |
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