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gforget |
1.1 |
%function: MITprof_create |
| 2 |
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%object: read netcdf data files in the "MIT format" |
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%author: Gael Forget (gforget@mit.edu) |
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%date: june 21th, 2006 |
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% |
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gforget |
1.5 |
%usage: [MITprof]=MITprof_create(fileOut,nProf,nLev); |
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gforget |
1.1 |
% ---> create an empty MITprof netcdf file that contains all T/S fields |
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gforget |
1.5 |
% [MITprof]=MITprof_create(fileOut,nProf,nLev,list_vars); |
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gforget |
1.1 |
% ---> same but specifying the list of variables in list_vars cell |
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% array (e.g. list_vars={'prof_T','prof_Tweight'}). |
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% |
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gforget |
1.4 |
%inputs: fileOut data file name |
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% nProf number of profiles |
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% nLev number of levels |
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% list_vars variable list (optional) |
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gforget |
1.1 |
% |
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gforget |
1.4 |
%outputs: (none) |
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gforget |
1.1 |
|
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gforget |
1.4 |
function []=MITprof_create(fileOut,nProf,nLev,varargin); |
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gforget |
1.1 |
|
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%=============list of variables that will actually be in the file==============% |
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gforget |
1.5 |
if nargin>3; list_vars=varargin{1}; |
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gforget |
1.2 |
else; list_vars={'prof_T','prof_Tweight','prof_Testim','prof_Terr','prof_Tflag',... |
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gforget |
1.5 |
'prof_S','prof_Sweight','prof_Sestim','prof_Serr','prof_Sflag'}; |
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gforget |
1.1 |
end; |
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list_vars_plus=[{'prof_depth','prof_date','prof_YYYYMMDD','prof_HHMMSS',... |
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gforget |
1.5 |
'prof_lon','prof_lat','prof_basin','prof_point'}... |
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list_vars]; |
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gforget |
1.1 |
|
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%==========masters table of variables, units, names and dimensions=============% |
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mt_v={'prof_depth'}; mt_u={'me'}; mt_n={'depth'}; mt_d={'iDEPTH'}; |
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%mt_v=[mt_v '']; mt_u=[mt_u ' ']; mt_n=[mt_n '']; mt_d=[mt_d '']; |
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mt_v=[mt_v 'prof_date']; mt_u=[mt_u ' ']; mt_n=[mt_n 'Julian day since Jan-1-0000']; mt_d=[mt_d 'iPROF']; |
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mt_v=[mt_v 'prof_YYYYMMDD']; mt_u=[mt_u ' ']; mt_n=[mt_n 'year (4 digits), month (2 digits), day (2 digits)']; mt_d=[mt_d 'iPROF']; |
| 37 |
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mt_v=[mt_v 'prof_HHMMSS']; mt_u=[mt_u ' ']; mt_n=[mt_n 'hour (2 digits), minute (2 digits), second (2 digits)']; mt_d=[mt_d 'iPROF']; |
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mt_v=[mt_v 'prof_lon']; mt_u=[mt_u ' ']; mt_n=[mt_n 'Longitude (degree East)']; mt_d=[mt_d 'iPROF']; |
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mt_v=[mt_v 'prof_lat']; mt_u=[mt_u ' ']; mt_n=[mt_n 'Latitude (degree North)']; mt_d=[mt_d 'iPROF']; |
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mt_v=[mt_v 'prof_basin']; mt_u=[mt_u ' ']; mt_n=[mt_n 'ocean basin index (ecco 4g)']; mt_d=[mt_d 'iPROF']; |
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mt_v=[mt_v 'prof_point']; mt_u=[mt_u ' ']; mt_n=[mt_n 'grid point index (ecco 4g)']; mt_d=[mt_d 'iPROF']; |
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% |
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mt_v=[mt_v 'prof_T']; mt_u=[mt_u 'degree C']; mt_n=[mt_n 'potential temperature']; mt_d=[mt_d 'iPROF,iDEPTH']; |
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mt_v=[mt_v 'prof_Tweight']; mt_u=[mt_u '(degree C)^-2']; mt_n=[mt_n 'pot. temp. least-square weight']; mt_d=[mt_d 'iPROF,iDEPTH']; |
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gforget |
1.2 |
mt_v=[mt_v 'prof_Testim']; mt_u=[mt_u 'degree C']; mt_n=[mt_n 'pot. temp. estimate (e.g. from atlas)']; mt_d=[mt_d 'iPROF,iDEPTH']; |
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gforget |
1.1 |
mt_v=[mt_v 'prof_Terr']; mt_u=[mt_u 'degree C']; mt_n=[mt_n 'pot. temp. instrumental error']; mt_d=[mt_d 'iPROF,iDEPTH']; |
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gforget |
1.2 |
mt_v=[mt_v 'prof_Tflag']; mt_u=[mt_u ' ']; mt_n=[mt_n 'flag = i > 0 means test i rejected data.']; mt_d=[mt_d 'iPROF,iDEPTH']; |
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gforget |
1.1 |
% |
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mt_v=[mt_v 'prof_S']; mt_u=[mt_u 'psu']; mt_n=[mt_n 'salinity']; mt_d=[mt_d 'iPROF,iDEPTH']; |
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mt_v=[mt_v 'prof_Sweight']; mt_u=[mt_u '(psu)^-2']; mt_n=[mt_n 'salinity least-square weight']; mt_d=[mt_d 'iPROF,iDEPTH']; |
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gforget |
1.2 |
mt_v=[mt_v 'prof_Sestim']; mt_u=[mt_u 'psu']; mt_n=[mt_n 'salinity estimate (e.g. from atlas)']; mt_d=[mt_d 'iPROF,iDEPTH']; |
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gforget |
1.1 |
mt_v=[mt_v 'prof_Serr']; mt_u=[mt_u 'psu']; mt_n=[mt_n 'salinity instrumental error']; mt_d=[mt_d 'iPROF,iDEPTH']; |
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gforget |
1.2 |
mt_v=[mt_v 'prof_Sflag']; mt_u=[mt_u ' ']; mt_n=[mt_n 'flag = i > 0 means test i rejected data.']; mt_d=[mt_d 'iPROF,iDEPTH']; |
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gforget |
1.1 |
% |
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mt_v=[mt_v 'prof_U']; mt_u=[mt_u 'm/s']; mt_n=[mt_n 'eastward velocity comp.']; mt_d=[mt_d 'iPROF,iDEPTH']; |
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mt_v=[mt_v 'prof_Uweight']; mt_u=[mt_u '(m/s)^-2']; mt_n=[mt_n 'east. v. least-square weight']; mt_d=[mt_d 'iPROF,iDEPTH']; |
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mt_v=[mt_v 'prof_V']; mt_u=[mt_u 'm/s']; mt_n=[mt_n 'northward velocity comp.']; mt_d=[mt_d 'iPROF,iDEPTH']; |
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mt_v=[mt_v 'prof_Vweight']; mt_u=[mt_u '(m/s)^-2']; mt_n=[mt_n 'north. v. least-square weight']; mt_d=[mt_d 'iPROF,iDEPTH']; |
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mt_v=[mt_v 'prof_ptr']; mt_u=[mt_u 'X']; mt_n=[mt_n 'passive tracer']; mt_d=[mt_d 'iPROF,iDEPTH']; |
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mt_v=[mt_v 'prof_ptrweight']; mt_u=[mt_u '(X)^-2']; mt_n=[mt_n 'pass. tracer least-square weight']; mt_d=[mt_d 'iPROF,iDEPTH']; |
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% |
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mt_v=[mt_v 'prof_bp']; mt_u=[mt_u 'cm']; mt_n=[mt_n 'bottom pressure']; mt_d=[mt_d 'iPROF']; |
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mt_v=[mt_v 'prof_bpweight']; mt_u=[mt_u '(cm)^-2']; mt_n=[mt_n 'bot. pres. least-square weight']; mt_d=[mt_d 'iPROF']; |
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mt_v=[mt_v 'prof_ssh']; mt_u=[mt_u 'cm']; mt_n=[mt_n 'sea surface height']; mt_d=[mt_d 'iPROF']; |
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mt_v=[mt_v 'prof_sshweight']; mt_u=[mt_u '(cm)^-2']; mt_n=[mt_n 'ssh least-square weight']; mt_d=[mt_d 'iPROF']; |
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%=============================create the file=================================% |
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if ~strcmp(fileOut(end-2:end),'.nc'); suff='.nc'; else; suff=''; end; |
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gforget |
1.3 |
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gforget |
1.1 |
%define netcdf dimensions : |
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gforget |
1.4 |
iPROF=nProf; iDEPTH=nLev; |
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lTXT=30; fillval=-9999; |
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gforget |
1.1 |
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gforget |
1.5 |
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global useNativeMatlabNetcdf; if isempty(useNativeMatlabNetcdf); useNativeMatlabNetcdf = ~isempty(which('netcdf.open')); end; |
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if (useNativeMatlabNetcdf); |
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ncid=netcdf.create([fileOut suff],'clobber'); |
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%put a couple global attributes |
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aa=sprintf(['Format: MITprof. This file was created using \n' ... |
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'the matlab toolbox which can be obtained (see README) from \n'... |
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'http://mitgcm.org/viewvc/MITgcm/MITgcm_contrib/gael/profilesMatlabProcessing/']); |
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netcdf.putAtt(ncid,-1,'description',aa); |
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netcdf.putAtt(ncid,-1,'date',date); |
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iPROFid = netcdf.defDim(ncid,'iPROF',iPROF); |
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iDEPTHid = netcdf.defDim(ncid,'iDEPTH',iDEPTH); |
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lTXTid = netcdf.defDim(ncid,'lTXT',lTXT); |
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%mt_v=[mt_v 'prof_descr']; mt_u=[mt_u ' ']; mt_n=[mt_n 'profile description']; mt_d=[mt_d 'iPROF,lTXT']; |
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varid = netcdf.defVar(ncid,'prof_descr','char',[lTXTid iPROFid]); |
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netcdf.putAtt(ncid,varid,'long_name','profile description'); |
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for ii=1:length(list_vars_plus); |
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jj=find(strcmp(mt_v,list_vars_plus{ii})); |
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if ~isempty(jj); |
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if strcmp(mt_d{jj},'iPROF,iDEPTH'); |
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varid = netcdf.defVar(ncid,mt_v{jj},'double',[iDEPTHid iPROFid]);%note the direction flip |
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else; |
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dimid = netcdf.inqDimID(ncid,mt_d{jj}); |
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varid = netcdf.defVar(ncid,mt_v{jj},'double',dimid); |
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end; |
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netcdf.putAtt(ncid,varid,'long_name',mt_n{jj}); |
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netcdf.putAtt(ncid,varid,'units',mt_u{jj}); |
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netcdf.putAtt(ncid,varid,'missing_value',fillval); |
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else; |
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warning([list_vars_plus{ii} ' not included -- it is not a MITprof variable']); |
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end; |
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gforget |
1.1 |
end; |
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gforget |
1.5 |
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netcdf.close(ncid); |
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else;%try to use old mex stuff |
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nc=netcdf([fileOut suff],'clobber'); |
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%put a couple global attributes |
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aa=sprintf(['Format: MITprof. This file was created using \n' ... |
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'the matlab toolbox which can be obtained (see README) from \n'... |
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'http://mitgcm.org/viewvc/MITgcm/MITgcm_contrib/gael/profilesMatlabProcessing/']); |
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nc.description=aa; |
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nc.date = date; |
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nc('iPROF') = iPROF; |
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nc('iDEPTH') = iDEPTH; |
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nc('lTXT') = lTXT; |
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%mt_v=[mt_v 'prof_descr']; mt_u=[mt_u ' ']; mt_n=[mt_n 'profile description']; mt_d=[mt_d 'iPROF,lTXT']; |
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nc{'prof_descr'} = ncchar('iPROF','lTXT'); |
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nc{'prof_descr'}.long_name='profile description'; |
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for ii=1:length(list_vars_plus); |
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jj=find(strcmp(mt_v,list_vars_plus{ii})); |
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if ~isempty(jj); |
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if strcmp(mt_d{jj},'iPROF,iDEPTH'); |
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nc{mt_v{jj}} = ncdouble('iPROF','iDEPTH'); |
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else; |
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nc{mt_v{jj}} = mt_d{jj}; |
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end; |
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nc{mt_v{jj}}.long_name = mt_n{jj}; |
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nc{mt_v{jj}}.units = mt_u{jj}; |
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nc{mt_v{jj}}.missing_value=fillval; |
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else; |
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warning([list_vars_plus{ii} ' not included -- it is not a MITprof varaiable']); |
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end; |
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end; |
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close(nc); |
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gforget |
1.1 |
end; |
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gforget |
1.5 |
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gforget |
1.1 |
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