| 1 |
function []=MITprof_create(fileOut,MITprofCur,varargin); |
| 2 |
% MITPROF_CREATE(fileOut,MITprofCur,list_vars) |
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% Creates a file in the MITprof format. The list of variables |
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% can further be specified via list_vars (optional). |
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|
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% check that file exists and add prefix and suffix if necessary |
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[pathstr, name, ext] = fileparts(fileOut); |
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if isempty(pathstr) | strcmp(pathstr,'.'), pathstr=pwd; end |
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if isempty(ext) | ~strcmp(ext,'.nc'), ext='.nc'; end |
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fileOut=[pathstr '/' name ext]; |
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|
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%define netcdf dimensions : |
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prof_depth=MITprofCur.prof_depth; |
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prof_depth=reshape(prof_depth,length(prof_depth),1); |
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iPROF=MITprofCur.np; iDEPTH=MITprofCur.nr; |
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if isfield(MITprofCur,'prof_interp_weights'); |
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iINTERP=size(MITprofCur.prof_interp_weights,2); |
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addGrid=1; |
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else; |
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iINTERP=1; |
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addGrid=0; |
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end; |
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lTXT=30; fillval=double(-9999); |
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|
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%=============list of variables that will actually be in the file==============% |
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if nargin>2; |
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list_vars=varargin{1}; |
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else; |
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list_vars={'prof_depth','prof_descr','prof_date','prof_YYYYMMDD','prof_HHMMSS',... |
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'prof_lon','prof_lat','prof_basin','prof_point','prof_flag','prof_T','prof_Tweight','prof_Testim','prof_Terr','prof_Tflag',... |
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'prof_S','prof_Sweight','prof_Sestim','prof_Serr','prof_Sflag','prof_D','prof_Destim'}; |
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if addGrid; |
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list_vars={list_vars{:},'prof_interp_XC11','prof_interp_YC11','prof_interp_XCNINJ','prof_interp_YCNINJ'}; |
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list_vars={list_vars{:},'prof_interp_i','prof_interp_j','prof_interp_lon','prof_interp_lat','prof_interp_weights'}; |
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end; |
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end; |
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|
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% eliminate duplicates |
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[list,m]=unique(list_vars); |
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list_vars=list_vars(sort(m)); |
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|
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list_vars_plus={}; |
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for ii=1:length(list_vars); |
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if ~isempty(strfind(list_vars{ii},'estim'))&... |
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~strcmp(list_vars{ii},'prof_Testim')&... |
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~strcmp(list_vars{ii},'prof_Sestim'); |
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list_vars_plus={list_vars_plus{:},list_vars{ii}(1:end-5)}; |
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end; |
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end; |
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|
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%==========masters table of variables, units, names and dimensions=============% |
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|
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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']; |
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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 'degrees_east']; 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 'degrees_north']; 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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mt_v=[mt_v 'prof_flag']; mt_u=[mt_u ' ']; mt_n=[mt_n 'flag = i > 0 for suspicious profile ']; 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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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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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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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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% |
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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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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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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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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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% |
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for ii=1:length(list_vars_plus); |
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mt_v=[mt_v list_vars_plus{ii}]; mt_u=[mt_u 'unknown']; mt_n=[mt_n 'unknown']; mt_d=[mt_d 'iPROF,iDEPTH']; |
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mt_v=[mt_v [list_vars_plus{ii} 'weight']]; mt_u=[mt_u '(unknown)^-2']; mt_n=[mt_n 'unknown least-square weight']; mt_d=[mt_d 'iPROF,iDEPTH']; |
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mt_v=[mt_v [list_vars_plus{ii} 'estim']]; mt_u=[mt_u 'unknown']; mt_n=[mt_n 'unknown estimate (e.g. from atlas)']; mt_d=[mt_d 'iPROF,iDEPTH']; |
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mt_v=[mt_v [list_vars_plus{ii} 'err']]; mt_u=[mt_u 'unknown']; mt_n=[mt_n 'unknown instrumental error']; mt_d=[mt_d 'iPROF,iDEPTH']; |
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mt_v=[mt_v [list_vars_plus{ii} 'flag']]; 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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end; |
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% |
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list_interpr={'prof_interp_XC11','prof_interp_YC11','prof_interp_XCNINJ','prof_interp_YCNINJ'}; |
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for ii=1:length(list_interpr); |
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mt_v=[mt_v list_interpr{ii}]; mt_u=[mt_u 'unknown']; mt_n=[mt_n 'interpolation variable']; mt_d=[mt_d 'iPROF']; |
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end; |
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list_interpr={'prof_interp_i','prof_interp_j','prof_interp_lon','prof_interp_lat','prof_interp_weights'}; |
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for ii=1:length(list_interpr); |
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mt_v=[mt_v list_interpr{ii}]; mt_u=[mt_u 'unknown']; mt_n=[mt_n 'interpolation variable']; mt_d=[mt_d 'iPROF,iINTERP']; |
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end; |
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% |
| 93 |
if 0; |
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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']; |
| 100 |
% |
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mt_v=[mt_v 'prof_D']; mt_u=[mt_u 'me']; mt_n=[mt_n 'variable depth']; mt_d=[mt_d 'iPROF,iDEPTH']; |
| 102 |
mt_v=[mt_v 'prof_Destim']; mt_u=[mt_u 'me']; mt_n=[mt_n 'variable depth estimate (e.g. from atlas)']; mt_d=[mt_d 'iPROF,iDEPTH']; |
| 103 |
% |
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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']; |
| 105 |
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']; |
| 106 |
mt_v=[mt_v 'prof_ssh']; mt_u=[mt_u 'cm']; mt_n=[mt_n 'sea surface height']; mt_d=[mt_d 'iPROF']; |
| 107 |
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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end; |
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|
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%=============================create the file=================================% |
| 111 |
|
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% write the netcdf structure |
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ncid=nccreateFile(fileOut,'clobber'); |
| 114 |
|
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aa=sprintf(['The contents of this MITprof file were processed \n' ... |
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'using the MITprof matlab toolbox which can be obtained from \n'... |
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'http://mitgcm.org/viewvc/MITgcm/MITgcm_contrib/gael/profilesMatlabProcessing/']); |
| 118 |
ncputAtt(ncid,'','Format',aa); |
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ncputAtt(ncid,'','date',date); |
| 120 |
|
| 121 |
ncdefDim(ncid,'iPROF',iPROF); |
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ncdefDim(ncid,'iDEPTH',iDEPTH); |
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if addGrid; ncdefDim(ncid,'iINTERP',iINTERP); end; |
| 124 |
ncdefDim(ncid,'lTXT',lTXT); |
| 125 |
|
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for ii=1:length(list_vars); |
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jj=find(strcmp(mt_v,list_vars{ii})); |
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if ~isempty(jj); |
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if strcmp(mt_d{jj},'iPROF,iDEPTH'); |
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ncdefVar(ncid,mt_v{jj},'double',{'iDEPTH','iPROF'});%note the direction flip |
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elseif strcmp(mt_d{jj},'iPROF,iINTERP'); |
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ncdefVar(ncid,mt_v{jj},'double',{'iINTERP','iPROF'});%note the direction flip |
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else; |
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ncdefVar(ncid,mt_v{jj},'double',{mt_d{jj}}); |
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end; |
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ncputAtt(ncid,mt_v{jj},'long_name',mt_n{jj}); |
| 137 |
ncputAtt(ncid,mt_v{jj},'units',mt_u{jj}); |
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ncputAtt(ncid,mt_v{jj},'missing_value',fillval); |
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ncputAtt(ncid,mt_v{jj},'_FillValue',fillval); |
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else; |
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if strcmp(list_vars{ii},'prof_descr') |
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ncdefVar(ncid,'prof_descr','char',{'lTXT','iPROF'}); |
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ncputAtt(ncid,'prof_descr','long_name','profile description'); |
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else |
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warning([list_vars{ii} ' not included -- it is not a MITprof variable']); |
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end |
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end; |
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end; |
| 149 |
|
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ncclose(ncid); |
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|
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%=============================set prof_depth=================================% |
| 153 |
|
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ncid=ncopen(fileOut,'write'); |
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ncputvar(ncid,'prof_depth',prof_depth); |
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ncclose(ncid); |
| 157 |
|
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