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gforget |
1.1 |
%function: MITprof_load |
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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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%usage: [MITprof]=MITprof_load(fileIn); |
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% ---> loads full data set |
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% [MITprof]=MITprof_load(fileIn,list_vars); |
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% ---> loads only the files listed in list_vars cell |
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% array (e.g. list_vars={'prof_T','prof_Tweight'}) |
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% plus the one dimensional information (prof_lon etc.) |
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% |
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%note: this does the same as MITprof_read, but |
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% - removes empty fields |
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% - replaces missing values with NaN |
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% - adds a couple fields |
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% - replaces prof_descr with a cell form |
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% |
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%inputs: fileIn data file name |
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% list_vars variables list (optional) |
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% |
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%outputs: MITprof structure containing the various fields/vectors |
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function [MITprof]=MITprof_load(fileIn,varargin); |
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gforget |
1.2 |
global useNativeMatlabNetcdf; if isempty(useNativeMatlabNetcdf); useNativeMatlabNetcdf = ~isempty(which('netcdf.open')); end; |
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gforget |
1.1 |
if nargin>1; list_vars=varargin{1}; |
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else; list_vars={'prof_T','prof_Tweight','prof_Tmask','prof_Testim','prof_Tflag',... |
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'prof_S','prof_Sweight','prof_Smask','prof_Sestim','prof_Sflag',... |
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'prof_U','prof_Uweight','prof_Umask',... |
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'prof_V','prof_Vweight','prof_Vmask',... |
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'prof_ptr','prof_ptrweight','prof_ptrmask',... |
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'prof_ssh','prof_sshweight','prof_sshmask'}; |
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end; |
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list_vars_plus=[{'prof_depth','prof_date','prof_YYYYMMDD','prof_HHMMSS',... |
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'prof_lon','prof_lat','prof_basin','prof_point','prof_descr'}... |
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list_vars]; |
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%get directory name: |
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tmp1=strfind(fileIn,'/'); |
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if ~isempty(tmp1); dirIn=fileIn(1:tmp1(end)); else; dirIn='./'; end; |
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%check that file exists: |
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tmp1=dir(fileIn); |
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if isempty(tmp1); tmp1=dir([fileIn '.nc']); end; |
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if isempty(tmp1); error([fileIn ' file not found']); end; |
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for ii=1:length(list_vars_plus); |
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ncload([dirIn tmp1.name],list_vars_plus{ii}); |
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%nan mask the data: |
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eval(['test0=~isempty(' list_vars_plus{ii} ');']); |
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gforget |
1.2 |
if test0&useNativeMatlabNetcdf; |
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gforget |
1.1 |
f = netcdf.open([dirIn tmp1.name], 'nowrite'); |
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varid = netcdf.inqVarId(f,list_vars_plus{ii}); |
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test1=~isempty(find(strcmp(ncatts(f,varid),'missing_value'))); |
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if test1; |
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spval = double(netcdf.getAtt(f,varid,'missing_value')); |
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eval([list_vars_plus{ii} '(' list_vars_plus{ii} '==spval)=NaN;']); |
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end; |
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netcdf.close(f); |
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gforget |
1.2 |
elseif test0; |
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f = netcdf(fileIn, 'nowrite'); |
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spval = f{list_vars_plus{ii}}.missing_value(:); |
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if isempty(spval); |
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spval = f{list_vars_plus{ii}}.FillValue_(:); |
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end |
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if ~isempty(spval); |
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eval([list_vars_plus{ii} '(' list_vars_plus{ii} '==spval)=NaN;']); |
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end; |
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close(f); |
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gforget |
1.1 |
end; |
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gforget |
1.3 |
%fix old name convention: |
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if ii==1&isempty(prof_depth); ncload([dirIn tmp1.name],'depth'); prof_depth=depth; clear depth; end; |
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gforget |
1.1 |
if ii==1; eval(['MITprof=struct(''prof_depth'',prof_depth);']); |
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elseif ~isempty(tmp1); eval(['MITprof.' list_vars_plus{ii} '=' list_vars_plus{ii} ';']); |
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end; eval(['clear ' list_vars_plus{ii} ']);']); |
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end; |
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gforget |
1.3 |
%make sure that lon is -180+180: |
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%------------------------------- |
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tmp_lon=MITprof.prof_lon; |
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tmp_lon(find(tmp_lon>180))=tmp_lon(find(tmp_lon>180))-360; |
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MITprof.prof_lon=tmp_lon; |
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gforget |
1.1 |
%replace prof_descr with cell array: |
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%---------------------------------- |
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gforget |
1.2 |
np=length(MITprof.prof_lon); prof_descr=cell(np,1); |
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gforget |
1.1 |
for pp=1:np; prof_descr(pp)={MITprof.prof_descr(pp,:)}; end; |
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gforget |
1.2 |
MITprof.prof_descr=prof_descr; |
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gforget |
1.1 |
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%get rid of empty variables: |
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%--------------------------- |
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fldNames=fieldnames(MITprof); |
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for iFld=1:length(fldNames); |
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eval(['test0=isempty(MITprof.' fldNames{iFld} ');']); |
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if test0; MITprof=rmfield(MITprof,fldNames{iFld}); end; |
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end; |
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%add a couple things: |
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%-------------------- |
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MITprof.np=length(MITprof.prof_lon); |
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MITprof.nr=length(MITprof.prof_depth); |
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