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function [S] = rdmnc(varargin) |
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% S=RDMNC(FILE1,FILE2,...) |
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% S=RDMNC(FILE1,...,ITER) |
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% S=RDMNC(FILE1,...,'VAR1','VAR2',...) |
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% S=RDMNC(FILE1,...,'VAR1','VAR2',...,ITER) |
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% |
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% FILE1 ... is either a single file name (e.g. 'state.nc') or a wild-card |
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% strings expanding to a group of file names (e.g. 'state.*.nc'). |
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% There are no assumptions about suffices (e.g. 'state.*' works) |
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% VAR1 ... are model variable names as written in the MNC/netcdf file |
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% ITER is a vector of time levels (consecutive indices referring to snap-shot |
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% in the MNC/netcdf file i.e. 1,2,3,... and not model time) |
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% S is a structure with mutliple fields |
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% |
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% rdmnc() is a rudimentary wrapper for joining and reading netcdf files |
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% produced by MITgcm. It does not give the same flexibility as opening the |
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% netcdf files directly using netcdf(). It is useful for quick loading of |
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% entire model fields which are distributed in multiple netcdf files. |
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% rdmnc() also reads non-MITgcm generated netcdf files. |
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% |
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% e.g. To plot the surface temperature in last time-level written to file |
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% >> S=rdmnd('state.*','XC','YC','RC','T',Inf); |
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% >> imagesc( S.XC, S.YC, S.T(:,:,1)' ); |
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% |
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% $Header: $ |
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|
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%Defaults |
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global verbose |
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file={}; |
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files={}; |
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verbose=0; |
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varlist={}; |
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timelevels=[]; |
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|
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% Process function arguments |
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for iarg=1:nargin; |
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arg=varargin{iarg}; |
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if ischar(arg) |
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switch char(arg) |
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case 'verbose', |
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verbose=1; |
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otherwise, |
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if isempty( dir(char(arg)) ) |
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varlist{end+1}={arg}; |
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else |
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file{end+1}={arg}; |
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end |
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end |
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else |
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if isempty(timelevels) |
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timelevels=arg; |
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else |
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error('Specify the time levels in a vector and not as multiple numeric arguments') |
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end |
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end |
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end |
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|
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if verbose; disp('Verbose mode enabled'); end |
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|
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% Create list of filenames |
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for eachfile=file |
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expandedEachFile=dir(char(eachfile{1})); |
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for i=1:size(expandedEachFile,1); |
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if expandedEachFile(i).isdir==0; files{end+1}=expandedEachFile(i).name; end |
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end |
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end |
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|
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% Open each file |
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S.attributes=[]; |
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for eachfile={files{1:end}} |
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nc=netcdf(char(eachfile),'read'); |
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if ismncfile(nc) |
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S=rdmnc_local(nc,varlist,timelevels,S); |
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else |
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S=rdnetcdf_local(nc,varlist,S); |
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end |
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end |
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|
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% ----------------------------------------------------------------------------- |
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function [result] = ismncfile(nc); |
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result=~isempty(nc.('MITgcm_mnc_ver')); |
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% ----------------------------------------------------------------------------- |
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function [A] = read_att(nc); |
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global verbose |
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allatt=ncnames(att(nc)); if verbose; allatt, end |
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A='none'; |
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for attr=allatt; |
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A.(char(attr))=nc.(char(attr))(:); |
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end |
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% ----------------------------------------------------------------------------- |
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function [i0,j0,fn] = findTileOffset(S); |
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global verbose |
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fn=0; |
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if isfield(S,'attributes') & isfield(S.attributes,'global') |
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G=S.attributes.global; |
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tn=G.tile_number; |
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snx=G.sNx; sny=G.sNy; nsx=G.nSx; nsy=G.nSy; npx=G.nPx; npy=G.nPy; |
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ntx=nsx*npx;nty=nsy*npy; |
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gbi=mod(tn-1,ntx); gbj=(tn-gbi-1)/ntx; |
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i0=snx*gbi; j0=sny*gbj; |
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if isfield(S.attributes.global,'exch2_myFace') |
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fn=G.exch2_myFace; |
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end |
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else |
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i0=0;j0=0; |
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end |
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% ----------------------------------------------------------------------------- |
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function [S] = rdnetcdf_local(nc,varlist,S) |
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% Read all attributes and variable data from a netcdf file |
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% with special operations for MNC style data |
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global verbose |
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|
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% No variables specified? Default to all |
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if isempty(varlist) |
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varlist=ncnames(var(nc)); if verbose; varlist, end |
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end |
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|
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% Attributes for structure |
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S.attributes=read_att(nc); |
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|
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% Read variable data |
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for ivar=1:size(varlist,2); |
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cvar=char(varlist{ivar}); |
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tmpdata=nc{cvar}(:); |
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if isempty(tmpdata) |
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disp(['No such variable ''' cvar ''' in netcdf file' name(nc)]) |
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else |
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tmpdata=squeeze(permute(tmpdata,[9:-1:1])); |
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S.(cvar)=tmpdata; |
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S.attributes.(cvar)=read_att(nc{cvar}); |
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end |
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end |
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% ----------------------------------------------------------------------------- |
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function [S] = rdmnc_local(nc,varlist,timelevels,S) |
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% Read all attributes and variable data from a netcdf file |
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% with special operations for MNC style data |
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global verbose |
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|
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nt=size( nc('T'), 1); if verbose; nt, end |
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|
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% No variables specified? Default to all |
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if isempty(varlist) |
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varlist=ncnames(var(nc)); if verbose; varlist, end |
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end |
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|
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% No iterations specified? Default to all |
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if isempty(timelevels) | isnan(timelevels) |
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timelevels=1:nt; |
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elseif timelevels == Inf |
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timelevels=nt; |
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end |
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|
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% Sanity checks |
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if max( find(timelevels > nt) ) |
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error('Requested time level is beyond time dimension in netcdf file') |
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end |
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|
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% Attributes for structure |
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if timelevels>0; S.timelevels_read_from_file=timelevels; end |
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S.attributes.global=read_att(nc); |
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|
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% Read variable data |
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for ivar=1:size(varlist,2); |
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cvar=char(varlist{ivar}); if verbose; cvar, end |
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if isempty(nc{cvar}) |
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disp(['No such variable ''' cvar ''' in MNC file ' name(nc)]) |
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continue |
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end |
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dims=ncnames(dim(nc{cvar})); |
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if dims{1}=='T' |
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if verbose; disp(['Reading variable ''' cvar ''' with record dimension']); end |
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tmpdata=nc{cvar}(timelevels,:); |
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else |
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if verbose; disp(['Reading variable ''' cvar '''']); end |
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tmpdata=nc{cvar}(:); |
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end |
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if isempty(tmpdata) |
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error(['No such variable ''' cvar ''' in MNC file ' name(nc)]) |
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else |
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tmpdata=squeeze(permute(tmpdata,[9:-1:1])); |
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[ni nj nk nm nn no np]=size(tmpdata); |
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if np~=1; error('Wow! This is a very high dimension variable...'); end |
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[i0,j0,fn]=findTileOffset(S); |
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cdim=dims{end}; if cdim(1)~='X'; i0=0; end |
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cdim=dims{end}; if cdim(1)=='Y'; i0=j0; j0=0; end |
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if length(dims)>1; |
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cdim=dims{end-1}; if cdim(1)~='Y'; j0=0; end |
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else |
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j0=0; |
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end |
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S.(cvar)(i0+(1:ni),j0+(1:nj),(1:nk),(1:nm),(1:nn),(1:no),(1:np))=tmpdata; |
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S.attributes.(cvar)=read_att(nc{cvar}); |
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end |
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end |
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|
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if isempty(S) |
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error('Something didn''t work!!!') |
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end |
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% ----------------------------------------------------------------------------- |
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