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function [S] = rdmnc(varargin) |
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|
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% Usage: |
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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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% Input: |
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% FILE1 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 Model variable names as written in the MNC/netcdf file. |
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% ITER Vector of iterations in the MNC/netcdf files, not model time. |
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% |
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% Output: |
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% S Structure with fields corresponding to 'VAR1', 'VAR2', ... |
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% |
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% Description: |
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% This function is a rudimentary wrapper for joining and reading netcdf |
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% files produced by MITgcm. It does not give the same flexibility as |
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% opening the netcdf files directly using netcdf(), but is useful for |
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% quick loading of entire model fields which are distributed in multiple |
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% netcdf files. |
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% |
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% Example: |
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% >> S=rdmnd('state.*','XC','YC','T'); |
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% >> imagesc( S.XC, S.YC, S.T(:,:,1)' ); |
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% |
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% Author: Alistair Adcroft |
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% Modifications: Daniel Enderton |
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|
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% $Header: /u/gcmpack/MITgcm/utils/matlab/rdmnc.m,v 1.16 2007/03/07 09:59:53 mlosch Exp $ |
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% $Name: $ |
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|
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% Initializations |
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dBug=0; |
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file={}; |
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filepaths={}; |
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files={}; |
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varlist={}; |
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iters=[]; |
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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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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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else |
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if isempty(iters) |
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iters=arg; |
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else |
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error(['The only allowed numeric argument is iterations',... |
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' to read in as a vector for the last argument']); |
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end |
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end |
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end |
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if isempty(file) |
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if isempty(varlist), |
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fprintf( 'No file name in argument list\n'); |
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else |
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fprintf(['No file in argument list:\n ==> ',char(varlist(1))]); |
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for i=2:size(varlist,2), fprintf([' , ',char(varlist(i))]); end |
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fprintf(' <==\n'); |
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end |
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error(' check argument list !!!'); |
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end |
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|
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% Create list of filenames |
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for eachfile=file |
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filepathtemp=eachfile{:}; |
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indecies = find(filepathtemp==filesep); |
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if ~isempty(indecies) |
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filepathtemp = filepathtemp(1:indecies(end)); |
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else |
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filepathtemp = ''; |
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end |
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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 |
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files{end+1}=expandedEachFile(i).name; |
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filepaths{end+1}=filepathtemp; |
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end |
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end |
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end |
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|
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|
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% If iterations unspecified, open all the files and make list of all the |
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% iterations that appear, use this iterations list for data extraction. |
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if isempty(iters) |
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iters = []; |
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for ieachfile=1:length(files) |
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eachfile = [filepaths{ieachfile},files{ieachfile}]; |
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nc=netcdf(char(eachfile),'read'); |
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nciters = nc{'iter'}(:); |
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if isempty(nciters), nciters = nc{'T'}(:); end |
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iters = [iters,nciters']; |
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close(nc); |
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end |
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iters = unique(iters'); |
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end |
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|
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% Cycle through files for data extraction. |
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S.attributes=[]; |
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for ieachfile=1:length(files) |
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eachfile = [filepaths{ieachfile},files{ieachfile}]; |
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if dBug > 0, fprintf([' open: ',eachfile]); end |
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nc=netcdf(char(eachfile),'read'); |
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S=rdmnc_local(nc,varlist,iters,S,dBug); |
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close(nc); |
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end |
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|
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|
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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% |
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% Local functions % |
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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% |
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|
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function [A] = read_att(nc); |
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allatt=ncnames(att(nc)); |
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if ~isempty(allatt) |
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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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else |
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A = 'none'; |
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end |
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|
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function [i0,j0,fn] = findTileOffset(S); |
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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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%[snx,sny,nsx,nsy,npx,npy,ntx,nty,i0,j0,fn]; |
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|
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function [S] = rdmnc_local(nc,varlist,iters,S,dBug) |
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|
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fiter = nc{'iter'}(:); % File iterations present |
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if isempty(fiter), fiter = nc{'T'}(:); end |
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if isinf(iters); iters = fiter(end); end |
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if isnan(iters); iters = fiter; end |
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[fii,dii] = ismember(fiter,iters); fii = find(fii); % File iteration index |
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dii = dii(find(dii ~= 0)); % Data interation index |
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if dBug > 0, |
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fprintf(' ; fii='); fprintf(' %i',fii); |
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fprintf(' ; dii='); fprintf(' %i',dii); fprintf(' \n'); |
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end |
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|
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% No variables specified? Default to all |
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if isempty(varlist), varlist=ncnames(var(nc)); end |
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|
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% Attributes for structure |
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if iters>0; S.iters_from_file=iters; end |
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S.attributes.global=read_att(nc); |
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[pstr,netcdf_fname,ext] = fileparts(name(nc)); |
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if strcmp(netcdf_fname(end-3:end),'glob') |
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% assume it is a global file produced by gluemnc and change some |
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% attributes |
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S.attributes.global.sNx = S.attributes.global.Nx; |
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S.attributes.global.sNy = S.attributes.global.Ny; |
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S.attributes.global.nPx = 1; |
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S.attributes.global.nSx = 1; |
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S.attributes.global.nPy = 1; |
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S.attributes.global.nSy = 1; |
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S.attributes.global.tile_number = 1; |
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S.attributes.global.nco_openmp_thread_number = 1; |
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end |
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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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|
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cvar=char(varlist{ivar}); |
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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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|
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dims = ncnames(dim(nc{cvar})); % Dimensions |
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sizVar = size(nc{cvar}); nDims=length(sizVar); |
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if dims{1} == 'T' |
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if isempty(find(fii)), error('Iters not found'); end |
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it = length(dims); |
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tmpdata = nc{cvar}(fii,:); |
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%- leading unity dimensions get lost; add them back: |
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tmpdata=reshape(tmpdata,[length(fii) sizVar(2:end)]); |
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else |
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it = 0; |
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tmpdata = nc{cvar}(:); |
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%- leading unity dimensions get lost; add them back: |
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tmpdata=reshape(tmpdata,sizVar); |
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end |
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|
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if dBug > 1, |
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fprintf([' var:',cvar,': nDims=%i ('],nDims);fprintf(' %i',size(nc{cvar})); |
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fprintf('):%i,nD=%i,it=%i ;',length(size(tmpdata)),length(dims),it); |
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end |
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if length(dims) > 1, |
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tmpdata=permute(tmpdata,[nDims:-1:1]); |
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end |
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if dBug > 1, |
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% fprintf('(tmpdata:');fprintf(' %i',size(tmpdata)); fprintf(')'); |
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end |
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[ni nj nk nm nn no np]=size(tmpdata); |
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|
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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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if dBug > 1, |
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fprintf(' i0,ni= %i %i; j,nj= %i %i; nk=%i :',i0,ni,j0,nj,nk); |
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end |
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|
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Sstr = ''; |
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for istr = 1:max(nDims,length(dims)), |
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if istr == it, Sstr = [Sstr,'dii,']; |
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elseif istr == 1, Sstr = [Sstr,'i0+(1:ni),']; |
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elseif istr == 2, Sstr = [Sstr,'j0+(1:nj),']; |
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elseif istr == 3, Sstr = [Sstr,'(1:nk),']; |
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elseif istr == 4, Sstr = [Sstr,'(1:nm),']; |
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elseif istr == 5, Sstr = [Sstr,'(1:nn),']; |
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elseif istr == 6, Sstr = [Sstr,'(1:no),']; |
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elseif istr == 7, Sstr = [Sstr,'(1:np),']; |
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else, error('Can''t handle this many dimensions!'); |
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end |
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end |
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eval(['S.(cvar)(',Sstr(1:end-1),')=tmpdata;']) |
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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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if dBug > 1, fprintf(' %i',size(S.(cvar))); fprintf('\n'); end |
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|
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S.attributes.(cvar)=read_att(nc{cvar}); |
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% replace missing or FillValues with NaN |
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attnames=fieldnames(S.attributes.(cvar)); |
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if ~isempty(attnames) |
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for k=1:length(attnames) |
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if strcmp(attnames{k},'missing_value') ... |
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| strcmp(attnames{k},'FillValue_') |
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S.(cvar)(S.(cvar) == S.attributes.(cvar).(attnames{k})) = NaN; |
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end |
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end |
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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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