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function [S] = rdmnc(varargin) |
2 |
|
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% Usage: |
4 |
% S=RDMNC(FILE1,FILE2,...) |
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% S=RDMNC(FILE1,...,ITER) |
6 |
% 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 1.21 2010/05/16 08:56:43 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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% find out if matlab's generic netcdf API is available |
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% if not assume that Chuck Denham's netcdf toolbox is installed |
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usemexcdf = isempty(which('netcdf.open')); |
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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; |
60 |
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) |
67 |
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'); |
73 |
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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if usemexcdf |
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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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close(nc); |
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else |
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% the parser complains about "netcdf.open" when the matlab netcdf |
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% API is not available, even when it is not used so we have to |
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% avoid the use of "netcdf.open", etc in this function |
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nciters = ncgetvar(char(eachfile),'iter'); |
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if isempty(nciters), nciters = ncgetvar(char(eachfile),'T'); end |
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end |
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iters = [iters,nciters']; |
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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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if usemexcdf |
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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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else |
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% the parser complains about "netcdf.open" when the matlab netcdf |
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% API is not available, even when it is not used so we have to |
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% avoid the use of "netcdf.open", etc in this function |
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S=rdmnc_local_matlabAPI(char(eachfile),varlist,iters,S,dBug); |
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end |
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end |
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|
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return |
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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}); |
206 |
if isempty(nc{cvar}) |
207 |
disp(['No such variable ''',cvar,''' in MNC file ',name(nc)]); |
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continue |
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end |
210 |
|
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dims = ncnames(dim(nc{cvar})); % Dimensions |
212 |
sizVar = size(nc{cvar}); nDims=length(sizVar); |
213 |
if dims{1} == 'T' |
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if isempty(find(fii)), error('Iters not found'); end |
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it = length(dims); |
216 |
tmpdata = nc{cvar}(fii,:); |
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% leading unity dimensions get lost; add them back: |
218 |
tmpdata=reshape(tmpdata,[length(fii) sizVar(2:end)]); |
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else |
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it = 0; |
221 |
tmpdata = nc{cvar}(:); |
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% leading unity dimensions get lost; add them back: |
223 |
tmpdata=reshape(tmpdata,sizVar); |
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end |
225 |
|
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if dBug > 1, |
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fprintf([' var:',cvar,': nDims=%i ('],nDims);fprintf(' %i',size(nc{cvar})); |
228 |
fprintf('):%i,nD=%i,it=%i ;',length(size(tmpdata)),length(dims),it); |
229 |
end |
230 |
if length(dims) > 1, |
231 |
tmpdata=permute(tmpdata,[nDims:-1:1]); |
232 |
end |
233 |
if dBug > 1, |
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% fprintf('(tmpdata:');fprintf(' %i',size(tmpdata)); fprintf(')'); |
235 |
end |
236 |
[ni nj nk nm nn no np]=size(tmpdata); |
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|
238 |
[i0,j0,fn]=findTileOffset(S); |
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cdim=dims{end}; if cdim(1)~='X'; i0=0; end |
240 |
cdim=dims{end}; if cdim(1)=='Y'; i0=j0; j0=0; end |
241 |
if length(dims)>1; |
242 |
cdim=dims{end-1}; if cdim(1)~='Y'; j0=0; end |
243 |
else |
244 |
j0=0; |
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end |
246 |
if dBug > 1, |
247 |
fprintf(' i0,ni= %i %i; j,nj= %i %i; nk=%i :',i0,ni,j0,nj,nk); |
248 |
end |
249 |
|
250 |
Sstr = ''; |
251 |
for istr = 1:max(nDims,length(dims)), |
252 |
if istr == it, Sstr = [Sstr,'dii,']; |
253 |
elseif istr == 1, Sstr = [Sstr,'i0+(1:ni),']; |
254 |
elseif istr == 2, Sstr = [Sstr,'j0+(1:nj),']; |
255 |
elseif istr == 3, Sstr = [Sstr,'(1:nk),']; |
256 |
elseif istr == 4, Sstr = [Sstr,'(1:nm),']; |
257 |
elseif istr == 5, Sstr = [Sstr,'(1:nn),']; |
258 |
elseif istr == 6, Sstr = [Sstr,'(1:no),']; |
259 |
elseif istr == 7, Sstr = [Sstr,'(1:np),']; |
260 |
else, error('Can''t handle this many dimensions!'); |
261 |
end |
262 |
end |
263 |
eval(['S.(cvar)(',Sstr(1:end-1),')=tmpdata;']) |
264 |
%S.(cvar)(i0+(1:ni),j0+(1:nj),(1:nk),(1:nm),(1:nn),(1:no),(1:np))=tmpdata; |
265 |
if dBug > 1, fprintf(' %i',size(S.(cvar))); fprintf('\n'); end |
266 |
|
267 |
S.attributes.(cvar)=read_att(nc{cvar}); |
268 |
% replace missing or FillValues with NaN |
269 |
if isfield(S.attributes.(cvar),'missing_value'); |
270 |
misval = S.attributes.(cvar).missing_value; |
271 |
S.(cvar)(S.(cvar) == misval) = NaN; |
272 |
end |
273 |
if isfield(S.attributes.(cvar),'FillValue_'); |
274 |
misval = S.attributes.(cvar).FillValue_; |
275 |
S.(cvar)(S.(cvar) == misval) = NaN; |
276 |
end |
277 |
|
278 |
end % for ivar |
279 |
|
280 |
if isempty(S) |
281 |
error('Something didn''t work!!!'); |
282 |
end |
283 |
|
284 |
return |
285 |
|
286 |
function [S] = rdmnc_local_matlabAPI(fname,varlist,iters,S,dBug) |
287 |
|
288 |
fiter = ncgetvar(fname,'iter'); % File iterations present |
289 |
if isempty(fiter), fiter = ncgetvar(fname,'T'); end |
290 |
if isinf(iters); iters = fiter(end); end |
291 |
if isnan(iters); iters = fiter; end |
292 |
[fii,dii] = ismember(fiter,iters); fii = find(fii); % File iteration index |
293 |
dii = dii(find(dii ~= 0)); % Data interation index |
294 |
if dBug > 0, |
295 |
fprintf(' ; fii='); fprintf(' %i',fii); |
296 |
fprintf(' ; dii='); fprintf(' %i',dii); fprintf(' \n'); |
297 |
end |
298 |
|
299 |
% now open the file for reading |
300 |
nc = netcdf.open(fname,'NC_NOWRITE'); |
301 |
% get basic information about netcdf file |
302 |
[ndims nvars natts recdim] = netcdf.inq(nc); |
303 |
|
304 |
% No variables specified? Default to all |
305 |
if isempty(varlist), |
306 |
for k=0:nvars-1 |
307 |
varlist{k+1} = netcdf.inqVar(nc,k); |
308 |
end |
309 |
end |
310 |
|
311 |
% Attributes for structure |
312 |
if iters>0; S.iters_from_file=iters; end |
313 |
S.attributes.global=ncgetatt(nc,'global'); |
314 |
[pstr,netcdf_fname,ext] = fileparts(fname); |
315 |
if strcmp(netcdf_fname(end-3:end),'glob') |
316 |
% assume it is a global file produced by gluemnc and change some |
317 |
% attributes |
318 |
S.attributes.global.sNx = S.attributes.global.Nx; |
319 |
S.attributes.global.sNy = S.attributes.global.Ny; |
320 |
S.attributes.global.nPx = 1; |
321 |
S.attributes.global.nSx = 1; |
322 |
S.attributes.global.nPy = 1; |
323 |
S.attributes.global.nSy = 1; |
324 |
S.attributes.global.tile_number = 1; |
325 |
S.attributes.global.nco_openmp_thread_number = 1; |
326 |
end |
327 |
|
328 |
% Read variable data |
329 |
for ivar=1:size(varlist,2) |
330 |
|
331 |
cvar=char(varlist{ivar}); |
332 |
varid=ncfindvarid(nc,cvar); |
333 |
if isempty(varid) |
334 |
disp(['No such variable ''',cvar,''' in MNC file ',fname]); |
335 |
continue |
336 |
end |
337 |
|
338 |
[varname,xtype,dimids,natts] = netcdf.inqVar(nc,varid); |
339 |
% does this variable contain a record (unlimited) dimension? |
340 |
[isrecvar,recpos] = ismember(recdim,dimids); |
341 |
|
342 |
% Dimensions |
343 |
clear sizVar dims |
344 |
for k=1:length(dimids) |
345 |
[dims{k}, sizVar(k)] = netcdf.inqDim(nc,dimids(k)); |
346 |
end |
347 |
nDims=length(sizVar); |
348 |
if isrecvar |
349 |
if isempty(find(fii)), error('Iters not found'); end |
350 |
it = length(dims); |
351 |
if length(dimids) == 1 |
352 |
% just a time or iteration variable, this will result in a vector |
353 |
% and requires special treatment |
354 |
icount=1; |
355 |
tmpdata = zeros(length(fii),1); |
356 |
for k=1:length(fii) |
357 |
istart = fii(k)-1; |
358 |
tmpdata(k) = netcdf.getVar(nc,varid,istart,icount,'double'); |
359 |
end |
360 |
else |
361 |
% from now on we assume that the record dimension is always the |
362 |
% last dimension. This may not always be the case |
363 |
if recpos ~= nDims |
364 |
error(sprintf('%s\n%s\n%s%s%i%s%i', ... |
365 |
['The current code assumes that the record ' ... |
366 |
'dimension is the last dimension,'], ... |
367 |
'this is not the case for variable', cvar, ... |
368 |
': nDims = ', nDims, ... |
369 |
', position of recDim = ', recpos)) |
370 |
end |
371 |
istart = zeros(1,it); % indexing starts a 0 |
372 |
icount = sizVar; |
373 |
% we always want to get only on time slice at a time |
374 |
icount(recpos) = 1; |
375 |
% make your life simpler by putting the time dimension first |
376 |
tmpdata = zeros([length(fii) sizVar(1:end-1)]); |
377 |
for k=1:length(fii) |
378 |
istart(recpos) = fii(k)-1; % indexing starts at 0 |
379 |
tmp = netcdf.getVar(nc,varid,istart,icount,'double'); |
380 |
tmpdata(k,:) = tmp(:); |
381 |
end |
382 |
% move time dimension to the end ... |
383 |
tmpdata = shiftdim(tmpdata,1); |
384 |
% ... and restore original shape |
385 |
tmpdata = reshape(tmpdata,[sizVar(1:end-1) length(fii)]); |
386 |
end |
387 |
else |
388 |
it = 0; |
389 |
tmpdata = netcdf.getVar(nc,varid,'double'); |
390 |
end |
391 |
% |
392 |
if dBug > 1, |
393 |
fprintf([' var:',cvar,': nDims=%i ('],nDims);fprintf(' %i',sizVar); |
394 |
fprintf('):%i,nD=%i,it=%i ;',length(size(tmpdata)),length(dims),it); |
395 |
end |
396 |
[ni nj nk nm nn no np]=size(tmpdata); |
397 |
% |
398 |
[i0,j0,fn]=findTileOffset(S); |
399 |
cdim=dims{1}; if cdim(1)~='X'; i0=0; end |
400 |
cdim=dims{1}; if cdim(1)=='Y'; i0=j0; j0=0; end |
401 |
if length(dims)>1; |
402 |
cdim=dims{2}; if cdim(1)~='Y'; j0=0; end |
403 |
else |
404 |
j0=0; |
405 |
end |
406 |
if dBug > 1, |
407 |
fprintf(' i0,ni= %i %i; j,nj= %i %i; nk=%i :',i0,ni,j0,nj,nk); |
408 |
end |
409 |
% |
410 |
Sstr = ''; |
411 |
for istr = 1:max(nDims,length(dims)), |
412 |
if istr == it, Sstr = [Sstr,'dii,']; |
413 |
elseif istr == 1, Sstr = [Sstr,'i0+(1:ni),']; |
414 |
elseif istr == 2, Sstr = [Sstr,'j0+(1:nj),']; |
415 |
elseif istr == 3, Sstr = [Sstr,'(1:nk),']; |
416 |
elseif istr == 4, Sstr = [Sstr,'(1:nm),']; |
417 |
elseif istr == 5, Sstr = [Sstr,'(1:nn),']; |
418 |
elseif istr == 6, Sstr = [Sstr,'(1:no),']; |
419 |
elseif istr == 7, Sstr = [Sstr,'(1:np),']; |
420 |
else, error('Can''t handle this many dimensions!'); |
421 |
end |
422 |
end |
423 |
eval(['S.(cvar)(',Sstr(1:end-1),')=tmpdata;']) |
424 |
%S.(cvar)(i0+(1:ni),j0+(1:nj),(1:nk),(1:nm),(1:nn),(1:no),(1:np))=tmpdata; |
425 |
if dBug > 1, fprintf(' %i',size(S.(cvar))); fprintf('\n'); end |
426 |
% |
427 |
S.attributes.(cvar)=ncgetatt(nc,cvar); |
428 |
% replace missing or FillValues with NaN |
429 |
if isfield(S.attributes.(cvar),'missing_value'); |
430 |
misval = S.attributes.(cvar).missing_value; |
431 |
S.(cvar)(S.(cvar) == misval) = NaN; |
432 |
end |
433 |
if isfield(S.attributes.(cvar),'FillValue_'); |
434 |
misval = S.attributes.(cvar).FillValue_; |
435 |
S.(cvar)(S.(cvar) == misval) = NaN; |
436 |
end |
437 |
|
438 |
end % for ivar |
439 |
|
440 |
% close the file |
441 |
netcdf.close(nc); |
442 |
|
443 |
if isempty(S) |
444 |
error('Something didn''t work!!!'); |
445 |
end |
446 |
|
447 |
return |
448 |
|
449 |
function vf = ncgetvar(fname,varname) |
450 |
% read a netcdf variable |
451 |
|
452 |
nc=netcdf.open(fname,'NC_NOWRITE'); |
453 |
% find out basics about the files |
454 |
[ndims nvars natts dimm] = netcdf.inq(nc); |
455 |
vf = []; |
456 |
varid = []; |
457 |
for k=0:nvars-1 |
458 |
if strcmp(netcdf.inqVar(nc,k),varname) |
459 |
varid = netcdf.inqVarId(nc,varname); |
460 |
end |
461 |
end |
462 |
if ~isempty(varid); |
463 |
[varn,xtype,dimids,natts] = netcdf.inqVar(nc,varid); |
464 |
% get data |
465 |
vf = double(netcdf.getVar(nc,varid)); |
466 |
else |
467 |
% do nothing |
468 |
end |
469 |
netcdf.close(nc); |
470 |
|
471 |
return |
472 |
|
473 |
function misval = ncgetmisval(nc,varid) |
474 |
|
475 |
[varname,xtype,dimids,natts] = netcdf.inqVar(nc,varid); |
476 |
misval = []; |
477 |
for k=0:natts-1 |
478 |
attn = netcdf.inqAttName(nc,varid,k); |
479 |
if strcmp(attn,'missing_value') | strcmp(attn,'_FillValue') |
480 |
misval = double(netcdf.getAtt(nc,varid,attname)); |
481 |
end |
482 |
end |
483 |
|
484 |
function A = ncgetatt(nc,varname) |
485 |
% get all attributes and put them into a struct |
486 |
|
487 |
% 1. get global properties of file |
488 |
[ndims nvars natts dimm] = netcdf.inq(nc); |
489 |
|
490 |
% get variable ID and properties |
491 |
if strcmp('global',varname) |
492 |
% "variable" is global |
493 |
varid = netcdf.getConstant('NC_GLOBAL'); |
494 |
else |
495 |
% find variable ID and properties |
496 |
varid = ncfindvarid(nc,varname); |
497 |
if ~isempty(varid) |
498 |
[varn,xtype,dimids,natts] = netcdf.inqVar(nc,varid); |
499 |
else |
500 |
warning(sprintf('variable %s not found',varname)) |
501 |
end |
502 |
end |
503 |
|
504 |
if natts > 1 |
505 |
for k=0:natts-1 |
506 |
attn = netcdf.inqAttName(nc,varid,k); |
507 |
[xtype attlen]=netcdf.inqAtt(nc,varid,attn); |
508 |
attval = netcdf.getAtt(nc,varid,attn); |
509 |
if ~ischar(attval) |
510 |
attval = double(attval); |
511 |
end |
512 |
A.(char(attn))=attval; |
513 |
end |
514 |
else |
515 |
A = 'none'; |
516 |
end |
517 |
|
518 |
return |
519 |
|
520 |
|
521 |
function varid = ncfindvarid(nc,varname) |
522 |
|
523 |
[ndims nvars natts dimm] = netcdf.inq(nc); |
524 |
varid=[]; |
525 |
for k=0:nvars-1 |
526 |
if strcmp(netcdf.inqVar(nc,k),varname); |
527 |
varid = netcdf.inqVarId(nc,varname); |
528 |
break |
529 |
end |
530 |
end |
531 |
|
532 |
return |