/[MITgcm]/MITgcm/utils/matlab/rdmnc.m
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Contents of /MITgcm/utils/matlab/rdmnc.m

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Revision 1.5 - (show annotations) (download)
Thu Oct 20 15:19:49 2005 UTC (18 years, 9 months ago) by enderton
Branch: MAIN
CVS Tags: checkpoint57y_post, checkpoint57y_pre, checkpoint58, checkpoint57x_post, checkpoint57w_post, checkpoint58a_post, checkpoint57z_post
Changes since 1.4: +1 -0 lines
Removed iteration check

1 function [S] = rdmnc_mod2(varargin)
2
3 % Usage:
4 % S=RDMNC(FILE1,FILE2,...)
5 % S=RDMNC(FILE1,...,ITER)
6 % S=RDMNC(FILE1,...,'VAR1','VAR2',...)
7 % S=RDMNC(FILE1,...,'VAR1','VAR2',...,ITER)
8 %
9 % Input:
10 % FILE1 Either a single file name (e.g. 'state.nc') or a wild-card
11 % strings expanding to a group of file names (e.g. 'state.*.nc').
12 % There are no assumptions about suffices (e.g. 'state.*' works).
13 % VAR1 Model variable names as written in the MNC/netcdf file.
14 % ITER Vector of iterations in the MNC/netcdf files, not model time.
15 %
16 % Output:
17 % S Structure with fields corresponding to 'VAR1', 'VAR2', ...
18 %
19 % Description:
20 % This function is a rudimentary wrapper for joining and reading netcdf
21 % files produced by MITgcm. It does not give the same flexibility as
22 % opening the netcdf files directly using netcdf(), but is useful for
23 % quick loading of entire model fields which are distributed in multiple
24 % netcdf files.
25 %
26 % Example:
27 % >> S=rdmnd('state.*','XC','YC','T');
28 % >> imagesc( S.XC, S.YC, S.T(:,:,1)' );
29 %
30 % Author: Alistair Adcroft
31 % Modifications: Daniel Enderton
32
33 % Initializations
34 file={};
35 filepaths={};
36 files={};
37 varlist={};
38 iters=[];
39
40 % Process function arguments
41 for iarg=1:nargin;
42 arg=varargin{iarg};
43 if ischar(arg)
44 if isempty(dir(char(arg)))
45 varlist{end+1}=arg;
46 else
47 file{end+1}=arg;
48 end
49 else
50 if isempty(iters)
51 iters=arg;
52 else
53 error(['The only allowed numeric argument is iterations',...
54 ' to read in as a vector for the last arguement']);
55 end
56 end
57 end
58
59 % Create list of filenames
60 for eachfile=file
61 filepathtemp=eachfile{:};
62 indecies = find(filepathtemp=='/');
63 if ~isempty(indecies)
64 filepathtemp = filepathtemp(1:indecies(end));
65 else
66 filepathtemp = '';
67 end
68 expandedEachFile=dir(char(eachfile{1}));
69 for i=1:size(expandedEachFile,1);
70 if expandedEachFile(i).isdir==0
71 files{end+1}=expandedEachFile(i).name;
72 filepaths{end+1}=filepathtemp;
73 end
74 end
75 end
76
77
78 % If iterations unspecified, open all the files and make list of all the
79 % iterations that appear, use this iterations list for data extraction.
80 if isempty(iters)
81 iters = [];
82 for ieachfile=1:length(files)
83 eachfile = [filepaths{ieachfile},files{ieachfile}];
84 nc=netcdf(char(eachfile),'read');
85 nciters = nc{'iter'}(:);
86 if isempty(nciters), nciters = nc{'T'}(:); end
87 iters = [iters,nciters];
88 close(nc);
89 end
90 iters = unique(iters);
91 end
92
93 % Cycle through files for data extraction.
94 S.attributes=[];
95 for ieachfile=1:length(files)
96 eachfile = [filepaths{ieachfile},files{ieachfile}];
97 nc=netcdf(char(eachfile),'read');
98 S=rdmnc_local(nc,varlist,iters,S);
99 close(nc);
100 end
101
102
103 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
104 % Local functions %
105 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
106
107 function [A] = read_att(nc);
108 allatt=ncnames(att(nc));
109 if ~isempty(allatt)
110 for attr=allatt;
111 A.(char(attr))=nc.(char(attr))(:);
112 end
113 else
114 A = 'none';
115 end
116
117 function [i0,j0,fn] = findTileOffset(S);
118 fn=0;
119 if isfield(S,'attributes') & isfield(S.attributes,'global')
120 G=S.attributes.global;
121 tn=G.tile_number;
122 snx=G.sNx; sny=G.sNy; nsx=G.nSx; nsy=G.nSy; npx=G.nPx; npy=G.nPy;
123 ntx=nsx*npx;nty=nsy*npy;
124 gbi=mod(tn-1,ntx); gbj=(tn-gbi-1)/ntx;
125 i0=snx*gbi; j0=sny*gbj;
126 if isfield(S.attributes.global,'exch2_myFace')
127 fn=G.exch2_myFace;
128 end
129 else
130 i0=0;j0=0;
131 end
132 %[snx,sny,nsx,nsy,npx,npy,ntx,nty,i0,j0,fn];
133
134 function [S] = rdmnc_local(nc,varlist,iters,S)
135
136 fiter = nc{'iter'}(:); % File iterations present
137 if isempty(fiter), fiter = nc{'T'}(:); end
138 [fii,dii] = ismember(fiter,iters); fii = find(fii); % File iteration index
139 dii = dii(find(dii ~= 0)); % Data interation index
140
141 % No variables specified? Default to all
142 if isempty(varlist), varlist=ncnames(var(nc)); end
143
144 % Attributes for structure
145 if iters>0; S.iters_read_from_file=iters; end
146 S.attributes.global=read_att(nc);
147
148 % Read variable data
149 for ivar=1:size(varlist,2)
150
151 cvar=char(varlist{ivar});
152 if isempty(nc{cvar})
153 disp(['No such variable ''',cvar,''' in MNC file ',name(nc)]);
154 continue
155 end
156
157 dims=ncnames(dim(nc{cvar})); % Dimensions
158
159 if dims{1}=='T'
160 if isempty(find(fii)), return, end
161 tmpdata=nc{cvar}(find(fii),:);
162 it = length(dims);
163 else
164 tmpdata=nc{cvar}(:);
165 it = 0;
166 end
167
168 tmpdata=squeeze(permute(tmpdata,[9:-1:1]));
169 [ni nj nk nm nn no np]=size(tmpdata);
170 [ni nj nk nm nn no np];
171
172 [i0,j0,fn]=findTileOffset(S);
173 cdim=dims{end}; if cdim(1)~='X'; i0=0; end
174 cdim=dims{end}; if cdim(1)=='Y'; i0=j0; j0=0; end
175 if length(dims)>1;
176 cdim=dims{end-1}; if cdim(1)~='Y'; j0=0; end
177 else
178 j0=0;
179 end
180
181 Sstr = '';
182 for istr = 1:7
183 if istr == it, Sstr = [Sstr,'dii,'];
184 elseif istr == 1, Sstr = [Sstr,'i0+(1:ni),'];
185 elseif istr == 2, Sstr = [Sstr,'j0+(1:nj),'];
186 elseif istr == 3, Sstr = [Sstr,'(1:nk),'];
187 elseif istr == 4, Sstr = [Sstr,'(1:nm),'];
188 elseif istr == 5, Sstr = [Sstr,'(1:nn),'];
189 elseif istr == 6, Sstr = [Sstr,'(1:no),'];
190 elseif istr == 7, Sstr = [Sstr,'(1:np),'];
191 else, error('Can''t handle this many dimensions!');
192 end
193 end
194 eval(['S.(cvar)(',Sstr(1:end-1),')=tmpdata;'])
195 %S.(cvar)(i0+(1:ni),j0+(1:nj),(1:nk),(1:nm),(1:nn),(1:no),(1:np))=tmpdata;
196 S.attributes.(cvar)=read_att(nc{cvar});
197 end
198
199 if isempty(S)
200 error('Something didn''t work!!!');
201 end

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