/[MITgcm]/MITgcm_contrib/gael/matlab_class/gcmfaces_IO/process2nctiles.m
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Contents of /MITgcm_contrib/gael/matlab_class/gcmfaces_IO/process2nctiles.m

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Revision 1.8 - (show annotations) (download)
Mon Jul 28 20:54:11 2014 UTC (10 years, 11 months ago) by gforget
Branch: MAIN
Changes since 1.7: +1 -1 lines
- fix windows PC compatibility (contributed by D.Spiegel).

1 function []=process2nctiles(dirModel,fileModel,fldModel,tileSize);
2 %process2nctiles(dirModel);
3 %object : convert MITgcm binary output to netcdf files (tiled)
4 %inputs : dirModel is the MITgcm run directory
5 % It is expected to contain binaries in
6 % 'diags/STATE/', 'diags/TRSP/', etc. as well
7 % as the 'available_diagnostics.log' text file.
8 % fileModel the file name base e.g. 'state_2d_set1'
9 % By default : all variables in e.g. 'state_2d_set1*'
10 % files will be processed, and writen individually to
11 % nctiles (tiled netcdf) that will be located in 'nctiles/'
12 % fldModel (by default []) can be specified (as e.g. 'ETAN')
13 % when fldModel is empty, all fields are processed
14 % tileSize (optional) is e.g. [90 90] (by default tiles=faces)
15 %output : (netcdf files)
16
17 gcmfaces_global;
18
19 %listFiles={'state_2d_set1','state_2d_set2','state_3d_set1','state_3d_set2'};
20 %listFiles={'trsp_3d_set1','trsp_3d_set2','trsp_3d_set3'};
21 %for ff=1:length(listFiles); process2nctiles('iter12/',listFiles{ff},[],[90 90]); end;
22
23 %directory names
24 listDirs={'STATE/','TRSP/'};
25 filAvailDiag=[dirModel 'available_diagnostics.log'];
26 filReadme=[dirModel 'README'];
27 dirOut=[dirModel 'nctiles/'];
28 if ~isdir(dirOut); mkdir(dirOut); end;
29
30 %seacrh in subdirectories
31 subDir=[];
32 for ff=1:length(listDirs);
33 tmp1=dir([dirModel 'diags/' listDirs{ff} fileModel '*']);
34 if ~isempty(tmp1); subDir=listDirs{ff}; end;
35 end;
36
37 if isempty(subDir);
38 error(['file ' fileModel ' was not found']);
39 else;
40 dirIn=[dirModel 'diags/' subDir];
41 nn=length(dir([dirIn fileModel '*data']));
42 fprintf('%s (%d files) was found in \n %s \n',fileModel,nn,dirIn);
43 end;
44
45 %set list of variables to process
46 if ~isempty(fldModel);
47 if ischar(fldModel); listFlds={fldModel};
48 else; listFlds=fldModel;
49 end;
50 else;
51 meta=read_meta([dirIn fileModel '*']);
52 listFlds=meta.fldList;
53 end;
54
55 %determine map of tile indices (by default tiles=faces)
56 if isempty(whos('tileSize'));
57 tileNo=mygrid.XC;
58 for ff=1:mygrid.nFaces; tileNo{ff}(:)=ff; end;
59 else;
60 tileNo=gcmfaces_loc_tile(tileSize(1),tileSize(2));
61 end;
62
63 %now do the actual processing
64 for vv=1:length(listFlds);
65 nameDiag=deblank(listFlds{vv})
66
67 %get meta information
68 meta=read_meta([dirIn fileModel '*']);
69 irec=find(strcmp(deblank(meta.fldList),nameDiag));
70 if length(irec)~=1; error('field not in file\n'); end;
71
72 %read time series
73 myDiag=rdmds2gcmfaces([dirIn fileModel '*'],NaN,'rec',irec);
74
75 %set ancilliary time variable
76 nn=length(size(myDiag{1}));
77 nn=size(myDiag{1},nn);
78 %tim=[1:nn];
79 tim=[1992*ones(nn,1) [1:nn]' 15*ones(nn,1)];
80 tim=datenum(tim)-datenum([1992 1 0]);
81 timUnits='days since 1992-1-1 0:0:0';
82
83 %get time step axis
84 [listTimes]=diags_list_times({[dirModel 'diags/STATE/']},{'state_2d_set1'});
85
86 %get units and long name from available_diagnostics.log
87 [avail_diag]=read_avail_diag(filAvailDiag,nameDiag);
88
89 %get description of estimate from README
90 [rdm]=read_readme(filReadme);
91 disp(rdm');
92
93 %convert to MITgcm format (90x1170 array)
94 myFile=[dirOut nameDiag];%first instance is for subdirectory name
95 if ~isdir(myFile); mkdir(myFile); end;
96 myFile=[myFile '/' nameDiag];%second instance is for file name base
97
98 %get grid params
99 [grid_diag]=set_grid_diag(avail_diag);
100
101 %apply mask, and convert to land mask
102 msk=grid_diag.msk;
103 if length(size(myDiag{1}))==3;
104 msk=repmat(msk,[1 1 size(myDiag{1},3)]);
105 end;
106 for kk=1:size(myDiag{1},4);
107 myDiag(:,:,:,kk)=myDiag(:,:,:,kk).*msk;
108 end;
109 clear msk;
110 %
111 land=isnan(grid_diag.msk);
112
113 %set 'coord' attribute
114 if avail_diag.nr~=1;
115 coord='lon lat dep tim';
116 else;
117 coord='lon lat tim';
118 end;
119
120 %create netcdf file using write2nctiles (works only with old matlab, thus far ...)
121 doCreate=1;
122 dimlist=write2nctiles(myFile,myDiag,doCreate,{'tileNo',tileNo},...
123 {'fldName',nameDiag},{'longName',avail_diag.longNameDiag},...
124 {'units',avail_diag.units},{'descr',nameDiag},{'coord',coord},{'rdm',rdm});
125
126 %determine relevant dimensions
127 for ff=1:length(dimlist);
128 dim.tim{ff}={dimlist{ff}{1}};
129 dim.twoD{ff}={dimlist{ff}{end-1:end}};
130 if avail_diag.nr~=1;
131 dim.threeD{ff}={dimlist{ff}{end-2:end}};
132 dim.dep{ff}={dimlist{ff}{end-2}};
133 else;
134 dim.threeD{ff}=dim.twoD{ff};
135 dim.dep{ff}=[];
136 end;
137 end;
138
139 %prepare to add fields
140 doCreate=0;
141
142 %now add fields
143 write2nctiles(myFile,tim,doCreate,{'tileNo',tileNo},...
144 {'fldName','tim'},{'longName','time'},...
145 {'units',timUnits},{'dimIn',dim.tim});
146 write2nctiles(myFile,listTimes,doCreate,{'tileNo',tileNo},...
147 {'fldName','step'},{'longName','final time step number'},...
148 {'units','1'},{'dimIn',dim.tim});
149 write2nctiles(myFile,grid_diag.lon,doCreate,{'tileNo',tileNo},...
150 {'fldName','lon'},{'units','degrees_east'},{'dimIn',dim.twoD});
151 write2nctiles(myFile,grid_diag.lat,doCreate,{'tileNo',tileNo},...
152 {'fldName','lat'},{'units','degrees_north'},{'dimIn',dim.twoD});
153 write2nctiles(myFile,grid_diag.msk,doCreate,{'tileNo',tileNo},...
154 {'fldName','land'},{'units','1'},{'longName','land mask'},{'dimIn',dim.threeD});
155 write2nctiles(myFile,grid_diag.RAC,doCreate,{'tileNo',tileNo},...
156 {'fldName','area'},{'units','m^2'},{'longName','grid cell area'},{'dimIn',dim.twoD});
157 if isfield(grid_diag,'dep');
158 write2nctiles(myFile,grid_diag.dep,doCreate,{'tileNo',tileNo},...
159 {'fldName','dep'},{'units','m'},{'dimIn',dim.dep});
160 write2nctiles(myFile,grid_diag.dz,doCreate,{'tileNo',tileNo},...
161 {'fldName','thic'},{'units','m'},{'dimIn',dim.dep});
162 end;
163
164 end;%for vv=1:length(listFlds);
165
166 function [meta]=read_meta(fileName);
167
168 %read meta file
169 tmp1=dir([fileName '*.meta']); tmp1=tmp1(1).name;
170 tmp2=strfind(fileName,filesep);
171 if ~isempty(tmp2); tmp2=tmp2(end); else; tmp2=0; end;
172 tmp1=[fileName(1:tmp2) tmp1]; fid=fopen(tmp1);
173 while 1;
174 tline = fgetl(fid);
175 if ~ischar(tline), break, end
176 if isempty(whos('tmp3')); tmp3=tline; else; tmp3=[tmp3 ' ' tline]; end;
177 end
178 fclose(fid);
179
180 %add meta variables to workspace
181 eval(tmp3);
182
183 %reformat to meta structure
184 meta.dataprec=dataprec;
185 meta.nDims=nDims;
186 meta.nFlds=nFlds;
187 meta.nrecords=nrecords;
188 meta.fldList=fldList;
189 meta.dimList=dimList;
190 if ~isempty(who('timeInterval')); meta.timeInterval=timeInterval; end;
191 if ~isempty(who('timeStepNumber')); meta.timeStepNumber=timeStepNumber; end;
192
193 %%
194
195 function [rdm]=read_readme(filReadme);
196
197 gcmfaces_global;
198
199 rdm=[];
200
201 fid=fopen(filReadme,'rt');
202 while ~feof(fid);
203 nn=length(rdm);
204 rdm{nn+1} = fgetl(fid);
205 end;
206 fclose(fid);
207
208 %%
209
210 function [avail_diag]=read_avail_diag(filAvailDiag,nameDiag);
211
212 gcmfaces_global;
213
214 avail_diag=[];
215
216 fid=fopen(filAvailDiag,'rt');
217 while ~feof(fid);
218 tline = fgetl(fid);
219 tmp1=8-length(nameDiag); tmp1=repmat(' ',[1 tmp1]);
220 tname = ['|' sprintf('%s',nameDiag) tmp1 '|'];
221 if ~isempty(strfind(tline,tname));
222 %e.g. tline=' 235 |SIatmQnt| 1 | |SM U1|W/m^2 |Net atmospheric heat flux, >0 decreases theta';
223 %
224 tmp1=strfind(tline,'|'); tmp1=tmp1(end-1:end);
225 avail_diag.units=strtrim(tline(tmp1(1)+1:tmp1(2)-1));
226 avail_diag.longNameDiag=tline(tmp1(2)+1:end);
227 %
228 tmp1=strfind(tline,'|'); tmp1=tmp1(4:5);
229 pars=tline(tmp1(1)+1:tmp1(2)-1);
230 %
231 if strcmp(pars(2),'M'); avail_diag.loc_h='C';
232 elseif strcmp(pars(2),'U'); avail_diag.loc_h='W';
233 elseif strcmp(pars(2),'V'); avail_diag.loc_h='S';
234 end;
235 %
236 avail_diag.loc_z=pars(9);
237 %
238 if strcmp(pars(10),'1'); avail_diag.nr=1;
239 else; avail_diag.nr=length(mygrid.RC);
240 end;
241 end;
242 end;
243 fclose(fid);
244
245 %%
246
247 function [grid_diag]=set_grid_diag(avail_diag);
248
249 gcmfaces_global;
250
251 %switch for non-tracer point values
252 if strcmp(avail_diag.loc_h,'C');
253 grid_diag.lon=mygrid.XC;
254 grid_diag.lat=mygrid.YC;
255 grid_diag.msk=mygrid.mskC(:,:,1:avail_diag.nr);
256 elseif strcmp(avail_diag.loc_h,'W');
257 grid_diag.lon=mygrid.XG;
258 grid_diag.lat=mygrid.YC;
259 grid_diag.msk=mygrid.mskW(:,:,1:avail_diag.nr);
260 elseif strcmp(avail_diag.loc_h,'S');
261 grid_diag.lon=mygrid.XC;
262 grid_diag.lat=mygrid.YG;
263 grid_diag.msk=mygrid.mskS(:,:,1:avail_diag.nr);
264 end;
265 grid_diag.RAC=mygrid.RAC;
266
267 %vertical grid
268 if avail_diag.nr~=1;
269 if strcmp(avail_diag.loc_z,'M');
270 grid_diag.dep=-mygrid.RC;
271 grid_diag.dz=mygrid.DRF;
272 elseif strcmp(avail_diag.loc_z,'L');
273 grid_diag.dep=-mygrid.RF(2:end);
274 grid_diag.dz=[mygrid.DRC(2:end) ; 228.25];%quick fix
275 else;
276 error('unknown vertical grid');
277 end;
278 grid_diag.dep=reshape(grid_diag.dep,[1 1 avail_diag.nr]);
279 grid_diag.dz=reshape(grid_diag.dz,[1 1 avail_diag.nr]);
280 end;

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