/[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 1.2 - (show annotations) (download)
Sat Feb 1 18:19:26 2014 UTC (11 years, 5 months ago) by gforget
Branch: MAIN
Changes since 1.1: +25 -5 lines
- add month (month index variable)
- embed README (optional) in global attributes

1 function []=process2nctiles(dirModel,fileModel,fldModel);
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 (optional) can be specifiec as e.g. 'ETAN'
13 %output : (netcdf files)
14
15 gcmfaces_global;
16
17 %directory names
18 listDirs={'STATE/','TRSP/'};
19 filAvailDiag=[dirModel 'available_diagnostics.log'];
20 filReadme=[dirModel 'README'];
21 dirOut=[dirModel 'nctiles/'];
22 if ~isdir(dirOut); mkdir(dirOut); end;
23
24 %seacrh in subdirectories
25 subDir=[];
26 for ff=1:length(listDirs);
27 tmp1=dir([dirModel 'diags/' listDirs{ff} fileModel '*']);
28 if ~isempty(tmp1); subDir=listDirs{ff}; end;
29 end;
30
31 if isempty(subDir);
32 error(['file ' fileModel ' was not found']);
33 else;
34 dirIn=[dirModel 'diags/' subDir];
35 nn=length(dir([dirIn fileModel '*data']));
36 fprintf('%s (%d files) was found in \n %s \n',fileModel,nn,dirIn);
37 end;
38
39 %set list of variables to process
40 if ~isempty(who('fldModel'));
41 if ischar(fldModel); listFlds={fldModel};
42 else; listFlds=fldModel;
43 end;
44 else;
45 meta=read_meta([dirIn fileModel '*']);
46 listFlds=meta.fldList;
47 end;
48
49 %now do the actual processing
50 for vv=1:length(listFlds);
51 nameDiag=deblank(listFlds{vv})
52
53 %get meta information
54 meta=read_meta([dirIn fileModel '*']);
55 irec=find(strcmp(deblank(meta.fldList),nameDiag));
56 if length(irec)~=1; error('field not in file\n'); end;
57
58 %read time series
59 myDiag=rdmds2gcmfaces([dirIn fileModel '*'],NaN,'rec',irec);
60
61 %ancilliary fields for netcdf file
62 tim=[1:size(myDiag{1},3)];
63 descr=nameDiag;
64
65 %get units and long name from available_diagnostics.log
66 [avail_diag]=read_avail_diag(filAvailDiag,nameDiag);
67
68 %get description of estimate from README
69 [rdm]=read_readme(filReadme);
70 disp(rdm');
71
72 %convert to MITgcm format (90x1170 array)
73 myFile=[dirOut nameDiag];
74
75 %get grid params
76 [grid_diag]=set_grid_diag(avail_diag);
77
78 %create netcdf file using write2nctiles (works only with old matlab, thus far ...)
79 doCreate=1;
80 dimOut=write2nctiles(myFile,myDiag,doCreate,...
81 {'fldName',nameDiag},{'longName',avail_diag.longNameDiag},...
82 {'units',avail_diag.units},{'descr',descr},{'rdm',rdm});
83
84 %prepare to add fields
85 doCreate=0;
86
87 %determine relevant dimensions (note the reverse order)
88 for ff=1:mygrid.nFaces;
89 dimtim{ff}={dimOut{ff}{1}};
90 dim2d{ff}={dimOut{ff}{end-1:end}};
91 if avail_diag.nr~=1;
92 dimmsk{ff}={dimOut{ff}{end-2:end}};
93 dimdep{ff}={dimOut{ff}{end-2}};
94 else;
95 dimmsk{ff}=dim2d{ff};
96 dimdep{ff}=[];
97 end;
98 end;
99
100 %now add fields
101 write2nctiles(myFile,tim,doCreate,{'fldName','month'},...
102 {'longName','month index starting Jan. 1992'},...
103 {'units',''},{'dimIn',dimtim});
104 write2nctiles(myFile,grid_diag.lon,doCreate,...
105 {'fldName','longitude'},{'units',''},{'dimIn',dim2d});
106 write2nctiles(myFile,grid_diag.lat,doCreate,...
107 {'fldName','latitude'},{'units',''},{'dimIn',dim2d});
108 write2nctiles(myFile,grid_diag.msk,doCreate,...
109 {'fldName','landmask'},{'units',''},...
110 {'longName','land mask'},{'dimIn',dimmsk});
111 write2nctiles(myFile,grid_diag.RAC,doCreate,...
112 {'fldName','cellarea'},{'units','m^2'},...
113 {'longName','grid cell area'},{'dimIn',dim2d});
114 if isfield(grid_diag,'dep');
115 write2nctiles(myFile,grid_diag.dep,doCreate,...
116 {'fldName','depth'},{'units','m'},{'dimIn',dimdep});
117 write2nctiles(myFile,grid_diag.dz,doCreate,...
118 {'fldName','cellthick'},{'units','m'},{'dimIn',dimdep});
119 end;
120
121 end;%for vv=1:length(listFlds);
122
123 function [meta]=read_meta(fileName);
124
125 %read meta file
126 tmp1=dir([fileName '*.meta']); tmp1=tmp1(1).name;
127 tmp2=strfind(fileName,'/');
128 if ~isempty(tmp2); tmp2=tmp2(end); else; tmp2=0; end;
129 tmp1=[fileName(1:tmp2) tmp1]; fid=fopen(tmp1);
130 while 1;
131 tline = fgetl(fid);
132 if ~ischar(tline), break, end
133 if isempty(whos('tmp3')); tmp3=tline; else; tmp3=[tmp3 ' ' tline]; end;
134 end
135 fclose(fid);
136
137 %add meta variables to workspace
138 eval(tmp3);
139
140 %reformat to meta structure
141 meta.dataprec=dataprec;
142 meta.nDims=nDims;
143 meta.nFlds=nFlds;
144 meta.nrecords=nrecords;
145 meta.fldList=fldList;
146 meta.dimList=dimList;
147 if ~isempty(who('timeInterval')); meta.timeInterval=timeInterval; end;
148 if ~isempty(who('timeStepNumber')); meta.timeStepNumber=timeStepNumber; end;
149
150 %%
151
152 function [rdm]=read_readme(filReadme);
153
154 gcmfaces_global;
155
156 rdm=[];
157
158 fid=fopen(filReadme,'rt');
159 while ~feof(fid);
160 nn=length(rdm);
161 rdm{nn+1} = fgetl(fid);
162 end;
163 fclose(fid);
164
165 %%
166
167 function [avail_diag]=read_avail_diag(filAvailDiag,nameDiag);
168
169 gcmfaces_global;
170
171 avail_diag=[];
172
173 fid=fopen(filAvailDiag,'rt');
174 while ~feof(fid);
175 tline = fgetl(fid);
176 tmp1=8-length(nameDiag); tmp1=repmat(' ',[1 tmp1]);
177 tname = ['|' sprintf('%s',nameDiag) tmp1 '|'];
178 if ~isempty(strfind(tline,tname));
179 %e.g. tline=' 235 |SIatmQnt| 1 | |SM U1|W/m^2 |Net atmospheric heat flux, >0 decreases theta';
180 %
181 tmp1=strfind(tline,'|'); tmp1=tmp1(end-1:end);
182 avail_diag.units=strtrim(tline(tmp1(1)+1:tmp1(2)-1));
183 avail_diag.longNameDiag=tline(tmp1(2)+1:end);
184 %
185 tmp1=strfind(tline,'|'); tmp1=tmp1(4:5);
186 pars=tline(tmp1(1)+1:tmp1(2)-1);
187 %
188 if strcmp(pars(2),'M'); avail_diag.loc_h='C';
189 elseif strcmp(pars(2),'U'); avail_diag.loc_h='W';
190 elseif strcmp(pars(2),'V'); avail_diag.loc_h='S';
191 end;
192 %
193 avail_diag.loc_z=pars(9);
194 %
195 if strcmp(pars(10),'1'); avail_diag.nr=1;
196 else; avail_diag.nr=length(mygrid.RC);
197 end;
198 end;
199 end;
200 fclose(fid);
201
202 %%
203
204 function [grid_diag]=set_grid_diag(avail_diag);
205
206 gcmfaces_global;
207
208 %switch for non-tracer point values
209 if strcmp(avail_diag.loc_h,'C');
210 grid_diag.lon=mygrid.XC;
211 grid_diag.lat=mygrid.YC;
212 grid_diag.msk=mygrid.mskC(:,:,1:avail_diag.nr);
213 elseif strcmp(avail_diag.loc_h,'W');
214 grid_diag.lon=mygrid.XG;
215 grid_diag.lat=mygrid.YC;
216 grid_diag.msk=mygrid.mskW(:,:,1:avail_diag.nr);
217 elseif strcmp(avail_diag.loc_h,'S');
218 grid_diag.lon=mygrid.XC;
219 grid_diag.lat=mygrid.YG;
220 grid_diag.msk=mygrid.mskS(:,:,1:avail_diag.nr);
221 end;
222 grid_diag.RAC=mygrid.RAC;
223
224 %vertical grid
225 if avail_diag.nr~=1;
226 if strcmp(avail_diag.loc_z,'M');
227 grid_diag.dep=-mygrid.RC;
228 grid_diag.dz=mygrid.DRF;
229 elseif strcmp(avail_diag.loc_z,'L');
230 grid_diag.dep=-mygrid.RF(2:end);
231 grid_diag.dz=[mygrid.DRC(2:end) ; 228.25];%quick fix
232 else;
233 error('unknown vertical grid');
234 end;
235 grid_diag.dep=reshape(grid_diag.dep,[1 1 avail_diag.nr]);
236 grid_diag.dz=reshape(grid_diag.dz,[1 1 avail_diag.nr]);
237 end;

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