matlab_class/gcmfaces_IO/process2nctiles.m

function []=process2nctiles(dirModel,fileModel,fldModel,tileSize);
%process2nctiles(dirModel);
%object : convert MITgcm binary output to netcdf files (tiled) 
%inputs : dirModel is the MITgcm run directory
%           It is expected to contain binaries in 
%           'diags/STATE/', 'diags/TRSP/', etc. as well
%           as the 'available_diagnostics.log' text file.
%         fileModel the file name base e.g. 'state_2d_set1'
%           By default : all variables in e.g. 'state_2d_set1*' 
%           files will be processed, and writen individually to
%           nctiles (tiled netcdf) that will be located in 'nctiles/'
%         fldModel (by default []) can be specified (as e.g. 'ETAN')
%            when fldModel is empty, all fields are processed
%         tileSize (optional) is e.g. [90 90] (by default tiles=faces) 
%output : (netcdf files)

gcmfaces_global;

%listFiles={'state_2d_set1','state_2d_set2','state_3d_set1','state_3d_set2'};
%listFiles={'trsp_3d_set1','trsp_3d_set2','trsp_3d_set3'};
%for ff=1:length(listFiles); process2nctiles('iter12/',listFiles{ff},[],[90 90]); end;

%directory names
listDirs={'STATE/','TRSP/'};
filAvailDiag=[dirModel 'available_diagnostics.log'];
filReadme=[dirModel 'README'];
dirOut=[dirModel 'nctiles/'];
if ~isdir(dirOut); mkdir(dirOut); end;

%seacrh in subdirectories
subDir=[];
for ff=1:length(listDirs);
tmp1=dir([dirModel 'diags/' listDirs{ff} fileModel '*']);
if ~isempty(tmp1); subDir=listDirs{ff}; end;
end;

if isempty(subDir); 
  error(['file ' fileModel ' was not found']);
else;
  dirIn=[dirModel 'diags/' subDir];
  nn=length(dir([dirIn fileModel '*data']));
  fprintf('%s (%d files) was found in \n %s \n',fileModel,nn,dirIn);
end;

%set list of variables to process
if ~isempty(fldModel);
   if ischar(fldModel); listFlds={fldModel};
   else; listFlds=fldModel;
   end;
else;
   meta=read_meta([dirIn fileModel '*']);
   listFlds=meta.fldList;
end;

%determine map of tile indices (by default tiles=faces)
if isempty(whos('tileSize'));
  tileNo=mygrid.XC; 
  for ff=1:mygrid.nFaces; tileNo{ff}(:)=ff; end;
else;
  tileNo=gcmfaces_loc_tile(tileSize(1),tileSize(2));
end;

%now do the actual processing
for vv=1:length(listFlds);
nameDiag=deblank(listFlds{vv}) 

%get meta information
meta=read_meta([dirIn fileModel '*']);
irec=find(strcmp(deblank(meta.fldList),nameDiag));
if length(irec)~=1; error('field not in file\n'); end;

%read time series
myDiag=rdmds2gcmfaces([dirIn fileModel '*'],NaN,'rec',irec);

%set ancilliary time variable
nn=length(size(myDiag{1}));
nn=size(myDiag{1},nn);
%tim=[1:nn];
tim=[1992*ones(nn,1) [1:nn]' 15*ones(nn,1)];
tim=datenum(tim)-datenum([1992 1 0]);
timUnits='days since 1992-1-1 0:0:0';

%get units and long name from available_diagnostics.log
[avail_diag]=read_avail_diag(filAvailDiag,nameDiag);

%get description of estimate from README
[rdm]=read_readme(filReadme);
disp(rdm');

%convert to MITgcm format (90x1170 array)
myFile=[dirOut nameDiag];%first instance is for subdirectory name
if ~isdir(myFile); mkdir(myFile); end;
myFile=[myFile '/' nameDiag];%second instance is for file name base

%get grid params
[grid_diag]=set_grid_diag(avail_diag);

%apply mask, and convert to land mask
msk=grid_diag.msk;
if length(size(myDiag{1}))==3;
  msk=repmat(msk,[1 1 size(myDiag{1},3)]);
end;
for kk=1:size(myDiag{1},4);
  myDiag(:,:,:,kk)=myDiag(:,:,:,kk).*msk;
end;
clear msk;
%
land=isnan(grid_diag.msk);

%set 'coord' attribute
if avail_diag.nr~=1;
  coord='lon lat dep tim';
else;
  coord='lon lat tim';
end;

%create netcdf file using write2nctiles (works only with old matlab, thus far ...)
doCreate=1; 
dimlist=write2nctiles(myFile,myDiag,doCreate,{'tileNo',tileNo},...
    {'fldName',nameDiag},{'longName',avail_diag.longNameDiag},...
    {'units',avail_diag.units},{'descr',nameDiag},{'coord',coord},{'rdm',rdm});

%determine relevant dimensions
for ff=1:length(dimlist);
  dim.tim{ff}={dimlist{ff}{1}};
  dim.twoD{ff}={dimlist{ff}{end-1:end}};
  if avail_diag.nr~=1;
    dim.threeD{ff}={dimlist{ff}{end-2:end}};
    dim.dep{ff}={dimlist{ff}{end-2}};
  else;
    dim.threeD{ff}=dim.twoD{ff};
    dim.dep{ff}=[];
  end;
end;

%prepare to add fields
doCreate=0;

%now add fields
write2nctiles(myFile,tim,doCreate,{'tileNo',tileNo},...
  {'fldName','tim'},{'longName','time'},...
  {'units',timUnits},{'dimIn',dim.tim});
write2nctiles(myFile,grid_diag.lon,doCreate,{'tileNo',tileNo},...
  {'fldName','lon'},{'units','degrees_east'},{'dimIn',dim.twoD});
write2nctiles(myFile,grid_diag.lat,doCreate,{'tileNo',tileNo},...
  {'fldName','lat'},{'units','degrees_north'},{'dimIn',dim.twoD});
write2nctiles(myFile,grid_diag.msk,doCreate,{'tileNo',tileNo},...
  {'fldName','land'},{'units','1'},{'longName','land mask'},{'dimIn',dim.threeD});
write2nctiles(myFile,grid_diag.RAC,doCreate,{'tileNo',tileNo},...
  {'fldName','area'},{'units','m^2'},{'longName','grid cell area'},{'dimIn',dim.twoD});
if isfield(grid_diag,'dep');
    write2nctiles(myFile,grid_diag.dep,doCreate,{'tileNo',tileNo},...
      {'fldName','dep'},{'units','m'},{'dimIn',dim.dep});
    write2nctiles(myFile,grid_diag.dz,doCreate,{'tileNo',tileNo},...
      {'fldName','thic'},{'units','m'},{'dimIn',dim.dep});
end;

end;%for vv=1:length(listFlds);

function [meta]=read_meta(fileName);

%read meta file
tmp1=dir([fileName '*.meta']); tmp1=tmp1(1).name;
tmp2=strfind(fileName,'/');
if ~isempty(tmp2); tmp2=tmp2(end); else; tmp2=0; end;
tmp1=[fileName(1:tmp2) tmp1]; fid=fopen(tmp1);
while 1;
    tline = fgetl(fid);
    if ~ischar(tline), break, end
    if isempty(whos('tmp3')); tmp3=tline; else; tmp3=[tmp3 ' ' tline]; end;
end
fclose(fid);

%add meta variables to workspace
eval(tmp3);

%reformat to meta structure
meta.dataprec=dataprec;
meta.nDims=nDims;
meta.nFlds=nFlds;
meta.nrecords=nrecords;
meta.fldList=fldList;
meta.dimList=dimList;
if ~isempty(who('timeInterval')); meta.timeInterval=timeInterval; end;
if ~isempty(who('timeStepNumber'));  meta.timeStepNumber=timeStepNumber; end;

%%

function [rdm]=read_readme(filReadme);

gcmfaces_global;

rdm=[];

fid=fopen(filReadme,'rt');
while ~feof(fid);
    nn=length(rdm);
    rdm{nn+1} = fgetl(fid);
end;
fclose(fid);

%%

function [avail_diag]=read_avail_diag(filAvailDiag,nameDiag);

gcmfaces_global;

avail_diag=[];

fid=fopen(filAvailDiag,'rt');
while ~feof(fid);
    tline = fgetl(fid);
    tmp1=8-length(nameDiag); tmp1=repmat(' ',[1 tmp1]);
    tname = ['|' sprintf('%s',nameDiag) tmp1 '|'];
    if ~isempty(strfind(tline,tname));
        %e.g. tline='   235 |SIatmQnt|  1 |       |SM      U1|W/m^2           |Net atmospheric heat flux, >0 decreases theta';
        %
        tmp1=strfind(tline,'|'); tmp1=tmp1(end-1:end);
        avail_diag.units=strtrim(tline(tmp1(1)+1:tmp1(2)-1));
        avail_diag.longNameDiag=tline(tmp1(2)+1:end);
        %
        tmp1=strfind(tline,'|'); tmp1=tmp1(4:5);
        pars=tline(tmp1(1)+1:tmp1(2)-1);
        %
        if strcmp(pars(2),'M'); avail_diag.loc_h='C';
        elseif strcmp(pars(2),'U'); avail_diag.loc_h='W';
        elseif strcmp(pars(2),'V'); avail_diag.loc_h='S';
        end;
        %
        avail_diag.loc_z=pars(9);
        %
        if strcmp(pars(10),'1'); avail_diag.nr=1;
        else; avail_diag.nr=length(mygrid.RC);
        end;
    end;
end;
fclose(fid);

%%

function [grid_diag]=set_grid_diag(avail_diag);

gcmfaces_global;

%switch for non-tracer point values
if strcmp(avail_diag.loc_h,'C');
    grid_diag.lon=mygrid.XC;
    grid_diag.lat=mygrid.YC;
    grid_diag.msk=mygrid.mskC(:,:,1:avail_diag.nr);
elseif strcmp(avail_diag.loc_h,'W');
    grid_diag.lon=mygrid.XG;
    grid_diag.lat=mygrid.YC;
    grid_diag.msk=mygrid.mskW(:,:,1:avail_diag.nr);
elseif strcmp(avail_diag.loc_h,'S');
    grid_diag.lon=mygrid.XC;
    grid_diag.lat=mygrid.YG;
    grid_diag.msk=mygrid.mskS(:,:,1:avail_diag.nr);
end;
grid_diag.RAC=mygrid.RAC;

%vertical grid
if avail_diag.nr~=1;
    if strcmp(avail_diag.loc_z,'M');
        grid_diag.dep=-mygrid.RC;
        grid_diag.dz=mygrid.DRF;
    elseif strcmp(avail_diag.loc_z,'L');
        grid_diag.dep=-mygrid.RF(2:end);
        grid_diag.dz=[mygrid.DRC(2:end) ; 228.25];%quick fix
    else;
        error('unknown vertical grid');
    end;
    grid_diag.dep=reshape(grid_diag.dep,[1 1 avail_diag.nr]);
    grid_diag.dz=reshape(grid_diag.dz,[1 1 avail_diag.nr]);
end;
1	gforget	1.4	function []=process2nctiles(dirModel,fileModel,fldModel,tileSize);
2	gforget	1.1	%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	gforget	1.4	% 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	gforget	1.1	%output : (netcdf files)
16
17			gcmfaces_global;
18
19	gforget	1.5	%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	gforget	1.1	%directory names
24			listDirs={'STATE/','TRSP/'};
25			filAvailDiag=[dirModel 'available_diagnostics.log'];
26	gforget	1.2	filReadme=[dirModel 'README'];
27	gforget	1.1	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	gforget	1.4	if ~isempty(fldModel);
47	gforget	1.1	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	gforget	1.4	%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	gforget	1.1	%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	gforget	1.5	%set ancilliary time variable
76	gforget	1.3	nn=length(size(myDiag{1}));
77	gforget	1.5	nn=size(myDiag{1},nn);
78			%tim=[1:nn];
79			tim=[1992ones(nn,1) [1:nn]' 15ones(nn,1)];
80			tim=datenum(tim)-datenum([1992 1 0]);
81			timUnits='days since 1992-1-1 0:0:0';
82	gforget	1.1
83			%get units and long name from available_diagnostics.log
84			[avail_diag]=read_avail_diag(filAvailDiag,nameDiag);
85
86	gforget	1.2	%get description of estimate from README
87			[rdm]=read_readme(filReadme);
88			disp(rdm');
89
90	gforget	1.1	%convert to MITgcm format (90x1170 array)
91	gforget	1.4	myFile=[dirOut nameDiag];%first instance is for subdirectory name
92			if ~isdir(myFile); mkdir(myFile); end;
93			myFile=[myFile '/' nameDiag];%second instance is for file name base
94	gforget	1.1
95			%get grid params
96			[grid_diag]=set_grid_diag(avail_diag);
97
98	gforget	1.5	%apply mask, and convert to land mask
99			msk=grid_diag.msk;
100	gforget	1.6	if length(size(myDiag{1}))==3;
101			msk=repmat(msk,[1 1 size(myDiag{1},3)]);
102			end;
103			for kk=1:size(myDiag{1},4);
104			myDiag(:,:,:,kk)=myDiag(:,:,:,kk).*msk;
105			end;
106	gforget	1.5	clear msk;
107			%
108			land=isnan(grid_diag.msk);
109
110			%set 'coord' attribute
111			if avail_diag.nr~=1;
112			coord='lon lat dep tim';
113			else;
114			coord='lon lat tim';
115			end;
116
117	gforget	1.1	%create netcdf file using write2nctiles (works only with old matlab, thus far ...)
118			doCreate=1;
119	gforget	1.4	dimlist=write2nctiles(myFile,myDiag,doCreate,{'tileNo',tileNo},...
120	gforget	1.1	{'fldName',nameDiag},{'longName',avail_diag.longNameDiag},...
121	gforget	1.5	{'units',avail_diag.units},{'descr',nameDiag},{'coord',coord},{'rdm',rdm});
122	gforget	1.1
123	gforget	1.4	%determine relevant dimensions
124			for ff=1:length(dimlist);
125			dim.tim{ff}={dimlist{ff}{1}};
126			dim.twoD{ff}={dimlist{ff}{end-1:end}};
127			if avail_diag.nr~=1;
128			dim.threeD{ff}={dimlist{ff}{end-2:end}};
129			dim.dep{ff}={dimlist{ff}{end-2}};
130	gforget	1.1	else;
131	gforget	1.4	dim.threeD{ff}=dim.twoD{ff};
132			dim.dep{ff}=[];
133	gforget	1.1	end;
134			end;
135
136	gforget	1.4	%prepare to add fields
137			doCreate=0;
138
139	gforget	1.1	%now add fields
140	gforget	1.4	write2nctiles(myFile,tim,doCreate,{'tileNo',tileNo},...
141	gforget	1.5	{'fldName','tim'},{'longName','time'},...
142			{'units',timUnits},{'dimIn',dim.tim});
143	gforget	1.4	write2nctiles(myFile,grid_diag.lon,doCreate,{'tileNo',tileNo},...
144	gforget	1.5	{'fldName','lon'},{'units','degrees_east'},{'dimIn',dim.twoD});
145	gforget	1.4	write2nctiles(myFile,grid_diag.lat,doCreate,{'tileNo',tileNo},...
146	gforget	1.5	{'fldName','lat'},{'units','degrees_north'},{'dimIn',dim.twoD});
147	gforget	1.4	write2nctiles(myFile,grid_diag.msk,doCreate,{'tileNo',tileNo},...
148	gforget	1.5	{'fldName','land'},{'units','1'},{'longName','land mask'},{'dimIn',dim.threeD});
149	gforget	1.4	write2nctiles(myFile,grid_diag.RAC,doCreate,{'tileNo',tileNo},...
150	gforget	1.5	{'fldName','area'},{'units','m^2'},{'longName','grid cell area'},{'dimIn',dim.twoD});
151	gforget	1.1	if isfield(grid_diag,'dep');
152	gforget	1.4	write2nctiles(myFile,grid_diag.dep,doCreate,{'tileNo',tileNo},...
153	gforget	1.5	{'fldName','dep'},{'units','m'},{'dimIn',dim.dep});
154	gforget	1.4	write2nctiles(myFile,grid_diag.dz,doCreate,{'tileNo',tileNo},...
155	gforget	1.5	{'fldName','thic'},{'units','m'},{'dimIn',dim.dep});
156	gforget	1.1	end;
157
158			end;%for vv=1:length(listFlds);
159
160			function [meta]=read_meta(fileName);
161
162			%read meta file
163			tmp1=dir([fileName '*.meta']); tmp1=tmp1(1).name;
164			tmp2=strfind(fileName,'/');
165			if ~isempty(tmp2); tmp2=tmp2(end); else; tmp2=0; end;
166			tmp1=[fileName(1:tmp2) tmp1]; fid=fopen(tmp1);
167			while 1;
168			tline = fgetl(fid);
169			if ~ischar(tline), break, end
170			if isempty(whos('tmp3')); tmp3=tline; else; tmp3=[tmp3 ' ' tline]; end;
171			end
172			fclose(fid);
173
174			%add meta variables to workspace
175			eval(tmp3);
176
177			%reformat to meta structure
178			meta.dataprec=dataprec;
179			meta.nDims=nDims;
180			meta.nFlds=nFlds;
181			meta.nrecords=nrecords;
182			meta.fldList=fldList;
183			meta.dimList=dimList;
184			if ~isempty(who('timeInterval')); meta.timeInterval=timeInterval; end;
185			if ~isempty(who('timeStepNumber')); meta.timeStepNumber=timeStepNumber; end;
186
187			%%
188
189	gforget	1.2	function [rdm]=read_readme(filReadme);
190
191			gcmfaces_global;
192
193			rdm=[];
194
195			fid=fopen(filReadme,'rt');
196			while ~feof(fid);
197			nn=length(rdm);
198			rdm{nn+1} = fgetl(fid);
199			end;
200			fclose(fid);
201
202			%%
203
204	gforget	1.1	function [avail_diag]=read_avail_diag(filAvailDiag,nameDiag);
205
206			gcmfaces_global;
207
208			avail_diag=[];
209
210			fid=fopen(filAvailDiag,'rt');
211			while ~feof(fid);
212			tline = fgetl(fid);
213			tmp1=8-length(nameDiag); tmp1=repmat(' ',[1 tmp1]);
214			tname = ['\|' sprintf('%s',nameDiag) tmp1 '\|'];
215			if ~isempty(strfind(tline,tname));
216			%e.g. tline=' 235 \|SIatmQnt\| 1 \| \|SM U1\|W/m^2 \|Net atmospheric heat flux, >0 decreases theta';
217			%
218			tmp1=strfind(tline,'\|'); tmp1=tmp1(end-1:end);
219			avail_diag.units=strtrim(tline(tmp1(1)+1:tmp1(2)-1));
220			avail_diag.longNameDiag=tline(tmp1(2)+1:end);
221			%
222			tmp1=strfind(tline,'\|'); tmp1=tmp1(4:5);
223			pars=tline(tmp1(1)+1:tmp1(2)-1);
224			%
225			if strcmp(pars(2),'M'); avail_diag.loc_h='C';
226			elseif strcmp(pars(2),'U'); avail_diag.loc_h='W';
227			elseif strcmp(pars(2),'V'); avail_diag.loc_h='S';
228			end;
229			%
230			avail_diag.loc_z=pars(9);
231			%
232			if strcmp(pars(10),'1'); avail_diag.nr=1;
233			else; avail_diag.nr=length(mygrid.RC);
234			end;
235			end;
236			end;
237			fclose(fid);
238
239			%%
240
241			function [grid_diag]=set_grid_diag(avail_diag);
242
243			gcmfaces_global;
244
245			%switch for non-tracer point values
246			if strcmp(avail_diag.loc_h,'C');
247			grid_diag.lon=mygrid.XC;
248			grid_diag.lat=mygrid.YC;
249			grid_diag.msk=mygrid.mskC(:,:,1:avail_diag.nr);
250			elseif strcmp(avail_diag.loc_h,'W');
251			grid_diag.lon=mygrid.XG;
252			grid_diag.lat=mygrid.YC;
253			grid_diag.msk=mygrid.mskW(:,:,1:avail_diag.nr);
254			elseif strcmp(avail_diag.loc_h,'S');
255			grid_diag.lon=mygrid.XC;
256			grid_diag.lat=mygrid.YG;
257			grid_diag.msk=mygrid.mskS(:,:,1:avail_diag.nr);
258			end;
259			grid_diag.RAC=mygrid.RAC;
260
261			%vertical grid
262			if avail_diag.nr~=1;
263			if strcmp(avail_diag.loc_z,'M');
264			grid_diag.dep=-mygrid.RC;
265			grid_diag.dz=mygrid.DRF;
266			elseif strcmp(avail_diag.loc_z,'L');
267			grid_diag.dep=-mygrid.RF(2:end);
268			grid_diag.dz=[mygrid.DRC(2:end) ; 228.25];%quick fix
269			else;
270			error('unknown vertical grid');
271			end;
272			grid_diag.dep=reshape(grid_diag.dep,[1 1 avail_diag.nr]);
273			grid_diag.dz=reshape(grid_diag.dz,[1 1 avail_diag.nr]);
274			end;