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;

%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);

%ancilliary fields for netcdf file
nn=length(size(myDiag{1}));
tim=[1:size(myDiag{1},nn)];
descr=nameDiag;

%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);

%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',descr},{'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','month'},{'longName','month index starting Jan. 1992'},...
  {'units',''},{'dimIn',dim.tim});
write2nctiles(myFile,grid_diag.lon,doCreate,{'tileNo',tileNo},...
  {'fldName','longitude'},{'units',''},{'dimIn',dim.twoD});
write2nctiles(myFile,grid_diag.lat,doCreate,{'tileNo',tileNo},...
  {'fldName','latitude'},{'units',''},{'dimIn',dim.twoD});
write2nctiles(myFile,grid_diag.msk,doCreate,{'tileNo',tileNo},...
  {'fldName','landmask'},{'units',''},...
  {'longName','land mask'},{'dimIn',dim.threeD});
write2nctiles(myFile,grid_diag.RAC,doCreate,{'tileNo',tileNo},...
  {'fldName','cellarea'},{'units','m^2'},...
  {'longName','grid cell area'},{'dimIn',dim.twoD});
if isfield(grid_diag,'dep');
    write2nctiles(myFile,grid_diag.dep,doCreate,{'tileNo',tileNo},...
      {'fldName','depth'},{'units','m'},{'dimIn',dim.dep});
    write2nctiles(myFile,grid_diag.dz,doCreate,{'tileNo',tileNo},...
      {'fldName','cellthick'},{'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			%directory names
20			listDirs={'STATE/','TRSP/'};
21			filAvailDiag=[dirModel 'available_diagnostics.log'];
22	gforget	1.2	filReadme=[dirModel 'README'];
23	gforget	1.1	dirOut=[dirModel 'nctiles/'];
24			if ~isdir(dirOut); mkdir(dirOut); end;
25
26			%seacrh in subdirectories
27			subDir=[];
28			for ff=1:length(listDirs);
29			tmp1=dir([dirModel 'diags/' listDirs{ff} fileModel '*']);
30			if ~isempty(tmp1); subDir=listDirs{ff}; end;
31			end;
32
33			if isempty(subDir);
34			error(['file ' fileModel ' was not found']);
35			else;
36			dirIn=[dirModel 'diags/' subDir];
37			nn=length(dir([dirIn fileModel '*data']));
38			fprintf('%s (%d files) was found in \n %s \n',fileModel,nn,dirIn);
39			end;
40
41			%set list of variables to process
42	gforget	1.4	if ~isempty(fldModel);
43	gforget	1.1	if ischar(fldModel); listFlds={fldModel};
44			else; listFlds=fldModel;
45			end;
46			else;
47			meta=read_meta([dirIn fileModel '*']);
48			listFlds=meta.fldList;
49			end;
50
51	gforget	1.4	%determine map of tile indices (by default tiles=faces)
52			if isempty(whos('tileSize'));
53			tileNo=mygrid.XC;
54			for ff=1:mygrid.nFaces; tileNo{ff}(:)=ff; end;
55			else;
56			tileNo=gcmfaces_loc_tile(tileSize(1),tileSize(2));
57			end;
58
59	gforget	1.1	%now do the actual processing
60			for vv=1:length(listFlds);
61			nameDiag=deblank(listFlds{vv})
62
63			%get meta information
64			meta=read_meta([dirIn fileModel '*']);
65			irec=find(strcmp(deblank(meta.fldList),nameDiag));
66			if length(irec)~=1; error('field not in file\n'); end;
67
68			%read time series
69			myDiag=rdmds2gcmfaces([dirIn fileModel '*'],NaN,'rec',irec);
70
71			%ancilliary fields for netcdf file
72	gforget	1.3	nn=length(size(myDiag{1}));
73			tim=[1:size(myDiag{1},nn)];
74	gforget	1.1	descr=nameDiag;
75
76			%get units and long name from available_diagnostics.log
77			[avail_diag]=read_avail_diag(filAvailDiag,nameDiag);
78
79	gforget	1.2	%get description of estimate from README
80			[rdm]=read_readme(filReadme);
81			disp(rdm');
82
83	gforget	1.1	%convert to MITgcm format (90x1170 array)
84	gforget	1.4	myFile=[dirOut nameDiag];%first instance is for subdirectory name
85			if ~isdir(myFile); mkdir(myFile); end;
86			myFile=[myFile '/' nameDiag];%second instance is for file name base
87	gforget	1.1
88			%get grid params
89			[grid_diag]=set_grid_diag(avail_diag);
90
91			%create netcdf file using write2nctiles (works only with old matlab, thus far ...)
92			doCreate=1;
93	gforget	1.4	dimlist=write2nctiles(myFile,myDiag,doCreate,{'tileNo',tileNo},...
94	gforget	1.1	{'fldName',nameDiag},{'longName',avail_diag.longNameDiag},...
95	gforget	1.2	{'units',avail_diag.units},{'descr',descr},{'rdm',rdm});
96	gforget	1.1
97	gforget	1.4	%determine relevant dimensions
98			for ff=1:length(dimlist);
99			dim.tim{ff}={dimlist{ff}{1}};
100			dim.twoD{ff}={dimlist{ff}{end-1:end}};
101			if avail_diag.nr~=1;
102			dim.threeD{ff}={dimlist{ff}{end-2:end}};
103			dim.dep{ff}={dimlist{ff}{end-2}};
104	gforget	1.1	else;
105	gforget	1.4	dim.threeD{ff}=dim.twoD{ff};
106			dim.dep{ff}=[];
107	gforget	1.1	end;
108			end;
109
110	gforget	1.4	%prepare to add fields
111			doCreate=0;
112
113	gforget	1.1	%now add fields
114	gforget	1.4	write2nctiles(myFile,tim,doCreate,{'tileNo',tileNo},...
115			{'fldName','month'},{'longName','month index starting Jan. 1992'},...
116			{'units',''},{'dimIn',dim.tim});
117			write2nctiles(myFile,grid_diag.lon,doCreate,{'tileNo',tileNo},...
118			{'fldName','longitude'},{'units',''},{'dimIn',dim.twoD});
119			write2nctiles(myFile,grid_diag.lat,doCreate,{'tileNo',tileNo},...
120			{'fldName','latitude'},{'units',''},{'dimIn',dim.twoD});
121			write2nctiles(myFile,grid_diag.msk,doCreate,{'tileNo',tileNo},...
122	gforget	1.1	{'fldName','landmask'},{'units',''},...
123	gforget	1.4	{'longName','land mask'},{'dimIn',dim.threeD});
124			write2nctiles(myFile,grid_diag.RAC,doCreate,{'tileNo',tileNo},...
125	gforget	1.1	{'fldName','cellarea'},{'units','m^2'},...
126	gforget	1.4	{'longName','grid cell area'},{'dimIn',dim.twoD});
127	gforget	1.1	if isfield(grid_diag,'dep');
128	gforget	1.4	write2nctiles(myFile,grid_diag.dep,doCreate,{'tileNo',tileNo},...
129			{'fldName','depth'},{'units','m'},{'dimIn',dim.dep});
130			write2nctiles(myFile,grid_diag.dz,doCreate,{'tileNo',tileNo},...
131			{'fldName','cellthick'},{'units','m'},{'dimIn',dim.dep});
132	gforget	1.1	end;
133
134			end;%for vv=1:length(listFlds);
135
136			function [meta]=read_meta(fileName);
137
138			%read meta file
139			tmp1=dir([fileName '*.meta']); tmp1=tmp1(1).name;
140			tmp2=strfind(fileName,'/');
141			if ~isempty(tmp2); tmp2=tmp2(end); else; tmp2=0; end;
142			tmp1=[fileName(1:tmp2) tmp1]; fid=fopen(tmp1);
143			while 1;
144			tline = fgetl(fid);
145			if ~ischar(tline), break, end
146			if isempty(whos('tmp3')); tmp3=tline; else; tmp3=[tmp3 ' ' tline]; end;
147			end
148			fclose(fid);
149
150			%add meta variables to workspace
151			eval(tmp3);
152
153			%reformat to meta structure
154			meta.dataprec=dataprec;
155			meta.nDims=nDims;
156			meta.nFlds=nFlds;
157			meta.nrecords=nrecords;
158			meta.fldList=fldList;
159			meta.dimList=dimList;
160			if ~isempty(who('timeInterval')); meta.timeInterval=timeInterval; end;
161			if ~isempty(who('timeStepNumber')); meta.timeStepNumber=timeStepNumber; end;
162
163			%%
164
165	gforget	1.2	function [rdm]=read_readme(filReadme);
166
167			gcmfaces_global;
168
169			rdm=[];
170
171			fid=fopen(filReadme,'rt');
172			while ~feof(fid);
173			nn=length(rdm);
174			rdm{nn+1} = fgetl(fid);
175			end;
176			fclose(fid);
177
178			%%
179
180	gforget	1.1	function [avail_diag]=read_avail_diag(filAvailDiag,nameDiag);
181
182			gcmfaces_global;
183
184			avail_diag=[];
185
186			fid=fopen(filAvailDiag,'rt');
187			while ~feof(fid);
188			tline = fgetl(fid);
189			tmp1=8-length(nameDiag); tmp1=repmat(' ',[1 tmp1]);
190			tname = ['\|' sprintf('%s',nameDiag) tmp1 '\|'];
191			if ~isempty(strfind(tline,tname));
192			%e.g. tline=' 235 \|SIatmQnt\| 1 \| \|SM U1\|W/m^2 \|Net atmospheric heat flux, >0 decreases theta';
193			%
194			tmp1=strfind(tline,'\|'); tmp1=tmp1(end-1:end);
195			avail_diag.units=strtrim(tline(tmp1(1)+1:tmp1(2)-1));
196			avail_diag.longNameDiag=tline(tmp1(2)+1:end);
197			%
198			tmp1=strfind(tline,'\|'); tmp1=tmp1(4:5);
199			pars=tline(tmp1(1)+1:tmp1(2)-1);
200			%
201			if strcmp(pars(2),'M'); avail_diag.loc_h='C';
202			elseif strcmp(pars(2),'U'); avail_diag.loc_h='W';
203			elseif strcmp(pars(2),'V'); avail_diag.loc_h='S';
204			end;
205			%
206			avail_diag.loc_z=pars(9);
207			%
208			if strcmp(pars(10),'1'); avail_diag.nr=1;
209			else; avail_diag.nr=length(mygrid.RC);
210			end;
211			end;
212			end;
213			fclose(fid);
214
215			%%
216
217			function [grid_diag]=set_grid_diag(avail_diag);
218
219			gcmfaces_global;
220
221			%switch for non-tracer point values
222			if strcmp(avail_diag.loc_h,'C');
223			grid_diag.lon=mygrid.XC;
224			grid_diag.lat=mygrid.YC;
225			grid_diag.msk=mygrid.mskC(:,:,1:avail_diag.nr);
226			elseif strcmp(avail_diag.loc_h,'W');
227			grid_diag.lon=mygrid.XG;
228			grid_diag.lat=mygrid.YC;
229			grid_diag.msk=mygrid.mskW(:,:,1:avail_diag.nr);
230			elseif strcmp(avail_diag.loc_h,'S');
231			grid_diag.lon=mygrid.XC;
232			grid_diag.lat=mygrid.YG;
233			grid_diag.msk=mygrid.mskS(:,:,1:avail_diag.nr);
234			end;
235			grid_diag.RAC=mygrid.RAC;
236
237			%vertical grid
238			if avail_diag.nr~=1;
239			if strcmp(avail_diag.loc_z,'M');
240			grid_diag.dep=-mygrid.RC;
241			grid_diag.dz=mygrid.DRF;
242			elseif strcmp(avail_diag.loc_z,'L');
243			grid_diag.dep=-mygrid.RF(2:end);
244			grid_diag.dz=[mygrid.DRC(2:end) ; 228.25];%quick fix
245			else;
246			error('unknown vertical grid');
247			end;
248			grid_diag.dep=reshape(grid_diag.dep,[1 1 avail_diag.nr]);
249			grid_diag.dz=reshape(grid_diag.dz,[1 1 avail_diag.nr]);
250			end;