matlab_class/gcmfaces_IO/struct2nctiles.m

function []=struct2nctiles(dirModel,fileOut,structIn,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/'
%         structIn is a structure containing descr, defs and vars
%            (see prep2nctiles.m for an example)
%         tileSize (optional) is e.g. [90 90] (by default tiles=faces)
%output : (netcdf files)

gcmfaces_global;

%directory names
filReadme=[dirModel 'README'];
dirOut=[dirModel 'tmp_nctiles/'];
if ~isdir(dirOut); mkdir(dirOut); end;

%set list of variables to process
listFlds={structIn(:).defs.fldName};
listDefs=listFlds;

%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;

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

%add structIn.descr to the beginning of rdm...
disp(structIn.descr');
descr=structIn.descr{1};
for ii=2:length(structIn.descr);
    descr=[descr ' ' structIn.descr{ii}];
end;

%set output directory/file name
myFile=[dirOut fileOut];%first instance is for subdirectory name
if ~isdir(myFile); mkdir(myFile); end;
myFile=[myFile filesep fileOut];%second instance is for file name base

%create netcdf file using write2nctiles
doCreate=1;

%sort by number of dimensions
ndimDiag=NaN*ones(1,length(listFlds));
for ii=1:length(listFlds);
    nameDiag=listFlds{ii};
    myDiag=getfield(structIn.vars,nameDiag);
    if isa(myDiag,'gcmfaces');
        ndimDiag(ii)=length(size(myDiag{1}));
    else;
        ndimDiag(ii)=sum(size(myDiag)~=1);
    end;
end;
[ndimDiag,ii]=sort(ndimDiag,'descend');
listFlds={listFlds{ii}};

%write first field
nameDiag=listFlds{1}; myDiag=getfield(structIn.vars,nameDiag); jj=find(strcmp(listDefs,nameDiag));
dimlist=write2nctiles(myFile,myDiag,doCreate,{'tileNo',tileNo},{'fldName',nameDiag},...
    {'units',structIn.defs(jj).units},{'longName',structIn.defs(jj).longName},...
    {'descr',descr},{'rdm',rdm});

%determine relevant dimensions
for ff=1:length(dimlist);
    dim.threeD{ff}=dimlist{ff};
    dim.twoD{ff}={dimlist{ff}{end-1:end}};
    dim.oneD{ff}={dimlist{ff}{1}};
end;

%prepare to add fields
doCreate=0;

%now add the other fields
for ii=2:length(listFlds);
    nameDiag=listFlds{ii};
    myDiag=getfield(structIn.vars,nameDiag);
    jj=find(strcmp(listDefs,nameDiag));
    if ndimDiag(ii)==1; tmpDim=dim.oneD;
    elseif ndimDiag(ii)==2; tmpDim=dim.twoD;
    elseif ndimDiag(ii)==3; tmpDim=dim.threeD;
    end;
    write2nctiles(myFile,myDiag',doCreate,{'tileNo',tileNo},...
        {'fldName',nameDiag},{'units',structIn.defs(jj).units},...
        {'longName',structIn.defs(jj).longName},{'dimIn',tmpDim});
end;

function [meta]=read_meta(fileName);

%read meta file
tmp1=dir([fileName '*.meta']); tmp1=tmp1(1).name;
tmp2=strfind(fileName,filesep);
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);

%%
1	function []=struct2nctiles(dirModel,fileOut,structIn,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	% structIn is a structure containing descr, defs and vars
13	% (see prep2nctiles.m for an example)
14	% tileSize (optional) is e.g. [90 90] (by default tiles=faces)
15	%output : (netcdf files)
16
17	gcmfaces_global;
18
19	%directory names
20	filReadme=[dirModel 'README'];
21	dirOut=[dirModel 'tmp_nctiles/'];
22	if ~isdir(dirOut); mkdir(dirOut); end;
23
24	%set list of variables to process
25	listFlds={structIn(:).defs.fldName};
26	listDefs=listFlds;
27
28	%determine map of tile indices (by default tiles=faces)
29	if isempty(whos('tileSize'));
30	tileNo=mygrid.XC;
31	for ff=1:mygrid.nFaces; tileNo{ff}(:)=ff; end;
32	else;
33	tileNo=gcmfaces_loc_tile(tileSize(1),tileSize(2));
34	end;
35
36	%get description of estimate from README
37	[rdm]=read_readme(filReadme);
38	disp(rdm');
39
40	%add structIn.descr to the beginning of rdm...
41	disp(structIn.descr');
42	descr=structIn.descr{1};
43	for ii=2:length(structIn.descr);
44	descr=[descr ' ' structIn.descr{ii}];
45	end;
46
47	%set output directory/file name
48	myFile=[dirOut fileOut];%first instance is for subdirectory name
49	if ~isdir(myFile); mkdir(myFile); end;
50	myFile=[myFile filesep fileOut];%second instance is for file name base
51
52	%create netcdf file using write2nctiles
53	doCreate=1;
54
55	%sort by number of dimensions
56	ndimDiag=NaN*ones(1,length(listFlds));
57	for ii=1:length(listFlds);
58	nameDiag=listFlds{ii};
59	myDiag=getfield(structIn.vars,nameDiag);
60	if isa(myDiag,'gcmfaces');
61	ndimDiag(ii)=length(size(myDiag{1}));
62	else;
63	ndimDiag(ii)=sum(size(myDiag)~=1);
64	end;
65	end;
66	[ndimDiag,ii]=sort(ndimDiag,'descend');
67	listFlds={listFlds{ii}};
68
69	%write first field
70	nameDiag=listFlds{1}; myDiag=getfield(structIn.vars,nameDiag); jj=find(strcmp(listDefs,nameDiag));
71	dimlist=write2nctiles(myFile,myDiag,doCreate,{'tileNo',tileNo},{'fldName',nameDiag},...
72	{'units',structIn.defs(jj).units},{'longName',structIn.defs(jj).longName},...
73	{'descr',descr},{'rdm',rdm});
74
75	%determine relevant dimensions
76	for ff=1:length(dimlist);
77	dim.threeD{ff}=dimlist{ff};
78	dim.twoD{ff}={dimlist{ff}{end-1:end}};
79	dim.oneD{ff}={dimlist{ff}{1}};
80	end;
81
82	%prepare to add fields
83	doCreate=0;
84
85	%now add the other fields
86	for ii=2:length(listFlds);
87	nameDiag=listFlds{ii};
88	myDiag=getfield(structIn.vars,nameDiag);
89	jj=find(strcmp(listDefs,nameDiag));
90	if ndimDiag(ii)==1; tmpDim=dim.oneD;
91	elseif ndimDiag(ii)==2; tmpDim=dim.twoD;
92	elseif ndimDiag(ii)==3; tmpDim=dim.threeD;
93	end;
94	write2nctiles(myFile,myDiag',doCreate,{'tileNo',tileNo},...
95	{'fldName',nameDiag},{'units',structIn.defs(jj).units},...
96	{'longName',structIn.defs(jj).longName},{'dimIn',tmpDim});
97	end;
98
99	function [meta]=read_meta(fileName);
100
101	%read meta file
102	tmp1=dir([fileName '*.meta']); tmp1=tmp1(1).name;
103	tmp2=strfind(fileName,filesep);
104	if ~isempty(tmp2); tmp2=tmp2(end); else; tmp2=0; end;
105	tmp1=[fileName(1:tmp2) tmp1]; fid=fopen(tmp1);
106	while 1;
107	tline = fgetl(fid);
108	if ~ischar(tline), break, end
109	if isempty(whos('tmp3')); tmp3=tline; else; tmp3=[tmp3 ' ' tline]; end;
110	end
111	fclose(fid);
112
113	%add meta variables to workspace
114	eval(tmp3);
115
116	%reformat to meta structure
117	meta.dataprec=dataprec;
118	meta.nDims=nDims;
119	meta.nFlds=nFlds;
120	meta.nrecords=nrecords;
121	meta.fldList=fldList;
122	meta.dimList=dimList;
123	if ~isempty(who('timeInterval')); meta.timeInterval=timeInterval; end;
124	if ~isempty(who('timeStepNumber')); meta.timeStepNumber=timeStepNumber; end;
125
126	%%
127
128	function [rdm]=read_readme(filReadme);
129
130	gcmfaces_global;
131
132	rdm=[];
133
134	fid=fopen(filReadme,'rt');
135	while ~feof(fid);
136	nn=length(rdm);
137	rdm{nn+1} = fgetl(fid);
138	end;
139	fclose(fid);
140
141	%%