matlab_class/gcmfaces_IO/write2nctiles.m

function [dimOut]=write2nctiles(fileOut,fldIn,doCreate,varargin);
%object : write gcmfaces object to netcdf files (tiled)
%inputs : fileOut is the name of the file to be created
%         fldIn is the array to write to disk
%         doCreate is a 0/1 switch; 1 => create file ; 0 => append to file. 
%optional paramaters :
%         can be provided in the form {'name',value}
%         those that are currently active are
%               'descr' is the file description (default '').
%               'rdm' is the extended estimate description (default '').
%               'fldName' is the nc variable name for fld (default : the outside name of fldIn).
%               'longName' is the corresponding long name (default : '').
%               'units' is the unit of fld (default : '(unknown)').
%               'missval' is the missing value (default : NaN).
%               'fillval' is the fill value (default : NaN).
%               'tileNo' is a map of tile indices (default is face number)
%               'coord' is auxilliary coordinates attribute (e.g. 'lon lat dep')
%netcdf dimensions : array dimensions are simply set to 'i1,i2,...'

gcmfaces_global;
if ~(myenv.useNativeMatlabNetcdf);
  error('only native matlab nectdf is supported in write2nctiles');
end;

doCheck=0;%set to one to print stuff to screen

%set more optional paramaters to default values
descr=''; 
rdm='';
fldName=inputname(2); longName=''; 
units='(unknown)'; missval=NaN; fillval=NaN; dimIn=[];
tileNo=mygrid.XC; for ff=1:mygrid.nFaces; tileNo{ff}(:)=ff; end;
coord='';

%set more optional paramaters to user defined values
for ii=1:nargin-3;
    if ~iscell(varargin{ii});
        warning('inputCheck:write2nctiles_1',...
            ['write2nctiles expects \n'...
            '         its optional parameters as cell arrays. \n'...
            '         Argument no. ' num2str(ii+1) ' was ignored \n'...
            '         Type ''help write2nctiles'' for details.']);
    elseif ~ischar(varargin{ii}{1});
        warning('inputCheck:write2nctiles_2',...
            ['write2nctiles expects \n'...
            '         its optional parameters cell arrays \n'...
            '         to start with character string. \n'...
            '         Argument no. ' num2str(ii+1) ' was ignored \n'...
            '         Type ''help write2nctiles'' for details.']);
    else;
        if strcmp(varargin{ii}{1},'descr')|...
                strcmp(varargin{ii}{1},'rdm')|...
                strcmp(varargin{ii}{1},'fldName')|...
                strcmp(varargin{ii}{1},'longName')|...
                strcmp(varargin{ii}{1},'units')|...
                strcmp(varargin{ii}{1},'missval')|...
                strcmp(varargin{ii}{1},'fillval')|...
                strcmp(varargin{ii}{1},'tileNo')|...
                strcmp(varargin{ii}{1},'coord')|...
                strcmp(varargin{ii}{1},'dimIn');
            eval([varargin{ii}{1} '=varargin{ii}{2};']);
        else;
            warning('inputCheck:write2nctiles_3',...
                ['unknown option ''' varargin{ii}{1} ''' was ignored']);
        end;
    end;
end;

%split fldIn (if isa gcmfaces) into tiles
tileList=unique(convert2vector(tileNo)); 
tileList=tileList(~isnan(tileList));
ntile=length(tileList);
%
if isa(fldIn,'gcmfaces'); 
 for ff=1:ntile; 
   tmp1=[];
   for gg=1:mygrid.nFaces;
     [tmpi,tmpj]=find(tileNo{gg}==ff);
     if ~isempty(tmpi);
       tmpi=[min(tmpi(:)):max(tmpi(:))];
       tmpj=[min(tmpj(:)):max(tmpj(:))];
       tmp1=fldIn{gg}(tmpi,tmpj,:,:);
     end;
   end;
   fldTiles{ff}=tmp1;
 end;
end;

%start processing loop
for ff=1:ntile;

if isa(fldIn,'gcmfaces');
  fldTile=fldTiles{ff};
  %reverse order of dimensions
  nn=length(size(fldTile));
  fldTile=permute(fldTile,[nn:-1:1]);
else;
  fldTile=fldIn;
end;
fileTile=[fileOut sprintf('.%04d.nc',ff)];

%select dimensions of relevance:
nDim=length(size(fldTile));
dimsize=size(fldTile);
for iDim=1:nDim;
if size(fldTile,iDim)~=1;
    dimlist{iDim}=['i' num2str(iDim)];
    dimName{iDim}=['array index ' num2str(iDim)];
    eval(['dimvec.i' num2str(iDim) '=[1:size(fldTile,iDim)];']);
end;
end;

%omit singleton dimensions:
ii=find(dimsize~=1);
dimsize=dimsize(ii);
dimlist={dimlist{ii}};
dimName={dimName{ii}};

%check : 
if doCheck;
whos fldTile
descr
fldName
longName
units
missval
fillval
dimlist
dimName
dimsize
dimvec
keyboard;
end;

%output dimension information
dimOut{ff}=dimlist;

if doCreate;
  %create netcdf file:
  %-------------------
% ncid=nccreate(fileTile,'NETCDF4');%to allow for big files
  ncid=nccreate(fileTile,'clobber');

  if ~isempty(rdm); 
    descr2=[descr ' -- ' rdm{1}];
  else;
    descr2=descr;
  end;
  ncputAtt(ncid,'','description',descr2);
  for pp=2:length(rdm);
  tmp1=char(pp+63);
  netcdf.putAtt(ncid,nc_global,tmp1,rdm{pp});
  end;
  %append readme
  pp=length(rdm)+1;
  netcdf.putAtt(ncid,nc_global,tmp1,'file created using gcmfaces_IO/write2nctiles.m');
  ncputAtt(ncid,'','date',date);
  netcdf.putAtt(ncid,nc_global,'Conventions','CF-1.6')   

  ncputAtt(ncid,'','_FillValue',fillval);
  ncputAtt(ncid,'','missing_value',missval);

  ncdefDim(ncid,'itxt',30);
  for dd=1:length(dimlist); ncdefDim(ncid,dimlist{dd},dimsize(dd)); end;

  for dd=1:length(dimlist);
    ncdefVar(ncid,dimlist{dd},'double',{dimlist{dd}});
    ncputAtt(ncid,dimlist{dd},'long_name',dimName{dd});
    ncputAtt(ncid,dimlist{dd},'units','1');
  end;
  ncclose(ncid);

  %fill in the dimensions dimensions values vectors:
  %-------------------------------------------------
  ncid=ncopen(fileTile,'write');
  for dd=1:length(dimlist);
    ncputvar(ncid,dimlist{dd},getfield(dimvec,dimlist{dd}));
  end;
  ncclose(ncid);
end;

%use dimentsion specified by user
if ~isempty(dimIn); dimlist=dimIn{ff}; end;

%define and fill field:
%----------------------
ncid=ncopen(fileTile,'write');
%
netcdf.reDef(ncid);
ncdefVar(ncid,fldName,'double',flipdim(dimlist,2));%note the direction flip
if ~isempty(longName); ncputAtt(ncid,fldName,'long_name',longName); end;
if ~isempty(units); ncputAtt(ncid,fldName,'units',units); end;
if ~isempty(coord); ncputAtt(ncid,fldName,'coordinates',coord); end; 
if strcmp(fldName,'lon'); ncputAtt(ncid,fldName,'standard_name','longitude'); end;
if strcmp(fldName,'lat'); ncputAtt(ncid,fldName,'standard_name','latitude'); end;
if strcmp(fldName,'dep'); ncputAtt(ncid,fldName,'standard_name','depth'); end;
if strcmp(fldName,'tim'); ncputAtt(ncid,fldName,'standard_name','time'); end;
if strcmp(fldName,'land'); ncputAtt(ncid,fldName,'standard_name','land_binary_mask'); end;
if strcmp(fldName,'area'); ncputAtt(ncid,fldName,'standard_name','cell_area'); end;
if strcmp(fldName,'thic'); ncputAtt(ncid,fldName,'standard_name','cell_thickness'); end;
netcdf.endDef(ncid);
%
ncputvar(ncid,fldName,fldTile);
ncclose(ncid);

end;%for ff=1:ntile;

1	gforget	1.1	function [dimOut]=write2nctiles(fileOut,fldIn,doCreate,varargin);
2			%object : write gcmfaces object to netcdf files (tiled)
3			%inputs : fileOut is the name of the file to be created
4			% fldIn is the array to write to disk
5			% doCreate is a 0/1 switch; 1 => create file ; 0 => append to file.
6			%optional paramaters :
7			% can be provided in the form {'name',value}
8			% those that are currently active are
9			% 'descr' is the file description (default '').
10	gforget	1.2	% 'rdm' is the extended estimate description (default '').
11	gforget	1.1	% 'fldName' is the nc variable name for fld (default : the outside name of fldIn).
12			% 'longName' is the corresponding long name (default : '').
13			% 'units' is the unit of fld (default : '(unknown)').
14			% 'missval' is the missing value (default : NaN).
15			% 'fillval' is the fill value (default : NaN).
16	gforget	1.4	% 'tileNo' is a map of tile indices (default is face number)
17	gforget	1.5	% 'coord' is auxilliary coordinates attribute (e.g. 'lon lat dep')
18	gforget	1.1	%netcdf dimensions : array dimensions are simply set to 'i1,i2,...'
19
20			gcmfaces_global;
21	gforget	1.5	if ~(myenv.useNativeMatlabNetcdf);
22			error('only native matlab nectdf is supported in write2nctiles');
23			end;
24	gforget	1.1
25			doCheck=0;%set to one to print stuff to screen
26
27			%set more optional paramaters to default values
28			descr='';
29	gforget	1.2	rdm='';
30	gforget	1.1	fldName=inputname(2); longName='';
31	gforget	1.4	units='(unknown)'; missval=NaN; fillval=NaN; dimIn=[];
32			tileNo=mygrid.XC; for ff=1:mygrid.nFaces; tileNo{ff}(:)=ff; end;
33	gforget	1.5	coord='';
34	gforget	1.1
35			%set more optional paramaters to user defined values
36			for ii=1:nargin-3;
37			if ~iscell(varargin{ii});
38			warning('inputCheck:write2nctiles_1',...
39			['write2nctiles expects \n'...
40			' its optional parameters as cell arrays. \n'...
41			' Argument no. ' num2str(ii+1) ' was ignored \n'...
42			' Type ''help write2nctiles'' for details.']);
43			elseif ~ischar(varargin{ii}{1});
44			warning('inputCheck:write2nctiles_2',...
45			['write2nctiles expects \n'...
46			' its optional parameters cell arrays \n'...
47			' to start with character string. \n'...
48			' Argument no. ' num2str(ii+1) ' was ignored \n'...
49			' Type ''help write2nctiles'' for details.']);
50			else;
51			if strcmp(varargin{ii}{1},'descr')\|...
52	gforget	1.2	strcmp(varargin{ii}{1},'rdm')\|...
53	gforget	1.1	strcmp(varargin{ii}{1},'fldName')\|...
54			strcmp(varargin{ii}{1},'longName')\|...
55			strcmp(varargin{ii}{1},'units')\|...
56			strcmp(varargin{ii}{1},'missval')\|...
57			strcmp(varargin{ii}{1},'fillval')\|...
58	gforget	1.4	strcmp(varargin{ii}{1},'tileNo')\|...
59	gforget	1.5	strcmp(varargin{ii}{1},'coord')\|...
60	gforget	1.1	strcmp(varargin{ii}{1},'dimIn');
61			eval([varargin{ii}{1} '=varargin{ii}{2};']);
62			else;
63			warning('inputCheck:write2nctiles_3',...
64			['unknown option ''' varargin{ii}{1} ''' was ignored']);
65			end;
66			end;
67			end;
68
69	gforget	1.4	%split fldIn (if isa gcmfaces) into tiles
70			tileList=unique(convert2vector(tileNo));
71			tileList=tileList(~isnan(tileList));
72			ntile=length(tileList);
73			%
74			if isa(fldIn,'gcmfaces');
75			for ff=1:ntile;
76			tmp1=[];
77			for gg=1:mygrid.nFaces;
78			[tmpi,tmpj]=find(tileNo{gg}==ff);
79			if ~isempty(tmpi);
80			tmpi=[min(tmpi(:)):max(tmpi(:))];
81			tmpj=[min(tmpj(:)):max(tmpj(:))];
82			tmp1=fldIn{gg}(tmpi,tmpj,:,:);
83			end;
84			end;
85			fldTiles{ff}=tmp1;
86			end;
87			end;
88
89			%start processing loop
90			for ff=1:ntile;
91	gforget	1.1
92			if isa(fldIn,'gcmfaces');
93	gforget	1.4	fldTile=fldTiles{ff};
94	gforget	1.1	%reverse order of dimensions
95			nn=length(size(fldTile));
96			fldTile=permute(fldTile,[nn:-1:1]);
97			else;
98			fldTile=fldIn;
99			end;
100	gforget	1.4	fileTile=[fileOut sprintf('.%04d.nc',ff)];
101	gforget	1.1
102			%select dimensions of relevance:
103			nDim=length(size(fldTile));
104			dimsize=size(fldTile);
105			for iDim=1:nDim;
106			if size(fldTile,iDim)~=1;
107			dimlist{iDim}=['i' num2str(iDim)];
108			dimName{iDim}=['array index ' num2str(iDim)];
109			eval(['dimvec.i' num2str(iDim) '=[1:size(fldTile,iDim)];']);
110			end;
111			end;
112
113			%omit singleton dimensions:
114			ii=find(dimsize~=1);
115			dimsize=dimsize(ii);
116			dimlist={dimlist{ii}};
117			dimName={dimName{ii}};
118
119			%check :
120			if doCheck;
121			whos fldTile
122			descr
123			fldName
124			longName
125			units
126			missval
127			fillval
128			dimlist
129			dimName
130			dimsize
131			dimvec
132			keyboard;
133			end;
134
135			%output dimension information
136			dimOut{ff}=dimlist;
137
138			if doCreate;
139			%create netcdf file:
140			%-------------------
141	gforget	1.4	% ncid=nccreate(fileTile,'NETCDF4');%to allow for big files
142			ncid=nccreate(fileTile,'clobber');
143	gforget	1.1
144	gforget	1.3	if ~isempty(rdm);
145			descr2=[descr ' -- ' rdm{1}];
146			else;
147			descr2=descr;
148			end;
149	gforget	1.4	ncputAtt(ncid,'','description',descr2);
150	gforget	1.2	for pp=2:length(rdm);
151			tmp1=char(pp+63);
152			netcdf.putAtt(ncid,nc_global,tmp1,rdm{pp});
153			end;
154			%append readme
155			pp=length(rdm)+1;
156			netcdf.putAtt(ncid,nc_global,tmp1,'file created using gcmfaces_IO/write2nctiles.m');
157	gforget	1.1	ncputAtt(ncid,'','date',date);
158	gforget	1.5	netcdf.putAtt(ncid,nc_global,'Conventions','CF-1.6')
159
160			ncputAtt(ncid,'','_FillValue',fillval);
161			ncputAtt(ncid,'','missing_value',missval);
162	gforget	1.1
163			ncdefDim(ncid,'itxt',30);
164			for dd=1:length(dimlist); ncdefDim(ncid,dimlist{dd},dimsize(dd)); end;
165
166			for dd=1:length(dimlist);
167			ncdefVar(ncid,dimlist{dd},'double',{dimlist{dd}});
168			ncputAtt(ncid,dimlist{dd},'long_name',dimName{dd});
169	gforget	1.5	ncputAtt(ncid,dimlist{dd},'units','1');
170	gforget	1.1	end;
171			ncclose(ncid);
172
173			%fill in the dimensions dimensions values vectors:
174			%-------------------------------------------------
175			ncid=ncopen(fileTile,'write');
176			for dd=1:length(dimlist);
177			ncputvar(ncid,dimlist{dd},getfield(dimvec,dimlist{dd}));
178			end;
179			ncclose(ncid);
180			end;
181
182			%use dimentsion specified by user
183			if ~isempty(dimIn); dimlist=dimIn{ff}; end;
184
185			%define and fill field:
186			%----------------------
187			ncid=ncopen(fileTile,'write');
188	gforget	1.5	%
189			netcdf.reDef(ncid);
190	gforget	1.1	ncdefVar(ncid,fldName,'double',flipdim(dimlist,2));%note the direction flip
191			if ~isempty(longName); ncputAtt(ncid,fldName,'long_name',longName); end;
192			if ~isempty(units); ncputAtt(ncid,fldName,'units',units); end;
193	gforget	1.5	if ~isempty(coord); ncputAtt(ncid,fldName,'coordinates',coord); end;
194			if strcmp(fldName,'lon'); ncputAtt(ncid,fldName,'standard_name','longitude'); end;
195			if strcmp(fldName,'lat'); ncputAtt(ncid,fldName,'standard_name','latitude'); end;
196			if strcmp(fldName,'dep'); ncputAtt(ncid,fldName,'standard_name','depth'); end;
197			if strcmp(fldName,'tim'); ncputAtt(ncid,fldName,'standard_name','time'); end;
198			if strcmp(fldName,'land'); ncputAtt(ncid,fldName,'standard_name','land_binary_mask'); end;
199			if strcmp(fldName,'area'); ncputAtt(ncid,fldName,'standard_name','cell_area'); end;
200			if strcmp(fldName,'thic'); ncputAtt(ncid,fldName,'standard_name','cell_thickness'); end;
201			netcdf.endDef(ncid);
202			%
203	gforget	1.1	ncputvar(ncid,fldName,fldTile);
204			ncclose(ncid);
205
206	gforget	1.4	end;%for ff=1:ntile;
207	gforget	1.1