Diagnostics/DiagUtility/rdmnc_mod.m

function [S] = rdmnc_mod(varargin)
% S=RDMNC(FILE1,FILE2,...)
% S=RDMNC(FILE1,...,ITER)
% S=RDMNC(FILE1,...,'VAR1','VAR2',...)
% S=RDMNC(FILE1,...,'VAR1','VAR2',...,ITER)
%
%  FILE1 ... is either a single file name (e.g. 'state.nc') or a wild-card
%        strings expanding to a group of file names (e.g. 'state.*.nc').
%        There are no assumptions about suffices (e.g. 'state.*' works)
%  VAR1 ... are model variable names as written in the MNC/netcdf file
%  ITER  is a vector of time levels (consecutive indices referring to snap-shot
%        in the MNC/netcdf file i.e. 1,2,3,... and not model time)
%  S     is a structure with mutliple fields
%
% rdmnc() is a rudimentary wrapper for joining and reading netcdf files
% produced by MITgcm.  It does not give the same flexibility as opening the
% netcdf files directly using netcdf(). It is useful for quick loading of
% entire model fields which are distributed in multiple netcdf files.
% rdmnc() also reads non-MITgcm generated netcdf files.
%
% e.g. To plot the surface temperature in last time-level written to file
% >> S=rdmnd('state.*','XC','YC','RC','T',Inf);
% >> imagesc( S.XC, S.YC, S.T(:,:,1)' );
%
% $Header: /u/gcmpack/MITgcm/utils/matlab/rdmnc.m,v 1.1 2004/03/08 16:45:56 adcroft Exp $

%Defaults
global verbose
file={};
filepaths={};
files={};
verbose=0;
varlist={};
timelevels=[];

% Process function arguments
for iarg=1:nargin;
    arg=varargin{iarg};
    if ischar(arg)
        switch char(arg)
        case 'verbose',
            verbose=1;
        otherwise,
            if isempty( dir(char(arg)) )
                varlist{end+1}={arg};
            else
                file{end+1}={arg};
            end
        end
    else
        if isempty(timelevels)
            timelevels=arg;
        else
            error('Specify the time levels in a vector and not as multiple numeric arguments')
        end
    end
end

if verbose; disp('Verbose mode enabled'); end

% Create list of filenames
for eachfile=file
        filepathtemp=eachfile{:}{:};
        indecies = find(filepathtemp=='/');
        if ~isempty(indecies)
        filepathtemp = filepathtemp(1:indecies(end));
        else
        filepathtemp = '';
        end
    expandedEachFile=dir(char(eachfile{1}));
    for i=1:size(expandedEachFile,1);
        if expandedEachFile(i).isdir==0
            files{end+1}=expandedEachFile(i).name;
            filepaths{end+1}=filepathtemp;
        end
    end
end

% Open each file
S.attributes=[];
for ieachfile=1:length(files)
    eachfile = [filepaths{ieachfile},files{ieachfile}];
    nc=netcdf(char(eachfile),'read');
    if ismncfile(nc)
        S=rdmnc_local(nc,varlist,timelevels,S);
    else
        S=rdnetcdf_local(nc,varlist,S);
    end
    close(nc);
end

% -----------------------------------------------------------------------------
function [result] = ismncfile(nc);
result=~isempty(nc.('MITgcm_mnc_ver'));
% -----------------------------------------------------------------------------
function [A] = read_att(nc);
global verbose
allatt=ncnames(att(nc)); if verbose; allatt, end
A='none';
for attr=allatt;
 A.(char(attr))=nc.(char(attr))(:);
end
% -----------------------------------------------------------------------------
function [i0,j0,fn] = findTileOffset(S);
global verbose
fn=0;
if isfield(S,'attributes') & isfield(S.attributes,'global')
 G=S.attributes.global;
 tn=G.tile_number;
 snx=G.sNx; sny=G.sNy; nsx=G.nSx; nsy=G.nSy; npx=G.nPx; npy=G.nPy;
 ntx=nsx*npx;nty=nsy*npy;
 gbi=mod(tn-1,ntx); gbj=(tn-gbi-1)/ntx;
 i0=snx*gbi; j0=sny*gbj;
 if isfield(S.attributes.global,'exch2_myFace')
  fn=G.exch2_myFace;
 end
else
 i0=0;j0=0;
end
[snx,sny,nsx,nsy,npx,npy,ntx,nty,i0,j0,fn];
% -----------------------------------------------------------------------------
function [S] = rdnetcdf_local(nc,varlist,S)
% Read all attributes and variable data from a netcdf file
% with special operations for MNC style data
global verbose

% No variables specified? Default to all
if isempty(varlist)
 varlist=ncnames(var(nc)); if verbose; varlist, end
end

% Attributes for structure
S.attributes=read_att(nc);

% Read variable data
for ivar=1:size(varlist,2);
 cvar=char(varlist{ivar});
 tmpdata=nc{cvar}(:);
 if isempty(tmpdata)
  disp(['No such variable ''' cvar ''' in netcdf file' name(nc)])
 else
  tmpdata=squeeze(permute(tmpdata,[9:-1:1]));
  S.(cvar)=tmpdata;
  S.attributes.(cvar)=read_att(nc{cvar});
 end
end
% -----------------------------------------------------------------------------
function [S] = rdmnc_local(nc,varlist,timelevels,S)
% Read all attributes and variable data from a netcdf file
% with special operations for MNC style data
global verbose

nt=size( nc('T'), 1); if verbose; nt, end

% No variables specified? Default to all
if isempty(varlist)
 varlist=ncnames(var(nc)); if verbose; varlist, end
end

% No iterations specified? Default to all
if isempty(timelevels) | isnan(timelevels)
 timelevels=1:nt;
elseif timelevels == Inf
 timelevels=nt;
end

% Sanity checks
if max( find(timelevels > nt) )
 error('Requested time level is beyond time dimension in netcdf file')
end

% Attributes for structure
if timelevels>0; S.timelevels_read_from_file=timelevels; end
S.attributes.global=read_att(nc);

% Read variable data
for ivar=1:size(varlist,2);
 cvar=char(varlist{ivar}); if verbose; cvar, end
 if isempty(nc{cvar})
  disp(['No such variable ''' cvar ''' in MNC file ' name(nc)])
  continue
 end
 dims=ncnames(dim(nc{cvar}));
 if dims{1}=='T'
  if verbose; disp(['Reading variable ''' cvar ''' with record dimension']); end
  tmpdata=nc{cvar}(timelevels,:);
 else
  if verbose; disp(['Reading variable ''' cvar '''']); end
  tmpdata=nc{cvar}(:);
 end
 if isempty(tmpdata)
  error(['No such variable ''' cvar ''' in MNC file ' name(nc)])
 else
  tmpdata=squeeze(permute(tmpdata,[9:-1:1]));
  [ni nj nk nm nn no np]=size(tmpdata);
  [ni nj nk nm nn no np];
  if np~=1; error('Wow! This is a very high dimension variable...'); end
  [i0,j0,fn]=findTileOffset(S);
  cdim=dims{end}; if cdim(1)~='X'; i0=0; end
  cdim=dims{end}; if cdim(1)=='Y'; i0=j0; j0=0; end
  if length(dims)>1;
   cdim=dims{end-1}; if cdim(1)~='Y'; j0=0; end
  else
   j0=0;
  end
  S.(cvar)(i0+(1:ni),j0+(1:nj),(1:nk),(1:nm),(1:nn),(1:no),(1:np))=tmpdata;
  S.attributes.(cvar)=read_att(nc{cvar});
 end
end

if isempty(S)
 error('Something didn''t work!!!')
end
% -----------------------------------------------------------------------------
1	enderton	1.1	function [S] = rdmnc_mod(varargin)
2			% S=RDMNC(FILE1,FILE2,...)
3			% S=RDMNC(FILE1,...,ITER)
4			% S=RDMNC(FILE1,...,'VAR1','VAR2',...)
5			% S=RDMNC(FILE1,...,'VAR1','VAR2',...,ITER)
6			%
7			% FILE1 ... is either a single file name (e.g. 'state.nc') or a wild-card
8			% strings expanding to a group of file names (e.g. 'state.*.nc').
9			% There are no assumptions about suffices (e.g. 'state.*' works)
10			% VAR1 ... are model variable names as written in the MNC/netcdf file
11			% ITER is a vector of time levels (consecutive indices referring to snap-shot
12			% in the MNC/netcdf file i.e. 1,2,3,... and not model time)
13			% S is a structure with mutliple fields
14			%
15			% rdmnc() is a rudimentary wrapper for joining and reading netcdf files
16			% produced by MITgcm. It does not give the same flexibility as opening the
17			% netcdf files directly using netcdf(). It is useful for quick loading of
18			% entire model fields which are distributed in multiple netcdf files.
19			% rdmnc() also reads non-MITgcm generated netcdf files.
20			%
21			% e.g. To plot the surface temperature in last time-level written to file
22			% >> S=rdmnd('state.*','XC','YC','RC','T',Inf);
23			% >> imagesc( S.XC, S.YC, S.T(:,:,1)' );
24			%
25			% $Header: /u/gcmpack/MITgcm/utils/matlab/rdmnc.m,v 1.1 2004/03/08 16:45:56 adcroft Exp $
26
27			%Defaults
28			global verbose
29			file={};
30			filepaths={};
31			files={};
32			verbose=0;
33			varlist={};
34			timelevels=[];
35
36			% Process function arguments
37			for iarg=1:nargin;
38			arg=varargin{iarg};
39			if ischar(arg)
40			switch char(arg)
41			case 'verbose',
42			verbose=1;
43			otherwise,
44			if isempty( dir(char(arg)) )
45			varlist{end+1}={arg};
46			else
47			file{end+1}={arg};
48			end
49			end
50			else
51			if isempty(timelevels)
52			timelevels=arg;
53			else
54			error('Specify the time levels in a vector and not as multiple numeric arguments')
55			end
56			end
57			end
58
59			if verbose; disp('Verbose mode enabled'); end
60
61			% Create list of filenames
62			for eachfile=file
63			filepathtemp=eachfile{:}{:};
64			indecies = find(filepathtemp=='/');
65			if ~isempty(indecies)
66			filepathtemp = filepathtemp(1:indecies(end));
67			else
68			filepathtemp = '';
69			end
70			expandedEachFile=dir(char(eachfile{1}));
71			for i=1:size(expandedEachFile,1);
72			if expandedEachFile(i).isdir==0
73			files{end+1}=expandedEachFile(i).name;
74			filepaths{end+1}=filepathtemp;
75			end
76			end
77			end
78
79			% Open each file
80			S.attributes=[];
81			for ieachfile=1:length(files)
82			eachfile = [filepaths{ieachfile},files{ieachfile}];
83			nc=netcdf(char(eachfile),'read');
84			if ismncfile(nc)
85			S=rdmnc_local(nc,varlist,timelevels,S);
86			else
87			S=rdnetcdf_local(nc,varlist,S);
88			end
89			close(nc);
90			end
91
92			% -----------------------------------------------------------------------------
93			function [result] = ismncfile(nc);
94			result=~isempty(nc.('MITgcm_mnc_ver'));
95			% -----------------------------------------------------------------------------
96			function [A] = read_att(nc);
97			global verbose
98			allatt=ncnames(att(nc)); if verbose; allatt, end
99			A='none';
100			for attr=allatt;
101			A.(char(attr))=nc.(char(attr))(:);
102			end
103			% -----------------------------------------------------------------------------
104			function [i0,j0,fn] = findTileOffset(S);
105			global verbose
106			fn=0;
107			if isfield(S,'attributes') & isfield(S.attributes,'global')
108			G=S.attributes.global;
109			tn=G.tile_number;
110			snx=G.sNx; sny=G.sNy; nsx=G.nSx; nsy=G.nSy; npx=G.nPx; npy=G.nPy;
111			ntx=nsxnpx;nty=nsynpy;
112			gbi=mod(tn-1,ntx); gbj=(tn-gbi-1)/ntx;
113			i0=snxgbi; j0=snygbj;
114			if isfield(S.attributes.global,'exch2_myFace')
115			fn=G.exch2_myFace;
116			end
117			else
118			i0=0;j0=0;
119			end
120			[snx,sny,nsx,nsy,npx,npy,ntx,nty,i0,j0,fn];
121			% -----------------------------------------------------------------------------
122			function [S] = rdnetcdf_local(nc,varlist,S)
123			% Read all attributes and variable data from a netcdf file
124			% with special operations for MNC style data
125			global verbose
126
127			% No variables specified? Default to all
128			if isempty(varlist)
129			varlist=ncnames(var(nc)); if verbose; varlist, end
130			end
131
132			% Attributes for structure
133			S.attributes=read_att(nc);
134
135			% Read variable data
136			for ivar=1:size(varlist,2);
137			cvar=char(varlist{ivar});
138			tmpdata=nc{cvar}(:);
139			if isempty(tmpdata)
140			disp(['No such variable ''' cvar ''' in netcdf file' name(nc)])
141			else
142			tmpdata=squeeze(permute(tmpdata,[9:-1:1]));
143			S.(cvar)=tmpdata;
144			S.attributes.(cvar)=read_att(nc{cvar});
145			end
146			end
147			% -----------------------------------------------------------------------------
148			function [S] = rdmnc_local(nc,varlist,timelevels,S)
149			% Read all attributes and variable data from a netcdf file
150			% with special operations for MNC style data
151			global verbose
152
153			nt=size( nc('T'), 1); if verbose; nt, end
154
155			% No variables specified? Default to all
156			if isempty(varlist)
157			varlist=ncnames(var(nc)); if verbose; varlist, end
158			end
159
160			% No iterations specified? Default to all
161			if isempty(timelevels) \| isnan(timelevels)
162			timelevels=1:nt;
163			elseif timelevels == Inf
164			timelevels=nt;
165			end
166
167			% Sanity checks
168			if max( find(timelevels > nt) )
169			error('Requested time level is beyond time dimension in netcdf file')
170			end
171
172			% Attributes for structure
173			if timelevels>0; S.timelevels_read_from_file=timelevels; end
174			S.attributes.global=read_att(nc);
175
176			% Read variable data
177			for ivar=1:size(varlist,2);
178			cvar=char(varlist{ivar}); if verbose; cvar, end
179			if isempty(nc{cvar})
180			disp(['No such variable ''' cvar ''' in MNC file ' name(nc)])
181			continue
182			end
183			dims=ncnames(dim(nc{cvar}));
184			if dims{1}=='T'
185			if verbose; disp(['Reading variable ''' cvar ''' with record dimension']); end
186			tmpdata=nc{cvar}(timelevels,:);
187			else
188			if verbose; disp(['Reading variable ''' cvar '''']); end
189			tmpdata=nc{cvar}(:);
190			end
191			if isempty(tmpdata)
192			error(['No such variable ''' cvar ''' in MNC file ' name(nc)])
193			else
194			tmpdata=squeeze(permute(tmpdata,[9:-1:1]));
195			[ni nj nk nm nn no np]=size(tmpdata);
196			[ni nj nk nm nn no np];
197			if np~=1; error('Wow! This is a very high dimension variable...'); end
198			[i0,j0,fn]=findTileOffset(S);
199			cdim=dims{end}; if cdim(1)~='X'; i0=0; end
200			cdim=dims{end}; if cdim(1)=='Y'; i0=j0; j0=0; end
201			if length(dims)>1;
202			cdim=dims{end-1}; if cdim(1)~='Y'; j0=0; end
203			else
204			j0=0;
205			end
206			S.(cvar)(i0+(1:ni),j0+(1:nj),(1:nk),(1:nm),(1:nn),(1:no),(1:np))=tmpdata;
207			S.attributes.(cvar)=read_att(nc{cvar});
208			end
209			end
210
211			if isempty(S)
212			error('Something didn''t work!!!')
213			end
214			% -----------------------------------------------------------------------------