utils/matlab/rdmnc.m

function [S] = rdmnc(varargin)

% Usage:
%   S=RDMNC(FILE1,FILE2,...)
%   S=RDMNC(FILE1,...,ITER)
%   S=RDMNC(FILE1,...,'VAR1','VAR2',...)
%   S=RDMNC(FILE1,...,'VAR1','VAR2',...,ITER)
%
% Input:
%   FILE1   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    Model variable names as written in the MNC/netcdf file.
%   ITER    Vector of iterations in the MNC/netcdf files, not model time.
%
% Output:
%   S       Structure with fields corresponding to 'VAR1', 'VAR2', ...
%
% Description:
%   This function 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(), but is useful for
%   quick loading of entire model fields which are distributed in multiple
%   netcdf files.
%
% Example:
%   >> S=rdmnd('state.*','XC','YC','T');
%   >> imagesc( S.XC, S.YC, S.T(:,:,1)' );
%
%  Author:  Alistair Adcroft
%  Modifications:  Daniel Enderton

% Initializations
file={};
filepaths={};
files={};
varlist={};
iters=[];

% Process function arguments
for iarg=1:nargin;
    arg=varargin{iarg};
    if ischar(arg)
        if isempty(dir(char(arg)))
            varlist{end+1}=arg;
        else
            file{end+1}=arg;
        end
    else
        if isempty(iters)
            iters=arg;
        else
            error(['The only allowed numeric argument is iterations',...
                   ' to read in as a vector for the last arguement']);
        end
    end
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


% If iterations unspecified, open all the files and make list of all the
% iterations that appear, use this iterations list for data extraction.
if isempty(iters)
    iters = [];
    for ieachfile=1:length(files)
        eachfile = [filepaths{ieachfile},files{ieachfile}];
        nc=netcdf(char(eachfile),'read');
        nciters = nc{'iter'}(:);
        if isempty(nciters), nciters = nc{'T'}(:); end
        iters = [iters,nciters];
        close(nc);
    end
    iters = unique(iters);
end

% Cycle through files for data extraction.
S.attributes=[];
for ieachfile=1:length(files)
    eachfile = [filepaths{ieachfile},files{ieachfile}];
    nc=netcdf(char(eachfile),'read');
    S=rdmnc_local(nc,varlist,iters,S);
    close(nc);
end


%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%                             Local functions                             %
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

function [A] = read_att(nc);
    allatt=ncnames(att(nc));
    if ~isempty(allatt)
        for attr=allatt;
            A.(char(attr))=nc.(char(attr))(:);
        end
    else
        A = 'none';
    end

function [i0,j0,fn] = findTileOffset(S);
    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] = rdmnc_local(nc,varlist,iters,S)

    fiter = nc{'iter'}(:);                               % File iterations present
    if isempty(fiter), fiter = nc{'T'}(:); end
    if isinf(iters); iters = fiter(end); end
    if isnan(iters); iters = fiter; end
    [fii,dii] = ismember(fiter,iters);  fii = find(fii); % File iteration index
    dii = dii(find(dii ~= 0));                           % Data interation index
    
    % No variables specified? Default to all
    if isempty(varlist), varlist=ncnames(var(nc)); end
    
    % Attributes for structure
    if iters>0; S.iters_read_from_file=iters; end
    S.attributes.global=read_att(nc);
    
        % Read variable data
        for ivar=1:size(varlist,2)
        
        cvar=char(varlist{ivar});
        if isempty(nc{cvar})
            disp(['No such variable ''',cvar,''' in MNC file ',name(nc)]);
            continue
        end
        
        dims = ncnames(dim(nc{cvar}));        % Dimensions
        adj = 0;
        if dims{1} == 'T'
            
            if isempty(find(fii)), disp('Iters not found'); return, end
            
            tmpdata = nc{cvar}(fii,:);
            if ismember('Zd000001' ,dims), adj = adj - 1; end
            if ismember('Zmd000001',dims), adj = adj - 1; end
            it = length(dims) + adj;
        else
            tmpdata = nc{cvar}(:);
            it = 0;
        end
        
        tmpdata=shiftdim(permute(tmpdata,[9:-1:1]));
        [ni nj nk nm nn no np]=size(tmpdata);
        
        [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
        
        Sstr = '';
        for istr = 1:7
            if     istr == it,  Sstr = [Sstr,'dii,'];
            elseif istr == 1,   Sstr = [Sstr,'i0+(1:ni),'];
            elseif istr == 2,   Sstr = [Sstr,'j0+(1:nj),'];
            elseif istr == 3,   Sstr = [Sstr,'(1:nk),'];
            elseif istr == 4,   Sstr = [Sstr,'(1:nm),'];
            elseif istr == 5,   Sstr = [Sstr,'(1:nn),'];
            elseif istr == 6,   Sstr = [Sstr,'(1:no),'];
            elseif istr == 7,   Sstr = [Sstr,'(1:np),'];
            else, error('Can''t handle this many dimensions!');
            end
        end
        
        eval(['S.(cvar)(',Sstr(1:end-1),')=tmpdata;'])
        %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

if isempty(S)
    error('Something didn''t work!!!');
end
1	enderton	1.6	function [S] = rdmnc(varargin)
2	enderton	1.3
3			% Usage:
4			% S=RDMNC(FILE1,FILE2,...)
5			% S=RDMNC(FILE1,...,ITER)
6			% S=RDMNC(FILE1,...,'VAR1','VAR2',...)
7			% S=RDMNC(FILE1,...,'VAR1','VAR2',...,ITER)
8			%
9			% Input:
10			% FILE1 Either a single file name (e.g. 'state.nc') or a wild-card
11			% strings expanding to a group of file names (e.g. 'state.*.nc').
12			% There are no assumptions about suffices (e.g. 'state.*' works).
13			% VAR1 Model variable names as written in the MNC/netcdf file.
14			% ITER Vector of iterations in the MNC/netcdf files, not model time.
15	adcroft	1.1	%
16	enderton	1.3	% Output:
17			% S Structure with fields corresponding to 'VAR1', 'VAR2', ...
18	adcroft	1.1	%
19	enderton	1.3	% Description:
20			% This function is a rudimentary wrapper for joining and reading netcdf
21			% files produced by MITgcm. It does not give the same flexibility as
22			% opening the netcdf files directly using netcdf(), but is useful for
23			% quick loading of entire model fields which are distributed in multiple
24			% netcdf files.
25	adcroft	1.1	%
26	enderton	1.3	% Example:
27			% >> S=rdmnd('state.*','XC','YC','T');
28			% >> imagesc( S.XC, S.YC, S.T(:,:,1)' );
29	adcroft	1.1	%
30	enderton	1.4	% Author: Alistair Adcroft
31	enderton	1.3	% Modifications: Daniel Enderton
32	adcroft	1.1
33	enderton	1.3	% Initializations
34	adcroft	1.1	file={};
35	enderton	1.3	filepaths={};
36	adcroft	1.1	files={};
37			varlist={};
38	enderton	1.3	iters=[];
39	adcroft	1.1
40			% Process function arguments
41			for iarg=1:nargin;
42	enderton	1.3	arg=varargin{iarg};
43			if ischar(arg)
44			if isempty(dir(char(arg)))
45			varlist{end+1}=arg;
46			else
47			file{end+1}=arg;
48			end
49			else
50			if isempty(iters)
51			iters=arg;
52			else
53			error(['The only allowed numeric argument is iterations',...
54			' to read in as a vector for the last arguement']);
55			end
56			end
57	adcroft	1.1	end
58
59			% Create list of filenames
60			for eachfile=file
61	enderton	1.3	filepathtemp=eachfile{:};
62			indecies = find(filepathtemp=='/');
63			if ~isempty(indecies)
64			filepathtemp = filepathtemp(1:indecies(end));
65			else
66			filepathtemp = '';
67			end
68			expandedEachFile=dir(char(eachfile{1}));
69			for i=1:size(expandedEachFile,1);
70			if expandedEachFile(i).isdir==0
71			files{end+1}=expandedEachFile(i).name;
72			filepaths{end+1}=filepathtemp;
73			end
74			end
75	adcroft	1.1	end
76
77
78	enderton	1.3	% If iterations unspecified, open all the files and make list of all the
79			% iterations that appear, use this iterations list for data extraction.
80			if isempty(iters)
81			iters = [];
82			for ieachfile=1:length(files)
83			eachfile = [filepaths{ieachfile},files{ieachfile}];
84			nc=netcdf(char(eachfile),'read');
85	enderton	1.4	nciters = nc{'iter'}(:);
86			if isempty(nciters), nciters = nc{'T'}(:); end
87			iters = [iters,nciters];
88	enderton	1.3	close(nc);
89			end
90			iters = unique(iters);
91	adcroft	1.1	end
92
93	enderton	1.3	% Cycle through files for data extraction.
94			S.attributes=[];
95			for ieachfile=1:length(files)
96			eachfile = [filepaths{ieachfile},files{ieachfile}];
97			nc=netcdf(char(eachfile),'read');
98			S=rdmnc_local(nc,varlist,iters,S);
99			close(nc);
100	adcroft	1.1	end
101
102	enderton	1.5
103	enderton	1.3	%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
104			% Local functions %
105			%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
106	adcroft	1.1
107	enderton	1.3	function [A] = read_att(nc);
108			allatt=ncnames(att(nc));
109			if ~isempty(allatt)
110			for attr=allatt;
111			A.(char(attr))=nc.(char(attr))(:);
112			end
113			else
114			A = 'none';
115			end
116	adcroft	1.1
117	enderton	1.3	function [i0,j0,fn] = findTileOffset(S);
118			fn=0;
119			if isfield(S,'attributes') & isfield(S.attributes,'global')
120			G=S.attributes.global;
121			tn=G.tile_number;
122			snx=G.sNx; sny=G.sNy; nsx=G.nSx; nsy=G.nSy; npx=G.nPx; npy=G.nPy;
123			ntx=nsxnpx;nty=nsynpy;
124			gbi=mod(tn-1,ntx); gbj=(tn-gbi-1)/ntx;
125			i0=snxgbi; j0=snygbj;
126			if isfield(S.attributes.global,'exch2_myFace')
127			fn=G.exch2_myFace;
128			end
129			else
130			i0=0;j0=0;
131			end
132			%[snx,sny,nsx,nsy,npx,npy,ntx,nty,i0,j0,fn];
133
134			function [S] = rdmnc_local(nc,varlist,iters,S)
135
136			fiter = nc{'iter'}(:); % File iterations present
137	enderton	1.4	if isempty(fiter), fiter = nc{'T'}(:); end
138	mlosch	1.10	if isinf(iters); iters = fiter(end); end
139			if isnan(iters); iters = fiter; end
140	enderton	1.3	[fii,dii] = ismember(fiter,iters); fii = find(fii); % File iteration index
141			dii = dii(find(dii ~= 0)); % Data interation index
142	enderton	1.4
143	enderton	1.3	% No variables specified? Default to all
144			if isempty(varlist), varlist=ncnames(var(nc)); end
145	enderton	1.4
146	enderton	1.3	% Attributes for structure
147			if iters>0; S.iters_read_from_file=iters; end
148			S.attributes.global=read_att(nc);
149	enderton	1.4
150	enderton	1.3	% Read variable data
151	enderton	1.4	for ivar=1:size(varlist,2)
152
153	enderton	1.3	cvar=char(varlist{ivar});
154			if isempty(nc{cvar})
155			disp(['No such variable ''',cvar,''' in MNC file ',name(nc)]);
156			continue
157			end
158
159	enderton	1.6	dims = ncnames(dim(nc{cvar})); % Dimensions
160			adj = 0;
161			if dims{1} == 'T'
162	jmc	1.9
163			if isempty(find(fii)), disp('Iters not found'); return, end
164	enderton	1.7
165			tmpdata = nc{cvar}(fii,:);
166	enderton	1.6	if ismember('Zd000001' ,dims), adj = adj - 1; end
167			if ismember('Zmd000001',dims), adj = adj - 1; end
168			it = length(dims) + adj;
169	enderton	1.3	else
170	enderton	1.6	tmpdata = nc{cvar}(:);
171	enderton	1.3	it = 0;
172			end
173	enderton	1.4
174	mlosch	1.11	tmpdata=shiftdim(permute(tmpdata,[9:-1:1]));
175	enderton	1.3	[ni nj nk nm nn no np]=size(tmpdata);
176
177			[i0,j0,fn]=findTileOffset(S);
178			cdim=dims{end}; if cdim(1)~='X'; i0=0; end
179			cdim=dims{end}; if cdim(1)=='Y'; i0=j0; j0=0; end
180			if length(dims)>1;
181			cdim=dims{end-1}; if cdim(1)~='Y'; j0=0; end
182			else
183			j0=0;
184			end
185
186			Sstr = '';
187			for istr = 1:7
188			if istr == it, Sstr = [Sstr,'dii,'];
189			elseif istr == 1, Sstr = [Sstr,'i0+(1:ni),'];
190			elseif istr == 2, Sstr = [Sstr,'j0+(1:nj),'];
191			elseif istr == 3, Sstr = [Sstr,'(1:nk),'];
192			elseif istr == 4, Sstr = [Sstr,'(1:nm),'];
193			elseif istr == 5, Sstr = [Sstr,'(1:nn),'];
194			elseif istr == 6, Sstr = [Sstr,'(1:no),'];
195			elseif istr == 7, Sstr = [Sstr,'(1:np),'];
196			else, error('Can''t handle this many dimensions!');
197			end
198			end
199	enderton	1.6
200	enderton	1.3	eval(['S.(cvar)(',Sstr(1:end-1),')=tmpdata;'])
201			%S.(cvar)(i0+(1:ni),j0+(1:nj),(1:nk),(1:nm),(1:nn),(1:no),(1:np))=tmpdata;
202			S.attributes.(cvar)=read_att(nc{cvar});
203			end
204	adcroft	1.1
205			if isempty(S)
206	enderton	1.3	error('Something didn''t work!!!');
207	adcroft	1.1	end