profilesMatlabProcessing/profiles_IO_v2/MITprof_read.m

%function:      MITprof_read
%object:        read netcdf data files in the "MIT format". Low-level function.
%                use MITprof_load instead to load data from a MITprof
%                netcdf file.
%author:        Gael Forget (gforget@mit.edu)
%date:          june 21th, 2006
%
%usage:    [MITprof]=MITprof_read(fileIn); 
%               ---> loads full data set
%          [MITprof]=MITprof_read(fileIn,list_vars); 
%               ---> loads only the files listed in list_vars cell
%               array (e.g. list_vars={'prof_T','prof_Tweight'}) 
%               plus the one dimensional information (prof_lon etc.)
%
%inputs:        fileIn          data file name
%           list_vars       variables list (optional)
%
%outputs:       MITprof structure containing the various fields/vectors

function [MITprof]=MITprof_read(fileIn,varargin);


% check that file exists and add prefix and suffix if necessary
[pathstr, name, ext] = fileparts(fileIn);
if isempty(pathstr) | strcmp(pathstr,'.'), pathstr=pwd; end
if isempty(ext) | ~strcmp(ext,'.nc'), ext='.nc'; end
fileIn=[pathstr '/' name ext];
if ~exist(fileIn,'file'), error([fileIn ' : file not found']); end

% list of variables to read
list_vars={'prof_depth','prof_date','prof_YYYYMMDD','prof_HHMMSS',...
    'prof_lon','prof_lat','prof_basin','prof_point','prof_descr'};

% load fields
if nargin>1; 
    list_vars=unique({list_vars{:},varargin{1}{:}});
    for ii=1:length(list_vars),
        ncload(fileIn,list_vars{ii});
    end
else;
    f = ncopen(fileIn,'nowrite');
    list_vars=ncvars(f);
    ncclose(f);
    ncload(fileIn);
end;

% fill the variable MITprof
MITprof=[];
N=length(prof_depth);
for ii=1:length(list_vars);
    var=eval(list_vars{ii});
    if ismember(list_vars{ii},{'prof_depth','prof_HHMMSS','prof_YYYYMMDD',...
            'prof_lat ','prof_lon','prof_point','prof_basin','prof_date'})
        MITprof=setfield(MITprof,list_vars{ii},reshape(var,length(var),1));
    else
        MITprof=setfield(MITprof,list_vars{ii},var);
    end
end;

%fix old name convention:
if isempty(prof_depth);
    ncload(fileIn,'depth');
    MITprof.prof_depth=depth;
    clear depth;
end;

%make sure that lon is -180+180:
%-------------------------------
tmp_lon=MITprof.prof_lon;
tmp_lon(find(tmp_lon>180))=tmp_lon(find(tmp_lon>180))-360;
MITprof.prof_lon=tmp_lon;

%get rid of empty variables:
%---------------------------
fldNames=fieldnames(MITprof);
for iFld=1:length(fldNames);
    eval(['test0=isempty(MITprof.' fldNames{iFld} ');']);
    if test0; MITprof=rmfield(MITprof,fldNames{iFld}); end;
end;
1	gforget	1.1	%function: MITprof_read
2	roquet	1.10	%object: read netcdf data files in the "MIT format". Low-level function.
3			% use MITprof_load instead to load data from a MITprof
4			% netcdf file.
5	gforget	1.1	%author: Gael Forget (gforget@mit.edu)
6			%date: june 21th, 2006
7			%
8	gforget	1.3	%usage: [MITprof]=MITprof_read(fileIn);
9	gforget	1.1	% ---> loads full data set
10	gforget	1.3	% [MITprof]=MITprof_read(fileIn,list_vars);
11	gforget	1.1	% ---> loads only the files listed in list_vars cell
12			% array (e.g. list_vars={'prof_T','prof_Tweight'})
13			% plus the one dimensional information (prof_lon etc.)
14			%
15	roquet	1.10	%inputs: fileIn data file name
16			% list_vars variables list (optional)
17	gforget	1.1	%
18			%outputs: MITprof structure containing the various fields/vectors
19
20	gforget	1.3	function [MITprof]=MITprof_read(fileIn,varargin);
21	gforget	1.1
22	roquet	1.7
23			% check that file exists and add prefix and suffix if necessary
24	roquet	1.8	[pathstr, name, ext] = fileparts(fileIn);
25			if isempty(pathstr) \| strcmp(pathstr,'.'), pathstr=pwd; end
26			if isempty(ext) \| ~strcmp(ext,'.nc'), ext='.nc'; end
27			fileIn=[pathstr '/' name ext];
28	roquet	1.9	if ~exist(fileIn,'file'), error([fileIn ' : file not found']); end
29	roquet	1.7
30			% list of variables to read
31			list_vars={'prof_depth','prof_date','prof_YYYYMMDD','prof_HHMMSS',...
32			'prof_lon','prof_lat','prof_basin','prof_point','prof_descr'};
33
34			% load fields
35			if nargin>1;
36			list_vars=unique({list_vars{:},varargin{1}{:}});
37			for ii=1:length(list_vars),
38			ncload(fileIn,list_vars{ii});
39			end
40			else;
41			f = ncopen(fileIn,'nowrite');
42			list_vars=ncvars(f);
43			ncclose(f);
44			ncload(fileIn);
45	gforget	1.1	end;
46
47	roquet	1.7	% fill the variable MITprof
48			MITprof=[];
49			N=length(prof_depth);
50			for ii=1:length(list_vars);
51			var=eval(list_vars{ii});
52			if ismember(list_vars{ii},{'prof_depth','prof_HHMMSS','prof_YYYYMMDD',...
53			'prof_lat ','prof_lon','prof_point','prof_basin','prof_date'})
54			MITprof=setfield(MITprof,list_vars{ii},reshape(var,length(var),1));
55			else
56			MITprof=setfield(MITprof,list_vars{ii},var);
57			end
58			end;
59
60			%fix old name convention:
61			if isempty(prof_depth);
62			ncload(fileIn,'depth');
63			MITprof.prof_depth=depth;
64			clear depth;
65	gforget	1.1	end;
66
67	gforget	1.5	%make sure that lon is -180+180:
68	roquet	1.7	%-------------------------------
69	gforget	1.5	tmp_lon=MITprof.prof_lon;
70			tmp_lon(find(tmp_lon>180))=tmp_lon(find(tmp_lon>180))-360;
71			MITprof.prof_lon=tmp_lon;
72
73	gforget	1.6	%get rid of empty variables:
74	roquet	1.7	%---------------------------
75	gforget	1.6	fldNames=fieldnames(MITprof);
76			for iFld=1:length(fldNames);
77			eval(['test0=isempty(MITprof.' fldNames{iFld} ');']);
78			if test0; MITprof=rmfield(MITprof,fldNames{iFld}); end;
79			end;