profilesMatlabProcessing/profiles_IO_v2/MITprof_read.m

%function:      MITprof_read
%object:        read netcdf data files in the "MIT format"
%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);


global useNativeMatlabNetcdf; 
if isempty(useNativeMatlabNetcdf); useNativeMatlabNetcdf = ~isempty(which('netcdf.open')); end;

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