profilesMatlabProcessing/profiles_IO_v2/MITprof_load.m

%function:      MITprof_load
%object:        read netcdf data files in the "MIT format"
%author:        Gael Forget (gforget@mit.edu)
%date:          june 21th, 2006
%
%usage:         [MITprof]=MITprof_load(fileIn);
%               ---> loads full data set
%           [MITprof]=MITprof_load(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.)
%
%note:          this does the same as MITprof_read, but
%               - replaces missing values with NaN
%               - adds a couple fields: np, nr, nd, list_descr
%               - replaces prof_descr with a cell form
%
%inputs:        fileIn          data file name
%           list_vars       variables list (optional)
%
%outputs:       MITprof structure containing the various fields/vectors

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


% load data using the low-level function MITprof_read
[MITprof]=MITprof_read(fileIn,varargin{:});

% re-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

% replace missing_values with NaNs
fldNames=fieldnames(MITprof);
for ii=1:length(fldNames);
    fld=getfield(MITprof,fldNames{ii});
    if ~isempty(fld)
        f = ncopen(fileIn, 'nowrite');
        varname=fldNames{ii};
        spval=ncgetFillVal(f,varname);
        if ~isempty(spval);
            fld(fld==spval)=NaN;
            MITprof=setfield(MITprof,fldNames{ii},fld);
        end;
        ncclose(f);
    end
end;

%convert prof_descr into a cell array:
%----------------------------------
MITprof.prof_descr=cellstr(MITprof.prof_descr);

%add a couple things:
%--------------------
MITprof.np=length(MITprof.prof_lon);
MITprof.nr=length(MITprof.prof_depth);
MITprof.list_descr=unique(MITprof.prof_descr);
MITprof.nd=length(MITprof.list_descr);

1	gforget	1.1	%function: MITprof_load
2			%object: read netcdf data files in the "MIT format"
3			%author: Gael Forget (gforget@mit.edu)
4			%date: june 21th, 2006
5			%
6			%usage: [MITprof]=MITprof_load(fileIn);
7	roquet	1.5	% ---> loads full data set
8			% [MITprof]=MITprof_load(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			%note: this does the same as MITprof_read, but
14	roquet	1.5	% - replaces missing values with NaN
15			% - adds a couple fields: np, nr, nd, list_descr
16			% - replaces prof_descr with a cell form
17	gforget	1.1	%
18			%inputs: fileIn data file name
19	roquet	1.9	% list_vars variables list (optional)
20	gforget	1.1	%
21			%outputs: MITprof structure containing the various fields/vectors
22
23			function [MITprof]=MITprof_load(fileIn,varargin);
24
25	gforget	1.2
26	roquet	1.9	% load data using the low-level function MITprof_read
27	roquet	1.5	[MITprof]=MITprof_read(fileIn,varargin{:});
28
29			% re-check that file exists and add prefix and suffix if necessary
30	roquet	1.7	[pathstr, name, ext] = fileparts(fileIn);
31			if isempty(pathstr) \| strcmp(pathstr,'.'), pathstr=pwd; end
32			if isempty(ext) \| ~strcmp(ext,'.nc'), ext='.nc'; end
33			fileIn=[pathstr '/' name ext];
34	roquet	1.8	if ~exist(fileIn,'file'), error([fileIn ' : file not found']); end
35	gforget	1.1
36	roquet	1.5	% replace missing_values with NaNs
37			fldNames=fieldnames(MITprof);
38			for ii=1:length(fldNames);
39			fld=getfield(MITprof,fldNames{ii});
40			if ~isempty(fld)
41	roquet	1.6	f = ncopen(fileIn, 'nowrite');
42			varname=fldNames{ii};
43			spval=ncgetFillVal(f,varname);
44			if ~isempty(spval);
45			fld(fld==spval)=NaN;
46			MITprof=setfield(MITprof,fldNames{ii},fld);
47			end;
48			ncclose(f);
49	roquet	1.5	end
50	gforget	1.1	end;
51
52	roquet	1.9	%convert prof_descr into a cell array:
53	gforget	1.1	%----------------------------------
54	gforget	1.4	MITprof.prof_descr=cellstr(MITprof.prof_descr);
55	gforget	1.1
56			%add a couple things:
57			%--------------------
58			MITprof.np=length(MITprof.prof_lon);
59			MITprof.nr=length(MITprof.prof_depth);
60	gforget	1.4	MITprof.list_descr=unique(MITprof.prof_descr);
61			MITprof.nd=length(MITprof.list_descr);
62	gforget	1.1