profilesMatlabProcessing/profiles_IO_v2/MITprof_load.m

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


% 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

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

% replace missing_values with NaNs
fldNames=fieldnames(MITprof);
fldNames=setdiff(fldNames,{'prof_depth','depth'}); % no NaNs in prof_depth
if isfield(MITprof,'prof_date'), % special case for prof_date
    fldNames=setdiff(fldNames,'prof_date');
    fldNames=[fldNames,{'prof_YYYYMMDD'}];
end
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;

% missing values for prof_date
if isfield(MITprof,'prof_date'),
    MITprof.prof_date( isnan(MITprof.prof_YYYYMMDD) )=NaN;
end

%convert prof_descr into a cell array:
%----------------------------------
if isfield(MITprof,'prof_descr')
    MITprof.prof_descr=cellstr(MITprof.prof_descr);
    MITprof.list_descr=unique(MITprof.prof_descr);
    MITprof.nd=length(MITprof.list_descr);
end

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

1	roquet	1.11	function [MITprof]=MITprof_load(fileIn,varargin);
2	gforget	1.1	%function: MITprof_load
3			%object: read netcdf data files in the "MIT format"
4			%author: Gael Forget (gforget@mit.edu)
5			%date: june 21th, 2006
6			%
7			%usage: [MITprof]=MITprof_load(fileIn);
8	roquet	1.5	% ---> loads full data set
9			% [MITprof]=MITprof_load(fileIn,list_vars);
10	gforget	1.1	% ---> loads only the files listed in list_vars cell
11			% array (e.g. list_vars={'prof_T','prof_Tweight'})
12			% plus the one dimensional information (prof_lon etc.)
13			%
14			%note: this does the same as MITprof_read, but
15	roquet	1.5	% - replaces missing values with NaN
16			% - adds a couple fields: np, nr, nd, list_descr
17			% - replaces prof_descr with a cell form
18	gforget	1.1	%
19			%inputs: fileIn data file name
20	roquet	1.10	% list_vars variables list (optional)
21	gforget	1.1	%
22			%outputs: MITprof structure containing the various fields/vectors
23
24
25	gforget	1.2
26	roquet	1.10	% check that file exists and add prefix and suffix if necessary
27	roquet	1.7	[pathstr, name, ext] = fileparts(fileIn);
28			if isempty(pathstr) \| strcmp(pathstr,'.'), pathstr=pwd; end
29			if isempty(ext) \| ~strcmp(ext,'.nc'), ext='.nc'; end
30			fileIn=[pathstr '/' name ext];
31	roquet	1.8	if ~exist(fileIn,'file'), error([fileIn ' : file not found']); end
32	gforget	1.1
33	roquet	1.10	% load data using the low-level function MITprof_read
34			[MITprof]=MITprof_read(fileIn,varargin{:});
35
36	roquet	1.5	% replace missing_values with NaNs
37			fldNames=fieldnames(MITprof);
38	roquet	1.11	fldNames=setdiff(fldNames,{'prof_depth','depth'}); % no NaNs in prof_depth
39			if isfield(MITprof,'prof_date'), % special case for prof_date
40			fldNames=setdiff(fldNames,'prof_date');
41			fldNames=[fldNames,{'prof_YYYYMMDD'}];
42			end
43	roquet	1.5	for ii=1:length(fldNames);
44			fld=getfield(MITprof,fldNames{ii});
45			if ~isempty(fld)
46	roquet	1.6	f = ncopen(fileIn, 'nowrite');
47			varname=fldNames{ii};
48			spval=ncgetFillVal(f,varname);
49			if ~isempty(spval);
50			fld(fld==spval)=NaN;
51			MITprof=setfield(MITprof,fldNames{ii},fld);
52			end;
53			ncclose(f);
54	roquet	1.5	end
55	gforget	1.1	end;
56
57	roquet	1.11	% missing values for prof_date
58			if isfield(MITprof,'prof_date'),
59			MITprof.prof_date( isnan(MITprof.prof_YYYYMMDD) )=NaN;
60			end
61
62	roquet	1.9	%convert prof_descr into a cell array:
63	gforget	1.1	%----------------------------------
64	roquet	1.10	if isfield(MITprof,'prof_descr')
65			MITprof.prof_descr=cellstr(MITprof.prof_descr);
66			MITprof.list_descr=unique(MITprof.prof_descr);
67			MITprof.nd=length(MITprof.list_descr);
68			end
69	gforget	1.1
70			%add a couple things:
71			%--------------------
72			MITprof.np=length(MITprof.prof_lon);
73			MITprof.nr=length(MITprof.prof_depth);
74