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);


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


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

% re-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

% replace missing_values with NaNs
fldNames=fieldnames(MITprof);
for ii=1:length(fldNames);

    fld=getfield(MITprof,fldNames{ii});
    if ~isempty(fld)
        if useNativeMatlabNetcdf;
            f = netcdf.open(fileIn, 'nowrite');
            varid = netcdf.inqVarID(f,fldNames{ii});
            if ~isempty(find(strcmp(ncatts(f,varid),'missing_value')));
                spval = double(netcdf.getAtt(f,varid,'missing_value'));
                fld(fld==spval)=NaN;
                MITprof=setfield(MITprof,fldNames{ii},fld);
            end;
            netcdf.close(f);
        else
            f = netcdf(fileIn, 'nowrite');
            spval = f{fldNames{ii}}.missing_value(:);
            if isempty(spval);
                spval = f{fldNames{ii}}.FillValue_(:);
            end
            if ~isempty(spval);
                fld(fld==spval)=NaN;
                MITprof=setfield(MITprof,fldNames{ii},fld);
            end;
            close(f);
        end
    end
    
end;

%replace prof_descr with 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			% list_vars variables list (optional)
20			%
21			%outputs: MITprof structure containing the various fields/vectors
22
23			function [MITprof]=MITprof_load(fileIn,varargin);
24
25	gforget	1.2
26	roquet	1.5
27			global useNativeMatlabNetcdf;
28			if isempty(useNativeMatlabNetcdf); useNativeMatlabNetcdf = ~isempty(which('netcdf.open')); end;
29
30
31
32			% load data using the function MITprof_read
33			[MITprof]=MITprof_read(fileIn,varargin{:});
34
35			% re-check that file exists and add prefix and suffix if necessary
36			if isempty(strfind(fileIn,'/'));
37			fileIn=['./' fileIn];
38	gforget	1.1	end;
39	roquet	1.5	if ~exist(fileIn,'file')
40			if ~exist([fileIn '.nc'],'file')
41			error([fileIn ' : file not found']);
42			else
43			fileIn=[fileIn '.nc'];
44			end
45			end
46	gforget	1.1
47	roquet	1.5	% replace missing_values with NaNs
48			fldNames=fieldnames(MITprof);
49			for ii=1:length(fldNames);
50
51			fld=getfield(MITprof,fldNames{ii});
52			if ~isempty(fld)
53			if useNativeMatlabNetcdf;
54			f = netcdf.open(fileIn, 'nowrite');
55			varid = netcdf.inqVarID(f,fldNames{ii});
56			if ~isempty(find(strcmp(ncatts(f,varid),'missing_value')));
57			spval = double(netcdf.getAtt(f,varid,'missing_value'));
58			fld(fld==spval)=NaN;
59			MITprof=setfield(MITprof,fldNames{ii},fld);
60			end;
61			netcdf.close(f);
62			else
63			f = netcdf(fileIn, 'nowrite');
64			spval = f{fldNames{ii}}.missing_value(:);
65			if isempty(spval);
66			spval = f{fldNames{ii}}.FillValue_(:);
67			end
68			if ~isempty(spval);
69			fld(fld==spval)=NaN;
70			MITprof=setfield(MITprof,fldNames{ii},fld);
71			end;
72			close(f);
73	gforget	1.2	end
74	roquet	1.5	end
75	gforget	1.3
76	gforget	1.1	end;
77
78			%replace prof_descr with cell array:
79			%----------------------------------
80	gforget	1.4	MITprof.prof_descr=cellstr(MITprof.prof_descr);
81	gforget	1.1
82			%add a couple things:
83			%--------------------
84			MITprof.np=length(MITprof.prof_lon);
85			MITprof.nr=length(MITprof.prof_depth);
86	gforget	1.4	MITprof.list_descr=unique(MITprof.prof_descr);
87			MITprof.nd=length(MITprof.list_descr);
88	gforget	1.1