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)
%               if no list_vars is provided, all fields are loaded.
%
%outputs:       MITprof structure containing the various fields/vectors

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


% check that file exists, and open it
if ~exist(fileIn,'file'), error([fileIn ' : file not found']); end

% open netcdf
nc=ncopen(fileIn);
MITprof=[];

% build the list of variable to load
if nargin>1; list_vars=varargin{1};
else, list_vars=ncvars(nc); end
if isempty(list_vars), return, end
%list_vars=[{'prof_lon','prof_lat'} list_vars];
%if ismember('prof_date',list_vars), list_vars=[{'prof_YYYYMMDD','prof_HHMMSS'} list_vars]; end
[list,m]=unique(list_vars);
list_vars=list_vars(sort(m));

% is there only one profile?
one_profile=0;
data=ncgetvar(nc,'prof_lon');
if length(data)==1, one_profile=1; end

% load fields into MITprof struct
for ii=1:length(list_vars),
    data=ncgetvar(nc,list_vars{ii});
    if size(data,1)==1 & ~one_profile,
        data=reshape(data,length(data),1);
    end
    MITprof=setfield(MITprof,list_vars{ii},data);
end

% load depth vector separately (either in prof_depth or depth variable)
if ismember('prof_depth', list_vars)
    data=ncgetvar(nc,'prof_depth');
elseif ismember('depth', list_vars)
    data=ncgetvar(nc,'depth');
end
data=reshape(data,length(data),1);
MITprof=setfield(MITprof,'prof_depth',data);

% add field prof_date if not already in the nc file
if ismember('prof_date',list_vars) & ~isfield(MITprof,'prof_date');
    MITprof.prof_date=datenum(num2str(MITprof.prof_YYYYMMDD*1e6+MITprof.prof_HHMMSS),'yyyymmddHHMMSS');
end;

% add prof_YYYYMMDD and prof_HHMMSS if possible
if isfield(MITprof,'prof_date') & ~isfield(MITprof,'prof_YYYYMMDD');
    tmp1=datevec(MITprof.prof_date);
    MITprof.prof_YYYYMMDD=tmp1(:,1)*1e4+tmp1(:,2)*1e2+tmp1(:,3);
    MITprof.prof_HHMMSS=tmp1(:,4)*1e4+tmp1(:,5)*1e2+tmp1(:,6);
end;

% close file
ncclose(nc);

%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	roquet	1.11	% if no list_vars is provided, all fields are loaded.
18	gforget	1.1	%
19			%outputs: MITprof structure containing the various fields/vectors
20
21	gforget	1.3	function [MITprof]=MITprof_read(fileIn,varargin);
22	gforget	1.1
23	roquet	1.7
24	roquet	1.11	% check that file exists, and open it
25	roquet	1.9	if ~exist(fileIn,'file'), error([fileIn ' : file not found']); end
26	roquet	1.7
27	roquet	1.11	% open netcdf
28			nc=ncopen(fileIn);
29			MITprof=[];
30	gforget	1.1
31	roquet	1.11	% build the list of variable to load
32			if nargin>1; list_vars=varargin{1};
33			else, list_vars=ncvars(nc); end
34			if isempty(list_vars), return, end
35	gforget	1.13	%list_vars=[{'prof_lon','prof_lat'} list_vars];
36			%if ismember('prof_date',list_vars), list_vars=[{'prof_YYYYMMDD','prof_HHMMSS'} list_vars]; end
37	roquet	1.11	[list,m]=unique(list_vars);
38			list_vars=list_vars(sort(m));
39
40	roquet	1.12	% is there only one profile?
41			one_profile=0;
42			data=ncgetvar(nc,'prof_lon');
43			if length(data)==1, one_profile=1; end
44
45	roquet	1.11	% load fields into MITprof struct
46			for ii=1:length(list_vars),
47			data=ncgetvar(nc,list_vars{ii});
48	roquet	1.12	if size(data,1)==1 & ~one_profile,
49	roquet	1.11	data=reshape(data,length(data),1);
50	roquet	1.7	end
51	roquet	1.12	MITprof=setfield(MITprof,list_vars{ii},data);
52			end
53	roquet	1.11
54	roquet	1.12	% load depth vector separately (either in prof_depth or depth variable)
55			if ismember('prof_depth', list_vars)
56			data=ncgetvar(nc,'prof_depth');
57			elseif ismember('depth', list_vars)
58			data=ncgetvar(nc,'depth');
59	roquet	1.11	end
60	roquet	1.12	data=reshape(data,length(data),1);
61			MITprof=setfield(MITprof,'prof_depth',data);
62	roquet	1.7
63	roquet	1.12	% add field prof_date if not already in the nc file
64			if ismember('prof_date',list_vars) & ~isfield(MITprof,'prof_date');
65			MITprof.prof_date=datenum(num2str(MITprof.prof_YYYYMMDD*1e6+MITprof.prof_HHMMSS),'yyyymmddHHMMSS');
66	gforget	1.1	end;
67
68	gforget	1.13	% add prof_YYYYMMDD and prof_HHMMSS if possible
69			if isfield(MITprof,'prof_date') & ~isfield(MITprof,'prof_YYYYMMDD');
70			tmp1=datevec(MITprof.prof_date);
71			MITprof.prof_YYYYMMDD=tmp1(:,1)1e4+tmp1(:,2)1e2+tmp1(:,3);
72			MITprof.prof_HHMMSS=tmp1(:,4)1e4+tmp1(:,5)1e2+tmp1(:,6);
73			end;
74
75	roquet	1.11	% close file
76			ncclose(nc);
77
78	gforget	1.5	%make sure that lon is -180+180:
79	roquet	1.7	%-------------------------------
80	gforget	1.5	tmp_lon=MITprof.prof_lon;
81			tmp_lon(find(tmp_lon>180))=tmp_lon(find(tmp_lon>180))-360;
82			MITprof.prof_lon=tmp_lon;
83
84	gforget	1.6	%get rid of empty variables:
85	roquet	1.7	%---------------------------
86	gforget	1.6	fldNames=fieldnames(MITprof);
87			for iFld=1:length(fldNames);
88			eval(['test0=isempty(MITprof.' fldNames{iFld} ');']);
89			if test0; MITprof=rmfield(MITprof,fldNames{iFld}); end;
90			end;