profilesMatlabProcessing/profiles_IO_v2/MITprof_write.m

function []=MITprof_write(fileOut,MITprof,varargin);
%function:      MITprof_write
%object:        write data in a MITprof netcdf file
%author:        Gael Forget (gforget@mit.edu)
%date:          Nov 5th, 2010
%
%usage:    []=MITprof_write(fileOut,MITprof, [list_vars] ); 
%
%inputs:        fileOut         data file name (absolute/relative path)
%                         .nc suffix is added if not already present
%           MITprof     struct containing profile data
%           list_vars   variable list (optional)
%
% Format description of MITprof struct input variable:
%   list of fields always available:
%       prof_depth      [nDepth x 1]
%       prof_descr      {nProf x 1} --> will be converted into a char array
%       prof_date       [nProf x 1]
%       prof_YYYYMMDD   [nProf x 1]
%       prof_HHMMSS     [nProf x 1]
%       prof_lon        [nProf x 1]
%       prof_lat        [nProf x 1]
%       prof_basin      [nProf x 1]
%       prof_point      [nProf x 1]
%
%   other fields generally available of size [nProf x nLev] :
%       prof_T, prof_Tflag, prof_Terr, prof_Tweight, prof_Testim
%       prof_S, prof_Sflag, prof_Serr, prof_Sweight, prof_Sestim
%
% if list_vars is not specified, every variables with a name starting 
%       with 'prof_', except prof_depth, will be saved in the MITprof
%       netcdf file. An error will occur if the program try to save a
%       variable that is not initialized in the MITprof netcdf file.
%
% if list_vars is specified, only variables present in the list will be
%       saved.
%
% NaN are auomatically replaced by missing_value attribute (or _FillValue).
% the file fileOut will be created using MITprof_create if needed.
%


% check that file exists and add prefix and suffix if necessary
[pathstr, name, ext] = fileparts(fileOut);
if isempty(pathstr) | strcmp(pathstr,'.'), pathstr=pwd; end
if isempty(ext) | ~strcmp(ext,'.nc'), ext='.nc'; end
fileOut=[pathstr '/' name ext];

% build the list of variables that must be loaded
if nargin>2,
    list_vars=varargin{1};
else
    list1=fieldnames(MITprof); list_vars={};
    I=strfind(list1,'prof_');
    for kk=1:length(I),
        if I{kk}==1 & ~strcmp(list1{kk},'prof_depth'),
            list_vars{end+1}=list1{kk};
        end
    end
end

% stop if there are no profile in MITprof
nProf=length(MITprof.prof_lon);
if nProf==0, return, end

% create the file if needed
if ~exist(fileOut,'file'),
    prof_depth=MITprof.prof_depth;
    MITprof_create(fileOut,nProf,prof_depth,list_vars);
end

% prof_descr: convert back from cell 2 array format
if isfield(MITprof,'prof_descr')
    ncload(fileOut,'prof_descr'); nb_char=size(prof_descr,2);
    prof_descr=char(MITprof.prof_descr);
    if size(prof_descr,2)<nb_char,
        prof_descr(:,size(prof_descr,2)+1:nb_char)=' ';
    elseif size(prof_descr,2)>nb_char
        disp('some profile descriptive strings have been shortened');
        prof_descr=prof_descr(:,1:nb_char);
    end
    MITprof.prof_descr=prof_descr;
end

% write to file:
nc=ncopen(fileOut,'write');
vars=ncvars(nc);
list_vars=intersect(vars,list_vars);
for ii=1:length(list_vars);
    varname=list_vars{ii};
    data=getfield(MITprof,varname);
    spval=ncgetFillVal(nc,varname);
    if isnumeric(data)
        if isempty(spval), 
            warning(['no FillVal for ' varname ': use of -9999 default value']);
            spval=double(-9999);
        end
        data(isnan(data))=spval;
        MITprof=setfield(MITprof,varname,data);
    end
    ncputvar(nc,varname,data);
end
ncclose(nc);


1	roquet	1.6	function []=MITprof_write(fileOut,MITprof,varargin);
2	gforget	1.1	%function: MITprof_write
3	roquet	1.6	%object: write data in a MITprof netcdf file
4	gforget	1.1	%author: Gael Forget (gforget@mit.edu)
5	gforget	1.3	%date: Nov 5th, 2010
6	gforget	1.1	%
7	roquet	1.6	%usage: []=MITprof_write(fileOut,MITprof, [list_vars] );
8			%
9			%inputs: fileOut data file name (absolute/relative path)
10			% .nc suffix is added if not already present
11			% MITprof struct containing profile data
12			% list_vars variable list (optional)
13			%
14			% Format description of MITprof struct input variable:
15			% list of fields always available:
16			% prof_depth [nDepth x 1]
17			% prof_descr {nProf x 1} --> will be converted into a char array
18			% prof_date [nProf x 1]
19			% prof_YYYYMMDD [nProf x 1]
20			% prof_HHMMSS [nProf x 1]
21			% prof_lon [nProf x 1]
22			% prof_lat [nProf x 1]
23			% prof_basin [nProf x 1]
24			% prof_point [nProf x 1]
25			%
26			% other fields generally available of size [nProf x nLev] :
27			% prof_T, prof_Tflag, prof_Terr, prof_Tweight, prof_Testim
28			% prof_S, prof_Sflag, prof_Serr, prof_Sweight, prof_Sestim
29			%
30			% if list_vars is not specified, every variables with a name starting
31			% with 'prof_', except prof_depth, will be saved in the MITprof
32			% netcdf file. An error will occur if the program try to save a
33			% variable that is not initialized in the MITprof netcdf file.
34			%
35			% if list_vars is specified, only variables present in the list will be
36			% saved.
37			%
38			% NaN are auomatically replaced by missing_value attribute (or _FillValue).
39			% the file fileOut will be created using MITprof_create if needed.
40	gforget	1.1	%
41
42	gforget	1.2
43	gforget	1.3
44	roquet	1.6	% check that file exists and add prefix and suffix if necessary
45	roquet	1.5	[pathstr, name, ext] = fileparts(fileOut);
46			if isempty(pathstr) \| strcmp(pathstr,'.'), pathstr=pwd; end
47			if isempty(ext) \| ~strcmp(ext,'.nc'), ext='.nc'; end
48			fileOut=[pathstr '/' name ext];
49	gforget	1.3
50	roquet	1.6	% build the list of variables that must be loaded
51			if nargin>2,
52			list_vars=varargin{1};
53			else
54			list1=fieldnames(MITprof); list_vars={};
55			I=strfind(list1,'prof_');
56			for kk=1:length(I),
57			if I{kk}==1 & ~strcmp(list1{kk},'prof_depth'),
58			list_vars{end+1}=list1{kk};
59			end
60			end
61			end
62
63	roquet	1.7	% stop if there are no profile in MITprof
64			nProf=length(MITprof.prof_lon);
65			if nProf==0, return, end
66
67	roquet	1.6	% create the file if needed
68			if ~exist(fileOut,'file'),
69			prof_depth=MITprof.prof_depth;
70			MITprof_create(fileOut,nProf,prof_depth,list_vars);
71			end
72
73			% prof_descr: convert back from cell 2 array format
74			if isfield(MITprof,'prof_descr')
75			ncload(fileOut,'prof_descr'); nb_char=size(prof_descr,2);
76			prof_descr=char(MITprof.prof_descr);
77			if size(prof_descr,2)<nb_char,
78			prof_descr(:,size(prof_descr,2)+1:nb_char)=' ';
79			elseif size(prof_descr,2)>nb_char
80			disp('some profile descriptive strings have been shortened');
81			prof_descr=prof_descr(:,1:nb_char);
82			end
83			MITprof.prof_descr=prof_descr;
84			end
85
86			% write to file:
87	roquet	1.4	nc=ncopen(fileOut,'write');
88	roquet	1.8	vars=ncvars(nc);
89			list_vars=intersect(vars,list_vars);
90	gforget	1.1	for ii=1:length(list_vars);
91	roquet	1.6	varname=list_vars{ii};
92			data=getfield(MITprof,varname);
93			spval=ncgetFillVal(nc,varname);
94			if isnumeric(data)
95	roquet	1.8	if isempty(spval),
96			warning(['no FillVal for ' varname ': use of -9999 default value']);
97			spval=double(-9999);
98			end
99	roquet	1.6	data(isnan(data))=spval;
100			MITprof=setfield(MITprof,varname,data);
101	roquet	1.8	end
102	roquet	1.6	ncputvar(nc,varname,data);
103	roquet	1.8	end
104	roquet	1.4	ncclose(nc);
105	roquet	1.8
106
107	gforget	1.1