profilesMatlabProcessing/profiles_IO_external/profiles_read_argo.m

function [varargout]=profile_read_argo(dataset,nf,m,varargin);
% read hydrographic data in the ARGO netcdf format
%  return the m-th profile from the nf-th file referenced in
%   dataset.fileInList.
%
% if m=0 :
%   [nprofiles,data_argo]=profile_read_argo(dataset,nf,0);
%       nprofiles: number of profiles in the nf-th file
%       data_argo: argo data in a struct variable
%
% if m~=0 :
%   profileCur=profile_read_argo(dataset,nf,m,data_argo);
%
% profileCur = (m-th profile of nf-th file)
%      pnum_txt: '5900841'
%           ymd: 20060101
%           hms: 3207
%           lat: -46.709
%           lon: 137.501
%         direc: 1
%             t: [1x115 single]
%             s: [1x115 single]
%             p: [1x115 single]
%         t_ERR: [1x115 single]
%         s_ERR: [1x115 single]
%     PorZisBAD: 0
%

fileIn=[dataset.dirIn dataset.fileInList(nf).name];

if m==0; % return the number of profile.
        
    %get the number of profiles:
    list_var={'JULD','LATITUDE','LONGITUDE','DIRECTION','PLATFORM_NUMBER',...
        'PRES_ADJUSTED','PRES_ADJUSTED_QC',...
        'TEMP_ADJUSTED','TEMP_ADJUSTED_QC','TEMP_ADJUSTED_ERROR',...
        'PSAL_ADJUSTED','PSAL_ADJUSTED_QC','PSAL_ADJUSTED_ERROR'};
    argo_data=[];
    for ii=1:length(list_var),
        ncload(fileIn,list_var{ii});
        argo_data=setfield(argo_data,list_var{ii},eval(list_var{ii}));
    end
    nprofiles = length(JULD);
    
    varargout{1}=nprofiles;
    varargout{2}=argo_data;
    
else;%if m==0;
    
    % load data
    argo_data=varargin{1};
    
    %date, position, etc
    juld=argo_data.JULD(m)+datenum(1950,1,1);
    [Y, M, D, H, MN, S] = datevec(juld);
    ymd=Y*1e4+M*1e2+D;
    hms=H*1e4+MN*1e2+S;
    
    lat=argo_data.LATITUDE(m);
    lon=argo_data.LONGITUDE(m); if lon < 0; lon=lon+360;end;
    
    direction=argo_data.DIRECTION(m);
    direc=0; 
    if(direction=='A');direc=1;end;
    if(direction=='D');direc=2;end
    
    pnum_txt=deblank(argo_data.PLATFORM_NUMBER(m,:));
    pnum_txt=pnum_txt(ismember(pnum_txt,'0123456789')); pnum=str2num(pnum_txt);
    if isempty(pnum_txt); pnum_txt='9999'; pnum=9999; disp(['no name for profile ' num2str(m)]); end;
    
    
    % pressure data
    
    p=argo_data.PRES_ADJUSTED(m,:);
    p_QC=argo_data.PRES_ADJUSTED_QC(m,:);
    p_QC(isnan(p))='5';
    
    for n=1:length(p)-1; % doubles
        tmp1=find(p(n+1:end)==p(n)); p(n+tmp1)=NaN; p_QC(n+tmp1)='5';
    end
    
    bad_P=0;
    tmp1=find(p_QC=='4');
    if(length(tmp1)<=5);
        %get rid of these few bad points and keep the profile
        p(tmp1)=NaN;p_QC(tmp1)='5';
    else;
        %flag the profile (will be masked in the main file)
        %but keep the bad points (to interp and be able to CHECK)
        bad_P=1;
    end;
    
    % temperature data
    t=argo_data.TEMP_ADJUSTED(m,:);
    t_QC=argo_data.TEMP_ADJUSTED_QC(m,:);
    t_ERR=argo_data.TEMP_ADJUSTED_ERROR(m,:);
    t_ERR(isnan(t_ERR))=0;
    
    % salinity data
    s=argo_data.PSAL_ADJUSTED(m,:);
    s_QC=argo_data.PSAL_ADJUSTED_QC(m,:);
    s_ERR=argo_data.PSAL_ADJUSTED_ERROR(m,:);
    s_ERR(isnan(s_ERR))=0;
    
    
    if isnan(t(1)); %this file does not contain temperature data...
        t=NaN*p; t_ERR=0*p;
    else;
        t(~ismember(t_QC,'12'))=NaN;
    end;
    if isnan(s(1)); %this file does not contain salinity data...
        s=NaN*p; s_ERR=0*p;
    else;
        s(~ismember(s_QC,'12'))=NaN;
    end;
    
    profileCur.pnum_txt=pnum_txt;
    profileCur.ymd=ymd; profileCur.hms=hms;
    profileCur.lat=lat; profileCur.lon=lon;
    profileCur.direc=direc;
    profileCur.t=t;
    profileCur.s=s;
    profileCur.p=p;
    profileCur.t_ERR=t_ERR;
    profileCur.s_ERR=s_ERR;
    profileCur.PorZisBAD=bad_P;
    
    varargout = {profileCur};
    
end;


1	roquet	1.3	function [varargout]=profile_read_argo(dataset,nf,m,varargin);
2			% read hydrographic data in the ARGO netcdf format
3			% return the m-th profile from the nf-th file referenced in
4			% dataset.fileInList.
5			%
6			% if m=0 :
7			% [nprofiles,data_argo]=profile_read_argo(dataset,nf,0);
8			% nprofiles: number of profiles in the nf-th file
9			% data_argo: argo data in a struct variable
10			%
11			% if m~=0 :
12			% profileCur=profile_read_argo(dataset,nf,m,data_argo);
13			%
14			% profileCur = (m-th profile of nf-th file)
15			% pnum_txt: '5900841'
16			% ymd: 20060101
17			% hms: 3207
18			% lat: -46.709
19			% lon: 137.501
20			% direc: 1
21			% t: [1x115 single]
22			% s: [1x115 single]
23			% p: [1x115 single]
24			% t_ERR: [1x115 single]
25			% s_ERR: [1x115 single]
26			% PorZisBAD: 0
27			%
28	gforget	1.1
29			fileIn=[dataset.dirIn dataset.fileInList(nf).name];
30
31	roquet	1.3	if m==0; % return the number of profile.
32	gforget	1.2
33	roquet	1.3	%get the number of profiles:
34			list_var={'JULD','LATITUDE','LONGITUDE','DIRECTION','PLATFORM_NUMBER',...
35			'PRES_ADJUSTED','PRES_ADJUSTED_QC',...
36			'TEMP_ADJUSTED','TEMP_ADJUSTED_QC','TEMP_ADJUSTED_ERROR',...
37			'PSAL_ADJUSTED','PSAL_ADJUSTED_QC','PSAL_ADJUSTED_ERROR'};
38			argo_data=[];
39			for ii=1:length(list_var),
40			ncload(fileIn,list_var{ii});
41			argo_data=setfield(argo_data,list_var{ii},eval(list_var{ii}));
42	gforget	1.2	end
43	roquet	1.3	nprofiles = length(JULD);
44	gforget	1.2
45	roquet	1.3	varargout{1}=nprofiles;
46			varargout{2}=argo_data;
47	gforget	1.2
48	roquet	1.3	else;%if m==0;
49	gforget	1.2
50	roquet	1.3	% load data
51			argo_data=varargin{1};
52	gforget	1.2
53			%date, position, etc
54	roquet	1.3	juld=argo_data.JULD(m)+datenum(1950,1,1);
55			[Y, M, D, H, MN, S] = datevec(juld);
56			ymd=Y1e4+M1e2+D;
57			hms=H1e4+MN1e2+S;
58	gforget	1.2
59	roquet	1.3	lat=argo_data.LATITUDE(m);
60			lon=argo_data.LONGITUDE(m); if lon < 0; lon=lon+360;end;
61	gforget	1.2
62	roquet	1.3	direction=argo_data.DIRECTION(m);
63			direc=0;
64			if(direction=='A');direc=1;end;
65			if(direction=='D');direc=2;end
66	gforget	1.2
67	roquet	1.3	pnum_txt=deblank(argo_data.PLATFORM_NUMBER(m,:));
68			pnum_txt=pnum_txt(ismember(pnum_txt,'0123456789')); pnum=str2num(pnum_txt);
69			if isempty(pnum_txt); pnum_txt='9999'; pnum=9999; disp(['no name for profile ' num2str(m)]); end;
70	gforget	1.2
71
72	roquet	1.3	% pressure data
73	gforget	1.2
74	roquet	1.3	p=argo_data.PRES_ADJUSTED(m,:);
75			p_QC=argo_data.PRES_ADJUSTED_QC(m,:);
76			p_QC(isnan(p))='5';
77	gforget	1.2
78	roquet	1.3	for n=1:length(p)-1; % doubles
79			tmp1=find(p(n+1:end)==p(n)); p(n+tmp1)=NaN; p_QC(n+tmp1)='5';
80	gforget	1.2	end
81
82			bad_P=0;
83			tmp1=find(p_QC=='4');
84			if(length(tmp1)<=5);
85			%get rid of these few bad points and keep the profile
86	roquet	1.3	p(tmp1)=NaN;p_QC(tmp1)='5';
87	gforget	1.2	else;
88			%flag the profile (will be masked in the main file)
89			%but keep the bad points (to interp and be able to CHECK)
90			bad_P=1;
91			end;
92
93	roquet	1.3	% temperature data
94			t=argo_data.TEMP_ADJUSTED(m,:);
95			t_QC=argo_data.TEMP_ADJUSTED_QC(m,:);
96			t_ERR=argo_data.TEMP_ADJUSTED_ERROR(m,:);
97			t_ERR(isnan(t_ERR))=0;
98
99			% salinity data
100			s=argo_data.PSAL_ADJUSTED(m,:);
101			s_QC=argo_data.PSAL_ADJUSTED_QC(m,:);
102			s_ERR=argo_data.PSAL_ADJUSTED_ERROR(m,:);
103			s_ERR(isnan(s_ERR))=0;
104	gforget	1.2
105
106	roquet	1.3	if isnan(t(1)); %this file does not contain temperature data...
107	gforget	1.2	t=NaNp; t_ERR=0p;
108			else;
109	roquet	1.3	t(~ismember(t_QC,'12'))=NaN;
110	gforget	1.2	end;
111	roquet	1.3	if isnan(s(1)); %this file does not contain salinity data...
112			s=NaNp; s_ERR=0p;
113	gforget	1.2	else;
114	roquet	1.3	s(~ismember(s_QC,'12'))=NaN;
115	gforget	1.2	end;
116
117			profileCur.pnum_txt=pnum_txt;
118			profileCur.ymd=ymd; profileCur.hms=hms;
119			profileCur.lat=lat; profileCur.lon=lon;
120			profileCur.direc=direc;
121			profileCur.t=t;
122			profileCur.s=s;
123			profileCur.p=p;
124			profileCur.t_ERR=t_ERR;
125			profileCur.s_ERR=s_ERR;
126			profileCur.PorZisBAD=bad_P;
127
128			varargout = {profileCur};
129
130	gforget	1.1	end;
131
132
133