profilesMatlabProcessing/profiles_IO_external/profiles_read_seals.m

function [varargout]=profile_read_seals(dataset,nf,m,varargin);
% read seal data in the ARGO netcdf format
%
% if m=0 :
%  return the information on the nf-th file referenced in
%  dataset.fileInList.
%   [nprofiles,data_seals]=profile_read_seals(dataset,nf,0);
%       nprofiles: number of profiles in the nf-th file
%       data_argo: argo data in a struct variable
%
% if m~=0 :
%  return the m-th profile from the nf-th file referenced in
%  dataset.fileInList.
%   profileCur=profile_read_seals(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','PRES_QC',...
        'TEMP','TEMP_QC',...
        'PSAL','PSAL_QC'};
    data_seals=[];
    for ii=1:length(list_var),
        ncload(fileIn,list_var{ii});
        data_seals=setfield(data_seals,list_var{ii},eval(list_var{ii}));
    end
    nprofiles = length(JULD);
    
    varargout{1}=nprofiles;
    varargout{2}=data_seals;
    
else;%if m==0;
    
    % load data
    data_seals=varargin{1};
    
    %date, position, etc
    juld=data_seals.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=data_seals.LATITUDE(m);
    lon=data_seals.LONGITUDE(m); if lon < 0; lon=lon+360;end;
    
    direction=data_seals.DIRECTION(m);
    direc=0; 
    if(direction=='A');direc=1;end;
    if(direction=='D');direc=2;end
    
    pnum_txt=deblank(data_seals.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=data_seals.PRES(m,:);
    p_QC=data_seals.PRES_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=data_seals.TEMP(m,:);
    t_QC=data_seals.TEMP_QC(m,:);
    t_ERR=t*0;
    
    % salinity data
    s=data_seals.PSAL(m,:);
    s_QC=data_seals.PSAL_QC(m,:);
    s_ERR=s*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	1.4	function [varargout]=profile_read_seals(dataset,nf,m,varargin);
2			% read seal data in the ARGO netcdf format
3			%
4			% if m=0 :
5			% return the information on the nf-th file referenced in
6			% dataset.fileInList.
7			% [nprofiles,data_seals]=profile_read_seals(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			% return the m-th profile from the nf-th file referenced in
13			% dataset.fileInList.
14			% profileCur=profile_read_seals(dataset,nf,m,data_argo);
15			%
16			% profileCur = (m-th profile of nf-th file)
17			% pnum_txt: '5900841'
18			% ymd: 20060101
19			% hms: 3207
20			% lat: -46.709
21			% lon: 137.501
22			% direc: 1
23			% t: [1x115 single]
24			% s: [1x115 single]
25			% p: [1x115 single]
26			% t_ERR: [1x115 single]
27			% s_ERR: [1x115 single]
28			% PorZisBAD: 0
29			%
30	gforget	1.1
31			fileIn=[dataset.dirIn dataset.fileInList(nf).name];
32
33	roquet	1.4	if m==0; % return the number of profile.
34
35			%get the number of profiles:
36			list_var={'JULD','LATITUDE','LONGITUDE', ...
37			'DIRECTION','PLATFORM_NUMBER',...
38			'PRES','PRES_QC',...
39			'TEMP','TEMP_QC',...
40			'PSAL','PSAL_QC'};
41			data_seals=[];
42			for ii=1:length(list_var),
43			ncload(fileIn,list_var{ii});
44			data_seals=setfield(data_seals,list_var{ii},eval(list_var{ii}));
45	gforget	1.1	end
46	roquet	1.4	nprofiles = length(JULD);
47	gforget	1.1
48	roquet	1.4	varargout{1}=nprofiles;
49			varargout{2}=data_seals;
50	gforget	1.1
51	roquet	1.4	else;%if m==0;
52	gforget	1.3
53	roquet	1.4	% load data
54			data_seals=varargin{1};
55	gforget	1.3
56	roquet	1.4	%date, position, etc
57			juld=data_seals.JULD(m)+datenum(1950,1,1);
58			[Y, M, D, H, MN, S] = datevec(juld);
59			ymd=Y1e4+M1e2+D;
60			hms=H1e4+MN1e2+S;
61	gforget	1.1
62	roquet	1.4	lat=data_seals.LATITUDE(m);
63			lon=data_seals.LONGITUDE(m); if lon < 0; lon=lon+360;end;
64	gforget	1.1
65	roquet	1.4	direction=data_seals.DIRECTION(m);
66			direc=0;
67			if(direction=='A');direc=1;end;
68			if(direction=='D');direc=2;end
69	gforget	1.1
70	roquet	1.4	pnum_txt=deblank(data_seals.PLATFORM_NUMBER(m,:));
71			pnum_txt=pnum_txt(ismember(pnum_txt,'0123456789')); pnum=str2num(pnum_txt);
72			if isempty(pnum_txt); pnum_txt='9999'; pnum=9999; disp(['no name for profile ' num2str(m)]); end;
73	gforget	1.1
74
75	roquet	1.4	% pressure data
76	gforget	1.1
77	roquet	1.4	p=data_seals.PRES(m,:);
78			p_QC=data_seals.PRES_QC(m,:);
79			p_QC(isnan(p))='5';
80	gforget	1.1
81	roquet	1.4	for n=1:length(p)-1; % doubles
82			tmp1=find(p(n+1:end)==p(n)); p(n+tmp1)=NaN; p_QC(n+tmp1)='5';
83	gforget	1.1	end
84
85			bad_P=0;
86			tmp1=find(p_QC=='4');
87			if(length(tmp1)<=5);
88			%get rid of these few bad points and keep the profile
89	roquet	1.4	p(tmp1)=NaN;p_QC(tmp1)='5';
90	gforget	1.1	else;
91			%flag the profile (will be masked in the main file)
92			%but keep the bad points (to interp and be able to CHECK)
93			bad_P=1;
94			end;
95
96	roquet	1.4	% temperature data
97			t=data_seals.TEMP(m,:);
98			t_QC=data_seals.TEMP_QC(m,:);
99			t_ERR=t*0;
100
101			% salinity data
102			s=data_seals.PSAL(m,:);
103			s_QC=data_seals.PSAL_QC(m,:);
104			s_ERR=s*0;
105
106
107			if isnan(t(1)); %this file does not contain temperature data...
108	gforget	1.1	t=NaNp; t_ERR=0p;
109			else;
110	roquet	1.4	t(~ismember(t_QC,'12'))=NaN;
111	gforget	1.1	end;
112	roquet	1.4	if isnan(s(1)); %this file does not contain salinity data...
113			s=NaNp; s_ERR=0p;
114	gforget	1.1	else;
115	roquet	1.4	s(~ismember(s_QC,'12'))=NaN;
116	gforget	1.1	end;
117
118			profileCur.pnum_txt=pnum_txt;
119			profileCur.ymd=ymd; profileCur.hms=hms;
120			profileCur.lat=lat; profileCur.lon=lon;
121			profileCur.direc=direc;
122			profileCur.t=t;
123			profileCur.s=s;
124			profileCur.p=p;
125			profileCur.t_ERR=t_ERR;
126			profileCur.s_ERR=s_ERR;
127			profileCur.PorZisBAD=bad_P;
128
129			varargout = {profileCur};
130
131			end;
132
133
134