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 :
%   dataset=profile_read_argo(dataset,nf,0);
%       dataset.nprofiles: number of profiles in the nf-th file
%       dataset.data_argo: argo data in a struct variable
%
% if m~=0 :
%   profileCur=profile_read_argo(dataset,nf,m);
%
% 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]
%     isBAD: 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','DATA_MODE',...
              'JULD_QC','POSITION_QC','PRES_ADJUSTED_QC','PRES_QC',...
              'TEMP_ADJUSTED_QC','TEMP_QC','PSAL_ADJUSTED_QC','PSAL_QC'};
    argo_data=[];
    for ii=1:length(list_var),
        ncload(fileIn,list_var{ii});
        data=eval(list_var{ii});
        if ~isempty(data);
        nc=ncopen(fileIn);
        FillVal=ncgetFillVal(nc,list_var{ii});
        ncclose(nc);
        if ischar(FillVal),
            data(strcmp(data,FillVal))=' ';
        else
            data(data==FillVal)=NaN;
        end
        end
        argo_data=setfield(argo_data,list_var{ii},data);
    end

    list_var={'PRES_ADJUSTED','PRES','TEMP_ADJUSTED','TEMP','TEMP_ADJUSTED_ERROR',...
        'PSAL_ADJUSTED','PSAL','PSAL_ADJUSTED_ERROR'};
    for ii=1:length(list_var),
        ncload(fileIn,list_var{ii});
        data=double(eval(list_var{ii}));
        if ~isempty(data);
        nc=ncopen(fileIn);
        FillVal=ncgetFillVal(nc,list_var{ii});
        ncclose(nc);
        data(data==FillVal)=NaN;
        end;
        argo_data=setfield(argo_data,list_var{ii},data);
    end
    
    dataset.argo_data=argo_data;
    dataset.nprofiles = length(JULD);
    if isempty(dataset.argo_data.TEMP); 
      dataset.nprofiles=0;
      fprintf(['empty file:' dataset.fileInList(nf).name '\n']);
    end;

    if ~isfield(dataset,'greyList');
      if ~isempty(dir([dataset.dirIn '../../ar_greylist.txt']));
        fidgrey=fopen([dataset.dirIn '../../ar_greylist.txt'],'rt');
        tmp1=fgetl(fidgrey);
        greylist=[]; ii=0;
        while ~feof(fidgrey);
            tmp1=fgetl(fidgrey); tmp2=strfind(tmp1,',');
    
            cur_pnum=double(tmp1(1:tmp2(1)-1));
            cur_pnum=cur_pnum(find(cur_pnum~=0&cur_pnum~=32));
            cur_pnum=char(cur_pnum);
    
            date_ref=double(tmp1(tmp2(2)+1:tmp2(3)-1));
            date_ref=date_ref(find(date_ref~=0&date_ref~=32));
            date_ref=char(date_ref);
            date_ref=[str2num(date_ref(1:4)) str2num(date_ref(5:6)) str2num(date_ref(7:8)) 0 0 0];
    
            vnam=tmp1(tmp2(1)+1:tmp2(2)-1);
    
            ii=ii+1;
            greylist(ii).pnum=cur_pnum;
            greylist(ii).start=date_ref;
            greylist(ii).vnam=vnam;
        end;
        fclose(fidgrey);

        dataset.greyList.pnum={greylist(:).pnum};
        dataset.greyList.start={greylist(:).start};
        dataset.greyList.vnam={greylist(:).vnam};
      else;
        dataset.greyList.pnum=[];
        dataset.greyList.start=[];
        dataset.greyList.vnam=[];  
      end;
    end;

    varargout{1}=dataset;
    
else;%if m==0;
   
    % load data
    argo_data=dataset.argo_data;
    
    %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,:);
    if all(isnan(p)), p=argo_data.PRES(m,:); p_QC=argo_data.PRES_QC(m,:); end
    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

    % QC on position, date and pressure    
    isBAD=0;

    if ~ismember(argo_data.POSITION_QC(m),'1258'); isBAD=1; end;
    if ~ismember(argo_data.JULD_QC(m),'1258'); isBAD=1; end;

    tmp1=find(~ismember(p_QC,'1258'));
    if(length(tmp1)<=5);
        %get rid of these few bad points and keep the profile
        p(tmp1)=NaN;
    else;
        %flag the profile (will be masked in the main file)
        %but keep the bad points (to interp and be able to CHECK)
        isBAD=1;
    end;
    
    % temperature data
    %[num2str(m) ' in ' dataset.fileInList(nf).name]
    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;
    if all(isnan(t)), t=argo_data.TEMP(m,:); t_QC=argo_data.TEMP_QC(m,:); end

    %accomodate files that have no salinity
    if isempty(argo_data.PSAL);
      argo_data.PSAL=NaN*argo_data.TEMP;    
      argo_data.PSAL_QC=char(32*ones(size(argo_data.TEMP_ADJUSTED_QC)));
      argo_data.PSAL_ADJUSTED=NaN*argo_data.TEMP;
      argo_data.PSAL_ADJUSTED_ERROR=NaN*argo_data.TEMP;
      argo_data.PSAL_ADJUSTED_QC=char(32*ones(size(argo_data.TEMP_ADJUSTED_QC)));
    end;

    % 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 all(isnan(s)), s=argo_data.PSAL(m,:); s_QC=argo_data.PSAL_QC(m,:); end
    
    if isnan(t(1)); %this file does not contain temperature data...
        t=NaN*p; t_ERR=0*p;
    else;
        t(~ismember(t_QC,'1258'))=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,'1258'))=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.isBAD=isBAD;
    profileCur.DATA_MODE=argo_data.DATA_MODE(m);
    
    varargout = {profileCur};
    
end;


1	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	% dataset=profile_read_argo(dataset,nf,0);
8	% dataset.nprofiles: number of profiles in the nf-th file
9	% dataset.data_argo: argo data in a struct variable
10	%
11	% if m~=0 :
12	% profileCur=profile_read_argo(dataset,nf,m);
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	% isBAD: 0
27	%
28
29	fileIn=[dataset.dirIn dataset.fileInList(nf).name];
30
31	if m==0; % return the number of profile.
32
33	%get the number of profiles:
34	list_var={'JULD','LATITUDE','LONGITUDE','DIRECTION','PLATFORM_NUMBER','DATA_MODE',...
35	'JULD_QC','POSITION_QC','PRES_ADJUSTED_QC','PRES_QC',...
36	'TEMP_ADJUSTED_QC','TEMP_QC','PSAL_ADJUSTED_QC','PSAL_QC'};
37	argo_data=[];
38	for ii=1:length(list_var),
39	ncload(fileIn,list_var{ii});
40	data=eval(list_var{ii});
41	if ~isempty(data);
42	nc=ncopen(fileIn);
43	FillVal=ncgetFillVal(nc,list_var{ii});
44	ncclose(nc);
45	if ischar(FillVal),
46	data(strcmp(data,FillVal))=' ';
47	else
48	data(data==FillVal)=NaN;
49	end
50	end
51	argo_data=setfield(argo_data,list_var{ii},data);
52	end
53
54	list_var={'PRES_ADJUSTED','PRES','TEMP_ADJUSTED','TEMP','TEMP_ADJUSTED_ERROR',...
55	'PSAL_ADJUSTED','PSAL','PSAL_ADJUSTED_ERROR'};
56	for ii=1:length(list_var),
57	ncload(fileIn,list_var{ii});
58	data=double(eval(list_var{ii}));
59	if ~isempty(data);
60	nc=ncopen(fileIn);
61	FillVal=ncgetFillVal(nc,list_var{ii});
62	ncclose(nc);
63	data(data==FillVal)=NaN;
64	end;
65	argo_data=setfield(argo_data,list_var{ii},data);
66	end
67
68	dataset.argo_data=argo_data;
69	dataset.nprofiles = length(JULD);
70	if isempty(dataset.argo_data.TEMP);
71	dataset.nprofiles=0;
72	fprintf(['empty file:' dataset.fileInList(nf).name '\n']);
73	end;
74
75	if ~isfield(dataset,'greyList');
76	if ~isempty(dir([dataset.dirIn '../../ar_greylist.txt']));
77	fidgrey=fopen([dataset.dirIn '../../ar_greylist.txt'],'rt');
78	tmp1=fgetl(fidgrey);
79	greylist=[]; ii=0;
80	while ~feof(fidgrey);
81	tmp1=fgetl(fidgrey); tmp2=strfind(tmp1,',');
82
83	cur_pnum=double(tmp1(1:tmp2(1)-1));
84	cur_pnum=cur_pnum(find(cur_pnum~=0&cur_pnum~=32));
85	cur_pnum=char(cur_pnum);
86
87	date_ref=double(tmp1(tmp2(2)+1:tmp2(3)-1));
88	date_ref=date_ref(find(date_ref~=0&date_ref~=32));
89	date_ref=char(date_ref);
90	date_ref=[str2num(date_ref(1:4)) str2num(date_ref(5:6)) str2num(date_ref(7:8)) 0 0 0];
91
92	vnam=tmp1(tmp2(1)+1:tmp2(2)-1);
93
94	ii=ii+1;
95	greylist(ii).pnum=cur_pnum;
96	greylist(ii).start=date_ref;
97	greylist(ii).vnam=vnam;
98	end;
99	fclose(fidgrey);
100
101	dataset.greyList.pnum={greylist(:).pnum};
102	dataset.greyList.start={greylist(:).start};
103	dataset.greyList.vnam={greylist(:).vnam};
104	else;
105	dataset.greyList.pnum=[];
106	dataset.greyList.start=[];
107	dataset.greyList.vnam=[];
108	end;
109	end;
110
111	varargout{1}=dataset;
112
113	else;%if m==0;
114
115	% load data
116	argo_data=dataset.argo_data;
117
118	%date, position, etc
119	juld=argo_data.JULD(m)+datenum(1950,1,1);
120	[Y, M, D, H, MN, S] = datevec(juld);
121	ymd=Y1e4+M1e2+D;
122	hms=H1e4+MN1e2+S;
123
124	lat=argo_data.LATITUDE(m);
125	lon=argo_data.LONGITUDE(m); if lon < 0; lon=lon+360;end;
126
127	direction=argo_data.DIRECTION(m);
128	direc=0;
129	if(direction=='A');direc=1;end;
130	if(direction=='D');direc=2;end
131
132	pnum_txt=deblank(argo_data.PLATFORM_NUMBER(m,:));
133	pnum_txt=pnum_txt(ismember(pnum_txt,'0123456789')); pnum=str2num(pnum_txt);
134	if isempty(pnum_txt); pnum_txt='9999'; pnum=9999; disp(['no name for profile ' num2str(m)]); end;
135
136
137	% pressure data
138
139	p=argo_data.PRES_ADJUSTED(m,:);
140	p_QC=argo_data.PRES_ADJUSTED_QC(m,:);
141	if all(isnan(p)), p=argo_data.PRES(m,:); p_QC=argo_data.PRES_QC(m,:); end
142	p_QC(isnan(p))='5';
143
144	for n=1:length(p)-1; % doubles
145	tmp1=find(p(n+1:end)==p(n)); p(n+tmp1)=NaN; p_QC(n+tmp1)='5';
146	end
147
148	% QC on position, date and pressure
149	isBAD=0;
150
151	if ~ismember(argo_data.POSITION_QC(m),'1258'); isBAD=1; end;
152	if ~ismember(argo_data.JULD_QC(m),'1258'); isBAD=1; end;
153
154	tmp1=find(~ismember(p_QC,'1258'));
155	if(length(tmp1)<=5);
156	%get rid of these few bad points and keep the profile
157	p(tmp1)=NaN;
158	else;
159	%flag the profile (will be masked in the main file)
160	%but keep the bad points (to interp and be able to CHECK)
161	isBAD=1;
162	end;
163
164	% temperature data
165	%[num2str(m) ' in ' dataset.fileInList(nf).name]
166	t=argo_data.TEMP_ADJUSTED(m,:);
167	t_QC=argo_data.TEMP_ADJUSTED_QC(m,:);
168	t_ERR=argo_data.TEMP_ADJUSTED_ERROR(m,:);
169	t_ERR(isnan(t_ERR))=0;
170	if all(isnan(t)), t=argo_data.TEMP(m,:); t_QC=argo_data.TEMP_QC(m,:); end
171
172	%accomodate files that have no salinity
173	if isempty(argo_data.PSAL);
174	argo_data.PSAL=NaN*argo_data.TEMP;
175	argo_data.PSAL_QC=char(32*ones(size(argo_data.TEMP_ADJUSTED_QC)));
176	argo_data.PSAL_ADJUSTED=NaN*argo_data.TEMP;
177	argo_data.PSAL_ADJUSTED_ERROR=NaN*argo_data.TEMP;
178	argo_data.PSAL_ADJUSTED_QC=char(32*ones(size(argo_data.TEMP_ADJUSTED_QC)));
179	end;
180
181	% salinity data
182	s=argo_data.PSAL_ADJUSTED(m,:);
183	s_QC=argo_data.PSAL_ADJUSTED_QC(m,:);
184	s_ERR=argo_data.PSAL_ADJUSTED_ERROR(m,:);
185	s_ERR(isnan(s_ERR))=0;
186	if all(isnan(s)), s=argo_data.PSAL(m,:); s_QC=argo_data.PSAL_QC(m,:); end
187
188	if isnan(t(1)); %this file does not contain temperature data...
189	t=NaNp; t_ERR=0p;
190	else;
191	t(~ismember(t_QC,'1258'))=NaN;
192	end;
193	if isnan(s(1)); %this file does not contain salinity data...
194	s=NaNp; s_ERR=0p;
195	else;
196	s(~ismember(s_QC,'1258'))=NaN;
197	end;
198
199	profileCur.pnum_txt=pnum_txt;
200	profileCur.ymd=ymd; profileCur.hms=hms;
201	profileCur.lat=lat; profileCur.lon=lon;
202	profileCur.direc=direc;
203	profileCur.T=t;
204	profileCur.S=s;
205	profileCur.p=p;
206	profileCur.T_ERR=t_ERR;
207	profileCur.S_ERR=s_ERR;
208	profileCur.isBAD=isBAD;
209	profileCur.DATA_MODE=argo_data.DATA_MODE(m);
210
211	varargout = {profileCur};
212
213	end;
214
215
216