profilesMatlabProcessing/profiles_IO_external/profiles_read_argo.m

function [varargout]=profile_read_argo(dataset,nf,m);

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

%output:
%       ymd     hms     imonth  lat     lon     direc   p       t       s       p_ERR   t_ERR   s_ERR

%common block:
global  PLATFORM_NUMBER_fillval PLATFORM_NUMBER;
global  VECdateOBS      LATITUDE        LONGITUDE       DIRECTION;
global  PRES    PRES_ADJUSTED   PRES_ADJUSTED_QC        PRES_fillval    PRES_QC;
global  TEMP    TEMP_ADJUSTED   TEMP_ADJUSTED_QC        TEMP_fillval    TEMP_QC TEMP_ADJUSTED_ERROR;
global  PSAL    PSAL_ADJUSTED   PSAL_ADJUSTED_QC        PSAL_fillval    PSAL_QC PSAL_ADJUSTED_ERROR;


if m==0;
%read the file and put the data in common blocks:

clear PRES* PSAL* TEMP*;
global  PRES    PRES_ADJUSTED   PRES_ADJUSTED_QC        PRES_fillval    PRES_QC;
global  TEMP    TEMP_ADJUSTED   TEMP_ADJUSTED_QC        TEMP_fillval    TEMP_QC TEMP_ADJUSTED_ERROR;
global  PSAL    PSAL_ADJUSTED   PSAL_ADJUSTED_QC        PSAL_fillval    PSAL_QC PSAL_ADJUSTED_ERROR;
TEMP=8888*ones(500,1);PSAL=8888*ones(500,1);

%WHAT IS WRONG HERE???
%if ( rep_nb~=1|isempty(findstr(fileIn,'20050911_prof')) )


eval(['ncload ' fileIn ';']);

%some dimensions inversions exist for _QC variables (!?)
if size(PRES_QC,1)~=size(PRES,1)
PRES_QC=PRES_QC'; 
if ~isempty(who('PRES_ADJUSTED_QC'));PRES_ADJUSTED_QC=PRES_ADJUSTED_QC';end;
if ~isempty(who('PSAL_QC'));PSAL_QC=PSAL_QC';end;
if ~isempty(who('PSAL_ADJUSTED_QC'));PSAL_ADJUSTED_QC=PSAL_ADJUSTED_QC';end;
if ~isempty(who('TEMP_QC'));TEMP_QC=TEMP_QC';end;
if ~isempty(who('TEMP_ADJUSTED_QC'));TEMP_ADJUSTED_QC=TEMP_ADJUSTED_QC';end;
end

if size(PLATFORM_NUMBER,1)~=size(PRES,1); PLATFORM_NUMBER=PLATFORM_NUMBER'; end; %'

%get the fillvalues:
nc = netcdf(fileIn, 'nowrite'); 
PRES_fillval=fillval(nc{'PRES'});
  if PSAL(1,1) ~= 8888; PSAL_fillval=fillval(nc{'PSAL'});end;
  if TEMP(1,1) ~= 8888; TEMP_fillval=fillval(nc{'TEMP'});end;
PLATFORM_NUMBER_fillval=fillval(nc{'PLATFORM_NUMBER'});
nc = close(nc);

REFdateOBS=str2num(strvcat(REFERENCE_DATE_TIME(1:4),REFERENCE_DATE_TIME(5:6),REFERENCE_DATE_TIME(7:8),REFERENCE_DATE_TIME(9:10),REFERENCE_DATE_TIME(11:12),REFERENCE_DATE_TIME(13:14)))';%'
REFdateOBS=jul_0h(REFdateOBS);
VECdateOBS=REFdateOBS+JULD;

xx=size(PRES);mloc=xx(1);mpts=xx(2);

varargout(1) = {length(LONGITUDE)};

else;%if m==0;
%select one profile for output:

%date, position, etc

tmp1=greg_0h(VECdateOBS(m));
ymd=tmp1(1)*1e4+tmp1(2)*1e2+tmp1(3);
hms=tmp1(4)*1e4+tmp1(5)*1e2+tmp1(6);

lat=LATITUDE(m);
lon=LONGITUDE(m); if lon < 0; lon=lon+360;end;

%%%%%%%ilon=find(((vec_lon-lon).^2)==min((vec_lon-lon).^2)); ilon=ilon(1);
%%%%%%%ilat=find(((vec_lat-lat).^2)==min((vec_lat-lat).^2)); ilat=ilat(1);

direc=0;if(DIRECTION(m)=='A');direc=1;end;if(DIRECTION(m)=='D');direc=2;end

pnum_txt=deblank(PLATFORM_NUMBER(m,:)); pnum_txt=pnum_txt(pnum_txt~=PLATFORM_NUMBER_fillval);
pnum=double(pnum_txt); pnum=pnum(find(pnum>=48&pnum<=57)); pnum=str2num(char(pnum));
if isempty(pnum); pnum_txt='9999'; pnum=9999; end;

%observations

 p=PRES_ADJUSTED(m,:);
 p_QC=PRES_ADJUSTED_QC(m,:);
 if isempty(find(p~=PRES_fillval)); p=PRES(m,:); p_QC=PRES_QC(m,:); end

        tmp1=find(isnan(p)); p(tmp1)=PRES_fillval; p_QC(tmp1)='5';
        for n=1:length(p)-1;
        tmp1=find(p(n+1:end)==p(n)&p(n+1:end)~=PRES_fillval);
        p(n+tmp1)=PRES_fillval;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)=PRES_fillval;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;

  if TEMP(m,1) ~= 8888
 t=TEMP_ADJUSTED(m,:);
 t_QC=TEMP_ADJUSTED_QC(m,:);
 t_ERR=TEMP_ADJUSTED_ERROR(m,:);tf=find(t_ERR==TEMP_fillval|isnan(t_ERR));t_ERR(tf)=0;
 if isempty(find(t~=TEMP_fillval)); t=TEMP(m,:); t_QC=TEMP_QC(m,:); end
  end

   if PSAL(m,1) ~= 8888
 s=PSAL_ADJUSTED(m,:);
 s_QC=PSAL_ADJUSTED_QC(m,:);
 s_ERR=PSAL_ADJUSTED_ERROR(m,:);sf=find(s_ERR==PSAL_fillval|isnan(s_ERR));,s_ERR(sf)=0;
 if isempty(find(s~=PSAL_fillval)); s=PSAL(m,:); s_QC=PSAL_QC(m,:); end
  end


p(p==PRES_fillval)=NaN;
p(p==PRES_fillval)=NaN;
if isempty(whos('t')); %this file does not contain salinity data... 
  t=NaN*p; t_ERR=0*p;
else;
  t(t_QC~='1'&t_QC~='2')=NaN;
end;
if isempty(whos('s')); %this file does not contain salinity data... 
  s=NaN*t; s_ERR=0*t_ERR;  
else;
  s(s_QC~='1'&s_QC~='2')=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;

%bad_latlon=0;
%if profileCur.lat<-90|profileCur.lat>90; bad_latlon=1; end;
%if profileCur.lon<-180|profileCur.lon>360; bad_latlon=1; end;
%profileCur.LONorLATisBAD=bad_latlon;

varargout = {profileCur};

end;


1	gforget	1.1	function [varargout]=profile_read_argo(dataset,nf,m);
2
3			fileIn=[dataset.dirIn dataset.fileInList(nf).name];
4
5			%output:
6			% ymd hms imonth lat lon direc p t s p_ERR t_ERR s_ERR
7
8			%common block:
9			global PLATFORM_NUMBER_fillval PLATFORM_NUMBER;
10			global VECdateOBS LATITUDE LONGITUDE DIRECTION;
11			global PRES PRES_ADJUSTED PRES_ADJUSTED_QC PRES_fillval PRES_QC;
12			global TEMP TEMP_ADJUSTED TEMP_ADJUSTED_QC TEMP_fillval TEMP_QC TEMP_ADJUSTED_ERROR;
13			global PSAL PSAL_ADJUSTED PSAL_ADJUSTED_QC PSAL_fillval PSAL_QC PSAL_ADJUSTED_ERROR;
14
15
16			if m==0;
17			%read the file and put the data in common blocks:
18
19			clear PRES* PSAL* TEMP*;
20			global PRES PRES_ADJUSTED PRES_ADJUSTED_QC PRES_fillval PRES_QC;
21			global TEMP TEMP_ADJUSTED TEMP_ADJUSTED_QC TEMP_fillval TEMP_QC TEMP_ADJUSTED_ERROR;
22			global PSAL PSAL_ADJUSTED PSAL_ADJUSTED_QC PSAL_fillval PSAL_QC PSAL_ADJUSTED_ERROR;
23			TEMP=8888ones(500,1);PSAL=8888ones(500,1);
24
25			%WHAT IS WRONG HERE???
26			%if ( rep_nb~=1\|isempty(findstr(fileIn,'20050911_prof')) )
27
28
29			eval(['ncload ' fileIn ';']);
30
31			%some dimensions inversions exist for _QC variables (!?)
32			if size(PRES_QC,1)~=size(PRES,1)
33			PRES_QC=PRES_QC';
34			if ~isempty(who('PRES_ADJUSTED_QC'));PRES_ADJUSTED_QC=PRES_ADJUSTED_QC';end;
35			if ~isempty(who('PSAL_QC'));PSAL_QC=PSAL_QC';end;
36			if ~isempty(who('PSAL_ADJUSTED_QC'));PSAL_ADJUSTED_QC=PSAL_ADJUSTED_QC';end;
37			if ~isempty(who('TEMP_QC'));TEMP_QC=TEMP_QC';end;
38			if ~isempty(who('TEMP_ADJUSTED_QC'));TEMP_ADJUSTED_QC=TEMP_ADJUSTED_QC';end;
39			end
40
41			if size(PLATFORM_NUMBER,1)~=size(PRES,1); PLATFORM_NUMBER=PLATFORM_NUMBER'; end; %'
42
43			%get the fillvalues:
44			nc = netcdf(fileIn, 'nowrite');
45			PRES_fillval=fillval(nc{'PRES'});
46			if PSAL(1,1) ~= 8888; PSAL_fillval=fillval(nc{'PSAL'});end;
47			if TEMP(1,1) ~= 8888; TEMP_fillval=fillval(nc{'TEMP'});end;
48			PLATFORM_NUMBER_fillval=fillval(nc{'PLATFORM_NUMBER'});
49			nc = close(nc);
50
51			REFdateOBS=str2num(strvcat(REFERENCE_DATE_TIME(1:4),REFERENCE_DATE_TIME(5:6),REFERENCE_DATE_TIME(7:8),REFERENCE_DATE_TIME(9:10),REFERENCE_DATE_TIME(11:12),REFERENCE_DATE_TIME(13:14)))';%'
52			REFdateOBS=jul_0h(REFdateOBS);
53			VECdateOBS=REFdateOBS+JULD;
54
55			xx=size(PRES);mloc=xx(1);mpts=xx(2);
56
57			varargout(1) = {length(LONGITUDE)};
58
59			else;%if m==0;
60			%select one profile for output:
61
62			%date, position, etc
63
64			tmp1=greg_0h(VECdateOBS(m));
65			ymd=tmp1(1)1e4+tmp1(2)1e2+tmp1(3);
66			hms=tmp1(4)1e4+tmp1(5)1e2+tmp1(6);
67
68			lat=LATITUDE(m);
69			lon=LONGITUDE(m); if lon < 0; lon=lon+360;end;
70
71			%%%%%%%ilon=find(((vec_lon-lon).^2)==min((vec_lon-lon).^2)); ilon=ilon(1);
72			%%%%%%%ilat=find(((vec_lat-lat).^2)==min((vec_lat-lat).^2)); ilat=ilat(1);
73
74			direc=0;if(DIRECTION(m)=='A');direc=1;end;if(DIRECTION(m)=='D');direc=2;end
75
76			pnum_txt=deblank(PLATFORM_NUMBER(m,:)); pnum_txt=pnum_txt(pnum_txt~=PLATFORM_NUMBER_fillval);
77			pnum=double(pnum_txt); pnum=pnum(find(pnum>=48&pnum<=57)); pnum=str2num(char(pnum));
78			if isempty(pnum); pnum_txt='9999'; pnum=9999; end;
79
80			%observations
81
82			p=PRES_ADJUSTED(m,:);
83			p_QC=PRES_ADJUSTED_QC(m,:);
84			if isempty(find(p~=PRES_fillval)); p=PRES(m,:); p_QC=PRES_QC(m,:); end
85
86			tmp1=find(isnan(p)); p(tmp1)=PRES_fillval; p_QC(tmp1)='5';
87			for n=1:length(p)-1;
88			tmp1=find(p(n+1:end)==p(n)&p(n+1:end)~=PRES_fillval);
89			p(n+tmp1)=PRES_fillval;p_QC(n+tmp1)='5';
90			end
91
92			bad_P=0;
93			tmp1=find(p_QC=='4');
94			if(length(tmp1)<=5);
95			%get rid of these few bad points and keep the profile
96			p(tmp1)=PRES_fillval;p_QC(tmp1)='5';
97			else;
98			%flag the profile (will be masked in the main file)
99			%but keep the bad points (to interp and be able to CHECK)
100			bad_P=1;
101			end;
102
103			if TEMP(m,1) ~= 8888
104			t=TEMP_ADJUSTED(m,:);
105			t_QC=TEMP_ADJUSTED_QC(m,:);
106			t_ERR=TEMP_ADJUSTED_ERROR(m,:);tf=find(t_ERR==TEMP_fillval\|isnan(t_ERR));t_ERR(tf)=0;
107			if isempty(find(t~=TEMP_fillval)); t=TEMP(m,:); t_QC=TEMP_QC(m,:); end
108			end
109
110			if PSAL(m,1) ~= 8888
111			s=PSAL_ADJUSTED(m,:);
112			s_QC=PSAL_ADJUSTED_QC(m,:);
113			s_ERR=PSAL_ADJUSTED_ERROR(m,:);sf=find(s_ERR==PSAL_fillval\|isnan(s_ERR));,s_ERR(sf)=0;
114			if isempty(find(s~=PSAL_fillval)); s=PSAL(m,:); s_QC=PSAL_QC(m,:); end
115			end
116
117
118			p(p==PRES_fillval)=NaN;
119			p(p==PRES_fillval)=NaN;
120			if isempty(whos('t')); %this file does not contain salinity data...
121			t=NaNp; t_ERR=0p;
122			else;
123			t(t_QC~='1'&t_QC~='2')=NaN;
124			end;
125			if isempty(whos('s')); %this file does not contain salinity data...
126			s=NaNt; s_ERR=0t_ERR;
127			else;
128			s(s_QC~='1'&s_QC~='2')=NaN;
129			end;
130
131
132			profileCur.pnum_txt=pnum_txt;
133			profileCur.ymd=ymd; profileCur.hms=hms;
134			profileCur.lat=lat; profileCur.lon=lon;
135			profileCur.direc=direc;
136			profileCur.t=t;
137			profileCur.s=s;
138			profileCur.p=p;
139			profileCur.t_ERR=t_ERR;
140			profileCur.s_ERR=s_ERR;
141			profileCur.PorZisBAD=bad_P;
142
143			%bad_latlon=0;
144			%if profileCur.lat<-90\|profileCur.lat>90; bad_latlon=1; end;
145			%if profileCur.lon<-180\|profileCur.lon>360; bad_latlon=1; end;
146			%profileCur.LONorLATisBAD=bad_latlon;
147
148			varargout = {profileCur};
149
150			end;
151
152
153