profilesMatlabProcessing/profiles_IO_external/profiles_read_wod05.m

function [varargout]=profile_read_wod05(dataset,nf,m);

fileIn=[dataset.dirIn dataset.fileInList(nf).name];
instrType=dataset.subset(3:end);
global fid_cur;

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

fid_cur=fopen(fileIn,'rt');
prof_cur=0;
while ~feof(fid_cur);
        line_cur = fgetl(fid_cur);
        if ~isempty(findstr(line_cur,'NODC Cruise ID')); 
                prof_cur=prof_cur+1;
%to jump over second possible occurence of NODC Cruise ID
                while isempty(findstr(line_cur,'END OF VARIABLES SECTION'));
                        line_cur = fgetl(fid_cur);
                end;
        end;
end;

varargout(1) = {prof_cur};

fclose(fid_cur);
fid_cur=fopen(fileIn,'rt');

else;%if m==0;

data_cur=NaN*zeros(10000,3); %array that is used to store one profile

line_cur = fgetl(fid_cur);
while isempty(findstr(line_cur,'NODC Cruise ID'));
        line_cur = fgetl(fid_cur);
end;
tmp1=findstr(line_cur,',,');
pnum_txt=['WOD-' instrType '//' deblank(line_cur(tmp1(1)+2:tmp1(2)-1))];

probe_type='-1'; Time=12.0;
lon=[]; lat=[]; Year=[]; Month=[]; Day=[];
 
while isempty(findstr(line_cur,'VARIABLES'));
        line_cur = fgetl(fid_cur);
        var_cur=textscan(line_cur,'%s','delimiter',','); var_cur=var_cur{1};

        if ~isempty(findstr(cell2mat(var_cur(1)),'Latitude')); 
                lat=str2num(cell2mat(var_cur(3)));
        end;
        if ~isempty(findstr(cell2mat(var_cur(1)),'Longitude')); 
                lon=str2num(cell2mat(var_cur(3)));
        end;
        if ~isempty(findstr(cell2mat(var_cur(1)),'Year')); 
                Year=str2num(cell2mat(var_cur(3)));
        end;
        if ~isempty(findstr(cell2mat(var_cur(1)),'Month')); 
                Month=str2num(cell2mat(var_cur(3)));
        end;
        if ~isempty(findstr(cell2mat(var_cur(1)),'Day'));
                Day=str2num(cell2mat(var_cur(3)));
        end;
        if ~isempty(findstr(cell2mat(var_cur(1)),'Time')); 
                Time=str2num(cell2mat(var_cur(3)));
        end;
        if ~isempty(findstr(cell2mat(var_cur(1)),'probe_type'));
                probe_type=cell2mat(var_cur(3));
        end;

end;

%case when necessary information missing: put dummy info
if isempty(lon)|isempty(lat)|isempty(Year)|isempty(Month)|isempty(Day)
        lat=-89.9; lon=0.1; Year=1800; Month=1; Day=1;
elseif Day==0;
        lat=-89.9; lon=0.1; Year=1800; Month=1; Day=1;
end;

if lon < 0; lon=lon+360;end;

pnum_txt=[pnum_txt '//' deblank(probe_type)];

var_cur=textscan(line_cur,'%s','delimiter',','); var_cur=var_cur{1};
v_cur=[];
for ii=1:length(var_cur);
        tmp1=cell2mat(var_cur(ii));
        if ~isempty(findstr(tmp1,'Depth')); v_cur=[v_cur; [1 ii]]; end;
        if ~isempty(findstr(tmp1,'Temperatur')); v_cur=[v_cur; [2 ii]]; end;
        if ~isempty(findstr(tmp1,'Salinity')); v_cur=[v_cur; [3 ii]]; end;
end;
line_cur = fgetl(fid_cur);
line_cur = fgetl(fid_cur);

data_tmp=cell2mat(textscan(line_cur,'%f','delimiter',',','treatAsEmpty',{'Prof-Flag'}));
qc_cast=zeros(1,3); 
%get cast qc??
qc_cast(v_cur(:,1))=data_tmp(v_cur(:,2)+1)';
qc_cast=1*(qc_cast==2|qc_cast==3|qc_cast==9);
%if ~isempty(find(qc_cast>0)); fprintf(['cast qc: ' num2str(qc_cast) ' for ' fileIn ' m=' num2str(m) '\n']); end;
%

data_cur(:)=NaN;
line_cur = fgetl(fid_cur);
count_cur=1;
data_tmp=cell2mat(textscan(line_cur,'%f','delimiter',',','treatAsEmpty',{'---.---','**********'}));
while ~isempty(data_tmp);
        %store data:
        data_cur(count_cur,v_cur(:,1))=data_tmp(v_cur(:,2))';
        %apply loc and global QC:
        qc_loc=zeros(1,3); qc_loc(v_cur(:,1))=data_tmp(v_cur(:,2)+1)'; 
        qc_bad=find(qc_loc(v_cur(:,1))>0|qc_cast(v_cur(:,1))>0);
        data_cur(count_cur,v_cur(qc_bad,1))=NaN;
        %read the next line:
        line_cur = fgetl(fid_cur);
        count_cur=count_cur+1;
        data_tmp=cell2mat(textscan(line_cur,'%f','delimiter',',','treatAsEmpty',{'---.---','**********'}));
end

if feof(fid_cur); fclose(fid_cur); end;

z=data_cur(1:count_cur-1,1);
t=data_cur(1:count_cur-1,2);
s=data_cur(1:count_cur-1,3);
t_ERR=zeros(size(t)); s_ERR=t_ERR; z_ERR=[];


ymd=1e4*Year+1e2*Month+Day;
  tmp1=(Time-floor(Time))*3600; 
  tmp2=floor(tmp1-floor(tmp1/60)*60);
  tmp1=floor(tmp1/60);
hms=1e4*floor(Time)+1e2*tmp1+tmp2;
direc=2;
PorZisBAD=0;

profileCur.pnum_txt=pnum_txt;
profileCur.ymd=ymd; profileCur.hms=hms;
profileCur.lat=lat; profileCur.lon=lon;
profileCur.direc=direc;
profileCur.PorZisBAD=PorZisBAD;
profileCur.t=t';
profileCur.s=s';
profileCur.z=z';
profileCur.t_ERR=t_ERR';
profileCur.s_ERR=s_ERR';
profileCur.z_ERR=z_ERR';
%by convention profileCur.z etc are line vectors

varargout = {profileCur};

end;


1	gforget	1.1	function [varargout]=profile_read_wod05(dataset,nf,m);
2
3			fileIn=[dataset.dirIn dataset.fileInList(nf).name];
4			instrType=dataset.subset(3:end);
5			global fid_cur;
6
7			if m==0;
8			%read the file and put the data in common blocks:
9
10			fid_cur=fopen(fileIn,'rt');
11			prof_cur=0;
12			while ~feof(fid_cur);
13			line_cur = fgetl(fid_cur);
14			if ~isempty(findstr(line_cur,'NODC Cruise ID'));
15			prof_cur=prof_cur+1;
16			%to jump over second possible occurence of NODC Cruise ID
17			while isempty(findstr(line_cur,'END OF VARIABLES SECTION'));
18			line_cur = fgetl(fid_cur);
19			end;
20			end;
21			end;
22
23			varargout(1) = {prof_cur};
24
25			fclose(fid_cur);
26			fid_cur=fopen(fileIn,'rt');
27
28			else;%if m==0;
29
30			data_cur=NaN*zeros(10000,3); %array that is used to store one profile
31
32			line_cur = fgetl(fid_cur);
33			while isempty(findstr(line_cur,'NODC Cruise ID'));
34			line_cur = fgetl(fid_cur);
35			end;
36			tmp1=findstr(line_cur,',,');
37			pnum_txt=['WOD-' instrType '//' deblank(line_cur(tmp1(1)+2:tmp1(2)-1))];
38
39			probe_type='-1'; Time=12.0;
40			lon=[]; lat=[]; Year=[]; Month=[]; Day=[];
41
42			while isempty(findstr(line_cur,'VARIABLES'));
43			line_cur = fgetl(fid_cur);
44			var_cur=textscan(line_cur,'%s','delimiter',','); var_cur=var_cur{1};
45
46			if ~isempty(findstr(cell2mat(var_cur(1)),'Latitude'));
47			lat=str2num(cell2mat(var_cur(3)));
48			end;
49			if ~isempty(findstr(cell2mat(var_cur(1)),'Longitude'));
50			lon=str2num(cell2mat(var_cur(3)));
51			end;
52			if ~isempty(findstr(cell2mat(var_cur(1)),'Year'));
53			Year=str2num(cell2mat(var_cur(3)));
54			end;
55			if ~isempty(findstr(cell2mat(var_cur(1)),'Month'));
56			Month=str2num(cell2mat(var_cur(3)));
57			end;
58			if ~isempty(findstr(cell2mat(var_cur(1)),'Day'));
59			Day=str2num(cell2mat(var_cur(3)));
60			end;
61			if ~isempty(findstr(cell2mat(var_cur(1)),'Time'));
62			Time=str2num(cell2mat(var_cur(3)));
63			end;
64			if ~isempty(findstr(cell2mat(var_cur(1)),'probe_type'));
65			probe_type=cell2mat(var_cur(3));
66			end;
67
68			end;
69
70			%case when necessary information missing: put dummy info
71			if isempty(lon)\|isempty(lat)\|isempty(Year)\|isempty(Month)\|isempty(Day)
72			lat=-89.9; lon=0.1; Year=1800; Month=1; Day=1;
73			elseif Day==0;
74			lat=-89.9; lon=0.1; Year=1800; Month=1; Day=1;
75			end;
76
77			if lon < 0; lon=lon+360;end;
78
79			pnum_txt=[pnum_txt '//' deblank(probe_type)];
80
81			var_cur=textscan(line_cur,'%s','delimiter',','); var_cur=var_cur{1};
82			v_cur=[];
83			for ii=1:length(var_cur);
84			tmp1=cell2mat(var_cur(ii));
85			if ~isempty(findstr(tmp1,'Depth')); v_cur=[v_cur; [1 ii]]; end;
86			if ~isempty(findstr(tmp1,'Temperatur')); v_cur=[v_cur; [2 ii]]; end;
87			if ~isempty(findstr(tmp1,'Salinity')); v_cur=[v_cur; [3 ii]]; end;
88			end;
89			line_cur = fgetl(fid_cur);
90			line_cur = fgetl(fid_cur);
91
92			data_tmp=cell2mat(textscan(line_cur,'%f','delimiter',',','treatAsEmpty',{'Prof-Flag'}));
93			qc_cast=zeros(1,3);
94			%get cast qc??
95			qc_cast(v_cur(:,1))=data_tmp(v_cur(:,2)+1)';
96			qc_cast=1*(qc_cast==2\|qc_cast==3\|qc_cast==9);
97			%if ~isempty(find(qc_cast>0)); fprintf(['cast qc: ' num2str(qc_cast) ' for ' fileIn ' m=' num2str(m) '\n']); end;
98			%
99
100			data_cur(:)=NaN;
101			line_cur = fgetl(fid_cur);
102			count_cur=1;
103			data_tmp=cell2mat(textscan(line_cur,'%f','delimiter',',','treatAsEmpty',{'---.---','**********'}));
104			while ~isempty(data_tmp);
105			%store data:
106			data_cur(count_cur,v_cur(:,1))=data_tmp(v_cur(:,2))';
107			%apply loc and global QC:
108			qc_loc=zeros(1,3); qc_loc(v_cur(:,1))=data_tmp(v_cur(:,2)+1)';
109			qc_bad=find(qc_loc(v_cur(:,1))>0\|qc_cast(v_cur(:,1))>0);
110			data_cur(count_cur,v_cur(qc_bad,1))=NaN;
111			%read the next line:
112			line_cur = fgetl(fid_cur);
113			count_cur=count_cur+1;
114			data_tmp=cell2mat(textscan(line_cur,'%f','delimiter',',','treatAsEmpty',{'---.---','**********'}));
115			end
116
117			if feof(fid_cur); fclose(fid_cur); end;
118
119			z=data_cur(1:count_cur-1,1);
120			t=data_cur(1:count_cur-1,2);
121			s=data_cur(1:count_cur-1,3);
122			t_ERR=zeros(size(t)); s_ERR=t_ERR; z_ERR=[];
123
124
125			ymd=1e4Year+1e2Month+Day;
126			tmp1=(Time-floor(Time))*3600;
127			tmp2=floor(tmp1-floor(tmp1/60)*60);
128			tmp1=floor(tmp1/60);
129			hms=1e4floor(Time)+1e2tmp1+tmp2;
130			direc=2;
131			PorZisBAD=0;
132
133			profileCur.pnum_txt=pnum_txt;
134			profileCur.ymd=ymd; profileCur.hms=hms;
135			profileCur.lat=lat; profileCur.lon=lon;
136			profileCur.direc=direc;
137			profileCur.PorZisBAD=PorZisBAD;
138			profileCur.t=t';
139			profileCur.s=s';
140			profileCur.z=z';
141			profileCur.t_ERR=t_ERR';
142			profileCur.s_ERR=s_ERR';
143			profileCur.z_ERR=z_ERR';
144			%by convention profileCur.z etc are line vectors
145
146			varargout = {profileCur};
147
148			end;
149
150
151