profilesMatlabProcessing/profiles_IO_external/profiles_read_wod05.m

function [varargout]=profile_read_wod05(dataset,nf,m,varargin);
% read hydrographic data in the WOD05 csv format
%  return the m-th profile from the nf-th file referenced in
%   dataset.fileInList.
%
% if m=0, return the number of profiles in the nf-th file
%   and the array index_prof giving the position of each
%   profile blocks.
%
% profileCur = 
%      pnum_txt: 'WOD-CTD//29-1103//4.'
%           ymd: 19900210
%           hms: 82659
%           lat: 40.94
%           lon: 2.6467
%         direc: 2
%     PorZisBAD: 0
%             t: [1x998 double]
%             s: [1x998 double]
%             z: [1x998 double]
%         t_ERR: [1x998 double]
%         s_ERR: [1x998 double]

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

if m==0;
    
    % return the number of profiles in the file
    % also build an index of first-line prosition of profiles: index_prof
    fid_cur=fopen(fileIn,'rt');
    prof_cur=0;index_prof=[];
    while ~feof(fid_cur);
        line_cur = fgetl(fid_cur);
        if ~isempty(findstr(line_cur,'NODC Cruise ID'));
            prof_cur=prof_cur+1;
            index_prof(end+1)=ftell(fid_cur)-length(line_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;
    fclose(fid_cur);
    
    varargout(1) = {prof_cur};
    varargout(2)= {index_prof};
    
    
else;%if m==0;
    
        
    % index_prof: position of beginning of each profile block in the .txt 
    index_prof=varargin{1};

    fid_cur=fopen(fileIn,'rt');
    fseek(fid_cur,index_prof(m),'bof');
    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
    
    fclose(fid_cur);
    
    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	roquet	1.2	function [varargout]=profile_read_wod05(dataset,nf,m,varargin);
2			% read hydrographic data in the WOD05 csv format
3			% return the m-th profile from the nf-th file referenced in
4			% dataset.fileInList.
5			%
6			% if m=0, return the number of profiles in the nf-th file
7			% and the array index_prof giving the position of each
8			% profile blocks.
9			%
10			% profileCur =
11			% pnum_txt: 'WOD-CTD//29-1103//4.'
12			% ymd: 19900210
13			% hms: 82659
14			% lat: 40.94
15			% lon: 2.6467
16			% direc: 2
17			% PorZisBAD: 0
18			% t: [1x998 double]
19			% s: [1x998 double]
20			% z: [1x998 double]
21			% t_ERR: [1x998 double]
22			% s_ERR: [1x998 double]
23	gforget	1.1
24			fileIn=[dataset.dirIn dataset.fileInList(nf).name];
25			instrType=dataset.subset(3:end);
26
27			if m==0;
28	roquet	1.2
29			% return the number of profiles in the file
30			% also build an index of first-line prosition of profiles: index_prof
31			fid_cur=fopen(fileIn,'rt');
32			prof_cur=0;index_prof=[];
33			while ~feof(fid_cur);
34			line_cur = fgetl(fid_cur);
35			if ~isempty(findstr(line_cur,'NODC Cruise ID'));
36			prof_cur=prof_cur+1;
37			index_prof(end+1)=ftell(fid_cur)-length(line_cur)-1;
38			%to jump over second possible occurence of NODC Cruise ID
39			while isempty(findstr(line_cur,'END OF VARIABLES SECTION'));
40			line_cur = fgetl(fid_cur);
41			end;
42			end;
43			end;
44			fclose(fid_cur);
45
46			varargout(1) = {prof_cur};
47			varargout(2)= {index_prof};
48
49
50	gforget	1.1	else;%if m==0;
51	roquet	1.2
52
53			% index_prof: position of beginning of each profile block in the .txt
54			index_prof=varargin{1};
55
56			fid_cur=fopen(fileIn,'rt');
57			fseek(fid_cur,index_prof(m),'bof');
58			data_cur=NaN*zeros(10000,3); %array that is used to store one profile
59
60			line_cur = fgetl(fid_cur);
61			while isempty(findstr(line_cur,'NODC Cruise ID'));
62	gforget	1.1	line_cur = fgetl(fid_cur);
63	roquet	1.2	end;
64			tmp1=findstr(line_cur,',,');
65			pnum_txt=['WOD-' instrType '//' deblank(line_cur(tmp1(1)+2:tmp1(2)-1))];
66
67			probe_type='-1'; Time=12.0;
68			lon=[]; lat=[]; Year=[]; Month=[]; Day=[];
69
70			while isempty(findstr(line_cur,'VARIABLES'));
71	gforget	1.1	line_cur = fgetl(fid_cur);
72	roquet	1.2	var_cur=textscan(line_cur,'%s','delimiter',','); var_cur=var_cur{1};
73
74			if ~isempty(findstr(cell2mat(var_cur(1)),'Latitude'));
75			lat=str2num(cell2mat(var_cur(3)));
76			end;
77			if ~isempty(findstr(cell2mat(var_cur(1)),'Longitude'));
78			lon=str2num(cell2mat(var_cur(3)));
79			end;
80			if ~isempty(findstr(cell2mat(var_cur(1)),'Year'));
81			Year=str2num(cell2mat(var_cur(3)));
82			end;
83			if ~isempty(findstr(cell2mat(var_cur(1)),'Month'));
84			Month=str2num(cell2mat(var_cur(3)));
85			end;
86			if ~isempty(findstr(cell2mat(var_cur(1)),'Day'));
87			Day=str2num(cell2mat(var_cur(3)));
88			end;
89			if ~isempty(findstr(cell2mat(var_cur(1)),'Time'));
90			Time=str2num(cell2mat(var_cur(3)));
91			end;
92			if ~isempty(findstr(cell2mat(var_cur(1)),'probe_type'));
93			probe_type=cell2mat(var_cur(3));
94			end;
95
96			end;
97
98			%case when necessary information missing: put dummy info
99			if isempty(lon)\|isempty(lat)\|isempty(Year)\|isempty(Month)\|isempty(Day)
100			lat=-89.9; lon=0.1; Year=1800; Month=1; Day=1;
101			elseif Day==0;
102			lat=-89.9; lon=0.1; Year=1800; Month=1; Day=1;
103			end;
104
105			if lon < 0; lon=lon+360;end;
106
107			pnum_txt=[pnum_txt '//' deblank(probe_type)];
108
109			var_cur=textscan(line_cur,'%s','delimiter',','); var_cur=var_cur{1};
110			v_cur=[];
111			for ii=1:length(var_cur);
112	gforget	1.1	tmp1=cell2mat(var_cur(ii));
113			if ~isempty(findstr(tmp1,'Depth')); v_cur=[v_cur; [1 ii]]; end;
114			if ~isempty(findstr(tmp1,'Temperatur')); v_cur=[v_cur; [2 ii]]; end;
115			if ~isempty(findstr(tmp1,'Salinity')); v_cur=[v_cur; [3 ii]]; end;
116	roquet	1.2	end;
117			line_cur = fgetl(fid_cur);
118			line_cur = fgetl(fid_cur);
119
120			data_tmp=cell2mat(textscan(line_cur,'%f','delimiter',',','treatAsEmpty',{'Prof-Flag'}));
121			qc_cast=zeros(1,3);
122			%get cast qc??
123			qc_cast(v_cur(:,1))=data_tmp(v_cur(:,2)+1)';
124			qc_cast=1*(qc_cast==2\|qc_cast==3\|qc_cast==9);
125			%if ~isempty(find(qc_cast>0)); fprintf(['cast qc: ' num2str(qc_cast) ' for ' fileIn ' m=' num2str(m) '\n']); end;
126			%
127
128			data_cur(:)=NaN;
129			line_cur = fgetl(fid_cur);
130			count_cur=1;
131			data_tmp=cell2mat(textscan(line_cur,'%f','delimiter',',','treatAsEmpty',{'---.---','**********'}));
132			while ~isempty(data_tmp);
133			%store data:
134	gforget	1.1	data_cur(count_cur,v_cur(:,1))=data_tmp(v_cur(:,2))';
135	roquet	1.2	%apply loc and global QC:
136			qc_loc=zeros(1,3); qc_loc(v_cur(:,1))=data_tmp(v_cur(:,2)+1)';
137			qc_bad=find(qc_loc(v_cur(:,1))>0\|qc_cast(v_cur(:,1))>0);
138			data_cur(count_cur,v_cur(qc_bad,1))=NaN;
139			%read the next line:
140	gforget	1.1	line_cur = fgetl(fid_cur);
141			count_cur=count_cur+1;
142			data_tmp=cell2mat(textscan(line_cur,'%f','delimiter',',','treatAsEmpty',{'---.---','**********'}));
143	roquet	1.2	end
144
145			fclose(fid_cur);
146
147			z=data_cur(1:count_cur-1,1);
148			t=data_cur(1:count_cur-1,2);
149			s=data_cur(1:count_cur-1,3);
150			t_ERR=zeros(size(t)); s_ERR=t_ERR; z_ERR=[];
151
152
153			ymd=1e4Year+1e2Month+Day;
154			tmp1=(Time-floor(Time))*3600;
155			tmp2=floor(tmp1-floor(tmp1/60)*60);
156			tmp1=floor(tmp1/60);
157			hms=1e4floor(Time)+1e2tmp1+tmp2;
158			direc=2;
159			PorZisBAD=0;
160
161			profileCur.pnum_txt=pnum_txt;
162			profileCur.ymd=ymd; profileCur.hms=hms;
163			profileCur.lat=lat; profileCur.lon=lon;
164			profileCur.direc=direc;
165			profileCur.PorZisBAD=PorZisBAD;
166			profileCur.t=t';
167			profileCur.s=s';
168			profileCur.z=z';
169			profileCur.t_ERR=t_ERR';
170			profileCur.s_ERR=s_ERR';
171			profileCur.z_ERR=z_ERR';
172			%by convention profileCur.z etc are line vectors
173
174			varargout = {profileCur};
175
176	gforget	1.1	end;
177
178
179