profilesMatlabProcessing/profiles_IO_external/profiles_read_odv.m

function [varargout]=profile_read_odv(dataset,nf,m,varargin);
% read seal data in the odv spreadsheet format
%
% if m=0 :
%  return the information on the nf-th file referenced in
%  dataset.fileInList.
%   [nprofiles,struct_odv]=profile_read_odv(dataset,nf,0);
%       nprofiles: number of profiles in the nf-th file
%       struct_odv: odv 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_odv(dataset,nf,m,struct_odv);
%
% 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 profiles in the file
    % also build an index of first-line prosition of profiles: index_prof
    fid_cur=fopen(fileIn,'rt');
    nprofiles=0;index_prof=[];
    
    % jump comment line at the beginning
    line_cur = fgetl(fid_cur);
    while ~feof(fid_cur) & strcmp(line_cur(1:2),'//')
        line_cur = fgetl(fid_cur);
        continue
    end
    
    % analyse data description line
    I=[0 find(double(line_cur)==9) length(line_cur)+1];
    nfields=length(I)-1;
    format=[];
    % column index for (in this order) :
    %   Cruise, Station, Date, Lon, Lat, Dep, Dep_qv, Temp,
    %   Temp_qv, Sal, Sal_qv
    for ii=1:length(I)-1,
        field=line_cur(I(ii)+1:I(ii+1)-1);
        field=field(1:min([6 length(field)]));
        switch field
            case 'Cruise'
                format(1)=ii;
            case 'Statio'
                format(2)=ii;
            case 'yyyy-m'
                format(3)=ii;
            case {'Longit'}
                format(4)=ii;
            case {'Latitu'}
                format(5)=ii;
            case {'Depth '}
                format([6 7])=[ii ii+1];
            case {'Temper'}
                format([8 9])=[ii ii+1];
            case {'Salini'}
                format([10 11])=[ii ii+1];
        end
    end
    
    % init struct_odv
    struct_odv=[];
    
    % read end of the textfile
    nlines=0;
    while ~feof(fid_cur);
        data_odv=cell(nfields,100000);
        for ii=1:100000,
            tline=fgetl(fid_cur);
            nlines=nlines+1;
            I_sep=[0 find(double(tline)==9)];
            for kk=1:length(I_sep)-1,
                data_odv{kk,ii}=tline(I_sep(kk)+1:I_sep(kk+1)-1);
            end
            if feof(fid_cur), break, end
        end
        if isempty(struct_odv),
            struct_odv.Cruise={data_odv{format(1),:}};
            struct_odv.Station={data_odv{format(2),:}};
            struct_odv.Date={data_odv{format(3),:}};
            struct_odv.Lon=str2double({data_odv{format(4),:}});
            struct_odv.Lat=str2double({data_odv{format(5),:}});
            struct_odv.Dep=str2double({data_odv{format(6),:}});
            struct_odv.Dep_qv=str2double({data_odv{format(7),:}});
            struct_odv.Temp=str2double({data_odv{format(8),:}});
            struct_odv.Temp_qv=str2double({data_odv{format(9),:}});
            struct_odv.Sal=str2double({data_odv{format(10),:}});
            struct_odv.Sal_qv=str2double({data_odv{format(11),:}});
        else
            struct_odv.Cruise={struct_odv.Cruise{:} data_odv{format(1),:}};
            struct_odv.Station={struct_odv.Station{:} data_odv{format(2),:}};
            struct_odv.Date={struct_odv.Date{:} data_odv{format(3),:}};
            struct_odv.Lon=[struct_odv.Lon str2double({data_odv{format(4),:}})];
            struct_odv.Lat=[struct_odv.Lat str2double({data_odv{format(5),:}})];
            struct_odv.Dep=[struct_odv.Dep str2double({data_odv{format(6),:}})];
            struct_odv.Dep_qv=[struct_odv.Dep_qv str2double({data_odv{format(7),:}})];
            struct_odv.Temp=[struct_odv.Temp str2double({data_odv{format(8),:}})];
            struct_odv.Temp_qv=[struct_odv.Temp_qv str2double({data_odv{format(9),:}})];
            struct_odv.Sal=[struct_odv.Sal str2double({data_odv{format(10),:}})];
            struct_odv.Sal_qv=[struct_odv.Sal_qv str2double({data_odv{format(11),:}})];
        end
        
    end
    fclose(fid_cur);
    
    struct_odv.Cruise=struct_odv.Cruise(1:nlines);
    struct_odv.Station=struct_odv.Station(1:nlines);
    struct_odv.Date=struct_odv.Date(1:nlines);
    struct_odv.Lon=struct_odv.Lon(1:nlines);
    struct_odv.Lat=struct_odv.Lat(1:nlines);
    struct_odv.Dep=struct_odv.Dep(1:nlines);
    struct_odv.Dep_qv=struct_odv.Dep_qv(1:nlines);
    struct_odv.Temp=struct_odv.Temp(1:nlines);
    struct_odv.Temp_qv=struct_odv.Temp_qv(1:nlines);
    struct_odv.Sal=struct_odv.Sal(1:nlines);
    struct_odv.Sal_qv=struct_odv.Sal_qv(1:nlines);
    

    % name of each profile
    struct_odv.pnum_txt=struct_odv.Cruise;
    for kk=1:length(struct_odv.Cruise),
        struct_odv.pnum_txt{kk}=[struct_odv.Cruise{kk} '//' struct_odv.Station{kk}];
    end
    
    % get rid of empty indicator string
    [pnum_txt,Iprof]=unique(struct_odv.pnum_txt);
    for kk=1:length(pnum_txt),
        if strcmp(pnum_txt{kk},'//'),
            pnum_txt=pnum_txt(setdiff(1:length(pnum_txt),kk));
            Iprof(kk)=[];
            break
        end
    end
    
    % sort index of profile
    [Iprof_sort,J]=sort(Iprof);
    pnum_txt_sort=pnum_txt(J);
    
    % write index of profile
    Iprof_sort=[Iprof_sort nlines+1];
    for kk=1:length(Iprof_sort)-1,
        for ii=Iprof_sort(kk):Iprof_sort(kk+1)-1,
            struct_odv.Iprof(ii)=kk;
        end
    end

    % number of profiles
    nprofiles=length(Iprof);

    varargout(1) = {nprofiles};
    varargout(2)= {struct_odv};
    
    
else;%if m==0;
    
    % data_odv: struct of strings: 
    struct_odv=varargin{1};
    
    
    % profile coordinates
    Iprof=find(struct_odv.Iprof==m);
    pnum_txt=struct_odv.pnum_txt{Iprof(1)};
    lon=struct_odv.Lon(Iprof(1));
    lat=struct_odv.Lat(Iprof(1));
    strdate=struct_odv.Date{Iprof(1)};
    if length(strdate)<10, varargout = {[]}; return; end
    ymd=str2num(strdate([1:4 6:7 9:10]));
    hms=0;  
    if length(strdate)==19, hms=str2num(strdate([12:13 15:16 18:19])); end
    if length(strdate)==16, hms=str2num(strdate([12:13 15:16]))*100; end
    if length(strdate)==13, hms=str2num(strdate([12:13]))*10000; end

    %case when necessary information missing: dont retrieve profile
    if isempty(lon)|isempty(lat)|isempty(ymd), varargout = {[]}; return; end
    if lon < 0; lon=lon+360; end;
    
    % get T/S data
    z=struct_odv.Dep(Iprof);
    t=struct_odv.Temp(Iprof);
    s=struct_odv.Sal(Iprof);
    z_qv=struct_odv.Dep_qv(Iprof);z_qv(isempty(z_qv))=1;
    t_qv=struct_odv.Temp_qv(Iprof);t_qv(isempty(t_qv))=1;
    s_qv=struct_odv.Sal_qv(Iprof);s_qv(isempty(s_qv))=1;

    I=find(isnan(z)|z_qv~=0);
    z(I)=[]; t(I)=[]; s(I)=[]; t_qv(I)=[]; s_qv(I)=[];
    t(t_qv~=0)=NaN; s(s_qv~=0)=NaN;
    t_ERR=t*0; s_ERR=s*0; 
    
    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;
    
    varargout = {profileCur};
    
end;


1	roquet	1.1	function [varargout]=profile_read_odv(dataset,nf,m,varargin);
2			% read seal data in the odv spreadsheet format
3			%
4			% if m=0 :
5			% return the information on the nf-th file referenced in
6			% dataset.fileInList.
7			% [nprofiles,struct_odv]=profile_read_odv(dataset,nf,0);
8			% nprofiles: number of profiles in the nf-th file
9			% struct_odv: odv 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_odv(dataset,nf,m,struct_odv);
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
31
32			fileIn=[dataset.dirIn dataset.fileInList(nf).name];
33
34			if m==0;
35
36			% return the number of profiles in the file
37			% also build an index of first-line prosition of profiles: index_prof
38			fid_cur=fopen(fileIn,'rt');
39			nprofiles=0;index_prof=[];
40
41			% jump comment line at the beginning
42			line_cur = fgetl(fid_cur);
43			while ~feof(fid_cur) & strcmp(line_cur(1:2),'//')
44			line_cur = fgetl(fid_cur);
45			continue
46			end
47
48			% analyse data description line
49			I=[0 find(double(line_cur)==9) length(line_cur)+1];
50			nfields=length(I)-1;
51			format=[];
52			% column index for (in this order) :
53			% Cruise, Station, Date, Lon, Lat, Dep, Dep_qv, Temp,
54			% Temp_qv, Sal, Sal_qv
55			for ii=1:length(I)-1,
56			field=line_cur(I(ii)+1:I(ii+1)-1);
57			field=field(1:min([6 length(field)]));
58			switch field
59			case 'Cruise'
60			format(1)=ii;
61			case 'Statio'
62			format(2)=ii;
63			case 'yyyy-m'
64			format(3)=ii;
65			case {'Longit'}
66			format(4)=ii;
67			case {'Latitu'}
68			format(5)=ii;
69			case {'Depth '}
70			format([6 7])=[ii ii+1];
71			case {'Temper'}
72			format([8 9])=[ii ii+1];
73			case {'Salini'}
74			format([10 11])=[ii ii+1];
75			end
76			end
77
78			% init struct_odv
79			struct_odv=[];
80
81			% read end of the textfile
82			nlines=0;
83			while ~feof(fid_cur);
84			data_odv=cell(nfields,100000);
85			for ii=1:100000,
86			tline=fgetl(fid_cur);
87			nlines=nlines+1;
88			I_sep=[0 find(double(tline)==9)];
89			for kk=1:length(I_sep)-1,
90			data_odv{kk,ii}=tline(I_sep(kk)+1:I_sep(kk+1)-1);
91			end
92			if feof(fid_cur), break, end
93			end
94			if isempty(struct_odv),
95			struct_odv.Cruise={data_odv{format(1),:}};
96			struct_odv.Station={data_odv{format(2),:}};
97			struct_odv.Date={data_odv{format(3),:}};
98			struct_odv.Lon=str2double({data_odv{format(4),:}});
99			struct_odv.Lat=str2double({data_odv{format(5),:}});
100			struct_odv.Dep=str2double({data_odv{format(6),:}});
101			struct_odv.Dep_qv=str2double({data_odv{format(7),:}});
102			struct_odv.Temp=str2double({data_odv{format(8),:}});
103			struct_odv.Temp_qv=str2double({data_odv{format(9),:}});
104			struct_odv.Sal=str2double({data_odv{format(10),:}});
105			struct_odv.Sal_qv=str2double({data_odv{format(11),:}});
106			else
107			struct_odv.Cruise={struct_odv.Cruise{:} data_odv{format(1),:}};
108			struct_odv.Station={struct_odv.Station{:} data_odv{format(2),:}};
109			struct_odv.Date={struct_odv.Date{:} data_odv{format(3),:}};
110			struct_odv.Lon=[struct_odv.Lon str2double({data_odv{format(4),:}})];
111			struct_odv.Lat=[struct_odv.Lat str2double({data_odv{format(5),:}})];
112			struct_odv.Dep=[struct_odv.Dep str2double({data_odv{format(6),:}})];
113			struct_odv.Dep_qv=[struct_odv.Dep_qv str2double({data_odv{format(7),:}})];
114			struct_odv.Temp=[struct_odv.Temp str2double({data_odv{format(8),:}})];
115			struct_odv.Temp_qv=[struct_odv.Temp_qv str2double({data_odv{format(9),:}})];
116			struct_odv.Sal=[struct_odv.Sal str2double({data_odv{format(10),:}})];
117			struct_odv.Sal_qv=[struct_odv.Sal_qv str2double({data_odv{format(11),:}})];
118			end
119
120			end
121			fclose(fid_cur);
122
123			struct_odv.Cruise=struct_odv.Cruise(1:nlines);
124			struct_odv.Station=struct_odv.Station(1:nlines);
125			struct_odv.Date=struct_odv.Date(1:nlines);
126			struct_odv.Lon=struct_odv.Lon(1:nlines);
127			struct_odv.Lat=struct_odv.Lat(1:nlines);
128			struct_odv.Dep=struct_odv.Dep(1:nlines);
129			struct_odv.Dep_qv=struct_odv.Dep_qv(1:nlines);
130			struct_odv.Temp=struct_odv.Temp(1:nlines);
131			struct_odv.Temp_qv=struct_odv.Temp_qv(1:nlines);
132			struct_odv.Sal=struct_odv.Sal(1:nlines);
133			struct_odv.Sal_qv=struct_odv.Sal_qv(1:nlines);
134
135
136			% name of each profile
137			struct_odv.pnum_txt=struct_odv.Cruise;
138			for kk=1:length(struct_odv.Cruise),
139			struct_odv.pnum_txt{kk}=[struct_odv.Cruise{kk} '//' struct_odv.Station{kk}];
140			end
141
142			% get rid of empty indicator string
143			[pnum_txt,Iprof]=unique(struct_odv.pnum_txt);
144			for kk=1:length(pnum_txt),
145			if strcmp(pnum_txt{kk},'//'),
146			pnum_txt=pnum_txt(setdiff(1:length(pnum_txt),kk));
147			Iprof(kk)=[];
148			break
149			end
150			end
151
152			% sort index of profile
153			[Iprof_sort,J]=sort(Iprof);
154			pnum_txt_sort=pnum_txt(J);
155
156			% write index of profile
157			Iprof_sort=[Iprof_sort nlines+1];
158			for kk=1:length(Iprof_sort)-1,
159			for ii=Iprof_sort(kk):Iprof_sort(kk+1)-1,
160			struct_odv.Iprof(ii)=kk;
161			end
162			end
163
164			% number of profiles
165			nprofiles=length(Iprof);
166
167			varargout(1) = {nprofiles};
168			varargout(2)= {struct_odv};
169
170
171			else;%if m==0;
172
173			% data_odv: struct of strings:
174			struct_odv=varargin{1};
175
176
177			% profile coordinates
178			Iprof=find(struct_odv.Iprof==m);
179			pnum_txt=struct_odv.pnum_txt{Iprof(1)};
180			lon=struct_odv.Lon(Iprof(1));
181			lat=struct_odv.Lat(Iprof(1));
182			strdate=struct_odv.Date{Iprof(1)};
183			if length(strdate)<10, varargout = {[]}; return; end
184			ymd=str2num(strdate([1:4 6:7 9:10]));
185			hms=0;
186			if length(strdate)==19, hms=str2num(strdate([12:13 15:16 18:19])); end
187			if length(strdate)==16, hms=str2num(strdate([12:13 15:16]))*100; end
188			if length(strdate)==13, hms=str2num(strdate([12:13]))*10000; end
189
190			%case when necessary information missing: dont retrieve profile
191			if isempty(lon)\|isempty(lat)\|isempty(ymd), varargout = {[]}; return; end
192			if lon < 0; lon=lon+360; end;
193
194			% get T/S data
195			z=struct_odv.Dep(Iprof);
196			t=struct_odv.Temp(Iprof);
197			s=struct_odv.Sal(Iprof);
198			z_qv=struct_odv.Dep_qv(Iprof);z_qv(isempty(z_qv))=1;
199			t_qv=struct_odv.Temp_qv(Iprof);t_qv(isempty(t_qv))=1;
200			s_qv=struct_odv.Sal_qv(Iprof);s_qv(isempty(s_qv))=1;
201
202			I=find(isnan(z)\|z_qv~=0);
203			z(I)=[]; t(I)=[]; s(I)=[]; t_qv(I)=[]; s_qv(I)=[];
204			t(t_qv~=0)=NaN; s(s_qv~=0)=NaN;
205			t_ERR=t0; s_ERR=s0;
206
207			direc=2;
208			PorZisBAD=0;
209
210			profileCur.pnum_txt=pnum_txt;
211			profileCur.ymd=ymd; profileCur.hms=hms;
212			profileCur.lat=lat; profileCur.lon=lon;
213			profileCur.direc=direc;
214			profileCur.PorZisBAD=PorZisBAD;
215			profileCur.t=t;
216			profileCur.s=s;
217			profileCur.z=z;
218			profileCur.t_ERR=t_ERR;
219			profileCur.s_ERR=s_ERR;
220
221			varargout = {profileCur};
222
223			end;
224
225
226