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function [varargout]=profile_read_odv(dataset,nf,m,varargin) |
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% read seal data in the odv spreadsheet format |
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% |
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% if m=0 : |
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% return the information on the nf-th file referenced in |
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% dataset.fileInList. |
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% dataset=profile_read_odv(dataset,nf,0); |
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% dataset.nprofiles: number of profiles in the nf-th file |
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% dataset.Iprofile: index referencing the profile for each dataline |
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% |
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% if m~=0 : |
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% return the m-th profile from the nf-th file referenced in |
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% dataset.fileInList. |
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% profileCur=profile_read_odv(dataset,nf,m); |
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% |
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% profileCur = (m-th profile of nf-th file) |
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% pnum_txt: '5900841' |
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% ymd: 20060101 |
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% hms: 3207 |
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% lat: -46.709 |
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% lon: 137.501 |
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% direc: 1 |
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% t: [1x115 single] |
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% s: [1x115 single] |
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% p: [1x115 single] |
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% t_ERR: [1x115 single] |
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% s_ERR: [1x115 single] |
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% isBAD: 0 |
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% |
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% IMPORTANT: Use three global variables: pnum Date and Data. |
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|
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global pnum Date Data |
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|
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fileIn=[dataset.dirIn dataset.fileInList(nf).name]; |
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|
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if m==0; |
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|
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% return the number of profiles in the file |
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% also build an index of first-line prosition of profiles: index_prof |
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fid_cur=fopen(fileIn,'rt'); |
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nprofiles=0;index_prof=[]; |
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|
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% jump comment line at the beginning |
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line_cur = fgetl(fid_cur); |
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while ~feof(fid_cur) & strcmp(line_cur(1:2),'//') |
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line_cur = fgetl(fid_cur); |
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continue |
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end |
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|
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% analyse data description line |
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I=[0 find(double(line_cur)==9) length(line_cur)+1]; |
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format=[]; |
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% column index for (in this order) : |
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% Cruise, Station, Date, Lon, Lat, Dep, Dep_qv, Temp, |
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% Temp_qv, Sal, Sal_qv |
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for ii=1:length(I)-1, |
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field=line_cur(I(ii)+1:I(ii+1)-1); |
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field=field(1:min([6 length(field)])); |
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switch field |
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case 'Cruise' |
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format(1)=ii; |
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case 'Statio' |
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format(2)=ii; |
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case 'yyyy-m' |
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format(3)=ii; |
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case {'Longit'} |
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format(4)=ii; |
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case {'Latitu'} |
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format(5)=ii; |
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case {'Depth '} |
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format([6 7])=[ii ii+1]; |
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case {'Temper'} |
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format([8 9])=[ii ii+1]; |
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case {'Salini'} |
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format([10 11])=[ii ii+1]; |
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end |
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end |
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|
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% read end of the textfile |
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nlines=0;nbuffer=100000;niter=0; |
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while ~feof(fid_cur); |
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niter=niter+1; |
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data_odv=cell(length(format)-1,nbuffer); |
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for ii=1:nbuffer, |
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tline=fgets(fid_cur); |
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nlines=nlines+1; |
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I_sep=[0 find(double(tline)==9)]; |
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data_odv{1,ii}=[ tline(I_sep(format(1))+1:I_sep(format(1)+1)-1) '//' ... |
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tline(I_sep(format(2))+1:I_sep(format(2)+1)-1) ]; |
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data_odv{2,ii}=tline(I_sep(format(3))+1:I_sep(format(3)+1)-1); |
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for kk=4:length(format), |
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I=I_sep(format(kk))+1:I_sep(format(kk)+1)-1; |
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if length(I)>1, |
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data_odv{kk-1,ii}=tline(I); |
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elseif isempty(I), |
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data_odv{kk-1,ii}='99999'; |
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else |
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val=tline(I); |
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if val==0, |
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data_odv{kk-1,ii}='99999'; |
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else |
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data_odv{kk-1,ii}=val; |
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end |
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end |
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end |
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if feof(fid_cur), break, end |
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end |
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data_odv=data_odv(:,1:ii); |
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data=data_odv(3:length(format)-1,:); |
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datanum=sscanf(sprintf('%s,',data{:}), '%g,'); |
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datanum(datanum==99999)=NaN; |
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|
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%no salinity case |
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if dataset.inclS, |
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datanum=reshape(datanum(:),8,ii); |
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else |
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datanum=reshape(datanum(:),6,ii); |
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end |
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|
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fprintf('%d lines\n',nlines); |
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if niter==1, |
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pnum=data_odv(1,:); |
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Date=data_odv(2,:); |
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Data=datanum; |
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else |
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pnum=[pnum data_odv(1,:)]; |
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Date=[Date data_odv(2,:)]; |
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Data=[Data datanum]; |
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end |
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|
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end |
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fclose(fid_cur); |
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|
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% get rid of empty indicator string |
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[pnum_txt_list,Iprof]=unique(pnum); |
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if size(Iprof,2)==1; Iprof=Iprof'; end; |
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for kk=1:length(pnum), |
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if strcmp(pnum_txt_list{kk},'//'), |
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pnum_txt_list=pnum_txt_list(setdiff(1:length(pnum_txt_list),kk)); |
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Iprof(kk)=[]; |
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break |
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end |
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end |
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|
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% sort index of profile |
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[Iprof_sort,J]=sort(Iprof); |
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pnum_txt_sort=pnum_txt_list(J); |
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|
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% write index of profile |
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Iprof_sort=[Iprof_sort nlines+1]; |
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Iprofile=zeros(nlines,1); |
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for kk=1:length(Iprof_sort)-1, |
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for ii=Iprof_sort(kk):Iprof_sort(kk+1)-1, |
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Iprofile(ii)=kk; |
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end |
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end |
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dataset.Iprofile=Iprofile; |
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|
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% number of profiles |
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dataset.nprofiles=length(Iprof); |
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|
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varargout(1) = {dataset}; |
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|
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|
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else;%if m==0; |
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|
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% profile coordinates |
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Iprof=find(dataset.Iprofile==m); |
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pnum_txt=pnum{Iprof(1)}; |
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lon=Data(1,Iprof(1)); |
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lat=Data(2,Iprof(1)); |
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strdate=Date{Iprof(1)}; |
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if length(strdate)<10, varargout = {[]}; return; end |
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ymd=str2num(strdate([1:4 6:7 9:10])); |
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hms=0; |
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if length(strdate)==19, hms=str2num(strdate([12:13 15:16 18:19])); end |
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if length(strdate)==16, hms=str2num(strdate([12:13 15:16]))*100; end |
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if length(strdate)==13, hms=str2num(strdate([12:13]))*10000; end |
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|
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%case when necessary information missing: dont retrieve profile |
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if isempty(lon)|isempty(lat)|isempty(ymd), varargout = {[]}; return; end |
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if lon < 0; lon=lon+360; end; |
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|
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% get T/S data |
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z=Data(3,Iprof); |
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z_qv=Data(4,Iprof);z_qv(isempty(z_qv))=1; |
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t=Data(5,Iprof); |
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t_qv=Data(6,Iprof);t_qv(isempty(t_qv))=1; |
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if dataset.inclS, |
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s=Data(7,Iprof); |
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s_qv=Data(8,Iprof);s_qv(isempty(s_qv))=1; |
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else |
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s=t*NaN; s_qv=t*NaN; s_ERR=t*NaN; |
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end |
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|
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I=find(isnan(z)|z_qv~=0); |
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z(I)=[]; t(I)=[]; t_qv(I)=[]; |
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t(t_qv~=0)=NaN; |
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t_ERR=t*0; |
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if dataset.inclS, |
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s_qv(I)=[]; s(I)=[]; |
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s(s_qv~=0)=NaN; s_ERR=s*0; |
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end |
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z_ERR=t*0; |
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|
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direc=2; |
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isBAD=0; |
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|
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profileCur.pnum_txt=pnum_txt; |
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profileCur.ymd=ymd; profileCur.hms=hms; |
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profileCur.lat=lat; profileCur.lon=lon; |
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profileCur.direc=direc; |
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profileCur.isBAD=isBAD; |
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profileCur.T=t; |
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profileCur.S=s; |
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profileCur.depth=z; |
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profileCur.T_ERR=t_ERR; |
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profileCur.S_ERR=s_ERR; |
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profileCur.depth_ERR=z_ERR; |
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|
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varargout = {profileCur}; |
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|
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end; |
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|
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