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roquet |
1.2 |
function [varargout]=profile_read_wod05(dataset,nf,m,varargin); |
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% read hydrographic data in the WOD05 csv format |
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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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% |
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roquet |
1.3 |
% 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_wod05(dataset,nf,0); |
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% dataset.nprofiles: number of profiles in the nf-th file |
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% dataset.index_prof: list of position number for each profile block |
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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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roquet |
1.2 |
% |
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% profileCur = |
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% pnum_txt: 'WOD-CTD//29-1103//4.' |
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% ymd: 19900210 |
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% hms: 82659 |
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% lat: 40.94 |
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% lon: 2.6467 |
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% direc: 2 |
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gforget |
1.5 |
% isBAD: 0 |
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roquet |
1.2 |
% t: [1x998 double] |
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% s: [1x998 double] |
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% z: [1x998 double] |
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% t_ERR: [1x998 double] |
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% s_ERR: [1x998 double] |
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gforget |
1.1 |
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fileIn=[dataset.dirIn dataset.fileInList(nf).name]; |
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instrType=dataset.subset(3:end); |
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if m==0; |
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roquet |
1.2 |
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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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prof_cur=0;index_prof=[]; |
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while ~feof(fid_cur); |
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line_cur = fgetl(fid_cur); |
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if ~isempty(findstr(line_cur,'NODC Cruise ID')); |
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prof_cur=prof_cur+1; |
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index_prof(end+1)=ftell(fid_cur)-length(line_cur)-1; |
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%to jump over second possible occurence of NODC Cruise ID |
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while isempty(findstr(line_cur,'END OF VARIABLES SECTION')); |
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line_cur = fgetl(fid_cur); |
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end; |
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end; |
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end; |
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fclose(fid_cur); |
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roquet |
1.3 |
dataset.nprofiles=prof_cur; |
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dataset.index_prof=index_prof; |
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varargout(1) = {dataset}; |
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roquet |
1.2 |
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gforget |
1.1 |
else;%if m==0; |
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roquet |
1.2 |
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% index_prof: position of beginning of each profile block in the .txt |
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roquet |
1.3 |
index_prof=dataset.index_prof; |
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roquet |
1.2 |
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fid_cur=fopen(fileIn,'rt'); |
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fseek(fid_cur,index_prof(m),'bof'); |
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data_cur=NaN*zeros(10000,3); %array that is used to store one profile |
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line_cur = fgetl(fid_cur); |
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while isempty(findstr(line_cur,'NODC Cruise ID')); |
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gforget |
1.1 |
line_cur = fgetl(fid_cur); |
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roquet |
1.2 |
end; |
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tmp1=findstr(line_cur,',,'); |
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pnum_txt=['WOD-' instrType '//' deblank(line_cur(tmp1(1)+2:tmp1(2)-1))]; |
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probe_type='-1'; Time=12.0; |
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lon=[]; lat=[]; Year=[]; Month=[]; Day=[]; |
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while isempty(findstr(line_cur,'VARIABLES')); |
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gforget |
1.1 |
line_cur = fgetl(fid_cur); |
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roquet |
1.2 |
var_cur=textscan(line_cur,'%s','delimiter',','); var_cur=var_cur{1}; |
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if ~isempty(findstr(cell2mat(var_cur(1)),'Latitude')); |
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lat=str2num(cell2mat(var_cur(3))); |
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end; |
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if ~isempty(findstr(cell2mat(var_cur(1)),'Longitude')); |
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lon=str2num(cell2mat(var_cur(3))); |
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end; |
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if ~isempty(findstr(cell2mat(var_cur(1)),'Year')); |
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Year=str2num(cell2mat(var_cur(3))); |
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end; |
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if ~isempty(findstr(cell2mat(var_cur(1)),'Month')); |
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Month=str2num(cell2mat(var_cur(3))); |
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end; |
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if ~isempty(findstr(cell2mat(var_cur(1)),'Day')); |
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Day=str2num(cell2mat(var_cur(3))); |
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end; |
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if ~isempty(findstr(cell2mat(var_cur(1)),'Time')); |
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Time=str2num(cell2mat(var_cur(3))); |
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end; |
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if ~isempty(findstr(cell2mat(var_cur(1)),'probe_type')); |
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probe_type=cell2mat(var_cur(3)); |
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end; |
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end; |
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%case when necessary information missing: put dummy info |
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if isempty(lon)|isempty(lat)|isempty(Year)|isempty(Month)|isempty(Day) |
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lat=-89.9; lon=0.1; Year=1800; Month=1; Day=1; |
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elseif Day==0; |
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lat=-89.9; lon=0.1; Year=1800; Month=1; Day=1; |
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end; |
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if lon < 0; lon=lon+360;end; |
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pnum_txt=[pnum_txt '//' deblank(probe_type)]; |
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var_cur=textscan(line_cur,'%s','delimiter',','); var_cur=var_cur{1}; |
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v_cur=[]; |
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for ii=1:length(var_cur); |
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gforget |
1.1 |
tmp1=cell2mat(var_cur(ii)); |
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if ~isempty(findstr(tmp1,'Depth')); v_cur=[v_cur; [1 ii]]; end; |
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if ~isempty(findstr(tmp1,'Temperatur')); v_cur=[v_cur; [2 ii]]; end; |
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if ~isempty(findstr(tmp1,'Salinity')); v_cur=[v_cur; [3 ii]]; end; |
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roquet |
1.2 |
end; |
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line_cur = fgetl(fid_cur); |
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line_cur = fgetl(fid_cur); |
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data_tmp=cell2mat(textscan(line_cur,'%f','delimiter',',','treatAsEmpty',{'Prof-Flag'})); |
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qc_cast=zeros(1,3); |
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%get cast qc?? |
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qc_cast(v_cur(:,1))=data_tmp(v_cur(:,2)+1)'; |
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qc_cast=1*(qc_cast==2|qc_cast==3|qc_cast==9); |
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%if ~isempty(find(qc_cast>0)); fprintf(['cast qc: ' num2str(qc_cast) ' for ' fileIn ' m=' num2str(m) '\n']); end; |
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% |
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data_cur(:)=NaN; |
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line_cur = fgetl(fid_cur); |
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count_cur=1; |
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data_tmp=cell2mat(textscan(line_cur,'%f','delimiter',',','treatAsEmpty',{'---.---','**********'})); |
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while ~isempty(data_tmp); |
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%store data: |
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gforget |
1.1 |
data_cur(count_cur,v_cur(:,1))=data_tmp(v_cur(:,2))'; |
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roquet |
1.2 |
%apply loc and global QC: |
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qc_loc=zeros(1,3); qc_loc(v_cur(:,1))=data_tmp(v_cur(:,2)+1)'; |
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qc_bad=find(qc_loc(v_cur(:,1))>0|qc_cast(v_cur(:,1))>0); |
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data_cur(count_cur,v_cur(qc_bad,1))=NaN; |
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%read the next line: |
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gforget |
1.1 |
line_cur = fgetl(fid_cur); |
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count_cur=count_cur+1; |
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data_tmp=cell2mat(textscan(line_cur,'%f','delimiter',',','treatAsEmpty',{'---.---','**********'})); |
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roquet |
1.2 |
end |
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fclose(fid_cur); |
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z=data_cur(1:count_cur-1,1); |
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t=data_cur(1:count_cur-1,2); |
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s=data_cur(1:count_cur-1,3); |
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t_ERR=zeros(size(t)); s_ERR=t_ERR; z_ERR=[]; |
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ymd=1e4*Year+1e2*Month+Day; |
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tmp1=(Time-floor(Time))*3600; |
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tmp2=floor(tmp1-floor(tmp1/60)*60); |
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tmp1=floor(tmp1/60); |
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hms=1e4*floor(Time)+1e2*tmp1+tmp2; |
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direc=2; |
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gforget |
1.5 |
isBAD=0; |
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roquet |
1.2 |
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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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gforget |
1.5 |
profileCur.isBAD=isBAD; |
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gforget |
1.4 |
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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roquet |
1.2 |
%by convention profileCur.z etc are line vectors |
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varargout = {profileCur}; |
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gforget |
1.1 |
end; |
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