Description of btl2mat

0001 function [btl_struct]=btl2mat(btl_file);
0002 % BTL2MAT Reads the SeaBird ASCII .BTL file format
0003 %
0004 %  Usage:   [lat,lon,gtime,data,names,sensors]=btl2mat(btl_file);
0005 %
0006 %     Input:  btl_file = name of .BTL file  (e.g. 'cast002.btl')
0007 %
0008 %     Output:btl_struct with fields:
0009 %             lon = longitude in decimal degrees, West negative
0010 %             lat = latitude in decimal degrees, North positive
0011 %           gtime = Gregorian time vector in UTC
0012 %            data = matrix containing all the columns of data in the .BTL file
0013 %           names = cell of string matrix containing the names of the columns
0014 %         sensors = string matrix containing the names of the sensors
0015 %
0016 %  NOTE: How lon,lat and time are written to the header of the .BTL
0017 %        file may vary with CTD setup.  For our .BTL files collected on
0018 %        the Oceanus, the lat, lon & time info look like this:
0019 %
0020 %    * System UpLoad Time = Mar 30 1998 18:48:42
0021 %    * NMEA Latitude = 42 32.15 N
0022 %    * NMEA Longitude = 069 28.69 W
0023 %    * NMEA UTC (Time) = 23:50:36
0024 %
0025 %  Modify the lat,lon and date string handling if your .BTL files are different.
0026 %  Also, There are several possibilities for the way time is stored.  Modify the
0027 %  time and gtime calculations based on whether or not the data ws logged in local time
0028 %  or gmt or utc.  The assumption here is that the system startup time is logged
0029 %  in local EST and the NMEA time is in GMT.  Watch out.
0030 %
0031 %  I do not store anything about the standard deviations.  If you feel like tackling
0032 %  that I'd love to see what you come up with.
0033 %
0034 % BUGS:  1. I have by no means encountered every possible variation in the way rossum
0035 %   stores data.  If something is wrong with the output check first that the variables
0036 %   stored in your btl file are all accounted for below.  I use only three cruises on
0037 %   three different ships as templates for creating this program.
0038 %   2. Does not account for the fact that a quantity can be output in several different units.
0039 %   i.e. if conductivity is output in S/m and mS/cm then the data in the matlab structure for
0040 %   conductivity is the last conductivity colummn encountered.
0041 %
0042 %  CALLER: user
0043 %
0044 %  DEPENDENCIES:
0045 %
0046 %  AUTHOR: 18 Oct 2001 Derrick Snowden (Derrick.Snowden@noaa.gov)
0047 %    based on cnv2mat by Rich Signell.
0048 %  4-8-98  Rich Signell (rsignell@usgs.gov)
0049 %     incorporates ideas from code by Derek Fong & Peter Brickley
0050 %
0051 
0052 % Open the .btl file as read-only text
0053 %
0054 fid=fopen(btl_file,'rt');
0055 if fid < 0 
0056     disp(['WARNING: btl2mat could not open ',btl_file]);
0057     btl=[];
0058     return
0059 end
0060 %
0061 % Read the header.
0062 % Start reading header lines of .BTL file,
0063 % Stop at line that starts with '*END*'
0064 %
0065 % Pull out NMEA lat & lon along the way and look
0066 % at the '# name' fields to see how many variables we have.
0067 %
0068 str='*START*';
0069 
0070 % This may change in different configurations.  I suppose it depends on your
0071 % shipboard processing scripts/procedures.  look through your files for
0072 %something that denots the end of the header but not the line containing the names ofthe columns.
0073 %while (~strncmp(str,'*END*',5));
0074 choose_nmea = 0;
0075 while (~strncmp(str,'# bottlesum_in',14));
0076     str=fgetl(fid);
0077     %-----------------------------------
0078     %
0079     %    Read the NMEA latitude string.  This may vary with CTD setup.
0080     %
0081     if (strncmp(str,'* NMEA Lat',10))
0082         choose_nmea = 1;
0083         is=findstr(str,'=');
0084         isub=is+1:length(str);
0085         dm=sscanf(str(isub),'%f',2);
0086         if(findstr(str(isub),'N'));
0087             lat=dm(1)+dm(2)/60;
0088         else  
0089             lat=-(dm(1)+dm(2)/60); 
0090         end
0091         %-------------------------------
0092         %
0093         %    Read the NMEA longitude string.  This may vary with CTD setup.
0094         %
0095     elseif (strncmp(str,'* NMEA Lon',10))
0096         choose_nmea = 1;
0097         is=findstr(str,'=');
0098         isub=is+1:length(str);
0099         dm=sscanf(str(isub),'%f',2);
0100         if(findstr(str(isub),'E'));
0101             lon=dm(1)+dm(2)/60;
0102         else  
0103             lon=-(dm(1)+dm(2)/60); 
0104         end
0105         %-----------------------------------
0106         %
0107         %    Read the NON NMEA latitude string.  This may vary with CTD setup.
0108         %
0109     elseif (strncmp(str,'** Lat',6))
0110         if choose_nmea == 0
0111             is=findstr(str,':');
0112             isub=is+1:length(str);
0113             dm=sscanf(str(isub),'%f',2);
0114             if(findstr(str(isub),'N'));
0115                 if length(dm) == 2
0116                     lat=dm(1)+dm(2)/60;
0117                 else
0118                     lat = dm(1); % assume they have used decimal degrees
0119                 end
0120             else 
0121                 if length(dm) == 2
0122                     lat=-(dm(1)+dm(2)/60);
0123                 else
0124                     lat = -(dm(1)); % assume they have used decimal degrees
0125                 end
0126                 
0127             end
0128         end
0129         %-------------------------------
0130         %
0131         %    Read the NON NMEA longitude string.  This may vary with CTD setup.
0132         %
0133     elseif (strncmp(str,'** Lon',6))
0134         if choose_nmea == 0
0135             is=findstr(str,':');
0136             isub=is+1:length(str);
0137             dm=sscanf(str(isub),'%f',2);
0138             if(findstr(str(isub),'E'));
0139                  if length(dm) == 2
0140                     lon =dm(1)+dm(2)/60;
0141                 else
0142                     lon = dm(1); % assume they have used decimal degrees
0143                 end
0144             else 
0145                 if length(dm) == 2
0146                     lon=-(dm(1)+dm(2)/60);
0147                 else
0148                     lon = -(dm(1)); % assume they have used decimal degrees
0149                 end
0150                 
0151            end
0152         end
0153         %------------------------
0154         %
0155         %    Read the 'System upload time' to get the date.
0156         %           This may vary with CTD setup.
0157         %
0158         %    I'm reading this in to get the date, since the NMEA time string
0159         %    does not contain date.  Unfortunately, the system upload time is
0160         %    in local time (here, EST), so I need to convert to UTC by adding
0161         %    5 hours (5/24 days).
0162         %
0163     elseif (strncmp(str,'* System UpLoad',15))
0164         is=findstr(str,'=');
0165         %    pick apart date string and reassemble in DATEFORM type 0 form
0166         datstr=[str(is+6:is+7) '-' str(is+2:is+4) '-' str(is+9:is+12)];
0167         datstr=[datstr ' ' str(is+14:is+21)];
0168         %    convert datstr to Julian time, add 5 hours to convert from EST to GMT
0169         n=datenum(datstr)+5/24;
0170         gtime=datevec(n);
0171         %----------------------------
0172         %
0173         %    Read the NMEA TIME string.  This may vary with CTD setup.
0174         %
0175         %      replace the System upload time with the NMEA time
0176     elseif (strncmp(str,'* NMEA UTC',10))
0177         is=findstr(str,':');
0178         isub=is(1)-2:length(str);
0179         gtime([4:6])=sscanf(str(isub),'%2d:%2d:%2d');
0180         %------------------------------
0181         %
0182         %    Read the variable names & units into a cell array
0183         %
0184     elseif (strncmp(str,'# name',6))  
0185         var=sscanf(str(7:10),'%d',1);
0186         var=var+1;  % .BTL file counts from 0, Matlab counts from 1
0187         %      stuff variable names into cell array
0188         names{var}=str;
0189         %------------------------------
0190         %
0191         %    Read the sensor names into a cell array
0192         %
0193     elseif (strncmp(str,'# sensor',8))  
0194         sens=sscanf(str(10:11),'%d',1);
0195         sens=sens+1;  % .BTL file counts from 0, Matlab counts from 1
0196         %      stuff sensor names into cell array
0197         sensors{sens}=str;
0198         %
0199         %  pick up bad flag value
0200     elseif (strncmp(str,'# bad_flag',10))  
0201         isub=13:length(str);
0202         bad_flag=sscanf(str(isub),'%g',1);
0203     end
0204 end
0205 %==============================================
0206 %
0207 %  Done reading header.  Now read the data!
0208 %
0209 %nvars=var;  %number of variables
0210 
0211 %==============================================
0212 %
0213 %  Start off with the column headings. which should occupy two lines.
0214 %
0215 col_headings = fgetl(fid);
0216 column_names1 = strread(col_headings,'%s','delimiter',' ');
0217 col_headings = fgetl(fid);
0218 column_names2 = strread(col_headings,'%s','delimiter',' ');
0219 % warn the user if there is not a Nbf column
0220 Nbf_flag=strmatch('Nbf',column_names1)|strmatch('Nbf',column_names2);
0221 %
0222 %if ~strmatch('Nbf',column_names1) | ~strmatch('Nbf',column_names2)
0223     if isempty(Nbf_flag)
0224     msg = sprintf('\n');
0225     msg = [msg sprintf([' WARNING BTL2MAT: There is no Nbf column in file:  ',btl_file,' \n'])];
0226     msg = [msg sprintf(['  Rerun rossum and configure to print number of bottles fired.\n'])];
0227     msg = [msg sprintf(['  Trying to continue anyway...\n'])];
0228     msg = [msg sprintf('\n')];
0229     disp(msg);
0230 end
0231 %==============
0232 % Going to need to do some looping but I don't know exactly how yet.
0233 % Maybe mark the spot here than count lines and come back here?
0234 %
0235 count = 1;
0236 while feof(fid)~=1
0237     str = fgetl(fid);
0238     avgcell{count} = strread(str,'%s' ,'delimiter',' ');
0239     % remove the string '(avg)'
0240     tmp = avgcell{count};
0241     tmp{end} = [];
0242     avgcell{count} = tmp;
0243     str = fgetl(fid);
0244     stdcell{count} = strread(str,'%s' ,'delimiter',' ');
0245     % remove the string '(avg)'
0246     tmp = stdcell{count};
0247     tmp{end} = [];
0248     stdcell{count} = tmp;
0249     count = count+1;
0250 end
0251 
0252 %  I'm going to exclude the std information for now DPS 19Oct2001
0253 % Assume that the date string will occupy 3 columns
0254 % Try to find the indices of the major known fields
0255 offset = 0;
0256 column_count = 0;
0257 for i = 1:length(column_names1)
0258     if strncmp('Bottle',column_names1{i},6); 
0259         column_count = column_count + 1;
0260         btl_pos_idx = column_count + offset; 
0261     end;
0262     if strncmp('Date',column_names1{i},4); 
0263         column_count = column_count + 1;
0264         date_idx = column_count; 
0265         offset = 2;
0266     end;
0267     if strncmp('Density00',column_names1{i},9); 
0268         column_count = column_count + 1;
0269         pri_pri_dens_idx = column_count + offset; 
0270     end;
0271     if strncmp('Density11',column_names1{i},9); 
0272         column_count = column_count + 1;
0273         sec_sec_dens_idx = column_count + offset; 
0274     end;
0275     if strncmp('Density01',column_names1{i},9); 
0276         column_count = column_count + 1;
0277         pri_sec_dens_idx = column_count + offset; 
0278     end;
0279     if strncmp('Density10',column_names1{i},9); 
0280         column_count = column_count + 1;
0281         sec_pri_dens_idx = column_count + offset; 
0282     end;
0283     if strncmp('Sigma-',column_names1{i},6); 
0284         %Parse the sigma into individual ascii representation
0285         %in order to compare non standard characters.
0286         % integer code 233 represents the e' in the column Skip it.
0287         sig = column_names1{i};
0288         if strncmp('00',sig(end-1:end),2)
0289             column_count = column_count + 1;
0290             pri_pri_sig_idx = column_count + offset;
0291         elseif strncmp('11',sig(end-1:end),2)
0292             column_count = column_count + 1;
0293             sec_sec_sig_idx = column_count + offset;
0294         elseif strncmp('10',sig(end-1:end),2)
0295             column_count = column_count + 1;
0296             sec_pri_sig_idx = column_count + offset;
0297         elseif strncmp('01',sig(end-1:end),2)
0298             column_count = column_count + 1;
0299             pri_sec_sig_idx = column_count + offset; 
0300         end
0301     end;
0302     
0303     if strncmp('Pr',column_names1{i},2); 
0304         column_count = column_count + 1;
0305         pr_idx = column_count + offset; 
0306     end;
0307     if strncmp('T068',column_names1{i},4); 
0308         column_count = column_count + 1;
0309         pri_t68_idx = column_count + offset; 
0310     end;
0311     if strncmp('T168',column_names1{i},4); 
0312         column_count = column_count + 1;
0313         sec_t68_idx = column_count + offset; 
0314     end;
0315     if strncmp('T090',column_names1{i},4); 
0316         column_count = column_count + 1;
0317         pri_t90_idx = column_count + offset; 
0318     end;
0319     if strncmp('T190',column_names1{i},4); 
0320         column_count = column_count + 1;
0321         sec_t90_idx = column_count + offset; 
0322     end;
0323     if strncmp('Sal00',column_names1{i},5); 
0324         column_count = column_count + 1;
0325         pri_pri_sal_idx = column_count + offset; 
0326     end;
0327     if strncmp('Sal11',column_names1{i},5); 
0328         column_count = column_count + 1;
0329         sec_sec_sal_idx = column_count + offset; 
0330     end;
0331     if strncmp('Sal01',column_names1{i},5); 
0332         column_count = column_count + 1;
0333         pri_sec_sal_idx = column_count + offset; 
0334     end;
0335     if strncmp('Sal10',column_names1{i},5); 
0336         column_count = column_count + 1;
0337         sec_pri_sal_idx = column_count + offset; 
0338     end;
0339     if strncmp('C0S/m',column_names1{i},5); 
0340         column_count = column_count + 1;
0341         pri_con_idx = column_count + offset; 
0342     end;
0343     if strncmp('C1S/m',column_names1{i},5); 
0344         column_count = column_count + 1;
0345         sec_con_idx = column_count + offset; 
0346     end;
0347     if strncmp('C0mS/cm',column_names1{i},5); 
0348         column_count = column_count + 1;
0349         pri_con_idx = column_count + offset; 
0350     end;
0351     if strncmp('C1mS/cm',column_names1{i},5); 
0352         column_count = column_count + 1;
0353         sec_con_idx = column_count + offset; 
0354     end;
0355     if strncmp('OxC',column_names1{i},3); 
0356         column_count = column_count + 1;
0357         pri_oxc_idx = column_count + offset; 
0358     end;
0359     if strncmp('OxsC',column_names1{i},4); 
0360         column_count = column_count + 1;
0361         sec_oxc_idx = column_count + offset; 
0362     end;
0363     if strncmp('OxT',column_names1{i},3); 
0364         column_count = column_count + 1;
0365         pri_oxt_idx = column_count + offset; 
0366     end;
0367     if strncmp('OxsT',column_names1{i},4); 
0368         column_count = column_count + 1;
0369         sec_oxt_idx = column_count + offset; 
0370     end;
0371     if strncmp('OxMm/Kg',column_names1{i},7); 
0372         column_count = column_count + 1;
0373         pri_do2_mmkg_idx = column_count + offset; 
0374     end;
0375     if strncmp('OxsMm/Kg',column_names1{i},8); 
0376         column_count = column_count + 1;
0377         sec_do2_mmkg_idx = column_count + offset; 
0378     end;
0379     if strncmp('Sbeox0Mm/Kg',column_names1{i},11); 
0380         column_count = column_count + 1;
0381         pri_sbedo2_mmkg_idx = column_count + offset; 
0382     end;
0383     if strncmp('Sbeox1Mm/Kg',column_names1{i},11); 
0384         column_count = column_count + 1;
0385         sec_sbedo2_mmkg_idx = column_count + offset; 
0386     end;
0387     if strncmp('OxdOC/dT',column_names1{i},8); 
0388         column_count = column_count + 1;
0389         pri_odocdt_idx = column_count + offset; 
0390     end;
0391     if strncmp('OxsdOC/dT',column_names1{i},9); 
0392         column_count = column_count + 1;
0393         sec_odocdt_idx = column_count + offset; 
0394     end;
0395     if strncmp('Sbeox0ML/L',column_names1{i},10); 
0396         column_count = column_count + 1;
0397         pri_sbedo2_mll_idx = column_count + offset; 
0398     end;
0399     if strncmp('Sbeox1ML/L',column_names1{i},10); 
0400         column_count = column_count + 1;
0401         sec_sbedo2_mll_idx = column_count + offset; 
0402     end;
0403     if strncmp('OxML/L',column_names1{i},6); 
0404         column_count = column_count + 1;
0405         pri_do2_mll_idx = column_count + offset; 
0406     end;
0407     if strncmp('OxsML/L',column_names1{i},7); 
0408         column_count = column_count + 1;
0409         sec_do2_mll_idx = column_count + offset; 
0410     end;
0411     if strncmp('Nbf',column_names1{i},3); 
0412         column_count = column_count + 1;
0413         btl_fired_idx = column_count + offset; 
0414     end;
0415  % CAF
0416        if strncmp('Potemp090C',column_names1{i},10); 
0417         column_count = column_count + 1;
0418         pot_temp_pri_idx = column_count + offset; 
0419        end;
0420        if strncmp('Potemp190C',column_names1{i},10); 
0421         column_count = column_count + 1;
0422         pot_temp_sec_idx = column_count + offset; 
0423        end;
0424        if strncmp('Sbeox0PS',column_names1{i},8); 
0425         column_count = column_count + 1;
0426         sbeox_pct_sat_pri_idx = column_count + offset; 
0427        end;
0428        if strncmp('Sbeox1PS',column_names1{i},8); 
0429         column_count = column_count + 1;
0430         sbeox_pct_sat_sec_idx = column_count + offset; 
0431        end;
0432        if strncmp('Sbeox0dOC/dT',column_names1{i},12); 
0433         column_count = column_count + 1;
0434         pri_sbedOC_dt_idx = column_count + offset; 
0435        end; 
0436        if strncmp('Sbeox1dOC/dT',column_names1{i},12); 
0437         column_count = column_count + 1;
0438         sec_sbedOC_dt_idx = column_count + offset; 
0439        end;
0440        if strncmp('Sbeox0V',column_names1{i},7); 
0441         column_count = column_count + 1;
0442         pri_sbeox_volt_idx = column_count + offset; 
0443        end;
0444        if strncmp('Sbeox1V',column_names1{i},7); 
0445         column_count = column_count + 1;
0446         sec_sbeox_volt_idx = column_count + offset; 
0447        end;
0448        if strncmp('Scan',column_names1{i},4); 
0449         column_count = column_count + 1;
0450         scan_idx = column_count + offset; 
0451        end;
0452        if strncmp('OxPS',column_names1{i},4); 
0453         column_count = column_count + 1;
0454         pct_sat_idx = column_count + offset; 
0455        end;
0456         if strncmp('OxsPS',column_names1{i},4); 
0457         column_count = column_count + 1;
0458         pct_sat_sec_idx = column_count + offset; 
0459        end;
0460        %CAF
0461     % repeat the above construct as you discover more parameters which rossum outputs.
0462 end
0463 column_count2 = 0;
0464 for i = 1:length(column_names2);
0465     if strncmp('Position',column_names2{i},8)
0466         %  This is redundant compared with Bottle above
0467     elseif strncmp('Time',column_names2{i},4)
0468         column_count2 = column_count2 + 1;
0469         time_idx = column_count2;
0470     end
0471 end
0472 
0473 % Begin to assemble the output matrix/structure.
0474 num_rows = length(avgcell);
0475 if ~isempty(date_idx)
0476     % date is parsed as a 3 column vector but we will combine into one.
0477     offset = 2;
0478 else
0479     offset = 0;
0480 end
0481 data = NaN.* ones(num_rows,(column_count-offset));
0482 for i = 1:num_rows
0483     if exist('btl_pos_idx','var') == 1
0484         data(i,btl_pos_idx) = str2num(avgcell{i}{btl_pos_idx});
0485         names{btl_pos_idx} = 'bottle_ros_position';
0486     end
0487     if exist('date_idx','var') == 1
0488         mnth = avgcell{i}{date_idx};
0489         day = avgcell{i}{date_idx + 1};
0490         yr = avgcell{i}{date_idx+2};
0491         if exist('time_idx','var') == 1
0492             timestr = stdcell{i}{time_idx};
0493             % dateform=0 == 'dd-mmm-yyyy HH:MM:SS'
0494             datestr = sprintf('%s',[day,'-',mnth,'-',yr,' ',timestr]);
0495         else
0496             datestr = sprintf('%s',[day,'-',mnth,'-',yr]);
0497         end
0498         data(i,date_idx) = datenum(datestr);
0499         names{date_idx} = 'date';
0500     end;
0501     if exist('pri_pri_dens_idx','var') == 1
0502         data(i,pri_pri_dens_idx) = str2num(avgcell{i}{pri_pri_dens_idx});
0503         names{pri_pri_dens_idx} = 'density_pri_pri';
0504     end;
0505     if exist('sec_sec_dens_idx','var') == 1
0506         data(i,sec_sec_dens_idx) = str2num(avgcell{i}{sec_sec_dens_idx});
0507         names{sec_sec_dens_idx} = 'density_sec_sec';
0508     end;
0509     if exist('pri_sec_dens_idx','var') == 1
0510         data(i,pri_sec_dens_idx) = str2num(avgcell{i}{pri_sec_dens_idx});
0511         names{pri_sec_dens_idx} = 'density_pri_sec';
0512     end;
0513     if exist('sec_pri_dens_idx','var') == 1
0514         data(i,sec_pri_dens_idx) = str2num(avgcell{i}{sec_pri_dens_idx});
0515         names{sec_pri_dens_idx} = 'density_sec_pri';
0516     end;
0517     if exist('pri_pri_sig_idx','var') == 1
0518         data(i,pri_pri_sig_idx) = str2num(avgcell{i}{pri_pri_sig_idx});
0519         names{pri_pri_sig_idx} = 'sigma_pri_pri';
0520     end;
0521     if exist('sec_sec_sig_idx','var') == 1
0522         data(i,sec_sec_sig_idx) = str2num(avgcell{i}{sec_sec_sig_idx});
0523         names{sec_sec_sig_idx} = 'sigma_sec_sec';
0524     end;
0525     if exist('pri_sec_sig_idx','var') == 1
0526         data(i,pri_sec_sig_idx) = str2num(avgcell{i}{pri_sec_sig_idx});
0527         names{pri_sec_sig_idx} = 'sigma_pri_sec';
0528     end;
0529     if exist('sec_pri_sig_idx','var') == 1
0530         data(i,sec_pri_sig_idx) = str2num(avgcell{i}{sec_pri_sig_idx});
0531         names{sec_pri_sig_idx} = 'sigma_sec_pri';
0532     end;
0533     if exist('pr_idx','var') == 1
0534         data(i,pr_idx) = str2num(avgcell{i}{pr_idx});
0535         names{pr_idx}='pressure';
0536     end;
0537     if exist('pri_t68_idx','var') == 1
0538         data(i,pri_t68_idx) = str2num(avgcell{i}{pri_t68_idx});
0539         names{pri_t68_idx} = 't68_pri';
0540     end;
0541     if exist('sec_t68_idx','var') == 1
0542         data(i,sec_t68_idx) = str2num(avgcell{i}{sec_t68_idx});
0543         names{sec_t68_idx} = 't68_sec';
0544     end;
0545     if exist('pri_t90_idx','var') == 1 
0546         data(i,pri_t90_idx) = str2num(avgcell{i}{pri_t90_idx});
0547         names{pri_t90_idx} = 't90_pri';
0548     end;
0549     if exist('sec_t90_idx','var') == 1
0550         data(i,sec_t90_idx) = str2num(avgcell{i}{sec_t90_idx});
0551         names{sec_t90_idx} = 't90_sec' ;
0552     end;
0553     if exist('pri_pri_sal_idx','var') == 1
0554         data(i,pri_pri_sal_idx) = str2num(avgcell{i}{pri_pri_sal_idx});
0555         names{pri_pri_sal_idx} = 'sal_pri_pri';
0556     end;
0557     if exist('sec_sec_sal_idx','var') == 1
0558         data(i,sec_sec_sal_idx) = str2num(avgcell{i}{sec_sec_sal_idx});
0559         names{sec_sec_sal_idx} = 'sal_sec_sec';
0560     end;
0561     if exist('pri_sec_sal_idx','var') == 1 
0562         data(i,pri_sec_sal_idx) = str2num(avgcell{i}{pri_sec_sal_idx});
0563         names{pri_sec_sal_idx} = 'sal_pri_sec';
0564     end;
0565     if exist('sec_pri_sal_idx','var') == 1
0566         data(i,sec_pri_sal_idx) = str2num(avgcell{i}{sec_pri_sal_idx});
0567         names{sec_pri_sal_idx} = 'sal_sec_pri';        
0568     end;
0569     if exist('pri_con_idx','var') == 1
0570         data(i,pri_con_idx) = str2num(avgcell{i}{pri_con_idx});
0571         names{pri_con_idx} = 'con_pri';                
0572     end;
0573     if exist('sec_con_idx','var') == 1
0574         data(i,sec_con_idx) = str2num(avgcell{i}{sec_con_idx});
0575         names{sec_con_idx} = 'con_sec';                
0576     end;
0577     if exist('pri_oxc_idx','var') == 1 
0578         data(i,pri_oxc_idx) = str2num(avgcell{i}{pri_oxc_idx});
0579         names{pri_oxc_idx} = 'oxc_pri';                
0580     end;
0581     if exist('sec_oxc_idx','var') == 1
0582         data(i,sec_oxc_idx) = str2num(avgcell{i}{sec_oxc_idx});
0583         names{sec_oxc_idx} = 'oxc_sec';                
0584     end;
0585     if exist('pri_oxt_idx','var') == 1
0586         data(i,pri_oxt_idx) = str2num(avgcell{i}{pri_oxt_idx});
0587         names{pri_oxt_idx} = 'oxt_pri';                
0588     end;
0589     if exist('sec_oxt_idx','var') == 1
0590         data(i,sec_oxt_idx) = str2num(avgcell{i}{sec_oxt_idx});
0591         names{sec_oxt_idx} = 'oxt_sec';                
0592     end;
0593     if exist('pri_do2_mmkg_idx','var') == 1 
0594         data(i,pri_do2_mmkg_idx) = str2num(avgcell{i}{pri_do2_mmkg_idx});
0595         names{pri_do2_mmkg_idx} = 'do2_pri';                
0596     end;
0597     if exist('sec_do2_mmkg_idx','var') == 1 
0598         data(i,sec_do2_mmkg_idx) = str2num(avgcell{i}{sec_do2_mmkg_idx});
0599         names{sec_do2_mmkg_idx} = 'do2_sec';                
0600     end;
0601     if exist('pri_do2_mll_idx','var') == 1
0602         data(i,pri_do2_mll_idx) = str2num(avgcell{i}{pri_do2_mll_idx});
0603         names{pri_do2_mll_idx} = 'do2_pri';                       
0604     end;
0605     if exist('sec_do2_mll_idx','var') == 1
0606         data(i,sec_do2_mll_idx) = str2num(avgcell{i}{sec_do2_mll_idx});
0607         names{sec_do2_mll_idx} = 'do2_sec';                               
0608     end;
0609     if exist('btl_fired_idx','var') == 1
0610         data(i,btl_fired_idx) = str2num(avgcell{i}{btl_fired_idx});
0611         names{btl_fired_idx} = 'bottle_fired_count';                                       
0612     end;
0613     if exist('scan_idx','var') == 1
0614         data(i,scan_idx) = str2num(avgcell{i}{scan_idx});
0615         names{scan_idx} = 'scan';                                       
0616     end;
0617     if exist('pri_odocdt_idx','var') == 1
0618         data(i,pri_odocdt_idx) = str2num(avgcell{i}{pri_odocdt_idx});
0619         names{pri_odocdt_idx} = 'odocdt_pri';                                       
0620     end;
0621     if exist('sec_odocdt_idx','var') == 1
0622         data(i,sec_odocdt_idx) = str2num(avgcell{i}{sec_odocdt_idx});
0623         names{sec_odocdt_idx} = 'odocdt_sec';                                       
0624     end;
0625     if exist('pri_sbedo2_mll_idx','var') == 1
0626         data(i,pri_sbedo2_mll_idx) = str2num(avgcell{i}{pri_sbedo2_mll_idx});
0627         names{pri_sbedo2_mll_idx} = 'sbedo2_mll_pri';                       
0628     end;
0629     if exist('sec_sbedo2_mll_idx','var') == 1
0630         data(i,sec_sbedo2_mll_idx) = str2num(avgcell{i}{sec_sbedo2_mll_idx});
0631         names{sec_sbedo2_mll_idx} = 'sbedo2_mll_sec';                               
0632     end;
0633     if exist('pri_sbedo2_mmkg_idx','var') == 1
0634         data(i,pri_sbedo2_mmkg_idx) = str2num(avgcell{i}{pri_sbedo2_mmkg_idx});
0635         names{pri_sbedo2_mmkg_idx} = 'sbedo2_mmkg_pri';                       
0636     end;
0637     if exist('sec_sbedo2_mmkg_idx','var') == 1
0638         data(i,sec_sbedo2_mmkg_idx) = str2num(avgcell{i}{sec_sbedo2_mmkg_idx});
0639         names{sec_sbedo2_mmkg_idx} = 'sbedo2_mmkg_sec';                               
0640     end;
0641    %CAF
0642    if exist('pot_temp_pri_idx','var') == 1
0643         data(i,pot_temp_pri_idx) = str2num(avgcell{i}{pot_temp_pri_idx});
0644         names{pot_temp_pri_idx} = 'pot_temp_pri';                               
0645     end;
0646     if exist('pot_temp_sec_idx','var') == 1
0647         data(i,pot_temp_sec_idx) = str2num(avgcell{i}{pot_temp_sec_idx});
0648         names{pot_temp_sec_idx} = 'pot_temp_sec';                               
0649     end;
0650     if exist('sbeox_pct_sat_pri_idx','var') == 1
0651         data(i,sbeox_pct_sat_pri_idx) = str2num(avgcell{i}{sbeox_pct_sat_pri_idx});
0652         names{sbeox_pct_sat_pri_idx} = 'sbeox_pct_sat_pri';                               
0653     end;
0654     if exist('sbeox_pct_sat_sec_idx','var') == 1
0655         data(i,sbeox_pct_sat_sec_idx) = str2num(avgcell{i}{sbeox_pct_sat_sec_idx});
0656         names{sbeox_pct_sat_sec_idx} = 'sbeox_pct_sat_sec';                               
0657     end;
0658     if exist('pri_sbedOC_dt_idx','var') == 1
0659         data(i,pri_sbedOC_dt_idx) = str2num(avgcell{i}{pri_sbedOC_dt_idx});
0660         names{pri_sbedOC_dt_idx} = 'sbeox_dOCdt_pri';                               
0661     end;
0662     if exist('sec_sbedOC_dt_idx','var') == 1
0663         data(i,sec_sbedOC_dt_idx) = str2num(avgcell{i}{sec_sbedOC_dt_idx});
0664         names{sec_sbedOC_dt_idx} = 'sbeox_dOCdt_sec';                               
0665     end;
0666     if exist('pri_sbeox_volt_idx','var') == 1
0667         data(i,pri_sbeox_volt_idx) = str2num(avgcell{i}{pri_sbeox_volt_idx});
0668         names{pri_sbeox_volt_idx} = 'sbeox_volt_pri';                               
0669     end;
0670     if exist('sec_sbeox_volt_idx','var') == 1
0671         data(i,sec_sbeox_volt_idx) = str2num(avgcell{i}{sec_sbeox_volt_idx});
0672         names{sec_sbeox_volt_idx} = 'sbeox_volt_sec';                               
0673     end;
0674      if exist('pct_sat_idx','var') == 1
0675         data(i,pct_sat_idx) = str2num(avgcell{i}{pct_sat_idx});
0676         names{pct_sat_idx} = 'pct_sat';                               
0677     end;
0678      if exist('pct_sat_sec_idx','var') == 1
0679         data(i,pct_sat_sec_idx) = str2num(avgcell{i}{pct_sat_sec_idx});
0680         names{pct_sat_sec_idx} = 'pct_sat_sec';                               
0681     end;
0682     %CAF
0683   % repeat the above construct as you discover more parameters which rossum outputs.
0684 end
0685 
0686 % Remove the empty cells from the names cell array
0687 % and the data matrix if the date_idx exists.
0688 offset = 0;
0689 if exist('date_idx','var') == 1
0690     data(:,[date_idx+1:date_idx+2]) = [];
0691     count = 1;
0692     for i = 1:(length(names))
0693         if ~isempty(names{i})
0694             tmp{count} = names{i};
0695             count = count + 1;
0696         end
0697     end
0698     names = tmp;
0699 end
0700     
0701 
0702 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
0703 %
0704 % Flag bad values with nan
0705 %
0706 if exist('bad_flag','var') == 1
0707     ind=find(data==bad_flag);
0708     data(ind)=data(ind)*nan;
0709 end
0710 
0711 
0712 btl_struct.lat = lat;
0713 btl_struct.lon = lon;
0714 btl_struct.gtime = gtime;
0715 btl_struct.sensors = char(sensors');
0716 % remove the spaces in the names cell
0717 for i = 1:length(names)
0718     str = names{i};
0719     idxspc = isspace(str);
0720     str(idxspc) = [];
0721     names{i} = str;
0722 end
0723 btl_struct.names = names;
0724 btl_struct.data = data;
0725 disp([btl_file,' loaded'])
0726 
0727 
0728 
0729 return
btl2mat_ab

PURPOSE

SYNOPSIS

DESCRIPTION

CROSS-REFERENCE INFORMATION

SOURCE CODE
