load_salts: Load the autosal samples into the cruise database.
CTD Calibration toolbox
INPUT:
cruiseid: character array containing the cruise id.
OUTPUT:
theSalts: Combined salinity structure
DESCRIPTION:
This file may need to be edited for each new cruise. It attempts to do four things,
each of which may be cruise dependent. First, it reads the Ron Brown autosal
dat and raw analysis files. Second, it attempts to recompute an average sample
bottle salinity by performing a more thorough quality control analysis than is done
by the autosal logging software. Third, it corrects for a linear drift in the autosal
between two standardizations using standard seawater samples. Finally, the cruise
database is updated with the results. Eventually it will become more cruise independent.
AUTHOR:
Derrick Snowden and Carlos Fonseca
NOAA/AOML/PhOD
Fri Oct 01 18:32:14 EDT 2004
CHANGELOG:
08-Jul-2004, Version 1.0
* Initial version.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%0001 function theResult = load_salts(cruiseid) 0002 % load_salts: Load the autosal samples into the cruise database. 0003 % 0004 % CTD Calibration toolbox 0005 % 0006 % INPUT: 0007 % cruiseid: character array containing the cruise id. 0008 % 0009 % OUTPUT: 0010 % theSalts: Combined salinity structure 0011 % 0012 % DESCRIPTION: 0013 % This file may need to be edited for each new cruise. It attempts to do four things, 0014 % each of which may be cruise dependent. First, it reads the Ron Brown autosal 0015 % dat and raw analysis files. Second, it attempts to recompute an average sample 0016 % bottle salinity by performing a more thorough quality control analysis than is done 0017 % by the autosal logging software. Third, it corrects for a linear drift in the autosal 0018 % between two standardizations using standard seawater samples. Finally, the cruise 0019 % database is updated with the results. Eventually it will become more cruise independent. 0020 % 0021 % 0022 % AUTHOR: 0023 % Derrick Snowden and Carlos Fonseca 0024 % NOAA/AOML/PhOD 0025 % Fri Oct 01 18:32:14 EDT 2004 0026 % 0027 % CHANGELOG: 0028 % 08-Jul-2004, Version 1.0 0029 % * Initial version. 0030 % 0031 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 0032 0033 % Check for correct number of inputs. 0034 error(nargchk(1,1,nargin)) 0035 0036 % Retrieve the necessary preferences for this cruise 0037 group = group_name(cruiseid); 0038 0039 % btl_dir is the calibration data directory 0040 if ispref(group,'cal_autosal_dir') 0041 cal_autosal_dir=getpref(group,'cal_autosal_dir'); 0042 else 0043 error(['The cal_autosal_dir preference was not set for cruise: ' cruiseid '. Run register_cruise.m']); 0044 end 0045 0046 % cruise_dir is the calibration data directory 0047 if ispref(group,'cal_data_dir') 0048 cruise_dir=getpref(group,'cal_data_dir'); 0049 else 0050 error(['The cal_data_dir preference was not set for cruise: ' cruiseid '. Run register_cruise.m']); 0051 end 0052 0053 % This file will contain the summary information 0054 % It is currently buggy and may not work. Nevertheless, it is intended 0055 % to be different for each cruise EDIT 0056 sumfile = fullfile(cal_autosal_dir,'salinity_summary.txt'); 0057 0058 % EDIT 0059 year = 2002; 0060 0061 % EDIT If you have more than one batch of standard water per cruise you may 0062 % need to include this in the loop below and change it for each autosal file. 0063 nominal_std_conductivity = 1.999; % This is fake for testing only.... 0064 std_water_label = '141'; 0065 mnth = 2; 0066 day =20; 0067 0068 % The cruise database. Don't edit this line. 0069 db_file = fullfile(cruise_dir,[cruiseid '_db.mat']); 0070 0071 % EDIT Maybe. The following two lines should be pretty standard on the Brown. 0072 dat_files = dir(fullfile(cal_autosal_dir,'*.dat')); 0073 raw_files = dir(fullfile(cal_autosal_dir,'*.raw')); 0074 0075 for idx_file = 1:length(dat_files) 0076 [pathstr,namestr,ext,vers] = fileparts(dat_files(idx_file).name); 0077 % EDIT The file naming convention I have encountered is MMDDHH or 2 dgit monthe 0078 % two digit day and two digit gmt hour at which the autosal analysis was performed. 0079 %[mnth,day,gmthr] = strread(namestr,'%02d%02d%02d'); 0080 this_dat = fullfile(cal_autosal_dir,dat_files(idx_file).name); 0081 this_raw = fullfile(cal_autosal_dir,raw_files(idx_file).name); 0082 % EDIT The raw files are pretty standard and should not need to be edited often. 0083 raw = read_autosal_raw(this_raw); 0084 % EDIT The dat files are likely different on each cruise. 0085 % Take an example read_autosal_dat_*.m and edit it according to your current configuration 0086 % then include it in the line below. NOTE it MUST have the same input/output syntax as 0087 % examples. 0088 salts = read_autosal_dat(this_dat,std_water_label,[year mnth day]); % specialized for your cruise 0089 % If you've done the read_autosal_dat correctly, the followind two lines will work. 0090 autosal=match_autosal_raw_dat(salts,raw,sumfile,[year mnth day]) 0091 cond = correct_autosal_drift(nominal_std_conductivity,autosal,sumfile); 0092 keyboard 0093 % Everything works to here for stc02. 0094 % 1. Concatentate the samples together so that they don't overwrite each other when 0095 % saved to the db_file. 0096 % 2. Verify that the autosal struct above is what carlos needs for the make_cond_sumfile. 0097 % 0098 end 0099 0100 0101 % Open the output file 0102 if exist(db_file)==2 0103 save(db_file,'cond','-append'); 0104 else 0105 save(db_file,'cond'); 0106 end 0107 if nargout==0 0108 assignin('caller','ans',cond); 0109 return 0110 else 0111 varargout{1}=cond; 0112 return 0113 end 0114 % 0115