% AOML/PhOD CTDO2 calibration toolbox - contents file
% CTDCal.m - AOML PhOD CTDO2 calibration toolbox
% 
% Data Management
% ---------------
% load_bl.m - Read and save the SeaBird ASCII .BL file format
% load_btl.m - Read and save the SeaBird ASCII .BTL file format
% load_cnv_beckman.m - Load the information in the *.cnv files into the cruise database
% load_cnv.m - Load the information in the *.cnv files into the cruise database
% load_oxy.m - Load a *.oxy files from the AOML Winkler titration system
% load_salts.m - Load the autosal samples into the cruise database
% parse_cnv_data_all_beckman.m -parse data columns read in from raw CNV files 
% parse_cnv_data_all.m - parse data columns read in from raw CNV files 
% parse_cnv_data.m - data columns read in from raw CNV files 
% read_oxy.m - Load a *.oxy file from the AOML Winkler titration system
% read_sbebl.m - Reads the SeaBird ASCII .BL file format
% read_sbebtl.m - Reads the SeaBird ASCII .BTL file format
% read_sbecnv.m - Reads the SeaBird BINARY or ASCII *.cnv file format
% 
% non_lin_fit.m - Nonlinear least-squares data fitting by the Gauss-Newton method
% normalqqplot.m - plot quantiles of data vs quantiles of normal distribution
% normqqplot.m - plot quantiles of data vs quantiles of normal distribution
% quantile.m - quantiles of the data x
% 
% Calibration Routines
% --------------------
% apply_calibration.m - Apply oxygen and conductivity calibration 
% apply_calibration1.m - Apply oxygen and conductivity calibration
% cond_cal1.m - Conductivity calibration calling routine
% cond_cal2.m - Conductivity calibration calling routine
% cond_cal.m - Conductivity calibration calling routine
% cond_cal_ORIGINAL.m - Conductivity calibration calling routine
% FS_apply_calibration.m - Apply oxygen and conductivity calibration 

% make_bottle_file.m - Apply oxygen and conductivity calibration 

% make_cond_sumfile.m - Makes conductivity bottle/ctd comparison summary file

% make_woce_bottle_file.m - Apply oxygen and conductivity calibration 
% make_woce_bottle_file_beckman.m - Apply oxygen and conductivity calibration 

% oxy_cal_beckman.m - Oxygen calibration calling routine
% oxy_cal.m - Oxygen calibration calling routine
% oxygen_fit_linear_beckman.m - to calculate the dissolved oxygen
% oxygen_fit_linear.m - to calculate the dissolved oxygen
% oxygen_fit_linearp_beckman.m - to calculate the dissolved oxygen
% oxygen_fit_linearp.m - to calculate the dissolved oxygen
% oxygen_fit_none_beckman.m - to calculate the dissolved oxygen
% oxygen_fit_none.m - to calculate the dissolved oxygen
% oxygen_fit_poly2_beckman.m - to calculate the dissolved oxygen
% oxygen_fit_poly2.m - to calculate the dissolved oxygen
% oxygen_fit_poly2p_beckman.m - to calculate the dissolved oxygen
% oxygen_fit_poly2p.m - to calculate the dissolved oxygen
% oxygen_fit_pres.m - to calculate the dissolved oxygen
% oxygen_fit_press_beckman.m - to calculate the dissolved oxygen
% 
% weim.m - Running weighted average of input data given a window
% ox_units.m - converts between 3 different oxygen units
% 
% Sensor Correction
% -----------------
% correct_autosal_drift.m - Correct for autosal drift with pre/post standard water analyses
% correct_pressure.m - Apply the correction for temperature sensors
% correct_temp.m - Apply the correction for temperature sensors
% deloop_beckman.m - Similar to LOOPEDIT on Seabird Data Processing
% deloop.m - Similar to LOOPEDIT on Seabird Data Processing
% despike1_beckman.m - Remove spikes in the primary sensors
% despike1.m - Remove spikes in the primary sensors
% despike2_beckman.m - Remove spikes in the secondary sensors
% despike2.m - Remove spikes in the secondary sensors
% fill_surface_beckman.m - Fill the CTD data up to the surface
% fill_surface.m - Fill the CTD data up to the surface
% 
% print_cal_figures.m - Print the output figures that come from FS_apply_calibration.m
% print_compare_cond.m - Print the output figures that come from compare_cond.m
% print_compare_ctd_sensors.m - Print the output figures that come from compare_ctd_sensors.m
% print_compare_oxy.m - Print the output figures that come from compare_oxy.m
% print_cond_cal.m - Print the output figures that come from cond_cal.m
% print_oxy_cal.m - Print the output figures that come from oxy_cal.m
% 
% Graphic Tools
% -------------
% boxparams_deep.m - calculate boxplot parameters for data vector x
% boxparams.m - calculate boxplot parameters for data vector x
% boxplotter1.m - make box or whisker plots
% 
% compare_cond.m - Diagnostics plots to compare conductivity values between CTD and bottle samples. 
% compare_ctd_sensors.m - Diagnostics plots to compare the sensors (conductivity, dissolved oxygen 
% compare_oxy.m - Diagnostics plots to compare CTD and samples dissolved oxygen values
% compare_tsplot.m - Makes ts-plots 
% compare_tsplot_original.m - Makes ts-plots
% plot_sensors_diff_beckman.m - Diagnostics plots to compare differences between the sensors
% plot_sensors_diff.m - Diagnostics plots to compare differences between the sensors
% 
% floatAxisX.m - create floating x-axis for multi-parameter plot
% floatAxisY.m - create floating y-axis for multi-parameter plot
% 
% window.m - Return a window of a given shape for smoothing data
% 
% Text and Matrix Manipulation
% ----------------------------
% ddeblank.m - Double deblank. Strip both leading and trailing blanks
% ddewhite.m - Double dewhite. Strip both leading and trailing whitespace
% meanmiss.m - Column matrix means with missing data
% 
% Station/Cruise Management
% -------------------------
% group_name.m - Get the preference group name for a given cruiseid
% make_cruise_dir.m - Setup a new working directory for CTD calibration
% make_cruise_dir_old.m - Setup a new working directory for CTD calibration
% make_oxy_sumfile_beckman.m - Makes oxygen bottle/ctd comparison summary file
% make_oxy_sumfile.m - Makes oxygen bottle/ctd comparison summary file
% oxy_struct.m - Return an empty oxygen calibration struct with minimum required fields
% rg_register_cruise.m - Input and manage cruise meta-data prior to calibration
% sample_struct.m - Return an empty data structure with the minimum required fields
% save_final_results.m - Apply oxygen and conductivity calibration and save
% write_aoml3.m - Write hydrographic profile data into aoml ascii format
% 
% ------------------------------------------------------------
% The following have bad help information. They need fixing up!
% 
% check_cal.m - script which does some cruise specific checking 
% cleaner.m - cleans up a data record
% cruise_setup.m - script to SETUP a CRUISE for data collection of LADCP, CTD,
% ctd_complete_process.m - script does the complete calibration process to the CTD data
% eval_fit.m - Looks like a one-off concoction for doing something
% FS_map_with_cast.m - script plots a map of the study region and adds on cable locations
% glitch.m - finds 'glitches' (?) in trace?
% linreg1.m - solves directly for the coefficients in linear model 
% linregctd.m - solves linear regression
% linreg.m - computes linear regression of y on x
% makeaxis.m - creates an axis of the size input in inches (sets some defaults)
% makefig.m - function creates full page figure
% make_plots.m - makes a series of plots of CTD data
% nan_mean.m - mean of data ignoring NaNs
% nan_std.m - std dev of data ignoring NaNs
% oxy_fit_linear_beckman.m - fit Beckman sensor to oxygen data
% oxy_fit_linear.m - fit oxygen sensor to oxygen data
% oxy_fit_linearp_beckman.m - fit Beckman sensor to oxygen data
% oxy_fit_linearp.m - fit oxygen sensor to oxygen data
% oxy_fit_none_beckman.m - fit Beckman sensor to oxygen data 
% oxy_fit_none.m - fit oxygen sensor to oxygen data
% oxy_fit_poly2_beckman.m - fit Beckman sensor to oxygen data 
% oxy_fit_poly2.m - fit oxygen sensor to oxygen data
% oxy_fit_poly2p_beckman.m - fit Beckman sensor to oxygen data 
% oxy_fit_poly2p.m - fit oxygen sensor to oxygen data
% oxy_fit_pres.m - fit oxygen sensor to oxygen data including pressure dep
% oxy_fit_press_beckman.m - fit Beckman sensor to oxygen data including pressure dep
% plot_sensors_residuals.m - plot sensor residuals
% save_plots.m - plot multiple parameters on same page
% t68tot90.m - Converts temperature from ITPS-68 to ITS-90
% t90tot68.m - Converts temperature from ITPS-90 to ITS-68
% 

% Bad Files, Typos
% 
% make_botlle_file.m - Apply oxygen and conductivity calibration 

% Contents file for ctdcal directory constructed from comments
% in m-files
%
%PROGRAM - 	MATLAB code by c.m.duncombe rae
%
%CREATED -	2007/11/09
%
%VERSION:
%	$Revision: 1.2 $
%	$Date: 2008/01/19 19:22:46 $
% 
%PROG MODS -	
% 		2007/12/19 CMDR
%		* introduce version tracking with RCS
%
%DISCLAIMER -	No responsibility can be accepted for failure or 
%		incorrect operation of this code. No guarantee, express 
%		or implied, is given. 
%

