OutputManager.m

%% OutputManager - SCRIPT which takes processed data, saved as an 
% ProcessedData object called "pd" and outputs SeaBASS data files and plots
%
%
% Requires: the .mat file saved in ProcessingManager, if not in memory
%
% Outputs:  SeaBASS txt files
%
% Other m-files required: readIngestParameters, ProcessedData, 
% Subfunctions: checkTimestamps
% MAT-files required: "acsPROC_(YEAR)_(DAY)" saved by PreProcessingManager,
%  "acsPREPROC_(YEAR)_(DAY)" saved by PreProcessingManager
%
% See also: readIngestParameters, ProcessedData, checkTimestamps
% 
% Author: Wendy Neary
% MISCLab, University of Maine
% email address: wendy.neary@maine.edu 
% Website: http://misclab.umeoce.maine.edu/index.php
% May 2015; Last revision: 4-Mar-16
% June 2016 - added bin_count and units to output files.
% July 2016 - changed to use new data
% Aug 2016 - removed bin_count wavelength-specific columns.

%----------------------------- BEGIN CODE ---------------------------------
%%Load data file from disk if necessary

if params.RUN.LOAD_OUTPUT_DATA_FROM_DISK

    matFileName = fullfile(params.INGEST.DATA_OUTPUT_DIRECTORY, ...
        strcat('acsPROC', '_', num2str(params.INGEST.YEAR), '_', num2str(params.INGEST.YEAR_DAY)));
    load(matFileName);
    clear matFileName;

    matFileName = fullfile(params.INGEST.DATA_OUTPUT_DIRECTORY, ...
        strcat('acsPREPROC', '_', num2str(params.INGEST.YEAR), '_', num2str(params.INGEST.YEAR_DAY)));
    load(matFileName); 
    clear matFileName;
    
end;

   
%% ----------------------------------------------------------------------- 
% SECTION 1: OUTPUT SEABASS FILES
% -----------------------------------------------------------------------

% VARIABLES TO GO IN PARAMS:

% ----------------------------------------------------------------------
% PART 1: GET DATA READY
% ----------------------------------------------------------------------

% get variables needed for output:
% ap, cp, ap_std, cp_std
% get timestamps - % this should be coming from L9 now.
ap_timestamps = pd.getVar('name', 'ap', 'data', 'timestamps');
cp_timestamps = pd.getVar('name', 'cp', 'data', 'timestamps');

% get ap - for each correction - more than one correction is possible
% this should be coming from L9 now.
if params.PROCESS.SCATTERING_CORR_SLADE
    ap_data_slade = pd.getVar('name', 'ap', 'data', 'data_slade'); %, 'level', 'corrected');
end;
if params.PROCESS.SCATTERING_CORR_ROTTGERS
    ap_data_rottgers = pd.getVar('name', 'ap', 'data', 'data_rottgers'); %, 'level', 'corrected');
end;
if params.PROCESS.SCATTERING_CORR_FLAT
    ap_data_flat = pd.getVar('name', 'ap', 'data', 'data_flat'); %, 'level', 'corrected');
end;

% get cp - this should be coming from L9 now.
cp_data = pd.getVar('name', 'cp', 'data', 'cp_data'); %, 'level', 'corrected');

% get ap uncertainty
% there can be more than one correction calculated - but we can only report
% one to seabass
% July2016 - Not using this anymore for SeaBASS
% if params.PROCESS.AP_UNCERTAINTY_BETWEEN_CORRECTIONS
%     ap_uncertainty = pd.getVar('name', 'ap', 'data', 'uncertainty_between_corrections', 'level', 'corrected');
% else
%     ap_uncertainty = pd.getVar('name', 'ap', 'data', 'uncertainty', 'level', 'corrected');
% end;
    
% get cp uncertainty
% July2016 - Not using this anymore for SeaBASS
% cp_uncertainty = pd.getVar('name', 'cp', 'data', 'uncertainty');

% added 3/3
% get std
cp_std_to_print = pd.getVar('name', 'cp', 'data', 'cp_std');
ap_std_to_print = pd.getVar('name', 'ap', 'data', 'ap_std');

% added 4/5/16
% JULY 16 - THIS NEEDS TO BE DESPIKED DATA BIN COUNT
cp_bin_count = pd.getVar('name', 'cp', 'data', 'cp_bin_count');
cp_bin_count = cp_bin_count(:,1);
ap_bin_count = pd.getVar('name', 'ap', 'data', 'ap_bin_count');
ap_bin_count = ap_bin_count(:,1);

% GET ANCILLARY DATA: Temperature, Salinity, GPS
temp_data = allData.TemperatureData.var.L3.BinnedLabTempData;
temp_timestamps = allData.TemperatureData.var.L3.BinnedTimestamps;
sal_timestamps = allData.SalinityData.var.L3.BinnedTimestamps;
sal_data = allData.SalinityData.var.L3.BinnedData;
lat_data = allData.GPSData.var.L3.BinnedLatData;
lon_data = allData.GPSData.var.L3.BinnedLonData;
gps_timestamps = allData.GPSData.var.L3.BinnedTimestamps;

% should all be the same
wavelengths = pd.var.ap.L7.wavelengths_slade;

%%
% check timestamps are all the same
% CHANGED 10/22
if checkTimestamps(ap_timestamps, cp_timestamps)
    L.debug('OutputManager', 'a and c timestamps same')
else
    L.error('OutputManager', 'a and c timestamps diff')
end;
if checkTimestamps(ap_timestamps, temp_timestamps)
    L.debug('OutputManager', 'a and temp timestamps same')
else
    L.error('OutputManager', 'a and temp timestamps diff')
end;
if checkTimestamps(ap_timestamps, gps_timestamps)
    L.debug('OutputManager', 'a and gps timestamps same')
else
    L.error('OutputManager', 'a and gps timestamps diff')
end;
if checkTimestamps(ap_timestamps, sal_timestamps)
    L.debug('OutputManager', 'a and sal timestamps same')
else
    L.error('OutputManager', 'a and sal timestamps diff')
end;

%%
goodrows = logical(isfinite(ap_data_slade(:,20)) .* isfinite(lat_data) .* ...
    isfinite(cp_data(:,20)));

%%
% Replace values below 0.005 with -9999
replaceWith999Index = cp_data < -0.005;
numReplaced = sum(replaceWith999Index);
totalNumReplaced = sum(numReplaced);
L.info('OutputManager', sprintf('Replaced %u values in cp_data with -9999', totalNumReplaced)); 

cp_data(replaceWith999Index) = -9999;
cp_uncertainty(replaceWith999Index) = -9999;
cp_std_to_print(replaceWith999Index) = -9999;

if params.PROCESS.SCATTERING_CORR_SLADE
    replaceWith999Index = ap_data_slade < -0.005;
    numReplaced = sum(replaceWith999Index);
    totalNumReplaced = sum(numReplaced);
    L.info('OutputManager', sprintf('Replaced %u values in ap_data_slade with -9999', totalNumReplaced));
    ap_data_slade(replaceWith999Index) = -9999;
end

if params.PROCESS.SCATTERING_CORR_ROTTGERS
    replaceWith999Index = ap_data_rottgers < -0.005;
    numReplaced = sum(replaceWith999Index);
    totalNumReplaced = sum(numReplaced);
    L.info('OutputManager', sprintf('Replaced %u values in ap_data_rottgers with -9999', totalNumReplaced));
    ap_data_rottgers(replaceWith999Index) = -9999;
end

if params.PROCESS.SCATTERING_CORR_FLAT
    replaceWith999Index = ap_data_flat < -0.005;
    numReplaced = sum(replaceWith999Index);
    totalNumReplaced = sum(numReplaced);
    L.info('OutputManager', sprintf('Replaced %u values in ap_data_flat with -9999', totalNumReplaced));    
    ap_data_flat(replaceWith999Index) = -9999;
end
ap_uncertainty(replaceWith999Index) = -9999;
ap_std_to_print(replaceWith999Index) = -9999;
    
% bin_tempc(isnan(bin_tempc)) = -9999;
replaceWith999Index = isnan(temp_data);
numReplaced = sum(replaceWith999Index);
totalNumReplaced = sum(numReplaced);
L.info('OutputManager', sprintf('Replaced %u values in temp_data with -9999', totalNumReplaced));  
temp_data(replaceWith999Index) = -9999;

replaceWith999Index = isnan(sal_data);
numReplaced = sum(replaceWith999Index);
totalNumReplaced = sum(numReplaced);
L.info('OutputManager', sprintf('Replaced %u values in sal_data with -9999', totalNumReplaced));  
sal_data(replaceWith999Index) = -9999;

% get start and end dates and times
% same for all files for this yearday
timestamps = cellstr(datestr(ap_timestamps));
temp_date = datestr(datenum(timestamps),'yyyymmdd');
temp_time = datestr(datenum(timestamps),'HH:MM:SS');
timestamps_date_to_print = cellstr(temp_date(goodrows,:));
timestamps_time_to_print = cellstr(temp_time(goodrows,:));

% same for all files for this yearday - NEEDS TO BE DONE AFTER BADROWS
% FILTERED OUT
start_date = timestamps_date_to_print{1,1};
end_date = timestamps_date_to_print{end,1};
start_time = timestamps_time_to_print{1,1};
end_time = timestamps_time_to_print{end,1};

% ----------------------------------------------------------------------
% PART 2: PRODUCE HEADER
% ----------------------------------------------------------------------
% ----------------------------------------------------------------------
% Step 1: Set up variables
% ----------------------------------------------------------------------
sb_fname_xls = [params.OUTPUT.SEABASS_FILE_PREFIX ...
    num2str(params.INGEST.YEAR) '_' num2str(params.INGEST.YEAR_DAY) '.xls'];
sb_fname_ascii = [params.OUTPUT.SEABASS_FILE_PREFIX ...
    num2str(params.INGEST.YEAR) '_' num2str(params.INGEST.YEAR_DAY)];
cruise = strrep(params.INGEST.CRUISE_LEG, ' ', '');

if params.OUTPUT.USE_SLADE
    data_type = {ap_data_slade, cp_data};
elseif params.OUTPUT.USE_ROTTGERS
    data_type = {ap_data_rottgers, cp_data};
elseif params.OUTPUT.USE_FLAT
    data_type = {ap_data_flat, cp_data};
else
    L.error('OutputManager','No ap data chosen for output');
end;

std_type = {ap_std_to_print, cp_std_to_print};
binCount_type = {ap_bin_count, cp_bin_count};
dataFiles = {'ap', 'cp'};
wlPrefix = {'ap', 'cp'};

if ~exist(params.INGEST.DATA_OUTPUT_DIRECTORY, 'dir')
    mkdir(params.INGEST.DATA_OUTPUT_DIRECTORY)
    L.info('OutputManager','made new direcotry for output');
end;
%%
for iData = 1:length(data_type)
    % ----------------------------------------------------------------------
    % Step 2: Create Header
    % ----------------------------------------------------------------------
    thisData = data_type{iData}; %ap_data_slade;
    thisSTD = std_type{iData};
    thisBinCount = binCount_type{iData};
    thisFileName = dataFiles{iData}; %;
    thisPrefix = wlPrefix{iData}; %;

    data_to_print = [lat_data lon_data temp_data sal_data thisData thisSTD thisBinCount];
    data_to_print = data_to_print(goodrows,:);
    
    data_size(:,:) = size(data_to_print);
    if data_size(1) == 0
        L.error('OutputManager', 'ERROR - NO DATA TO OUTPUT FOR SEABASS FILES');
        continue;
    end;

    northLat = max(data_to_print(:,1));
    southLat = min(data_to_print(:,1));
    eastLon = max(data_to_print(:,2));
    westLon = min(data_to_print(:,2));
    
    % create list of units, get rid of last ','
    apcp_units = char(repmat(uint8(strcat(params.INGEST.AC_UNITS, ',')),...
        1, 2*(length(wavelengths))));
    % create units for bin_count
    units_to_print = strcat(apcp_units, 'none');


    
    % build the extension name from the dataFile
    extension = strcat(thisFileName, '.txt');
    seabassFileName = fullfile(params.INGEST.DATA_OUTPUT_DIRECTORY, strcat(sb_fname_ascii, extension));

    sb_hdr = {'date', 'time', 'lat', 'lon', 'Wt', 'sal'};
    % put all these fields into a matrix
    sb_hdr = [sb_hdr strcat(thisPrefix, cellstr(num2str(wavelengths)))' ...
        strcat(thisPrefix, cellstr(num2str(wavelengths)), '_sd')' 'bincount'];
    % remove whitespace
    sb_hdr = strrep(sb_hdr, ' ', '');

    % name file
    fid = fopen(seabassFileName, 'w', 'n', 'US-ASCII');
    
    if fid ~= -1
        fprintf(fid,'/begin_header\n');
        fprintf(fid,'/investigators=%s\n', params.OUTPUT.INVESTIGATOR );
        fprintf(fid,'/affiliations=%s\n', params.OUTPUT.AFFILIATION );
        fprintf(fid,'/contact=%s\n', params.OUTPUT.CONTACT);
        fprintf(fid,'/experiment=%s\n', params.OUTPUT.EXPERIMENT);
        fprintf(fid,'/cruise=');
        fprintf(fid,cruise);
        fprintf(fid,'\n');
        fprintf(fid,'/station=NA\n');
        fprintf(fid,'/data_file_name=');
        fprintf(fid,strcat(sb_fname_ascii,extension));
        fprintf(fid,'\n');
        fprintf(fid,'/documents=%s\n', params.OUTPUT.DOCUMENTATION);
        fprintf(fid,'/calibration_files=%s\n', params.OUTPUT.CALIBRATION_FILES);
        fprintf(fid,'/data_type=%s\n', params.OUTPUT.DATA_TYPE);
        fprintf(fid,'/data_status=%s\n', params.OUTPUT.DATA_STATUS);
        fprintf(fid, '/start_date=%s\n', start_date);
        fprintf(fid, '/end_date=%s\n', end_date);
        fprintf(fid,'/start_time=%s[GMT]\n', start_time);
        fprintf(fid,'/end_time=%s[GMT]\n', end_time);
        fprintf(fid,'/north_latitude=%5.3f[DEG]\n', northLat);
        fprintf(fid,'/south_latitude=%5.3f[DEG]\n', southLat);
        fprintf(fid,'/east_longitude=%5.3f[DEG]\n', eastLon);
        fprintf(fid,'/west_longitude=%5.3f[DEG]\n', westLon);
        fprintf(fid,'/water_depth=NA\n');
        fprintf(fid,'/measurement_depth=%s\n', params.OUTPUT.MEASUREMENT_DEPTH); % not allowed if depth is in the data
        fprintf(fid,'/secchi_depth=NA\n');
        fprintf(fid,'/cloud_percent=NA\n');
        fprintf(fid,'/wind_speed=NA\n');
        fprintf(fid,'/wave_height=NA\n');
        fprintf(fid,'/missing=-9999\n');
        fprintf(fid,'/delimiter=space\n');
        % new 9/8/16
        fprintf(fid, '!\n');
        fprintf(fid, '! COMMENTS\n');
        fprintf(fid, '!\n');
        fprintf(fid, '! Filters used for designating bins as SUSPECT:\n');
        comment_1 = 'abs(TSW_bin_median - TSW_bin_mean))./(TSW_bin_median-FSW_interp_median) > max(';
        comment_2 = ', ';
        comment_3 = ' ./(TSW_bin_median-FSW_interp_median))';
        fprintf(fid, '! mean/median filter:');
        fprintf(fid, '%s %5.3f %s %5.3f %s\n', comment_1, ...
            params.PROCESS.MEAN_MEDIAN_FILTER_1, ...
            comment_2, params.PROCESS.MEAN_MEDIAN_FILTER_2, ...
            comment_3);
        fprintf(fid, '! std filter: std_fail_index = TSW_bin_std > stdThreshold\n');
        fprintf(fid, '! where stdThreshold = %5.3f for a and %5.3f for c\n', ...
            params.PROCESS.a_STD_THRESH, params.PROCESS.c_STD_THRESH);
        fprintf(fid, '!\n');
        fprintf(fid,'/fields=');
        for j=1:length(sb_hdr)
            if j < length(sb_hdr)
                fprintf(fid, '%s,',cell2mat(sb_hdr(j)));
            else
                fprintf(fid, '%s',cell2mat(sb_hdr(j)));
            end;
        end
        fprintf(fid,'\n');
        fprintf(fid,['/units=yyyymmdd,hh:mm:ss,degrees,degrees,degreesC,PSU,' units_to_print '\n']);
        fprintf(fid,'/end_header\n');

        % ----------------------------------------------------------------------
        % Step 3: Create Data
        % ----------------------------------------------------------------------

        [nRows, ~]=size(data_to_print);
        for thisRow = 1:nRows
            fprintf(fid, '%8s ', cell2mat( timestamps_date_to_print( thisRow,1 )));
            fprintf(fid, '%8s ', cell2mat( timestamps_time_to_print( thisRow,1 )));

            % print all columns except last with a space after
            fprintf(fid,'%6.4f ', data_to_print(thisRow,1:end-1));
            
            % print last column without a space
            fprintf(fid,'%6.4f', data_to_print(thisRow,end));
            fprintf(fid,'\n');
        end
        fclose(fid);
        clear seabassFileName;
    else
        L.error('Outputmanager', sprintf('Failed to open file: %s', seabassFileName));
    end;
    
end   % for loop for data


%% ---------------------------------------------------------------------- 
% SECTION 2: CREATE FINAL PLOTS
% -----------------------------------------------------------------------
%%
fignum = 41;
wavelengthToPlot = 20;

figure(fignum);
ax1 = subplot(2,1,1);
hold on;
grid on;
plot(pd.var.c.L1.timestamps, pd.var.c.L1.data(:, wavelengthToPlot), 'b');
scatter(pd.var.cFSW.L3.binnedTime, pd.var.cFSW.L3.median(:,20), 5, 'o', 'fill', 'MarkerFaceColor', 'green', 'MarkerEdgeColor','green');
xlabel('Timestamps');
ylabel('c Data');
dynamicDateTicks;
xlim([ datenum(params.INGEST.YEAR, params.INGEST.MONTH, params.INGEST.DAY, 0, 0, 0) ,...
       datenum(params.INGEST.YEAR, params.INGEST.MONTH, params.INGEST.DAY + 1, 0, 0, 0) ] );
% ylim([-0.1, .5])
legend('Synchronized c data', 'FSW Bins');
title_text = sprintf('Filtered c Data - using median\n Cruise: %s Leg: %s \n%u-%s-%u (Yearday: %u)', ...
    params.INGEST.CRUISE, params.INGEST.CRUISE_LEG, params.INGEST.DAY, ...
    params.INGEST.MONTH_TEXT, params.INGEST.YEAR, params.INGEST.YEAR_DAY);    
title(title_text,'fontsize',12);

ax2 = subplot(2,1,2);
hold on;
grid on;
plot(pd.var.a.L1.timestamps, pd.var.a.L1.data(:, wavelengthToPlot), 'b');
scatter(pd.var.aFSW.L3.binnedTime, pd.var.aFSW.L3.median(:,20), 5, 'o', 'fill', 'MarkerFaceColor', 'green', 'MarkerEdgeColor','green');
xlabel('Timestamps');
ylabel('a Data');
dynamicDateTicks;
xlim([ datenum(params.INGEST.YEAR, params.INGEST.MONTH, params.INGEST.DAY, 0, 0, 0) ,...
       datenum(params.INGEST.YEAR, params.INGEST.MONTH, params.INGEST.DAY + 1, 0, 0, 0) ] );
% ylim([ -0.05, 0.15])
legend('Synchronized a data', 'FSW Bins');
title_text = sprintf('Filtered a Data - using median\n Cruise: %s Leg: %s \n%u-%s-%u (Yearday: %u)', ...
    params.INGEST.CRUISE, params.INGEST.CRUISE_LEG, params.INGEST.DAY, ...
    params.INGEST.MONTH_TEXT, params.INGEST.YEAR, params.INGEST.YEAR_DAY);
title(title_text,'fontsize',12);

linkaxes([ax1, ax2], 'x')
saveas(gcf,  fullfile(params.INGEST.DATA_OUTPUT_DIRECTORY, strcat(num2str(params.INGEST.YEAR), ...
    '_', num2str(params.INGEST.YEAR_DAY),  '_filtered')));
saveas(gcf,  fullfile(params.INGEST.DATA_OUTPUT_DIRECTORY, strcat(num2str(params.INGEST.YEAR), ...
    '_', num2str(params.INGEST.YEAR_DAY), '_filtered.jpg')));
    
%% FIGURE 2: "PEACHY"
fignum = 42;
figure(fignum);
ax1 = subplot(2,1,1);
hold on;
grid on;
plot(pd.var.c.L1.timestamps, pd.var.c.L1.data(:, wavelengthToPlot), 'k');
scatter(pd.var.cTSW.L3.binnedTime, pd.var.cTSW.L3.median(:,20), 5, 'o', 'MarkerFaceColor', 'green', 'MarkerEdgeColor','green');
scatter(pd.var.cFSW.L4.binnedTime, pd.var.cFSW.L4.interpolatedData(:,20),10,'o','fill','MarkerEdgeColor','blue');
xlabel('Timestamps');
ylabel('c Data');
dynamicDateTicks;
xlim([ datenum(params.INGEST.YEAR, params.INGEST.MONTH, params.INGEST.DAY, 0, 0, 0) ,...
       datenum(params.INGEST.YEAR, params.INGEST.MONTH, params.INGEST.DAY + 1, 0, 0, 0) ] );
% ylim([ -0.05, 0.5])
legend('Synchronized c data', 'TSW Bins', 'Interpolated data');
    title_text = sprintf('Interpolated Filtered c Data - using median\n Cruise: %s Leg: %s \n%u-%s-%u (Yearday: %u)', ...
    params.INGEST.CRUISE, params.INGEST.CRUISE_LEG, params.INGEST.DAY, ...
    params.INGEST.MONTH_TEXT, params.INGEST.YEAR, params.INGEST.YEAR_DAY);
title(title_text,'fontsize',12);

% dynamicDateTicks;
ax2 = subplot(2,1,2);
hold on;
grid on;
plot(pd.var.a.L1.timestamps, pd.var.a.L1.data(:, wavelengthToPlot), 'k');
scatter(pd.var.aTSW.L3.binnedTime, pd.var.aTSW.L3.median(:,20), 5, 'o', 'fill', 'MarkerFaceColor', 'green', 'MarkerEdgeColor','green');
scatter(pd.var.aFSW.L4.binnedTime, pd.var.aFSW.L4.interpolatedData(:,20), 5, 'fill', 'MarkerEdgeColor', 'blue');
xlabel('Timestamps');
ylabel('a Data');
dynamicDateTicks;
xlim([ datenum(params.INGEST.YEAR, params.INGEST.MONTH, params.INGEST.DAY, 0, 0, 0) ,...
       datenum(params.INGEST.YEAR, params.INGEST.MONTH, params.INGEST.DAY + 1, 0, 0, 0) ] );
% ylim([ -0.03, 0.5])
legend('Synchronized a data', 'TSW Bins', 'Interpolated data');
    title_text = sprintf('Interpolated Filtered a Data - using median\n Cruise: %s Leg: %s \n%u-%s-%u (Yearday: %u)', ...
    params.INGEST.CRUISE, params.INGEST.CRUISE_LEG, params.INGEST.DAY, ...
    params.INGEST.MONTH_TEXT, params.INGEST.YEAR, params.INGEST.YEAR_DAY);
title(title_text,'fontsize',12);
% 
 linkaxes([ax1, ax2], 'x')

saveas(gcf,  fullfile(params.INGEST.DATA_OUTPUT_DIRECTORY, ...
    strcat(num2str(params.INGEST.YEAR), '_', num2str(params.INGEST.YEAR_DAY), '_interp')));
saveas(gcf,  fullfile(params.INGEST.DATA_OUTPUT_DIRECTORY, ...
    strcat(num2str(params.INGEST.YEAR), '_',num2str(params.INGEST.YEAR_DAY), '_interp.jpg')));    

%% FIGURE 3: wlap
fignum=43;
figure(fignum)
hold on;
grid on;
plot(pd.var.ap.L7.wavelengths_slade, pd.var.ap.L9.data_slade);
xlabel('Wavelength')
ylabel('ap - corrected using Slade')
title_text = sprintf('Corrected ap vs. Wavelength\n Cruise: %s Leg: %s \n%u-%s-%u (Yearday: %u)', ...
    params.INGEST.CRUISE, params.INGEST.CRUISE_LEG, params.INGEST.DAY, ...
    params.INGEST.MONTH_TEXT, params.INGEST.YEAR, params.INGEST.YEAR_DAY);
title(title_text, 'fontsize', 12);

saveas(gcf,  fullfile(params.INGEST.DATA_OUTPUT_DIRECTORY, ...
    strcat(num2str(params.INGEST.YEAR), '_', num2str(params.INGEST.YEAR_DAY), '_wlap')));
saveas(gcf,  fullfile(params.INGEST.DATA_OUTPUT_DIRECTORY, ...
    strcat(num2str(params.INGEST.YEAR), '_', num2str(params.INGEST.YEAR_DAY), '_wlap.jpg')));        

 %% FIGURE 4: wlap
fignum=44;
figure(fignum)
hold on;
grid on;
plot(pd.var.ap.L7.wavelengths_rottgers, pd.var.ap.L9.data_rottgers);
xlabel('Wavelength')
ylabel('ap - corrected using Rottgers')
title_text = sprintf('Corrected ap vs. Wavelength\n Cruise: %s Leg: %s \n%u-%s-%u (Yearday: %u)', ...
    params.INGEST.CRUISE, params.INGEST.CRUISE_LEG, params.INGEST.DAY, ...
    params.INGEST.MONTH_TEXT, params.INGEST.YEAR, params.INGEST.YEAR_DAY);
title(title_text, 'fontsize', 12);

saveas(gcf,  fullfile(params.INGEST.DATA_OUTPUT_DIRECTORY, ...
    strcat(num2str(params.INGEST.YEAR), '_', num2str(params.INGEST.YEAR_DAY), '_wlap_rottgers')));
saveas(gcf,  fullfile(params.INGEST.DATA_OUTPUT_DIRECTORY, ...
    strcat(num2str(params.INGEST.YEAR), '_', num2str(params.INGEST.YEAR_DAY), '_wlap_rottgers.jpg')));     

%% FIGURE 5: wlcp
fignum=45;
figure(fignum)
hold on;
grid on;
plot(pd.var.cp.L7.wavelengths, pd.var.cp.L9.cp_data);
xlabel('Wavelength')
ylabel('cp - corrected')
title_text = sprintf('Corrected cp vs. Wavelength\n Cruise: %s Leg: %s \n%u-%s-%u (Yearday: %u)', ...
    params.INGEST.CRUISE, params.INGEST.CRUISE_LEG, params.INGEST.DAY, ...
    params.INGEST.MONTH_TEXT, params.INGEST.YEAR, params.INGEST.YEAR_DAY);
title(title_text, 'fontsize', 12);  

saveas(gcf,  fullfile(params.INGEST.DATA_OUTPUT_DIRECTORY, ...
    strcat(num2str(params.INGEST.YEAR), '_', num2str(params.INGEST.YEAR_DAY), '_wlcp')));
saveas(gcf,  fullfile(params.INGEST.DATA_OUTPUT_DIRECTORY, ...
    strcat(num2str(params.INGEST.YEAR), '_', num2str(params.INGEST.YEAR_DAY), '_wlcp.jpg'))); 
    

%% write params to .ini file
struct2ini( fullfile(params.INGEST.DATA_OUTPUT_DIRECTORY, ...
    strcat(num2str(params.INGEST.YEAR), '_',num2str(params.INGEST.YEAR_DAY), '.ini')), params );
   
%% close variables

if params.INGEST.CLEAR_VARS
    clear ans;
    clear ap_bin_count;
    clear ap_std_to_print;
    clear ap_data_rottgers;
    clear ap_data_slade;
    clear ap_timestamps;
    clear ap_uncertainty;
    clear apcp_units;
    clear ax1;
    clear ax2;
    clear binCount_type;
    clear cp_bin_count;
    clear cp_std_to_print;
    clear cp_data;
    clear cp_timestamps;
    clear cp_uncertainty;
    clear cruise;
    clear data;
    clear data_size;
    clear data_type;
    clear data_to_print;
    clear dataFiles;
    clear eastLon;
    clear end_date;
    clear end_time;
    clear extension;
    clear fid;
    clear fignum;
    clear goodrows;
    clear gps_timestamps;
    clear iData;
    clear j;
    clear lat_data;
    clear lon_data;
    clear northLat;
    clear nRows;
    clear numReplaced;
    clear replaceWith999Index;
    clear sal_data;
    clear sal_timestamps;
    clear sb_fname_ascii;
    clear sb_fname_xls;
    clear sb_hdr;
    clear seabassFileName;
    clear southLat;
    clear start_date;
    clear start_time;
    clear std_type;
    clear temp_data;
    clear temp_date;
    clear temp_time;
    clear temp_timestamps;
    clear thisBinCount;
    clear thisSTD;
    clear thisData;
    clear thisFileName;
    clear thisPrefix;
    clear thisRow;
    clear timestamps;
    clear timestamps_date_to_print;
    clear timestamps_time_to_print;
    clear title_text;
    clear totalNumReplaced;
    clear wavelengths;
    clear wavelengthToPlot;
    clear westLon;
    clear wlPrefix;
    
end;