function attn_temp_curr(theSite)
%   attn_temp_curr(theSite)
%
%Program to create time series plots of beam attenuation, temperature, and
%current for theSite.

%Soupy Alexander, 4/2004

%This Matlab m-file was used to create portions of U.S. Geological Survey 
%Data Series 85. Although this program has been used by the USGS, no 
%warranty, expressed or implied, is made by the USGS or the United States 
%Government as to the accuracy and functioning of the program and related 
%program material nor shall the fact of distribution constitute any such 
%warranty, and no responsibility is assumed by the USGS in connection 
%therewith.

%Citation:  Butman, Bradford, Alexander, P. Soupy, Anderson, S.P., 
%Lightsom, F.L., Scotti, Alberto, and Beardsley, R.C., 2004, The 
%Massachusetts Bay Internal Wave Experiment, August 1998:  Data Report:  
%U.S. Geological Survey Data Series 85, 1 DVD-ROM.

theDir = 'C:\SCHTUFF\MASS_BAY\MBAY_IWAVE\REPORT\DATAFILES';
printDir = 'C:\SCHTUFF\MASS_BAY\MBAY_IWAVE\REPORT\';

thePlotTypes = {'all'; '0819_0824'; '0822'};

for indexType = 3%1:length(thePlotTypes)
    plotType = thePlotTypes{indexType};
    
    if strcmp(plotType, 'all')
        %Full Record
        theTimeFrame = [datenum(1998, 07, 29, 00, 00, 00) datenum(1998, 09, 02, 00, 00, 00)];
        theTicks = min(theTimeFrame):5:max(theTimeFrame);
        theCode = 6;
        theExt = '-a1h';
        
    elseif strcmp(plotType, '0819_0824')
        %August 19-24
        theTimeFrame = [datenum(1998, 8, 19, 00, 00, 00) datenum(1998, 08, 25, 00, 00, 00)];
        theTicks = min(theTimeFrame):1:max(theTimeFrame);
        theCode = 6;
        theExt = '-a';
    elseif strcmp(plotType, '0822')
        % August 22
        theTimeFrame = [datenum(1998, 8, 22, 00, 00, 00) datenum(1998, 08, 23, 00, 00, 00)];
        theTicks = min(theTimeFrame):2/24:max(theTimeFrame);
        theCode = 15;
        theExt = '-a';
    end
    
    if strcmp(upper(theSite), 'B')
        files1 = {['5383att' theExt '.cdf']; ['5371tcp' theExt '.nc']};
        files2 = {['5383sc' theExt '.cdf']; ['5371tcp' theExt '.nc']};
        files3 = {['5371v' theExt '_d1.nc']; ['5371v' theExt '_d2.nc']};
        if ~strcmp(plotType, 'all')
            theLimits = {[0 4]; [4.5 5.5]; [0 50]};
        else
            theLimits = {[0 4]; [4.5 5.5]; [0 20]};
        end
        waterDepth = 85;
    elseif strcmp(upper(theSite), 'C')
        files1 = {['5343att' theExt '.cdf']; ['5351tcp' theExt '.nc']};
        files2 = {['5343sc' theExt '.cdf']; ['5351tcp' theExt '.nc']};
        files3 = {['5344' theExt '.nc']};
        if ~strcmp(plotType, 'all')
            theLimits = {[0 4]; [5 15]; [0 70]};
        else
            theLimits = {[0 4]; [5 10]; [0 50]};
        end
        waterDepth = 51;
    end
    
    theMult = [1 1 1];
    
    plotTitles = {'Beam Attenuation'; 'Temperature'; 'Current Speed'};
    
    colList = {'r'; 'b'; 'g'; 'm'; 'c'; 'k'};
    
    figure, orient landscape
    
    for indexPlot = 1:3
        eval(['targFiles = files' num2str(indexPlot)' ';']);
        subplot(3,1,indexPlot), hold on
        
        clear thePlots theDepths theTitles
        
        for indexFile = 1:length(targFiles)
            ncID = netcdf(fullfile(theDir, targFiles{indexFile}), 'nowrite');
            theTime = singlejd(ncID{'time'}(:), ncID{'time2'}(:));
            %if strcmp(targFiles{indexFile}, 'vmcm0009.epic')
            %    waterDepth = 85;
            %else
            %     waterDepth = ncID.water_depth{:};
            %end
            
            if indexPlot == 1
                theData = ncID{'ATTN_55'}(:);
                if isempty(theData)
                    theData = ncID{'att_1'}(:);
                end
                
                theDepths(indexFile) = ncID{'depth'}(:);
                theTitles{indexFile} = [num2str(waterDepth - theDepths(indexFile), ...
                        '%.1f') ' mab'];
                thePlots(indexFile) = plot(julian2datenum(theTime), theData, colList{indexFile});
                ylabel('Attn (m^-^1)')
            elseif indexPlot == 2
                theData = ncID{'T_20'}(:);
                if isempty(theData)
                    theData = ncID{'temperature'}(:);
                end
                if isempty(theData)
                    theData = ncID{'temp'}(:);
                end
                theDepths(indexFile) = ncID{'depth'}(:);
                theTitles{indexFile} = [num2str(waterDepth - theDepths(indexFile), ...
                        '%.1f') ' mab'];
                thePlots(indexFile) = plot(julian2datenum(theTime), theData, colList{indexFile});
                ylabel('Temp (^oC)')
            else
                theU = ncID{'u_1205'}(:);
                theV = ncID{'v_1206'}(:);
                if isempty(theU)
                    theU = ncID{'east'}(:);
                    theV = ncID{'north'}(:);
                end
                
                [theTheta, theMag] = cart2pol(theU, theV);
                newTheta = 20*(pi/180)-theTheta;    
                %theData = theMag.*cos(newTheta) * theMult(indexPlot);
                theData = sqrt(theU.^2 + theV.^2);
                
                theDepths(indexFile) = ncID{'depth'}(:);
                theTitles{indexFile} = [num2str(waterDepth - theDepths(indexFile), ...
                        '%.1f') ' mab'];
                thePlots(indexFile) = plot(julian2datenum(theTime), theData, colList{indexFile});
                ylabel('Current (cm/s)')
                
                l = line([min(theTimeFrame) max(theTimeFrame)], [0 0]);
                set(l, 'color', 'k')
            end
        end
        
        ylim(theLimits{indexPlot})
        xlim(theTimeFrame)
        set(gca, 'xtick', theTicks)
        datetick('x', theCode, 'keepticks', 'keeplimits')
        box('on')
        
        l = legend(thePlots, theTitles);
        set(l, 'fontsize', 8)
        
        title(['Site ' upper(theSite) ', ' plotTitles{indexPlot}])
    end
    
    printTitle = ['atc_' lower(theSite) '_' plotType '.pdf'];
    print(gcf, '-dpdf', fullfile(printDir, printTitle))
    close
end