function fix_tripod_depthKJR(MOORING,WD,note,datum)
%
%   function to fix the water_depth attributes within a netcdf file based
%   on a better estimate of the water depth. Will take the current water 
%   depth value in the file, and fix all the attributes based on the
%   difference between the two. Make sure you are in the root directory for
%   the mooring, and this will go through each folder, look for netcdf
%   files, and fix the water depth values of each file. If the water depth
%   supplied is not significantly different than the water depth in the
%   file, it won't change that file.
%
%   inputs:   MOORING - the mooring number, as a string, e.g. '847'
%             WD - the correct water depth for that mooring
%             note - note on the source of water depth info, as a string, e.g. 'Water
%               depth from mean pressure on tripod' or 'Water depth from MLLW
%               of NOAA survey'
%             datum - datum of water depth, e.g., MSL, MLLW, MTL, etc.

if nargin<1
    help(mfilename)
    return
end
if isnumeric(MOORING)
    MOORING = num2str(MOORING);
end
tstr = datestr(now,30);
outfile = ['FixWaterDepth',MOORING,'on',tstr,'.txt'];
diary(sprintf(outfile))
sprintf(['Run on ' tstr])
disp(['Checking mooring ' MOORING ' for files to have depth corrected'])
disp(['New water depth: ' num2str(WD)])
disp(note)
disp(['Datum of new water depth: ' datum])

D = dir;
for i = 3:length(dir);  %go through the folders, skipping the first two (i.e., '.' and '..');
    if D(i).isdir
        disp(['Looking in ' D(i).name ' for files to be corrected'])
        cd(D(i).name)
        ncfiles = dir('*.nc');cdffiles = dir('*.cdf');files = [cdffiles;ncfiles];
        if length(files)<1,
            disp(['There are no netCDF data files in folder ' D(i).name ' to correct; moving on'])
            break
        elseif length(files)>=1
            disp(['-There are ' num2str(length(files)) ' netCDF files to check'])
            for j = 1:length(files)
                fname = files(j).name;
                if strcmp(files(j).name,'ep_standard.nc')
                    disp('File ep_standard skipped')   %dont want to work on ep_standard
                    break
                end;    
                disp(['--Checking ' fname ' for attributes to fix'])
                nc = netcdf(fname,'write');
                %first check to see if depth exists, i.e., is it just a raw
                %data file with no attributes
                if isempty(nc{'depth'})
                    disp('---No depth variable exists, moving on...')
                elseif ~isempty(nc{'depth'})
                    vnames = ncnames(var(nc));vars = var(nc);
                    Gdepth = nc.WATER_DEPTH(:);
                    diff = WD - Gdepth;
                    %if the difference is less than 10cm, it's not really worth
                    %changing, because the tripod could settle that much on
                    %deployment...
                    if abs(diff)<0.1,
                        disp('---Difference in water depth is too minimal, moving on....')
                        close(nc)
                    elseif abs(diff)>0.1
                        disp(['----Fixing global attributes of file ' files(j).name ])
                        % save the original value, insert new WATER_DEPTH & add comments
                        if ~isempty(nc.WATER_DEPTH)
                            water_depth_ori = nc.WATER_DEPTH(:);
                        elseif ~isempty(nc.water_depth)
                            water_depth_ori = nc.water_depth(:);
                        else
                            water_depth_ori = 'unknown';
                        end
                        nc.WATER_DEPTH_ORI = water_depth_ori;
                        if isempty(nc.WATER_DEPTH_SOURCE)
                            nc.WATER_DEPTH_ORI_NOTE = ncchar(nc.WATER_DEPTH_NOTE);
                        elseif ~isempty(nc.WATER_DEPTH_SOURCE)      %i.e. this is an adcp file
                            nc.WATER_DEPTH_ORI_NOTE = ncchar(nc.WATER_DEPTH_SOURCE);
                            nc.WATER_DEPTH_SOURCE = [];
                        end
                        % if water_depth doesn't exist it shows up as empty
                        % we don't want the lc. water_depth anyway- use WATER_DEPTH
                        if ~isempty(nc.water_depth(:));
                            nc.water_depth=[];
                        end
                        nc.WATER_DEPTH=ncfloat(WD);
                        newnote = strcat([note ' Datum: ' datum]);
                        if(isempty(nc.WATER_DEPTH_NOTE))
                            nc.WATER_DEPTH_NOTE = ncchar(newnote);
                        else
                            nc.WATER_DEPTH_NOTE = ncchar(newnote);
                        end
                        if ~isempty(nc.INST_DEPTH)&&~isempty(nc.INST_HEIGHT)
                            nc.INST_DEPTH = nc.WATER_DEPTH-nc.INST_HEIGHT;
                            nc.INST_HEIGHT_NOTE=ncchar('height in meters above bottom: nominal for moorings');
                            nc.INST_DEPTH_NOTE=ncchar('inst_depth = (water_depth - inst_height); nominal depth below the surface');
                        end
                        nc.WATER_DEPTH = nc.WATER_DEPTH_ORI(:) + diff;
                        %now fix the variable 'depth' - doesn't matter if depth
                        %is a vector or a scalar, still want to remove the same
                        %difference
                         dep = nc{'depth'}(:);
                         newdep = dep + diff;
                         nc{'depth'}.ori_water_depth=water_depth_ori;
                         nc{'depth'}(:) = newdep;
                         nc{'depth'}.CMNT=ncchar('adjusted using new water_depth');
                        disp('----Now fixing variable attributes')
                        for k = 1:length(vars)
                            vark = vnames{k};ncobj = nc{vark};
                            if ~isempty(ncobj.sensor_depth)
                                newdepth = ncobj.sensor_depth + diff;
                                ncobj.sensor_depth = newdepth;
                                disp(['-----Variable ' char(vnames(k)) ' sensor depth attribute changed'])
                            elseif isempty(ncobj.sensor_depth)&&~isempty(ncobj.initial_sensor_height)
                                ncobj.sensor_depth = nc.WATER_DEPTH(:) - ncobj.initial_sensor_height;
                                disp(['-----Variable ' char(vnames(k)) ' sensor depth attribute added'])
                            end
                            if ~isempty(ncobj.sensor_depth)&&isempty(ncobj.initial_sensor_height)
                                ncobj.initial_sensor_height = nc.WATER_DEPTH(:) - ncobj.sensor_depth;
                                disp(['-----Variable ' char(vnames(k)) ' sensor height above bottom attribute added'])
                            end
                        end
                        % now add info to the history to record the change
                        hist = nc.history(:);cmnt = 'Water depth variable and attributes changed to reflect more accurate values';
                        nc.history = ncchar([cmnt ';' hist]);
                        close(nc)
                    end
                end
            end
        end
        cd ..
    end
end

disp(['Done checking files for mooring ' MOORING ' for water depth attributes to be corrected.'])

diary off