function corr_inst_depth(fname,WD,inst_ht,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. Allows the user to input instrument height in
%   case it was missing. This program forces all variables to have the same
%   inst_height so will mess things up for files with sensors at several
%   heights- use fix_tripod_depthKJR for these instead.

%   inputs:   fname- name of the file to open
%             WD - the correct water depth for that mooring
%             inst_ht - the installed height of the instrument above the seafloor
%             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.
%
%  emontgomery@usgs.gov 3/11/11
%
% note - this program will crash if a file with no depth variable is used.


if nargin<1
    help(mfilename)
    return
end
tstr = datestr(now,30);
outfile = ['Fix',fname,'on',tstr,'.txt'];
diary(sprintf(outfile))
sprintf(['Run on ' tstr])
disp(['New water depth: ' num2str(WD)])
disp(note)
disp(['Datum of new water depth: ' datum])

if strcmp(fname,'ep_standard.nc')
    disp('File ep_standard skipped')   %dont want to work on ep_standard
    return
    
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
vnames = ncnames(var(nc));vars = var(nc);
Gdepth = nc.WATER_DEPTH(:);
if isnan(Gdepth)
    Gdepth=0;
end
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...
wdep_eq=0;      % set a flag to not mess with depth variable if WD's are equal
if abs(diff)<0.1,
    keepon=input('---Difference in water depth is minimal, do you want to continue? ','s')
    wdep_eq=1;
    if strcmp(lower(keepon(1)),'n')
        disp('as requested, exiting program')
        close(nc)
        retun
    end
end
disp(['----Fixing global attributes of file ' fname ])
% only mess with the WATER_DEPTH attribute if it's different
if ~wdep_eq
    % 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
    % now put the new info in the exising variables
    nc.WATER_DEPTH(:)=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
end
if (nc{'depth'}(1) - (WD-inst_ht) ~= 0)
    % now insert the new measurement depth
    newdep = WD-inst_ht;
    nc{'depth'}.ori_water_depth=water_depth_ori;
    nc{'depth'}(:) = newdep;
    nc{'depth'}.CMNT=ncchar('adjusted using new water_depth');
elseif (length(nc{'depth'}(:)) > 1)  % for vectors, use diff to correct
    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');
end
if isempty(nc.initial_instrument_height(:))
    nc.initial_instrument_height=ncfloat(inst_ht);
else
    nc.initial_instrument_height(:)=inst_ht;
end

disp('----Now fixing variable attributes')
for k = 6:length(vars)
    vark = vnames{k};ncobj = nc{vark};
    if isempty(ncobj.initial_sensor_height(:))
        ncobj.initial_sensor_height=ncfloat(inst_ht);
    end
    if ~isempty(ncobj.sensor_depth)
        if isnan(ncobj.sensor_depth(:))  % waves should all be here
            ncobj.initial_sensor_height(:)=inst_ht;
            ncobj.sensor_depth(:) = nc.WATER_DEPTH(:) - ncobj.initial_sensor_height(:);
            disp(['-----Variable ' char(vnames(k)) ' sensor depth and inst ht fixed'])
        else
            %newdepth = ncobj.sensor_depth + diff;
            %ncobj.sensor_depth = newdepth;
            ncobj.sensor_depth(:) = nc.WATER_DEPTH(:) - ncobj.initial_sensor_height(:);
            ncobj.initial_sensor_height(:)=inst_ht;
            disp(['-----Variable ' char(vnames(k)) ' sensor depth attribute changed'])
        end
    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 by corr_inst_depth';
nc.history = ncchar([cmnt ';' hist]);
close(nc)

disp(['Done fixing water depth attributes for ' fname])

diary off