function retn = fix_mooringdepth(mooring_struct)
% fix_mooringdepth adjust all global metadata and depth variable to a new depth
%
% function to adjust all global metadata to be consistent for one tripod
%  using a scientist supplied water_depth.  The original value should be
%  that from the mooring log. 
%
%   usage : retn_status = fix_mooringdepth(struct_name)
%         where the retn_status is 1 if no problems
%         the input structure is comprised of:
%           mooring number (.moor_no),
%           new water depth (.new_water_depth)
%           (next 3 have as many items as instruments)
%           instrument index (from filenames (.hgtind)
%           new sensor depth (.new_sens_depth)
%           new inst height (.new_inst_height)
%           comment describing source of new water depth (.cmnt)
%           see do_fix_mooringdepth for how to make the structure
%  emontgomery@usgs.gov 11/7/08
%
% 10/15/07 added modification of nc{'depth'} variable along with the attributes
%
% For moorings, the heights and depths are pretty nominal, since the
% mooring moves around some with the waves and tides.  So each instrument
% gets one instrument height and sensor_depth

% check for arguments and exit if the right number aren't present
if nargin ~= 1; help (mfilename); retn=0; return; end

% if nothing in the sens_depth field, compute it from instrument heights
% from mooring log
if (isempty (mooring_struct.new_sens_depth))
    mooring_struct.new_sens_depth=mooring_struct.new_water_depth-mooring_struct.new_inst_height;
end

retn = 1;
tripno=num2str(mooring_struct.moor_no);

%  NOTE : this only works on files in the cwd-
% it doesn't traverse dirs to find files to modify !!
if ispc
    eval(['d=dir(''*' tripno '*.nc'');'])
    for jj=1:length(d)
        fn{jj}=d(jj).name;
    end
else              % for unix
    eval(['[stat,fnames]=unix(''ls ' tripno '*.nc'');'])
    xx=findstr(tripno,fnames);
    xx=[xx length(fnames)+1];
    knt=1;
    for ik=1:length(xx)-1
        vv=char(deblank(fnames(xx(ik):xx(ik+1)-1)));
        if findstr(vv,'old')
            disp(['not processing ' vv]);
        else
            fn{knt}=deblank(fnames(xx(ik):xx(ik+1)-1));
            knt=knt+1;
        end
    end
end

% loop through to manipulate each file on the tripod
for ik=1:length(fn)
    ncfilename=fn{ik};
    perloc=findstr('.',ncfilename);
    new_nm=[ncfilename(1:perloc-1) '_old.nc'];

    result=fcopy(ncfilename,new_nm);
    nc = netcdf(ncfilename, 'write');
    if isempty(nc), disp('read of ncfile failed, try another name'), return, end

    % modify history & modification date:
    lfeed = char(10);
    nc.CREATION_DATE = ncchar(datestr(now,0));
    history = ['WATER_DEPTH related attributes corrected by ', mfilename , ': ' nc.history(:)];
    ifeed = findstr(history,lfeed);
    history(ifeed) = ':';
    nc.history = ncchar(history);
    flg=0;

    % fix global attributes related to WATER_DEPTH
    ga=att(nc);

    % 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
    
    % 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(mooring_struct.new_water_depth);
    if(isempty(nc.WATER_DEPTH_NOTE))
        nc.WATER_DEPTH_NOTE = ncchar([mooring_struct.cmnt ': (m) ']);
    else
        nc.WATER_DEPTH_NOTE = ncchar([mooring_struct.cmnt ': (m) ' nc.WATER_DEPTH_NOTE]);
    end
    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');

  % pick which depth and height to use based on the file name
   val=find(str2num(ncfilename(4))==(mooring_struct.hgtind)); 
    nc.inst_height=ncfloat(mooring_struct.new_inst_height(val));
    nc.inst_depth=ncfloat(mooring_struct.new_sens_depth(val));

    % now deal with adjusting the variable attributes ...
    vn=var(nc);
    for ik=6:length(vn)
        nc{name(vn{ik})}.sensor_depth=ncfloat(mooring_struct.new_sens_depth(val));
        nc{name(vn{ik})}.sensor_hab=ncfloat(mooring_struct.new_inst_height(val));
    end     % for each variable

    %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
    % this section changes the contents of the depth() variable
    % we're going to change the contents of the variable depth here!
    %  sokeep the original depth info in attributes
    nc{'depth'}.ori_water_depth=water_depth_ori;
    dp=nc{'depth'}(:);
    dnp=num2str(dp(1));
    for kk=2:length(dp)
        dnp=[dnp ', ' num2str(dp(kk))];
    end
    nc{'depth'}.oridepth=dnp;
    % Finally insert adjusted measurement depths
    nc{'depth'}(:)=mooring_struct.new_sens_depth(val);
    nc{'depth'}.CMNT=ncchar('adjusted using new sensor_depth');
    close(nc)
end

% finally, verify that all the variables seem reasonable and match
for jj=1:length(fn)
    ncfilename=fn{jj};
    disp_ncdepth(ncfilename);
end