function retn = fix_depth_meta(tripod_no, new_water_depth, cmnt)
%fix_depth_meta: adjusts metadata and depth variable to a new water_depth
%
%  function to adjust all global metadata to be consistent for one tripod
%  using a scientist supplied water_depth.  The default value should be
%  that from the mooring log.
%
%  adjusts the sensor_depth attribute for each variable, the WATER_DEPTH,
%  and the depth variable.
%
%   usage : retn_status = fix_depth_meta(726, 9.3, 'computed from adv pressure')
%         where the retn_status is 1 if no problems
%         arg1= mooring number, arg2= new water depth, arg3 = comment
%         describing how the new water depth was computed
%  emontgomery@usgs.gov 6/7/06

if nargin ~= 3; help (mfilename); retn=0; return; end

retn = 1;
tripno=num2str(tripod_no);
%
%  NOTE : this only works on files in the cwd- it doesn't traverse dirs to
%  find files to modify !!
%   ** needs to work with either nc or cdf
if ispc
    eval(['d1=dir(''*' tripno '*.nc'');'])
    eval(['d2=dir(''*' tripno '*.cdf'');'])
    d=[d1;d2];
    for jj=1:length(d)
        fn{jj}=d(jj).name;
    end
else              % for unix
    eval(['[stat,fnames]=unix(''ls *' tripno '*'');'])
    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(~isempty(findstr(vv,'cdf')) | ~isempty(findstr(vv,'nc')))
            fn{knt}=deblank(fnames(xx(ik):xx(ik+1)-1));
            knt=knt+1;
        else
            disp(['not processing ' vv]);

        end
    end
end
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.: ' nc.history(:)];
    ifeed = findstr(history,lfeed);
    history(ifeed) = ':';
    nc.history = ncchar(history);
    flg=0;

    % fix global attributes related to WATER_DEPTH
    ga=att(nc);
    for j=1:length(ga)
        attname=name(ga{j});
        % capitalize the attribute names in sc, mc, and pt
        if (strcmp(attname,'inst_depth'))
            flg=flg+1;
        elseif (strcmp(attname,'water_depth'))
            nc.WATER_DEPTH=nc.water_depth(:);
            nc.water_depth=[];
            flg=flg+1;
        end
    end
    % this is data that doesn't have the inst_height attribute
    if (flg ==2)
        nc.inst_height=nc.inst_depth(:); %use a dummy to create attribute
        %so compute it from what's there
        nc.inst_height=ncfloat(nc.WATER_DEPTH-nc.inst_depth);
    end

    % NOW fix the water depth & add comments
    water_depth_ori = nc.WATER_DEPTH(:);        % save the original value
    nc.WATER_DEPTH=ncfloat(new_water_depth);
    if(isempty(nc.WATER_DEPTH_NOTE))
        nc.WATER_DEPTH_NOTE = ncchar([cmnt ': (m) ']);
    else
        nc.WATER_DEPTH_NOTE = ncchar([cmnt ': (m) ' nc.WATER_DEPTH_NOTE]);
    end

    if (~isempty(nc.ADVProbeHeight))
        nc.inst_height=ncfloat(nc.ADVProbeHeight);
        nc{'depth'}(:)=new_water_depth - nc.inst_height;
    elseif (~isempty(nc.PCADPProbeHeight))
        nc.inst_height=ncfloat(nc.PCADPProbeHeight);
    elseif (~isempty(nc.sensor_height))
        nc.inst_height=ncfloat(nc.sensor_height);
        nc.sensor_height=[];
    elseif flg==2
        nc{'depth'}(:)=new_water_depth - nc.inst_height;
    end
    % this is  *NOT* tested 12/28/06
    % for data types where depth is a vector, not a point, you need do do something like
    % if (length(nc{'depth'}(:) > 1))
    %   nc{'depth'}(:)= nc{'depth'}(:) + (water_depth_ori-new_water_depth);
    % end

    if nc.inst_height(:)>0
        disp(['Instrument height above bottom is: ', num2str(nc.inst_height(:))])
        gd_ih=input('Is this correct? (y/n) \n','s');
        gd_ih=upper(gd_ih);
    end

    if (isempty(nc.inst_height) | strfind(gd_ih,'N'))
        disp(['NO instrument height available in the metadata for ' ncfilename]);
        disp('please select a value to use from these options from the mooring log')
        rd_mlog_mno_hgt(tripno)
        hgt=input('  enter the value as decimal meters (such as: 2.05): \n');
        if isempty(hgt)
            disp ('can not use that answer, exiting')
            close(nc)
            return
        else
            nc.inst_height = ncfloat(hgt);
        end
    end

    nc.inst_height_note=ncchar('height in meters above bottom: accurate for tripod mounted intstruments');
    nc.inst_depth=ncfloat(nc.WATER_DEPTH - nc.inst_height);
    nc.inst_depth_note=ncchar('inst_depth = (water_depth - inst_height); nominal depth below the surface');


    % need to deal with the variable attributes next....
    % variable attributes
    % nc{'T_28'}.sensor_depth=ncfloat(inst_depth);

    vn=var(nc);
    for ik=6:length(vn)
        if (~isempty(vn{ik}.sensor_depth(:)))
            % this part is for hydra's that may have sensors attached to it
            % at many heights- the likely sensor names are P_402?, SDP_850
            % sed_??, and NEP*, so are using the names to separate...
            if (strncmpi(name(vn{ik}),'NEP',3) | strncmpi(name(vn{ik}),'SED',3) | strfind(name(vn{ik}),'P_'))
                [name(vn{ik}) ' ' num2str(nc{name(vn{ik})}.sensor_depth(:))]
                s_ih=water_depth_ori-  vn{ik}.sensor_depth(:)
                nc{name(vn{ik})}.sensor_depth=ncfloat(nc.WATER_DEPTH - s_ih);
                [name(vn{ik}) ' ' num2str(nc{name(vn{ik})}.sensor_depth(:))]
            else  % for everything else use nc.inst_height
                nc{name(vn{ik})}.sensor_depth=ncfloat(nc.WATER_DEPTH - nc.inst_height);
            end
        end
    end

    close(nc)
end

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