function retn = fix_depth_all(tripod_no, new_water_depth, cmnt)
% fix_depth_meta is superceeded by adj_tripod_depth (used for MASS BAY data
% and handles a lot of odd stuff- requires an .xls to work) or
% fix_tripod_depthKJR or fix_tripod_depthEM.
% it 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 default value should be
%  that from the mooring log.  Adds comments
%1.01
%   usage : retn_status = fix_depth_all(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 source of new water depth
%  emontgomery@usgs.gov 6/7/06
%
% 10/15/07 added modification of nc{'depth'} variable along with the attributes
%
% most recent mods allow the program to detect orientation sensors that are
% probably at a different height than the sensors they're with

% check for arguments and exit if the right number aren't present
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 !!
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);
    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
    
    % display the file being evaluated
    % 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

    % save the original value, insert new WATER_DEPTH & add comments
    water_depth_ori = nc.WATER_DEPTH(:);
    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
    nc.inst_height_note=ncchar('height in meters above bottom: accurate for tripod mounted intstruments');
    nc.inst_depth_note=ncchar('inst_depth = (water_depth - inst_height); nominal depth below the surface');

    % some instruments have metadata with the height info -use it!
    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=[];
    end

    % now try to sort out the sensor_depths using inst_height (or similar)
    if (isempty(nc.inst_height))
        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
    else
       disp([ncfilename]);
       hgt=nc.inst_height;
    end
    nc.inst_depth=ncfloat(nc.WATER_DEPTH - nc.inst_height);

    % now deal with adjusting the variable attributes ...
    vn=var(nc);
    for ik=6:length(vn)
        if (~isempty(vn{ik}.sensor_depth(:)))
            s_ih=water_depth_ori - 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*, ATTN*, tran* so are using the names to separate...
            isNEP=strncmpi(name(vn{ik}),'NEP',3);  % transmissometers are
            isSED=strncmpi(name(vn{ik}),'SED',3);  % always different
            isATTN=strncmpi(name(vn{ik}),'ATTN',4);
            istran=strncmpi(name(vn{ik}),'tran',4);
            isCTD=strncmpi(name(vn{ik}),'CTD',3);
            isPr=strncmpi(name(vn{ik}),'P_',2);
            % not all C & T sensors are co-located...
            isCnd=strncmpi(name(vn{ik}),'C_',2);
            isSal=strncmpi(name(vn{ik}),'S_',2);
            iscmp=strncmpi(name(vn{ik}),'comp',4);    % orientation data is usually
            istlt=strncmpi(name(vn{ik}),'tilt',4);    % in the logger, but may
            isptc=strncmpi(name(vn{ik}),'pitch',4);   % not be given a separate
            isrol=strncmpi(name(vn{ik}),'roll',4);    % height
            % strncmpi used here because it returns a true or false.
            % strfind is [] if it fails, and the {if a|b} doesn't work as
            % expected with []
            if (isNEP | isSED | isATTN | istran | isCTD | isPr | isCnd | isSal)
                % use initial_sensor_height, if available
                sh=vn{ik}.initial_sensor_height(:);
                if isempty(sh)
                    sh=s_ih;
                end
                use_hgt=input(['is ' num2str(sh) 'm the correct height_above bottom for ' name(vn{ik}) '? '],'s');
                if strfind(lower(use_hgt),'n')
                    ori_hgt=input('enter a new height for the orientation sensor: ');
                else
                    ori_hgt=sh;
                end

                if (~isempty(sh))
                    nc{name(vn{ik})}.sensor_depth=ncfloat(new_water_depth - sh);
                else
                    nc{name(vn{ik})}.sensor_depth=ncfloat(nc.WATER_DEPTH - hgt);
                    nc{name(vn{ik})}.sensor_hab=ncfloat(hgt);
                    % [name(vn{ik}) ' ' num2str(nc{name(vn{ik})}.sensor_depth(:))]
                end
                % or if orientation, ask what height to put in the attribute
            elseif (iscmp | istlt | isptc | isrol)
                use_hgt=input(['is ' num2str(hgt) 'm the correct height_above bottom for ' name(vn{ik}) '? '],'s');
                if strfind(lower(use_hgt),'n')
                    ori_hgt=input('enter a new height for the orientation sensor: ');
                else
                    ori_hgt=hgt;
                end
                nc{name(vn{ik})}.sensor_depth=ncfloat(nc.WATER_DEPTH - ori_hgt);
                nc{name(vn{ik})}.sensor_hab=ncfloat(ori_hgt);
                %otherwise use the unrounded instrument height
            elseif (~isempty('s_ih'))
                % even though there is a sensor height, it is often rounded
                % by using the hght input, it can regain the precision lost
                nc{name(vn{ik})}.sensor_depth=ncfloat(nc.WATER_DEPTH - hgt);
                nc{name(vn{ik})}.sensor_hab=ncfloat(hgt);
                disp([name(vn{ik}) ' is '  num2str(nc{name(vn{ik})}.sensor_depth(:)) 'm deep or ' num2str(s_ih) 'MAB'])
            else  % for everything else use nc.inst_height
                nc{name(vn{ik})}.sensor_depth=ncfloat(nc.WATER_DEPTH - nc.inst_height);
                disp([name(vn{ik}) ' is '  num2str(nc{name(vn{ik})}.sensor_depth(:)) 'm deep or ' num2str(nc.inst_height(:)) 'MAB'])
            end    % if
        end     % for each variable
    end      % for each file

    %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
    % this section changes the contents of the depth() variable
    % {'depth'} is for the depth of the measurements
    dif_wd = new_water_depth-water_depth_ori;
    % are the new and old WATER_DEPTHs are the same?
    if abs(dif_wd) > .01
        % 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 ik=2:length(dp)
            dnp=[dnp ', ' num2str(dp(ik))];
        end
        nc{'depth'}.oridepth=dnp;
        % Finally insert adjusted measurement depths
        if (length(nc{'depth'}(:)) > 1) %for vectors (adv, pca)
            nc{'depth'}(:)= nc{'depth'}(:) + (dif_wd);
        else    % for single depth sensors
            nc{'depth'}(:)=new_water_depth - nc.inst_height;
        end
        nc{'depth'}.CMNT=ncchar('adjusted using new water_depth- original depth data in depth.oridepth attribute');
    else       % if the depths are the same don't change stuff
        nc{'depth'}.CMNT=ncchar('no change needed');
    end
    % recompute min and max of depth
    nc{'depth'}.minimum=ncfloat(min(nc{'depth'}(:)));
    nc{'depth'}.maximum=ncfloat(max(nc{'depth'}(:)));

    close(nc)
end

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