function retn = adj_tripod_depth(new_struct, tripod_struct)
% adj_tripod_depth 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, but ofter a pressure based one is preferred.
%
%   usage : retn_status = adj_tripod_depth(new_struct, tripod_struct)
%         where the retn_status is 1 if no problems
%         two input structure are needed- one is for the new info
%         new_struct: tripod number (.tripod_no),
%                     new water depth (.new_water_depth)
%                     comment describing source of new water depth (.cmnt)
%         tripod_struct: (made by running extract_hab on the mooring log with additions for varname_cmab)
%         tripod_struct may contain the data from one or more tripods
%           tripod number (.tirpodid)
%           new inst. height (.hab)
%           name of sensor to which the height applies (.habname)
%           serial number of instrument (.sn)
%           hab, habname and sn may be row arrays if more than one sensor/instrument
%  the sensor_depth attribute done with new water depth and instrument hab
%  a sensor_hab attribute is added to hold deployment inst. heights.
%  nc{'depth'} variable is changed along with the attributes- if it is a
%  MIDAS or ADV logger, the depth of the velocity measurement is used.  A
%  note is added saying which variable is the source for depth.
%
%  emontgomery@usgs.gov 1/12/09
%
% Program written in Matlab v7.4.0336 (R2007a)
% Program updated in Matlab 7.6.0.324 (R2008a)
% Program ran on PC with Windows XP Professional OS.
%
% "Although this program has been used by the USGS, no warranty,
% expressed or implied, is made by the USGS or the United States
% Government as to the accuracy and functioning of the program
% and related program material nor shall the fact of distribution
% constitute any such warranty, and no responsibility is assumed
% by the USGS in connection therewith."

%
% check for arguments and exit if the right number aren't present
if nargin ~= 2; help (mfilename); retn=0; return; end

retn = 1;
tripno=num2str(new_struct.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=copyfile(ncfilename,new_nm);
    nc = netcdf(ncfilename, 'write');
    if isempty(nc), disp('read of nc_file failed, try another name')
        retn=0;
        return
    end
    % a few have no depth dimension- this can't work on those files
    if isempty(nc{'depth'})
        disp(['no depth dimension in ' ncfilename '. Remedy this first!'])
        retn=0;
        return
    end

    % save all the original values to compare later:
    [r,dval]=extract_ncdepth(nc);

    % 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
    % remove the other option, if it exists
    lx=strmatch('water_depth(m)',[ncnames(ga)]);
    % because of the (m) the above syntax won't remove the attribute
    if ~isempty(lx);
        disp(['water_depth(m) attribute present- remove with ncatted later'])
    end
    nc.WATER_DEPTH=ncfloat(new_struct.new_water_depth);
    if(isempty(nc.WATER_DEPTH_NOTE))
        nc.WATER_DEPTH_NOTE = ncchar([new_struct.cmnt ': (m) ']);
    else
        nc.WATER_DEPTH_NOTE = ncchar([new_struct.cmnt ': (m) ' nc.WATER_DEPTH_NOTE]);
    end
    % not doing inst_depth as a global attribute- see hab for each sensor
    % nc.inst_depth_note=ncchar('inst_depth = (water_depth - variable_depth)');

    % select which information is appropriate to the file:
    resp='n'; fls=0;
    fidx=find(strncmp([tripod_struct.tripodid],cellstr(ncfilename(1:4)),3));
    if length(fidx) ~=1
        disp(['did not get an exact match to use on ' ncfilename '- select which should be used.'])
        for k=1:length(fidx)
            resp=input(['how about: ' char(tripod_struct(fidx(k)).tripodid) '  ?  (y or n)\n'],'s');
            if strncmpi(resp,'y',1)
                fidx(1)=fidx(k);
                fidx(2:end)=[];
                flg=1;
            end
            if flg==1; break; end
        end
    end
    % Aanderraa rcm's are a bit different- they have t, ox and u,v in 1 file

    % now deal with adjusting the variable attributes ...
    vn=var(nc);
    ncnms=ncnames(var(nc));
    % set up names that map possible variable names in our files
    names_for_pressure={'p_1' 'p_4' 'p_4023' 'sdp_850' 'p_4022' 'p_4020'};
    names_for_velocity={'u_1205' 'v_1206' 'w_1204' 'werr_1201' 'cd_310' 'cs_300'};
    names_for_var1={'uvar_4050' 'uvcov_4051' 'vvar_4052' 'uwcov_4053' 'vwcov_4054' 'wvar_4055'};
    names_for_var2={'nav_105' 'peru_4056' 'perv_4057' };
    names_for_var3={'ustd_' 'vstd_' 'wstd_' 'agc' 'cor' 'hsd_' 'psd_' 'rsd_' 'tx_1211'};
    names_for_velvar=[names_for_var1 names_for_var2 names_for_var3];
    names_for_vel=[names_for_velocity];
    names_for_t={'t_24' 't_20' 't_28'};
    names_for_c={'c_50','c_51' 's_40', 's_41' 'sth_71'};
    names_for_ox={'o_60' 'o2raw' 'ost_62'};
    names_for_trans={'attn_55' 'tran_4010' 'trn_107'};
    names_for_obs={'neph_56' 'nep1' 'nep2'};
    %names_for_abss={};
    names_for_orientation={'tiltx_4017' 'tilty_4018' 'comp_1406' 'comp_1404'};
    names_for_orientn2={'hdg_1215' 'ptch_1216' 'roll_1217'};

    % it's really critical that it found the right _cmab's for the data in the
    % .xls.  If your file has a temperature variable, but there's no TEMP_cmab
    % displayed, it won't treat the T_xx variable, and it won't be in the
    % output file.  SO check this carefully!
    disp('this was read- are all the needed params here???')
    [ tripod_struct(fidx).tripodid tripod_struct(fidx).habname]
     resp=input('(y or  n?) ','s');
     
     if strcmp(lower(resp),'y')
         for g=6:length(vn)
             sval=char(lower(ncnms(g)));
             if (length(sval)> 3)
                 sval=sval(1:3);
             end
             matches_vel=~isempty(strmatch(sval,names_for_vel));
             matches_velvar=~isempty(strmatch(sval,names_for_velvar));
             matches_ori1=~isempty(strmatch(sval,names_for_orientation));
             matches_ori2=~isempty(strmatch(sval,names_for_orientn2));
             if (strmatch(lower(ncnms(g)),names_for_pressure))
                 j=find(strncmpi([tripod_struct(fidx).habname],'pres',4));
                 nih=tripod_struct(fidx).hab(j)/100;        %must convert to meters
             elseif (matches_vel || matches_velvar)
                 if ~isempty(strfind(ncfilename,'_d1'))  % midas with bass, pod1
                     j=find(strncmpi([tripod_struct(fidx).habname],'basspod1',8));
                     nih=tripod_struct(fidx).hab(j)/100;        %must convert to meters
                 elseif ~isempty(strfind(ncfilename,'_d2'))  % midas with bass, pod2
                     j=find(strncmpi([tripod_struct(fidx).habname],'basspod2',8));
                     nih=tripod_struct(fidx).hab(j)/100;        %must convert to meters
                 elseif ~isempty(strfind(ncfilename,'adv'))  % adv
                     j=find(strncmpi([tripod_struct(fidx).habname],'adv',3));
                     nih=tripod_struct(fidx).hab(j)/100;        %must convert to meters
                 elseif ~isempty(strfind(ncfilename,'pca'))  % pcadp
                     j=find(strncmpi([tripod_struct(fidx).habname],'pca',3));
                     nih=tripod_struct(fidx).hab(j)/100;        %must convert to meters
                 elseif ~isempty(strfind(ncfilename,'rcm'))  % aanderraa
                     j=find(strncmpi([tripod_struct(fidx).habname],'opt',3));
                     nih=tripod_struct(fidx).hab(j)/100;        %must convert to meters
                 elseif find(strncmpi([tripod_struct(fidx).habname],'dlcm',4))  % dlcm
                     j=find(strncmpi([tripod_struct(fidx).habname],'dlcm',4));
                     nih=tripod_struct(fidx).hab(j)/100;        %must convert to meters
                 else
                     disp([lower(ncnms(g)) 'this current measurement did not find a category, so nothing done'])
                 end
             elseif (matches_ori1 || matches_ori2)
                 % MIDAS with bass orientation is 1.3m above pod1 and 1.9 above
                 % pod2
                 if ~isempty(strfind(ncfilename,'_d1'))  % midas with bass, pod1
                     j=find(strncmpi([tripod_struct(fidx).habname],'basspod1',8));
                     nih=(tripod_struct(fidx).hab(j)/100)+1.29;   %must convert to meters
                 elseif ~isempty(strfind(ncfilename,'_d2'))  % midas with bass, pod2
                     j=find(strncmpi([tripod_struct(fidx).habname],'basspod2',8));
                     nih=(tripod_struct(fidx).hab(j)/100)+1.89;   %must convert to meters
                 elseif ~isempty(strfind(ncfilename,'_d0'))  % might be any data
                     % bass orientation was usually 2.29mab, so use this value
                     nih=2.29;   %must convert to meters
                     % use instrument height for these
                 elseif ~isempty(strfind(ncfilename,'adv'))  % adv
                     j=find(strncmpi([tripod_struct(fidx).habname],'adv',3));
                     nih=tripod_struct(fidx).hab(j)/100;        %must convert to meters
                 elseif ~isempty(strfind(ncfilename,'pca'))  % adv
                     j=find(strncmpi([tripod_struct(fidx).habname],'pca',3));
                     nih=tripod_struct(fidx).hab(j)/100;        %must convert to meters
                 else
                     disp([lower(ncnms(g)) 'this current measurement did not find a category, so nothing done'])
                 end
             elseif (strmatch(lower(ncnms(g)),names_for_t))
                 j=find(strncmpi([tripod_struct(fidx).habname],'temp',4));
                 nih=tripod_struct(fidx).hab(j)/100;        %must convert to meters
             elseif (strmatch(lower(ncnms(g)),names_for_c))
                 j=find(strncmpi([tripod_struct(fidx).habname],'cond',4));
                 nih=tripod_struct(fidx).hab(j)/100;        %must convert to meters
             elseif (strmatch(sval,names_for_trans))
                 j=find(strncmpi([tripod_struct(fidx).habname],'tran',4));
                 nih=tripod_struct(fidx).hab(j)/100;        %must convert to meters
             elseif (strmatch(sval,names_for_obs))
                 j=find(strncmpi([tripod_struct(fidx).habname],'obs',3));
                 nih=tripod_struct(fidx).hab(j)/100;        %must convert to meters
             elseif (strmatch(lower(ncnms(g)),names_for_ox))
                 j=find(strncmpi([tripod_struct(fidx).habname],'o2',2));
                 nih=tripod_struct(fidx).hab(j)/100;        %must convert to meters
             else
                 disp(['no match for ' char(ncnms(g)) ' in ' char(ncfilename) ])
                 nih=input('Enter the instrument height (m) to use\n','s');
                 nih=str2double(nih);
             end
             %now put the outcome into the variable attributes
             if (~exist('nih'))
                 disp('no instrument height known- please enter one (m):')
                 disp(' use: nih=###; return')
                 keyboard
             end
             nc{name(vn{g})}.sensor_hab=ncfloat(nih);
             nc{name(vn{g})}.sensor_depth=ncfloat(new_struct.new_water_depth-nih);
             if ~isempty(nc{name(vn{g})}.initial_sensor_height(:))
                 nc{name(vn{g})}.initial_sensor_height=ncfloat(nih);
             end
             clear j nih
         end     % for each variable
     else
         disp('OK, time to go back to the drawing board')
         return
     end
     
    [r2,dval2]=extract_ncdepth(nc);

    %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
    % this section changes the contents of the depth() coordinate variable
    %  so keep the original depth info in attributes
    nc{'depth'}.ori_water_depth=water_depth_ori;
    dp=nc{'depth'}(:);  % should be the original measurement_depth
    dnp=num2str(dp(1));
    if length(dp) > 1
        for kk=2:length(dp)
            dnp=[dnp ', ' num2str(dp(kk))];
        end
    end
    nc{'depth'}.oridepth=dnp;   % save the original measurement depth(s)

    % Finally insert adjusted measurement depths- in almost all cases
    % it should be the depth of the measurement(s)
    % for velocity files
    isvel=union(strfind(ncfilename,'v-'), strfind(ncfilename,'v'));  %midas and adv
    isvel2=union(strfind(ncfilename,'s1-'), strfind(ncfilename,'spd'));  %midas and adv
    isvar=strfind(ncfilename,'var-');  % variance stats
    ispr=union(strfind(ncfilename,'p-'), strfind(ncfilename,'psd'));  %pr
    ispca=strfind(ncfilename,'pca');  %pcadp
    istcp=union(strfind(ncfilename,'tc'), strfind(ncfilename,'tp-'));  % older temp and cond
    issb=union(strfind(ncfilename,'mc'), strfind(ncfilename,'sc'));  % seacat
    isaanderaa=union(strfind(ncfilename,'rcm'), strfind(ncfilename,'aa'));  % rcm ctd
    istct=strfind(ncfilename,'tct-');  % tct can have just about anything in it
    iscs=strfind(ncfilename,'cs');  % these only have c & s, no t
    isatt=strfind(ncfilename,'att');  % rcm ctd
    isox=strfind(ncfilename,'ox');  % any oxygen
    isysi=strfind(ncfilename,'ysi');  % any ysi

    if (~isvel & ~isvar & ~istcp & ~issc & ~ismc & ~isatt & ~isox ...
            & ~isvel2 & ~ispca & ~istct & ~iscs & ~isaanderaa)
        disp (['Cannot identify file type for ' ncfilname]);
    end

    if (~isempty(isvar))  % must be before vel- var will be true for both
        tx=(strmatch('uvar_4050',lower(ncnms)));
        eval(['nc{''depth''}(:)=nc{''' char(ncnms(tx)) '''}.sensor_depth(:);']);
        nc{'depth'}.CMNT=ncchar('adjusted using depth of u_variance measurement');
    elseif (~isempty(isvel) || ~isempty(isvel2))
        tx=(strmatch('u_',lower(ncnms)));
        eval(['nc{''depth''}(:)=nc{''' char(ncnms(tx(1))) '''}.sensor_depth(:);']);
        nc{'depth'}.CMNT=ncchar('adjusted using depth of velocity measurement');
    elseif (~isempty(ispr))
        tx=(strmatch('p_4',lower(ncnms)));  % might be p_1, p_4, p_4023
        if isempty(tx)
            tx=(strmatch('p_1',lower(ncnms)));
            if isempty(tx)
                tx=(strmatch('p_4023',lower(ncnms)));
            end
        end
        eval(['nc{''depth''}(:)=nc{''' char(ncnms(tx(1))) '''}.sensor_depth(:);']);
        nc{'depth'}.CMNT=ncchar('adjusted using depth of pressure sensor');
    elseif (~isempty(istct))  % has to be before the ones looking for t_
        tx=length(lower(ncnms));    % use the last variable name
        eval(['nc{''depth''}(:)=nc{''' char(ncnms(tx)) '''}.sensor_depth(:);']);
        nc{'depth'}.CMNT=ncchar('adjusted using depth of last variable');
    elseif (~isempty(issb) || ~isempty(istcp) || ~isempty(isysi))
        tx=(strmatch('t_20',lower(ncnms)));  % might be t_20 or t_24
        if isempty(tx)
            tx=(strmatch('t_24',lower(ncnms)));
            if isempty(tx)
                tx=(strmatch('t_28',lower(ncnms)));
            end
        end
        if ~isempty(tx)
        eval(['nc{''depth''}(:)=nc{''' char(ncnms(tx)) '''}.sensor_depth(:);']);
        nc{'depth'}.CMNT=ncchar('adjusted using depth of temperature measurement');
        end
    elseif (~isempty(iscs))
        tx=(strmatch('s_40',lower(ncnms)));
        eval(['nc{''depth''}(:)=nc{''' char(ncnms(tx)) '''}.sensor_depth(:);']);
        nc{'depth'}.CMNT=ncchar('adjusted using depth of attn measurement');
    elseif (~isempty(isatt))
        tx=(strmatch('attn_55',lower(ncnms)));
        eval(['nc{''depth''}(:)=nc{''' char(ncnms(tx)) '''}.sensor_depth(:);']);
        nc{'depth'}.CMNT=ncchar('adjusted using depth of attn measurement');
    elseif (~isempty(isox))
        tx=(strmatch('o_60',lower(ncnms)));
        eval(['nc{''depth''}(:)=nc{''' char(ncnms(tx)) '''}.sensor_depth(:);']);
        nc{'depth'}.CMNT=ncchar('adjusted using depth of oxygen measurement');
    elseif (~isempty(ispca))
        wd_dif=nc.WATER_DEPTH(:)-water_depth_ori
        new_dp=dp+wd_dif
        nc{'depth'}.CMNT=ncchar('adjusted using dufference between original and new water_depth');
    elseif (~isempty(isaanderaa))
        tx=(strmatch('u_1205',lower(ncnms)));
        nc{'depth'}.CMNT=ncchar('adjusted using depth of velocity measurement');
        if isempty(tx)
            tx=(strmatch('t_',lower(ncnms)));
            nc{'depth'}.CMNT=ncchar('adjusted using depth of temperature measurement');
            if isempty(tx)
                tx=(strmatch('o_60',lower(ncnms)));
                nc{'depth'}.CMNT=ncchar('adjusted using depth of oxygen measurement');
            end
        end
        eval(['nc{''depth''}(:)=nc{''' char(ncnms(tx)) '''}.sensor_depth(:);']);
    else
        disp('not accounted for yet- please modify nc{''depth''} as appropriate')
        keyboard
    end
    % file names with _d3, _d4 will land here, along with any other name
    % that's not "normal"
    if isempty(tx)  %means depth was unchanged
        disp('bad depth variable, trying to fix')
        tnm=ncnames(var(nc));
        [p,q]=size(tnm);
        td=eval(['nc{''' char(tnm(q)) '''}.sensor_depth(:);']);
        eval(['nc{''depth''}(:)=nc{''' char(tnm(q)) '''}.sensor_depth(:);']);
        cmnt=['nc{''depth''}.CMNT=ncchar(''adjusted using depth of ' char(tnm(q)) ' measurement.'')'];
        eval(cmnt);
       % return
       disp ('fixed....')
    end
       if isempty(strmatch('oridepth',ncnames(att(nc{'depth'})))) %depth NOT adjusted
           disp ('unable to repair. exiting')
           return
    end
    [r3,dval3]=extract_ncdepth(nc);

    % check the new file has the right stuff  **uncomment for debugging
    % [char(fn{ik}) ': ']
    % disp([dval.strs{1:2} dval.strs{3}])
    % disp(dval.vals)
    % disp(dval2.vals)
    % disp(dval3.vals)

    % since depth is accounted for, don't do a inst_height in the global
    % metadata- just use the sensor_hab info in each variable
    close(nc)
end

% finally, verify that all the variables seem reasonable and match
eval(['diary log' tripno '.txt'])
for jj=1:length(fn)
    disp_ncdepth(fn{jj});
end
diary off