function cleanup_ysi_tb(ncfilename)
% cleanup_ysi_tb: creates a consistent timebase to use in netCDF file
%  ysi's are patched together from smaller parts so there are usually gaps,
%  but they aren't filled with NaN, so the timebase isn't uniform
% this program adds the missing time steps, and fills all variables at
% those times with fill_Value
%  etm mod  02/17/11

%%% START USGS BOILERPLATE -------------
% These programs are intened for us in adjusting metadata terms in
% netCDF files from the USGS CMGP Oceanographic time-series data
% archive
%
% Program written Matlab 7.6.0.342 (R2008a)
% Program ran on Linux PC with RHEL4 and on Windows XP PC.
%
% "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."
%%% END USGS BOILERPLATE --------------


perloc=findstr('.',ncfilename);
new_nm=[ncfilename(1:perloc-1) '_new.cdf'];

% open input file
nc = netcdf(ncfilename);   % open the a (file named b)
if isempty(nc), return, end
% and the NEW EMPTY output file to take trimmed data
outc = netcdf(new_nm,'clobber');

%% set the dimensions (only applies to coordinate variables)

outc('time') = 0;
outc('depth')=length(nc{'depth'}(:));
outc('lon') = 1;
outc('lat') = 1;

%copy the info over - this is a way of DEFINING the variables
%  this happens in the loop below : copy(nc{'time'},outc,0,1);
% have to copy the structure of the variable into the new array with
% size 0 initially, then copy new contents to determine the size.
vnam=ncnames(var(nc));
% use the names from nc, but get the empty variables from ep-standard.
eps = netcdf('ep_standard.nc');
if isempty(eps)
    [epsfile,epspath] = uigetfile('*.nc','Choose epic standard file');
    eps = netcdf(epsfile);
    if isempty(eps)
        disp (['Cannot open epic standard file ' epsfile]);
        disp (['Execution ends.']);
        ncclose;
        return;
    end
end

for ik=1:length(vnam)% create the non-record variables
    epvar=eps{vnam{ik}};
    if isempty(epvar)  %get from nc, if not in eps
        eval(['copy(nc{''' char(vnam(ik)) '''},outc,0,1);'])
    else
        copy(epvar,outc,0,1);
    end
    % eval(['copy(nc{''' char(vnam(ik)) '''},outc,0,1);'])
end
close(eps)

% endef must be used to terminate the variable definition
% and the termination *MUST* come before values are written to any
% variable!
endef(outc)

% need to copy over all the global attributes here
atn=ncnames(att(nc));
for j=1:length(atn)
    eval( ['copy(nc.' char(atn(j)) ',outc);'])
end

%% Global attributes:
lfeed = char(10);
outc.CREATION_DATE = ncchar(datestr(now,0));
history = ['timebase made even by cleaup_ysy_tb.m:' nc.history(:)];
ifeed = findstr(history,lfeed);
history(ifeed) = ':';
outc.history = ncchar(history);

% NOW set the values of some of the coordinate vars, but don't do time yet!
outc{'lat'}(:)=nc{'lat'}(:);
outc{'lon'}(:)=nc{'lon'}(:);
outc{'depth'}(:)=nc{'depth'}(:);

tt=nc{'time'}(:)+(nc{'time2'}(:)/86400000);
if isnumeric(nc.DELTA_T(:))
    dtjd=(nc.DELTA_T(:)./86400);
else
    dtjd=(str2num(nc.DELTA_T(:)))/86400;
end
tgap=find(diff(tt)> dtjd*1.25);  % not sure why, but the threshold needed to be a bit bigger

%  here we want to insert the shorter strings into the first nlen items
%  later we use nctrim to get rid of the trailing irrelevant junk
nlen=length(tgap)
tnew=tt(1:tgap(1));
for ik=1:nlen
    tdiff=(tt(tgap(ik)+1)-tt(tgap(ik)));
    nskip=round(tdiff/dtjd);
    new_times=tt(tgap(ik))+dtjd:dtjd:tt(tgap(ik))+(nskip-1)*dtjd;
    if (new_times(end)-tt(tgap(ik)+1) ==0)
        new_times(end)=[];
    end
    eval(['nf' num2str(ik) '=ones(length(new_times),1).*nc.VAR_FILL(:);'])
    tnew=[tnew; new_times'];
    if ik==nlen
        tnew=[tnew; tt(tgap(ik)+1:end)];
    else
        tnew=[tnew; tt(tgap(ik)+1:tgap(ik+1))];
    end
    clear nskip new_times tdiff
end
% time part works to here
% put the new time into the coordinate variable
% eptime expects a matlab time string, so we must convert to get it back
% ntime=ep_time(tnew);
% nl=length(ntime);
% outc{'time'}(1:nl)=ntime(:,1);
% outc{'time2'}(1:nl)=ntime(:,2);

t1=floor(tnew);
t2=rem(tnew,floor(tnew));
nl=length(t1);
outc{'time'}(1:nl)=t1;
outc{'time2'}(1:nl)=t2.*86400000;

for ik=[6:length(vnam)]
    %copy the attributes of each variable over
    eval(['copy(nc{''' char(vnam(ik)) ''' }, outc{''' char(vnam(ik)) ''' },0,1);'])
    if strmatch(vnam(ik),'time_cf')
        tmp=linspace(nc{'time_cf'}(1), nc{'time_cf'}(end),length(t1));
    else
    tmp=ones(size(tnew));
    eval(['ori_dat = nc{''' char(vnam(ik)) '''}(:);'])
    % separate indecies are needed because tmp will index by all the flens
    idx1=tgap(1);tidx1=idx1;tidx2=tidx1;
    tmp(1:tidx1)=ori_dat(1:idx1); flentot=0;
    for jj=1:nlen
        eval(['flen=length(nf' num2str(jj) ');']);
        flentot=flentot+flen;
        tidx1=tidx2;
        tidx2=tidx1+flen;
        [tidx1+1 tidx2];
        eval(['tmp(tidx1+1:tidx2)=nf' num2str(jj) ';']);
        if jj<nlen
            tidx1=tidx2; tidx2=tgap(jj+1)+flentot;
            [tidx1+1 tidx2];
            tmp(tidx1+1:tidx2)=ori_dat(idx1+1:tgap(jj+1));
            idx1=tgap(jj+1);
         else
            tidx1=tidx2; tidx2=length(ori_dat)+flentot;
            [tidx1+1 tidx2];
            tmp(tidx1+1:tidx2)=ori_dat(idx1+1:length(ori_dat));
        end     
    end
    end
    eval(['outc{''' char(vnam(ik)) '''}(:) = tmp;'])
end

close (outc);
close (nc);