function statrtn=cvt_nep2sed_brst(infile,outfile, extmeta)
% cvt_nep2sed_brst: computes sediment concentration from nep (raw volts)
%  uses equation from dohydraoptic to correct or compute sed. conc. from OBS.
% works on burst files.
%
% ** this is very slow, and doesn't put optic into sed_981 properly.  It
%    can be used to remove the bad sed from the data, but not putting new
%    in
%
%  usage :
%       extm.height = 0.99; % m
%       extm.cals.gain = .33; % for OBS gain setting, g/l per volt
%       extm.cals.coef = [2.4687 133.1316];
%       extm.remove_minVolt=0;  % remove minimum voltage (1 for yes)
%       status ==cvt_nep2sed_brst('8446advb-cal.nc','8446advb-new.nc',extm)
% emontgomery 9/3/09

if exist(infile,'file')
    nc = netcdf(infile);
else
    [infile,inpath] = uigetfile('*.cdf','Choose input file');
    nc = netcdf(infile);
    if isempty(nc)
        disp (['Cannot open input file ' infile]);
        statrtn=0;
        disp (['Execution ends.']);
        return;
    end
end

[nvarin,chosen] = em_dollyvar(nc,'y');
nvarout=nvarin;

% Get the global attributes
keepatts = att(nc);
ngatts=length(keepatts);

% get the variablenames
for ivar = 1:nvarin;
    invar = nc{chosen{ivar}};
    invar = autonan(invar,1);
    inname{ivar} = name(invar);
end

% get the length of the data- this won't change
ntimes=length(nc{'time'}(:));

%get existing neph data 
% so far we only have one OBS/logger, so we don't need to handle more than
% one thing in loc (yet)
loc=strmatch('NEP',chosen);
loc2=strmatch('Sed',chosen);

extvolts=nc{chosen{loc}}(:,:);
sz=size(nc{'time'}); 
  p=sz(1); q=sz(2);  % p = #bursts, q = pts in burst
  % find the number of the ext connector
  extno=chosen{loc}(4);

% this is the part from dohydraoptic
if ~isempty(findstr('OBS',extmeta.serial)),
    if ~(isfield(extmeta,'remove_minVolt'))
        extmeta.remove_minVolt=0;
    end
    if extmeta.remove_minVolt
       adj_evolt =extvolts-min(extvolts);
    else 
       adj_evolt=extvolts;
    end     
    if isfield(extmeta.cals,'coef') && ~isempty(extmeta.cals.coef),
        % user has supplied coefficients
         optic = min(min(extvolts)).*ones(size(extvolts));      
        for n = 2:length(extmeta.cals.coef),
            optic = optic + extmeta.cals.coef(n).*(extvolts.^(n-1));
        end
    else
        % No coefficients, no conversion
        %disp('dohydraoptic: No coefficients supplied for the OBS')
        optic = [];
    end
else
    optic = extvolts;
end
% end part from dohydraoptic

% Open output cdf
outc = netcdf(outfile,'noclobber');
if isempty(outc)
    [outfile,outpath] = uiputfile('*.nc','Choose output file');
    outc = netcdf(fullfile(outpath,outfile),'noclobber'); % MM 11/18/04 add path
    if isempty(outc)
        disp (['Cannot open output file ' outfile]);
        disp (['Data will be parked in temporary.nc']);
        outc = netcdf('temporary.nc','clobber');
    end
end

%Update global attributes and variables in output file.
history =['Sed_981 created or modified by cvt_nep2sed_brst :' nc.history(:)]

vardesc=nc.VAR_DESC(:);
if isempty(strfind(vardesc,'sed'))  % add sed to the list, if missing
    vardesc = [vardesc ':sed' extno];
    nvarout=nvarout+1;
    loc2=nvarout;        % new cases of sed will be added to the end
end

% Dimensions:
outc('time') = p;
outc('depth') = 1;
outc('lon') = 1;
outc('lat') = 1;
outc('sample') = q;
% Variables and attributes:
%   ncvar/copy with 1,1,1 == copy data, copy attributes, copy dimensions
copy(nc{'time'},outc,1,1,1);
copy(nc{'time2'},outc,1,1,1);
copy(nc{'depth'},outc,1,1,1);
copy(nc{'lon'},outc,1,1,1);
copy(nc{'lat'},outc,1,1,1);
copy(nc{'burst'},outc,1,1,1);

% Copy global attributes from input file to output file.
for i = 1 : length(keepatts);
    copy(keepatts{i},outc);
end
% now add the ones that needed updating
outc.history = history;
outc.VAR_DESC = ncchar(vardesc);
outc.CREATION_DATE = ncchar(datestr(now,0));

for i = 2: nvarout;
    disp (['creating output variable ' inname{i}]);
    ivar = nc{inname{i}};
    if ~isempty(strmatch('Sed',chosen{i}))
        copy(ivar,outc,1,1,1);
    else
        sedname=['Sed' extno '_981'];
        nc{sedname} = ncfloat('time', 'depth', 'lat', 'lon', 'sample')
        nc{sedname}.name = ncchar('Sed');
        nc{sedname}.long_name = ncchar('Sediment concentration ');
        nc{sedname}.generic_name = ncchar('sed');
        nc{sedname}.FORTRAN_format = ncchar('f10.2');
        nc{sedname}.units = ncchar('g/l');
        nc{sedname}.epic_code = nclong(981);
        nc{sedname}.code = ncchar('R');
        nc{sedname}.sensor_depth = ncfloat(0);
        nc{sedname}.serial_number = ncchar('OBS2181');
        nc{sedname}.minimum = ncfloat(0);
        nc{sedname}.maximum = ncfloat(0);
        nc{sedname}.valid_range = ncfloat([0 1500]);
        nc{sedname}.FillValue_ = 1.0e35;
    end
end

%disable define mode
    endef(outc)
    % put new optic data in the file           
        outc{chosen{loc2}}(1:p,1:q) = optic;
        outc{chosen{loc2}}.minimum = ncfloat(min(min(optic)));
        outc{chosen{loc2}}.maximum = ncfloat(max(max(optic)));

% now close the ncfiles
close (outc);
close (nc);
statrtn=1;