%------------------------------------------------------------------------
% NAME:     qp_x2arts
%
%           Maps a state vector to ARTS variables.
%
%           The function can be used for iterative retrievals to apply the
%           present state.
%
%           If the RECALC_ABS=0, the absorption is scaled to match the
%           retrieved species profiles. If RECALC_ABS=1, only the species
%           profiles are stored and the absorption must be recalculed in
%           next iteration.
%
%           The function is developed for qpcls but can maybe be useful
%           for other purposes.
%
% FORMAT:   map_x( Q, x, basename, Kx, kx_names, kx_index, kx_aux, 
%                          recalc_abs, logspecies, p_abs, vmrs, Abs, Absp, za )
%
% IN:       Q           Q structure.
%           x           The state vector.
%           basename    Basename for the ARTS calculations.
%           Kx          Weighting function matrix.
%           kx_names    As the corresponding ARTS variable.
%           kx_index    Start and stop index for each retrieval identity.
%                       A 2 column matrix.
%           kx_aux      As the corresponding ARTS variable.
%           recalc_abs  Flag to determine if absorption will be recalculated
%           logspecies  Flag for retrieval of the log. of species.
%           p_abs       As ARTS variable p_abs.
%           f_mono      As ARTS variable f_mono.
%           vmrs        As ARTS variable vmrs.
%           Abs         As ARTS variable abs.
%           Absp        As ARTS variable abs_per_tg.
%           za          As ARTS variable za_pencil.
%------------------------------------------------------------------------

% HISTORY: 2001.01.04  Started by by Patrick Eriksson.


function qp_x2arts( Q, x, basename, Kx, kx_names, kx_index, kx_aux, recalc_abs, logspecies, p_abs, f_mono, vmrs, Abs, Absp, za )


yc       = 0;
ispecies = 0;
nf       = length( f_mono );
Cabs     = [];                % Matrix for continuum absorption


i = 0;
%
while i < size(kx_names,1)

  i = i + 1;

  [group,name,par1] = qp_kinfo( kx_names{i} );

  ind = kx_index(i,1):kx_index(i,2);

  %=== Species
  %
  if strcmp( group, 'Species' )
    %
    ispecies = ispecies + 1;
    %
    xp = interpp( kx_aux(ind,1), x(ind), p_abs );
    %
    if logspecies
      xp = exp( xp );
    end
    %
    vmrs(ispecies,:) = vmrs(ispecies,:) .* xp'; 
    %
    if ~recalc_abs
      %
      dAbs = Absp{ispecies} .* ( ones(nf,1) * (xp-1)' );
      Absp{ispecies} = Absp{ispecies} + dAbs; 
      Abs = Abs + dAbs;
      %
    end


  %=== Temperature
  %
  elseif strcmp( group, 'Temperature' )
    %
    t_abs = interpp( kx_aux(ind,1), x(ind), p_abs );
    write_artsvar( basename, 't_abs', t_abs, 'b' );


  %=== Continuum fit
  %
  elseif strcmp( group, 'Continuum' )
    %
    [ flimits, fp, f_mono ] = qp_contabs_freqs( Q );
    %
    indf = find( f_mono>=flimits(1) & f_mono<=flimits(2) );
    indp = find( p_abs<=kx_aux(ind(1),1) & p_abs>=kx_aux(last(ind),1) );
    % 
    np = length(fp);
    nx = length(ind);
    Xv = zeros( np, nx );
    %
    for ii = 1 : length(fp)
      ind      = kx_index(i+ii-1,1):kx_index(i+ii-1,2);
      Xv(ii,:) = 1e-3 * x(ind)';                      % conversion 1/km to 1/m
    end
    %
    fp = fp' /1e9;
    fm = f_mono/1e9;
    %
    Xe = zeros( length(indf), nx );
    %
    for ii = 1:nx
      Xe(:,ii) = polyval( polyfit( fp, Xv(:,ii), Q.CONTABS_ORDER ), fm(indf) );
    end
    %
    Cabs            = zeros( nf, length(p_abs) );
    Cabs(indf,indp) = interpp( kx_aux(ind,1), Xe', p_abs(indp) )';   
    %
    i = i + np - 1;
    %
    clear fp fm Xv Xe indf indp


  %=== Pointing off-set
  %
  elseif strcmp( name, 'Pointing: off-set' )
    %
    za = za + x(ind);
    write_artsvar( basename, 'za_pencil', za, 'b' );


  %=== Frequency off-set
  %
  %  MHz is used here as internal unit.
  % 
  elseif strcmp( name, 'Frequency: off-set' )
    %
    f_mono = f_mono + x(ind) * 1e6;
    write_artsvar( basename, 'f_mono', f_mono, 'b' );


  %=== Ground emission
  %
  elseif strcmp( group, 'Ground emission' )
    %
    x(ind) = check_minmax( x(ind), Q.EGROUND_MINMAX );
    %
    e_ground = read_artsvar( basename, 'e_ground' );
    f_mono   = read_artsvar( basename, 'f_mono' );
    [ fp, findex ] = qp_eground_lims( f_mono, Q.EGROUND_LIMITS );
    %
    for ii = 1 : length(fp)
      is = findex(ii,1) : findex(ii,2); 
      e_ground(is) = x(ind(ii));
    end
    write_artsvar( basename, 'e_ground', e_ground, 'b' );


  %=== Baseline fits
  %
  elseif strcmp( group, 'Baseline' )
    %
    yc = yc + Kx(:,ind) * x(ind);


  %=== Quantities handled by qp_x2y are ioncluded here so it can be checked
  %=== that all quantities are handled.
  %
  elseif strcmp( group, 'Baseline' )
    %

  elseif strcmp( name, 'Reference load temperatures' )
    %

  elseif strcmp( name, 'Proportional calibration error' )
    %

  else
     error(sprintf( 'Unknown retrieval identity: %s', name ));
  end
end



%=== Save profile/absorption data
%
write_artsvar( basename, 'vmrs', vmrs, 'b' );
%
if ~recalc_abs
  if ~isempty( Cabs )
    Abs = Abs + Cabs;
  end
  write_artsvar( basename, 'abs', Abs, 'b' );
  write_artsvar( basename, 'abs_per_tg', Absp, 'b' );

else
  if isempty( Cabs )
    Cabs = zeros( nf, length(p_abs) );
  end
  write_artsvar( basename, 'abs0', Cabs, 'b' );

end
  




function x = check_minmax( x, minmax );

  if isempty( minmax )
    return
  end

  if length(minmax) ~= 2
    error( ...
        'The length of a vector with min and max values must have length 2.');
  end

  i = find ( x < minmax(1) );
  if ~isempty(i)
     x(i) = minmax(1);
  end

  i = find ( x > minmax(2) );
  if ~isempty(i)
     x(i) = minmax(2);
  end

return