% ARTS_Y   Calculates spectra using ARTS
%
%    Qarts fields for atmosphere, absorption, sensor and RT must be
%    specified.
%
% FORMAT   [y,dy,J,jq,ji] = arts_y( Q )
%        
% OUT   y   Spectrum vector.
%       dy  Estimate of calculation accuracy.
%       J   Jacobian. NaN returned if Q.J not defined.
%       jq  Jacobian quantities. NaN returned if Q.J not defined.
%       ji  Jacobian indices. NaN returned if Q.J not defined.
%           Indices are 1-based (that is, ARTS indices + 1);
% IN    Q   Qarts structure.

% 2004-09-17   Created by Patrick Eriksson.


function [y,dy,J,jq,ji] = arts_y( Q )


%- Avoid unnecessary Jacobian calculations
%
do_j = 1;
%
if nargout <= 2  |  isnan(Q.SENSOR_RESPONSE)  |  Q.SENSOR_RESPONSE == 0
  do_j = 0;
end


tmpfolder   = create_tmpfolder;

try
  %
  if do_j
    parts = qarts2cfile( 'y+j' );
  else
    parts = qarts2cfile( 'y+j' );
  end
  S     = qarts2cfile( Q, parts, tmpfolder );
  cfile = fullfile( tmpfolder, 'cfile.arts' );
  qtool( S, cfile, [] );
  arts( cfile );

catch
  delete_tmpfolder( tmpfolder );
  rethrow(lasterror);
end


if isstruct( Q.CLOUDBOX )  
  if strcmp(upper(Q.CLOUDBOX.METHOD),'MC')
    dy = xmlLoad( fullfile( tmpfolder, 'mc_error.xml' ) );
  else
    dy = NaN;
  end
else
  dy = NaN;
end

y = xmlLoad( fullfile( tmpfolder, 'y.xml' ) );


if do_j
  J = xmlLoad( fullfile( tmpfolder, 'jacobian.xml' ) );
  if nargout >= 4
    jq = xmlLoad( fullfile( tmpfolder, 'jacobian_quantities.xml' ) );
    ji = xmlLoad( fullfile( tmpfolder, 'jacobian_indices.xml' ) );
    for i = 1 : length(ji)
      for j = 1 : length(ji{i})
        ji{i}{j} = ji{i}{j} + 1;
      end
    end
  end
else
  J  = NaN;
  jq = NaN;
  ji = NaN;
end


delete_tmpfolder( tmpfolder );