% ARTS_Y   Calculates spectra and jacobians using ARTS
%
%    Takes a qarts structure and calculates corresponding spectra.
%
%    Auxilary data and jacobians are also returned. The later requires an
%    active selection through J_DO. Otherwise NaN is returned.
%    variables.
%
% FORMAT   [y,y_aux,J,jq,ji] = arts_y( Q [, workfolder] )
%        
% OUT   y            Spectrum vector.
%       y_aux        Auxilary data (see *y_aux*).
%       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.
% OPT   workfolder   If not defined or empty, a temporary folder is created.
%                    Otherwise this is interpreted as the path to a folder 
%                    where calculation output can be stored. These files
%                    will be left in the folder. The files are not read if
%                    corresponding output argument is not considered.
%                    Default is [].

% 2004-09-17   Created by Patrick Eriksson.

function [y,y_aux,J,jq,ji] = arts_y( Q, workfolder )
%
if nargin < 2, workfolder = []; end
%
if atmlab( 'STRICT_ASSERT' )
  rqre_datatype( Q, @isstruct );
  rqre_datatype( workfolder, {@isempty,@ischar} );
end


%- Default output
%
[y_aux,J,jq,ji] = deal( NaN );


%- Create workfolder?
%
if isempty( workfolder )
  workfolder = create_tmpfolder;
  cu = onCleanup( @()delete_tmpfolder( workfolder ) );
end


%- Avoid unnecessary calculations
%
if nargout < 3
  Q.J_DO = false;
end


%- Run ARTS
%
parts = qarts2cfile( 'y' );    
S     = qarts2cfile( Q, parts, workfolder );
cfile = fullfile( workfolder, 'cfile.arts' );
strs2file( cfile, S );
arts( cfile );


%- Load data

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


if nargout >= 2
  y_aux = xmlLoad( fullfile( workfolder, 'y_aux.xml' ) );
end

if nargout >= 3  & qarts_isset( Q.J_DO ) &  Q.J_DO
  %
  J = xmlLoad( fullfile( workfolder, 'jacobian.xml' ) );
  %
  if nargout >= 4
    jq = xmlLoad( fullfile( workfolder, 'jacobian_quantities.xml' ) );
    ji = xmlLoad( fullfile( workfolder, 'jacobian_indices.xml' ) );
    for i = 1 : length(ji)
      for j = 1 : length(ji{i})
        ji{i}{j} = ji{i}{j} + 1;
      end
    end
  end
end