% ARTS_ABSTABLE_FROM_ARTS1   Creates an ARTS absorption lookup table
%
%    ARTS1 is used to generate the absorption lookup table. Spectrocopic
%    settings follows Qarts1. See needed fields below.
%
%    Gas species, grids and atmospheric state are specified following Qarts.
%    Needed fields are listed below. The frequency and pressure grid in the
%    absorption table will be Q.F_GRID and Q.P_GRID. If the atmospheric
%    dimension, the VMR reference state is taken as a mean over all latitude
%    and longitude profiles.
%
%    Needed Qarts fields:
%       ABS_SPECIES
%       P_GRID
%       F_GRID
%       ATMOSPHERE_DIM
%       USE_RAW_ATMOSPHERE 
%       atmospheric fields following value of USE_RAW_ATMOSPHERE  
%
%    Needed Qarts1 fields:
%       LINEFORMAT
%       LINEDATA  
%       LINESHAPE  
%       LINESHAPE_FACTOR 
%       LINESHAPE_CUTOFF 
%       ABSMODELS 
%
% FORMAT   A = arts_abstable_from_arts1( Q, Q1, dt [, workfolder ] )
%        
% OUT   A    Absorption table structure.
% IN    Q    ARTS settings.
% IN    Q1   ARTS1 settings.
%       dt   Vector with temperature perturbations. Default is 0.
% 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 not is considered.
%                    Default is [].

% 2004-09-08   Created by Patrick Eriksson.


function A = arts_abstable_from_arts1( Q, Q1, dt, workfolder )


%= Default values
%
dt_DEFAULT         = 0;
workfolder_DEFAULT = [];
%
set_defaults;


%- Check input
%
rqre_datatype( 'struct', Q );
rqre_datatype( {'empty','char'}, workfolder );


folder_created = 0;
%
if isempty( workfolder )
  workfolder   = create_tmpfolder;
end



try 
  %=== Obtain profiles through ARTS
  %
  rqre_bool( 'ARTS field USE_RAW_ATMOSPHERE', Q.USE_RAW_ATMOSPHERE );
  %
  p_grid   = qarts_get( Q.P_GRID );
  %
  if Q.USE_RAW_ATMOSPHERE
    %
    [t_field,z_field,vmr_field] = arts_get_atmfields( Q ); 
  else
    t_field   = qarts_get( Q.T_FIELD );
    z_field   = qarts_get( Q.Z_FIELD );
    vmr_field = qarts_get( Q.VMR_FIELD );
    %
    np = length( p_grid );
    if np~=size(t_field,1)  |  np~=size(z_field,1)  |  np~=size(vmr_field,2)
      error( 'Either T_FIELD, Z_FIELD or VMR_FIELD does not match P_GRID' );
    end
  end


  %=== Compact to 1D
  %
  if Q.ATMOSPHERE_DIM == 3
   t_field = mean( t_field, 3 );
   z_field = mean( z_field, 3 );
   vmr_field = mean( vmr_field, 4 );
  end
  if Q.ATMOSPHERE_DIM > 1
   t_field = mean( t_field, 2 );
   z_field = mean( z_field, 2 );
   vmr_field = mean( vmr_field, 3 );
  end


  %=== Assign obtained fields corresponding Qarts1 fields
  %
  Q1.USE_RAW_ATMOSPHERE = 0;
  Q1.P_ABS = p_grid;
  Q1.Z_ABS = z_field;
  Q1.VMRS  = vmr_field;


  %=== Copy some fields from Q to Q1
  %
  Q1.TGS    = Q.ABS_SPECIES;
  if ischar(  Q.F_GRID )
    Q1.F_MONO = xmlLoad( Q.F_GRID );
  else
    Q1.F_MONO = Q.F_GRID;
  end


  %=== Define control file for ARTS1 run
  %
  cfile = fullfile( workfolder, 'cfile.arts' );
  parts = {'tgs','load_atm','pf_grids','spectroscopy','calc_abs',...
           'save_abs_per_tg'};


  %=== Create absorption table
  %
  A.species           = Q.ABS_SPECIES;
  A.nonlinear_species = {};
  A.f_grid            = vec2col( qarts_get( Q.F_GRID ) );
  A.p_grid            = vec2col( qarts_get( Q.P_GRID ) );
  A.vmrs_ref          = vmr_field;
  A.t_ref             = vec2col( t_field );
  A.t_pert            = dt;
  A.nls_pert          = [];
  %
  nt = length(dt);
  nf = length(A.f_grid);
  %
  A.xsec = zeros( nt, length(A.species), nf, length(A.p_grid) );
  %
  for i = 1 : nt
    %
    Q1.T_ABS = t_field + dt(i);
    %
    S = qarts12cfile( Q1, parts, workfolder );
    qtool( S, cfile, [] );
    arts1( cfile );
    %
    X = arts1_loadfile( workfolder, 'abs_per_tg', 'AOMATRIX' );
    %
    for j = 1 : length(A.species)
      A.xsec(i,j,:,:) = X{j} ./ ...
                repmat( vmr2nd( A.vmrs_ref(j,:), A.p_grid, Q1.T_ABS )', nf, 1 );
    end
    %
  end

  if folder_created
    delete_tmpfolder( workfolder );
  end


catch
  if folder_created
    delete_tmpfolder( workfolder );
  end

  rethrow(lasterror);
end