xsh_absorp.c

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/*                                                                            *
 *   This file is part of the ESO X-shooter Pipeline                          *
 *   Copyright (C) 2006 European Southern Observatory                         *
 *                                                                            *
 *   This library is free software; you can redistribute it and/or modify     *
 *   it under the terms of the GNU General Public License as published by     *
 *   the Free Software Foundation; either version 2 of the License, or        *
 *   (at your option) any later version.                                      *
 *                                                                            *
 *   This program is distributed in the hope that it will be useful,          *
 *   but WITHOUT ANY WARRANTY; without even the implied warranty of           *
 *   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the            *
 *   GNU General Public License for more details.                             *
 *                                                                            *
 *   You should have received a copy of the GNU General Public License        *
 *   along with this program; if not, write to the Free Software              *
 *   Foundation, 51 Franklin St, Fifth Floor, Boston, MA  02111-1307  USA     *
 *                                                                            */
 
/*
 * $Author: amodigli $
 * $Date: 2012-12-18 14:12:51 $
 * $Revision: 1.13 $
*/
 
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
 
/*----------------------------------------------------------------------------*/
/*----------------------------------------------------------------------------*/
/*-----------------------------------------------------------------------------
  Includes
  ----------------------------------------------------------------------------*/
 
 
/* DRL steps */
 
/* Error handling */
#include <xsh_error.h>
/* Utility fonctions */
#include <xsh_utils.h>
#include <xsh_utils_scired_slit.h>
#include <xsh_msg.h>
/* DFS functions */
#include <xsh_dfs.h>
#include <xsh_pfits.h>
/* DRL functions */
#include <xsh_utils_image.h>
#include <xsh_utils_scired_slit.h>
#include <xsh_data_instrument.h>
#include <xsh_data_spectrum1D.h>
#include <xsh_drl_check.h>
#include <xsh_drl.h>
#include <xsh_model_utils.h>
/* Library */
#include <cpl.h>
/* CRH Remove */
 
/*-----------------------------------------------------------------------------
  Defines
  ----------------------------------------------------------------------------*/
 
#define RECIPE_ID "xsh_absorp"
#define RECIPE_AUTHOR "P.Goldoni, L.Guglielmi, R. Haigron, F. Royer, A. Modigliani"
#define RECIPE_CONTACT "regis.haigron@obspm.fr,amodigli@eso.org"
 
/*-----------------------------------------------------------------------------
  Functions prototypes
  ----------------------------------------------------------------------------*/
 
/*
 *   Plugin initalization, execute and cleanup handlers
 */
 
 
static int xsh_absorp_create(cpl_plugin *);
static int xsh_absorp_exec(cpl_plugin *);
static int xsh_absorp_destroy(cpl_plugin *);
 
/* The actual executor function */
static cpl_error_code xsh_absorp(cpl_parameterlist *, cpl_frameset *);
 
/*-----------------------------------------------------------------------------
  Static variables
  ----------------------------------------------------------------------------*/
static char xsh_absorp_description_short[] =
"Create a telluric absorption mask";
 
static char xsh_absorp_description[] =
"This recipe creates a mask corresponding to the positions of telluric absorption\n\
Input Frames : \n\
  - A set of n Science frames ( n == 1 or >=3, Tag = STD_TELL_SLIT_STARE_arm)\n\
  - A spectral format table (Tag = SPECTRAL_FORMAT_TAB_arm)\n\
  - [UVB,VIS] A master bias frame (Tag = MASTER_BIAS_arm)\n\
  - [OPTIONAL]A master dark frame (Tag = MASTER_DARK_arm)\n\
  - A master flat frame (Tag = MASTER_FLAT_SLIT_arm)\n\
  - An order table frame(Tag = ORDER_TAB_EDGES_SLIT_arm)\n\
  - [OPTIONAL] A table with dispersion coefficients (Tag = DISP_TAB_arm,\n\
    required if rectify-conserve-flux=TRUE or do_wavemap=TRUE and poly mode\n\
  - [poly mode] A wave solution frame(Tag = WAVE_TAB_2D_arm)\n\
  - [physical model mode] A model cfg table (Format = TABLE, Tag = XSH_MOD_CFG_TAB_arm)\n\
  - [OPTIONAL] A table specifying multiplying factor for break points \n\
    (Tag = SKY_SUB_BKPTS_arm) to generate\n\
  - [OPTIONAL] A badpixel map (Tag = BADPIXEL_MAP_arm)\n\
  - [OPTIONAL,physmod mode] A table listing sky line positions (Tag = SKY_LINE_LIST_arm)\n\
    this is used to be able to control quality of sky subtraction, for example\n\
    projecting guess positions on the product SCI_SLIT_STARE_SUB_SKY_arm\n\
Products : \n\
  - TELL_MASK_arm telluric mask\n\
  - PREFIX_ORDER2D_arm extracted spectrum, order-by-order, 2D\n\
  - PREFIX_ORDER1D_arm extracted spectrum, order-by-order, 1D\n\
  - PREFIX_MERGE2D_arm merged spectrum, 2D\n\
  - PREFIX_MERGE1D_arm merged spectrum, 1D\n\
  - PREFIX_ON_arm bias (dark) subtracted sci frame\n\
  - PREFIX_SUB_BACK_SLIT_arm sci frame bias, (dark), inter-order bkg subtracted\n\
  - PREFIX_NOCRH_arm sci frame corrected from cosmic ray hits\n\
  - [OPTIONAL,-compute-map=TRUE] PREFIX_WAVE_MAP_arm, wave map image\n\
  - [OPTIONAL,-compute-map=TRUE] PREFIX_SLIT_MAP_arm, slit map image\n\
  - PREFIX_DIVFF_arm as PREFIX_SUB_BACK_SLIT_arm, flat fielded\n\
  - PREFIX_SUB_SKY_arm, as PREFIX_DIVFF_arm, sky subtracted\n\
  - PREFIX_SKY_arm, 2D sky frame\n\
  - PREFIX_SKY_ORD1D_arm, 1D sky image (order-by-order)\n\
  - PREFIX_SCI_SLIT_STARE_BACK_SLIT_arm, inter-order background image\n\
  - OBJECT_SLIT_STARE_arm, sci frame in PRE format\n\
  - where PREFIX is SCI, FLUX, TELL if input raw DPR.TYPE contains OBJECT or FLUX or TELLURIC";
 
/*-----------------------------------------------------------------------------
  Functions code
  ----------------------------------------------------------------------------*/
/*----------------------------------------------------------------------------*/
/*----------------------------------------------------------------------------*/
 
int cpl_plugin_get_info(cpl_pluginlist *list) {
  cpl_recipe *recipe = NULL;
  cpl_plugin *plugin = NULL;
 
  recipe = cpl_calloc(1, sizeof(*recipe));
  if ( recipe == NULL ){
    return -1;
  }
 
  plugin = &recipe->interface ;
 
  cpl_plugin_init(plugin,
                  CPL_PLUGIN_API,                    /* Plugin API */
                  XSH_BINARY_VERSION,             /* Plugin version */
                  CPL_PLUGIN_TYPE_RECIPE,            /* Plugin type */
                  RECIPE_ID,                         /* Plugin name */
                  xsh_absorp_description_short, /* Short help */
                  xsh_absorp_description,       /* Detailed help */
                  RECIPE_AUTHOR,                     /* Author name */
                  RECIPE_CONTACT,                    /* Contact address */
                  xsh_get_license(),                 /* Copyright */
                  xsh_absorp_create,
                  xsh_absorp_exec,
                  xsh_absorp_destroy);
 
  cpl_pluginlist_append(list, plugin);
 
  return (cpl_error_get_code() != CPL_ERROR_NONE);
}
 
/*----------------------------------------------------------------------------*/
/*----------------------------------------------------------------------------*/
 
static int xsh_absorp_create(cpl_plugin *plugin){
  cpl_recipe *recipe = NULL;
  cpl_parameter* p=NULL;
 
  xsh_clipping_param crh_clip_param = {5.0, 5, 0.7, 0, 0.3};
  /* First param (conv_kernel) should be initialized correctly ! */
  xsh_remove_crh_single_param crh_single = { 0.1, 5, 2.0, 4} ;
  xsh_rectify_param rectify = { "default", 
                                CPL_KERNEL_DEFAULT, 
                                4, 
                                XSH_WAVE_BIN_SIZE_PIPE_NIR, 
                                XSH_SLIT_BIN_SIZE_PIPE_NIR,
                                1,
                0, 0. }; 
 
  xsh_subtract_sky_single_param sky_single = {3000, 3000,7,20, 5., -1, -1,
                                              BSPLINE_METHOD, FINE,7, 1.5,
                                             0.0, 0.0,
                                             0.0, 0.0} ;
  xsh_stack_param stack_param = {"median",5.,5.,5};
  /* 2nd and 3rd params should be initialized correctly */
  xsh_localize_obj_param loc_obj = 
    {10, 0.1, 0, 0, LOC_MANUAL_METHOD, 0, 2.0,3,3, FALSE};
  xsh_extract_param extract_par = 
    { LOCALIZATION_METHOD };
 
  xsh_opt_extract_param opt_extract_par = 
     { 5, 10, 10, 0.01, 10.0, 1., 2, 2, GAUSS_METHOD }; 
 
  /* Parameters init */
  opt_extract_par.oversample = 5;
  opt_extract_par.box_hsize = 10;
  opt_extract_par.chunk_size = 50;
  opt_extract_par.lambda_step = 0.02;
  opt_extract_par.clip_kappa = 3;
  opt_extract_par.clip_frac = 0.4;
  opt_extract_par.clip_niter = 2;
  opt_extract_par.niter = 1;
  opt_extract_par.method = GAUSS_METHOD;
  /* Reset library state */
  xsh_init();
 
  /* Check input */
  assure( plugin != NULL, CPL_ERROR_NULL_INPUT, "Null plugin");
 
  /* Get the recipe out of the plugin */
  assure( cpl_plugin_get_type(plugin) == CPL_PLUGIN_TYPE_RECIPE,
          CPL_ERROR_TYPE_MISMATCH,
          "Plugin is not a recipe");
 
  recipe = (cpl_recipe *)plugin;
 
  /* Create the parameter list in the cpl_recipe object */
  recipe->parameters = cpl_parameterlist_new();
  assure( recipe->parameters != NULL,
          CPL_ERROR_ILLEGAL_OUTPUT,
          "Memory allocation failed!");
 
  /* Set generic parameters (common to all recipes) */
  check( xsh_parameters_generic( RECIPE_ID, recipe->parameters ) ) ;
  xsh_parameters_decode_bp(RECIPE_ID,recipe->parameters,-1);
  check( xsh_parameters_pre_overscan( RECIPE_ID, recipe->parameters ) ) ;
  check(xsh_parameters_stack_create(RECIPE_ID,recipe->parameters,stack_param));
 
  /* crh clipping params */
  check(xsh_parameters_clipping_crh_create(RECIPE_ID,recipe->parameters,
    crh_clip_param));
 
  /* subtract_background_params */
  check(xsh_parameters_background_create(RECIPE_ID,recipe->parameters));
 
 
  check(p=xsh_parameters_find(recipe->parameters,RECIPE_ID,"background-method"));
  cpl_parameter_set_default_string(p,"poly");
 
 
  /* remove_crh_single */
  check(xsh_parameters_remove_crh_single_create(RECIPE_ID,recipe->parameters,
                        crh_single )) ;
 
  /* xsh_rectify */
  check(xsh_parameters_rectify_create(RECIPE_ID,recipe->parameters,
                        rectify )) ;
 
  /* xsh_localize_object */
  check(xsh_parameters_localize_obj_create(RECIPE_ID,recipe->parameters,
                       loc_obj )) ;
 
  /* xsh_remove_sky_single */
  check(xsh_parameters_subtract_sky_single_create(RECIPE_ID,recipe->parameters,
                          sky_single )) ;
 
  /* trivial extract (Just temporary) */
  check(xsh_parameters_extract_create(RECIPE_ID,
                      recipe->parameters,
                      extract_par,LOCALIZATION_METHOD )) ;
 
  /* optimal extract */
  check( xsh_parameters_new_boolean( recipe->parameters, RECIPE_ID,
    "do-optextract", FALSE, 
    "TRUE if we do the optimal extraction"));
 
  check( xsh_parameters_opt_extract_create( RECIPE_ID, recipe->parameters,
    opt_extract_par));
 
  /* absorp parameters */
  check( xsh_parameters_new_int( recipe->parameters, RECIPE_ID,
    "absorp-filter-hsize", 5,
     "Half size of median filter use to detect tellurics"));
  check( xsh_parameters_new_double( recipe->parameters, RECIPE_ID,
    "absorp-threshold", 0.02,
     "Threshold use to detect tellurics"));
 
  check( xsh_parameters_new_boolean( recipe->parameters, RECIPE_ID,
    "do-flatfield", TRUE, 
    "TRUE if we do the flatfielding"));
 
  check( xsh_parameters_new_boolean( recipe->parameters, RECIPE_ID,
    "compute-map", TRUE,
     "if TRUE recompute (wave and slit) maps from the dispersion solution. If sky-subtract is set to TRUE this must be set to TRUE."));
 
  check( xsh_parameters_new_boolean( recipe->parameters, RECIPE_ID,
    "trace-obj", FALSE,
     "if TRUE compute object position trace via Gaussian fit."));
 
  
 cleanup:
  if ( cpl_error_get_code() != CPL_ERROR_NONE ){
    xsh_error_dump(CPL_MSG_ERROR);
    return 1;
  }
  else {
    return 0;
  }
}
 
/*----------------------------------------------------------------------------*/
/*----------------------------------------------------------------------------*/
 
static int xsh_absorp_exec(cpl_plugin *plugin) {
  cpl_recipe *recipe = NULL;
 
  /* Check parameter */
 
  assure( plugin != NULL, CPL_ERROR_NULL_INPUT, "Null plugin" );
 
  /* Get the recipe out of the plugin */
  assure( cpl_plugin_get_type(plugin) == CPL_PLUGIN_TYPE_RECIPE,
          CPL_ERROR_TYPE_MISMATCH, "Plugin is not a recipe");
 
  recipe = (cpl_recipe *)plugin;
 
  /* Check recipe */
  xsh_absorp(recipe->parameters, recipe->frames);
 
 cleanup:
  if ( cpl_error_get_code() != CPL_ERROR_NONE ) {
    xsh_error_dump(CPL_MSG_ERROR);
    xsh_error_reset();
    return 1;
  }
  else {
    return 0;
  }
}
 
/*----------------------------------------------------------------------------*/
/*----------------------------------------------------------------------------*/
static int xsh_absorp_destroy(cpl_plugin *plugin)
{
  cpl_recipe *recipe = NULL;
 
  /* reset error state before detroying recipe */
  xsh_error_reset(); 
  /* Check parameter */
  assure( plugin != NULL, CPL_ERROR_NULL_INPUT, "Null plugin" );
 
  /* Get the recipe out of the plugin */
  assure( cpl_plugin_get_type(plugin) == CPL_PLUGIN_TYPE_RECIPE,
      CPL_ERROR_TYPE_MISMATCH, "Plugin is not a recipe");
 
  recipe = (cpl_recipe *)plugin;
 
  xsh_free_parameterlist(&recipe->parameters);
 
 cleanup:
  if (cpl_error_get_code() != CPL_ERROR_NONE)
    {
      return 1;
    }
  else
    {
      return 0;
    }
}
 
static cpl_error_code 
xsh_params_set_defaults(cpl_parameterlist* pars,
                        const char* rec_id,
                         xsh_instrument* inst,
                        xsh_rectify_param * rectify_par,
                        xsh_background_param* backg)
{
 
   cpl_parameter* p=NULL;
   check(p=xsh_parameters_find(pars,RECIPE_ID,"background-radius-x"));
   if(cpl_parameter_get_int(p) <= 0) {
      if (xsh_instrument_get_arm(inst) == XSH_ARM_NIR){
         backg->radius_x=1;
      } else {
         backg->radius_x=2;
      }
   }
 
   check(xsh_rectify_params_set_defaults(pars,rec_id,inst,rectify_par));
 
 cleanup:
 
  return cpl_error_get_code();
 
}
 
 
static cpl_error_code 
xsh_params_monitor(xsh_background_param* backg,
                   xsh_rectify_param * rectify_par,
                   xsh_localize_obj_param * loc_obj_par,
                   xsh_opt_extract_param *opt_extract_par,
                   int sub_sky_nbkpts1,
                   int sub_sky_nbkpts2)
{
 
 
  xsh_msg_dbg_low("bkg params: sampley=%d radius_y=%d smooth_y=%d",
      backg->sampley,backg->radius_y,backg->smooth_y);
 
  xsh_msg_dbg_low("bkg params: radius_x=%d smooth_x=%d",
      backg->radius_x,backg->smooth_x);
 
  xsh_msg_dbg_low("rectify params: radius=%g bin_lambda=%g bin_space=%g",
      rectify_par->rectif_radius,rectify_par->rectif_bin_lambda,
      rectify_par->rectif_bin_space);
 
  xsh_msg_dbg_low("localize params: chunk_nb=%d nod_step=%g",
      loc_obj_par->loc_chunk_nb,loc_obj_par->nod_step);
 
  xsh_msg_dbg_low("opt extract params: chunk_size=%d lambda_step=%g box_hsize=%d",
      opt_extract_par->chunk_size,opt_extract_par->lambda_step,
      opt_extract_par->box_hsize);
 
  xsh_msg_dbg_low("sky params: nbkpts1=%d nbkpts2=%d",
      sub_sky_nbkpts1,sub_sky_nbkpts2);
 
  return cpl_error_get_code();
 
}
/*--------------------------------------------------------------------------*/
/*--------------------------------------------------------------------------*/
 
static cpl_error_code 
xsh_params_bin_scale(cpl_frameset* raws,
                     xsh_background_param* backg,
                     xsh_opt_extract_param *opt_extract_par,
                     int* sub_sky_nbkpts1,
                     int* sub_sky_nbkpts2)
{
 
  cpl_frame* frame=NULL;
  const char* name=NULL;
  cpl_propertylist *plist=NULL;
  int binx=0;
  int biny=0;
 
  check(frame=cpl_frameset_get_first(raws));
  check(name=cpl_frame_get_filename(frame));
  check(plist=cpl_propertylist_load(name,0));
  check(binx=xsh_pfits_get_binx(plist));
  check(biny=xsh_pfits_get_biny(plist));
  xsh_free_propertylist( &plist);
 
  if(biny>1) {
 
    /* backg->sampley=backg->sampley/biny;
    number of points of the grid in y direction.
    Not to be bin dependent
    */
 
    backg->radius_y=backg->radius_y/biny;
 
    /* bin dependent */
    *sub_sky_nbkpts1*=0.75*biny;
    *sub_sky_nbkpts2*=0.75*biny;
 
    /*
    if(backg->smooth_y>0) {
      backg->smooth_y=backg->smooth_y/biny;
    }
    Smoothing radius' half size in x direction.
    For the moment not bin dependent, but for optimal results probably yes
    */
    /*
    rectify_par->rectif_radius=rectify_par->rectif_radius/biny;
    Rectify Interpolation radius
    For the moment not bin dependent, but for optimal results probably yes
    */
 
    /*
    rectify_par->rectif_bin_lambda=rectify_par->rectif_bin_lambda/biny;
    Rectify Wavelength Step
    For the moment not bin dependent, but for optimal results probably yes
    */
 
    /*
    loc_obj_par->loc_chunk_nb=loc_obj_par->loc_chunk_nb/biny;
    Localization Nb of chunks
    Not bin dependent
    */
 
    /*
    opt_extract_par->chunk_size=opt_extract_par->chunk_size/biny;
    Chunk size.
    */
 
    /*
    opt_extract_par->lambda_step=opt_extract_par->lambda_step/biny;
    Lambda step.
    For the moment not bin dependent, but for optimal results probably yes
    */
 
 
  }
 
 
  if(binx>1) {
 
    backg->radius_x=backg->radius_x/binx;
 
    /*
    if(backg->smooth_x>0) {
      backg->smooth_x=backg->smooth_x/binx;
    }
    Smoothing radius' half size in x direction
    For the moment not bin dependent, but for optimal results probably yes
    */
 
    /*
    rectify_par->rectif_bin_space=rectify_par->rectif_bin_space/binx;
    Rectify Position Step
    For the moment not bin dependent, but for optimal results probably yes
    */
 
    /*
    loc_obj_par->nod_step=loc_obj_par->nod_step/binx;
    Step (arcsec) between A and B images in nodding mode
    Not bin dependent
    */
 
    opt_extract_par->box_hsize=opt_extract_par->box_hsize/binx;
 
  }
 
 cleanup:
  xsh_free_propertylist(&plist);
  return cpl_error_get_code();
 
}
 
/*----------------------------------------------------------------------------*/
/*----------------------------------------------------------------------------*/
static cpl_error_code 
xsh_absorp(cpl_parameterlist* parameters,
                  cpl_frameset* frameset)
{
   const char* recipe_tags[1] = {XSH_STD_TELL_SLIT_STARE};
  int recipe_tags_size = 1;
 
  /* Input frames */
  cpl_frameset *raws = NULL;
  cpl_frameset *calib = NULL;
  /* Beware, do not "free" the following input frames, they are part
     of the input frameset */
  cpl_frame *bpmap = NULL;
  cpl_frame *master_bias = NULL;
  cpl_frame *master_dark = NULL;
  cpl_frame *master_flat = NULL;
  cpl_frame *order_tab_edges = NULL;
  cpl_frame *wave_tab = NULL ;
  cpl_frame *model_config_frame = NULL ;
  cpl_frame *wavemap_frame = NULL ;
  cpl_frame *slitmap_frame = NULL ;
  cpl_frame *disp_tab_frame = NULL;
  cpl_frame *spectralformat_frame = NULL ;
  cpl_frame *tell_list_frame = NULL;
  /* Parameters */
  xsh_clipping_param* crh_clipping_par = NULL;
  xsh_background_param* backg_par = NULL;
  xsh_remove_crh_single_param * crh_single_par = NULL ;
  xsh_rectify_param * rectify_par = NULL ;
  xsh_localize_obj_param * loc_obj_par = NULL ;
  int sub_sky_nbkpts1 = SUBTRACT_SKY_SINGLE_NBKPTS ; 
  int sub_sky_nbkpts2 = SUBTRACT_SKY_SINGLE_NBKPTS ; 
  int do_sub_sky = FALSE;       
  int recipe_use_model = 0;
  int do_optextract = 0;
  int do_flatfield = 0; 
  int do_compute_map = 0;
  int do_trace_obj = 0;
 
  int merge_par = 0;
  xsh_extract_param *extract_par = NULL ;
  xsh_opt_extract_param *opt_extract_par = NULL;
  xsh_subtract_sky_single_param *sky_par = NULL;
 
  xsh_instrument* instrument = NULL;
  int nb_raw_frames ;
  char rec_name[256];
 
  /* Intermediate frames */
#if 0
  cpl_frameset * on = NULL, * off = NULL ; 
#endif
  cpl_frame * crhm_frame = NULL ;   
  cpl_frame * rmbias = NULL;    
  cpl_frame * rmdark = NULL;    
  cpl_frame * rmbkg = NULL ;    
  cpl_frame * div_frame = NULL ; 
  cpl_frame * sub_sky_frame = NULL ; 
  cpl_frame * sub_sky2_frame = NULL ; 
  cpl_frame * rect_frame = NULL ; 
  cpl_frame * loc_table_frame = NULL ; 
  cpl_frame * clean_frame = NULL ; 
  cpl_frame * rect2_frame = NULL ;
  cpl_frame * rect2_frame_eso = NULL ;
  cpl_frame * rect2_frame_tab = NULL ;
 
  /* Output Frames (results)*/
  cpl_frame * sky_frame = NULL ; 
  cpl_frame * sky_frame_eso = NULL ; 
  cpl_frame * res_1D_frame = NULL ; 
  cpl_frame * res_2D_frame = NULL ; 
  cpl_frame * fluxcal_rect_1D_frame = NULL ;    
  cpl_frame * fluxcal_rect_2D_frame = NULL ;    
  cpl_frame * fluxcal_1D_frame = NULL ; 
  cpl_frame * fluxcal_2D_frame = NULL ; 
 
  cpl_frame * ext_frame = NULL ;
  cpl_frame * ext_frame_eso = NULL ;
 
  cpl_frame *orderoxt1d_eso_frame = NULL;
  cpl_frame *orderext1d_frame = NULL;
  cpl_frame *orderoxt1d_frame = NULL;
  cpl_frame *mergeext1d_frame = NULL;
  cpl_frame *mergeoxt1d_frame = NULL;
 
  cpl_frame* grid_backg=NULL;
  cpl_frame* frame_backg=NULL;
  cpl_frame* sky_frame_ima=NULL;
  char prefix[256];
  const char* ftag=NULL;
 
  cpl_frame* single_frame_sky_sub_tab_frame=NULL;
/*
  char sky_name[256];
  xsh_pre* pre_sci=NULL;
  cpl_image* sky_image=NULL;
*/
  cpl_frame* clean_obj=NULL;
  char *rec_prefix = NULL;
  cpl_frame* sky_list_frame=NULL;
  cpl_frame* qc_sky_frame=NULL;
  cpl_propertylist* plist=NULL;
  cpl_frame* qc_obj_trace_ord=NULL;
  cpl_frame* qc_obj_trace_mer=NULL;
 
  const char* name=NULL;
  int pre_overscan_corr=0;
  /* absorp */
  cpl_frame *tell_mask_frame = NULL;
  int absorp_filter_hsize = 5;
  double absorp_thresh = 0.0;
  cpl_frame *qc_subex_frame = NULL;
  cpl_frame *qc_s2ddiv1d_frame = NULL;
  cpl_frame *qc_model_frame = NULL;
  cpl_frame *qc_weight_frame = NULL;
 
  xsh_stack_param* stack_par=NULL;
 
  /**************************************************************************/
  /* DFS management */
  /**************************************************************************/
  check( xsh_begin( frameset, parameters, &instrument, &raws, &calib,
                    recipe_tags, recipe_tags_size,
                    RECIPE_ID, XSH_BINARY_VERSION,
                    xsh_absorp_description_short ) ) ;
 
  /*
  assure( instrument->mode == XSH_MODE_SLIT, CPL_ERROR_ILLEGAL_INPUT,
      "Instrument NOT in Slit Mode" ) ;
  */
  xsh_recipe_params_check(parameters,instrument,RECIPE_ID);
  if(instrument->arm == XSH_ARM_NIR) {
    xsh_instrument_nir_corr_if_JH(raws,instrument);
  }
  /**************************************************************************/
  /* Recipe frames */
  /**************************************************************************/
  /* One should have 1 or >=3 input frames. 2 is not permitted */
  check( nb_raw_frames = cpl_frameset_get_size( raws ) ) ;
  xsh_msg_dbg_low("nb_raw_frames=%d",nb_raw_frames);
  XSH_ASSURE_NOT_ILLEGAL_MSG( nb_raw_frames == 1 || nb_raw_frames >= 3, 
                              "This recipes accepts either one or at least 3 input frames" ) ;
  check( pre_overscan_corr = xsh_parameters_get_int( parameters, RECIPE_ID,
                                                       "pre-overscan-corr"));
  check(xsh_slit_stare_get_calibs(calib,instrument, &spectralformat_frame,
                                  &master_bias,&master_dark,&master_flat,
                                  &order_tab_edges,&model_config_frame,
                                  &wave_tab,&sky_list_frame,&qc_sky_frame,
                                  &bpmap,&single_frame_sky_sub_tab_frame,
                                  &wavemap_frame,&slitmap_frame,RECIPE_ID,
                  &recipe_use_model,pre_overscan_corr));
  
  /* tell line list */
  check( tell_list_frame = xsh_find_frame_with_tag(calib,XSH_TELL_LINE_LIST,
                                               instrument));
  if ( tell_list_frame == NULL){
    xsh_msg_error("Provide telluric line list frame");
     return CPL_ERROR_DATA_NOT_FOUND;
  }
  
  /**************************************************************************/
  /* Recipe parameters */
  /**************************************************************************/
 
  check(xsh_slit_stare_get_params(parameters,RECIPE_ID, &pre_overscan_corr,
                                  &crh_clipping_par,&backg_par,&loc_obj_par,
                                  &rectify_par,&crh_single_par,&sub_sky_nbkpts1,
                                  &do_flatfield,&sub_sky_nbkpts2,&sky_par,
                                  &extract_par,&do_optextract,
                                  &opt_extract_par,&do_trace_obj));
 
  check( absorp_filter_hsize = xsh_parameters_get_int( parameters, RECIPE_ID,
    "absorp-filter-hsize"));
  check( absorp_thresh = xsh_parameters_get_double( parameters, RECIPE_ID,
    "absorp-threshold"));  
  check(xsh_params_set_defaults(parameters,RECIPE_ID,instrument,rectify_par,
                                backg_par));
   /* special parameters */
   check( xsh_parameters_dosky_get( RECIPE_ID, parameters,&do_sub_sky));
 
  /* adjust relevant parameter to binning */
  if ( xsh_instrument_get_arm(instrument) != XSH_ARM_NIR) {
     check(xsh_params_bin_scale(raws,backg_par,
                                opt_extract_par,
                                &sub_sky_nbkpts1,&sub_sky_nbkpts2));
  }
 
  /* parameters dependent input */
  check( stack_par = xsh_stack_frames_get( RECIPE_ID, parameters));
  if ( rectify_par->conserve_flux){
     check_msg(disp_tab_frame = xsh_find_disp_tab( calib, instrument),
               "rectify-conserve-flux=TRUE, you must give a DISP_TAB_ARM input");
  }
  if ( do_compute_map && recipe_use_model==FALSE){
     check_msg(disp_tab_frame = xsh_find_disp_tab( calib, instrument), 
               "compute-map=TRUE, physmodel mode, you must give a DISP_TAB_ARM input");
  }
  check(xsh_params_monitor(backg_par,rectify_par,loc_obj_par,opt_extract_par,
               sub_sky_nbkpts1,sub_sky_nbkpts2));
 
  /**************************************************************************/
  /* Recipe code */
  /**************************************************************************/
 
  /* prepare RAW frames in XSH format */
  check(xsh_prepare(raws, bpmap, master_bias, XSH_OBJECT_SLIT_STARE,
            instrument,pre_overscan_corr,CPL_TRUE));
  check( rec_prefix = xsh_set_recipe_file_prefix( raws,
    "xsh_absorp"));
 
  /* pre CRH removal (method multi) as scired may have more than 2 in frames */
  ftag = XSH_GET_TAG_FROM_ARM( XSH_SLIT_STARE_REMOVE_CRH, instrument);
  check( crhm_frame = xsh_check_remove_crh_multiple( raws, ftag,stack_par,
   crh_clipping_par, instrument, NULL, NULL));
 
 
  check(xsh_slit_stare_get_maps(calib,
                                do_compute_map,recipe_use_model,rec_prefix,
                                instrument,model_config_frame,crhm_frame,
                                disp_tab_frame,order_tab_edges,
                                &wavemap_frame, &slitmap_frame));
 
  sprintf(prefix,"%s_",rec_prefix);
  /* Subtract bias if necessary */
  /* AMO here one should check is pre-overscan was corrected */
  check( rmbias = xsh_check_subtract_bias( crhm_frame, master_bias, 
                        instrument, prefix,
                                           pre_overscan_corr,0));
 
  /* Subtract Dark if necessary */
  check( rmdark = xsh_check_subtract_dark( rmbias, master_dark,
    instrument, rec_prefix));
 
  /* subtract inter-order background */
  xsh_msg("Subtract inter-order background");
  check(rmbkg = xsh_subtract_background( rmdark,
                     order_tab_edges,
                     backg_par, instrument,rec_prefix,
                                         &grid_backg,&frame_backg,0));
 
  /* In case CRH single or localize auto do preliminar sky subtraction */
  xsh_slit_stare_correct_crh_and_sky(loc_obj_par,crh_single_par,rectify_par,
                                     do_sub_sky,rec_prefix,rmbkg,
                                     order_tab_edges, slitmap_frame, 
                                     wavemap_frame,model_config_frame,
                                     single_frame_sky_sub_tab_frame,instrument,
                                     sub_sky_nbkpts1, sky_par,
                                     &sky_frame,&sky_frame_eso,&sky_frame_ima,
                                     wave_tab,disp_tab_frame,
                                     spectralformat_frame,nb_raw_frames,
                                     &loc_table_frame,&clean_frame,&clean_obj);
 
 
 
  /* now we divide by the flat for proper sky subtraction */
  check( div_frame = xsh_check_divide_flat( do_flatfield, clean_obj,
    master_flat, instrument, rec_prefix));
 
 
  check( sub_sky2_frame = xsh_check_subtract_sky_single( do_sub_sky, div_frame,
      order_tab_edges, slitmap_frame, wavemap_frame, loc_table_frame,
      single_frame_sky_sub_tab_frame, instrument, sub_sky_nbkpts2, sky_par,
      &sky_frame, &sky_frame_eso, &sky_frame_ima, rec_prefix,0));
 
  xsh_msg( "Prepare S2D products" ) ; 
  xsh_msg( "Rectify") ;
  sprintf(rec_name,"%s_%s_%s.fits",rec_prefix,XSH_ORDER2D,
      xsh_instrument_arm_tostring( instrument));
 
  check( rect2_frame = xsh_rectify( sub_sky2_frame, order_tab_edges,
                                    wave_tab, model_config_frame, instrument, 
                                    rectify_par,spectralformat_frame, 
                                    disp_tab_frame,rec_name, 
                                    &rect2_frame_eso,&rect2_frame_tab,
                    rec_prefix));
  xsh_msg( "Extract" ) ;
  check(ext_frame=xsh_extract(rect2_frame, loc_table_frame,
                  instrument, extract_par,&ext_frame_eso,
                  rec_prefix)) ;
 
  xsh_msg( "Merge orders with 1D frame" ) ;
  check( res_1D_frame = xsh_merge_ord( ext_frame, instrument,
                       merge_par,rec_prefix ));
  check(xsh_monitor_spectrum1D_flux(res_1D_frame,instrument));
 
  xsh_msg( "Calling xsh_merge_ord with 2D frame" ) ;
  check( res_2D_frame = xsh_merge_ord( rect2_frame, instrument,
                       merge_par,rec_prefix ));
 
  xsh_msg("Prepare S1D products" ) ;
  /* doing optimal extraction */
  int hsize=0;
  int naxis2=0;
  if ( do_optextract){
    xsh_msg( "Optimal extraction");
    check( xsh_opt_extract( sub_sky2_frame, order_tab_edges,
                wave_tab, model_config_frame, wavemap_frame, 
                slitmap_frame, loc_table_frame, 
                spectralformat_frame, master_flat, instrument,
                opt_extract_par, rec_prefix,
                &orderext1d_frame, &orderoxt1d_frame,
                            &orderoxt1d_eso_frame,
                &qc_subex_frame,
                &qc_s2ddiv1d_frame,
                &qc_model_frame,
                &qc_weight_frame));
                
    check( mergeext1d_frame = xsh_merge_ord( orderext1d_frame, instrument,
                         merge_par,rec_prefix));
    check( mergeoxt1d_frame = xsh_merge_ord( orderoxt1d_frame, instrument,
                         merge_par,rec_prefix));
  }
 
  if( do_trace_obj) {
     name=cpl_frame_get_filename(res_2D_frame);
     plist=cpl_propertylist_load(name,0);
     naxis2=xsh_pfits_get_naxis2(plist);
     xsh_free_propertylist(&plist);
     hsize=naxis2/4;
     check(qc_obj_trace_ord=xsh_frame_image_ext_qc_trace_window(rect2_frame_eso,
                                                            instrument,
                                                            rec_prefix,
                                                            hsize,0));
 
     check(qc_obj_trace_mer=xsh_frame_image_qc_trace_window(res_2D_frame,
                                                        instrument,
                                                        rec_prefix,
                                                        hsize,0));
  }
 
  /* Produce telluric mask */
  if ( mergeoxt1d_frame != NULL){
    check( tell_mask_frame = xsh_compute_absorp( mergeoxt1d_frame, tell_list_frame,
      absorp_filter_hsize, absorp_thresh, instrument));
  }
  else{
    check( tell_mask_frame = xsh_compute_absorp( res_1D_frame, tell_list_frame,
      absorp_filter_hsize, absorp_thresh, instrument));    
  }
 
  /* saving products */   
 
  xsh_msg( "Saving products" ) ;
 
  check( xsh_add_product_vector( tell_mask_frame, frameset, parameters,
                   RECIPE_ID, instrument,
                   cpl_frame_get_tag( tell_mask_frame)));
 
 
 
  check( xsh_add_product_image(rect2_frame_eso, frameset, parameters,
                   RECIPE_ID, instrument,
                   cpl_frame_get_tag(rect2_frame_eso)));
 
  check( xsh_add_product_image(ext_frame_eso, frameset, parameters,
                   RECIPE_ID, instrument,
                   cpl_frame_get_tag(ext_frame_eso)));
 
  check( xsh_add_product_spectrum( res_2D_frame, frameset, parameters, 
                   RECIPE_ID, instrument,NULL,NULL));
 
 
  check( xsh_add_product_spectrum( res_1D_frame, frameset, parameters, 
                   RECIPE_ID, instrument,NULL,NULL));
 
  check( xsh_add_product_pre( rmbias, frameset, parameters, 
                  RECIPE_ID, instrument,NULL));
 
  check( xsh_add_product_image( rmbkg, frameset, parameters, 
                RECIPE_ID, instrument,
                cpl_frame_get_tag(rmbkg)));
 
  if ( do_sub_sky == 1 && nb_raw_frames == 1 && crh_single_par->nb_iter > 0){
 
  check( xsh_add_product_image( clean_frame, frameset, parameters, 
                RECIPE_ID, instrument,
                cpl_frame_get_tag(clean_frame)));
 
  }
  if (do_compute_map){
    sprintf(prefix,"%s_WAVE_MAP_%s",rec_prefix,
        xsh_instrument_arm_tostring(instrument));
 
 
    check(xsh_add_product_image( wavemap_frame, frameset,
      parameters, RECIPE_ID, instrument, prefix));
 
    check(sprintf(prefix,"%s_SLIT_MAP_%s",rec_prefix,
               xsh_instrument_arm_tostring(instrument)));
 
    check(xsh_add_product_image( slitmap_frame, frameset,
      parameters, RECIPE_ID, instrument, prefix));
  }
  if(do_flatfield) {
 
  check( xsh_add_product_image( div_frame, frameset, parameters, 
                    RECIPE_ID, instrument,
                    cpl_frame_get_tag(div_frame)));
  }
 
  if ( do_optextract){
    check( xsh_add_product_table( orderext1d_frame, frameset,
      parameters, RECIPE_ID, instrument, NULL));
    check( xsh_add_product_table( orderoxt1d_frame, frameset,
      parameters, RECIPE_ID, instrument, NULL));
    check( xsh_add_product_spectrum( mergeext1d_frame, frameset, parameters,
      RECIPE_ID, instrument,NULL,NULL));
    check( xsh_add_product_spectrum( mergeoxt1d_frame, frameset, 
      parameters, RECIPE_ID, instrument,NULL,NULL));
    check( xsh_add_product_image( qc_subex_frame, frameset, parameters, 
                    RECIPE_ID, instrument,
                    cpl_frame_get_tag(qc_subex_frame)));
    check( xsh_add_product_image( qc_s2ddiv1d_frame, frameset, parameters, 
                    RECIPE_ID, instrument,
                    cpl_frame_get_tag(qc_s2ddiv1d_frame)));
    check( xsh_add_product_image( qc_model_frame, frameset, parameters, 
                    RECIPE_ID, instrument,
                    cpl_frame_get_tag(qc_model_frame)));
    check( xsh_add_product_image( qc_weight_frame, frameset, parameters, 
                    RECIPE_ID, instrument,
                    cpl_frame_get_tag(qc_weight_frame)));
  }
  if ( do_sub_sky == 1 ) {
    check( xsh_add_product_pre( sub_sky2_frame, frameset, parameters,
                RECIPE_ID, instrument,NULL));
    check( xsh_add_product_image( sky_frame_ima, frameset, parameters,
                  RECIPE_ID, instrument,
                  cpl_frame_get_tag(sky_frame_ima)));
    check( xsh_add_product_image( sky_frame_eso, frameset,
                                  parameters, RECIPE_ID, instrument,
                                  cpl_frame_get_tag(sky_frame_eso)));
  }
  check( xsh_add_product_image( frame_backg, frameset, parameters, 
                    RECIPE_ID, instrument,
                    cpl_frame_get_tag(frame_backg)));
 
  if(crhm_frame != NULL) {
     check( xsh_add_product_image( crhm_frame, frameset, parameters, 
                                   RECIPE_ID, instrument,
                                   cpl_frame_get_tag(crhm_frame)));
 
  }
 
  if(qc_sky_frame != NULL) {
    check( xsh_add_product_table(qc_sky_frame, frameset,
                       parameters, RECIPE_ID, instrument,NULL));
  
  }
 
  if(do_trace_obj) {
    check( xsh_add_product_table(qc_obj_trace_ord, frameset,
                       parameters, RECIPE_ID, instrument, NULL));
 
   check( xsh_add_product_table(qc_obj_trace_mer, frameset,
                       parameters, RECIPE_ID, instrument, NULL));
  }
 
 
  cleanup:
    xsh_end( RECIPE_ID, frameset, parameters );
    XSH_FREE( rec_prefix);
    XSH_FREE( crh_clipping_par);
    XSH_FREE( backg_par);
    XSH_FREE( crh_single_par);
    XSH_FREE( rectify_par);
    XSH_FREE( sky_par);
    XSH_FREE( loc_obj_par);
    XSH_FREE( extract_par);
    XSH_FREE( opt_extract_par);
    xsh_instrument_free(&instrument);
 
    xsh_free_frameset(&raws);
    xsh_free_frameset(&calib);
    xsh_free_frame( &crhm_frame);
    xsh_free_frame( &qc_sky_frame);
 
    xsh_free_frame( &wavemap_frame);
    xsh_free_frame( &slitmap_frame);
    
    xsh_free_frame(&rmbias);
    xsh_free_frame(&rmdark);
    xsh_free_frame(&rmbkg);
    xsh_free_frame(&div_frame);
    xsh_free_frame(&sub_sky_frame);
    
    xsh_free_frame(&sub_sky2_frame);
    xsh_free_frame(&sky_frame);
    xsh_free_frame(&sky_frame_eso);
    xsh_free_frame(&sky_frame_ima);
 
    xsh_free_frame(&rect_frame) ;
    xsh_free_frame(&rect2_frame_eso) ;
    xsh_free_frame(&rect2_frame_tab) ;
 
    xsh_free_frame( &orderext1d_frame);
    xsh_free_frame( &orderoxt1d_frame);
    xsh_free_frame( &mergeext1d_frame);
    xsh_free_frame( &mergeoxt1d_frame);
 
    xsh_free_frame(&loc_table_frame) ;
    xsh_free_frame( &clean_frame);
    xsh_free_frame( &clean_obj);
    xsh_free_frame( &ext_frame);
    xsh_free_frame( &ext_frame_eso);
    xsh_free_frame(&res_1D_frame) ;
    xsh_free_frame(&res_2D_frame) ;
    xsh_free_frame(&fluxcal_rect_1D_frame) ;
    xsh_free_frame(&fluxcal_rect_2D_frame) ;
    xsh_free_frame(&fluxcal_1D_frame) ;
    xsh_free_frame(&fluxcal_2D_frame) ;
 
    xsh_free_frame(&rect2_frame) ;
    xsh_free_frame(&grid_backg) ;
    xsh_free_frame(&frame_backg) ;
    xsh_free_frame( &tell_mask_frame);
    xsh_free_propertylist(&plist);
   
    xsh_free_frame( &single_frame_sky_sub_tab_frame);
    xsh_free_frame( &qc_subex_frame);
    xsh_free_frame(&qc_s2ddiv1d_frame);
    xsh_free_frame(&qc_model_frame);
    xsh_free_frame(&qc_weight_frame);
                                     
    return CPL_ERROR_NONE;
}