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NAME

       sinfo_rec_jitter - Object or STD star or PSF star data reduction

SYNOPSIS

       esorex sinfo_rec_jitter [OPTIONS] FILE.sof

DESCRIPTION

       This recipe performs science data reduction.

       The   input  files  are:  science  object  and  sky  frames  with  tags
       OBJECT_NODDING and SKY_NODDING or Telluric standard star frames and sky
       frames  with  tags  STD and SKY_STD or PSF standard star and sky frames
       with tags PSF_CALIBRATOR and SKY_PSF_CALIBRATOR and Master  calibration
       frames:  A corresponding (band,preoptics) wavelength map image with tag
       WAVE_MAP A corresponding (band,preoptics) master flat  field  with  tag
       MASTER_FLAT_LAMP  A corresponding (band,preoptics) master bad pixel map
       with  tag  MASTER_BP_MAP  A  corresponding  (band,preoptics)   slitlets
       position  frame  with  tag  SLIT_POS  A corresponding (band) distortion
       table with tag DISTORTION A corresponding (band) slitlet distance table
       with  tag  SLITLETS_DISTANCE  The output is an image resulting from the
       IMA1 op IMA2 where op indicates A reference table with the position  of
       the  first  column with tag FIRST_COLUMN Relevant outputs are: combined
       cubes     (PRO.CATG=x_OBS     x=STD,OBJ,PSF)     reconstructed     cube
       (PRO.CATG=COADD_x_OBS   x=STD,OBJ,PSF)   An  average  along  Z  of  the
       reconstructed cube (PRO.CATG=MED_x_OBS x=STD,OBJ,PSF) The bad pixel map
       associated to the cube (PRO.CATG=BP_MAP_COADD_x_OBS x=STD,OBJ,PSF)

OPTIONS

       --gen-overpar <bool>
              Overwrite  DRS  ini parameters:  (bool; default: True). The full
              name of  this  option  for  the  EsoRex  configuration  file  is
              sinfoni.general.overwrite_parameters [default = True].

       --lc_sw <bool>
              Correct for bad lines introduced by instrument software:  (bool;
              default: False). The full name of this  option  for  the  EsoRex
              configuration file is sinfoni.general.lc_sw [default = False].

       --lc_kappa <long>
              Kappa  sigma  value  (long;  default: 18). The full name of this
              option    for    the    EsoRex     configuration     file     is
              sinfoni.general.lc_kappa [default = 18].

       --lc_filt_rad <long>
              Filtering  radii  applied  during median filter. Should be small
              (long; default: 3). The full name of this option for the  EsoRex
              configuration file is sinfoni.general.lc_filt_rad [default = 3].

       --product-density <long>
              Density  of  pipeline  products:  0  (low),  1  (low+skycor),  2
              (med-QC), 3 (high-debug+skycor) (long;  default:  2).  The  full
              name  of  this  option  for  the  EsoRex  configuration  file is
              sinfoni.product.density [default = 2].

       --stack-lo_rej <float>
              lower rejection (float; default: 0.1). The  full  name  of  this
              option     for     the     EsoRex    configuration    file    is
              sinfoni.stacked.low_rejection [default = 0.1].

       --stack-hi_rej <float>
              higher rejection (float; default: 0.1). The full  name  of  this
              option     for     the     EsoRex    configuration    file    is
              sinfoni.stacked.high_rejection [default = 0.1].

       --stack-flat_ind <bool>
              Flat Index:  (bool; default: True). The full name of this option
              for  the EsoRex configuration file is sinfoni.stacked.flat_index
              [default = True].

       --stack-mflat_norm_smooth <long>
              Normalize master flat to its  smoothed  value  (to  remove  lamp
              response  curve).  0 (no smooth). 1 (apply fft filter along y).2
              (apply running median filter along y). (long; default:  0).  The
              full  name  of  this option for the EsoRex configuration file is
              sinfoni.stacked.mflat_norm_smooth [default = 0].

       --stack-mflat_smooth_rad <long>
              Normalization smoothing radii  (long;  default:  16).  The  full
              name  of  this  option  for  the  EsoRex  configuration  file is
              sinfoni.stacked.mflat_smooth_rad [default = 16].

       --stack-mask_ind <long>
              BP Mask Interpolation Switch: indicates if the  bad  pixel  mask
              should  be  applied (1) or not (0)  (long; default: 1). The full
              name of  this  option  for  the  EsoRex  configuration  file  is
              sinfoni.stacked.mask_index [default = 1].

       --stack-ind_ind <bool>
              indicates  if  the  bad  pixels  should  be  indicated  (yes) or
              interpolated (no) (bool; default: False). The full name of  this
              option     for     the     EsoRex    configuration    file    is
              sinfoni.stacked.ind_index [default = False].

       --stack-mask_rad <long>
              Max distance bad-good pix:  (long; default: 4). The full name of
              this    option    for   the   EsoRex   configuration   file   is
              sinfoni.stacked.mask_rad [default = 4].

       --stack-gauss_ind <bool>
              Gaussian Convolution Switch:  (bool; default: False).  The  full
              name  of  this  option  for  the  EsoRex  configuration  file is
              sinfoni.stacked.gauss_index [default = False].

       --stack-khw <long>
              Kernel Half Width (long; default: 2).  The  full  name  of  this
              option     for     the     EsoRex    configuration    file    is
              sinfoni.stacked.kernel_half_width [default = 2].

       --stack-warpfix_ind <bool>
              Warp Fix Index:  (bool; default: True). The full  name  of  this
              option     for     the     EsoRex    configuration    file    is
              sinfoni.stacked.warpfix_ind [default = True].

       --stack-warpfix_kernel <str>
              Warpfix kernel:  (str; default: ´tanh´). The full name  of  this
              option     for     the     EsoRex    configuration    file    is
              sinfoni.stacked.warpfix_kernel [default = tanh].

       --stack-qc_thresh_min <long>
              qc_thresh_min (long; default: 0). The full name of  this  option
              for       the       EsoRex       configuration      file      is
              sinfoni.stacked.qc_thresh_min [default = 0].

       --stack-qc_thresh_max <long>
              qc_thresh_max (long; default: 49000).  The  full  name  of  this
              option     for     the     EsoRex    configuration    file    is
              sinfoni.stacked.qc_thresh_max [default = 49000].

       --stack-sub_raw_sky <bool>
              indicates if the raw sky frame should be  subtracted  (TRUE)  or
              (FALSE)  (bool; default: True). The full name of this option for
              the EsoRex  configuration  file  is  sinfoni.stacked.sub_raw_sky
              [default = True].

       --objnod-aj_method <long>
              Method  to  reduce  autojitter  template  frames  Raw frames are
              object only exposures. object-fake_sky pairs are  generated.  0:
              no  sky  for  all  objects  (long; default: 1). The full name of
              this   option   for   the   EsoRex   configuration    file    is
              sinfoni.objnod.autojitter_method [default = 1].

       --objnod-scales_sky <bool>
              Spatial    median    (sky)    subtraction    from    cube:   (If
              autojitter_method==1),indicates if the spatial  median  of  each
              plane  should be subtracted (TRUE) or not (FALSE) from each cube
              plane (bool; default: False). The full name of this  option  for
              the   EsoRex  configuration  file  is  sinfoni.objnod.scales_sky
              [default = False].

       --objnod-ks_clip <bool>
              Kappa-sigma clipping of coadded cube: indicates if a kappa-sigma
              clipping should be performed (TRUE) or not (FALSE) on each plane
              of the coadded cube (bool; default: True). The full name of this
              option     for     the     EsoRex    configuration    file    is
              sinfoni.objnod.ks_clip [default = True].

       --objnod-kappa <float>
              kappa value for kappa-sigma clipping  of  coadded  cube  (float;
              default:  2.0).  The  full  name  of  this option for the EsoRex
              configuration file is sinfoni.objnod.kappa [default = 2.0].

       --objnod-size_x <long>
              Cube x size: x-pixel size of the final combined  data  cube,must
              lie between 64 and 128. If 0 it is computed automatically (long;
              default: 0). The  full  name  of  this  option  for  the  EsoRex
              configuration file is sinfoni.objnod.size_x [default = 0].

       --objnod-size_y <long>
              Cube  y  size: y-pixel size of the final combined data cube,must
              lie between 64 and 128.If 0 it is computed automatically  (long;
              default:  0).  The  full  name  of  this  option  for the EsoRex
              configuration file is sinfoni.objnod.size_y [default = 0].

       --objnod-no_coeffs <long>
              number of coefficients for the polynomial interpolation   (long;
              default:  3).  The  full  name  of  this  option  for the EsoRex
              configuration file is sinfoni.objnod.n_coeffs [default = 3].

       --objnod-ns_ind <bool>
              Nord South Index Switch: indicates if the slitlet distances  are
              determined  by  a  north-south-test  (TRUE) or slitlet edge fits
              (FALSE) (bool; default: True). The full name of this option  for
              the EsoRex configuration file is sinfoni.objnod.nord_south_index
              [default = True].

       --objnod-fine_tune_mtd <str>
              Fine Tuning Method: indicator for the shifting method to use (P:
              polynomial  interpolation,  S: cubic spline interpolation) (str;
              default: ´P´). The full name  of  this  option  for  the  EsoRex
              configuration file is sinfoni.objnod.fine_tuning_method [default
              = P].

       --objnod-order <long>
              Fine Tuning polynomial order: order of  the  polynomial  if  the
              polynomial   interpolation   shifting  method  is  used.  (long;
              default: 2). The  full  name  of  this  option  for  the  EsoRex
              configuration file is sinfoni.objnod.order [default = 2].

       --objnod-lo_rej <float>
              lower  rejection:  percentage  of  rejected low value pixels for
              averaging the sky spectra (float; default: 10.0). The full  name
              of   this   option   for   the   EsoRex  configuration  file  is
              sinfoni.objnod.low_rejection [default = 10.0].

       --objnod-hi_rej <float>
              higher rejection: percentage of rejected high value  pixels  for
              averaging  the sky spectra (float; default: 10.0). The full name
              of  this  option  for   the   EsoRex   configuration   file   is
              sinfoni.objnod.high_rejection [default = 10.0].

       --objnod-tol <long>
              Tolerance:  pixel  tolerance,  this  distance  tolerance  to the
              diagonal dividing line is not considered for the sky  extraction
              to  be sure to have a clean sky due to positioning tolerance and
              crossing through pixels (long; default: 2).  The  full  name  of
              this    option    for   the   EsoRex   configuration   file   is
              sinfoni.objnod.tolerance [default = 2].

       --objnod-jit_ind <bool>
              Jitter Index: jitter mode indicator: TRUE:  Auto-Jitter,  FALSE:
              user  defined jitterThe size_x size_y kernel_type parameters are
              only  used  if  jitterInd  is  set  to  yes,   that   means   in
              auto-jittering  mode!  (bool;  default:  True). The full name of
              this   option   for   the   EsoRex   configuration    file    is
              sinfoni.objnod.jitter_index [default = True].

       --objnod-kernel_typ <str>
              Kernel  Type:the  name  of the interpolation kernel to shift the
              single cubes  to the correct places inside the big combined cube
              (str;  default:  ´tanh´).  The  full name of this option for the
              EsoRex configuration file is sinfoni.objnod.kernel_type [default
              = tanh].

       --objnod-vllx <long>
              Vignetting  on  llx:  pixels  vignetted from lower left corner X
              coordinate  of  contributing  cubes  before  coaddition   (long;
              default:  0).  The  full  name  of  this  option  for the EsoRex
              configuration file is sinfoni.objnod.vllx [default = 0].

       --objnod-vlly <long>
              Vignetting on lly: pixels vignetted from  lower  left  corner  Y
              coordinate  of  contributing  cubes  before  coaddition   (long;
              default: 0). The  full  name  of  this  option  for  the  EsoRex
              configuration file is sinfoni.objnod.vlly [default = 0].

       --objnod-vurx <long>
              Vignetting  on  urx:  pixels vignetted from upper right corner X
              coordinate  of  contributing  cubes  before  coaddition   (long;
              default:  0).  The  full  name  of  this  option  for the EsoRex
              configuration file is sinfoni.objnod.vurx [default = 0].

       --objnod-vury <long>
              Vignetting on ury: pixels vignetted from upper  right  corner  Y
              coordinate  of  contributing  cubes  before  coaddition   (long;
              default: 0). The  full  name  of  this  option  for  the  EsoRex
              configuration file is sinfoni.objnod.vury [default = 0].

       --objnod-fcol <float>
              First  column  offset:   (float; default: 0.0). The full name of
              this   option   for   the   EsoRex   configuration    file    is
              sinfoni.objnod.fcol [default = 0.0].

       --objnod-sky_cor <bool>
              Sky  residuals correction:  (bool; default: True). The full name
              of  this  option  for   the   EsoRex   configuration   file   is
              sinfoni.objnod.sky_cor [default = True].

       --objnod-flux_cor <bool>
              Apply  flux  correction after rebinning:  (bool; default: True).
              The full name of this option for the EsoRex  configuration  file
              is sinfoni.objnod.flux_cor [default = True].

       --objnod-mosaic_max_size <long>
              Maximum  allowed  size  for  cubes mosaic is 100*mosaic_max_size
              (long; default: 14196). The full name of  this  option  for  the
              EsoRex   configuration  file  is  sinfoni.objnod.mosaic_max_size
              [default = 14196].

       --skycor-mask_ws <float>
              Starting wavelength for  object-sky  cross  correlation  (float;
              default:  1.4).  The  full  name  of  this option for the EsoRex
              configuration file is sinfoni.sinfo_utl_skycor.mask_ws  [default
              = 1.4].

       --skycor-mask_we <float>
              End wavelength for object-sky cross correlation (float; default:
              2.5). The full name of this option for the EsoRex  configuration
              file is sinfoni.sinfo_utl_skycor.mask_we [default = 2.5].

       --skycor-min_frac <float>
              Threshold value for fraction of spatial pixels to be sky (float;
              default: 0.8). The full name  of  this  option  for  the  EsoRex
              configuration file is sinfoni.sinfo_utl_skycor.min_frac [default
              = 0.8].

       --skycor-sky_bkg_filter_width <long>
              Width of sky-thermal background pre filter (to  remove  emission
              lines  before  fitting  a  Black Body). (long; default: 12). The
              full name of this option for the EsoRex  configuration  file  is
              sinfoni.sinfo_utl_skycor.sky_bkg_filter_width [default = 12].

       --skycor-line_hw <float>
              Threshold  value for full width in pixels of unresolved emission
              line.   Lines  with  FWHM  smaller  than  this  value  are   not
              considered   in   the   object-sky   cross  correlation  and  in
              computation of the optimal  sky  lines  scaling  factor  (float;
              default:  4.0).  The  full  name  of  this option for the EsoRex
              configuration file  is  sinfoni.sinfo_utl_skycor.line_half_width
              [default = 4.0].

       --skycor-scale_method <long>
              Optimal  sky lines scaling factor computation method: amoeba fit
              (0), maximum likelihood (1)  (long; default: 1). The  full  name
              of   this   option   for   the   EsoRex  configuration  file  is
              sinfoni.sinfo_utl_skycor.scale_method [default = 1].

       --skycor-rot_cor <bool>
              Computes scaling factor  correction  due  to  rotational  levels
              transitions (bool; default: False). The full name of this option
              for      the      EsoRex       configuration       file       is
              sinfoni.sinfo_utl_skycor.rot_cor [default = False].

       --skycor-fit_obj_noise <bool>
              Do Gaussian fit of object noise (bool; default: False). The full
              name of  this  option  for  the  EsoRex  configuration  file  is
              sinfoni.sinfo_utl_skycor.fit_obj_noise [default = False].

       --skycor-niter <long>
              Number  of iterations of background fit (long; default: 10). The
              full name of this option for the EsoRex  configuration  file  is
              sinfoni.sinfo_utl_skycor.niter [default = 10].

       --skycor-pshift <float>
              Sky  spectrum shift towar object (float; default: 0.0). The full
              name of  this  option  for  the  EsoRex  configuration  file  is
              sinfoni.sinfo_utl_skycor.pshift [default = 0.0].

       --skycor-llx <long>
              Lower  left  X defining object spectrum location (long; default:
              1). The full name of this option for  the  EsoRex  configuration
              file is sinfoni.sinfo_utl_skycor.llx [default = 1].

       --skycor-lly <long>
              Lower  left  Y defining object spectrum location (long; default:
              1). The full name of this option for  the  EsoRex  configuration
              file is sinfoni.sinfo_utl_skycor.lly [default = 1].

       --skycor-urx <long>
              Upper  right X defining object spectrum location (long; default:
              64). The full name of this option for the  EsoRex  configuration
              file is sinfoni.sinfo_utl_skycor.urx [default = 64].

       --skycor-ury <long>
              Upper  right Y defining object spectrum location (long; default:
              64). The full name of this option for the  EsoRex  configuration
              file is sinfoni.sinfo_utl_skycor.ury [default = 64].

       --skycor-sub_thr_bkg_from_obj <bool>
              Subtract  thermal background contribute from object spectra. Set
              it to TRUE if stack-sub_raw_sky is set to FALSE (bool;  default:
              False).   The   full   name   of  this  option  for  the  EsoRex
              configuration                      file                       is
              sinfoni.sinfo_utl_skycor.sub_thr_bkg_from_obj [default = False].

       --std_star-switch <bool>
              Switch  to  activate  spectrum extraction (bool; default: True).
              The full name of this option for the EsoRex  configuration  file
              is sinfoni.std_star.switch [default = True].

       --std_star-lo_rej <float>
              lower  rejection  (float;  default:  0.1). The full name of this
              option    for    the    EsoRex     configuration     file     is
              sinfoni.std_star.low_rejection [default = 0.1].

       --std_star-hi_rej <float>
              high  rejection  (float;  default:  0.1).  The full name of this
              option    for    the    EsoRex     configuration     file     is
              sinfoni.std_star.high_rejection [default = 0.1].

       --std_star-fwhm_fct <float>
              Factor   to   find   2D-Gauss   FWHM.  The  extraction  box  is:
              halfbox_x=halfbox_y=fwhm_factor*(fwhm_x+fwhm_y)*0.5      (float;
              default:  5.0).  The  full  name  of  this option for the EsoRex
              configuration file is  sinfoni.std_star.fwhm_factor  [default  =
              5.0].

       --std_star-conv_ind <bool>
              Intensity  Conversion  Index:   (bool;  default: True). The full
              name of  this  option  for  the  EsoRex  configuration  file  is
              sinfoni.std_star.conversion_index [default = True].

       --std_star-compute_eff <bool>
              Compute  efficiency:  TRUE/FALSE (bool; default: True). The full
              name of  this  option  for  the  EsoRex  configuration  file  is
              sinfoni.std_star.compute_eff [default = True].

       --psf-switch <bool>
              Switch   to   activate   PSF-related  (Strehl/Encircled  energy)
              computation (bool; default: True). The full name of this  option
              for the EsoRex configuration file is sinfoni.psf.switch [default
              = True].

       Note that it is possible to  create  a  configuration  file  containing
       these  options, along with suitable default values. Please refer to the
       details provided by the 'esorex --help' command.

SEE ALSO

       The full documentation for the sinfo pipeline can be  downloaded  as  a
       PDF file using the following URL:

              ftp://ftp.eso.org/pub/dfs/pipelines/sinfoni/sinfo-pipeline-manual-19.0.pdf

       An overview over the existing ESO pipelines can be  found  on  the  web
       page http://www.eso.org/sci/software/pipelines/.

       Basic documentation about the EsoRex program can be found at the esorex
       (1) man page.

       It is possible to call the pipelines from python using  the  python-cpl
       package.    See   http://packages.python.org/python-cpl/index.php  for
       further information.

       The other  recipes  of  the  sinfo  pipeline  are  sinfo_utl_skycor(7),
       sinfo_rec_wavecal(7),  sinfo_rec_detlin(7), sinfo_utl_ima_line_corr(7),
       sinfo_utl_bp_mask_add(7),                   sinfo_utl_cube2spectrum(7),
       sinfo_utl_cube_create(7),                           sinfo_rec_mflat(7),
       sinfo_utl_spectrum_divide_by_blackbody(7), sinfo_utl_line_oh_select(7),
       sinfo_utl_cube2ima(7),   sinfo_rec_distortion(7),   sinfo_rec_pupil(7),
       sinfo_utl_cube_combine(7),                      sinfo_utl_ima_arith(7),
       sinfo_utl_cube_arith(7),        sinfo_utl_spectrum_wavelength_shift(7),
       sinfo_utl_skymap(7), sinfo_rec_mdark(7)

VERSION

       sinfo_rec_jitter 2.5.2

AUTHOR

       Andrea Modigliani <Andrea.Mdigliani@eso.org>

BUG REPORTS

       Please report any problems to Andrea.Mdigliani@eso.org.  Alternatively,
       you   may   send   a   report   to  the  ESO  User  Support  Department
       <usd-help@eso.org>.

LICENSE

       This file is part of the  SINFONI  Instrument  Pipeline  Copyright  (C)
       2002,2003 European Southern Observatory

       This program 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, Inc.,
       59 Temple Place, Suite 330, Boston, MA  02111-1307  USA



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