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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) Information  on  relevant  parameters  can  be
       found with esorex --params sinfo_rec_jitter esorex --help sinfo_rec_jitter

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.html for further information.

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

VERSION

       sinfo_rec_jitter 2.4.0

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