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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].

       --std_star-extract <str>
              Extraction  Method:  simple/optimal (str; default: ´simple´). The full name of this
              option for the EsoRex configuration file  is  sinfoni.std_star.extract  [default  =
              simple].

       --std_star-pfm <str>
              Object   Mask   Post  Filtering  Method:  erosion/dilation/closing  (str;  default:
              ´erosion´). The full name of this option  for  the  EsoRex  configuration  file  is
              sinfoni.std_star.pfm [default = erosion].

       --std_star-pfx <long>
              X  Size  of  the  post  filtering kernel. (long; default: 3). The full name of this
              option for the EsoRex configuration file is sinfoni.std_star.pfx [default = 3].

       --std_star-pfy <long>
              Y Size of the post filtering kernel. (long; default: 3).  The  full  name  of  this
              option for the EsoRex configuration file is sinfoni.std_star.pfy [default = 3].

       --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_distortion(7),
       sinfo_rec_mdark(7),    sinfo_rec_mflat(7),    sinfo_rec_pupil(7),    sinfo_rec_wavecal(7),
       sinfo_utl_bp_mask_add(7),        sinfo_utl_cube2ima(7),        sinfo_utl_cube2spectrum(7),
       sinfo_utl_cube_arith(7),        sinfo_utl_cube_combine(7),       sinfo_utl_cube_create(7),
       sinfo_utl_ima_arith(7),      sinfo_utl_ima_line_corr(7),      sinfo_utl_line_oh_select(7),
       sinfo_utl_skycor(7),    sinfo_utl_skymap(7),    sinfo_utl_spectrum_divide_by_blackbody(7),
       sinfo_utl_spectrum_wavelength_shift(7)

VERSION

       sinfo_rec_jitter 3.0.0

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