Provided by: cpl-plugin-visir-doc_4.3.7+dfsg-1build2_all bug

NAME

       visir_old_img_combine - Old DRS detector: Images combination recipe

SYNOPSIS

       esorex visir_old_img_combine [OPTIONS] FILE.sof

DESCRIPTION

       This  recipe recombines the data observed in chopping/nodding or chopping or nodding modes
       into one combined image using optionally cross-correlation methods.

       The   files   listed   in   the   Set   Of   Frames    (sof-file)    must    be    tagged:
       VISIR-observation-file.fits      IM_OBS_CHO_NOD_JIT     or     VISIR-observation-file.fits
       IM_OBS_CHO_JIT       or        VISIR-observation-file.fits        IM_OBS_NOD_JIT        or
       VISIR-observation-file.fits IM_OBS_DIR_JIT

       The  corresponding  primary  product  will have a FITS card ´HIERARCH ESO PRO CATG´ with a
       value  of  IMG_OBS_COMBINED_CNJ   or   IMG_OBS_COMBINED_CJ   or   IMG_OBS_COMBINED_NJ   or
       IMG_OBS_COMBINED_DJ  and  the  corresponding  beam-collapsed product will have a FITS card
       ´HIERARCH ESO PRO CATG´ with a  value  of  IMG_OBS_ONEBEAM_CNJ  or  IMG_OBS_ONEBEAM_CJ  or
       IMG_OBS_ONEBEAM_NJ or IMG_OBS_ONEBEAM_DJ

       Additionally, a bad pixel map with a PRO.CATG of IMG_BPM may be added to the Set Of Frames
       with tag: BPM.

OPTIONS

       --nod <str>
              An optional ASCII specification of the nodding positions (in case they are  missing
              from the FITS-file). The file must consist of one line per input FITS-file and each
              line must consist of an integer (which is  ignored)  followed  by  a  0  or  1  (to
              indicate  object or sky).  (str; default: ´NONE´). The full name of this option for
              the EsoRex configuration file  is  visir.visir_old_img_combine.nodding  [default  =
              NONE].

       --auto_bpm <bool>
              Automatic  detection  and  correction of bad pixels (bool; default: True). The full
              name    of    this    option    for    the    EsoRex    configuration    file    is
              visir.visir_old_img_combine.auto_bpm [default = True].

       --g <bool>
              Automatic  filtering  of  glitches  (bool;  default:  False). The full name of this
              option for the EsoRex configuration file is  visir.visir_old_img_combine.rem_glitch
              [default = False].

       --p <bool>
              Automatic  purging  of  half-cycle  images whose median deviates more than a factor
              three from the mean of the medians of half-cycle images or whose standard deviation
              deviates more than a factor three from the mean of their standard deviations (bool;
              default: False). The full name of this option for the EsoRex configuration file  is
              visir.visir_old_img_combine.purge_bad [default = False].

       --union <bool>
              Combine  images using their union, as opposed to their intersection (deprecated and
              ignored, see --combine_method) (bool; default: True). The full name of this  option
              for  the  EsoRex configuration file is visir.visir_old_img_combine.union [default =
              True].

       --rej <str>
              Each resulting pixel is the average of the corresponding (interpolated) pixel value
              in  each  jittered  image.  A positive value, n1, for the first of the two integers
              specifies that for each pixel the smallest n1 pixel values shall be ignored in  the
              averaging.   Similarly,  a  positive  value, n2, for the second of the two integers
              specifies that for each pixel the largest n2 pixel values shall be ignored  in  the
              averaging.  (str;  default:  ´0-0´).  The  full  name of this option for the EsoRex
              configuration file is visir.visir_old_img_combine.rej [default = 0-0].

       --plot <int>
              The recipe can produce a number of predefined plots. Zero means that  none  of  the
              plots  are  produced, while increasing values (e.g. 1 or 2) increases the number of
              plots produced. If the plotting  fails  a  warning  is  produced,  and  the  recipe
              continues.  The  default  behaviour  of the plotting is to use gnuplot (with option
              -persist). The recipe currently  produces  1D-plots  using  gnuplot  commands.  The
              recipe  user  can  control the actual plotting-command used by the recipe to create
              the plot by setting the environment variable CPL_PLOTTER. Currently, if CPL_PLOTTER
              is   set   it   must   contain   the   string  ´gnuplot´.  Setting  it  to  ´cat  >
              my_gnuplot_$$.txt´ causes a number of ASCII-files to be created, which each produce
              a  plot  when  given  as  standard  input  to gnuplot (e.g. later or on a different
              computer). A finer control of the plotting options can be obtained  by  writing  an
              executable  script,  e.g.  my_gnuplot.pl,  that  executes gnuplot after setting the
              desired gnuplot  options  (e.g.  set  terminal  pslatex  color)  and  then  setting
              CPL_PLOTTER  to  my_gnuplot.pl.  The  predefined  plots include plotting of images.
              Images can be plotted not only with gnuplot, but also using the pnm format. This is
              controlled  with  the  environment  variable  CPL_IMAGER. If CPL_IMAGER is set to a
              string that does not contain the word gnuplot, the recipe will generate the plot in
              pnm  format.  E.g.   setting  CPL_IMAGER to ´display - &´ will produce a gray-scale
              image using the image viewer display. (int; default: 0).  The  full  name  of  this
              option  for  the  EsoRex  configuration  file  is  visir.visir_old_img_combine.plot
              [default = 0].

       --off <str>
              An optional ASCII specification of the offsets in case those in FITS-  headers  are
              missing  or  wrong. The file must consist of one line per input pair of FITS-files,
              and each line must consist of two numbers which represent the shift  in  pixels  of
              that  image  relative  to  the first image. The first line should thus comprise two
              zeros. Correct FITS-header offsets mean that the i´th X offset can be  gotten  from
              Xoffset_0  -  Xoffset_i,  where  Xoffset_i  is  the value of ESO SEQ CUMOFFSETX and
              likewise for Y. (str; default: ´NONE´). The full name of this option for the EsoRex
              configuration file is visir.visir_old_img_combine.offsets [default = NONE].

       --ref <bool>
              User-defined  refining  of  the  image  offsets.  See options objs and xcorr (bool;
              default: False). The full name of this option for the EsoRex configuration file  is
              visir.visir_old_img_combine.refine [default = False].

       --objs <str>
              The  shift and add of images needs anchor points that typically are bright objects.
              These are normally detected automatically but with user-defined refining of offsets
              enabled,  they  must  be  provided by the user through an ASCII file containing one
              line per anchor point with each line consisting of  its  x  and  y  coordinate  (in
              pixels). This file is ignored with user-defined refining of offsets disabled. (str;
              default: ´NONE´). The full name of this option for the EsoRex configuration file is
              visir.visir_old_img_combine.objects [default = NONE].

       --xcorr <str>
              If user-defined refining of offsets is enabled a cross-correlation of the images is
              performed. In order to speed up this process, this cross-correlation  is  performed
              only  on  smaller  rectangles around the anchor points. The first two parameters is
              the half-size of this rectangle in pixels. The second pair is the maximum shift  in
              x  and y (pixels) evaluated by the cross-correlation on the rectangle. Used only if
              user-defined refining of offsets is enabled.  (str;  default:  ´10-10-25-25´).  The
              full    name    of   this   option   for   the   EsoRex   configuration   file   is
              visir.visir_old_img_combine.xcorr [default = 10-10-25-25].

       --combine_method <str>
              Combine images using one of: 1) Onto  the  first  image  (first);  2)  Their  union
              (union);  3)  Their  intersection  (inter). NB: Only the ´first´-method produces an
              image product with WCS coordinates. A successful ´first´-method always  produces  a
              combined  image  with  dimensions  equal  to  those  of  the  input images. For the
              ´union´-method the result image is at least as large as the input images while  for
              the  ´inter´-method  the result image is at most as large as the input images (str;
              default: ´union´). The full name of this option for the EsoRex  configuration  file
              is visir.visir_old_img_combine.comb_meth [default = union].

       --destripe_iterations <int>
              Max  number  of  destriping  iterations  (0  to  disable  destriping).   Horizontal
              destriping is done first and  if  no  horizontal  striping  is  detected,  vertical
              destriping  is  performed  (int; default: 15). The full name of this option for the
              EsoRex configuration file is visir.visir_old_img_combine.nstripe [default = 15].

       --destripe_morpho <bool>
              Destripe with morphological cleaning (bool; default: False). The full name of  this
              option  for  the  EsoRex  configuration file is visir.visir_old_img_combine.mstripe
              [default = False].

       --eccmax <float>
              The maximum eccentricity allowed in the  combination  of  the  three  (in  parallel
              nod/chopping)  or  four  (in  perpendicular nod/chopping) beams.  In parallel mode,
              three perfectly aligned points spaced with the chopnod throw will have eccentricity
              0,  while  in  perpedicular mode a square with the chopnod throw as the side length
              will have eccentricity 0 (float; default: 0.25). The full name of this  option  for
              the  EsoRex  configuration  file  is  visir.visir_old_img_combine.eccmax [default =
              0.25].

       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 visir pipeline can be downloaded as a PDF  file  using  the
       following URL:

              ftp://ftp.eso.org/pub/dfs/pipelines/visir/visir-pipeline-manual-1.4.pdf

       An   overview   over   the   existing   ESO  pipelines  can  be  found  on  the  web  page
       https://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
       https://packages.python.org/python-cpl/index.html for further information.

       The   other   recipes  of  the  visir  pipeline  are  visir_img_dark(7),  visir_img_ff(7),
       visir_img_reduce(7),  visir_img_trans(7),   visir_old_img_phot(7),   visir_old_spc_obs(7),
       visir_old_spc_obs_ech(7),         visir_old_spc_phot(7),        visir_old_spc_phot_ech(7),
       visir_old_spc_wcal(7),       visir_old_spc_wcal_ech(7),        visir_old_util_destripe(7),
       visir_spc_reduce(7),             visir_util_apply_calib(7),            visir_util_clip(7),
       visir_util_convert_weight(7),    visir_util_detect_shift(7),    visir_util_img_std_cat(7),
       visir_util_join(7),   visir_util_qc(7),   visir_util_repack(7),   visir_util_run_swarp(7),
       visir_util_spc_std_cat(7), visir_util_spc_txt2fits(7), visir_util_undistort(7)

VERSION

       visir_old_img_combine 4.3.7

AUTHOR

       Lars Lundin <usd-help@eso.org>

BUG REPORTS

       Please report any problems to usd-help@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  VISIR Instrument Pipeline Copyright (C) 2004, 2005 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., 51 Franklin St, Fifth Floor, Boston,
       MA  02111-1307  USA