Name
       jitter - ISAAC (SW and LW) / SOFI / NACO jitter imaging reduction

Synopsis
       jitter [flags] [options]

Description
       jitter reduces images taken in infrared jitter imaging mode. It makes a
       number of assumptions on the input signal and has  a  list  of  several
       possible  algorithms  with  associated  parameters  for  each reduction
       stage.

       jitter has been developped to reduce jitter  imaging  data  taken  from
       infrared  instruments,  e.g.  IRAC2, SOFI, ISAAC or NACO. Although some
       features are specific to the two latter instruments, it  is  reasonable
       to think that the same algorithms should work on similar data.

       jitter  is  configured through an initialization file. The name of this
       file is defaulted to jitter.ini but can be changed through the  use  of
       the -f option. In the following documentation, this file is referred to
       as the ini file.

Process
       The jitter data reduction process is  divided  into  flat-fielding/dark
       subtraction/bad pixel correction, sky estimation and subtraction, frame
       offset detection, frame re-centering, frame stacking to a single frame,
       and  optional  post-processing tasks. Some processes may be deactivated
       depending on what you intend to do with the data.  Describing  all  the
       algorithms in this command is far beyond the scope of this manual page.
       A documentation about the jitter algorithm can be found on the  eclipse
       web site.

       To  setup  the process, you need first to generate a default jitter.ini
       file and then change parameters according to your needs. This  initial-
       ization file is self-documented.

Flags
       Flags which can be activated on the command-line are the following:

       -t or --time
              Activate  time  estimation tools. This actually triggers a clock
              when the process is running and produces duration estimations in
              CPU and user time at the end.

Options
       -c or --calib  calib.ascii
              This  option  can  only  be used together with the -g option. It
              will generate a default ini file where the names of the calibra-
              tion  files  are  deduced  from  the  contents  of  the provided
              ’calib.ascii’ file. This file should contain  two  columns:  the
              first one gives the name of the calibration file, the second one
              specifies its type.

       -f or --file  filename
              Changes the name of the ini file from jitter.ini to filename.

       -g or --generate
              Generates a default ini file in the  current  directory,  and  a
              default  empty  frame list called framelist.ascii.  You can fill
              up the ASCII list of input names by using the ls command:
              ls -1 *.fits >> framelist.ascii
              or:
              dfits *.fits | fitsort DPR.TYPE >> framelist.ascii
              Of  course,   the   list   of   frames   need   not   be   named
              ’framelist.ascii’,  this  is the default name only. Change it if
              you wish in the ini file.

       -A or --algorithm  algo
              is used together with the -g option to generate an ini file with
              the  defaults  set for the specified instrument. Possible values
              for algo are isaac-sw, isaac-lw, naco-sw or auto.

       -w or --gui
              Launches a GUI to use jitter

       -h or --help
              Displays a short reminder of possible options and flags.

       -i or --in  filename
              This option can only be used together with  the  -g  option.  It
              will  generate  a  default  ini file where the name of the input
              framelist is not the  default  but  the  one  provided  to  this
              option.

       -o or --out  basename
              This  option  can  only  be used together with the -g option. It
              will generate a default ini file where the  output  basename  is
              not the default but the one provided to this option.

Files
       The  ini  file  which is generated by using the -g option is self-docu-
       mented, all parameters are described in the file comments.

       The ini file consists of [Sections] followed by
       keyword = value lines.

       Section names and keywords are case-insensitive. Values  associated  to
       keuwords  may be integer, floating point numbers, character strings, or
       flags. Types associated to keywords are usually indicated in  the  com-
       ment  section.  Character strings as keyword values are case-sensitive.
       Flags are given as Yes/Y/yes or No/N/no.

       Comments in the ini file are identified by lines starting with  a  hash
       (#) sign, and generally everything after a semicolon (;) and before the
       end of the line. The semicolon is not mandatory, the two  5A  following
       lines are strictly equivalent:

       ExposureTime = 1000 ; integer value in seconds
       ExposureTime = 1000

       It  is  advised  to  use  the -A option when the ini file is generated.
       jitter can reduce data from several instruments.  Each  instrument  has
       its own defaults. To generate an ini file with the defaults for a given
       instrument, specify the instrument with this -A option.