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.