Provided by: cpl-plugin-visir-doc_4.3.8+dfsg-1_all 
NAME
visir_img_reduce - Combines a stack of chopped, jittered and/or nodded exposures and can compute the
sensitivity for standard star observations
SYNOPSIS
esorex visir_img_reduce [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 or VISIR-observation-file.fits BURST
VISIR-Standard-star-catalog IMG_STD_CATALOG (optional) VISIR-linearty-table.fits LINEARITY_TABLE
(optional) Additionally, a bad pixel map with a PRO.CATG of IMG_BPM may be added to the Set Of Frames
with tag: BPM.
OPTIONS
--planestart <int>
Plane number to start repacking from in each nod cycle,earlier planes are skipped. (int; default:
0). The full name of this option for the EsoRex configuration file is
visir.visir_util_repack.planestart [default = 0].
--planelimit <int>
Limit number of processed inputplanes. It will repack until at least this number of input images
have been processed or the full dataset has been repacked. Always full chop cycles need to be
repacked so the number is adjusted upward to the next multiple of images per chop cycle. <= 0 for
no limit. (int; default: -1). The full name of this option for the EsoRex configuration file is
visir.visir_util_repack.planelimit [default = -1].
--trimlow <int>
Burst data only. Number of additional planes to cut from before each plane with chopper movement.
(int; default: 0). The full name of this option for the EsoRex configuration file is
visir.visir_util_repack.trimlow [default = 0].
--trimhigh <int>
Burst data only. Number of additional planes to cut from after each plane with chopper movement.
A value of -1 does not skip the plane of the movement. (int; default: 0). The full name of this
option for the EsoRex configuration file is visir.visir_util_repack.trimhigh [default = 0].
--lincorrect <bool>
Apply linearity correction. Should only be enabled on high flux observations, may degrade results
otherwise. (bool; default: False). The full name of this option for the EsoRex configuration file
is visir.visir_util_repack.lincorrect [default = False].
--template <str>
Correlation template used to detect shifts and reject bad images. If none given an averaged image
is used (str; default: ´NONE´). The full name of this option for the EsoRex configuration file is
visir.visir_util_detect_shift.template [default = NONE].
--min-correlation <float>
Minimal correlation to the template required to be accepted (float; default: 0.5). The full name
of this option for the EsoRex configuration file is visir.visir_util_detect_shift.min-correlation
[default = 0.5].
--max-shift <float>
Maximal allowed object shift for an image to be accepted (float; default: 10.0). The full name of
this option for the EsoRex configuration file is visir.visir_util_detect_shift.max-shift [default
= 10.0].
--max-mad <float>
Maximal allowed median absolute deviation for an image to be accepted. <= 0 equals no limit
(float; default: 0.0). The full name of this option for the EsoRex configuration file is
visir.visir_util_detect_shift.max-mad [default = 0.0].
--naverage <int>
Number of planes to average before attempting to detect the shifts. (int; default: 1). The full
name of this option for the EsoRex configuration file is visir.visir_util_detect_shift.naverage
[default = 1].
--method <str>
Method to determine beam shifts. xcorrelate: use the cross correlation shift. brightest: use the
position of the brightest pixel (str; default: ´xcorrelate´). The full name of this option for the
EsoRex configuration file is visir.visir_util_detect_shift.method [default = xcorrelate].
--no-shift <bool>
Sets whether to apply the determined shifts in following recipes. Set to TRUE of shifts appear too
large. (bool; default: False). The full name of this option for the EsoRex configuration file is
visir.visir_util_detect_shift.no-shift [default = False].
--no-reject <bool>
If true images with bad statistics will not be rejected and no shift correction is done (bool;
default: True). The full name of this option for the EsoRex configuration file is
visir.visir_util_detect_shift.no-reject [default = True].
--beampos <str>
Define the positions of the beams. These positions are cut by the window to extract the single
beam images. Format: sign:x,y,window;sign:x,y,window;... where sign is "pos" or "neg" depending
on whether the beam is positive or negative. The window is optional and defines the size of the
cut image around the beam. The default window is the chop throw. E.g.: pos:50,60;neg:50,160; By
default autodetection is attempted. (str; default: ´NONE´). The full name of this option for the
EsoRex configuration file is visir.visir_util_detect_shift.beampos [default = NONE].
--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: 3.0). The full name
of this option for the EsoRex configuration file is visir.visir_util_detect_shift.eccmax [default
= 3.0].
--keepfrac <float>
The fraction of pixels to keep for the initialmedian (float; default: 0.9). The full name of this
option for the EsoRex configuration file is visir.visir_util_clip.keepfrac [default = 0.9].
--kappa <float>
Clip outside + or - kappa * sigma (the standard deviation) (float; default: 5.0). The full name of
this option for the EsoRex configuration file is visir.visir_util_clip.kappa [default = 5.0].
--maxite <int>
Max number of kappa-sigma clipping iterations (int; default: 3). The full name of this option for
the EsoRex configuration file is visir.visir_util_clip.maxite [default = 3].
--shift-beams <bool>
Account for movements of the object defined in CRPIX[12] (bool; default: True). The full name of
this option for the EsoRex configuration file is visir.visir_util_clip.shift-beams [default =
True].
--error-source <str>
Defines the way errors are generated: img-stdev: stdev of image timeseries: stdev of each pixel
over the time axis of the cube none: no error generation (str; default: ´img-stdev´). The full
name of this option for the EsoRex configuration file is visir.visir_util_clip.error-source
[default = img-stdev].
--badimage <float>
If percentage of clipped pixels above this value the whole image is considered bad (float;
default: 0.2). The full name of this option for the EsoRex configuration file is
visir.visir_util_clip.badimage [default = 0.2].
--output-all <bool>
Output a coadded image for each input file in addition to the complete coaddition. (bool; default:
False). The full name of this option for the EsoRex configuration file is
visir.visir_util_run_swarp.output-all [default = False].
--extra_config <str>
Additional configuration parameters (str; default: ´NONE´). The full name of this option for the
EsoRex configuration file is visir.visir_util_run_swarp.extra_config [default = NONE].
--config_fname <str>
Swarp configure file name. (str; default: ´/usr/share/cpl-
plugins/visir-4.3.8/config/visir_default.swarp´). The full name of this option for the EsoRex
configuration file is visir.visir_util_run_swarp.config_fname [default =
/usr/share/cpl-plugins/visir-4.3.8/config/visir_default.swarp].
--nprocs <int>
Maximum number of swarp processes that can be spawned simultaneously. (int; default: -1). The
full name of this option for the EsoRex configuration file is visir.visir_util_run_swarp.nprocs
[default = -1].
--jy_val <float>
The flux of the standard star in Jansky (float; default: -999.0). The full name of this option for
the EsoRex configuration file is visir.visir_old_img_phot.jy_val [default = -999.0].
--radii <str>
Radii : star_max bg_int bg_ext (str; default: ´20-20-30´). The full name of this option for the
EsoRex configuration file is visir.visir_old_img_phot.radii [default = 20-20-30].
--delete-temp <bool>
Delete temporary files created during processing (bool; default: True). The full name of this
option for the EsoRex configuration file is visir.visir_img_reduce.delete-temp [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 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_trans(7),
visir_old_img_combine(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_img_reduce 4.3.8
AUTHOR
Julian Taylor <jtaylor@partner.eso.org>
BUG REPORTS
Please report any problems to jtaylor@partner.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) 2015 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