visir_img_reduce - Combines a stack of chopped, jittered and/or
nodded exposures and can compute the sensitivity for standard star
observations
esorex visir_img_reduce [OPTIONS] FILE.sof
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.
- --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].
- 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-4.4.2/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-4.4.2/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.
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)
Julian Taylor <jtaylor@partner.eso.org>
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>.
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