Provided by: cpl-plugin-visir-doc_4.4.2+dfsg-1build1_all 
NAME
visir_spc_reduce - Spectroscopic Observation recipe
SYNOPSIS
esorex visir_spc_reduce [OPTIONS] FILE.sof
DESCRIPTION
This recipe performs a wavelength calibration followed by spectrum extraction from a combined image. It
can also compute sensitivities for standard star observations.
It works for low and high resolution including echelle mode.
The files listed in the Set Of Frames (sof-file) must be tagged: VISIR-Long-Slit-Spectroscopy-file.fits
SPEC_OBS_LMR VISIR-Quantum-Efficiency-Calibration-file.fits SPEC_CAL_QEFF
VISIR-Atmospheric-Emission-Lines-Calibration-file.fits SPEC_CAL_LINES
VISIR-Standard-Star-Flux-Catalog.fits (optional)SPEC_STD_CATALOG 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].
--xl <int>
Coordinate in spatial direction. Together with yl it defines the lower point of a rectangle
containing only skylines for the wavelength shift detection (int; default: 117). The full name of
this option for the EsoRex configuration file is visir.visir_util_undistort.xl [default = 117].
--yl <int>
Coordinate in wavelength direction. See xl (int; default: 110). The full name of this option for
the EsoRex configuration file is visir.visir_util_undistort.yl [default = 110].
--xh <int>
Coordinate in spatial direction. Together with yl it defines the higher point of a rectangle
containing only skylines for the wavelength shift detection (int; default: 125). The full name of
this option for the EsoRex configuration file is visir.visir_util_undistort.xh [default = 125].
--yh <int>
Coordinate in wavelength direction. See xh (int; default: 150). The full name of this option for
the EsoRex configuration file is visir.visir_util_undistort.yh [default = 150].
--slit_skew <float>
Distortion correction: Skew of slit (degrees) (clockwise) (float; default: 0.52). The full name of
this option for the EsoRex configuration file is visir.visir_util_undistort.phi [default = 0.52].
--spectrum_skew <float>
Distortion correction: LMR Skew of spectrum (degrees) (counter- clockwise). Not used in High
Resolution (float; default: 1.73). The full name of this option for the EsoRex configuration file
is visir.visir_util_undistort.ksi [default = 1.73].
--vert_arc <float>
Distortion correction: LR Detector vertical curvature (pixel). Reduced by a factor 4 in MR. Not
used in HR A-side. Increased by a factor 115/52 in HR B-side (float; default: -0.8). The full name
of this option for the EsoRex configuration file is visir.visir_util_undistort.eps [default =
-0.8].
--hori_arc <float>
Distortion correction: LMR Detector horizontal curvature (pixel). Increased by a factor 1.5 in HR
A-side. Reduced by a factor 2 in HR B-side (float; default: 0.0). The full name of this option for
the EsoRex configuration file is visir.visir_util_undistort.delta [default = 0.0].
--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_util_destripe.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_util_destripe.mstripe [default = False].
--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_spc_obs.rej [default = 0-0].
--bkgcorrect <bool>
Subtract the median from the spectral column before extracting the wavelength. This is required
when the skylines do not correctly cancel due to gratting oscillations (bool; default: True). The
full name of this option for the EsoRex configuration file is visir.visir_old_spc_obs.bkgcorrect
[default = True].
--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_spc_obs.plot [default = 0].
--slit_skew <float>
Distortion correction: Skew of slit (degrees) (clockwise) (float; default: 0.52). The full name of
this option for the EsoRex configuration file is visir.visir_old_spc_obs.phi [default = 0.52].
--spectrum_skew <float>
Distortion correction: LMR Skew of spectrum (degrees) (counter- clockwise). Not used in High
Resolution (float; default: 1.73). The full name of this option for the EsoRex configuration file
is visir.visir_old_spc_obs.ksi [default = 1.73].
--vert_arc <float>
Distortion correction: LR Detector vertical curvature (pixel). Reduced by a factor 4 in MR. Not
used in HR A-side. Increased by a factor 115/52 in HR B-side (float; default: -0.8). The full name
of this option for the EsoRex configuration file is visir.visir_old_spc_obs.eps [default = -0.8].
--hori_arc <float>
Distortion correction: LMR Detector horizontal curvature (pixel). Increased by a factor 1.5 in HR
A-side. Reduced by a factor 2 in HR B-side (float; default: 0.0). The full name of this option for
the EsoRex configuration file is visir.visir_old_spc_obs.delta [default = 0.0].
--fixcombi <bool>
Perform the distortion correction on the combined image, and not on each of the jittered images.
This will reduce excution time and degrade the quality of the combined image (bool; default:
False). The full name of this option for the EsoRex configuration file is
visir.visir_old_spc_obs.fixcombi [default = False].
--emis_tol <float>
The computation of the mean and standard deviation of the sensitivity is done for wavelengths with
an atmospheric emissivity of at most emis_min + emis_tol * (emis_max - emis_min), where emis_min
is the minimum emissivity in the observed wavelength range and emis_max is the ditto maximum. Thus
emis_tol = 1 means that all wavelengths are included. (float; default: 1.0). The full name of this
option for the EsoRex configuration file is visir.visir_old_spc_obs.emis_tol [default = 1.0].
--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_spc_obs.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_spc_obs.mstripe [default = False].
--rl <int>
Reject leftmost columns in spectrum extraction, zero means all columns on the left are used. In
cross-dispersion mode a (small) negative number may be used (pixel) (int; default: 0). The full
name of this option for the EsoRex configuration file is visir.visir_old_spc_obs.reject_left
[default = 0].
--rr <int>
Reject rightmost columns in spectrum extraction, zero means all columns on the right are used. In
cross-dispersion mode a (small) negative number may be used (pixel) (int; default: 0). The full
name of this option for the EsoRex configuration file is visir.visir_old_spc_obs.reject_right
[default = 0].
--apfile <str>
An optional ASCII file specification of the aperture definitions to use during spectral
extraction. Each line must contain either 3 fields for optimal extraction, or an even number of
fields greater than 5 for aperture extraction. For optimal extraction, the 1st field should be
´O´, and for aperture extraction it should be ´A´. In both cases the next pair of fields indicate
the left & right edges of the source aperture in pixel coordinates. For aperture extraction,
fields after the 3rd define the sky apertures coordinates, with the 4th field indicating the
method used to determine the sky background [one of ´A´ (average), ´F´ (linear fit), or ´M´
(median)] followed by at least one pair of pixel coordinates representing the left & right edge of
a sky aperture. You may supply more sky apertures by supplying additional pixel coordinate pairs
after the first. Multiple lines targeting the same order are allowed. (str; default: ´NONE´). The
full name of this option for the EsoRex configuration file is visir.visir_old_spc_obs.apfile
[default = NONE].
--ro_noise <float>
Readout noise of the detector (float; default: 14.5). The full name of this option for the EsoRex
configuration file is visir.visir_old_spc_obs.ron [default = 14.5].
--ox_sigma <float>
Sigma to use for clipping in optimal extraction (float; default: 5.0). The full name of this
option for the EsoRex configuration file is visir.visir_old_spc_obs.optex_sigma [default = 5.0].
--ox_niters <int>
Number of optimal extraction iterations to perform (int; default: 2). The full name of this option
for the EsoRex configuration file is visir.visir_old_spc_obs.optex_niters [default = 2].
--ox_smooth <int>
Width of smoothing window to use along spectral dimension during optimal extraction. A median
filter is used. (int; default: 31). The full name of this option for the EsoRex configuration file
is visir.visir_old_spc_obs.optex_smooth [default = 31].
--gain <float>
Detector gain (float; default: 0.75). The full name of this option for the EsoRex configuration
file is visir.visir_old_spc_obs.gain [default = 0.75].
--ox_kernel <int>
Size of square smoothing kernel, in pixels, to apply to science frame before optimal extraction
(ignored during aperture extraction). A median filter is used. (int; default: 3). The full name of
this option for the EsoRex configuration file is visir.visir_old_spc_obs.optex_kernel [default =
3].
--respcal <str>
An optional path to a FITS file containing a 1-D fringe model to be divided into the 1-D extracted
spectra in order to remove the fringes. (str; default: ´NONE´). The full name of this option for
the EsoRex configuration file is visir.visir_old_spc_obs.respcal [default = NONE].
--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_spc_reduce.delete-temp [default = True].
--destripe <bool>
Attempt to remove stripes (bool; default: False). The full name of this option for the EsoRex
configuration file is visir.visir_spc_reduce.destripe [default = False].
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_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_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_spc_reduce 4.4.2
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
visir_spc_reduce 4.4.2 VISIR_SPC_REDUCE(7)