Provided by: cpl-plugin-visir-doc_4.1.0+dfsg-2_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 <long>
Plane number to start repacking from, earlier planes are skipped. (long; default: 0). The full
name of this option for the EsoRex configuration file is visir.visir_util_repack.planestart
[default = 0].
--ncycles <long>
Number of full on-off cycles to repack. <= 0 for all. (long; default: -1). The full name of this
option for the EsoRex configuration file is visir.visir_util_repack.ncycles [default = -1].
--trimlow <long>
Burst data only. Number of additional planes to cut from before each plane with chopper movement.
(long; default: 0). The full name of this option for the EsoRex configuration file is
visir.visir_util_repack.trimlow [default = 0].
--trimhigh <long>
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. (long; default: 0). The full name of this
option for the EsoRex configuration file is visir.visir_util_repack.trimhigh [default = 0].
--xl <long>
Coordinate in spatial direction. Together with yl it defines the lower point of a rectangle
containing only skylines for the wavelength shift detection (long; default: 117). The full name of
this option for the EsoRex configuration file is visir.visir_util_undistort.xl [default = 117].
--yl <long>
Coordinate in wavelength direction. See xl (long; default: 110). The full name of this option for
the EsoRex configuration file is visir.visir_util_undistort.yl [default = 110].
--xh <long>
Coordinate in spatial direction. Together with yl it defines the higher point of a rectangle
containing only skylines for the wavelength shift detection (long; default: 125). The full name of
this option for the EsoRex configuration file is visir.visir_util_undistort.xh [default = 125].
--yh <long>
Coordinate in wavelength direction. See xh (long; 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 <long>
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 (long; 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: False). The
full name of this option for the EsoRex configuration file is visir.visir_old_spc_obs.bkgcorrect
[default = False].
--plot <long>
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. (long; 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].
--orderoffset <long>
Echelle order offset. The offset is relative to the main order. The allowed range of offsets
depend on the selected grism. The offset can never exceed +/-4. If the main order is e.g. 8 an
order offset of +1 will cause the recipe to base the data reduction on order 9. With a positive
order offset the central wavelength becomes smaller while for a negative order offset the central
wavelength becomes larger. (long; default: 0). The full name of this option for the EsoRex
configuration file is visir.visir_old_spc_obs.orderoffset [default = 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 <long>
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 (long; 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 <long>
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) (long; default: 0). The full
name of this option for the EsoRex configuration file is visir.visir_old_spc_obs.reject_left
[default = 0].
--rr <long>
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) (long; default: 0). The full
name of this option for the EsoRex configuration file is visir.visir_old_spc_obs.reject_right
[default = 0].
--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
http://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
http://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 4.1.0
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 4.1.0 VISIR_SPC_REDUCE(7)