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