Provided by: cpl-plugin-visir-doc_4.4.2+dfsg-1_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