Provided by: cpl-plugin-visir-doc_4.3.11+dfsg-1_all 
NAME
visir_old_spc_obs_ech - Old DRS detector: Spectroscopic Observation recipe in Echelle mode
SYNOPSIS
esorex visir_old_spc_obs_ech [OPTIONS] FILE.sof
DESCRIPTION
This recipe estimates the dispersion relation using the atmospheric spectrum in a grism spectroscopy
half-cycle frame.
It also extracts the spectrum of an observed object using a combined frame.
The files listed in the Set Of Frames (sof-file) must be tagged: VISIR-Echelle-Spectroscopy-file.fits
SPEC_OBS_HRG VISIR-Quantum-Efficiency-Calibration-file.fits SPEC_CAL_QEFF
VISIR-Atmospheric-Emission-Lines-Calibration-file.fits SPEC_CAL_LINES
Additionally, a bad pixel map with a PRO.CATG of SPEC_BPM may be added to the Set Of Frames with tag:
BPM.
OPTIONS
--nod <str>
An optional ASCII specification of the nodding positions (in case they are missing from the
FITS-file). The file must consist of one line per input FITS-file and each line must consist of an
integer (which is ignored) followed by a 0 or 1 (to indicate object or sky). (str; default:
´NONE´). The full name of this option for the EsoRex configuration file is
visir.visir_old_spc_obs_ech.nodding [default = NONE].
--auto_bpm <bool>
Automatic detection and correction of bad pixels (bool; default: True). The full name of this
option for the EsoRex configuration file is visir.visir_old_spc_obs_ech.auto_bpm [default = True].
--g <bool>
Automatic filtering of glitches (bool; default: False). The full name of this option for the
EsoRex configuration file is visir.visir_old_spc_obs_ech.rem_glitch [default = False].
--p <bool>
Automatic purging of half-cycle images whose median deviates more than a factor three from the
mean of the medians of half-cycle images or whose standard deviation deviates more than a factor
three from the mean of their standard deviations (bool; default: False). The full name of this
option for the EsoRex configuration file is visir.visir_old_spc_obs_ech.purge_bad [default =
False].
--union <bool>
Combine images using their union, as opposed to their intersection (deprecated and ignored, see
--combine_method) (bool; default: True). The full name of this option for the EsoRex configuration
file is visir.visir_old_spc_obs_ech.union [default = True].
--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_ech.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_ech.bkgcorrect [default = False].
--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_ech.plot [default = 0].
--slit_skew <float>
Distortion correction: Skew of slit (degrees) (clockwise) (float; default: 0.0). The full name of
this option for the EsoRex configuration file is visir.visir_old_spc_obs_ech.phi [default = 0.0].
--spectrum_skew <float>
Distortion correction: LMR Skew of spectrum (degrees) (counter- clockwise). Not used in High
Resolution (float; default: 0.0). The full name of this option for the EsoRex configuration file
is visir.visir_old_spc_obs_ech.ksi [default = 0.0].
--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: 0.0). The full name
of this option for the EsoRex configuration file is visir.visir_old_spc_obs_ech.eps [default =
0.0].
--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_ech.delta [default = 0.0].
--orderoffset <int>
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. (int; default: 0). The full name of this option for the EsoRex
configuration file is visir.visir_old_spc_obs_ech.orderoffset [default = 0].
--off <str>
An optional ASCII specification of the offsets in case those in FITS- headers are missing or
wrong. The file must consist of one line per input pair of FITS-files, and each line must consist
of two numbers which represent the shift in pixels of that image relative to the first image. The
first line should thus comprise two zeros. Correct FITS-header offsets mean that the i´th X offset
can be gotten from Xoffset_0 - Xoffset_i, where Xoffset_i is the value of ESO SEQ CUMOFFSETX and
likewise for Y. (str; default: ´NONE´). The full name of this option for the EsoRex configuration
file is visir.visir_old_spc_obs_ech.offsets [default = NONE].
--ref <bool>
User-defined refining of the image offsets. See options objs and xcorr (bool; default: False). The
full name of this option for the EsoRex configuration file is visir.visir_old_spc_obs_ech.refine
[default = False].
--objs <str>
The shift and add of images needs anchor points that typically are bright objects. These are
normally detected automatically but with user-defined refining of offsets enabled, they must be
provided by the user through an ASCII file containing one line per anchor point with each line
consisting of its x and y coordinate (in pixels). This file is ignored with user-defined refining
of offsets disabled. (str; default: ´NONE´). The full name of this option for the EsoRex
configuration file is visir.visir_old_spc_obs_ech.objects [default = NONE].
--xcorr <str>
If user-defined refining of offsets is enabled a cross-correlation of the images is performed. In
order to speed up this process, this cross-correlation is performed only on smaller rectangles
around the anchor points. The first two parameters is the half-size of this rectangle in pixels.
The second pair is the maximum shift in x and y (pixels) evaluated by the cross-correlation on the
rectangle. Used only if user-defined refining of offsets is enabled. (str; default:
´10-10-25-25´). The full name of this option for the EsoRex configuration file is
visir.visir_old_spc_obs_ech.xcorr [default = 10-10-25-25].
--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_ech.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_ech.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_ech.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_ech.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_ech.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_ech.reject_right
[default = 0].
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_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)
VERSION
visir_old_spc_obs_ech 4.3.11
AUTHOR
Lars Lundin <usd-help@eso.org>
BUG REPORTS
Please report any problems to usd-help@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) 2004, 2005 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_old_spc_obs_ech 4.3.11 VISIR_OLD_SPC_OBS_ECH(7)