visir_spc_reduce - Spectroscopic Observation recipe
esorex visir_spc_reduce [OPTIONS] FILE.sof
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.
- --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.
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)
Julian Taylor <jtaylor@partner.eso.org>
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>.
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