visir_old_spc_phot - Old DRS detector: Sensitivity computation in
spectroscopy
esorex visir_old_spc_phot [OPTIONS] FILE.sof
This recipe estimates the dispersion relation using the
atmospheric spectrum in a long-slit spectroscopy half-cycle frame.
It also extracts the spectrum of an observed object using a
combined frame.
Lastly, it computes the spectral photometry of an observed
standard star.
The files listed in the Set Of Frames (sof-file) must be tagged:
VISIR-Long-Slit-Spectroscopy-file.fits SPEC_CAL_PHOT
VISIR-Quantum-Efficiency-Calibration-file.fits SPEC_CAL_QEFF
VISIR-Atmospheric-Emission-Lines-Calibration-file.fits SPEC_CAL_LINES
VISIR-Spectroscopic-Standard-Star-Catalog.fits SPEC_STD_CATALOG
Additionally, a bad pixel map with a PRO.CATG of SPEC_BPM may be
added to the Set Of Frames with tag: BPM.
- --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_phot.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_phot.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_phot.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_phot.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_phot.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_phot.rej [default =
0-0].
- --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_phot.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_phot.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_phot.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_phot.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_phot.delta [default =
0.0].
- --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_phot.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_phot.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_phot.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_phot.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_phot.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_phot.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_phot.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_phot.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_phot.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_phot.reject_right
[default = 0].
- --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_phot.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_phot.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_phot.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_phot.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_phot.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_phot.optex_kernel
[default = 3].
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_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)
Lars Lundin <https://support.eso.org>
Please report any problems to https://support.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)
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