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visir_spc_reduce - Spectroscopic Observation recipe

VISIR_SPC_REDUCE(7) visir recipes VISIR_SPC_REDUCE(7)

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 in each nod cycle,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].
--planelimit <long>
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. (long; default: -1). The full name of this option for the EsoRex configuration file is visir.visir_util_repack.planelimit [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].
--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 <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 4.3.3
 

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
4.3.3 visir_spc_reduce