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xsh_orderpos - Create the orders centre traces table file
esorex xsh_orderpos [OPTIONS] FILE.sof
This recipe creates the orders centre traces table. Input Frames for UVB and VIS: Raw file (Tag = ORDERDEF_arm_D2) Master Dark (Tag = MASTER_DARK_arm) Master Bias (Tag = MASTER_BIAS_arm) Input Frames for NIR: Raw file ON(Tag = ORDERDEF_NIR_ON) Raw file OFF(Tag = ORDERDEF_NIR_OFF) Input Frames for all arms Guess order table (Tag = ORDER_TAB_GUESS_arm) Spectral format table (Tag = SPECTRAL_FORMAT_TAB_arm) - [OPTIONAL] A map of non linear bad pixels (Format=QUP, Tag = BP_MAP_NL_arm) - [OPTIONAL] A map of reference bad pixels (Format = QUP,RAW, Tag = BP_MAP_RP_arm) Prepare PRE structures. For NIR, subtract NIR-OFF from NIR-ON. For UVB and NIR, Substract the master Bias and master dark. Detect Orders and calculate the order table. The final products are: An updated Order Table, PRO.CATG=ORDER_TABLE_CENTR_arm. A order trace residuals Table, PRO.CATG=ORDERPOS_RESID_TAB_arm. The order pos frame bias subtracted, PRO.CATG=ORDERDEF_ON_arm.
--keep-temp <str> If ´no´, temporary files are deleted. (str; default: ´no´). The full name of this option for the EsoRex configuration file is xsh.xsh_orderpos.keep-temp [default = no]. --debug-level <str> Additional xshooter debug level. One of ´none´, ´low´, ´medium´, ´high´ (str; default: ´none´). The full name of this option for the EsoRex configuration file is xsh.xsh_orderpos.debug-level [default = none]. --time-stamp <bool> Add timestamp to product file name. (bool; default: False). The full name of this option for the EsoRex configuration file is xsh.xsh_orderpos.time-stamp [default = False]. --decode-bp <int> Integer representation of the bits to be considered bad when decoding the bad pixel mask pixel values. Most frequent codes relevant for the user: 0: good pixel, 8: pick-up noise, 16: cosmic-ray removed, 32: cosmic-ray unremoved, 128: calibration file defect, 256: hot pixel, 512: dark pixel, 4096: A/D converted saturation, 32768: non linear pixel, 1048576: extrapolated flux in NIR, 4194304: Interpolated flux during extraction. (int; default: 2144337919). The full name of this option for the EsoRex configuration file is xsh.xsh_orderpos.decode-bp [default = 2144337919]. --pre-overscan-corr <int> pre-overscan correction.0: no correction1: mean overscan correction2: mean prescan correction3: (mean pre+mean overscan)/2 correction (int; default: 1). The full name of this option for the EsoRex configuration file is xsh.xsh_orderpos.pre-overscan-corr [default = 1]. --detectcontinuum-search-win-hsize <int> Half window size in pixels for the 1D box to search for the maximum in the cross-dispersion profile (int; default: 5). The full name of this option for the EsoRex configuration file is xsh.xsh_orderpos.detectcontinuum-search-win-hsize [default = 5]. --detectcontinuum-running-win-hsize <int> Half window size for the running median box during the search for the maximum in the cross-dispersion profile (int; default: 0). The full name of this option for the EsoRex configuration file is xsh.xsh_orderpos.detectcontinuum-running-win-hsize [default = 0]. --detectcontinuum-fit-win-hsize <int> Half window size for the fit of the cross-dispersion profile (int; default: 5). The full name of this option for the EsoRex configuration file is xsh.xsh_orderpos.detectcontinuum-fit-win-hsize [default = 5]. --detectcontinuum-center-thresh-fac <float> Threshold factor applied to check that the flux at the fitted peak is higher than error. (float; default: 0.0). The full name of this option for the EsoRex configuration file is xsh.xsh_orderpos.detectcontinuum-center-thresh-fac [default = 0.0]. --detectcontinuum-ordertab-step-y <int> Step in Y for order centroid detection (int; default: 1). The full name of this option for the EsoRex configuration file is xsh.xsh_orderpos.detectcontinuum-ordertab-step-y [default = 1]. --detectcontinuum-ordertab-deg-y <int> Degree in Y in the polynomial order tracing X=f(Y) (int; default: 5). The full name of this option for the EsoRex configuration file is xsh.xsh_orderpos.detectcontinuum-ordertab-deg-y [default = 5]. --detectcontinuum-clip-res-max <float> Maximum allowed residual (before kappa-sigma clip) (float; default: 0.5). The full name of this option for the EsoRex configuration file is xsh.xsh_orderpos.detectcontinuum-clip-res-max [default = 0.5]. --detectcontinuum-clip-sigma <float> Kappa value in sigma clipping during order trace polynomial fit (float; default: 5.0). The full name of this option for the EsoRex configuration file is xsh.xsh_orderpos.detectcontinuum-clip-sigma [default = 5.0]. --detectcontinuum-clip-niter <int> Number of iterations in sigma clipping during order trace polynomial fit (int; default: 5). The full name of this option for the EsoRex configuration file is xsh.xsh_orderpos.detectcontinuum-clip-niter [default = 5]. --detectcontinuum-clip-frac <float> Minimal fractions of points accepted / total in sigma clippingduring order trace polynomial fit (float; default: 0.4). The full name of this option for the EsoRex configuration file is xsh.xsh_orderpos.detectcontinuum-clip-frac [default = 0.4]. 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 xshoo pipeline can be downloaded as a PDF file using the following URL: ftp://ftp.eso.org/pub/dfs/pipelines/xshoo/xshoo-pipeline-manual-12.1.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 xshoo pipeline are xsh_2dmap(7), xsh_cfg_recover(7), xsh_flexcomp(7), xsh_geom_ifu(7), xsh_lingain(7), xsh_mbias(7), xsh_mdark(7), xsh_mflat(7), xsh_predict(7), xsh_respon_slit_nod(7), xsh_respon_slit_offset(7), xsh_respon_slit_stare(7), xsh_scired_ifu_offset(7), xsh_scired_ifu_offset_drl(7), xsh_scired_ifu_stare(7), xsh_scired_ifu_stare_drl(7), xsh_scired_slit_nod(7), xsh_scired_slit_offset(7), xsh_scired_slit_stare(7), xsh_util_physmod(7), xsh_wavecal(7)
L.Guglielmi,R.Haigron,P.Goldoni,F.Royer, A. Modigliani <email@example.com>
Please report any problems to firstname.lastname@example.org. Alternatively, you may send a report to the ESO User Support Department <email@example.com>.
This file is part of the X-shooter Instrument Pipeline Copyright (C) 2006 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., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA