--- name: "xsh_scired_ifu_offset" section: "7" platform: "linux" package: "cpl-plugin-xshoo-doc" version: "3.5.0+dfsg-4" release: "Debian 11 (Bullseye)" platforms: ["linux"] url: "https://new.carta.tech/xsh_scired_ifu_offset" --- # xsh\_scired\_ifu\_offset(7) Reduce science IFU on-off exposures and build a 3D cube ## NAME xsh\_scired\_ifu\_offset - Reduce science IFU on-off exposures and build a 3D cube ## SYNOPSIS esorex **xsh\_scired\_ifu\_offset** \[OPTIONS\] FILE.sof ## DESCRIPTION This recipe Reduce science IFU on-off exposures and build a 3D cube Input Frames : \ \- A set of 2xn Science frames, Tag = OBJECT\_IFU\_OFFSET\_arm, SKY\_IFU\_arm\ \- A spectral format table (Tag = SPECTRAL\_FORMAT\_TAB\_arm)\ \- A master flat frame (Tag = MASTER\_FLAT\_IFU\_arm)\ \- An order table frame(Tag = ORDER\_TABLE\_EDGES\_IFU\_arm)\ \- 3 wave solution frames, one per slitlet (Tag = WAVE\_TAB\_ARC\_IFU\_slitlet\_arm)\ where ´slitlet´ is DOWN, CEN or UP\ \- \[OPTIONAL\] A dispersion table (Tag = DISP\_TAB\_IFU\_arm)\ \- \[OPTIONAL\] A non-linear badpixel map (Tag = BP\_MAP\_NL\_arm)\ \- \[OPTIONAL\] A reference badpixel map (Tag = BP\_MAP\_RP\_arm) Products : \ \- Merged 3D data cube (PREFIX\_MERGE3D\_DATA\_OBJ\_arm)\ \- QC Traces of 3D data cube (PREFIX\_MERGE3D\_TRACE\_OBJ\_arm)\ \- Order by order 3D data cube (PREFIX\_ORDER3D\_DATA\_OBJ\_arm)\ \- Order by order 3D qual cube (IFU\_CFG\_COR\_arm)\ \- Order by order 3D qual cube (PREFIX\_MERGE3D\_DATA\_SKY\_arm)\ \- where PREFIX is SCI, FLUX, TELL if input raw DPR.TYPE contains OBJECT or FLUX or TELLURIC\ \- 1 Spectrum merge 3D, PRO.CATG=MERGE3D\_IFU\_arm ## OPTIONS - **--keep-temp** *\* If ´no´, temporary files are deleted. (str; default: ´no´). The full name of this option for the EsoRex configuration file is **xsh.xsh\_scired\_ifu\_offset.keep-temp** \[default = *no*\]. - **--debug-level** *\* 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\_scired\_ifu\_offset.debug-level** \[default = *none*\]. - **--time-stamp** *\* Add timestamp to product file name. (bool; default: False). The full name of this option for the EsoRex configuration file is **xsh.xsh\_scired\_ifu\_offset.time-stamp** \[default = *False*\]. - **--decode-bp** *\* 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\_scired\_ifu\_offset.decode-bp** \[default = *2144337919*\]. - **--pre-overscan-corr** *\* pre-overscan correction. 0: no correction 1: mean overscan correction 2: mean prescan correction 3: (mean pre+mean overscan)/2 correction (int; default: 1). The full name of this option for the EsoRex configuration file is **xsh.xsh\_scired\_ifu\_offset.pre-overscan-corr** \[default = *1*\]. - **--stack-method** *\* Method used to build master frame. (str; default: ´median´). The full name of this option for the EsoRex configuration file is **xsh.xsh\_scired\_ifu\_offset.stack-method** \[default = *median*\]. - **--klow** *\* Kappa used to clip low level values, when method is set to ´mean´ (float; default: 5.0). The full name of this option for the EsoRex configuration file is **xsh.xsh\_scired\_ifu\_offset.klow** \[default = *5.0*\]. - **--khigh** *\* Kappa used to clip high level values, when method is set to ´mean´ (float; default: 5.0). The full name of this option for the EsoRex configuration file is **xsh.xsh\_scired\_ifu\_offset.khigh** \[default = *5.0*\]. - **--crh-clip-kappa** *\* Kappa value in sigma clipping during CRH rejection using multiple frames (float; default: 5.0). The full name of this option for the EsoRex configuration file is **xsh.xsh\_scired\_ifu\_offset.crh-clip-kappa** \[default = *5.0*\]. - **--crh-clip-niter** *\* Number of iterations in sigma clipping during CRH rejection using multiple frames (int; default: 5). The full name of this option for the EsoRex configuration file is **xsh.xsh\_scired\_ifu\_offset.crh-clip-niter** \[default = *5*\]. - **--crh-clip-frac** *\* Minimal ratio of points accepted / total in sigma clipping during CRH rejection using multiple frames (float; default: 0.7). The full name of this option for the EsoRex configuration file is **xsh.xsh\_scired\_ifu\_offset.crh-clip-frac** \[default = *0.7*\]. - **--removecrhsingle-sigmalim** *\* Poisson fluctuation threshold to flag CRHs (see van Dokkum, PASP,113,2001,p1420-27) (float; default: 5.0). The full name of this option for the EsoRex configuration file is **xsh.xsh\_scired\_ifu\_offset.removecrhsingle-sigmalim** \[default = *5.0*\]. - **--removecrhsingle-flim** *\* Minimum contrast between the Laplacian image and the fine structure image that a point must have to be flagged as CRH. (see van Dokkum, PASP,113,2001,p1420-27) (float; default: 2.0). The full name of this option for the EsoRex configuration file is **xsh.xsh\_scired\_ifu\_offset.removecrhsingle-flim** \[default = *2.0*\]. - **--removecrhsingle-niter** *\* Max number of iterations (int; default: 4). The full name of this option for the EsoRex configuration file is **xsh.xsh\_scired\_ifu\_offset.removecrhsingle-niter** \[default = *4*\]. - **--rectify-kernel** *\* Name of the Interpolation Kernel Used. Possible values are: tanh, sinc, sinc2, lanczos, hamming, hann. (str; default: ´tanh´). The full name of this option for the EsoRex configuration file is **xsh.xsh\_scired\_ifu\_offset.rectify-kernel** \[default = *tanh*\]. - **--rectify-radius** *\* Rectify Interpolation radius \[bin units\]. (float; default: 2.0). The full name of this option for the EsoRex configuration file is **xsh.xsh\_scired\_ifu\_offset.rectify-radius** \[default = *2.0*\]. - **--rectify-bin-lambda** *\* Wavelength step in the output spectrum \[nm\] (float; default: -1.0). The full name of this option for the EsoRex configuration file is **xsh.xsh\_scired\_ifu\_offset.rectify-bin-lambda** \[default = *-1.0*\]. - **--rectify-bin-slit** *\* Spatial step along the slit in the output spectrum \[arcsec\] (float; default: -1.0). The full name of this option for the EsoRex configuration file is **xsh.xsh\_scired\_ifu\_offset.rectify-bin-slit** \[default = *-1.0*\]. - **--localize-method** *\* Localization method (MANUAL, MAXIMUM, GAUSSIAN) used to detect the object centroid and height on the slit (str; default: ´MANUAL´). The full name of this option for the EsoRex configuration file is **xsh.xsh\_scired\_ifu\_offset.localize-method** \[default = *MANUAL*\]. - **--localize-chunk-nb** *\* Number of chunks in the full spectrum to localize the object (int; default: 10). The full name of this option for the EsoRex configuration file is **xsh.xsh\_scired\_ifu\_offset.localize-chunk-nb** \[default = *10*\]. - **--localize-thresh** *\* Threshold relative to the peak intensity below which the edges of the object are detected for MAXIMUM localization (float; default: 0.1). The full name of this option for the EsoRex configuration file is **xsh.xsh\_scired\_ifu\_offset.localize-thresh** \[default = *0.1*\]. - **--localize-deg-lambda** *\* Degree in lambda in the localization polynomial expression slit=f(lambda), used only for MAXIMUM and GAUSSIAN (int; default: 0). The full name of this option for the EsoRex configuration file is **xsh.xsh\_scired\_ifu\_offset.localize-deg-lambda** \[default = *0*\]. - **--localize-slit-position** *\* Object position on the slit for MANUAL localization \[arcsec\] (float; default: 0.0). The full name of this option for the EsoRex configuration file is **xsh.xsh\_scired\_ifu\_offset.localize-slit-position** \[default = *0.0*\]. - **--localize-slit-hheight** *\* Object half height on the slit for MANUAL localization \[arcsec\] (float; default: 2.0). The full name of this option for the EsoRex configuration file is **xsh.xsh\_scired\_ifu\_offset.localize-slit-hheight** \[default = *2.0*\]. - **--localize-kappa** *\* Kappa value for sigma clipping in the localization polynomial fit (float; default: 3.0). The full name of this option for the EsoRex configuration file is **xsh.xsh\_scired\_ifu\_offset.localize-kappa** \[default = *3.0*\]. - **--localize-niter** *\* Number of iterations for sigma clipping in the localization polynomial fit (int; default: 3). The full name of this option for the EsoRex configuration file is **xsh.xsh\_scired\_ifu\_offset.localize-niter** \[default = *3*\]. - **--localize-use-skymask** *\* TRUE if we want to mask sky lines using SKY\_LINE\_LIST file. (bool; default: False). The full name of this option for the EsoRex configuration file is **xsh.xsh\_scired\_ifu\_offset.localize-use-skymask** \[default = *False*\]. - **--compute-map** *\* if TRUE recompute (wave and slit) maps from the dispersion solution. If sky-subtract is set to TRUE this must be set to TRUE. (bool; default: False). The full name of this option for the EsoRex configuration file is **xsh.xsh\_scired\_ifu\_offset.compute-map** \[default = *False*\]. - **--trace-obj** *\* if TRUE trace object position on each IFU slice. In this case order TAB edges is required (bool; default: False). The full name of this option for the EsoRex configuration file is **xsh.xsh\_scired\_ifu\_offset.trace-obj** \[default = *False*\]. - **--check-afc** *\* Input AFC corrected model/wave solution and science frame check. If TRUE the recipe verify that the input mode/wave solution is AFC corrected, its INS.OPTIi.NAME is ´Pin\_0.5 ´, and its OBS.ID and OBS.TARG.NAME values matches with the corresponding values of the science frame. (bool; default: True). The full name of this option for the EsoRex configuration file is **xsh.xsh\_scired\_ifu\_offset.check-afc** \[default = *True*\]. - **--cut-uvb-spectrum** *\* TRUE if recipe cuts the UVB spectrum at 556 nm (dichroich) (bool; default: True). The full name of this option for the EsoRex configuration file is **xsh.xsh\_scired\_ifu\_offset.cut-uvb-spectrum** \[default = *True*\]. 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 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_2dmap/7.md), [*xsh\_cfg\_recover*(7)](/xsh_cfg_recover/7.md), [*xsh\_flexcomp*(7)](/xsh_flexcomp/7.md), [*xsh\_geom\_ifu*(7)](/xsh_geom_ifu/7.md), [*xsh\_lingain*(7)](/xsh_lingain/7.md), [*xsh\_mbias*(7)](/xsh_mbias/7.md), [*xsh\_mdark*(7)](/xsh_mdark/7.md), [*xsh\_mflat*(7)](/xsh_mflat/7.md), [*xsh\_orderpos*(7)](/xsh_orderpos/7.md), [*xsh\_predict*(7)](/xsh_predict/7.md), [*xsh\_respon\_slit\_nod*(7)](/xsh_respon_slit_nod/7.md), [*xsh\_respon\_slit\_offset*(7)](/xsh_respon_slit_offset/7.md), [*xsh\_respon\_slit\_stare*(7)](/xsh_respon_slit_stare/7.md), [*xsh\_scired\_ifu\_offset\_drl*(7)](/xsh_scired_ifu_offset_drl/7.md), [*xsh\_scired\_ifu\_stare*(7)](/xsh_scired_ifu_stare/7.md), [*xsh\_scired\_ifu\_stare\_drl*(7)](/xsh_scired_ifu_stare_drl/7.md), [*xsh\_scired\_slit\_nod*(7)](/xsh_scired_slit_nod/7.md), [*xsh\_scired\_slit\_offset*(7)](/xsh_scired_slit_offset/7.md), [*xsh\_scired\_slit\_stare*(7)](/xsh_scired_slit_stare/7.md), [*xsh\_util\_physmod*(7)](/xsh_util_physmod/7.md), [*xsh\_wavecal*(7)](/xsh_wavecal/7.md) ## VERSION xsh\_scired\_ifu\_offset 3.5.0 ## AUTHOR A.Modigliani, J.Vernet, P. Bristow \ ## BUG REPORTS Please report any problems to Andrea.Modigliani@eso.org. Alternatively, you may send a report to the ESO User Support Department \. ## LICENSE 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