--- name: "xsh_geom_ifu" 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_geom_ifu" --- # xsh\_geom\_ifu(7) Produces the spatial geometry of the IFU pattern on the sky ## NAME xsh\_geom\_ifu - Produces the spatial geometry of the IFU pattern on the sky ## SYNOPSIS esorex **xsh\_geom\_ifu** \[OPTIONS\] FILE.sof ## DESCRIPTION This recipe Produces the spatial geometry of the IFU pattern on the sky Input Frames : \ \- A set of n science frames ( n == 1 or \>=3, Tag = TRACE\_arm)\ \- \[UVB,VIS\] A master bias frame (Tag = MASTER\_BIAS\_arm)\ \- \[OPTIONAL\] A master dark frame (Tag = MASTER\_DARK\_arm)\ \- A master flat frame (Tag = MASTER\_FLAT\_IFU\_arm)\ \- An AFC corrected model order edges table for IFU frame (Tag = ORDER\_TAB\_AFC\_IFU\_arm)\ \- \[PHYSMOD\] An AFC corrected model cfg frame (Tag = XSH\_MOD\_CFG\_OPT\_AFC\_arm)\ \- \[POLY\] An AFC corrected model wavesol frame (Tag = WAVE\_TAB\_AFC\_arm)\ \- An AFC corrected dispersion solution frame (Tag = DISP\_TAB\_AFC\_arm)\ \- \[OPTIONAL\] A badpixel map (Tag = BADPIXEL\_MAP\_arm) Products : \ \- A set of shift offset tables (Tag = OFFSET\_TAB\_slitlet\_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\_geom\_ifu.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\_geom\_ifu.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\_geom\_ifu.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\_geom\_ifu.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\_geom\_ifu.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\_geom\_ifu.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\_geom\_ifu.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\_geom\_ifu.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\_geom\_ifu.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\_geom\_ifu.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\_geom\_ifu.crh-clip-frac** \[default = *0.7*\]. - **--background-edges-margin** *\* X margin to order edge to define background sampling points (int; default: 1). The full name of this option for the EsoRex configuration file is **xsh.xsh\_geom\_ifu.background-edges-margin** \[default = *1*\]. - **--background-poly-deg-y** *\* Poly mode fit deg along Y. (int; default: 9). The full name of this option for the EsoRex configuration file is **xsh.xsh\_geom\_ifu.background-poly-deg-y** \[default = *9*\]. - **--background-poly-deg-x** *\* Poly mode fit deg along X. (int; default: 9). The full name of this option for the EsoRex configuration file is **xsh.xsh\_geom\_ifu.background-poly-deg-x** \[default = *9*\]. - **--background-poly-kappa** *\* Poly mode kappa value of kappa-sigma-clip outliers removal. (float; default: 10.0). The full name of this option for the EsoRex configuration file is **xsh.xsh\_geom\_ifu.background-poly-kappa** \[default = *10.0*\]. - **--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\_geom\_ifu.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\_geom\_ifu.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\_geom\_ifu.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\_geom\_ifu.rectify-kernel** \[default = *tanh*\]. - **--rectify-radius** *\* Rectify Interpolation radius \[bin units\]. (float; default: 4.0). The full name of this option for the EsoRex configuration file is **xsh.xsh\_geom\_ifu.rectify-radius** \[default = *4.0*\]. - **--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\_geom\_ifu.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\_geom\_ifu.rectify-bin-slit** \[default = *-1.0*\]. - **--localizeifu-bckg-deg** *\* Degree (\<=2) of the polynomial component in the cross-dispersion profile fit (int; default: 50). The full name of this option for the EsoRex configuration file is **xsh.xsh\_geom\_ifu.localizeifu-bckg-deg** \[default = *50*\]. - **--localizeifu-smooth-hsize** *\* Half-size of the median filter for smoothing the cross-dispersion profile prior to localization (int; default: 3). The full name of this option for the EsoRex configuration file is **xsh.xsh\_geom\_ifu.localizeifu-smooth-hsize** \[default = *3*\]. - **--localizeifu-wavelet-nscales** *\* Number of scales used for wavelet a trous algorithm (int; default: 5). The full name of this option for the EsoRex configuration file is **xsh.xsh\_geom\_ifu.localizeifu-wavelet-nscales** \[default = *5*\]. - **--localizeifu-wavelet-hf-skip** *\* Number of high frequency scales skipped from the wavelet decomposition (int; default: 2). The full name of this option for the EsoRex configuration file is **xsh.xsh\_geom\_ifu.localizeifu-wavelet-hf-skip** \[default = *2*\]. - **--localizeifu-sigma-low** *\* Gaussian fits of the cross-dispersion profile whose FWHM is lower than this value are rejected (float; default: 0.05). The full name of this option for the EsoRex configuration file is **xsh.xsh\_geom\_ifu.localizeifu-sigma-low** \[default = *0.05*\]. - **--localizeifu-sigma-up** *\* Gaussian fits of the cross-dispersion profile whose FWHM is larger than this value are rejected (float; default: 0.95). The full name of this option for the EsoRex configuration file is **xsh.xsh\_geom\_ifu.localizeifu-sigma-up** \[default = *0.95*\]. - **--localizeifu-snr-low** *\* Gaussian fits of the cross-dispersion profile whose SNR is lower than this value are rejected (float; default: 0.05). The full name of this option for the EsoRex configuration file is **xsh.xsh\_geom\_ifu.localizeifu-snr-low** \[default = *0.05*\]. - **--localizeifu-snr-up** *\* Gaussian fits of the cross-dispersion profile whose SNR is larger than this value are rejected (float; default: 0.95). The full name of this option for the EsoRex configuration file is **xsh.xsh\_geom\_ifu.localizeifu-snr-up** \[default = *0.95*\]. - **--localizeifu-slitlow-edges-mask** *\* in arsec (float; default: 0.0). The full name of this option for the EsoRex configuration file is **xsh.xsh\_geom\_ifu.localizeifu-slitlow-edges-mask** \[default = *0.0*\]. - **--localizeifu-slitup-edges-mask** *\* in arsec (float; default: 0.0). The full name of this option for the EsoRex configuration file is **xsh.xsh\_geom\_ifu.localizeifu-slitup-edges-mask** \[default = *0.0*\]. - **--localizeifu-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\_geom\_ifu.localizeifu-use-skymask** \[default = *False*\]. - **--localizeifu-chunk-hsize** *\* Half size of chunk \[bin\] (int; default: 0). The full name of this option for the EsoRex configuration file is **xsh.xsh\_geom\_ifu.localizeifu-chunk-hsize** \[default = *0*\]. - **--correctifu-niter** *\* Number of iterations in computing the localization shifts of the IFU slitlets (int; default: 3). The full name of this option for the EsoRex configuration file is **xsh.xsh\_geom\_ifu.correctifu-niter** \[default = *3*\]. - **--correctifu-lambdaref** *\* Reference wavelength where the reference localization on the slit is chosen (float; default: -1.0). The full name of this option for the EsoRex configuration file is **xsh.xsh\_geom\_ifu.correctifu-lambdaref** \[default = *-1.0*\]. - **--correctifu-lambdaref-hsize** *\* HAlf size in nm to estimate reference wavelength (float; default: 2.5). The full name of this option for the EsoRex configuration file is **xsh.xsh\_geom\_ifu.correctifu-lambdaref-hsize** \[default = *2.5*\]. - **--do-cube** *\* if TRUE creates a data cube (bool; default: False). The full name of this option for the EsoRex configuration file is **xsh.xsh\_geom\_ifu.do-cube** \[default = *False*\]. - **--compute-map** *\* if TRUE recompute (wave and slit) maps from the dispersion solution. (bool; default: True). The full name of this option for the EsoRex configuration file is **xsh.xsh\_geom\_ifu.compute-map** \[default = *True*\]. - **--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\_geom\_ifu.check-afc** \[default = *True*\]. - **--flat-method** *\* method adopted for flat: (str; default: ´blaze´). The full name of this option for the EsoRex configuration file is **xsh.xsh\_geom\_ifu.flat-method** \[default = *blaze*\]. 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\_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*(7)](/xsh_scired_ifu_offset/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\_geom\_ifu 3.5.0 ## AUTHOR P.Goldoni, L.Guglielmi, R. Haigron, F. Royer \ ## BUG REPORTS Please report any problems to regis.haigron@obspm.fr. 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