--- name: "sinfo_rec_pupil" section: "7" platform: "linux" package: "cpl-plugin-sinfo-doc" version: "2.5.2+dfsg-2" release: "Debian 8 (Jessie)" platforms: ["linux"] url: "https://new.carta.tech/sinfo_rec_pupil" --- # sinfo\_rec\_pupil(7) Pupil data reduction ## NAME sinfo\_rec\_pupil - Pupil data reduction ## SYNOPSIS esorex **sinfo\_rec\_pupil** \[OPTIONS\] FILE.sof ## DESCRIPTION This recipe performs science data reduction. The input files are science object and sky frames with tags OBJECT\_NODDING and SKY\_NODDING Master calibration frames: A corresponding (band,preoptics) wavelength map image with tag WAVE\_MAP A corresponding (band,preoptics) master flat field with tag MASTER\_FLAT\_LAMP A corresponding (band,preoptics) master bad pixel map with tag MASTER\_BP\_MAP A corresponding (band,preoptics) slitlets position frame with tag SLIT\_POS A corresponding (band) distortion table with tag DISTORTION A corresponding (band) slitlet distance table with tag SLITLETS\_DISTANCE The output is an image resulting from the IMA1 op IMA2 where op indicates A reference table with the position of the 1st column with tag FIRST\_COLUMN Relevant outputs are: combined cubes (PRO.CATG=x\_OBS x=STD,OBJ,PSF) reconstructed cube (PRO.CATG=COADD\_x\_OBS x=STD,OBJ,PSF) An average along Z of the reconstructed cube (PRO.CATG=MED\_x\_OBS x=STD,OBJ,PSF) The bad pixel map associated to the cube (PRO.CATG=BP\_MAP\_COADD\_x\_OBS x=STD,OBJ,PSF) ## OPTIONS - **--product-density** *\* Density of pipeline products: 0 (low), 1 (low+skycor), 2 (med-QC), 3 (high-debug+skycor) (long; default: 2). The full name of this option for the EsoRex configuration file is **sinfoni.product.density** \[default = *2*\]. - **--stack-lo\_rej** *\* lower rejection (float; default: 0.1). The full name of this option for the EsoRex configuration file is **sinfoni.stacked.low\_rejection** \[default = *0.1*\]. - **--stack-hi\_rej** *\* higher rejection (float; default: 0.1). The full name of this option for the EsoRex configuration file is **sinfoni.stacked.high\_rejection** \[default = *0.1*\]. - **--stack-flat\_ind** *\* Flat Index: (bool; default: True). The full name of this option for the EsoRex configuration file is **sinfoni.stacked.flat\_index** \[default = *True*\]. - **--stack-mflat\_norm\_smooth** *\* Normalize master flat to its smoothed value (to remove lamp response curve). 0 (no smooth). 1 (apply fft filter along y).2 (apply running median filter along y). (long; default: 0). The full name of this option for the EsoRex configuration file is **sinfoni.stacked.mflat\_norm\_smooth** \[default = *0*\]. - **--stack-mflat\_smooth\_rad** *\* Normalization smoothing radii (long; default: 16). The full name of this option for the EsoRex configuration file is **sinfoni.stacked.mflat\_smooth\_rad** \[default = *16*\]. - **--stack-mask\_ind** *\* BP Mask Interpolation Switch: indicates if the bad pixel mask should be applied (1) or not (0) (long; default: 1). The full name of this option for the EsoRex configuration file is **sinfoni.stacked.mask\_index** \[default = *1*\]. - **--stack-ind\_ind** *\* indicates if the bad pixels should be indicated (yes) or interpolated (no) (bool; default: False). The full name of this option for the EsoRex configuration file is **sinfoni.stacked.ind\_index** \[default = *False*\]. - **--stack-mask\_rad** *\* Max distance bad-good pix: (long; default: 4). The full name of this option for the EsoRex configuration file is **sinfoni.stacked.mask\_rad** \[default = *4*\]. - **--stack-gauss\_ind** *\* Gaussian Convolution Switch: (bool; default: False). The full name of this option for the EsoRex configuration file is **sinfoni.stacked.gauss\_index** \[default = *False*\]. - **--stack-khw** *\* Kernel Half Width (long; default: 2). The full name of this option for the EsoRex configuration file is **sinfoni.stacked.kernel\_half\_width** \[default = *2*\]. - **--stack-warpfix\_ind** *\* Warp Fix Index: (bool; default: True). The full name of this option for the EsoRex configuration file is **sinfoni.stacked.warpfix\_ind** \[default = *True*\]. - **--stack-warpfix\_kernel** *\* Warpfix kernel: (str; default: ´tanh´). The full name of this option for the EsoRex configuration file is **sinfoni.stacked.warpfix\_kernel** \[default = *tanh*\]. - **--stack-qc\_thresh\_min** *\* qc\_thresh\_min (long; default: 0). The full name of this option for the EsoRex configuration file is **sinfoni.stacked.qc\_thresh\_min** \[default = *0*\]. - **--stack-qc\_thresh\_max** *\* qc\_thresh\_max (long; default: 49000). The full name of this option for the EsoRex configuration file is **sinfoni.stacked.qc\_thresh\_max** \[default = *49000*\]. - **--stack-sub\_raw\_sky** *\* indicates if the raw sky frame should be subtracted (TRUE) or (FALSE) (bool; default: True). The full name of this option for the EsoRex configuration file is **sinfoni.stacked.sub\_raw\_sky** \[default = *True*\]. - **--objnod-aj\_method** *\* Method to reduce autojitter template frames Raw frames are object only exposures. object-fake\_sky pairs are generated. 0: no sky for all objects (long; default: 1). The full name of this option for the EsoRex configuration file is **sinfoni.objnod.autojitter\_method** \[default = *1*\]. - **--objnod-scales\_sky** *\* Spatial median (sky) subtraction from cube: (If autojitter\_method==1),indicates if the spatial median of each plane should be subtracted (TRUE) or not (FALSE) from each cube plane (bool; default: False). The full name of this option for the EsoRex configuration file is **sinfoni.objnod.scales\_sky** \[default = *False*\]. - **--objnod-ks\_clip** *\* Kappa-sigma clipping of coadded cube: indicates if a kappa-sigma clipping should be performed (TRUE) or not (FALSE) on each plane of the coadded cube (bool; default: True). The full name of this option for the EsoRex configuration file is **sinfoni.objnod.ks\_clip** \[default = *True*\]. - **--objnod-kappa** *\* kappa value for kappa-sigma clipping of coadded cube (float; default: 2.0). The full name of this option for the EsoRex configuration file is **sinfoni.objnod.kappa** \[default = *2.0*\]. - **--objnod-size\_x** *\* Cube x size: x-pixel size of the final combined data cube,must lie between 64 and 128. If 0 it is computed automatically (long; default: 0). The full name of this option for the EsoRex configuration file is **sinfoni.objnod.size\_x** \[default = *0*\]. - **--objnod-size\_y** *\* Cube y size: y-pixel size of the final combined data cube,must lie between 64 and 128.If 0 it is computed automatically (long; default: 0). The full name of this option for the EsoRex configuration file is **sinfoni.objnod.size\_y** \[default = *0*\]. - **--objnod-no\_coeffs** *\* number of coefficients for the polynomial interpolation (long; default: 3). The full name of this option for the EsoRex configuration file is **sinfoni.objnod.n\_coeffs** \[default = *3*\]. - **--objnod-ns\_ind** *\* Nord South Index Switch: indicates if the slitlet distances are determined by a north-south-test (TRUE) or slitlet edge fits (FALSE) (bool; default: True). The full name of this option for the EsoRex configuration file is **sinfoni.objnod.nord\_south\_index** \[default = *True*\]. - **--objnod-fine\_tune\_mtd** *\* Fine Tuning Method: indicator for the shifting method to use (P: polynomial interpolation, S: cubic spline interpolation) (str; default: ´P´). The full name of this option for the EsoRex configuration file is **sinfoni.objnod.fine\_tuning\_method** \[default = *P*\]. - **--objnod-order** *\* Fine Tuning polynomial order: order of the polynomial if the polynomial interpolation shifting method is used. (long; default: 2). The full name of this option for the EsoRex configuration file is **sinfoni.objnod.order** \[default = *2*\]. - **--objnod-lo\_rej** *\* lower rejection: percentage of rejected low value pixels for averaging the sky spectra (float; default: 10.0). The full name of this option for the EsoRex configuration file is **sinfoni.objnod.low\_rejection** \[default = *10.0*\]. - **--objnod-hi\_rej** *\* higher rejection: percentage of rejected high value pixels for averaging the sky spectra (float; default: 10.0). The full name of this option for the EsoRex configuration file is **sinfoni.objnod.high\_rejection** \[default = *10.0*\]. - **--objnod-tol** *\* Tolerance: pixel tolerance, this distance tolerance to the diagonal dividing line is not considered for the sky extraction to be sure to have a clean sky due to positioning tolerance and crossing through pixels (long; default: 2). The full name of this option for the EsoRex configuration file is **sinfoni.objnod.tolerance** \[default = *2*\]. - **--objnod-jit\_ind** *\* Jitter Index: jitter mode indicator: TRUE: Auto-Jitter, FALSE: user defined jitterThe size\_x size\_y kernel\_type parameters are only used if jitterInd is set to yes, that means in auto-jittering mode! (bool; default: True). The full name of this option for the EsoRex configuration file is **sinfoni.objnod.jitter\_index** \[default = *True*\]. - **--objnod-kernel\_typ** *\* Kernel Type:the name of the interpolation kernel to shift the single cubes to the correct places inside the big combined cube (str; default: ´tanh´). The full name of this option for the EsoRex configuration file is **sinfoni.objnod.kernel\_type** \[default = *tanh*\]. - **--objnod-vllx** *\* Vignetting on llx: pixels vignetted from lower left corner X coordinate of contributing cubes before coaddition (long; default: 0). The full name of this option for the EsoRex configuration file is **sinfoni.objnod.vllx** \[default = *0*\]. - **--objnod-vlly** *\* Vignetting on lly: pixels vignetted from lower left corner Y coordinate of contributing cubes before coaddition (long; default: 0). The full name of this option for the EsoRex configuration file is **sinfoni.objnod.vlly** \[default = *0*\]. - **--objnod-vurx** *\* Vignetting on urx: pixels vignetted from upper right corner X coordinate of contributing cubes before coaddition (long; default: 0). The full name of this option for the EsoRex configuration file is **sinfoni.objnod.vurx** \[default = *0*\]. - **--objnod-vury** *\* Vignetting on ury: pixels vignetted from upper right corner Y coordinate of contributing cubes before coaddition (long; default: 0). The full name of this option for the EsoRex configuration file is **sinfoni.objnod.vury** \[default = *0*\]. - **--objnod-fcol** *\* First column offset: (float; default: 0.0). The full name of this option for the EsoRex configuration file is **sinfoni.objnod.fcol** \[default = *0.0*\]. - **--objnod-sky\_cor** *\* Sky residuals correction: (bool; default: True). The full name of this option for the EsoRex configuration file is **sinfoni.objnod.sky\_cor** \[default = *True*\]. - **--objnod-flux\_cor** *\* Apply flux correction after rebinning: (bool; default: True). The full name of this option for the EsoRex configuration file is **sinfoni.objnod.flux\_cor** \[default = *True*\]. - **--objnod-mosaic\_max\_size** *\* Maximum allowed size for cubes mosaic is 100\*mosaic\_max\_size (long; default: 14196). The full name of this option for the EsoRex configuration file is **sinfoni.objnod.mosaic\_max\_size** \[default = *14196*\]. 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 sinfo pipeline can be downloaded as a PDF file using the following URL: - **ftp://ftp.eso.org/pub/dfs/pipelines/sinfoni/sinfo-pipeline-manual-19.0.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 sinfo pipeline are [*sinfo\_utl\_cube2spectrum*(7)](/sinfo_utl_cube2spectrum/7.md), [*sinfo\_rec\_jitter*(7)](/sinfo_rec_jitter/7.md), [*sinfo\_utl\_ima\_line\_corr*(7)](/sinfo_utl_ima_line_corr/7.md), [*sinfo\_utl\_cube\_combine*(7)](/sinfo_utl_cube_combine/7.md), [*sinfo\_utl\_bp\_mask\_add*(7)](/sinfo_utl_bp_mask_add/7.md), [*sinfo\_utl\_skycor*(7)](/sinfo_utl_skycor/7.md), [*sinfo\_utl\_spectrum\_divide\_by\_blackbody*(7)](/sinfo_utl_spectrum_divide_by_blackbody/7.md), [*sinfo\_rec\_mflat*(7)](/sinfo_rec_mflat/7.md), [*sinfo\_utl\_cube\_create*(7)](/sinfo_utl_cube_create/7.md), [*sinfo\_utl\_line\_oh\_select*(7)](/sinfo_utl_line_oh_select/7.md), [*sinfo\_utl\_cube2ima*(7)](/sinfo_utl_cube2ima/7.md), [*sinfo\_utl\_spectrum\_wavelength\_shift*(7)](/sinfo_utl_spectrum_wavelength_shift/7.md), [*sinfo\_rec\_distortion*(7)](/sinfo_rec_distortion/7.md), [*sinfo\_rec\_wavecal*(7)](/sinfo_rec_wavecal/7.md), [*sinfo\_utl\_ima\_arith*(7)](/sinfo_utl_ima_arith/7.md), [*sinfo\_utl\_cube\_arith*(7)](/sinfo_utl_cube_arith/7.md), [*sinfo\_rec\_detlin*(7)](/sinfo_rec_detlin/7.md), [*sinfo\_utl\_skymap*(7)](/sinfo_utl_skymap/7.md), [*sinfo\_rec\_mdark*(7)](/sinfo_rec_mdark/7.md) ## VERSION sinfo\_rec\_pupil 2.5.2 ## AUTHOR Andrea Modigliani \ ## 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 SINFONI Instrument Pipeline Copyright (C) 2002,2003 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