--- name: "vmmoscalib" section: "7" platform: "linux" package: "cpl-plugin-vimos-doc" version: "4.1.7+dfsg-2" release: "Debian 12 (Bookworm)" platforms: ["linux"] url: "https://new.carta.tech/vmmoscalib" --- # vmmoscalib(7) Determination of the extraction mask ## NAME vmmoscalib - Determination of the extraction mask ## SYNOPSIS esorex **vmmoscalib** \[OPTIONS\] FILE.sof ## DESCRIPTION This recipe is used to identify reference lines on MOS arc lamp exposures, and trace the spectral edges on the corresponding flat field exposures. This information is used to determine the spectral extraction mask to be applied in the scientific data reduction, performed with the recipe vimos\_science. The input arc lamp and flat field exposures are assumed to be obtained quasi-simultaneously, so that they would be described by exactly the same instrument distortions. A line catalog must be specified, containing the wavelengths of the reference arc lamp lines used for the wavelength calibration. A grism table (typically depending on the instrument mode, and in particular on the grism used) may also be specified: this table contains a default recipe parameter setting to control the way spectra are extracted for a specific instrument mode, as it is used for automatic run of the pipeline on Paranal and in Garching. If this table is specified, it will modify the default recipe parameter setting, with the exception of those parameters which have been explicitly modifyed on the command line. If a grism table is not specified, the input recipe parameters values will always be read from the command line, or from an esorex configuration file if present, or from their generic default values (that are rarely meaningful). Finally a master bias frame must be input to this recipe. In the table below the MOS\_CURV\_COEFF, MOS\_CURV\_TRACES, MOS\_SPATIAL\_MAP MOS\_ARC\_SPECTRUM\_EXTRACTED, MOS\_SPECTRA\_DETECTION, MOS\_SLIT\_MAP, and MOS\_SLIT\_LOCATION, are never created in case of long-slit-like data. The products MOS\_SPECTRA\_DETECTION, MOS\_SLIT\_MAP, and MOS\_DISP\_RESIDUALS, are just created if the --check parameter is set to true. The product GLOBAL\_DISTORTION\_TABLE is just created if more than 12 separate spectra are found in the CCD. Input files: DO category: Type: Explanation: Required:\ MOS\_SCREEN\_FLAT Raw Flat field exposures Y\ MOS\_ARC\_SPECTRUM Raw Arc lamp exposure Y\ MASTER\_BIAS Calib Bias frame Y\ LINE\_CATALOG Calib Line catalog Y\ CONFIG\_TABLE Calib Grism table . Output files: DO category: Data type: Explanation:\ MOS\_COMBINED\_SCREEN\_FLAT FITS image Combined (sum) flat field\ MOS\_MASTER\_SCREEN\_FLAT FITS image Normalised flat field\ MOS\_ARC\_SPECTRUM\_EXTRACTED FITS image Wavelength calibrated arc spectrum\ MOS\_DISP\_COEFF FITS table Inverse dispersion coefficients\ MOS\_DISP\_RESIDUALS FITS image Residuals in wavelength calibration\ MOS\_DISP\_RESIDUALS\_TABLE FITS table Residuals in wavelength calibration\ MOS\_DELTA\_IMAGE FITS image Offset vs linear wavelength calib\ MOS\_WAVELENGTH\_MAP FITS image Wavelength for each pixel on CCD\ MOS\_SPECTRA\_DETECTION FITS image Check for preliminary detection\ MOS\_SLIT\_MAP FITS image Map of central wavelength on CCD\ MOS\_CURV\_TRACES FITS table Spectral curvature traces\ MOS\_CURV\_COEFF FITS table Spectral curvature coefficients\ MOS\_SPATIAL\_MAP FITS image Spatial position along slit on CCD\ MOS\_SPECTRAL\_RESOLUTION FITS table Resolution at reference arc lines\ MOS\_SLIT\_LOCATION FITS table Slits on product frames and CCD\ GLOBAL\_DISTORTION\_TABLE FITS table Global distortions table ## OPTIONS - **--dispersion** *\* Expected spectral dispersion (Angstrom/pixel) (float; default: 0.0). The full name of this option for the EsoRex configuration file is **vimos.vmmoscalib.dispersion** \[default = *0.0*\]. - **--peakdetection** *\* Initial peak detection threshold (ADU) (float; default: 0.0). The full name of this option for the EsoRex configuration file is **vimos.vmmoscalib.peakdetection** \[default = *0.0*\]. - **--wdegree** *\* Degree of wavelength calibration polynomial (int; default: 0). The full name of this option for the EsoRex configuration file is **vimos.vmmoscalib.wdegree** \[default = *0*\]. - **--wradius** *\* Search radius if iterating pattern-matching with first-guess method (pixel) (int; default: 4). The full name of this option for the EsoRex configuration file is **vimos.vmmoscalib.wradius** \[default = *4*\]. - **--wreject** *\* Rejection threshold in dispersion relation fit (pixel) (float; default: 1.0). The full name of this option for the EsoRex configuration file is **vimos.vmmoscalib.wreject** \[default = *1.0*\]. - **--wmodelss** *\* Interpolation mode of wavelength solution (0 = no interpolation, 1 = fill gaps, 2 = global model) (int; default: 2). The full name of this option for the EsoRex configuration file is **vimos.vmmoscalib.wmodelss** \[default = *2*\]. - **--wmodemos** *\* Interpolation mode of wavelength solution (0 = no interpolation, 1 = local (slit) solution, 2 = global model) (int; default: 1). The full name of this option for the EsoRex configuration file is **vimos.vmmoscalib.wmodemos** \[default = *1*\]. - **--ignore\_lines** *\* Catalog lines nearest to wavelengths in this list will be ignored for wavelength calibration (str; default: ´´). The full name of this option for the EsoRex configuration file is **vimos.vmmoscalib.ignore\_lines** \[default = \]. - **--used\_linesets** *\* Linesets to use. Valid are ´standard´ and´extended´ (see column LINE\_SET in the line catalogue) (str; default: ´standard´). The full name of this option for the EsoRex configuration file is **vimos.vmmoscalib.used\_linesets** \[default = *standard*\]. - **--cdegree** *\* Degree of spectral curvature polynomial (int; default: 0). The full name of this option for the EsoRex configuration file is **vimos.vmmoscalib.cdegree** \[default = *0*\]. - **--cmode** *\* Interpolation mode of curvature solution applicable to MOS-like data (0 = no interpolation, 1 = fill gaps, 2 = global model) (int; default: 1). The full name of this option for the EsoRex configuration file is **vimos.vmmoscalib.cmode** \[default = *1*\]. - **--startwavelength** *\* Start wavelength in spectral extraction (float; default: 0.0). The full name of this option for the EsoRex configuration file is **vimos.vmmoscalib.startwavelength** \[default = *0.0*\]. - **--endwavelength** *\* End wavelength in spectral extraction (float; default: 0.0). The full name of this option for the EsoRex configuration file is **vimos.vmmoscalib.endwavelength** \[default = *0.0*\]. - **--reference** *\* Reference wavelength for slit map (float; default: 0.0). The full name of this option for the EsoRex configuration file is **vimos.vmmoscalib.reference** \[default = *0.0*\]. - **--slit\_ident** *\* Attempt slit identification.For multiplexing data slit identification is always performed. Switching it off will cause systematic errors in the absolute flux calibration if the FLAT\_SED correction is used (see pipeline manual for details) (bool; default: True). The full name of this option for the EsoRex configuration file is **vimos.vmmoscalib.slit\_ident** \[default = *True*\]. - **--s\_degree** *\* Polynomial degree for the flat field fitting along spatial direction (int; default: -1). The full name of this option for the EsoRex configuration file is **vimos.vmmoscalib.s\_degree** \[default = *-1*\]. - **--sradius** *\* Smooth box radius for flat field along spatial direction (used if s\_degree \< 0) (int; default: -1). The full name of this option for the EsoRex configuration file is **vimos.vmmoscalib.sradius** \[default = *-1*\]. - **--d\_nknots** *\* Number of knots in flat field fitting splines along dispersion direction (int; default: -1). The full name of this option for the EsoRex configuration file is **vimos.vmmoscalib.d\_nknots** \[default = *-1*\]. - **--dradius** *\* Smooth box radius for flat field along dispersion direction (if d\_knots \< 0) (int; default: 10). The full name of this option for the EsoRex configuration file is **vimos.vmmoscalib.dradius** \[default = *10*\]. - **--fit\_threshold** *\* Threshold percentage for flat spline fitting with respect to the maximum (float; default: 0.01). The full name of this option for the EsoRex configuration file is **vimos.vmmoscalib.fit\_threshold** \[default = *0.01*\]. - **--line\_ident\_tol** *\* Tolerance for the ratio of detected lines vs reference lines. This is used during for arc line identification. (float; default: 0.05). The full name of this option for the EsoRex configuration file is **vimos.vmmoscalib.line\_ident\_tol** \[default = *0.05*\]. - **--normalise\_spa\_local** *\* If TRUE the normalization along the spatial axis is performed row-by- row otherwise a collapsed slit is used. (bool; default: True). The full name of this option for the EsoRex configuration file is **vimos.vmmoscalib.normalise\_spa\_local** \[default = *True*\]. 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 vimos pipeline can be downloaded as a PDF file using the following URL: - **ftp://ftp.eso.org/pub/dfs/pipelines/vimos/vimos-pipeline-manual-6.9.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 vimos pipeline are [*vimos\_ima\_bias*(7)](/vimos_ima_bias/7.md), [*vimos\_ima\_dark*(7)](/vimos_ima_dark/7.md), [*vimos\_ima\_det\_noise*(7)](/vimos_ima_det_noise/7.md), [*vimos\_ima\_fringe*(7)](/vimos_ima_fringe/7.md), [*vimos\_ima\_science*(7)](/vimos_ima_science/7.md), [*vimos\_ima\_standard*(7)](/vimos_ima_standard/7.md), [*vimos\_ima\_twilight\_flat*(7)](/vimos_ima_twilight_flat/7.md), [*vmbias*(7)](/vmbias/7.md), [*vmdark*(7)](/vmdark/7.md), [*vmdet*(7)](/vmdet/7.md), [*vmifucalib*(7)](/vmifucalib/7.md), [*vmifucombine*(7)](/vmifucombine/7.md), [*vmifucombinecube*(7)](/vmifucombinecube/7.md), [*vmifuscience*(7)](/vmifuscience/7.md), [*vmifustandard*(7)](/vmifustandard/7.md), [*vmmosscience*(7)](/vmmosscience/7.md), [*vmspphot*(7)](/vmspphot/7.md) ## VERSION vmmoscalib 4.1.7 ## AUTHOR Carlo Izzo \ ## BUG REPORTS Please report any problems to https://support.eso.org. Alternatively, you may send a report to the ESO User Support Department \. ## LICENSE This file is currently part of the VIMOS Instrument Pipeline Copyright (C) 2002-2006 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., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA