--- name: "vmmosscience" 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/vmmosscience" --- # vmmosscience(7) Extraction of scientific spectra ## NAME vmmosscience - Extraction of scientific spectra ## SYNOPSIS esorex **vmmosscience** \[OPTIONS\] FILE.sof ## DESCRIPTION This recipe is used to reduce scientific spectra using the extraction mask and the products created by the recipe vimos\_calib. The spectra are bias subtracted, flat fielded (if a normalised flat field is specified) and remapped eliminating the optical distortions. The wavelength calibration can be optionally upgraded using a number of sky lines: if no sky lines catalog of wavelengths is specified, an internal one is used instead. If the alignment to the sky lines is performed, the input dispersion coefficients table is upgraded and saved to disk, and a new CCD wavelengths map is created. A configuration table (typically depending on the grism in use) 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 configuration 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 (which are rarely meaningful). Either a scientific or a standard star exposure can be specified in input. Only in case of a standard star exposure input, the atmospheric extinction table and a table with the physical fluxes of the observed standard star must be specified in input, and a spectro-photometric table is created in output. This table can then be input again to this recipe, always with an atmospheric extinction table, and if a photometric calibration is requested then flux calibrated spectra (in units of erg/cm/cm/s/Angstrom) are also written in output. Input files: DO category: Type: Explanation: Required:\ MOS\_SCIENCE Raw Scientific exposure Y\ or MOS\_STANDARD Raw Standard star exposure Y MASTER\_BIAS Calib Master bias Y\ SKY\_LINE\_CATALOG Calib Sky lines catalog . MOS\_MASTER\_SCREEN\_FLAT Calib Normalised flat field . MOS\_DISP\_COEFF Calib Inverse dispersion Y\ MOS\_CURV\_COEFF Calib Spectral curvature Y\ MOS\_SLIT\_LOCATION Calib Slits positions table Y\ CONFIG\_TABLE Calib Configuration table . In case MOS\_STANDARD is specified in input, EXTINCT\_TABLE Calib Atmospheric extinction Y\ STD\_FLUX\_TABLE Calib Standard star flux Y\ TELLURIC\_CONTAMINATION Calib Telluric regions list . In case a photometric calibration is requested for scientific\ data, the following inputs are mandatory: EXTINCT\_TABLE Calib Atmospheric extinction Y\ MOS\_SPECPHOT\_TABLE Calib Response curves Y If requested for standard star data, the SPECPHOT\_TABLE can be dropped:\ in this case the correction is applied using the SPECPHOT\_TABLE produced\ in the same run. Output files (acronym \_STD\_ replaces \_SCI\_ and \_STANDARD\_ replaces \_SCIENCE\_ in case input is MOS\_STANDARD rather than MOS\_SCIENCE): DO category: Data type: Explanation:\ MOS\_SCIENCE\_REDUCED Image Extracted scientific spectra\ MOS\_SCI\_SKY\_REDUCED Image Extracted sky spectra\ MOS\_SCI\_ERROR\_REDUCED Image Errors on extracted spectra\ MOS\_UNMAPPED\_SCIENCE Image Sky subtracted scientific spectra\ MOS\_SCIENCE\_EXTRACTED Image Rectified scientific spectra\ MOS\_SCIENCE\_SKY\_EXTRACTED Image Rectified science spectra with sky\ MOS\_SCIENCE\_SKY Image Rectified sky spectra\ MOS\_SCI\_UNMAPPED\_SKY Image Sky on CCD\ MOS\_SCI\_GLOBAL\_SKY\_SPECTRUM Table Global sky spectrum\ OBJECT\_SCI\_TABLE Table Positions of detected objects Only if fringing correction is requested (dithered exposures):\ MOS\_SCI\_FRINGES Image Fringe map Only if the sky-alignment of the wavelength solution is requested:\ MOS\_SCI\_SKYLINES\_OFFSETS\_SLIT Table Sky lines offsets\ MOS\_SCI\_DISP\_COEFF\_SKY Table Upgraded dispersion coefficients\ MOS\_SCI\_WAVELENGTH\_MAP\_SKY Image Upgraded wavelength map Only if a MOS\_STANDARD is specified in input:\ MOS\_SPECPHOT\_TABLE Table Efficiency and response curves Only if MOS\_SPECPHOT\_TABLE or MOS\_MASTER\_RESPONSE are specified in input:\ MOS\_SCIENCE\_FLUX\_REDUCED Image Flux calibrated scientific spectra\ MOS\_SCI\_ERROR\_FLUX\_REDUCED Image Errors on flux calibrated spectra\ MOS\_SCIENCE\_FLUX\_EXTRACTED Image Flux calibrated slit spectra ## OPTIONS - **--skyalign** *\* Polynomial order for sky lines alignment, or -1 to avoid alignment (int; default: -1). The full name of this option for the EsoRex configuration file is **vimos.vmmosscience.skyalign** \[default = *-1*\]. - **--flatfield** *\* Apply flat field (bool; default: True). The full name of this option for the EsoRex configuration file is **vimos.vmmosscience.flatfield** \[default = *True*\]. - **--skyglobal** *\* Subtract global sky spectrum from CCD (bool; default: False). The full name of this option for the EsoRex configuration file is **vimos.vmmosscience.skyglobal** \[default = *False*\]. - **--skymedian** *\* Sky subtraction from extracted slit spectra (bool; default: False). The full name of this option for the EsoRex configuration file is **vimos.vmmosscience.skymedian** \[default = *False*\]. - **--skylocal** *\* Sky subtraction from CCD slit spectra (bool; default: True). The full name of this option for the EsoRex configuration file is **vimos.vmmosscience.skylocal** \[default = *True*\]. - **--cosmics** *\* Eliminate cosmic rays hits (only if global or local sky subtraction is also requested) (bool; default: True). The full name of this option for the EsoRex configuration file is **vimos.vmmosscience.cosmics** \[default = *True*\]. - **--slit\_margin** *\* Number of pixels to exclude at each slit in object detection and extraction (int; default: 3). The full name of this option for the EsoRex configuration file is **vimos.vmmosscience.slit\_margin** \[default = *3*\]. - **--ext\_radius** *\* Maximum extraction radius for detected objects (pixel) (int; default: 6). The full name of this option for the EsoRex configuration file is **vimos.vmmosscience.ext\_radius** \[default = *6*\]. - **--cont\_radius** *\* Minimum distance at which two objects of equal luminosity do not contaminate each other (pixel) (int; default: 0). The full name of this option for the EsoRex configuration file is **vimos.vmmosscience.cont\_radius** \[default = *0*\]. - **--ext\_mode** *\* Object extraction method: 0 = aperture, 1 = Horne optimal extraction (int; default: 1). The full name of this option for the EsoRex configuration file is **vimos.vmmosscience.ext\_mode** \[default = *1*\]. - **--detection** *\* Object detection threshold (ADU) (float; default: 2.0). The full name of this option for the EsoRex configuration file is **vimos.vmmosscience.detection** \[default = *2.0*\]. - **--resp\_fit\_nknots** *\* Number of knots in spline fitting of the instrument response. (-1: No fitting. -2: Read from grism table) (int; default: -2). The full name of this option for the EsoRex configuration file is **vimos.vmmosscience.resp\_fit\_nknots** \[default = *-2*\]. - **--resp\_fit\_degree** *\* Degree of polynomial in fitting of the instrument response. (-1: No fitting. -2: Read from grism table) (int; default: -2). The full name of this option for the EsoRex configuration file is **vimos.vmmosscience.resp\_fit\_degree** \[default = *-2*\]. - **--resp\_ignore\_mode** *\* Types of lines/regions to ignore in response. Valid ones are ´stellar\_absorption´, ´telluric´ and ´command\_line´ (from parameter resp\_ignore\_lines) (str; default: ´stellar\_absorption,telluric,command\_line´). The full name of this option for the EsoRex configuration file is **vimos.vmmosscience.resp\_ignore\_mode** \[default = *stellar\_absorption,telluric,command\_line*\]. - **--resp\_ignore\_points** *\* Extra lines/regions to ignore in response. Use a comma separated list of values. A range can be specified like 4500.0-4600.0 (str; default: ´´). The full name of this option for the EsoRex configuration file is **vimos.vmmosscience.resp\_ignore\_points** \[default = \]. - **--resp\_use\_flat\_sed** *\* Use the flat SED to normalise the observed spectra. Value are true, false, grism\_table. (str; default: ´grism\_table´). The full name of this option for the EsoRex configuration file is **vimos.vmmosscience.resp\_use\_flat\_sed** \[default = *grism\_table*\]. - **--resp\_shift** *\* The extracted standard star will be shifted these many angstroms before using it to compute the response. This is useful for observed std stars not centered in the slits. Positive values will shift the spectrum to the red. Shift is given in Angstroms but no fraction of pixels will be shifted. (float; default: 0.0). The full name of this option for the EsoRex configuration file is **vimos.vmmosscience.resp\_shift** \[default = *0.0*\]. - **--time\_normalise** *\* Normalise output spectra by the exposure time (bool; default: True). The full name of this option for the EsoRex configuration file is **vimos.vmmosscience.time\_normalise** \[default = *True*\]. - **--anyframe** *\* Look for a standard star in any frame classified as MOS\_STANDARD (bool; default: False). The full name of this option for the EsoRex configuration file is **vimos.vmmosscience.anyframe** \[default = *False*\]. - **--alignment** *\* Type of alignment of dithered frames, either to the nearest neighbour pixel or to fractions of pixel (str; default: ´integer´). The full name of this option for the EsoRex configuration file is **vimos.vmmosscience.alignment** \[default = *integer*\]. - **--stack\_method** *\* Frames combination method (str; default: ´average´). The full name of this option for the EsoRex configuration file is **vimos.vmmosscience.stack\_method** \[default = *average*\]. - **--minrejection** *\* Number of lowest values to be rejected (int; default: 1). The full name of this option for the EsoRex configuration file is **vimos.vmmosscience.minrejection** \[default = *1*\]. - **--maxrejection** *\* Number of highest values to be rejected (int; default: 1). The full name of this option for the EsoRex configuration file is **vimos.vmmosscience.maxrejection** \[default = *1*\]. - **--klow** *\* Low threshold in ksigma method (float; default: 3.0). The full name of this option for the EsoRex configuration file is **vimos.vmmosscience.klow** \[default = *3.0*\]. - **--khigh** *\* High threshold in ksigma method (float; default: 3.0). The full name of this option for the EsoRex configuration file is **vimos.vmmosscience.khigh** \[default = *3.0*\]. - **--kiter** *\* Max number of iterations in ksigma method (int; default: 999). The full name of this option for the EsoRex configuration file is **vimos.vmmosscience.kiter** \[default = *999*\]. - **--dither** *\* Align dithered frames before stacking(for multiple input frames) (bool; default: True). The full name of this option for the EsoRex configuration file is **vimos.vmmosscience.dither** \[default = *True*\]. - **--compute** *\* Compute offsets of dithered images from detected objects (true), or read offsets from header (false) (bool; default: False). The full name of this option for the EsoRex configuration file is **vimos.vmmosscience.dither.compute** \[default = *False*\]. - **--fringing** *\* Apply fringing correction (only for dithered observations) (bool; default: True). The full name of this option for the EsoRex configuration file is **vimos.vmmosscience.fringing** \[default = *True*\]. - **--offset** *\* Minimum required offset between exposures for applying the sky fringing correction. (float; default: 3.0). The full name of this option for the EsoRex configuration file is **vimos.vmmosscience.fringing.offset** \[default = *3.0*\]. - **--generate\_idp** *\* Generate IDP products (bool; default: False). The full name of this option for the EsoRex configuration file is **vimos.vmmosscience.generate\_idp** \[default = *False*\]. 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), [*vmmoscalib*(7)](/vmmoscalib/7.md), [*vmspphot*(7)](/vmspphot/7.md) ## VERSION vmmosscience 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 part of the VIMOS Instrument Pipeline Copyright (C) 2019 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