--- name: "vmifuscience" 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/vmifuscience" --- # vmifuscience(7) Extract spectra from an IFU scientific exposure. ## NAME vmifuscience - Extract spectra from an IFU scientific exposure. ## SYNOPSIS esorex **vmifuscience** \[OPTIONS\] FILE.sof ## DESCRIPTION This recipe extracts IFU scientific spectra using the input extraction mask, after aligning it to the brightest fiber spectra detected on the input exposure. The extracted spectra are then resampled at a constant wavelength step, after aligning the input wavelength calibration to the positions of a set of identified sky lines. The extracted spectra are eventually corrected for the relative differences in transmission from fiber to fiber. Input files: DO category: Type: Explanation: Required:\ IFU\_SCIENCE Raw Scientific spectra Y\ MASTER\_BIAS Calib Master bias Y\ IFU\_TRACE Calib Extraction mask Y\ IFU\_IDS Calib Wavelength calibration Y\ IFU\_TRANSMISSION Calib Transmission correction Y\ EXTINCT\_TABLE Calib Atmospheric extinction . IFU\_SPECPHOT\_TABLE Calib Response curve . CCD\_TABLE Calib Bad pixel table . Output files: DO category: Data type: Explanation:\ IFU\_SCIENCE\_REDUCED FITS image Reduced scientific spectra\ IFU\_SCIENCE\_FLUX\_REDUCED FITS image Reduced scientific spectra\ IFU\_FOV FITS image Reconstructed IFU field-of-view\ IFU\_SKY\_TRACE FITS table Science aligned extraction mask Only if sky alignment is requested:\ IFU\_SKY\_IDS FITS table Sky aligned wavelength solution The extraction mask, the wavelength calibration, and the relative transmission table, are those generated by the recipe vmifucalib. A CCD table must be specified only if a bad pixel cleaning is requested. For more details, please refer to the VIMOS Pipeline User´s Guide. ## OPTIONS - **--BiasMethod** *\* Bias removal method. (str; default: ´Zmaster´). The full name of this option for the EsoRex configuration file is **vimos.Parameters.bias.removing.method** \[default = *Zmaster*\]. - **--CleanBadPixel** *\* Bad pixel correction on master flat field. (bool; default: False). The full name of this option for the EsoRex configuration file is **vimos.Parameters.badpixel.clean** \[default = *False*\]. - **--ApplyTransmission** *\* Apply transmission correction to extracted scientific spectra (bool; default: True). The full name of this option for the EsoRex configuration file is **vimos.Parameters.apply.transmission** \[default = *True*\]. - **--CalibrateFlux** *\* Extracted spectra are flux calibrated. (bool; default: False). The full name of this option for the EsoRex configuration file is **vimos.Parameters.flux.calibration** \[default = *False*\]. - **--UseSkylines** *\* Use sky lines to refine the wavelength calibration (bool; default: True). The full name of this option for the EsoRex configuration file is **vimos.Parameters.sky.align** \[default = *True*\]. - **--UseSkyIndividual** *\* Use sky lines to refine the wavelength calibration individually for each spectrum (bool; default: False). The full name of this option for the EsoRex configuration file is **vimos.Parameters.sky.individual** \[default = *False*\]. - **--ComputeQC** *\* Compute QC1 parameters (bool; default: False). The full name of this option for the EsoRex configuration file is **vimos.Parameters.quality.enable** \[default = *False*\]. 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), [*vmifustandard*(7)](/vmifustandard/7.md), [*vmmoscalib*(7)](/vmmoscalib/7.md), [*vmmosscience*(7)](/vmmosscience/7.md), [*vmspphot*(7)](/vmspphot/7.md) ## VERSION vmifuscience 4.1.7 ## AUTHOR ESO VIMOS Pipeline Team \ ## 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) 2002-2005 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