--- name: "kmos_sci_red" section: "7" platform: "linux" package: "cpl-plugin-kmos-doc" version: "2.1.0+dfsg-1" release: "Debian 10 (Buster)" platforms: ["linux"] url: "https://new.carta.tech/kmos_sci_red" --- # kmos\_sci\_red(7) Reconstruct obj/sky-pairs individually and combine them afterwards ## NAME kmos\_sci\_red - Reconstruct obj/sky-pairs individually and combine them afterwards ## SYNOPSIS esorex **kmos\_sci\_red** \[OPTIONS\] FILE.sof ## DESCRIPTION Two data frames are expected in order to have a sky IFU for the IFU Objects. If an OH spectrum is given in the SOF file the lambda axis will be corrected using the OH lines as reference. Every IFU containing an object will be reconstructed and divided by telluric and illumination correction. By default these intermediate cubes are saved to disk. The reconstructed objects with the same object name are combined. In order to combine a specific object, the parameters --name or --ifus can be used. For exposures taken with the templates KMOS\_spec\_obs\_mapping8 and KMOS\_spec\_obs\_mapping24, all active IFUs are combined. Input files: DO KMOS \ category Type Explanation Required #Frames\ \-------- ----- ----------- -------- -------\ SCIENCE RAW The science frames Y \>=1 \ XCAL F2D x calibration frame Y 1 \ YCAL F2D y calibration frame Y 1 \ LCAL F2D Wavelength calib. frame Y 1 \ WAVE\_BAND F2L Table with start-/end-wavelengths Y 1 \ MASTER\_FLAT F2D Master flat Y 0,1 \ ILLUM\_CORR F2I Illumination correction N 0,1 \ TELLURIC F1I normalised telluric spectrum N 0,1 \ TELLURIC\_GEN F1I normalised telluric spectrum N 0,1 \ OH\_SPEC F1S Vector holding OH lines N 0,1 Output files: DO KMOS\ category Type Explanation\ \-------- ----- -----------\ SCI\_COMBINED F3I Combined cubes with noise\ SCI\_RECONSTRUCTED F3I Reconstructed cube with noise\ EXP\_MASK F3I Exposure time mask (not for mapping-templates!)\ SCI\_INTERIM\_OBJECT F3I (optional) Intermediate reconstructed object \ cubes used for sky tweaking, no noise \ (set --sky\_tweak and --save\_interims)\ SCI\_INTERIM\_SKY F3I (optional) Intermediate reconstructed sky \ cubes used for sky tweaking, no noise\ (set --sky\_tweak and --save\_interims)\ SCI\_COMBINED\_COLL (optional) Collapsed combined cube\ (set --collapse\_combined)\ SCI\_RECONSTRUCTED\_COLL (optional) Collapsed reconstructed cube\ (set --collapse\_reconstructed) ## OPTIONS - **--imethod** *\* Method to use for interpolation during reconstruction. \["NN" (nearest neighbour), "lwNN" (linear weighted nearest neighbor), "swNN" (square weighted nearest neighbor), "MS" (Modified Shepard´s method)"CS" (Cubic spline)\] (str; default: ´CS´). The full name of this option for the EsoRex configuration file is **kmos.kmos\_sci\_red.imethod** \[default = *CS*\]. - **--smethod** *\* Method to use for interpolation during shifting. \["NN" (nearest neighbour), "CS" (Cubic spline)\] (str; default: ´CS´). The full name of this option for the EsoRex configuration file is **kmos.kmos\_sci\_red.smethod** \[default = *CS*\]. - **--method** *\* The shifting method: ´none´: no shifting, combined directly, ´header´: shift according to WCS (default), ´center´: centering algorithm, ´user´: read shifts from file (str; default: ´header´). The full name of this option for the EsoRex configuration file is **kmos.kmos\_sci\_red.method** \[default = *header*\]. - **--fmethod** *\* The fitting method (applies only when method=´center´): ´gauss´: fit a gauss function to collapsed image (default), ´moffat´: fit a moffat function to collapsed image (str; default: ´gauss´). The full name of this option for the EsoRex configuration file is **kmos.kmos\_sci\_red.fmethod** \[default = *gauss*\]. - **--name** *\* Name of the object to combine. (str; default: ´´). The full name of this option for the EsoRex configuration file is **kmos.kmos\_sci\_red.name** \[default = \]. - **--ifus** *\* The indices of the IFUs to combine. "ifu1;ifu2;..." (str; default: ´´). The full name of this option for the EsoRex configuration file is **kmos.kmos\_sci\_red.ifus** \[default = \]. - **--oscan** *\* Apply Overscan Correction (bool; default: True). The full name of this option for the EsoRex configuration file is **kmos.kmos\_sci\_red.oscan** \[default = *True*\]. - **--pix\_scale** *\* Change the pixel scale \[arcsec\]. Default of 0.2" results into cubes of 14x14pix, a scale of 0.1" results into cubes of 28x28pix, etc. (float; default: 0.2). The full name of this option for the EsoRex configuration file is **kmos.kmos\_sci\_red.pix\_scale** \[default = *0.2*\]. - **--suppress\_extension** *\* Suppress arbitrary filename extension.(TRUE (apply) or FALSE (don´t apply) (bool; default: False). The full name of this option for the EsoRex configuration file is **kmos.kmos\_sci\_red.suppress\_extension** \[default = *False*\]. - **--neighborhoodRange** *\* Defines the range to search for neighbors in pixels (float; default: 1.001). The full name of this option for the EsoRex configuration file is **kmos.kmos\_sci\_red.neighborhoodRange** \[default = *1.001*\]. - **--filename** *\* The path to the file with the shift vectors.(Applies only to method=´user´) (str; default: ´´). The full name of this option for the EsoRex configuration file is **kmos.kmos\_sci\_red.filename** \[default = \]. - **--flux** *\* TRUE: Apply flux conservation. FALSE: otherwise (bool; default: False). The full name of this option for the EsoRex configuration file is **kmos.kmos\_sci\_red.flux** \[default = *False*\]. - **--background** *\* TRUE: Apply background removal. FALSE: otherwise (bool; default: False). The full name of this option for the EsoRex configuration file is **kmos.kmos\_sci\_red.background** \[default = *False*\]. - **--fast\_mode** *\* FALSE: cubes are shifted and combined,TRUE: cubes are collapsed and then shifted and combined (bool; default: False). The full name of this option for the EsoRex configuration file is **kmos.kmos\_sci\_red.fast\_mode** \[default = *False*\]. - **--extrapolate** *\* Applies only to ´smethod=CS´ when doing sub-pixel shifts: FALSE: shifted IFU will be filled with NaN´s at the borders,TRUE: shifted IFU will be extrapolated at the borders (bool; default: False). The full name of this option for the EsoRex configuration file is **kmos.kmos\_sci\_red.extrapolate** \[default = *False*\]. - **--xcal\_interpolation** *\* TRUE: Interpolate xcal between rotator angles. FALSE: otherwise (bool; default: True). The full name of this option for the EsoRex configuration file is **kmos.kmos\_sci\_red.xcal\_interpolation** \[default = *True*\]. - **--edge\_nan** *\* Set borders of cubes to NaN before combining them.(TRUE (apply) or FALSE (don´t apply) (bool; default: False). The full name of this option for the EsoRex configuration file is **kmos.kmos\_sci\_red.edge\_nan** \[default = *False*\]. - **--no\_combine** *\* Don´t combine cubes after reconstruction.(TRUE (apply) or FALSE (don´t apply) (bool; default: False). The full name of this option for the EsoRex configuration file is **kmos.kmos\_sci\_red.no\_combine** \[default = *False*\]. - **--no\_subtract** *\* Don´t sky subtract object and references.(TRUE (apply) or FALSE (don´t apply) (bool; default: False). The full name of this option for the EsoRex configuration file is **kmos.kmos\_sci\_red.no\_subtract** \[default = *False*\]. - **--sky\_tweak** *\* Use modified sky cube for sky subtraction.(TRUE (apply) or FALSE (don´t apply) (bool; default: False). The full name of this option for the EsoRex configuration file is **kmos.kmos\_sci\_red.sky\_tweak** \[default = *False*\]. - **--skip\_sky\_oh\_align** *\* Skip the OH alignment for the SKY (bool; default: False). The full name of this option for the EsoRex configuration file is **kmos.kmos\_sci\_red.skip\_sky\_oh\_align** \[default = *False*\]. - **--discard\_subband** *\* Ignore last sub-band in the sky tweaking (bool; default: False). The full name of this option for the EsoRex configuration file is **kmos.kmos\_sci\_red.discard\_subband** \[default = *False*\]. - **--stretch** *\* Stretch sky in the sky tweaking (bool; default: False). The full name of this option for the EsoRex configuration file is **kmos.kmos\_sci\_red.stretch\_sky** \[default = *False*\]. - **--stretch\_degree** *\* Stretch polynomial degree (int; default: 8). The full name of this option for the EsoRex configuration file is **kmos.kmos\_sci\_red.stretch\_degree** \[default = *8*\]. - **--stretch\_resampling** *\* Stretch resampling method (linear/spline) (str; default: ´spline´). The full name of this option for the EsoRex configuration file is **kmos.kmos\_sci\_red.stretch\_resampling** \[default = *spline*\]. - **--tbsub** *\* Subtract thermal background from input cube.(TRUE (apply) or FALSE (don´t apply) (bool; default: True). The full name of this option for the EsoRex configuration file is **kmos.kmos\_sci\_red.tbsub** \[default = *True*\]. - **--b\_samples** *\* The number of samples in wavelength for the reconstructed cube (int; default: 2048). The full name of this option for the EsoRex configuration file is **kmos.kmos\_sci\_red.b\_samples** \[default = *2048*\]. - **--obj\_sky\_table** *\* The path to the file with the modified obj/sky associations. (str; default: ´´). The full name of this option for the EsoRex configuration file is **kmos.kmos\_sci\_red.obj\_sky\_table** \[default = \]. - **--velocity\_offset** *\* Specify velocity offset correction in km/s for lambda scale (float; default: 0.0). The full name of this option for the EsoRex configuration file is **kmos.kmos\_sci\_red.velocity\_offset** \[default = *0.0*\]. - **--save\_interims** *\* Save interim object and sky cubes. Can only be used together with --sky\_tweak (bool; default: False). The full name of this option for the EsoRex configuration file is **kmos.kmos\_sci\_red.save\_interims** \[default = *False*\]. - **--collapse\_reconstructed** *\* Flag to collapse the reconstructed images (bool; default: False). The full name of this option for the EsoRex configuration file is **kmos.kmos\_sci\_red.collapse\_reconstructed** \[default = *False*\]. - **--collapse\_combined** *\* Flag to collapse the combined images (bool; default: False). The full name of this option for the EsoRex configuration file is **kmos.kmos\_sci\_red.collapse\_combined** \[default = *False*\]. - **--cmethod** *\* Apply "average", "median", "sum", "min\_max." or "ksigma". (str; default: ´ksigma´). The full name of this option for the EsoRex configuration file is **kmos.kmos\_sci\_red.cmethod** \[default = *ksigma*\]. - **--cpos\_rej** *\* The positive rejection threshold for kappa-sigma-clipping (sigma). (float; default: 3.0). The full name of this option for the EsoRex configuration file is **kmos.kmos\_sci\_red.cpos\_rej** \[default = *3.0*\]. - **--cneg\_rej** *\* The negative rejection threshold for kappa-sigma-clipping (sigma). (float; default: 3.0). The full name of this option for the EsoRex configuration file is **kmos.kmos\_sci\_red.cneg\_rej** \[default = *3.0*\]. - **--citer** *\* The number of iterations for kappa-sigma-clipping. (int; default: 3). The full name of this option for the EsoRex configuration file is **kmos.kmos\_sci\_red.citer** \[default = *3*\]. - **--cmax** *\* The number of maximum pixel values to clip with min/max-clipping. (int; default: 1). The full name of this option for the EsoRex configuration file is **kmos.kmos\_sci\_red.cmax** \[default = *1*\]. - **--cmin** *\* The number of minimum pixel values to clip with min/max-clipping. (int; default: 1). The full name of this option for the EsoRex configuration file is **kmos.kmos\_sci\_red.cmin** \[default = *1*\]. 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 kmos pipeline can be downloaded as a PDF file using the following URL: - **ftp://ftp.eso.org/pub/dfs/pipelines/kmos/kmos-pipeline-manual-2.9.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 kmos pipeline are [*kmo\_arithmetic*(7)](/kmo_arithmetic/7.md), [*kmo\_copy*(7)](/kmo_copy/7.md), [*kmo\_fit\_profile*(7)](/kmo_fit_profile/7.md), [*kmo\_fits\_strip*(7)](/kmo_fits_strip/7.md), [*kmo\_make\_image*(7)](/kmo_make_image/7.md), [*kmo\_noise\_map*(7)](/kmo_noise_map/7.md), [*kmo\_rotate*(7)](/kmo_rotate/7.md), [*kmo\_shift*(7)](/kmo_shift/7.md), [*kmo\_sky\_mask*(7)](/kmo_sky_mask/7.md), [*kmo\_stats*(7)](/kmo_stats/7.md), [*kmos\_combine*(7)](/kmos_combine/7.md), [*kmos\_dark*(7)](/kmos_dark/7.md), [*kmos\_extract\_spec*(7)](/kmos_extract_spec/7.md), [*kmos\_flat*(7)](/kmos_flat/7.md), [*kmos\_gen\_reflines*(7)](/kmos_gen_reflines/7.md), [*kmos\_gen\_telluric*(7)](/kmos_gen_telluric/7.md), [*kmos\_illumination*(7)](/kmos_illumination/7.md), [*kmos\_reconstruct*(7)](/kmos_reconstruct/7.md), [*kmos\_sky\_tweak*(7)](/kmos_sky_tweak/7.md), [*kmos\_std\_star*(7)](/kmos_std_star/7.md), [*kmos\_test*(7)](/kmos_test/7.md), [*kmos\_wave\_cal*(7)](/kmos_wave_cal/7.md) ## VERSION kmos\_sci\_red 2.1.0 ## AUTHOR Alex Agudo Berbel, Yves Jung \ ## BUG REPORTS Please report any problems to usd-help@eso.org. Alternatively, you may send a report to the ESO User Support Department \. ## LICENSE This file is part of the CRIRES 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