--- name: "sinfo_rec_wavecal" 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_wavecal" --- # sinfo\_rec\_wavecal(7) Wavelength calibration and slitpos determination ## NAME sinfo\_rec\_wavecal - Wavelength calibration and slitpos determination ## SYNOPSIS esorex **sinfo\_rec\_wavecal** \[OPTIONS\] FILE.sof ## DESCRIPTION This recipe performs wavelength calibration. The input files are on/off arc lamp frames with tag WAVE\_LAMP Master calibration frame input is: A corresponding (band) reference line table with tag REF\_LINE\_ARC A corresponding (band) distortion table with tag DISTORTION A corresponding (band,preoptic) master flat with tag MASTER\_FLAT\_LAMP A corresponding (band,preoptics) master bad pixel map with tag MASTER\_BP\_MAP If wcal-estimate\_ind=TRUE, a corresponding (band,preoptics) slitlet position guess table SLIT\_POS\_GUESS (for example a copy of the SLIT\_POS product) If wcal-calib\_indicator=FALSE, a corresponding (band,preoptics) parabolic fit coefficients table WAVE\_COEF\_SLIT If sinfoni.wavecal.slitpos\_boostrap\_switch=FALSE (wcal-calib-slitpos\_bootstrap=0), a corresponding (band,preoptics) slitlets position table with tag SLIT\_POS The main products are: The master flat field corrected for distortions (PRO.CATG=MFLAT\_STACKED\_DIST) The arc lamp frames stacked (PRO.CATG=WAVE\_LAMP\_STACKED) The wavelength map (PRO.CATG=WAVE\_MAP) The slitlet position table (PRO.CATG=SLIT\_POS) A parabolic fit coefficients table (PRO.CATG=WAVE\_COEF\_SLIT) Parameters relative to arc lamp line fit: (PRO.CATG=WAVE\_FIT\_PARAMS) ## OPTIONS - **--gen-overpar** *\* Overwrite DRS ini parameters: (bool; default: True). The full name of this option for the EsoRex configuration file is **sinfoni.general.overwrite\_parameters** \[default = *True*\]. - **--lc\_sw** *\* Correct for bad lines introduced by instrument software: (bool; default: False). The full name of this option for the EsoRex configuration file is **sinfoni.general.lc\_sw** \[default = *False*\]. - **--lc\_kappa** *\* Kappa sigma value (long; default: 18). The full name of this option for the EsoRex configuration file is **sinfoni.general.lc\_kappa** \[default = *18*\]. - **--lc\_filt\_rad** *\* Filtering radii applied during median filter. Should be small (long; default: 3). The full name of this option for the EsoRex configuration file is **sinfoni.general.lc\_filt\_rad** \[default = *3*\]. - **--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** \[default = *True*\]. - **--wcal-slitpos\_bootstrap** *\* Switch to get a new slitpos without a reference: (bool; default: False). The full name of this option for the EsoRex configuration file is **sinfoni.wavecal.slitpos\_boostrap** \[default = *False*\]. - **--wcal-calib\_indicator** *\* Calib Indicator: FALSE: if the dispersion relation is already known, the routine can jump to the sinfo\_waveMap section TRUE: if the dispersion relation must first be determined (bool; default: True). The full name of this option for the EsoRex configuration file is **sinfoni.wavecal.calib\_indicator** \[default = *True*\]. - **--wcal-min\_diff** *\* Minimum Of Difference: minimum difference of mean and sinfo\_median column intensity to carry out the cross sinfo\_correlation (float; default: 1.0). The full name of this option for the EsoRex configuration file is **sinfoni.wavecal.min\_diff** \[default = *1.0*\]. - **--wcal-hw** *\* Half Width: half width of a box within which the line must be placed (long; default: 7). The full name of this option for the EsoRex configuration file is **sinfoni.wavecal.half\_width** \[default = *7*\]. - **--wcal-sigma** *\* Sigma: sigma of Gaussian which is convolved with the artificial spectrum generated using the line list (float; default: 2.0). The full name of this option for the EsoRex configuration file is **sinfoni.wavecal.sigma** \[default = *2.0*\]. - **--wcal-fwhm** *\* FWHM: initial guess value for the fwhm of the Gaussian used for the line fit (float; default: 2.83). The full name of this option for the EsoRex configuration file is **sinfoni.wavecal.fwhm** \[default = *2.83*\]. - **--wcal-min\_amplitude** *\* Minimum Of Amplitude: of the Gaussian to do the fit (float; default: 5.0). The full name of this option for the EsoRex configuration file is **sinfoni.wavecal.min\_amplitude** \[default = *5.0*\]. - **--wcal-max\_residual** *\* Maximum Residuals value: beyond this value the fit is rejected (float; default: 0.5). The full name of this option for the EsoRex configuration file is **sinfoni.wavecal.max\_residual** \[default = *0.5*\]. - **--wcal-n\_a\_coeffs** *\* Number of A coefficients: number of polynomial coefficients for the dispersion relation (long; default: 4). The full name of this option for the EsoRex configuration file is **sinfoni.wavecal.n\_a\_coefficients** \[default = *4*\]. - **--wcal-n\_b\_coeffs** *\* Number of B coefficients: number of polynomial coefficients for the polynomial fit of the dispersion coefficients (long; default: 2). The full name of this option for the EsoRex configuration file is **sinfoni.wavecal.n\_b\_coefficients** \[default = *2*\]. - **--wcal-sigma\_factor** *\* Sigma Factor: Factor of the standard deviation of the polynomial coefficients of the dispersion relation beyond which the coefficients are not used for the fit (float; default: 1.5). The full name of this option for the EsoRex configuration file is **sinfoni.wavecal.sigma\_factor** \[default = *1.5*\]. - **--wcal-wcoeff\_ind** *\* Write Coefficients Index: indicates if the coefficients should be written into a file or not (bool; default: True). The full name of this option for the EsoRex configuration file is **sinfoni.wavecal.write\_coeffs\_ind** \[default = *True*\]. - **--wcal-par\_ind** *\* Write Parameter Index: indicates if the fit parameters should be written into a file or not (bool; default: True). The full name of this option for the EsoRex configuration file is **sinfoni.wavecal.write\_par\_ind** \[default = *True*\]. - **--wcal-pixel\_dist** *\* Minimal Slitlets´s Distance in spectral direction (long; default: 15). The full name of this option for the EsoRex configuration file is **sinfoni.wavecal.pixel\_dist** \[default = *15*\]. - **--wcal-pixel\_tol** *\* Pixel Tolerance: allowed pixel position tolerance between estimated and fitted line position (float; default: 5.0). The full name of this option for the EsoRex configuration file is **sinfoni.wavecal.pixel\_tol** \[default = *5.0*\]. - **--wcal-wave\_map\_ind** *\* Wavelength Map Indicator: indicates if the wavelength calibration map should be generated (TRUE) or not (FALSE) (bool; default: False). The full name of this option for the EsoRex configuration file is **sinfoni.wavecal.wave\_map\_ind** \[default = *False*\]. - **--wcal-mag\_factor** *\* Magnificator Factor: magnifying factor for the number of pixels in the columns needed for FFT (long; default: 8). The full name of this option for the EsoRex configuration file is **sinfoni.wavecal.mag\_factor** \[default = *8*\]. - **--wcal-slit\_pos\_ind** *\* Slit Position Indicator: indicates if the fits of the slitlet edge positions should be carried through or not (bool; default: True). The full name of this option for the EsoRex configuration file is **sinfoni.wavecal.slit\_pos\_indicator** \[default = *True*\]. - **--wcal-fit\_boltz\_ind** *\* Fit Boltzmann Indicator: indicates if the fits of the slitlet edge positions is carried trough by using a Boltzmann function as model function (bool; default: True). The full name of this option for the EsoRex configuration file is **sinfoni.wavecal.fit\_boltz\_indicator** \[default = *True*\]. - **--wcal-fit\_edge\_ind** *\* Fit Edge Indicator: indicates if the fits of the slitlet edge positions is carried through by using a simple edge function as model function (bool; default: False). The full name of this option for the EsoRex configuration file is **sinfoni.wavecal.fit\_edge\_indicator** \[default = *False*\]. - **--wcal-estimate\_ind** *\* Estimate Indicator: indicates if the fits of the slitlet edge positions is carried through by using a list of estimated guess positions in a file (TRUE)or if the initial positions are calculated automatically (FALSE). The estimation case is more stable (bool; default: False). The full name of this option for the EsoRex configuration file is **sinfoni.wavecal.estimate\_indicator** \[default = *False*\]. - **--wcal-box\_len** *\* Box Length: pixel length of the row box within which the fit is carried out (long; default: 32). The full name of this option for the EsoRex configuration file is **sinfoni.wavecal.box\_length** \[default = *32*\]. - **--wcal-y\_box** *\* Y Box: half width of a small box in spectral direction within which the maximal intensity pixel is searched (float; default: 5.0). The full name of this option for the EsoRex configuration file is **sinfoni.wavecal.y\_box** \[default = *5.0*\]. - **--wcal-diff\_toll** *\* Difference Tolearance: maximal tolerable difference of the resulting fit positions of the slitlet edges with respect to the expected positions (float; default: 2.0). The full name of this option for the EsoRex configuration file is **sinfoni.wavecal.diff\_tol** \[default = *2.0*\]. - **--wcal-qc\_thresh\_min** *\* qc\_thresh\_min (long; default: 0). The full name of this option for the EsoRex configuration file is **sinfoni.wavecal.qc\_thresh\_min** \[default = *0*\]. - **--wcal-qc\_thresh\_max** *\* qc\_thresh\_max (long; default: 49000). The full name of this option for the EsoRex configuration file is **sinfoni.wavecal.qc\_thresh\_max** \[default = *49000*\]. - **--wcal-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.wavecal.n\_coeffs** \[default = *3*\]. 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\_pupil*(7)](/sinfo_rec_pupil/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\_wavecal 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