Provided by: cpl-plugin-uves-doc_5.9.1+dfsg-1build2_all bug

NAME

       uves_cal_tflat - Reduces a TFLAT frame

SYNOPSIS

       esorex uves_cal_tflat [OPTIONS] FILE.sof

DESCRIPTION

       This recipe reduces a TFLAT_xxx frame (xxx = BLUE,RED). This is achieved by 1) combining
       all provided TFLAT frames to a MASTER_TFLAT frame, then 2) doing a normal science
       reduction on the first input TFLAT frame Input frames are raw TFLAT_xxx  frames, and:
       order table(s) for each chip, ORDER_TABLE_xxxx (where xxxx=BLUE, REDL, REDU), line
       table(s) for each chip, LINE_TABLE_xxxx, a master bias frame, MASTER_BIAS_xxxx, a master
       flat, MASTER_FLAT_xxxx,

OPTIONS

       --debug <bool>
              Whether or not to save intermediate results to local directory (bool; default:
              False). The full name of this option for the EsoRex configuration file is
              uves.debug [default = False].

       --plotter <str>
              Any plots produced by the recipe are redirected to the command specified by this
              parameter. The plotting command must contain the substring ´gnuplot´ and must be
              able to parse gnuplot syntax on its standard input. Valid examples of such a
              command may include ´gnuplot -persist´ and ´cat > mygnuplot$$.gp´. A finer control
              of the plotting options can be obtained by writing an executable script, e.g.
              my_gnuplot.pl, that executes gnuplot after setting the desired gnuplot options
              (e.g. set terminal pslatex color). To turn off plotting, set this parameter to ´no´
              (str; default: ´no´). The full name of this option for the EsoRex configuration
              file is uves.plotter [default = no].

       --process_chip <str>
              For RED arm data process the redl, redu, or both chip(s) (str; default: ´both´).
              The full name of this option for the EsoRex configuration file is uves.process_chip
              [default = both].

       --clean_traps <bool>
              Clean detector traps. If TRUE detector traps are interpolated.The bad pixels are
              replaced by the average of thenearest good pixels in the same column, or simply
              marked as bad. The positions of bad pixels are hard-coded (as function of UVES
              chip). (bool; default: False). The full name of this option for the EsoRex
              configuration file is uves_cal_tflat.clean_traps [default = False].

       --norm_method <str>
              Method used to build master frame  (str; default: ´explevel´). The full name of
              this option for the EsoRex configuration file is uves_cal_tflat.norm_method
              [default = explevel].

       --reduce.slitlength <float>
              Extraction slit length (in pixels). If negative, the value inferred from the raw
              frame header is used (float; default: -1.0). The full name of this option for the
              EsoRex configuration file is uves_cal_tflat.reduce.slitlength [default = -1.0].

       --reduce.skysub <bool>
              Do sky-subtraction (only applicable to linear and average extractions)? (bool;
              default: False). The full name of this option for the EsoRex configuration file is
              uves_cal_tflat.reduce.skysub [default = False].

       --reduce.objoffset <float>
              Offset (in pixels) of extraction slit with respect to center of order.  This
              parameter applies to linear/average/optimal extraction. For linear/average
              extraction, if the related parameter objslit is negative, the offset is
              automatically determined by measuring the actual object position.  (float; default:
              0.0). The full name of this option for the EsoRex configuration file is
              uves_cal_tflat.reduce.objoffset [default = 0.0].

       --reduce.objslit <float>
              Object window size (in pixels). This must be less than the total slit length. If
              negative, the default value (half of full slit length) is used. The upper and lower
              sky windows are defined as the part of the full slit (if any) outside the object
              window. The center of the object window is determined by the offset parameter. This
              parameter does not apply to optimal extraction. (float; default: -1.0). The full
              name of this option for the EsoRex configuration file is
              uves_cal_tflat.reduce.objslit [default = -1.0].

       --reduce.tiltcorr <bool>
              If enabled (recommended), the provided dispersion solutions obtained at different
              slit positions are interpolated linearly at the actually measured position of the
              object/sky. Line tilt correction is currently not supported for 2d extraction, in
              which case the dispersion solution obtained at the middle of the slit is always
              used. (bool; default: True). The full name of this option for the EsoRex
              configuration file is uves_cal_tflat.reduce.tiltcorr [default = True].

       --reduce.ffmethod <str>
              Flat-fielding method. If set to ´pixel´, flat-fielding is done in pixel-pixel space
              (before extraction); if set to ´extract´, flat- fielding is performed in
              pixel-order space (i.e. after extraction). If set to ´no´, no flat-field correction
              is done (str; default: ´extract´). The full name of this option for the EsoRex
              configuration file is uves_cal_tflat.reduce.ffmethod [default = extract].

       --reduce.merge <str>
              Order merging method. If ´optimal´, the flux in the overlapping region is set to
              the (optimally computed, using the uncertainties) average of single order spectra.
              If ´sum´, the flux in the overlapping region is computed as the sum of the single
              order spectra. If ´noappend´ the spectrum is simply rebinned but not merged.If
              flat-fielding is done, method ´optimal´ is recommended, otherwise ´sum´. (str;
              default: ´optimal´). The full name of this option for the EsoRex configuration file
              is uves_cal_tflat.reduce.merge [default = optimal].

       --reduce.merge_delt1 <float>
              Order merging left hand (short wavelength) cut. To reduce the amount of order
              overlapping regions we allow to cut short and long wavelength ranges. This may
              reduce the ripple possibly introduced by the order merging. Suggested values are:
              10 (W<=390), 12 (390<W<=437, 520<W<=564), 14 (437<W<=520, 564<W)  (float; default:
              0.0). The full name of this option for the EsoRex configuration file is
              uves_cal_tflat.reduce.merge_delt1 [default = 0.0].

       --reduce.merge_delt2 <float>
              Order merging right hand (long wavelength) cut. To reduce the amount of order
              overlapping regions we allow to cut short and long wavelength ranges. This may
              reduce the ripple possibly introduced by the order merging. Suggested values is 4
              (float; default: 0.0). The full name of this option for the EsoRex configuration
              file is uves_cal_tflat.reduce.merge_delt2 [default = 0.0].

       --reduce.extract.method <str>
              Extraction method. (2d/optimal not supported by uves_cal_wavecal, weighted
              supported only by uves_cal_wavecal, 2d not supported by uves_cal_response) (str;
              default: ´average´). The full name of this option for the EsoRex configuration file
              is uves_cal_tflat.reduce.extract.method [default = average].

       --reduce.extract.kappa <float>
              In optimal extraction mode, this is the threshold for bad (i.e.  hot/cold) pixel
              rejection. If a pixel deviates more than kappa*sigma (where sigma is the
              uncertainty of the pixel flux) from the inferred spatial profile, its weight is set
              to zero. Range: [-1,100]. If this parameter is negative, no rejection is performed.
              (float; default: 10.0). The full name of this option for the EsoRex configuration
              file is uves_cal_tflat.reduce.extract.kappa [default = 10.0].

       --reduce.extract.chunk <int>
              In optimal extraction mode, the chunk size (in pixels) used for fitting the
              analytical profile (a fit of the analytical profile to single bins would suffer
              from low statistics). (int; default: 32). The full name of this option for the
              EsoRex configuration file is uves_cal_tflat.reduce.extract.chunk [default = 32].

       --reduce.extract.profile <str>
              In optimal extraction mode, the kind of profile to use. ´gauss´ gives a Gaussian
              profile, ´moffat´ gives a Moffat profile with beta=4 and a possible linear sky
              contribution. ´virtual´ uses a virtual resampling algorithm (i.e. measures and uses
              the actual object profile).  ´constant´ assumes a constant spatial profile and
              allows optimal extraction of wavelength calibration frames. ´auto´ will
              automatically select the best method based on the estimated S/N of the object. For
              low S/N, ´moffat´ or ´gauss´ are recommended (for robustness). For high S/N,
              ´virtual´ is recommended (for accuracy). In the case of virtual resampling, a
              precise determination of the order positions is required; therefore the
              order-definition is repeated using the (assumed non-low S/N) science frame (str;
              default: ´auto´). The full name of this option for the EsoRex configuration file is
              uves_cal_tflat.reduce.extract.profile [default = auto].

       --reduce.extract.skymethod <str>
              In optimal extraction mode, the sky subtraction method to use.  ´median´ estimates
              the sky as the median of pixels along the slit (ignoring pixels close to the
              object), whereas ´optimal´ does a chi square minimization along the slit to obtain
              the best combined object and sky levels. The optimal method gives the most accurate
              sky determination but is also a bit slower than the median method (str; default:
              ´optimal´). The full name of this option for the EsoRex configuration file is
              uves_cal_tflat.reduce.extract.skymethod [default = optimal].

       --reduce.extract.oversample <int>
              The oversampling factor used for the virtual resampling algorithm. If negative, the
              value 5 is used for S/N <=200, and the value 10 is used if the estimated S/N is >
              200 (int; default: -1). The full name of this option for the EsoRex configuration
              file is uves_cal_tflat.reduce.extract.oversample [default = -1].

       --reduce.extract.best <bool>
              (optimal extraction only) If false (fastest), the spectrum is extracted only once.
              If true (best), the spectrum is extracted twice, the second time using improved
              variance estimates based on the first iteration. Better variance estimates slightly
              improve the obtained signal to noise but at the cost of increased execution time
              (bool; default: True). The full name of this option for the EsoRex configuration
              file is uves_cal_tflat.reduce.extract.best [default = True].

       --reduce.rebin.wavestep <float>
              The bin size (in w.l.u.) in wavelength space. If negative, a step size of 2/3 * (
              average pixel size ) is used. (float; default: -1.0). The full name of this option
              for the EsoRex configuration file is uves_cal_tflat.reduce.rebin.wavestep [default
              = -1.0].

       --reduce.rebin.scale <bool>
              Whether or not to multiply by the factor dx/dlambda (pixels per wavelength) during
              the rebinning. This option is disabled as default in concordance with the method
              used in the MIDAS pipeline. This option should be set to true to convert the
              observed flux (in pixel-space) to a flux per wavelength (in wavelength-space).
              (bool; default: False). The full name of this option for the EsoRex configuration
              file is uves_cal_tflat.reduce.rebin.scale [default = False].

       --reduce.backsub.mmethod <str>
              Background measuring method. If equal to ´median´ the background is sampled using
              the median of a subwindow. If ´minimum´, the subwindow minimum value is used. If
              ´no´, no background subtraction is done.  (str; default: ´median´). The full name
              of this option for the EsoRex configuration file is
              uves_cal_tflat.reduce.backsub.mmethod [default = median].

       --reduce.backsub.npoints <int>
              This is the number of columns in interorder space used to sample the background.
              (int; default: 82). The full name of this option for the EsoRex configuration file
              is uves_cal_tflat.reduce.backsub.npoints [default = 82].

       --reduce.backsub.radiusy <int>
              The height (in pixels) of the background sampling window is (2*radiusy + 1). This
              parameter is not corrected for binning. (int; default: 2). The full name of this
              option for the EsoRex configuration file is uves_cal_tflat.reduce.backsub.radiusy
              [default = 2].

       --reduce.backsub.sdegree <int>
              Degree of interpolating splines. Currently only degree = 1 is supported (int;
              default: 1). The full name of this option for the EsoRex configuration file is
              uves_cal_tflat.reduce.backsub.sdegree [default = 1].

       --reduce.backsub.smoothx <float>
              If spline interpolation is used to measure the background, the x-radius of the
              post-smoothing window is (smoothx * image_width).  Here, ´image_width´ is the image
              width after binning. If negative, the default values are used: (25.0/4096) for blue
              flat-field frames, (50.0/4096) for red flat-field frames, (300.0/4096) for blue
              science frames and (300.0/4096) for red science frames. (float; default: -1.0). The
              full name of this option for the EsoRex configuration file is
              uves_cal_tflat.reduce.backsub.smoothx [default = -1.0].

       --reduce.backsub.smoothy <float>
              If spline interpolation is used to measure the background, the y-radius of the
              post-smoothing window is (smoothy * image_height).  Here, ´image_height´ is the
              image height after binning. If negative, the default values are used: (100.0/2048)
              for blue flat-field frames, (300.0/2048) for red flat-field frames, (200.0/2048)
              for blue science frames and (500.0/2048) for red science frames. (float; default:
              -1.0). The full name of this option for the EsoRex configuration file is
              uves_cal_tflat.reduce.backsub.smoothy [default = -1.0].

       --backsub.mmethod <str>
              Background measuring method. If equal to ´median´ the background is sampled using
              the median of a subwindow. If ´minimum´, the subwindow minimum value is used. If
              ´no´, no background subtraction is done.  (str; default: ´median´). The full name
              of this option for the EsoRex configuration file is uves_cal_tflat.backsub.mmethod
              [default = median].

       --backsub.npoints <int>
              This is the number of columns in interorder space used to sample the background.
              (int; default: 82). The full name of this option for the EsoRex configuration file
              is uves_cal_tflat.backsub.npoints [default = 82].

       --backsub.radiusy <int>
              The height (in pixels) of the background sampling window is (2*radiusy + 1). This
              parameter is not corrected for binning. (int; default: 2). The full name of this
              option for the EsoRex configuration file is uves_cal_tflat.backsub.radiusy [default
              = 2].

       --backsub.sdegree <int>
              Degree of interpolating splines. Currently only degree = 1 is supported (int;
              default: 1). The full name of this option for the EsoRex configuration file is
              uves_cal_tflat.backsub.sdegree [default = 1].

       --backsub.smoothx <float>
              If spline interpolation is used to measure the background, the x-radius of the
              post-smoothing window is (smoothx * image_width).  Here, ´image_width´ is the image
              width after binning. If negative, the default values are used: (25.0/4096) for blue
              flat-field frames, (50.0/4096) for red flat-field frames, (300.0/4096) for blue
              science frames and (300.0/4096) for red science frames. (float; default: -1.0). The
              full name of this option for the EsoRex configuration file is
              uves_cal_tflat.backsub.smoothx [default = -1.0].

       --backsub.smoothy <float>
              If spline interpolation is used to measure the background, the y-radius of the
              post-smoothing window is (smoothy * image_height).  Here, ´image_height´ is the
              image height after binning. If negative, the default values are used: (100.0/2048)
              for blue flat-field frames, (300.0/2048) for red flat-field frames, (200.0/2048)
              for blue science frames and (500.0/2048) for red science frames. (float; default:
              -1.0). The full name of this option for the EsoRex configuration file is
              uves_cal_tflat.backsub.smoothy [default = -1.0].

       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 uves pipeline can be downloaded as a PDF file using the
       following URL:

              ftp://ftp.eso.org/pub/dfs/pipelines/uves/uves-pipeline-manual-5.9.1.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 uves pipeline are flames_cal_mkmaster(7), flames_cal_orderpos(7),
       flames_cal_predict(7), flames_cal_prep_sff_ofpos(7), flames_cal_wavecal(7),
       flames_obs_redchain(7), flames_obs_scired(7), flames_utl_unpack(7), uves_cal_cd_align(7),
       uves_cal_mbias(7), uves_cal_mdark(7), uves_cal_mflat(7), uves_cal_mflat_combine(7),
       uves_cal_mkmaster(7), uves_cal_orderpos(7), uves_cal_predict(7), uves_cal_response(7),
       uves_cal_wavecal(7), uves_obs_redchain(7), uves_obs_scired(7), uves_utl_ima_arith(7),
       uves_utl_remove_crh_single(7)

VERSION

       uves_cal_tflat 5.9.1

AUTHOR

       Jonas M. Larsen <cpl@eso.org>

BUG REPORTS

       Please report any problems to cpl@eso.org. Alternatively, you may send a report to the ESO
       User Support Department <usd-help@eso.org>.

LICENSE

       This file is part of the FLAMES/UVES Pipeline Copyright (C) 2004, 2005, 2006, 2007
       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  02111-1307  USA