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

NAME

       flames_obs_redchain - Runs the full UVES-FIBRE reduction chain

SYNOPSIS

       esorex flames_obs_redchain [OPTIONS] FILE.sof

DESCRIPTION

       This recipe does a complete science reduction. It runs all necessary calibration recipes
       depending on the availability of raw/processed calibration frames.

       Input frames are all UVES-FIBER raw and reference frames: formatchecks,
       FIB_ARC_LAMP_FORM_RED, order definition frames, FIB_ORDER_FLAT_RED, biases, BIAS_RED,
       darks, DARK_RED, flats, SFLAT_RED, arc lamps, FIB_ARC_LAMP_RED, standard stars,
       FIB_STANDARD_RED a wavelength catalogue table,LINE_REFER_TABLE, and optionally a
       wavelength table of bright lines,LINE_INTMON_TABLE, used only for computing Quality
       Control parameters.

       a reference standard star flux table, FLUX_STD_TABLE, a table describing the atmospheric
       extintion,EXTCOEFF_TABLE.

       Optionally, science frames, SCIENCE_xxx, or UVES_SCI_POINT_xxx, or UVES_SCI_EXTND_xxx, or
       UVES_SCI_SLICER_xxx.

       For further details on the data reduction and the input frame types refer to the man page
       of the individual recipes.

OPTIONS

       --scired <bool>
              Whether or not to do science reduction. If false, only master calibration frames
              are created. If false, either zero or all necessary calibration frames must be
              provided for each arm (bool; default: True). The full name of this option for the
              EsoRex configuration file is flames_obs_redchain.scired [default = True].

       --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].

       --flames_obs_scired.ext_method <str>
              Extraction method (str; default: ´opt´). The full name of this option for the
              EsoRex configuration file is flames_obs_redchain.flames_obs_scired.ext_method
              [default = opt].

       --flames_obs_scired.cor_max_fnd <str>
              Find correlation maximum? (str; default: ´Y´). The full name of this option for the
              EsoRex configuration file is flames_obs_redchain.flames_obs_scired.cor_max_fnd
              [default = Y].

       --flames_obs_scired.cor_def_rng <float>
              Correlation range size? (float; default: 6.0). The full name of this option for the
              EsoRex configuration file is flames_obs_redchain.flames_obs_scired.cor_def_rng
              [default = 6.0].

       --flames_obs_scired.cor_def_pnt <int>
              Correlation sampling points? (int; default: 25). The full name of this option for
              the EsoRex configuration file is flames_obs_redchain.flames_obs_scired.cor_def_pnt
              [default = 25].

       --flames_obs_scired.cor_def_off <float>
              Correlation center offset? (float; default: 0.0). The full name of this option for
              the EsoRex configuration file is flames_obs_redchain.flames_obs_scired.cor_def_off
              [default = 0.0].

       --flames_obs_scired.corvel_iter <int>
              Velocity correlation iteration number (SimCal) (int; default: 1). The full name of
              this option for the EsoRex configuration file is
              flames_obs_redchain.flames_obs_scired.corvel_iter [default = 1].

       --flames_obs_scired.bias_method <str>
              Bias subtraction method (str; default: ´M´). The full name of this option for the
              EsoRex configuration file is flames_obs_redchain.flames_obs_scired.bias_method
              [default = M].

       --flames_obs_scired.bias_value <int>
              Bias value (only if bias_method = V) (int; default: 200). The full name of this
              option for the EsoRex configuration file is
              flames_obs_redchain.flames_obs_scired.bias_value [default = 200].

       --flames_obs_scired.cubify_sw <str>
              Cubify switch (str; default: ´N´). The full name of this option for the EsoRex
              configuration file is flames_obs_redchain.flames_obs_scired.cubify_sw [default =
              N].

       --flames_obs_scired.filt_sw <str>
              Filter switch (str; default: ´none´). The full name of this option for the EsoRex
              configuration file is flames_obs_redchain.flames_obs_scired.filt_sw [default =
              none].

       --flames_obs_scired.bkg_max_io_win <int>
              Background window number in each full inter order (int; default: 500). The full
              name of this option for the EsoRex configuration file is
              flames_obs_redchain.flames_obs_scired.bkg_max_io_win [default = 500].

       --flames_obs_scired.bkg_xy_win_sz_x <int>
              x maximum size of each background window:  (int; default: 6). The full name of this
              option for the EsoRex configuration file is
              flames_obs_redchain.flames_obs_scired.bkg_xy_win_sz_x [default = 6].

       --flames_obs_scired.bkg_xy_win_sz_y <int>
              y maximum size of each background window:  (int; default: 2). The full name of this
              option for the EsoRex configuration file is
              flames_obs_redchain.flames_obs_scired.bkg_xy_win_sz_y [default = 2].

       --flames_obs_scired.pixel_thresh_max <int>
              Pixel saturation threshold max (int; default: 55000). The full name of this option
              for the EsoRex configuration file is
              flames_obs_redchain.flames_obs_scired.pixel_thresh_max [default = 55000].

       --flames_obs_scired.pixel_thresh_min <int>
              Pixel saturation threshold min (int; default: -20). The full name of this option
              for the EsoRex configuration file is
              flames_obs_redchain.flames_obs_scired.pixel_thresh_min [default = -20].

       --flames_obs_scired.drs_k_s_thre <float>
              Kappa sigma threshold (float; default: 10.0). The full name of this option for the
              EsoRex configuration file is flames_obs_redchain.flames_obs_scired.drs_k_s_thre
              [default = 10.0].

       --flames_obs_scired.drs_base_name <str>
              Base name for science products (str; default: ´fxb´). The full name of this option
              for the EsoRex configuration file is
              flames_obs_redchain.flames_obs_scired.drs_base_name [default = fxb].

       --flames_obs_scired.drs_maxyshift <float>
              Half width of the interval to scan for correlation, when determining y shift
              (float; default: 3.0). The full name of this option for the EsoRex configuration
              file is flames_obs_redchain.flames_obs_scired.drs_maxyshift [default = 3.0].

       --flames_obs_scired.drs_ext_w_siz <float>
              Integration window size good: 10 (if fibre deconvolution works fine) (float;
              default: 10.0). The full name of this option for the EsoRex configuration file is
              flames_obs_redchain.flames_obs_scired.drs_ext_w_siz [default = 10.0].

       --flames_obs_scired.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 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 flames_obs_redchain.flames_obs_scired.merge [default =
              optimal].

       --flames_obs_scired.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<860), 4 (W>=860)
              (float; default: -1.0). The full name of this option for the EsoRex configuration
              file is flames_obs_redchain.flames_obs_scired.merge_delt1 [default = -1.0].

       --flames_obs_scired.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
              for W<860, else 0 (float; default: -1.0). The full name of this option for the
              EsoRex configuration file is flames_obs_redchain.flames_obs_scired.merge_delt2
              [default = -1.0].

       --flames_obs_scired.clean_tmp_products <bool>
              Input data format (bool; default: False). The full name of this option for the
              EsoRex configuration file is
              flames_obs_redchain.flames_obs_scired.clean_tmp_products [default = False].

       --flames_obs_scired.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
              flames_obs_redchain.flames_obs_scired.rebin.wavestep [default = -1.0].

       --flames_obs_scired.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 flames_obs_redchain.flames_obs_scired.rebin.scale [default = False].

       --flames_cal_orderpos.use_guess_tab <int>
              If a Guess order table is provided this parameter set how it is used:0: No usage,
              1: use it to set lower/upper Y raws where order are searched 2: the order table try
              to fully match the guess (int; default: 1). The full name of this option for the
              EsoRex configuration file is
              flames_obs_redchain.flames_cal_orderpos.preproc.use_guess_tab [default = 1].

       --flames_cal_orderpos.radx <int>
              Half X size of median filtering window (int; default: 2). The full name of this
              option for the EsoRex configuration file is
              flames_obs_redchain.flames_cal_orderpos.preproc.radx [default = 2].

       --flames_cal_orderpos.rady <int>
              Half Y size of median filtering window (int; default: 1). The full name of this
              option for the EsoRex configuration file is
              flames_obs_redchain.flames_cal_orderpos.preproc.rady [default = 1].

       --flames_cal_orderpos.mmethod <str>
              Background subtraction method. If equal to ´median´ the background is sampled using
              the median of a sub-window. If ´minimum´, the minimum sub-window 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
              flames_obs_redchain.flames_cal_orderpos.preproc.mmethod [default = median].

       --flames_cal_orderpos.backsubgrid <int>
              Number of grid points (in x- and y-direction) used to estimate the background
              (mode=poly). (int; default: 50). The full name of this option for the EsoRex
              configuration file is flames_obs_redchain.flames_cal_orderpos.preproc.backsubgrid
              [default = 50].

       --flames_cal_orderpos.backsubradiusy <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
              flames_obs_redchain.flames_cal_orderpos.preproc.backsubradiusy [default = 2].

       --flames_cal_orderpos.backsubkappa <float>
              The value of kappa in the one-sided kappa-sigma clipping used to estimate the
              background (mode=poly). (float; default: 4.0). The full name of this option for the
              EsoRex configuration file is
              flames_obs_redchain.flames_cal_orderpos.preproc.backsubkappa [default = 4.0].

       --flames_cal_orderpos.backsubdegx <int>
              Degree (in x) of polynomial used to estimate the background (mode=poly). (int;
              default: 2). The full name of this option for the EsoRex configuration file is
              flames_obs_redchain.flames_cal_orderpos.preproc.backsubdegx [default = 2].

       --flames_cal_orderpos.backsubdegy <int>
              Degree (in y) of polynomial used to estimate the background (mode=poly). (int;
              default: 2). The full name of this option for the EsoRex configuration file is
              flames_obs_redchain.flames_cal_orderpos.preproc.backsubdegy [default = 2].

       --flames_cal_orderpos.samplewidth <int>
              Separation of sample traces (used by Hough transform) in input image (int; default:
              50). The full name of this option for the EsoRex configuration file is
              flames_obs_redchain.flames_cal_orderpos.hough.samplewidth [default = 50].

       --flames_cal_orderpos.minslope <float>
              Minimum possible line slope. This should be the ´physical´ slope on the chip, i.e.
              not taking binning factors into account, which is handled by the recipe (float;
              default: 0.0). The full name of this option for the EsoRex configuration file is
              flames_obs_redchain.flames_cal_orderpos.hough.minslope [default = 0.0].

       --flames_cal_orderpos.maxslope <float>
              Maximum possible line slope (float; default: 0.2). The full name of this option for
              the EsoRex configuration file is
              flames_obs_redchain.flames_cal_orderpos.hough.maxslope [default = 0.2].

       --flames_cal_orderpos.sloperes <int>
              Resolution (width in pixels) of Hough space (int; default: 120). The full name of
              this option for the EsoRex configuration file is
              flames_obs_redchain.flames_cal_orderpos.hough.sloperes [default = 120].

       --flames_cal_orderpos.pthres <float>
              In automatic mode, or if the number of orders to detect is read from a guess table,
              the detection of new lines stops when the intensity of a candidate line drops to
              less than ´pthres´ times the intensity of the previous detection.  (float; default:
              0.2). The full name of this option for the EsoRex configuration file is
              flames_obs_redchain.flames_cal_orderpos.hough.pthres [default = 0.2].

       --flames_cal_orderpos.tracestep <int>
              The step size used when tracing the orders (int; default: 10). The full name of
              this option for the EsoRex configuration file is
              flames_obs_redchain.flames_cal_orderpos.trace.tracestep [default = 10].

       --flames_cal_orderpos.minthresh <float>
              The minimum threshold value is (min + minthres*(max - min)). Here ´min´ and ´max´
              are the lowest and highest pixel values in the central bin of the order (float;
              default: 0.2). The full name of this option for the EsoRex configuration file is
              flames_obs_redchain.flames_cal_orderpos.trace.minthresh [default = 0.2].

       --flames_cal_orderpos.maxgap <float>
              If the order line drops below detection threshold, the order tracing algorithm will
              try to jump a gap of maximum size ´maxgap´ multiplied by the image width (float;
              default: 0.2). The full name of this option for the EsoRex configuration file is
              flames_obs_redchain.flames_cal_orderpos.trace.maxgap [default = 0.2].

       --flames_cal_orderpos.maxrms <float>
              When fitting the orders with straight lines, this is the maximum allowed RMS
              relative to the median RMS of all orders (float; default: 100.0). The full name of
              this option for the EsoRex configuration file is
              flames_obs_redchain.flames_cal_orderpos.reject.maxrms [default = 100.0].

       --flames_cal_orderpos.defpol1 <int>
              The degree of the bivarite fit (cross dispersion direction). If negative, the
              degree is optimized to give the best fit (int; default: -1). The full name of this
              option for the EsoRex configuration file is
              flames_obs_redchain.flames_cal_orderpos.reject.defpol1 [default = -1].

       --flames_cal_orderpos.defpol2 <int>
              The degree of the bivarite fit (order number). If negative, the degree is optimized
              to give the best fit (int; default: -1). The full name of this option for the
              EsoRex configuration file is flames_obs_redchain.flames_cal_orderpos.reject.defpol2
              [default = -1].

       --flames_cal_orderpos.kappa <float>
              Used for kappa-sigma clipping of the final polynomial fit. If negative, no clipping
              is done (float; default: 4.0). The full name of this option for the EsoRex
              configuration file is flames_obs_redchain.flames_cal_orderpos.reject.kappa [default
              = 4.0].

       --uves_cal_mbias.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 flames_obs_redchain.uves_cal_mbias.clean_traps [default =
              False].

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

       --uves_cal_mbias.klow <float>
              Kappa used to clip low level values, when method is set to ´mean´ (float; default:
              5.0). The full name of this option for the EsoRex configuration file is
              flames_obs_redchain.uves_cal_mbias.klow [default = 5.0].

       --uves_cal_mbias.khigh <float>
              Kappa used to clip high level values, when method is set to ´mean´ (float; default:
              5.0). The full name of this option for the EsoRex configuration file is
              flames_obs_redchain.uves_cal_mbias.khigh [default = 5.0].

       --uves_cal_mbias.niter <int>
              Number of kappa sigma iterations, when method is set to ´mean´  (int; default: 5).
              The full name of this option for the EsoRex configuration file is
              flames_obs_redchain.uves_cal_mbias.niter [default = 5].

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

       --uves_cal_mflat.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
              flames_obs_redchain.uves_cal_mflat.backsub.mmethod [default = median].

       --uves_cal_mflat.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 flames_obs_redchain.uves_cal_mflat.backsub.npoints [default = 82].

       --uves_cal_mflat.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
              flames_obs_redchain.uves_cal_mflat.backsub.radiusy [default = 2].

       --uves_cal_mflat.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
              flames_obs_redchain.uves_cal_mflat.backsub.sdegree [default = 1].

       --uves_cal_mflat.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
              flames_obs_redchain.uves_cal_mflat.backsub.smoothx [default = -1.0].

       --uves_cal_mflat.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
              flames_obs_redchain.uves_cal_mflat.backsub.smoothy [default = -1.0].

       --flames_cal_predict.mbox_x <int>
              Match box X size (int; default: 40). The full name of this option for the EsoRex
              configuration file is flames_obs_redchain.flames_cal_predict.mbox_x [default = 40].

       --flames_cal_predict.mbox_y <int>
              Match box Y size (int; default: 40). The full name of this option for the EsoRex
              configuration file is flames_obs_redchain.flames_cal_predict.mbox_y [default = 40].

       --flames_cal_predict.trans_x <float>
              Detector translation along X (float; default: 0.0). The full name of this option
              for the EsoRex configuration file is flames_obs_redchain.flames_cal_predict.trans_x
              [default = 0.0].

       --flames_cal_predict.trans_y <float>
              Detector translation along Y (float; default: 0.0). The full name of this option
              for the EsoRex configuration file is flames_obs_redchain.flames_cal_predict.trans_y
              [default = 0.0].

       --flames_cal_predict.ech_angle_off <float>
              Offset on echelle angle (float; default: 0.0). The full name of this option for the
              EsoRex configuration file is flames_obs_redchain.flames_cal_predict.ech_angle_off
              [default = 0.0].

       --flames_cal_predict.cd_angle_off <float>
              Offset on cross disperser angle (float; default: 0.0). The full name of this option
              for the EsoRex configuration file is
              flames_obs_redchain.flames_cal_predict.cd_angle_off [default = 0.0].

       --flames_cal_predict.ccd_rot_angle_off <float>
              Offset on CCD rotation angle (float; default: 0.0). The full name of this option
              for the EsoRex configuration file is
              flames_obs_redchain.flames_cal_predict.ccd_rot_angle_off [default = 0.0].

       --flames_cal_predict.compute_regression_sw <bool>
              Compute regression? (bool; default: True). The full name of this option for the
              EsoRex configuration file is
              flames_obs_redchain.flames_cal_predict.compute_regression_sw [default = True].

       --flames_cal_predict.def_pol1 <int>
              Polynomial X deg (int; default: 4). The full name of this option for the EsoRex
              configuration file is flames_obs_redchain.flames_cal_predict.def_pol1 [default =
              4].

       --flames_cal_predict.def_pol2 <int>
              Polynomial Y deg (int; default: 5). The full name of this option for the EsoRex
              configuration file is flames_obs_redchain.flames_cal_predict.def_pol2 [default =
              5].

       --flames_cal_predict.kappa <float>
              Kappa value in kappa sigma clipping on RESIDUAL between YFIT and Y columns (float;
              default: 4.5). The full name of this option for the EsoRex configuration file is
              flames_obs_redchain.flames_cal_predict.kappa [default = 4.5].

       --flames_cal_predict.tol <float>
              Tolerance in kappa sigma clipping on RESIDUAL between YFIT and Y columns (float;
              default: 2.0). The full name of this option for the EsoRex configuration file is
              flames_obs_redchain.flames_cal_predict.tol [default = 2.0].

       --flames_cal_wavecal.nwindows <int>
              Number of extraction windows per trace. The windows will be aligned (i.e. no
              overlap and no spacing between adjacent windows). Unless an offset is specified,
              the middle window(s) is centered on the trace (int; default: 1). The full name of
              this option for the EsoRex configuration file is
              flames_obs_redchain.flames_cal_wavecal.nwindows [default = 1].

       --flames_cal_wavecal.length <float>
              Length (in pixels) of each extraction window. This parameter is also equal to the
              seperation of adjacent window centers, causing the extraction windows to always be
              aligned. The parameter is automatically adjusted according to the binning of the
              input raw frame. If negative, the extraction window length is determined
              automatically to cover the full slit (float; default: 7.0). The full name of this
              option for the EsoRex configuration file is
              flames_obs_redchain.flames_cal_wavecal.length [default = 7.0].

       --flames_cal_wavecal.offset <float>
              A global offset (in pixels) of all extraction windows (float; default: 0.0). The
              full name of this option for the EsoRex configuration file is
              flames_obs_redchain.flames_cal_wavecal.offset [default = 0.0].

       --flames_cal_wavecal.range <int>
              Width (pix) of search window is 2*range + 1. This parameter is automatically
              adjusted according to binning. (int; default: 8). The full name of this option for
              the EsoRex configuration file is
              flames_obs_redchain.flames_cal_wavecal.search.range [default = 8].

       --flames_cal_wavecal.minlines <int>
              Minimum number of lines to detect. If zero, the default value (1100 for BLUE/REDL
              chips; 1000 for REDU chip) is used. (int; default: 0). The full name of this option
              for the EsoRex configuration file is
              flames_obs_redchain.flames_cal_wavecal.search.minlines [default = 0].

       --flames_cal_wavecal.maxlines <int>
              Maximum number of lines to detect. If zero, the default value (1600 for BLUE/REDL
              chip; 1400 for REDU chip) is used. (int; default: 0). The full name of this option
              for the EsoRex configuration file is
              flames_obs_redchain.flames_cal_wavecal.search.maxlines [default = 0].

       --flames_cal_wavecal.shiftmax <float>
              The maximum shift (pix) in either direction compared to guess solution. This
              parameter is automatically corrected for binning (float; default: 10.0). The full
              name of this option for the EsoRex configuration file is
              flames_obs_redchain.flames_cal_wavecal.first.shiftmax [default = 10.0].

       --flames_cal_wavecal.shiftstep <float>
              The step size (pix) used when searching for the optimum shift. This parameter is
              automatically corrected for binning (float; default: 0.1). The full name of this
              option for the EsoRex configuration file is
              flames_obs_redchain.flames_cal_wavecal.first.shiftstep [default = 0.1].

       --flames_cal_wavecal.shifttoler <float>
              Tolerance (pix) when matching shifted lines. This parameter is not adjusted
              according to binning (float; default: 0.05). The full name of this option for the
              EsoRex configuration file is
              flames_obs_redchain.flames_cal_wavecal.first.shifttoler [default = 0.05].

       --flames_cal_wavecal.alpha <float>
              The parameter that controls the distance to the nearest neighbours (float; default:
              0.1). The full name of this option for the EsoRex configuration file is
              flames_obs_redchain.flames_cal_wavecal.identify.alpha [default = 0.1].

       --flames_cal_wavecal.maxerror <float>
              This parameter controls the graceful exit of the identification loop.  If the RMS
              of the global fit exceeds this value (pix) the iteration stops (float; default:
              20.0). The full name of this option for the EsoRex configuration file is
              flames_obs_redchain.flames_cal_wavecal.identify.maxerror [default = 20.0].

       --flames_cal_wavecal.degree <int>
              Degrees of the global 2d dispersion polynomial. If a negative number is specified,
              the polynomial degrees are automatically selected by starting from (1, 1) and
              inreasing the degrees as long as the RMS residual decreases significantly (int;
              default: 4). The full name of this option for the EsoRex configuration file is
              flames_obs_redchain.flames_cal_wavecal.identify.degree [default = 4].

       --flames_cal_wavecal.tolerance <float>
              Tolerance of fit. If positive, the tolerance is in pixel units. If negative,
              abs(tolerance) is in wavelength units. Lines with residuals worse than the
              tolerance are excluded from the final fit. Unlike in previous versions, this
              parameter is not corrected for CCD binning.  This rejection based on the absolute
              residual in pixel can be effectively disabled by setting the tolerance to a very
              large number (e.g. 9999). In that case outliers will be rejected using only kappa
              sigma clipping. (float; default: 0.6). The full name of this option for the EsoRex
              configuration file is flames_obs_redchain.flames_cal_wavecal.calibrate.tolerance
              [default = 0.6].

       --flames_cal_wavecal.kappa <float>
              Lines with residuals more then kappa stdev are rejected from the final fit (float;
              default: 4.0). The full name of this option for the EsoRex configuration file is
              flames_obs_redchain.flames_cal_wavecal.calibrate.kappa [default = 4.0].

       --flames_cal_wavecal.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
              flames_obs_redchain.flames_cal_wavecal.rebin.wavestep [default = -1.0].

       --flames_cal_wavecal.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 flames_obs_redchain.flames_cal_wavecal.rebin.scale [default = False].

       --flames_cal_wavecal.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 flames_obs_redchain.flames_cal_wavecal.extract.method [default = average].

       --flames_cal_wavecal.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 flames_obs_redchain.flames_cal_wavecal.extract.kappa [default = 10.0].

       --flames_cal_wavecal.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 flames_obs_redchain.flames_cal_wavecal.extract.chunk
              [default = 32].

       --flames_cal_wavecal.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
              flames_obs_redchain.flames_cal_wavecal.extract.profile [default = auto].

       --flames_cal_wavecal.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
              flames_obs_redchain.flames_cal_wavecal.extract.skymethod [default = optimal].

       --flames_cal_wavecal.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 flames_obs_redchain.flames_cal_wavecal.extract.oversample [default = -1].

       --flames_cal_wavecal.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 flames_obs_redchain.flames_cal_wavecal.extract.best [default = True].

       --flames_cal_prep_sff_ofpos.ext_method <str>
              Extraction method (str; default: ´opt´). The full name of this option for the
              EsoRex configuration file is
              flames_obs_redchain.flames_cal_prep_sff_ofpos.ext_method [default = opt].

       --flames_cal_prep_sff_ofpos.bias_method <str>
              Bias subtraction method, M for master bias frame, N for no bias subtraction, V to
              subtract a constant bias level defined by the parameter bias_value (str; default:
              ´M´). The full name of this option for the EsoRex configuration file is
              flames_obs_redchain.flames_cal_prep_sff_ofpos.bias_method [default = M].

       --flames_cal_prep_sff_ofpos.bias_value <int>
              Bias value (only if bias_method = V) (int; default: 200). The full name of this
              option for the EsoRex configuration file is
              flames_obs_redchain.flames_cal_prep_sff_ofpos.bias_value [default = 200].

       --flames_cal_prep_sff_ofpos.filter_switch <str>
              Filter switch (str; default: ´none´). The full name of this option for the EsoRex
              configuration file is flames_obs_redchain.flames_cal_prep_sff_ofpos.filter_switch
              [default = none].

       --flames_cal_prep_sff_ofpos.sat_thr <int>
              Saturation threshold (int; default: 55000). The full name of this option for the
              EsoRex configuration file is flames_obs_redchain.flames_cal_prep_sff_ofpos.sat_thr
              [default = 55000].

       --flames_cal_prep_sff_ofpos.fileprep <bool>
              Slitff* and Fibreff* file preparation. If fast extraction method is used it should
              be set to FALSE (bool; default: True). The full name of this option for the EsoRex
              configuration file is flames_obs_redchain.flames_cal_prep_sff_ofpos.fileprep
              [default = True].

       --flames_cal_prep_sff_ofpos.cubify <bool>
              Cubify switch (bool; default: True). The full name of this option for the EsoRex
              configuration file is flames_obs_redchain.flames_cal_prep_sff_ofpos.cubify [default
              = True].

       --flames_cal_prep_sff_ofpos.save_flat_size <int>
              To be sure to use the flat part of a slit flatsone may need to subtract this bit.
              The default value -1, is used for automatic setting: if WCEN=520 save_flat_size=0,
              else save_flat_size=2. Values explicitly set by user overwrite this rule. (int;
              default: -1). The full name of this option for the EsoRex configuration file is
              flames_obs_redchain.flames_cal_prep_sff_ofpos.save_flat_size [default = -1].

       --flames_cal_prep_sff_ofpos.clean_tmp_products <bool>
              Input data format (bool; default: False). The full name of this option for the
              EsoRex configuration file is
              flames_obs_redchain.flames_cal_prep_sff_ofpos.clean_tmp_products [default = False].

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

       --uves_cal_mdark.klow <float>
              Kappa used to clip low level values, when method is set to ´mean´ (float; default:
              5.0). The full name of this option for the EsoRex configuration file is
              flames_obs_redchain.uves_cal_mdark.klow [default = 5.0].

       --uves_cal_mdark.khigh <float>
              Kappa used to clip high level values, when method is set to ´mean´ (float; default:
              5.0). The full name of this option for the EsoRex configuration file is
              flames_obs_redchain.uves_cal_mdark.khigh [default = 5.0].

       --uves_cal_mdark.niter <int>
              Number of kappa sigma iterations, when method is set to ´mean´  (int; default: 5).
              The full name of this option for the EsoRex configuration file is
              flames_obs_redchain.uves_cal_mdark.niter [default = 5].

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

       --uves_cal_mdark.klow <float>
              Kappa used to clip low level values, when method is set to ´mean´ (float; default:
              5.0). The full name of this option for the EsoRex configuration file is
              flames_obs_redchain.uves_cal_mdark.klow [default = 5.0].

       --uves_cal_mdark.khigh <float>
              Kappa used to clip high level values, when method is set to ´mean´ (float; default:
              5.0). The full name of this option for the EsoRex configuration file is
              flames_obs_redchain.uves_cal_mdark.khigh [default = 5.0].

       --uves_cal_mdark.niter <int>
              Number of kappa sigma iterations, when method is set to ´mean´  (int; default: 5).
              The full name of this option for the EsoRex configuration file is
              flames_obs_redchain.uves_cal_mdark.niter [default = 5].

       --uves_cal_mdark.qc_dark.reg.num_x <int>
              Number of regions along the X axis (where mean/med/rms are computed).  (int;
              default: 4). The full name of this option for the EsoRex configuration file is
              flames_obs_redchain.uves_cal_mdark.qc_dark.reg.num_x [default = 4].

       --uves_cal_mdark.qc_dark.reg.num_y <int>
              Number of regions along the Y axis(where mean/med/rms are computed).  (int;
              default: 4). The full name of this option for the EsoRex configuration file is
              flames_obs_redchain.uves_cal_mdark.qc_dark.reg.num_y [default = 4].

       --uves_cal_mdark.qc_dark.reg.box_sx <int>
              Region X size [pix] (int; default: 100). The full name of this option for the
              EsoRex configuration file is flames_obs_redchain.uves_cal_mdark.qc_dark.reg.box_sx
              [default = 100].

       --uves_cal_mdark.qc_dark.reg.box_sy <int>
              Region Y size [pix] (int; default: 100). The full name of this option for the
              EsoRex configuration file is flames_obs_redchain.uves_cal_mdark.qc_dark.reg.box_sy
              [default = 100].

       --uves_cal_mdark.qc_dark.reg.border_x <int>
              X distance between the left hand side of the detector and the left hand side of the
              region [pix] (int; default: 100). The full name of this option for the EsoRex
              configuration file is flames_obs_redchain.uves_cal_mdark.qc_dark.reg.border_x
              [default = 100].

       --uves_cal_mdark.qc_dark.reg.border_y <int>
              X distance between the left hand side of the detector and the left hand side of the
              region [pix] (int; default: 100). The full name of this option for the EsoRex
              configuration file is flames_obs_redchain.uves_cal_mdark.qc_dark.reg.border_y
              [default = 100].

       --uves_cal_mdark.qc_dark.reg.when <int>
              When QC analysis is performed. 0: on each raw frame or 1: on the master frame (int;
              default: 0). The full name of this option for the EsoRex configuration file is
              flames_obs_redchain.uves_cal_mdark.qc_dark.reg.when [default = 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_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_tflat(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

       flames_obs_redchain 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