SYNOPSIS

esorex xsh_scired_slit_stare [OPTIONS] FILE.sof

DESCRIPTION

This recipe reduces science exposure in SLIT configuration and stare mode Input Frames :
  - A set of n Science frames ( n == 1 or >=3, Tag = OBJECT_SLIT_STARE_UVB)
  - A spectral format table (Tag = SPECTRAL_FORMAT_TAB_arm)
  - [UVB,VIS] A master bias frame (Tag = MASTER_BIAS_arm)
  - [OPTIONAL]A master dark frame (Tag = MASTER_DARK_arm)
  - A master flat frame (Tag = MASTER_FLAT_SLIT_arm)
  - An order table frame(Tag = ORDER_TAB_EDGES_SLIT_arm)
  - [OPTIONAL] A table with dispersion coefficients (Tag = DISP_TAB_arm,
    required in poly mode
  - [poly mode] A wave solution frame(Tag = WAVE_TAB_2D_arm)
  - [physical model mode] A model cfg table (Format = TABLE, Tag = XSH_MOD_CFG_TAB_arm)
  - [OPTIONAL] A table specifying multiplying factor for break points 
    (Tag = SKY_SUB_BKPTS_arm) to generate
  - [OPTIONAL] A non-linear badpixel map (Tag = BP_MAP_NL_arm)
  - [OPTIONAL] A reference badpixel map (Tag = BP_MAP_RP_arm)
  - [OPTIONAL,physmod mode] A table listing sky line positions (Tag = SKY_LINE_LIST_arm)
    this is used to be able to control quality of sky subtraction, for example
    projecting guess positions on the product SCI_SLIT_STARE_SUB_SKY_arm
  - [OPTIONAL] The instrument response table (Tag = RESPONSE_ORDER1D_SLIT_arm)
  - [OPTIONAL] An atmospheric extinction table (Tag = ATMOS_EXT_arm)
  - [OPTIONAL] A telluric mask (Tag = TELL_MASK_arm) Products :
  - PREFIX_ORDER2D_arm extracted spectrum, order-by-order, 2D
  - PREFIX_ORDER1D_arm extracted spectrum, order-by-order, 1D
  - PREFIX_MERGE2D_arm merged spectrum, 2D
  - PREFIX_MERGE1D_arm merged spectrum, 1D
  - SKY_SLIT_MERGE2D_arm merged spectrum sky, 2D
  - PREFIX_SUB_BACK_SLIT_arm sci frame bias, (dark), inter-order bkg subtracted
  - PREFIX_WAVE_MAP_arm, wave map image
  - PREFIX_SLIT_MAP_arm, slit map image
  - PREFIX_DIVFF_arm as PREFIX_SUB_BACK_SLIT_arm, flat fielded
  - PREFIX_SUB_SKY_arm, as PREFIX_DIVFF_arm, sky subtracted
  - PREFIX_SKY_arm, 2D sky frame
  - PREFIX_SKY_ORD1D_arm, 1D sky image (order-by-order)
  - PREFIX_BACK_SLIT_arm, inter order background image 
  - where PREFIX is SCI, FLUX, TELL if input raw DPR.TYPE contains OBJECT or FLUX or TELLURIC
  - [OPTIONAL, if response and atm ext are provided]  PREFIX_FLUX_ORDER2D_arm (2 dimension)
  - [OPTIONAL, if response and atm ext are provided]  PREFIX_FLUX_ORDER1D_arm (1 dimension)
  - [OPTIONAL, if response and atm ext are provided]  PREFIX_FLUX_MERGE2D_arm (2 dimension)
  - [OPTIONAL, if response and atm ext are provided]  PREFIX_FLUX_MERGE1D_arm (1 dimension)
  - PREFIX_ON_arm bias (dark) subtracted sci frame

OPTIONS

--keep-temp <str>

If 'no', temporary files are deleted. (str; default: 'no'). The full name of this option for the EsoRex configuration file is xsh.xsh_scired_slit_stare.keep-temp [default = no].

--debug-level <str>

Additional xshooter debug level. One of 'none', 'low', 'medium', 'high' (str; default: 'none'). The full name of this option for the EsoRex configuration file is xsh.xsh_scired_slit_stare.debug-level [default = none].

--time-stamp <bool>

Add timestamp to product file name. (bool; default: False). The full name of this option for the EsoRex configuration file is xsh.xsh_scired_slit_stare.time-stamp [default = False].

--decode-bp <long>

Integer representation of the bits to be considered bad when decoding the bad pixel mask pixel values. Most frequent codes relevant for the user: 0: good pixel, 8: pick-up noise, 16: cosmic-ray removed, 32: cosmic-ray unremoved, 128: calibration file defect, 256: hot pixel, 512: dark pixel, 4096: A/D converted saturation, 32768: non linear pixel, 1048576: extrapolated flux in NIR, 4194304: Interpolated flux during extraction. (long; default: 2144337919). The full name of this option for the EsoRex configuration file is xsh.xsh_scired_slit_stare.decode-bp [default = 2144337919].

--pre-overscan-corr <long>

pre-overscan correction.0: no correction1: mean overscan correction2: mean prescan correction3: (mean pre+mean overscan)/2 correction (long; default: 1). The full name of this option for the EsoRex configuration file is xsh.xsh_scired_slit_stare.pre-overscan-corr [default = 1].

--stack-method <str>

Method used to build master frame. (str; default: 'median'). The full name of this option for the EsoRex configuration file is xsh.xsh_scired_slit_stare.stack-method [default = median].

--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 xsh.xsh_scired_slit_stare.klow [default = 5.0].

--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 xsh.xsh_scired_slit_stare.khigh [default = 5.0].

--background-edges-margin <long>

X margin to order edge to define background sampling points (long; default: 1). The full name of this option for the EsoRex configuration file is xsh.xsh_scired_slit_stare.background-edges-margin [default = 1].

--background-poly-deg-y <long>

Poly mode fit deg along Y. (long; default: 9). The full name of this option for the EsoRex configuration file is xsh.xsh_scired_slit_stare.background-poly-deg-y [default = 9].

--background-poly-deg-x <long>

Poly mode fit deg along X. (long; default: 9). The full name of this option for the EsoRex configuration file is xsh.xsh_scired_slit_stare.background-poly-deg-x [default = 9].

--background-poly-kappa <float>

Poly mode kappa value of kappa-sigma-clip outliers removal. (float; default: 10.0). The full name of this option for the EsoRex configuration file is xsh.xsh_scired_slit_stare.background-poly-kappa [default = 10.0].

--removecrhsingle-sigmalim <float>

Poisson fluctuation threshold to flag CRHs (see van Dokkum, PASP,113,2001,p1420-27) (float; default: 20.0). The full name of this option for the EsoRex configuration file is xsh.xsh_scired_slit_stare.removecrhsingle-sigmalim [default = 20.0].

--removecrhsingle-flim <float>

Minimum contrast between the Laplacian image and the fine structure image that a point must have to be flagged as CRH. (see van Dokkum, PASP,113,2001,p1420-27) (float; default: 2.0). The full name of this option for the EsoRex configuration file is xsh.xsh_scired_slit_stare.removecrhsingle-flim [default = 2.0].

--removecrhsingle-niter <long>

Max number of iterations (long; default: 4). The full name of this option for the EsoRex configuration file is xsh.xsh_scired_slit_stare.removecrhsingle-niter [default = 4].

--rectify-kernel <str>

Name of the Interpolation Kernel Used. Possible values are: tanh, sinc, sinc2, lanczos, hamming, hann. (str; default: 'tanh'). The full name of this option for the EsoRex configuration file is xsh.xsh_scired_slit_stare.rectify-kernel [default = tanh].

--rectify-radius <float>

Rectify Interpolation radius [bin units]. (float; default: 2.0). The full name of this option for the EsoRex configuration file is xsh.xsh_scired_slit_stare.rectify-radius [default = 2.0].

--rectify-bin-lambda <float>

Wavelength step in the output spectrum [nm] (float; default: -1.0). The full name of this option for the EsoRex configuration file is xsh.xsh_scired_slit_stare.rectify-bin-lambda [default = -1.0].

--rectify-bin-slit <float>

Spatial step along the slit in the output spectrum [arcsec] (float; default: -1.0). The full name of this option for the EsoRex configuration file is xsh.xsh_scired_slit_stare.rectify-bin-slit [default = -1.0].

--localize-method <str>

Localization method (MANUAL, MAXIMUM, GAUSSIAN) used to detect the object centroid and height on the slit (str; default: 'MANUAL'). The full name of this option for the EsoRex configuration file is xsh.xsh_scired_slit_stare.localize-method [default = MANUAL].

--localize-chunk-nb <long>

Number of chunks in the full spectrum to localize the object (long; default: 10). The full name of this option for the EsoRex configuration file is xsh.xsh_scired_slit_stare.localize-chunk-nb [default = 10].

--localize-thresh <float>

Threshold relative to the peak intensity below which the edges of the object are detected for MAXIMUM localization (float; default: 0.1). The full name of this option for the EsoRex configuration file is xsh.xsh_scired_slit_stare.localize-thresh [default = 0.1].

--localize-deg-lambda <long>

Degree in lambda in the localization polynomial expression slit=f(lambda), used only for MAXIMUM and GAUSSIAN (long; default: 0). The full name of this option for the EsoRex configuration file is xsh.xsh_scired_slit_stare.localize-deg-lambda [default = 0].

--localize-slit-position <float>

Object position on the slit for MANUAL localization [arcsec] (float; default: 0.0). The full name of this option for the EsoRex configuration file is xsh.xsh_scired_slit_stare.localize-slit-position [default = 0.0].

--localize-slit-hheight <float>

Object half height on the slit for MANUAL localization [arcsec] (float; default: 2.0). The full name of this option for the EsoRex configuration file is xsh.xsh_scired_slit_stare.localize-slit-hheight [default = 2.0].

--localize-kappa <float>

Kappa value for sigma clipping in the localization polynomial fit (float; default: 3.0). The full name of this option for the EsoRex configuration file is xsh.xsh_scired_slit_stare.localize-kappa [default = 3.0].

--localize-niter <long>

Number of iterations for sigma clipping in the localization polynomial fit (long; default: 3). The full name of this option for the EsoRex configuration file is xsh.xsh_scired_slit_stare.localize-niter [default = 3].

--localize-use-skymask <bool>

TRUE if we want to mask sky lines using SKY_LINE_LIST file. (bool; default: False). The full name of this option for the EsoRex configuration file is xsh.xsh_scired_slit_stare.localize-use-skymask [default = False].

--sky-subtract <bool>

TRUE to use subtract sky single. (bool; default: True). The full name of this option for the EsoRex configuration file is xsh.xsh_scired_slit_stare.sky-subtract [default = True].

--sky-bspline-nbkpts-first <long>

Nb of break points for Bezier curve fitting (without localization) (long; default: 3000). The full name of this option for the EsoRex configuration file is xsh.xsh_scired_slit_stare.sky-bspline-nbkpts-first [default = 3000].

--sky-bspline-nbkpts-second <long>

Nb of break points for Bezier curve fitting (with localization) (long; default: 3000). The full name of this option for the EsoRex configuration file is xsh.xsh_scired_slit_stare.sky-bspline-nbkpts-second [default = 3000].

--sky-bspline-order <long>

Bezier spline order (long; default: 7). The full name of this option for the EsoRex configuration file is xsh.xsh_scired_slit_stare.sky-bspline-order [default = 7].

--sky-bspline-niter <long>

Nb of iterations (long; default: 20). The full name of this option for the EsoRex configuration file is xsh.xsh_scired_slit_stare.sky-bspline-niter [default = 20].

--sky-bspline-kappa <float>

Kappa value used to kappa-sigma-clip object (float; default: 5.0). The full name of this option for the EsoRex configuration file is xsh.xsh_scired_slit_stare.sky-bspline-kappa [default = 5.0].

--sky-method <str>

Sky subtract Method (BSPLINE, MEDIAN) (str; default: 'MEDIAN'). The full name of this option for the EsoRex configuration file is xsh.xsh_scired_slit_stare.sky-method [default = MEDIAN].

--bspline-sampling <str>

BSPLINE sampling. UNIFORM-uses the user defined nbkpts value, corrected for binning, for all orders. FINE: multiplies the user defined nbkpts value, corrected for binning, by a hard coded coefficient optimized on each arm-order) (str; default: 'FINE'). The full name of this option for the EsoRex configuration file is xsh.xsh_scired_slit_stare.bspline-sampling [default = FINE].

--sky-median-hsize <long>

Half size of the running median. If sky-method=MEDIAN . (long; default: 20). The full name of this option for the EsoRex configuration file is xsh.xsh_scired_slit_stare.sky-median-hsize [default = 20].

--sky-slit-edges-mask <float>

Size of edges mask in arcsec (float; default: 0.5). The full name of this option for the EsoRex configuration file is xsh.xsh_scired_slit_stare.sky-slit-edges-mask [default = 0.5].

--sky-position1 <float>

Central position of the sky window #1 [arcsec] (float; default: 0.0). The full name of this option for the EsoRex configuration file is xsh.xsh_scired_slit_stare.sky-position1 [default = 0.0].

--sky-hheight1 <float>

Half size of sky window #1 [arcsec] (float; default: 0.0). The full name of this option for the EsoRex configuration file is xsh.xsh_scired_slit_stare.sky-hheight1 [default = 0.0].

--sky-position2 <float>

Central position of the sky window #2 [arcsec] (float; default: 0.0). The full name of this option for the EsoRex configuration file is xsh.xsh_scired_slit_stare.sky-position2 [default = 0.0].

--sky-hheight2 <float>

Half size of the sky window #2 [arcsec] (float; default: 0.0). The full name of this option for the EsoRex configuration file is xsh.xsh_scired_slit_stare.sky-hheight2 [default = 0.0].

--stdextract-interp-hsize <long>

Half size of mask used to define object cross order profile (long; default: 30). The full name of this option for the EsoRex configuration file is xsh.xsh_scired_slit_stare.stdextract-interp-hsize [default = 30].

--do-optextract <bool>

TRUE if we do the optimal extraction (bool; default: False). The full name of this option for the EsoRex configuration file is xsh.xsh_scired_slit_stare.do-optextract [default = False].

--optextract-oversample <long>

Oversample factor for the science image (long; default: 5). The full name of this option for the EsoRex configuration file is xsh.xsh_scired_slit_stare.optextract-oversample [default = 5].

--optextract-box-half-size <long>

Extraction box [pixel] (long; default: 10). The full name of this option for the EsoRex configuration file is xsh.xsh_scired_slit_stare.optextract-box-half-size [default = 10].

--optextract-chunk-size <long>

Chunk size [bin] (long; default: 50). The full name of this option for the EsoRex configuration file is xsh.xsh_scired_slit_stare.optextract-chunk-size [default = 50].

--optextract-step-lambda <float>

Lambda step [nm] (float; default: 0.02). The full name of this option for the EsoRex configuration file is xsh.xsh_scired_slit_stare.optextract-step-lambda [default = 0.02].

--optextract-clip-kappa <float>

Kappa for cosmics ray hits rejection (float; default: 3.0). The full name of this option for the EsoRex configuration file is xsh.xsh_scired_slit_stare.optextract-clip-kappa [default = 3.0].

--optextract-clip-frac <float>

Maximum bad pixels fraction for cosmics ray hits rejection (float; default: 0.4). The full name of this option for the EsoRex configuration file is xsh.xsh_scired_slit_stare.optextract-clip-frac [default = 0.4].

--optextract-clip-niter <long>

Maximum number of iterations for cosmics ray hits rejection (long; default: 2). The full name of this option for the EsoRex configuration file is xsh.xsh_scired_slit_stare.optextract-clip-niter [default = 2].

--optextract-niter <long>

Number of iterations (long; default: 1). The full name of this option for the EsoRex configuration file is xsh.xsh_scired_slit_stare.optextract-niter [default = 1].

--optextract-method <str>

Extraction method GAUSSIAN | GENERAL (str; default: 'GAUSSIAN'). The full name of this option for the EsoRex configuration file is xsh.xsh_scired_slit_stare.optextract-method [default = GAUSSIAN].

--cut-uvb-spectrum <bool>

TRUE if recipe cuts the UVB spectrum at 556 nm (dichroich) (bool; default: True). The full name of this option for the EsoRex configuration file is xsh.xsh_scired_slit_stare.cut-uvb-spectrum [default = True].

--generate-SDP-format <bool>

TRUE if additional files should be generated in Science Data Product (SDP) format. (bool; default: False). The full name of this option for the EsoRex configuration file is xsh.xsh_scired_slit_stare.generate-SDP-format [default = False].

--dummy-association-keys <long>

Sets the number of dummy (empty) ASSONi, ASSOCi and ASSOMi keywords to create. (long; default: 0). The full name of this option for the EsoRex configuration file is xsh.xsh_scired_slit_stare.dummy-association-keys [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.

VERSION

xsh_scired_slit_stare 2.7.1

AUTHOR

P.Goldoni, L.Guglielmi, R. Haigron, F. Royer, D. Bramich, A. Modigliani <[email protected]>

LICENSE

This file is part of the X-shooter Instrument Pipeline Copyright (C) 2006 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