.TH XSH_SCIRED_SLIT_STARE "7" "2.5.2" "xsh_scired_slit_stare" "xshoo recipes"
.SH NAME
xsh_scired_slit_stare \- Reduce science exposure in SLIT configuration and stare mode

.SH SYNOPSIS
esorex
.B xsh_scired_slit_stare
[OPTIONS] FILE.sof

.SH 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

.SH OPTIONS
.TP
\fB\-\-keep\-temp\fR \fI<str>\fR
If \'no\', temporary files are deleted. (str; default: \'no\'). The full name of this option for the EsoRex configuration
file is \fBxsh.xsh_scired_slit_stare.keep\-temp\fR [default = \fIno\fR].
.TP
\fB\-\-debug\-level\fR \fI<str>\fR
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 \fBxsh.xsh_scired_slit_stare.debug\-level\fR [default = \fInone\fR].
.TP
\fB\-\-time\-stamp\fR \fI<bool>\fR
Add timestamp to product file name. (bool; default: False). The full name of this option for the EsoRex configuration
file is \fBxsh.xsh_scired_slit_stare.time\-stamp\fR [default = \fIFalse\fR].
.TP
\fB\-\-decode\-bp\fR \fI<long>\fR
Integer representation of the bits to be considered bad when decoding
the bad pixel mask pixel values. (long; default: 2144337919). The full name of this option for the EsoRex configuration
file is \fBxsh.xsh_scired_slit_stare.decode\-bp\fR [default = \fI2144337919\fR].
.TP
\fB\-\-pre\-overscan\-corr\fR \fI<long>\fR
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 \fBxsh.xsh_scired_slit_stare.pre\-overscan\-corr\fR [default = \fI1\fR].
.TP
\fB\-\-stack\-method\fR \fI<str>\fR
Method used to build master frame. (str; default: \'median\'). The full name of this option for the EsoRex configuration
file is \fBxsh.xsh_scired_slit_stare.stack\-method\fR [default = \fImedian\fR].
.TP
\fB\-\-klow\fR \fI<float>\fR
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 \fBxsh.xsh_scired_slit_stare.klow\fR [default = \fI5.0\fR].
.TP
\fB\-\-khigh\fR \fI<float>\fR
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 \fBxsh.xsh_scired_slit_stare.khigh\fR [default = \fI5.0\fR].
.TP
\fB\-\-background\-edges\-margin\fR \fI<long>\fR
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 \fBxsh.xsh_scired_slit_stare.background\-edges\-margin\fR [default = \fI1\fR].
.TP
\fB\-\-background\-poly\-deg\-y\fR \fI<long>\fR
Poly mode fit deg along Y. (long; default: 9). The full name of this option for the EsoRex configuration
file is \fBxsh.xsh_scired_slit_stare.background\-poly\-deg\-y\fR [default = \fI9\fR].
.TP
\fB\-\-background\-poly\-deg\-x\fR \fI<long>\fR
Poly mode fit deg along X. (long; default: 9). The full name of this option for the EsoRex configuration
file is \fBxsh.xsh_scired_slit_stare.background\-poly\-deg\-x\fR [default = \fI9\fR].
.TP
\fB\-\-background\-poly\-kappa\fR \fI<float>\fR
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 \fBxsh.xsh_scired_slit_stare.background\-poly\-kappa\fR [default = \fI10.0\fR].
.TP
\fB\-\-removecrhsingle\-sigmalim\fR \fI<float>\fR
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 \fBxsh.xsh_scired_slit_stare.removecrhsingle\-sigmalim\fR [default = \fI20.0\fR].
.TP
\fB\-\-removecrhsingle\-flim\fR \fI<float>\fR
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 \fBxsh.xsh_scired_slit_stare.removecrhsingle\-flim\fR [default = \fI2.0\fR].
.TP
\fB\-\-removecrhsingle\-niter\fR \fI<long>\fR
Max number of iterations (long; default: 4). The full name of this option for the EsoRex configuration
file is \fBxsh.xsh_scired_slit_stare.removecrhsingle\-niter\fR [default = \fI4\fR].
.TP
\fB\-\-rectify\-kernel\fR \fI<str>\fR
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 \fBxsh.xsh_scired_slit_stare.rectify\-kernel\fR [default = \fItanh\fR].
.TP
\fB\-\-rectify\-radius\fR \fI<float>\fR
Rectify Interpolation radius [bin units]. (float; default: 2.0). The full name of this option for the EsoRex configuration
file is \fBxsh.xsh_scired_slit_stare.rectify\-radius\fR [default = \fI2.0\fR].
.TP
\fB\-\-rectify\-bin\-lambda\fR \fI<float>\fR
Wavelength step in the output spectrum [nm] (float; default: \-1.0). The full name of this option for the EsoRex configuration
file is \fBxsh.xsh_scired_slit_stare.rectify\-bin\-lambda\fR [default = \fI\-1.0\fR].
.TP
\fB\-\-rectify\-bin\-slit\fR \fI<float>\fR
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 \fBxsh.xsh_scired_slit_stare.rectify\-bin\-slit\fR [default = \fI\-1.0\fR].
.TP
\fB\-\-localize\-method\fR \fI<str>\fR
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 \fBxsh.xsh_scired_slit_stare.localize\-method\fR [default = \fIMANUAL\fR].
.TP
\fB\-\-localize\-chunk\-nb\fR \fI<long>\fR
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 \fBxsh.xsh_scired_slit_stare.localize\-chunk\-nb\fR [default = \fI10\fR].
.TP
\fB\-\-localize\-thresh\fR \fI<float>\fR
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 \fBxsh.xsh_scired_slit_stare.localize\-thresh\fR [default = \fI0.1\fR].
.TP
\fB\-\-localize\-deg\-lambda\fR \fI<long>\fR
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 \fBxsh.xsh_scired_slit_stare.localize\-deg\-lambda\fR [default = \fI0\fR].
.TP
\fB\-\-localize\-slit\-position\fR \fI<float>\fR
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 \fBxsh.xsh_scired_slit_stare.localize\-slit\-position\fR [default = \fI0.0\fR].
.TP
\fB\-\-localize\-slit\-hheight\fR \fI<float>\fR
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 \fBxsh.xsh_scired_slit_stare.localize\-slit\-hheight\fR [default = \fI2.0\fR].
.TP
\fB\-\-localize\-kappa\fR \fI<float>\fR
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 \fBxsh.xsh_scired_slit_stare.localize\-kappa\fR [default = \fI3.0\fR].
.TP
\fB\-\-localize\-niter\fR \fI<long>\fR
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 \fBxsh.xsh_scired_slit_stare.localize\-niter\fR [default = \fI3\fR].
.TP
\fB\-\-localize\-use\-skymask\fR \fI<bool>\fR
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 \fBxsh.xsh_scired_slit_stare.localize\-use\-skymask\fR [default = \fIFalse\fR].
.TP
\fB\-\-sky\-subtract\fR \fI<bool>\fR
TRUE to use subtract sky single. (bool; default: True). The full name of this option for the EsoRex configuration
file is \fBxsh.xsh_scired_slit_stare.sky\-subtract\fR [default = \fITrue\fR].
.TP
\fB\-\-sky\-bspline\-nbkpts\-first\fR \fI<long>\fR
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 \fBxsh.xsh_scired_slit_stare.sky\-bspline\-nbkpts\-first\fR [default = \fI3000\fR].
.TP
\fB\-\-sky\-bspline\-nbkpts\-second\fR \fI<long>\fR
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 \fBxsh.xsh_scired_slit_stare.sky\-bspline\-nbkpts\-second\fR [default = \fI3000\fR].
.TP
\fB\-\-sky\-bspline\-order\fR \fI<long>\fR
Bezier spline order (long; default: 7). The full name of this option for the EsoRex configuration
file is \fBxsh.xsh_scired_slit_stare.sky\-bspline\-order\fR [default = \fI7\fR].
.TP
\fB\-\-sky\-bspline\-niter\fR \fI<long>\fR
Nb of iterations (long; default: 20). The full name of this option for the EsoRex configuration
file is \fBxsh.xsh_scired_slit_stare.sky\-bspline\-niter\fR [default = \fI20\fR].
.TP
\fB\-\-sky\-bspline\-kappa\fR \fI<float>\fR
Kappa value used to kappa\-sigma\-clip object (float; default: 5.0). The full name of this option for the EsoRex configuration
file is \fBxsh.xsh_scired_slit_stare.sky\-bspline\-kappa\fR [default = \fI5.0\fR].
.TP
\fB\-\-sky\-method\fR \fI<str>\fR
Sky subtract Method (BSPLINE, MEDIAN) (str; default: \'MEDIAN\'). The full name of this option for the EsoRex configuration
file is \fBxsh.xsh_scired_slit_stare.sky\-method\fR [default = \fIMEDIAN\fR].
.TP
\fB\-\-bspline\-sampling\fR \fI<str>\fR
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 \fBxsh.xsh_scired_slit_stare.bspline\-sampling\fR [default = \fIFINE\fR].
.TP
\fB\-\-sky\-median\-hsize\fR \fI<long>\fR
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 \fBxsh.xsh_scired_slit_stare.sky\-median\-hsize\fR [default = \fI20\fR].
.TP
\fB\-\-sky\-slit\-edges\-mask\fR \fI<float>\fR
Size of edges mask in arcsec (float; default: 0.5). The full name of this option for the EsoRex configuration
file is \fBxsh.xsh_scired_slit_stare.sky\-slit\-edges\-mask\fR [default = \fI0.5\fR].
.TP
\fB\-\-sky\-position1\fR \fI<float>\fR
Central position of the sky window #1 [arcsec] (float; default: 0.0). The full name of this option for the EsoRex configuration
file is \fBxsh.xsh_scired_slit_stare.sky\-position1\fR [default = \fI0.0\fR].
.TP
\fB\-\-sky\-hheight1\fR \fI<float>\fR
Half size of sky window #1 [arcsec] (float; default: 0.0). The full name of this option for the EsoRex configuration
file is \fBxsh.xsh_scired_slit_stare.sky\-hheight1\fR [default = \fI0.0\fR].
.TP
\fB\-\-sky\-position2\fR \fI<float>\fR
Central position of the sky window #2 [arcsec] (float; default: 0.0). The full name of this option for the EsoRex configuration
file is \fBxsh.xsh_scired_slit_stare.sky\-position2\fR [default = \fI0.0\fR].
.TP
\fB\-\-sky\-hheight2\fR \fI<float>\fR
Half size of the sky window #2 [arcsec] (float; default: 0.0). The full name of this option for the EsoRex configuration
file is \fBxsh.xsh_scired_slit_stare.sky\-hheight2\fR [default = \fI0.0\fR].
.TP
\fB\-\-stdextract\-interp\-hsize\fR \fI<long>\fR
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 \fBxsh.xsh_scired_slit_stare.stdextract\-interp\-hsize\fR [default = \fI30\fR].
.TP
\fB\-\-do\-optextract\fR \fI<bool>\fR
TRUE if we do the optimal extraction (bool; default: False). The full name of this option for the EsoRex configuration
file is \fBxsh.xsh_scired_slit_stare.do\-optextract\fR [default = \fIFalse\fR].
.TP
\fB\-\-optextract\-oversample\fR \fI<long>\fR
Oversample factor for the science image (long; default: 5). The full name of this option for the EsoRex configuration
file is \fBxsh.xsh_scired_slit_stare.optextract\-oversample\fR [default = \fI5\fR].
.TP
\fB\-\-optextract\-box\-half\-size\fR \fI<long>\fR
Extraction box [pixel] (long; default: 10). The full name of this option for the EsoRex configuration
file is \fBxsh.xsh_scired_slit_stare.optextract\-box\-half\-size\fR [default = \fI10\fR].
.TP
\fB\-\-optextract\-chunk\-size\fR \fI<long>\fR
Chunk size [bin] (long; default: 50). The full name of this option for the EsoRex configuration
file is \fBxsh.xsh_scired_slit_stare.optextract\-chunk\-size\fR [default = \fI50\fR].
.TP
\fB\-\-optextract\-step\-lambda\fR \fI<float>\fR
Lambda step [nm] (float; default: 0.02). The full name of this option for the EsoRex configuration
file is \fBxsh.xsh_scired_slit_stare.optextract\-step\-lambda\fR [default = \fI0.02\fR].
.TP
\fB\-\-optextract\-clip\-kappa\fR \fI<float>\fR
Kappa for cosmics ray hits rejection (float; default: 3.0). The full name of this option for the EsoRex configuration
file is \fBxsh.xsh_scired_slit_stare.optextract\-clip\-kappa\fR [default = \fI3.0\fR].
.TP
\fB\-\-optextract\-clip\-frac\fR \fI<float>\fR
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 \fBxsh.xsh_scired_slit_stare.optextract\-clip\-frac\fR [default = \fI0.4\fR].
.TP
\fB\-\-optextract\-clip\-niter\fR \fI<long>\fR
Maximum number of iterations for cosmics ray hits rejection (long;
default: 2). The full name of this option for the EsoRex configuration
file is \fBxsh.xsh_scired_slit_stare.optextract\-clip\-niter\fR [default = \fI2\fR].
.TP
\fB\-\-optextract\-niter\fR \fI<long>\fR
Number of iterations (long; default: 1). The full name of this option for the EsoRex configuration
file is \fBxsh.xsh_scired_slit_stare.optextract\-niter\fR [default = \fI1\fR].
.TP
\fB\-\-optextract\-method\fR \fI<str>\fR
Extraction method GAUSSIAN | GENERAL (str; default: \'GAUSSIAN\'). The full name of this option for the EsoRex configuration
file is \fBxsh.xsh_scired_slit_stare.optextract\-method\fR [default = \fIGAUSSIAN\fR].
.TP
\fB\-\-cut\-uvb\-spectrum\fR \fI<bool>\fR
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 \fBxsh.xsh_scired_slit_stare.cut\-uvb\-spectrum\fR [default = \fITrue\fR].
.TP
\fB\-\-generate\-SDP\-format\fR \fI<bool>\fR
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 \fBxsh.xsh_scired_slit_stare.generate\-SDP\-format\fR [default = \fIFalse\fR].
.TP
\fB\-\-dummy\-association\-keys\fR \fI<long>\fR
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 \fBxsh.xsh_scired_slit_stare.dummy\-association\-keys\fR [default = \fI0\fR].

.PP
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.

.SH SEE ALSO
The full documentation for the xshoo pipeline can be downloaded as 
a PDF file using the following URL:
.IP
.B ftp://ftp.eso.org/pub/dfs/pipelines/xshoo/xshoo\-pipeline\-manual\-12.1.pdf
.PP
An overview over the existing ESO pipelines can be found on the web page
\fBhttp://www.eso.org/sci/software/pipelines/\fR.
.PP
Basic documentation about the EsoRex program can be found at the esorex (1) 
man page.
.PP
It is possible to call the pipelines from python using the python\-cpl package.
See \fBhttp://packages.python.org/python\-cpl/index.html\fR for further
information.
.PP
The other recipes of the xshoo pipeline are
.IR xsh_cfg_recover (7),
.IR xsh_lingain (7),
.IR xsh_geom_ifu (7),
.IR xsh_wavecal (7),
.IR xsh_scired_slit_nod (7),
.IR xsh_respon_slit_nod (7),
.IR xsh_mdark (7),
.IR xsh_respon_slit_offset (7),
.IR xsh_orderpos (7),
.IR xsh_scired_ifu_stare_drl (7),
.IR xsh_scired_ifu_stare (7),
.IR xsh_flexcomp (7),
.IR xsh_scired_ifu_offset_drl (7),
.IR xsh_util_physmod (7),
.IR xsh_respon_slit_stare (7),
.IR xsh_2dmap (7),
.IR xsh_mflat (7),
.IR xsh_mbias (7),
.IR xsh_predict (7),
.IR xsh_scired_ifu_offset (7),
.IR xsh_scired_slit_offset (7)

.SH VERSION
xsh_scired_slit_stare 2.5.2

.SH AUTHOR
P.Goldoni, L.Guglielmi, R. Haigron, F. Royer, D. Bramich, A. Modigliani <amodigli@eso.org>

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

.SH 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