xsh_scired_slit_stare - Reduce science exposure in SLIT
configuration and stare mode
esorex xsh_scired_slit_stare [OPTIONS] FILE.sof
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_MERGE1D_SLIT_arm)
- [OPTIONAL] An atmospheric extinction table (Tag = ATMOS_EXT_arm)
- [OPTIONAL] A telluric mask (Tag = TELL_MASK_arm)
- [OPTIONAL] The instrument master response table (Tag =
MRESPONSE_MERGE1D_SLIT_arm).
If both master and individual response are provided the individual response
is preferred.
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
- --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
<int>
- 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.
(int; 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
<int>
- pre-overscan correction.0: no correction1: mean overscan correction2: mean
prescan correction3: (mean pre+mean overscan)/2 correction (int; 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
<int>
- X margin to order edge to define background sampling points (int; 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
<int>
- Poly mode fit deg along Y. (int; 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
<int>
- Poly mode fit deg along X. (int; 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
<int>
- Max number of iterations (int; 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
<int>
- Number of chunks in the full spectrum to localize the object (int;
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
<int>
- Degree in lambda in the localization polynomial expression slit=f(lambda),
used only for MAXIMUM and GAUSSIAN (int; 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
<int>
- Number of iterations for sigma clipping in the localization polynomial fit
(int; 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
<int>
- Nb of break points for Bezier curve fitting (without localization) (int;
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
<int>
- Nb of break points for Bezier curve fitting (with localization) (int;
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
<int>
- Bezier spline order (int; 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
<int>
- Nb of iterations (int; 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, BSPLINE1, BSPLINE2 MEDIAN). BSPLINE is
equivalent to BSPLINE1 (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
<int>
- Half size of the running median. If sky-method=MEDIAN . (int; 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].
- Half size of mask used to define object cross order profile (int; 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].
- Oversample factor for the science image (int; default: 5). The full name
of this option for the EsoRex configuration file is
xsh.xsh_scired_slit_stare.optextract-oversample [default =
5].
- Extraction box [pixel] (int; 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].
- Chunk size [bin] (int; default: 50). The full name of this option for the
EsoRex configuration file is
xsh.xsh_scired_slit_stare.optextract-chunk-size [default =
50].
- 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].
- 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].
- 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].
- Maximum number of iterations for cosmics ray hits rejection (int; default:
2). The full name of this option for the EsoRex configuration file is
xsh.xsh_scired_slit_stare.optextract-clip-niter [default =
2].
- Number of iterations (int; default: 1). The full name of this option for
the EsoRex configuration file is
xsh.xsh_scired_slit_stare.optextract-niter [default =
1].
- 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
<int>
- Sets the number of dummy (empty) ASSONi, ASSOCi and ASSOMi keywords to
create. (int; 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.
The full documentation for the xshoo pipeline can be downloaded as
a PDF file using the following URL:
- ftp://ftp.eso.org/pub/dfs/pipelines/xshoo/xshoo-pipeline-manual-12.1.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 xshoo pipeline are xsh_2dmap(7),
xsh_cfg_recover(7), xsh_flexcomp(7), xsh_geom_ifu(7),
xsh_lingain(7), xsh_mbias(7), xsh_mdark(7),
xsh_mflat(7), xsh_orderpos(7), xsh_predict(7),
xsh_respon_slit_nod(7), xsh_respon_slit_offset(7),
xsh_respon_slit_stare(7), xsh_scired_ifu_offset(7),
xsh_scired_ifu_offset_drl(7), xsh_scired_ifu_stare(7),
xsh_scired_ifu_stare_drl(7), xsh_scired_slit_nod(7),
xsh_scired_slit_offset(7), xsh_util_physmod(7),
xsh_wavecal(7)
xsh_scired_slit_stare 3.2.0
P.Goldoni, L.Guglielmi, R. Haigron, F. Royer, D. Bramich, A.
Modigliani <amodigli@eso.org>
Please report any problems to amodigli@eso.org. Alternatively, you
may send a report to the ESO User Support Department
<usd-help@eso.org>.
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