Provided by: cpl-plugin-xshoo-doc_3.5.3+dfsg-1build1_all 
NAME
xsh_mflat - Create the master flat and the orders edges traces table frames
SYNOPSIS
esorex xsh_mflat [OPTIONS] FILE.sof
DESCRIPTION
This recipe creates the master flat and the orders edges traces table frames.
Input Frames :
- [UVB] A set of n RAW frames (Format = RAW, n>=3, Tag = FLAT_D2_mode_UVB,
mode=SLIT/IFU)
- [UVB] A set of n RAW frames (Format = RAW, n>=3, Tag = FLAT_QTH_mode_UVB)
- [VIS] A set of n RAW frames (Format = RAW, n>=3, Tag = FLAT_mode_VIS)
- [NIR] A set of n x n RAW frames ((Format = RAW, n>=3, Tag = FLAT_mode_NIR_ON,
FLAT_mode_NIR_OFF)
- A spectral format table (Format = PRE, Tag = SPECTRAL_FORMAT_TAB_arm)
- An order table (Format = TABLE, Tag = ORDER_TAB_CENTR_arm)
- [UVB,VIS] A master bias (Format = PRE, Tag = MASTER_BIAS_arm)
- [OPTIONAL] A map of reference bad pixel (Format = QUP,RAW, Tag = BP_MAP_RP_arm)
- [OPTIONAL] A map of non linear pixel (Format = QUP,RAW, Tag = BP_MAP_NL_arm)
- [OPTIONAL,UVB,VIS] A master dark (Format = PRE, Tag = MASTER_DARK_arm)
Products :
- An updated order table with edge UP and edge LOW (Format = TABLE, TAG =
ORDER_TAB_EDGES_mode_arm)
- A master flat (Format = PRE, PRO.CATG = MASTER_FLAT_mode_arm)
- The inter-order background frame (Format = PRE, PRO.CATG = MFLAT_BACK_mode_arm)
- The inter-order background sampling points grid table
(Format = PRE, PRO.CATG = MFLAT_GRID_BACK_mode_arm)
Prepare the flat frames.
Stack and sigma clip all the flat frames.
Subtract master bias.
Subtract master dark.
Detect order edge.
Subtract background.
Create the Master Flat.
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_mflat.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_mflat.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_mflat.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_mflat.decode-bp [default =
2144337919].
--pre-overscan-corr <int>
pre-overscan correction. 0: no correction 1: mean overscan correction 2: mean
prescan correction 3: (mean pre+mean overscan)/2 correction (int; default: 1). The
full name of this option for the EsoRex configuration file is
xsh.xsh_mflat.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_mflat.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_mflat.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_mflat.khigh [default = 5.0].
--detectorder-edges-search-win-hsize <int>
During extraction the local spatial profile (=cross-order) of the spectrum is
determined by collapsing the 2-dimensional spectrum along the dispersion axis. This
parameter defines the half size of the region across which the spectrum is
collapsed. This parameter affects flagged pixels interpolation. In case of spectrum
gaps the recommended optimal value is: (size_of_gap [nm]/(2*size_of_pixel [nm])+1)
(int; default: 50). The full name of this option for the EsoRex configuration file
is xsh.xsh_mflat.detectorder-edges-search-win-hsize [default = 50].
--detectorder-edges-flux-thresh <float>
Threshold in relative flux (compared to the central flux) below which the order
edges are defined (float; default: 0.4). The full name of this option for the
EsoRex configuration file is xsh.xsh_mflat.detectorder-edges-flux-thresh [default =
0.4].
--detectorder-min-sn <float>
Minimum signal-to-noise ratio at the centroid of the orders (60 for
SLIT-UVB,VIS,NIR, 20 for IFU-UVB,VIS, 4 for IFU-NIR (float; default: -1.0). The
full name of this option for the EsoRex configuration file is
xsh.xsh_mflat.detectorder-min-sn [default = -1.0].
--detectorder-min-order-size-x <int>
Minimum order size in pixels along X direction [60 for UVB,VIS, 40 for NIR] (int;
default: -1). The full name of this option for the EsoRex configuration file is
xsh.xsh_mflat.detectorder-min-order-size-x [default = -1].
--detectorder-chunk-half-size <int>
Half size in pixels of the chunks in Y direction (int; default: 1). The full name
of this option for the EsoRex configuration file is
xsh.xsh_mflat.detectorder-chunk-half-size [default = 1].
--detectorder-slitlet-low-factor <float>
Factor for slitlet on lower edge slitlet (IFU) (float; default: 1.0). The full name
of this option for the EsoRex configuration file is
xsh.xsh_mflat.detectorder-slitlet-low-factor [default = 1.0].
--detectorder-slitlet-up-factor <float>
Factor for slitlet on upper edge (IFU) (float; default: 1.0). The full name of this
option for the EsoRex configuration file is
xsh.xsh_mflat.detectorder-slitlet-up-factor [default = 1.0].
--detectorder-fixed-slice <bool>
If true the size of slitlet is fixed (IFU) (bool; default: True). The full name of
this option for the EsoRex configuration file is
xsh.xsh_mflat.detectorder-fixed-slice [default = True].
--detectorder-slice-trace-method <str>
method adopted for IFU slice tracing (´fixed´ for SLIT and ´sobel´ for IFU): (str;
default: ´auto´). The full name of this option for the EsoRex configuration file is
xsh.xsh_mflat.detectorder-slice-trace-method [default = auto].
--detectorder-qc-mode <bool>
If true allows one to skip edge detection on orders below detectorder- min-sn (oly
for QC mode, not to be set by normal users) (bool; default: False). The full name
of this option for the EsoRex configuration file is
xsh.xsh_mflat.detectorder-qc-mode [default = False].
--detectorder-d2-min-sn <float>
minimum signal noise ratio in D2 lamp frame in order (float; default: 60.0). The
full name of this option for the EsoRex configuration file is
xsh.xsh_mflat.detectorder-d2-min-sn [default = 60.0].
--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_mflat.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_mflat.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_mflat.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_mflat.background-poly-kappa [default = 10.0].
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 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_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_scired_slit_stare(7), xsh_util_physmod(7), xsh_wavecal(7)
VERSION
xsh_mflat 3.5.3
AUTHOR
P.Goldoni, L.Guglielmi, R. Haigron, F. Royer, D. Bramich, A. Modigliani <amodigli@eso.org>
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>.
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