Provided by: cpl-plugin-xshoo-doc_3.5.3+dfsg-1build1_all 
NAME
xsh_lingain - Computes detector's gain/linearity-map
SYNOPSIS
esorex xsh_lingain [OPTIONS] FILE.sof
DESCRIPTION
This recipe computes detector linearity coefficients and gain Input Frames :
arm = UVB-VIS:
- A set of n RAW linearity frames (Format=RAW, n >=8, Tag = LINEARITY_arm_ON)
- A set of n RAW bias frames (Format=RAW, n >=1, Tag = LINEARITY_arm_OFF)
arm = NIR:
- A set of n RAW linearity on frames (Format=RAW, n >=8, Tag = LINEARITY_arm_ON)
- A set of n RAW linearity off frames (Format=RAW, n >=8, Tag = LINEARITY_arm_OFF)
- [OPTIONAL] a static bad pixel map (PRO.CATG=BP_MAP_RP_arm)
Note: on and off frames are taken in pairs sequence: OFF-ON-ON-OFF,
at least 16 frames.
Products :
- A linearity map table, PRO.CATG = BP_MAP_LIN_NIR
- A gain table, PRO.CATG = GAIN_INFO
- A cube cointaining the linearity coefficients, PRO.CATG = COEFFS_CUBE_arm
- A linearity map image (RAW format), PRO.CATG = RAW_BP_MAP_NL_arm
- A linearity map image (PRE format), PRO.CATG = BP_MAP_NL_arm
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_lingain.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_lingain.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_lingain.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_lingain.decode-bp [default
= 2144337919].
--method <str>
Method to be used when computing GAIN. Methods appliable: <PTC | MED>. By default
PTC method will be applied. (str; default: ´PTC´). The full name of this option for
the EsoRex configuration file is xshoo.xsh_lingain.method [default = PTC].
--order <int>
Polynomial order for the fit (Linearity) (int; default: 3). The full name of this
option for the EsoRex configuration file is xshoo.xsh_lingain.order [default = 3].
--kappa <float>
Kappa value for the kappa-sigma clipping (Gain) (float; default: 3.0). The full
name of this option for the EsoRex configuration file is xshoo.xsh_lingain.kappa
[default = 3.0].
--niter <int>
Number of iterations to compute rms (Gain) (int; default: 5). The full name of this
option for the EsoRex configuration file is xshoo.xsh_lingain.niter [default = 5].
--llx <int>
x coordinate of the lower-left point of the region of interest. If not modified,
default value will be 1. (int; default: -1). The full name of this option for the
EsoRex configuration file is xshoo.xsh_lingain.llx [default = -1].
--lly <int>
y coordinate of the lower-left point of the region of interest. If not modified,
default value will be 1. (int; default: -1). The full name of this option for the
EsoRex configuration file is xshoo.xsh_lingain.lly [default = -1].
--urx <int>
x coordinate of the upper-right point of the region of interest. If not modified,
default value will be X dimension of the input image. (int; default: -1). The full
name of this option for the EsoRex configuration file is xshoo.xsh_lingain.urx
[default = -1].
--ury <int>
y coordinate of the upper-right point of the region of interest. If not modified,
default value will be Y dimension of the input image. (int; default: -1). The full
name of this option for the EsoRex configuration file is xshoo.xsh_lingain.ury
[default = -1].
--ref_level <int>
User reference level (int; default: 10000). The full name of this option for the
EsoRex configuration file is xshoo.xsh_lingain.ref_level [default = 10000].
--intermediate <bool>
De-/Activate intermediate products (bool; default: False). The full name of this
option for the EsoRex configuration file is xshoo.xsh_lingain.intermediate [default
= False].
--autocorr <bool>
De-/Activate the autocorr option (bool; default: False). The full name of this
option for the EsoRex configuration file is xshoo.xsh_lingain.autocorr [default =
False].
--collapse <bool>
De-/Activate the collapse option (bool; default: True). The full name of this
option for the EsoRex configuration file is xshoo.xsh_lingain.collapse [default =
True].
--rescale <bool>
De-/Activate the image rescale option (bool; default: True). The full name of this
option for the EsoRex configuration file is xshoo.xsh_lingain.rescale [default =
True].
--pix2pix <bool>
De-/Activate the computation with pixel to pixel accuracy (bool; default: True).
The full name of this option for the EsoRex configuration file is
xshoo.xsh_lingain.pix2pix [default = True].
--bpmbin <bool>
De-/Activate the binary bpm option (bool; default: False). The full name of this
option for the EsoRex configuration file is xshoo.xsh_lingain.bpmbin [default =
False].
--m <int>
Maximum x-shift for the autocorr (int; default: 26). The full name of this option
for the EsoRex configuration file is xshoo.xsh_lingain.m [default = 26].
--filter <int>
Upper limit of Median flux to be filtered (int; default: -1). The full name of this
option for the EsoRex configuration file is xshoo.xsh_lingain.filter [default =
-1].
--n <int>
Maximum y-shift for the autocorr (int; default: 26). The full name of this option
for the EsoRex configuration file is xshoo.xsh_lingain.n [default = 26].
--tolerance <float>
Tolerance for pair discrimination (float; default: 0.1). The full name of this
option for the EsoRex configuration file is xshoo.xsh_lingain.tolerance [default =
0.1].
--pafgen <bool>
Generate PAF file (bool; default: False). The full name of this option for the
EsoRex configuration file is xshoo.xsh_lingain.pafgen [default = False].
--pafname <str>
Specific name for PAF file (str; default: ´xsh_lingain´). The full name of this
option for the EsoRex configuration file is xshoo.xsh_lingain.pafname [default =
xsh_lingain].
--exts <int>
Activate the multi-exts option. Choose -1 to process all extensions. Choose an
extension number to process the appropriate extension. (int; default: 0). The full
name of this option for the EsoRex configuration file is xshoo.xsh_lingain.exts
[default = 0].
--fpn_method <str>
Method for computing Fixed Pattern Noise (SMOOTH or HISTOGRAM) (str; default:
´HISTOGRAM´). The full name of this option for the EsoRex configuration file is
xshoo.xsh_lingain.fpn_method [default = HISTOGRAM].
--fpn_smooth <int>
template size in pixels for smoothing during FPN computation (only for SMOOTH
method) (int; default: 13). The full name of this option for the EsoRex
configuration file is xshoo.xsh_lingain.fpn_smooth [default = 13].
--saturation_limit <float>
all frames with mean saturation above the limit would not be used in linearity
calculation (float; default: 65535.0). The full name of this option for the EsoRex
configuration file is xshoo.xsh_lingain.saturation_limit [default = 65535.0].
--gain_threshold <float>
all frames with mean flux above the threshold would not be used in gain calculation
(float; default: 65535.0). The full name of this option for the EsoRex
configuration file is xshoo.xsh_lingain.gain_threshold [default = 65535.0].
--coeffs_cube_split <bool>
if TRUE, the recipe writes as many COEFFS_CUBE_Pi (i=0..order) as the value of the
order parameter in a separate file (bool; default: False). The full name of this
option for the EsoRex configuration file is xshoo.xsh_lingain.coeffs_cube_split
[default = False].
--llx1 <int>
x coord of the lower-left point of the first field used for contamination
measurement. If not modified, default value will be 1. (int; default: -1). The
full name of this option for the EsoRex configuration file is
xshoo.xsh_lingain.llx1 [default = -1].
--lly1 <int>
y coord of the lower-left point of the first field used for contamination
measurement. If not modified, default value will be 1. (int; default: -1). The
full name of this option for the EsoRex configuration file is
xshoo.xsh_lingain.lly1 [default = -1].
--urx1 <int>
x coord of the upper-right point of the first field used for contamination
measurement. If not modified, default value will be X dimension of the input image.
(int; default: -1). The full name of this option for the EsoRex configuration file
is xshoo.xsh_lingain.urx1 [default = -1].
--ury1 <int>
y coord of the upper-right point of the first field used for contamination
measurement. If not modified, default value will be Y dimension of the input image.
(int; default: -1). The full name of this option for the EsoRex configuration file
is xshoo.xsh_lingain.ury1 [default = -1].
--llx2 <int>
x coord of the lower-left point of the second field used for contamination
measurement. If not modified, default value will be 1. (int; default: -1). The
full name of this option for the EsoRex configuration file is
xshoo.xsh_lingain.llx2 [default = -1].
--lly2 <int>
y coord of the lower-left point of the second field used for contamination
measurement. If not modified, default value will be 1. (int; default: -1). The
full name of this option for the EsoRex configuration file is
xshoo.xsh_lingain.lly2 [default = -1].
--urx2 <int>
x coord of the upper-right point of the second field used for contamination
measurement. If not modified, default value will be half of the X dimension of the
input image. (int; default: -1). The full name of this option for the EsoRex
configuration file is xshoo.xsh_lingain.urx2 [default = -1].
--ury2 <int>
y coord of the upper-right point of the second field used for contamination
measurement. If not modified, default value will be half of the Y dimension of the
input image. (int; default: -1). The full name of this option for the EsoRex
configuration file is xshoo.xsh_lingain.ury2 [default = -1].
--llx3 <int>
x coord of the lower-left point of the third field used for contamination
measurement. If not modified, default value will be 1. (int; default: -1). The
full name of this option for the EsoRex configuration file is
xshoo.xsh_lingain.llx3 [default = -1].
--lly3 <int>
y coord of the lower-left point of the third field used for contamination
measurement. If not modified, default value will be half of the Y dimension of the
input image. (int; default: -1). The full name of this option for the EsoRex
configuration file is xshoo.xsh_lingain.lly3 [default = -1].
--urx3 <int>
x coord of the upper-right point of the third field used for contamination
measurement. If not modified, default value will be half of X dimension of the
image. (int; default: -1). The full name of this option for the EsoRex
configuration file is xshoo.xsh_lingain.urx3 [default = -1].
--ury3 <int>
y coord of the upper-right point of the third field used for contamination
measurement. If not modified, default value will be Y dimension of the image. (int;
default: -1). The full name of this option for the EsoRex configuration file is
xshoo.xsh_lingain.ury3 [default = -1].
--llx4 <int>
x coord of the lower-left point of the fourth field used for contamination
measurement. If not modified, default value will be half of X dimension of the
image. (int; default: -1). The full name of this option for the EsoRex
configuration file is xshoo.xsh_lingain.llx4 [default = -1].
--lly4 <int>
y coord of the lower-left point of the fourth field used for contamination
measurement. If not modified, default value will be half of the Y dimension of the
input image. (int; default: -1). The full name of this option for the EsoRex
configuration file is xshoo.xsh_lingain.lly4 [default = -1].
--urx4 <int>
x coord of the upper-right point of the fourth field used for contamination
measurement. If not modified, default value will be X dimension of the image. (int;
default: -1). The full name of this option for the EsoRex configuration file is
xshoo.xsh_lingain.urx4 [default = -1].
--ury4 <int>
y coord of the upper-right point of the fourth field used for contamination
measurement. If not modified, default value will be Y dimension of the input image.
(int; default: -1). The full name of this option for the EsoRex configuration file
is xshoo.xsh_lingain.ury4 [default = -1].
--llx5 <int>
x coord of the lower-left point of the fifth field used for contamination
measurement. If not modified, default value will be half of the X dimension of the
input image. (int; default: -1). The full name of this option for the EsoRex
configuration file is xshoo.xsh_lingain.llx5 [default = -1].
--lly5 <int>
y coord of the lower-left point of the fifth field used for contamination
measurement. If not modified, default value will be 1. (int; default: -1). The
full name of this option for the EsoRex configuration file is
xshoo.xsh_lingain.lly5 [default = -1].
--urx5 <int>
x coord of the upper-right point of the fifth field used for contamination
measurement. If not modified, default value will be X dimension of the image. (int;
default: -1). The full name of this option for the EsoRex configuration file is
xshoo.xsh_lingain.urx5 [default = -1].
--ury5 <int>
y coord of the upper-right point of the fifth field used for contamination
measurement. If not modified, default value will be half of Y dimension of the
input image. (int; default: -1). The full name of this option for the EsoRex
configuration file is xshoo.xsh_lingain.ury5 [default = -1].
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_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_scired_slit_stare(7), xsh_util_physmod(7), xsh_wavecal(7)
VERSION
xsh_lingain 3.5.3
AUTHOR
Lander de Bilbao,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