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 <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_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 <long>

Polynomial order for the fit (Linearity) (long; 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 <long>

Number of iterations to compute rms (Gain) (long; default: 5). The full name of this option for the EsoRex configuration file is xshoo.xsh_lingain.niter [default = 5].

--llx <long>

x coordinate of the lower-left point of the region of interest. If not modified, default value will be 1. (long; default: -1). The full name of this option for the EsoRex configuration file is xshoo.xsh_lingain.llx [default = -1].

--lly <long>

y coordinate of the lower-left point of the region of interest. If not modified, default value will be 1. (long; default: -1). The full name of this option for the EsoRex configuration file is xshoo.xsh_lingain.lly [default = -1].

--urx <long>

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. (long; default: -1). The full name of this option for the EsoRex configuration file is xshoo.xsh_lingain.urx [default = -1].

--ury <long>

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. (long; default: -1). The full name of this option for the EsoRex configuration file is xshoo.xsh_lingain.ury [default = -1].

--ref_level <long>

User reference level (long; 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 <long>

Maximum x-shift for the autocorr (long; default: 26). The full name of this option for the EsoRex configuration file is xshoo.xsh_lingain.m [default = 26].

--filter <long>

Upper limit of Median flux to be filtered (long; default: -1). The full name of this option for the EsoRex configuration file is xshoo.xsh_lingain.filter [default = -1].

--n <long>

Maximum y-shift for the autocorr (long; 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 <long>

Activate the multi-exts option. Choose -1 to process all extensions. Choose an extension number to process the appropriate extension. (long; 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 <long>

template size in pixels for smoothing during FPN computation (only for SMOOTH method) (long; 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 <long>

x coord of the lower-left point of the first field used for contamination measurement. If not modified, default value will be 1. (long; default: -1). The full name of this option for the EsoRex configuration file is xshoo.xsh_lingain.llx1 [default = -1].

--lly1 <long>

y coord of the lower-left point of the first field used for contamination measurement. If not modified, default value will be 1. (long; default: -1). The full name of this option for the EsoRex configuration file is xshoo.xsh_lingain.lly1 [default = -1].

--urx1 <long>

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. (long; default: -1). The full name of this option for the EsoRex configuration file is xshoo.xsh_lingain.urx1 [default = -1].

--ury1 <long>

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. (long; default: -1). The full name of this option for the EsoRex configuration file is xshoo.xsh_lingain.ury1 [default = -1].

--llx2 <long>

x coord of the lower-left point of the second field used for contamination measurement. If not modified, default value will be 1. (long; default: -1). The full name of this option for the EsoRex configuration file is xshoo.xsh_lingain.llx2 [default = -1].

--lly2 <long>

y coord of the lower-left point of the second field used for contamination measurement. If not modified, default value will be 1. (long; default: -1). The full name of this option for the EsoRex configuration file is xshoo.xsh_lingain.lly2 [default = -1].

--urx2 <long>

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. (long; default: -1). The full name of this option for the EsoRex configuration file is xshoo.xsh_lingain.urx2 [default = -1].

--ury2 <long>

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. (long; default: -1). The full name of this option for the EsoRex configuration file is xshoo.xsh_lingain.ury2 [default = -1].

--llx3 <long>

x coord of the lower-left point of the third field used for contamination measurement. If not modified, default value will be 1. (long; default: -1). The full name of this option for the EsoRex configuration file is xshoo.xsh_lingain.llx3 [default = -1].

--lly3 <long>

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. (long; default: -1). The full name of this option for the EsoRex configuration file is xshoo.xsh_lingain.lly3 [default = -1].

--urx3 <long>

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. (long; default: -1). The full name of this option for the EsoRex configuration file is xshoo.xsh_lingain.urx3 [default = -1].

--ury3 <long>

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. (long; default: -1). The full name of this option for the EsoRex configuration file is xshoo.xsh_lingain.ury3 [default = -1].

--llx4 <long>

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. (long; default: -1). The full name of this option for the EsoRex configuration file is xshoo.xsh_lingain.llx4 [default = -1].

--lly4 <long>

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. (long; default: -1). The full name of this option for the EsoRex configuration file is xshoo.xsh_lingain.lly4 [default = -1].

--urx4 <long>

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. (long; default: -1). The full name of this option for the EsoRex configuration file is xshoo.xsh_lingain.urx4 [default = -1].

--ury4 <long>

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. (long; default: -1). The full name of this option for the EsoRex configuration file is xshoo.xsh_lingain.ury4 [default = -1].

--llx5 <long>

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. (long; default: -1). The full name of this option for the EsoRex configuration file is xshoo.xsh_lingain.llx5 [default = -1].

--lly5 <long>

y coord of the lower-left point of the fifth field used for contamination measurement. If not modified, default value will be 1. (long; default: -1). The full name of this option for the EsoRex configuration file is xshoo.xsh_lingain.lly5 [default = -1].

--urx5 <long>

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. (long; default: -1). The full name of this option for the EsoRex configuration file is xshoo.xsh_lingain.urx5 [default = -1].

--ury5 <long>

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. (long; 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.

VERSION

xsh_lingain 2.7.1

AUTHOR

Lander de Bilbao,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