xsh_lingain - Computes detector's gain/linearity-map
esorex xsh_lingain [OPTIONS] FILE.sof
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
- --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.
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)
Lander de Bilbao,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