Provided by: cpl-plugin-kmos-doc_1.3.17+dfsg-1_all 
NAME
kmos_sci_red - Reconstruct obj/sky-pairs individually and combine them afterwards
SYNOPSIS
esorex kmos_sci_red [OPTIONS] FILE.sof
DESCRIPTION
Two data frames are expected in order to have a sky IFU for the IFU Objects.
If an OH spectrum is given in the SOF file the lambda axis will be corrected using the OH lines as
reference.
Every IFU containing an object will be reconstructed and divided by telluric and illumination correction.
By default these intermediate cubes are saved to disk. The reconstructed objects with the same object
name are combined.
In order to combine a specific object, the parameters --name or --ifus can be used.
For exposures taken with the templates KMOS_spec_obs_mapping8 and KMOS_spec_obs_mapping24, all active
IFUs are combined.
Input files:
DO KMOS
category Type Explanation Required #Frames
-------- ----- ----------- -------- -------
SCIENCE RAW The science frames Y >=1
XCAL F2D x calibration frame Y 1
YCAL F2D y calibration frame Y 1
LCAL F2D Wavelength calib. frame Y 1
WAVE_BAND F2L Table with start-/end-wavelengths Y 1
MASTER_FLAT F2D Master flat Y 0,1
ILLUM_CORR F2I Illumination correction N 0,1
TELLURIC F1I normalised telluric spectrum N 0,1
OH_SPEC F1S Vector holding OH lines N 0,1
Output files:
DO KMOS
category Type Explanation
-------- ----- -----------
SCI_COMBINED F3I Combined cubes with noise
SCI_RECONSTRUCTED F3I Reconstructed cube with noise
EXP_MASK F3I Exposure time mask (not for mapping-templates!)
SCI_INTERIM_OBJECT F3I (optional) Intermediate reconstructed object
cubes used for sky tweaking, no noise
(set --sky_tweak and --save_interims)
SCI_INTERIM_SKY F3I (optional) Intermediate reconstructed sky
cubes used for sky tweaking, no noise
(set --sky_tweak and --save_interims)
SCI_COMBINED_COLL (optional) Collapsed combined cube
(set --collapse_combined)
SCI_RECONSTRUCTED_COLL (optional) Collapsed reconstructed cube
(set --collapse_reconstructed)
OPTIONS
--imethod <str>
Method to use for interpolation during reconstruction. ["NN" (nearest neighbour), "lwNN" (linear
weighted nearest neighbor), "swNN" (square weighted nearest neighbor), "MS" (Modified Shepard´s
method)"CS" (Cubic spline)] (str; default: ´CS´). The full name of this option for the EsoRex
configuration file is kmos.kmos_sci_red.imethod [default = CS].
--smethod <str>
Method to use for interpolation during shifting. ["NN" (nearest neighbour), "CS" (Cubic spline)]
(str; default: ´CS´). The full name of this option for the EsoRex configuration file is
kmos.kmos_sci_red.smethod [default = CS].
--method <str>
The shifting method: ´none´: no shifting, combined directly, ´header´: shift according to WCS
(default), ´center´: centering algorithm, ´user´: read shifts from file (str; default: ´header´).
The full name of this option for the EsoRex configuration file is kmos.kmos_sci_red.method
[default = header].
--fmethod <str>
The fitting method (applies only when method=´center´): ´gauss´: fit a gauss function to
collapsed image (default), ´moffat´: fit a moffat function to collapsed image (str; default:
´gauss´). The full name of this option for the EsoRex configuration file is
kmos.kmos_sci_red.fmethod [default = gauss].
--name <str>
Name of the object to combine. (str; default: ´´). The full name of this option for the EsoRex
configuration file is kmos.kmos_sci_red.name [default = ].
--ifus <str>
The indices of the IFUs to combine. "ifu1;ifu2;..." (str; default: ´´). The full name of this
option for the EsoRex configuration file is kmos.kmos_sci_red.ifus [default = ].
--oscan <bool>
Apply Overscan Correction (bool; default: True). The full name of this option for the EsoRex
configuration file is kmos.kmos_sci_red.oscan [default = True].
--pix_scale <float>
Change the pixel scale [arcsec]. Default of 0.2" results into cubes of 14x14pix, a scale of 0.1"
results into cubes of 28x28pix, etc. (float; default: 0.2). The full name of this option for the
EsoRex configuration file is kmos.kmos_sci_red.pix_scale [default = 0.2].
--suppress_extension <bool>
Suppress arbitrary filename extension.(TRUE (apply) or FALSE (don´t apply) (bool; default: False).
The full name of this option for the EsoRex configuration file is
kmos.kmos_sci_red.suppress_extension [default = False].
--neighborhoodRange <float>
Defines the range to search for neighbors in pixels (float; default: 1.001). The full name of this
option for the EsoRex configuration file is kmos.kmos_sci_red.neighborhoodRange [default = 1.001].
--filename <str>
The path to the file with the shift vectors.(Applies only to method=´user´) (str; default: ´´).
The full name of this option for the EsoRex configuration file is kmos.kmos_sci_red.filename
[default = ].
--flux <bool>
TRUE: Apply flux conservation. FALSE: otherwise (bool; default: False). The full name of this
option for the EsoRex configuration file is kmos.kmos_sci_red.flux [default = False].
--background <bool>
TRUE: Apply background removal. FALSE: otherwise (bool; default: False). The full name of this
option for the EsoRex configuration file is kmos.kmos_sci_red.background [default = False].
--fast_mode <bool>
FALSE: cubes are shifted and combined,TRUE: cubes are collapsed and then shifted and combined
(bool; default: False). The full name of this option for the EsoRex configuration file is
kmos.kmos_sci_red.fast_mode [default = False].
--extrapolate <bool>
Applies only to ´smethod=CS´ when doing sub-pixel shifts: FALSE: shifted IFU will be filled with
NaN´s at the borders,TRUE: shifted IFU will be extrapolated at the borders (bool; default: False).
The full name of this option for the EsoRex configuration file is kmos.kmos_sci_red.extrapolate
[default = False].
--xcal_interpolation <bool>
TRUE: Interpolate xcal between rotator angles. FALSE: otherwise (bool; default: True). The full
name of this option for the EsoRex configuration file is kmos.kmos_sci_red.xcal_interpolation
[default = True].
--edge_nan <bool>
Set borders of cubes to NaN before combining them.(TRUE (apply) or FALSE (don´t apply) (bool;
default: False). The full name of this option for the EsoRex configuration file is
kmos.kmos_sci_red.edge_nan [default = False].
--no_combine <bool>
Don´t combine cubes after reconstruction.(TRUE (apply) or FALSE (don´t apply) (bool; default:
False). The full name of this option for the EsoRex configuration file is
kmos.kmos_sci_red.no_combine [default = False].
--no_subtract <bool>
Don´t sky subtract object and references.(TRUE (apply) or FALSE (don´t apply) (bool; default:
False). The full name of this option for the EsoRex configuration file is
kmos.kmos_sci_red.no_subtract [default = False].
--sky_tweak <bool>
Use modified sky cube for sky subtraction.(TRUE (apply) or FALSE (don´t apply) (bool; default:
False). The full name of this option for the EsoRex configuration file is
kmos.kmos_sci_red.sky_tweak [default = False].
--discard_subband <bool>
Ignore last sub-band in the sky tweaking (bool; default: False). The full name of this option for
the EsoRex configuration file is kmos.kmos_sci_red.discard_subband [default = False].
--tbsub <bool>
Subtract thermal background from input cube.(TRUE (apply) or FALSE (don´t apply) (bool; default:
True). The full name of this option for the EsoRex configuration file is kmos.kmos_sci_red.tbsub
[default = True].
--b_samples <long>
The number of samples in wavelength for the reconstructed cube (long; default: 2048). The full
name of this option for the EsoRex configuration file is kmos.kmos_sci_red.b_samples [default =
2048].
--b_start <float>
The lowest wavelength [um] to use when reconstructing. Derived by default, depending on the band
(float; default: -1.0). The full name of this option for the EsoRex configuration file is
kmos.kmos_sci_red.b_start [default = -1.0].
--b_end <float>
The highest wavelength [um] to use when reconstructing. Derived by default, depending on the band
(float; default: -1.0). The full name of this option for the EsoRex configuration file is
kmos.kmos_sci_red.b_end [default = -1.0].
--obj_sky_table <str>
The path to the file with the modified obj/sky associations. (str; default: ´´). The full name of
this option for the EsoRex configuration file is kmos.kmos_sci_red.obj_sky_table [default = ].
--velocity_offset <float>
Specify velocity offset correction in km/s for lambda scale (float; default: 0.0). The full name
of this option for the EsoRex configuration file is kmos.kmos_sci_red.velocity_offset [default =
0.0].
--save_interims <bool>
Save interim object and sky cubes. Can only be used together with --sky_tweak (bool; default:
False). The full name of this option for the EsoRex configuration file is
kmos.kmos_sci_red.save_interims [default = False].
--collapse_reconstructed <bool>
Flag to collapse the reconstructed images (bool; default: False). The full name of this option for
the EsoRex configuration file is kmos.kmos_sci_red.collapse_reconstructed [default = False].
--collapse_combined <bool>
Flag to collapse the combined images (bool; default: False). The full name of this option for the
EsoRex configuration file is kmos.kmos_sci_red.collapse_combined [default = False].
--cmethod <str>
Apply "average", "median", "sum", "min_max." or "ksigma". (str; default: ´ksigma´). The full name
of this option for the EsoRex configuration file is kmos.kmos_sci_red.cmethod [default = ksigma].
--cpos_rej <float>
The positive rejection threshold for kappa-sigma-clipping (sigma). (float; default: 3.0). The
full name of this option for the EsoRex configuration file is kmos.kmos_sci_red.cpos_rej [default
= 3.0].
--cneg_rej <float>
The negative rejection threshold for kappa-sigma-clipping (sigma). (float; default: 3.0). The
full name of this option for the EsoRex configuration file is kmos.kmos_sci_red.cneg_rej [default
= 3.0].
--citer <long>
The number of iterations for kappa-sigma-clipping. (long; default: 3). The full name of this
option for the EsoRex configuration file is kmos.kmos_sci_red.citer [default = 3].
--cmax <long>
The number of maximum pixel values to clip with min/max-clipping. (long; default: 1). The full
name of this option for the EsoRex configuration file is kmos.kmos_sci_red.cmax [default = 1].
--cmin <long>
The number of minimum pixel values to clip with min/max-clipping. (long; default: 1). The full
name of this option for the EsoRex configuration file is kmos.kmos_sci_red.cmin [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 kmos pipeline can be downloaded as a PDF file using the following URL:
ftp://ftp.eso.org/pub/dfs/pipelines/kmos/kmos-pipeline-manual-2.9.pdf
An overview over the existing ESO pipelines can be found on the web page
http://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
http://packages.python.org/python-cpl/index.html for further information.
The other recipes of the kmos pipeline are kmo_arithmetic(7), kmo_copy(7), kmo_fit_profile(7),
kmo_fits_check(7), kmo_fits_strip(7), kmo_illumination_flat(7), kmo_make_image(7), kmo_noise_map(7),
kmo_rotate(7), kmo_shift(7), kmo_sky_mask(7), kmo_stats(7), kmos_combine(7), kmos_dark(7),
kmos_extract_spec(7), kmos_flat(7), kmos_gen_reflines(7), kmos_illumination(7), kmos_reconstruct(7),
kmos_sky_tweak(7), kmos_std_star(7), kmos_test(7), kmos_wave_cal(7)
VERSION
kmos_sci_red 1.3.17
AUTHOR
Alex Agudo Berbel, Yves Jung <usd-help@eso.org>
BUG REPORTS
Please report any problems to usd-help@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 CRIRES Instrument Pipeline Copyright (C) 2002,2003 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