Provided by: cpl-plugin-kmos-doc_1.3.17+dfsg-1_all 
NAME
kmos_combine - Combine reconstructed cubes
SYNOPSIS
esorex kmos_combine [OPTIONS] FILE.sof
DESCRIPTION
This recipe shifts several exposures of an object and combines them. Diffe- rent methods to match the
exposures are described here (--method parameter).
The output cube is larger than the input cubes, according to the shifts to be applied. Additionally a
border of NaN values is added. The WCS is the same as for the first exposure.
For each spatial/spectral pixel a new value is calculated (according the --cmethod parameter) and written
into the output cube.
Only exposures with the same WCS orientation can be combined (except -–method=”none”), north must point
to the same direction. It is recommended to apply any rotation possibly after combining.
The behavior of the selection of IFUs to combine differs for some templates and can be controlled with
the parameters --name and --ifus.
If the input data cubes stem from templates KMOS_spec_obs_mapping8 or KMOS_spec_obs_mapping24 all
extensions from all input frames are combined into a single map by default (like in recipe kmo_sci_red).
If just the area of a specific IFU should be combined, the parameter --ifus can be specified, or more
easily --name.
If the input data cubes stem from other templates like e.g.
KMOS_spec_obs_freedither all extensions of all input frames are combined into several output frames by
default. The input IFUs are grouped according to their targeted object name stored in the keywords ESO
OCS ARMx NAME. If just a specific object should be combined, its name can be specified with --name. If
arbitrary IFUs shoukd be comined, one can specify these with the parameter --ifus.
The default mapping mode is done via the --name parameter, where the name of the object has to be
provided. The recipe searches in input data cubes IFUs pointing to that object.
Input files:
DO KMOS
category Type Explanation Required #Frames
-------- ----- ----------- -------- -------
<none or any> F3I data frame Y 2-n
Output files:
DO KMOS
category Type Explanation
-------- ----- -----------
COMBINE_<ESO PRO CATG> F3I Combined data cube
EXP_MASK_<ESO PRO CATG> F3I Exposure time mask
SCI_COMBINED_COLL (optional) Collapsed combined cube
(set --collapse_combined)
OPTIONS
--name <str>
Name of the object to combine. (str; default: ´´). The full name of this option for the EsoRex
configuration file is kmos.kmos_combine.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_combine.ifus [default = ].
--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: ´none´).
The full name of this option for the EsoRex configuration file is kmos.kmos_combine.method
[default = none].
--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_combine.fmethod [default = gauss].
--filename <str>
The path to the file with the shift vectors (method=´user´) (str; default: ´´). The full name of
this option for the EsoRex configuration file is kmos.kmos_combine.filename [default = ].
--flux <bool>
Apply flux conservation: (TRUE (apply) or FALSE (don´t apply) (bool; default: False). The full
name of this option for the EsoRex configuration file is kmos.kmos_combine.flux [default = False].
--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_combine.edge_nan [default = False].
--skipped_frames <str>
Comma separated List of IFUs to skip for the combination. An IFU is specified with R:I.R is the
index (starting at 1) of the reconstructed frame, I the IFU number (str; default: ´´). The full
name of this option for the EsoRex configuration file is kmos.kmos_combine.skipped_frames [default
= ].
--suppress_extension <bool>
Suppress arbitrary filename extension. (bool; default: False). The full name of this option for
the EsoRex configuration file is kmos.kmos_combine.suppress_extension [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_combine.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_combine.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_combine.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_combine.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_combine.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_combine.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_combine.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_dark(7), kmos_extract_spec(7),
kmos_flat(7), kmos_gen_reflines(7), kmos_illumination(7), kmos_reconstruct(7), kmos_sci_red(7),
kmos_sky_tweak(7), kmos_std_star(7), kmos_test(7), kmos_wave_cal(7)
VERSION
kmos_combine 1.3.17
AUTHOR
Alex Agudo Berbel, Y. 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