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kmos_combine - Combine reconstructed cubes

KMOS_COMBINE(7) kmos recipes KMOS_COMBINE(7)

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
-------- ----- ----------- -------- -------
CUBE_OBJECT F3I data frame Y 2-n
 

Output files:
 

DO KMOS
category Type Explanation
-------- ----- -----------
COMBINE_ F3I Combined data cube
EXP_MASK 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 (start 1) of the recons. frame, I the IFU nb (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_strip(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_gen_telluric(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 1.4.3
 

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
1.4.3 kmos_combine