kmos_combine(7) 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.

VERSION

kmos_combine 1.3.19

AUTHOR

Alex Agudo Berbel, Y. Jung <[email protected]>

BUG REPORTS

Please report any problems to [email protected] Alternatively, you may send a report to the ESO User Support Department <[email protected]>.

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