Provided by: cpl-plugin-kmos-doc_1.2.8+dfsg-2_all 
NAME
kmo_combine - Combine reconstructed cubes
SYNOPSIS
esorex kmo_combine [OPTIONS] FILE.sof
DESCRIPTION
This recipe shifts several exposures of an object and combines them. The diffe- rent
methods to match the exposures are described below (--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 will be calculated (according the --cmethod
parameter) and written into the output cube.
Only exposures with equal orientation regarding the WCS 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 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 parameter --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 all input data cubes IFUs pointing to that
object.
BASIC PARAMETERS
--name --ifus Since an object can be present only once per exposure and since it can be
located in different IFUs for the existing exposures, there are two modes to identify the
objects:
* Combine by object names (default)
In this case the object name must be provided via the --name parameter. The
object name will be searched for in all primary headers of all provided frames
in the keyword ESO OCS ARMx NAME.
* Combine by index (advanced)
In this case the --ifus parameter must be provided. The parameter must have
the same number of entries as frames are provided, e.g. "3;1;24" for 3 expo-
sures. The index doesn´t reference the extension in the frame but the real
index of the IFU as defined in the EXTNAME keyword (e.g. ´IFU.3.DATA´).
--method There are following sources to get the shift parameters from:
* ´none´ (default)
The cubes are directly recombined, not shifting at all. The output frame will
have the same dimensions as the input cubes.
If the size differs a warning will be emitted and the cubes will be aligned
to the lower left corner. If the orientation differs a warning will be emit-
ted, but the cubes are combined anyway.
* ´header´
The shifts are calculated according to the WCS information stored in the
header of every IFU. The output frame will get larger, except the object is
at the exact same position for all exposures. The size of the exposures can
differ, but the orientation must be the same for all exposures.
* ´center´
The shifts are calculated using a centering algorithm. The cube will be col-
lapsed and a 2D profile will be fitted to it to identify the centre. With
the parameter --fmethod the function to fit can be provided. The size of the
exposures can differ, but the orientation must be the same for all exposures.
* ´user´
Read the shifts from a user specified file. The path of the file must be pro-
vided using the --filename parameter. For every exposure (except the first one)
two shift values are expected per line, they have to be separated with simple
spaces. The values indicate pixel shifts and are referenced to the first
frame. The 1st value is the shift in x-direction to the left, the 2nd the
shift in y-direction upwards. The size of the exposures can differ, but the
orientation must be the same for all exposures.
--cmethod Following methods of frame combination are available:
* ´ksigma´ (Default)
An iterative sigma clipping. For each position all pixels in the spectrum
are examined. If they deviate significantly, they will be rejected according
to the conditions:
val > mean + stdev * cpos_rej
and
val < mean - stdev * cneg_rej
where --cpos_rej, --cneg_rej and --citer are the corresponding configuration
parameters. In the first iteration median and percentile level are used.
* ´median´
At each pixel position the median is calculated.
* ´average´
At each pixel position the average is calculated.
* ´sum´
At each pixel position the sum is calculated.
* ´min_max´
The specified number of minimum and maximum pixel values will be rejected.
--cmax and --cmin apply to this method.
ADVANCED PARAMETERS
--edge_nan Set borders of two sides of the cubes to NaN before combining them. This
minimises unwanted border effects when dithering.
--fmethod see --method=´center´ The type of function that should be fitted spatially to
the collapsed image.
This fit is used to create a mask to extract the spectrum of the object. Valid values are
“gauss” and “moffat”.
--filename see --method=´user´
--cpos_rej --cneg_rej --citer see --cmethod=´ksigma´
--cmax --cmin see --cmethod=´min_max´
--flux Specify if flux conservation should be applied.
--suppress_extension If set to TRUE, the arbitrary filename extensions are supressed. If
multiple products with the same category are produced, they will be numered consecutively
starting from 0.
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
OPTIONS
--name <str>
Name of the object to combine. (str; default: ´´). The full name of this option for
the EsoRex configuration file is kmos.kmo_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.kmo_combine.ifus
[default = ].
--method <str>
The shifting method: ´none´: no shifting, combined directly (default), ´header´:
shift according to WCS, ´center´: centering algorithm, ´user´: read shifts from
file (str; default: ´none´). The full name of this option for the EsoRex
configuration file is kmos.kmo_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.kmo_combine.fmethod [default = gauss].
--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.kmo_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.kmo_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.kmo_combine.edge_nan [default = False].
--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.kmo_combine.suppress_extension [default = False].
--cmethod <str>
Either apply "average", "median", "sum", "min_max." or "ksigma". (str; default:
´ksigma´). The full name of this option for the EsoRex configuration file is
kmos.kmo_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.kmo_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.kmo_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.kmo_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.kmo_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.kmo_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_dev_setup(7), kmo_copy(7), kmo_flat(7),
kmo_fits_check(7), kmo_sci_red(7), kmo_illumination(7), kmo_fits_stack(7),
kmo_noise_map(7), kmo_rotate(7), kmo_extract_spec(7), kmo_multi_reconstruct(7),
kmo_stats(7), kmo_shift(7), kmo_wave_cal(7), kmo_dark(7), kmo_arithmetic(7),
kmo_std_star(7), kmo_fits_strip(7), kmo_illumination_flat(7), kmo_make_image(7),
kmo_sky_tweak(7), kmo_fit_profile(7), kmo_sky_mask(7), kmo_reconstruct(7)
VERSION
kmo_combine 1.2.8
AUTHOR
Alex Agudo Berbel <kmos-spark@mpe.mpg.de>
BUG REPORTS
Please report any problems to kmos-spark@mpe.mpg.de. Alternatively, you may send a report
to the ESO User Support Department <usd-help@eso.org>.
LICENSE
This file is part of the KMOS 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, 51 Franklin Street, Suite 500, Boston, MA
02110-1335 USA