Provided by: cpl-plugin-kmos-doc_1.2.8+dfsg-2_all 
NAME
kmo_extract_spec - Extract a spectrum from a cube.
SYNOPSIS
esorex kmo_extract_spec [OPTIONS] FILE.sof
DESCRIPTION
This recipe extracts a spectrum from a datacube. The datacube must be in F3I KMOS FITS
format (either with or without noise). The output will be a similarly formatted F1I KMOS
FITS file.
BASIC PARAMETERS
--mask_method There are several ways to define the region to consider for spectrum
calculation:
* ´integrated´´ (default)
A circular mask with defined centre and radius is created (--centre and
--radius have to be defined). This mask is applied to all extensions.
* ´mask´
An arbitrary mask can be provided (for example the mask created by kmo_sky_mask
can be used). The mask must be in F2I KMOS FITS format, mustn´t contain noise
and must have as many extensions as the input cube. The mask can be binary as
well as it can contain float values, so a weighted mask is also possible.
(0: pixels is ignored, 1: pixel is included) The mask must be of the same size
that the input datacube.
* ´optimal´
The mask is created automatically by fitting a normalised profile (using
kmo_fit_profile) to the image of the datacube (using kmo_make_image the data-
cube is summed up in spectral direction according to the specified --cmethod).
This profile is then used as mask input. When --save_mask is set to true the
mask is saved on disk. The remaining parameters not described here apply to
the fitting of the profile.
If the spectra of several objects in a IFU should be extracted, --mask_method= ´mask´ is
recommended. With several calls to kmo_extract_spec using different masks all spectra can
be extracted.
ADVANCED PARAMETERS
--centre --radius see --mask_method = ´integrated´
--save_mask see --mask_method = ´optimal´
--cmethod Applies only if –mask_method = ´integral´ 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.
--cpos_rej --cneg_rej --citer see --cmethod=´ksigma´
--cmax --cmin see --cmethod=´min_max´
Input files:
DO KMOS
category Type Explanation Required #Frames
-------- ----- ----------- -------- -------
<none or any> F3I The datacubes Y 1
<none or any> F2I The mask N 0,1
Output files:
DO KMOS
category Type Explanation
-------- ----- -----------
EXTRACT_SPEC F1I Extracted spectrum
EXTRACT_SPEC_MASK F2I (optional, if --save_mask=true and
--mask_method=´optimal´: The calculated mask)
OPTIONS
--mask_method <str>
Either apply ´mask´, ´integrated´ or ´optimal´ masking method. (str; default:
´integrated´). The full name of this option for the EsoRex configuration file is
kmos.kmo_extract_spec.mask_method [default = integrated].
--centre <str>
The centre of the circular mask (pixel). (str; default: ´7.5,7.5´). The full name
of this option for the EsoRex configuration file is kmos.kmo_extract_spec.centre
[default = 7.5,7.5].
--radius <float>
The radius of the circular mask (pixel). (float; default: 3.0). The full name of
this option for the EsoRex configuration file is kmos.kmo_extract_spec.radius
[default = 3.0].
--save_mask <bool>
True if the calculated mask should be saved. (bool; default: False). The full name
of this option for the EsoRex configuration file is kmos.kmo_extract_spec.save_mask
[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_extract_spec.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_extract_spec.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_extract_spec.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_extract_spec.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_extract_spec.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_extract_spec.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_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_combine(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_extract_spec 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