.TH KMO_EXTRACT_SPEC "7" "1.3.5" "kmo_extract_spec" "kmos recipes"
.SH NAME
kmo_extract_spec \- Extract a spectrum from a cube.

.SH SYNOPSIS
esorex
.B kmo_extract_spec
[OPTIONS] FILE.sof

.SH 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.
.PP

.SS 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.
.PP

  * \'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.
.PP
  (0: pixels is ignored, 1: pixel is included) The mask must be of the same size
  that the input datacube.
.PP

  * \'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).
.PP
  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.
.PP

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.
.PP

.SS 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.
.PP

   * \'median\'
   At each pixel position the median is calculated.
.PP

   * \'average\'
   At each pixel position the average is calculated.
.PP

   * \'sum\'
   At each pixel position the sum is calculated.
.PP

   * \'min_max\'
   The specified number of minimum and maximum pixel values will be rejected.
.PP
   \-\-cmax and \-\-cmin apply to this method.
.PP

\-\-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)  




.SH OPTIONS
.TP
\fB\-\-mask_method\fR \fI<str>\fR
Either apply \'mask\', \'integrated\' or \'optimal\' masking method. (str;
default: \'integrated\'). The full name of this option for the EsoRex configuration
file is \fBkmos.kmo_extract_spec.mask_method\fR [default = \fIintegrated\fR].
.TP
\fB\-\-centre\fR \fI<str>\fR
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 \fBkmos.kmo_extract_spec.centre\fR [default = \fI7.5,7.5\fR].
.TP
\fB\-\-radius\fR \fI<float>\fR
The radius of the circular mask (pixel). (float; default: 3.0). The full name of this option for the EsoRex configuration
file is \fBkmos.kmo_extract_spec.radius\fR [default = \fI3.0\fR].
.TP
\fB\-\-save_mask\fR \fI<bool>\fR
True if the calculated mask should be saved. (bool; default: False). The full name of this option for the EsoRex configuration
file is \fBkmos.kmo_extract_spec.save_mask\fR [default = \fIFalse\fR].
.TP
\fB\-\-cmethod\fR \fI<str>\fR
Apply "average", "median", "sum", "min_max." or "ksigma". (str;
default: \'ksigma\'). The full name of this option for the EsoRex configuration
file is \fBkmos.kmo_extract_spec.cmethod\fR [default = \fIksigma\fR].
.TP
\fB\-\-cpos_rej\fR \fI<float>\fR
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 \fBkmos.kmo_extract_spec.cpos_rej\fR [default = \fI3.0\fR].
.TP
\fB\-\-cneg_rej\fR \fI<float>\fR
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 \fBkmos.kmo_extract_spec.cneg_rej\fR [default = \fI3.0\fR].
.TP
\fB\-\-citer\fR \fI<long>\fR
The number of iterations for kappa\-sigma\-clipping. (long; default: 3). The full name of this option for the EsoRex configuration
file is \fBkmos.kmo_extract_spec.citer\fR [default = \fI3\fR].
.TP
\fB\-\-cmax\fR \fI<long>\fR
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 \fBkmos.kmo_extract_spec.cmax\fR [default = \fI1\fR].
.TP
\fB\-\-cmin\fR \fI<long>\fR
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 \fBkmos.kmo_extract_spec.cmin\fR [default = \fI1\fR].

.PP
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.

.SH SEE ALSO
The full documentation for the kmos pipeline can be downloaded as 
a PDF file using the following URL:
.IP
.B ftp://ftp.eso.org/pub/dfs/pipelines/kmos/kmos\-pipeline\-manual\-2.9.pdf
.PP
An overview over the existing ESO pipelines can be found on the web page
\fBhttp://www.eso.org/sci/software/pipelines/\fR.
.PP
Basic documentation about the EsoRex program can be found at the esorex (1) 
man page.
.PP
It is possible to call the pipelines from python using the python\-cpl package.
See \fBhttp://packages.python.org/python\-cpl/index.html\fR for further
information.
.PP
The other recipes of the kmos pipeline are
.IR kmo_copy (7),
.IR kmo_fits_check (7),
.IR kmo_sci_red (7),
.IR kmo_fits_stack (7),
.IR kmo_noise_map (7),
.IR kmo_rotate (7),
.IR kmo_multi_reconstruct (7),
.IR kmo_sky_tweak (7),
.IR kmo_shift (7),
.IR kmos_gen_reflines (7),
.IR kmo_stats (7),
.IR kmo_arithmetic (7),
.IR kmos_dark (7),
.IR kmo_fits_strip (7),
.IR kmo_combine (7),
.IR kmo_std_star (7),
.IR kmo_illumination_flat (7),
.IR kmo_make_image (7),
.IR kmos_flat (7),
.IR kmo_fit_profile (7),
.IR kmo_sky_mask (7),
.IR kmos_illumination (7),
.IR kmos_wave_cal (7),
.IR kmo_reconstruct (7)

.SH VERSION
kmo_extract_spec 1.3.5

.SH AUTHOR
Alex Agudo Berbel <usd\-help@eso.org>

.SH 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>.

.SH 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