.TH KMO_MAKE_IMAGE "7" "1.3.5" "kmo_make_image" "kmos recipes"
.SH NAME
kmo_make_image \- Collapse a cube to create a spatial image

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

.SH DESCRIPTION
This recipe collapses a cube along the spectral axis using rejection. By 
default all spectral slices are averaged.
.PP
Errors are propagated for the same spectral ranges as for the input data if
a noise map is provided.
.PP

.SS BASIC PARAMETERS
\-\-range
The spectral range can be delimited to one or several sub\-ranges like 
"1.8,1.9" or "1.8,1.9; 2.0,2.11"

\-\-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 wished 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 min and max pixel values will be rejected.
.PP
       \-\-cmax and \-\-cmin apply to this method.
.PP

.SS ADVANCED PARAMETERS
\-\-threshold
Optionally an OH spectrum can be provided. In this case a threshold can be
defined. The wavelengths of values above the threshold level in the OH
spectrum are omitted in the input frame. This parameter can be combined with
the \-\-range parameter. Negative threshold values are ignored.
.PP
Own spectra can be converted into the required F1S KMOS FITS format for the
OH spectrum using kmo_fits_stack.
.PP

\-\-cpos_rej
\-\-cneg_rej
\-\-citer
   see \-\-cmethod=\'ksigma\'
\-\-cmax
\-\-cmin
   see \-\-cmethod=\'min_max\'


  Input files:
   DO CATG           Type   Explanation                    Required #Frames
   \-\-\-\-\-\-\-           \-\-\-\-\-  \-\-\-\-\-\-\-\-\-\-\-                    \-\-\-\-\-\-\-\- \-\-\-\-\-\-\-
   <none or any>     F3I    data frame                         Y       1   
   <none or any>     F1S    OH line spectrum                   N      0,1  

  Output files:
   DO CATG           Type   Explanation
   \-\-\-\-\-\-\-           \-\-\-\-\-  \-\-\-\-\-\-\-\-\-\-\-
   MAKE_IMAGE        F2I    Collapsed data cubes




.SH OPTIONS
.TP
\fB\-\-range\fR \fI<str>\fR
The spectral ranges to combine. e.g."x1_start,x1_end;x2_start,x2_end"
(microns) (str; default: \'\'). The full name of this option for the EsoRex configuration
file is \fBkmos.kmo_make_image.range\fR [default = \fI\fR].
.TP
\fB\-\-threshold\fR \fI<float>\fR
The OH threshold level (%) (float; default: 0.1). The full name of this option for the EsoRex configuration
file is \fBkmos.kmo_make_image.threshold\fR [default = \fI0.1\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_make_image.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_make_image.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_make_image.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_make_image.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_make_image.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_make_image.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_extract_spec (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 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_make_image 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