.TH KMO_ILLUMINATION_FLAT "7" "1.4.0" "kmo_illumination_flat" "kmos recipes"
.SH NAME
kmo_illumination_flat \- Alternative to kmo_illumination based on flatfield frames.

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

.SH DESCRIPTION
This recipe creates the spatial non\-uniformity calibration frame needed for
all three detectors. It must be called after the kmo_wave_cal\-recipe, which
generates the spectral calibration frame needed in this recipe. As input at
least a flatfield frame is required.
.PP
Contrary to kmo_illumination it doesn\'t use flat sky frames but rather the
flatfield frames from the internal flat lamp. This recipe can be used if no
acceptable flat sky frames are available.
.PP
The created product, the illumination correction, can be used as input for
kmo_std_star and kmo_sci_red.
.PP

.SS BASIC PARAMETERS
\-\-imethod
The interpolation method used for reconstruction.
.PP

.SS ADVANCED PARAMETERS
\-\-flux
Specify if flux conservation should be applied.
.PP

\-\-neighborhoodRange
Defines the range to search for neighbors during reconstruction

\-\-b_samples
The number of samples in spectral direction for the reconstructed cube.
.PP
Ideally this number should be greater than 2048, the detector size.
.PP

\-\-b_start
\-\-b_end
Used to define manually the start and end wavelength for the reconstructed
cube. By default the internally defined values are used.
.PP

\-\-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.
.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\'

\-\-pix_scale
Change the pixel scale [arcsec]. Default of 0.2" results into cubes of
14x14pix, a scale of 0.1" results into cubes of 28x28pix, etc.
.PP

\-\-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.
.PP


  Input files:

   DO                    KMOS                                                  
   category              Type   Explanation                    Required #Frames
   \-\-\-\-\-\-\-\-              \-\-\-\-\-  \-\-\-\-\-\-\-\-\-\-\-                    \-\-\-\-\-\-\-\- \-\-\-\-\-\-\-
   FLAT_SKY_FLAT          F2D   Flatlamp\-on exposures             Y      1\-n   
                                (at least 3 frames recommended)                
   XCAL                   F2D   x calibration frame               Y       1    
   YCAL                   F2D   y calibration frame               Y       1    
   LCAL                   F2D   Wavelength calib. frame           Y       1    
   WAVE_BAND              F2L   Table with start\-/end\-wavelengths Y       1    

  Output files:

   DO                    KMOS
   category              Type   Explanation
   \-\-\-\-\-\-\-\-              \-\-\-\-\-  \-\-\-\-\-\-\-\-\-\-\-
   ILLUM_CORR             F2I    Illumination calibration frame   




.SH OPTIONS
.TP
\fB\-\-imethod\fR \fI<str>\fR
Method to use for interpolation: ["NN" (nearest neighbour), "lwNN"
(linear weighted nearest neighbor), "swNN" (square weighted nearest
neighbor), "MS" (Modified Shepard\'s method), "CS" (Cubic spline)]
(str; default: \'CS\'). The full name of this option for the EsoRex configuration
file is \fBkmos.kmo_illumination_flat.imethod\fR [default = \fICS\fR].
.TP
\fB\-\-neighborhoodRange\fR \fI<float>\fR
Defines the range to search for neighbors. in pixels (float; default:
1.001). The full name of this option for the EsoRex configuration
file is \fBkmos.kmo_illumination_flat.neighborhoodRange\fR [default = \fI1.001\fR].
.TP
\fB\-\-flux\fR \fI<bool>\fR
TRUE: Apply flux conservation. FALSE: otherwise (bool; default: False). The full name of this option for the EsoRex configuration
file is \fBkmos.kmo_illumination_flat.flux\fR [default = \fIFalse\fR].
.TP
\fB\-\-pix_scale\fR \fI<float>\fR
Change the pixel scale [arcsec]. Default of 0.2" results into cubes of
14x14pix, a scale of 0.1" results into cubes of 28x28pix, etc. (float;
default: 0.2). The full name of this option for the EsoRex configuration
file is \fBkmos.kmo_illumination_flat.pix_scale\fR [default = \fI0.2\fR].
.TP
\fB\-\-suppress_extension\fR \fI<bool>\fR
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 \fBkmos.kmo_illumination_flat.suppress_extension\fR [default = \fIFalse\fR].
.TP
\fB\-\-b_samples\fR \fI<long>\fR
The number of samples in wavelength for the reconstructed cube (long;
default: 2048). The full name of this option for the EsoRex configuration
file is \fBkmos.kmo_illumination_flat.b_samples\fR [default = \fI2048\fR].
.TP
\fB\-\-b_start\fR \fI<float>\fR
The lowest wavelength [um] to use when reconstructing. Derived by
default, depending on the band (float; default: \-1.0). The full name of this option for the EsoRex configuration
file is \fBkmos.kmo_illumination_flat.b_start\fR [default = \fI\-1.0\fR].
.TP
\fB\-\-b_end\fR \fI<float>\fR
The highest wavelength [um] to use when reconstructing. Derived by
default, depending on the band (float; default: \-1.0). The full name of this option for the EsoRex configuration
file is \fBkmos.kmo_illumination_flat.b_end\fR [default = \fI\-1.0\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_illumination_flat.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_illumination_flat.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_illumination_flat.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_illumination_flat.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_illumination_flat.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_illumination_flat.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_arithmetic (7),
.IR kmo_copy (7),
.IR kmo_fit_profile (7),
.IR kmo_fits_strip (7),
.IR kmo_make_image (7),
.IR kmo_noise_map (7),
.IR kmo_rotate (7),
.IR kmo_shift (7),
.IR kmo_sky_mask (7),
.IR kmo_stats (7),
.IR kmos_combine (7),
.IR kmos_dark (7),
.IR kmos_extract_spec (7),
.IR kmos_flat (7),
.IR kmos_gen_reflines (7),
.IR kmos_illumination (7),
.IR kmos_reconstruct (7),
.IR kmos_sci_red (7),
.IR kmos_sky_tweak (7),
.IR kmos_std_star (7),
.IR kmos_test (7),
.IR kmos_wave_cal (7)

.SH VERSION
kmo_illumination_flat 1.4.0

.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