Provided by: cpl-plugin-kmos-doc_1.3.17+dfsg-1_all 
NAME
kmos_flat - Create master flatfield frame and badpixel map
SYNOPSIS
esorex kmos_flat [OPTIONS] FILE.sof
DESCRIPTION
This recipe creates the master flat field and calibration frames needed for spatial calibration for all
three detectors. It must be called after the kmo_dark-recipe, which generates a bad pixel mask
(badpixel_dark.fits). The bad pixel mask will be updated in this recipe.
As input at least 3 dark frames, 3 frames with the flat lamp on are recommended. Additionally a badpixel
mask from kmo_dark is required.
The badpixel mask contains 0 for bad pixels and 1 for good ones.
The structure of the resulting xcal and ycal frames is quite complex since the arrangement of the IFUs
isn´t just linear on the detector. Basically the integer part of the calibration data shows the offset of
each pixels centre in mas (Milli arcsec) from the field centre. The viewing of an IFU is 2800 mas
(14pix*0.2arcsec/pix). So the values in these two frames will vary between +/-1500 (One would expect
1400, but since the slitlets aren´t expected to be exactly vertical, the values can even go up to around
1500).
Additionally in the calibration data in y-direction the decimal part of the data designates the IFU to
which the slitlet corresponds to (for each detector from 1 to 8).
Because of the irregular arrangement of the IFUs not all x-direction calibration data is found in xcal
and similarly not all y-direction calibration data is located in ycal. For certain IFUs they are switched
and/or flipped in x- or y-direction: For IFUs 1,2,3,4,13,14,15,16: x- and y- data is switched For IFUs
17,18,19,20: y-data is flipped For IFUs 21,22,23,24: x-data is flipped For IFUs
5,6,7,8,9,10,11,12: x- and y- data is switched and
x- and y- data is flipped
Furthermore frames can be provided for several rotator angles. In this case the resulting calibration
frames for each detector are repeatedly saved as extension for every angle.
Advanced features: ------------------ To create the badpixel mask the edges of all slitlets are fitted to
a polynomial. Since it can happen that some of these fits (3 detectors 8 IFUs * 14slitlets * 2 edges
(left and right edge of slitlet)= 672 edges) fail, the fit parameters are themselves fitted again to
detect any outliers.
By default, the parameters of all left and all right edges are grouped individually and then fitted using
chebyshev polynomials. The advantage of a chebyshev polynomial is, that it consists in fact of a series
of orthogonal polynomials. This implies that the parameters of the polynomials are independent. This fact
predestines the use of chebyshev polynomials for our case. So each individual parameter can be examined
independently.
The reason why the left and right edges are fitted individually is that there is a systematic pattern
specific to these groups. The reason for this pattern is probably to be found in the optical path the
light is traversing.
The behaviour of this fitting step can be influenced via environment parameters: * KF_ALLPARS (default:
1)
When set to 1 all coefficients of the polynomial of an edge are to be
corrected, also when just one of these coefficients is an outlier. When
set to 0 only the outlier is to be corrected.
* KF_CH (default: 1)
When set to 1 chebyshev polynomials are used to fit the fitted parameters.
When set to 0 normal polynomials are used.
* KF_SIDES (default: 2)
This variable can either be set to 1 or 2. When set to 2 the left and
right edges are examined individually. When set to 1 all edges are
examined as one group.
* KF_FACTOR(default: 4)
This factor defines the threshold factor. All parameters deviating
KF_FACTOR*stddev are to be corrected
BASIC PARAMETERS
--badpix_thresh The threshold level to mark pixels as bad on the dark subtracted frames [%]
--surrounding_pixels The amount of bad pixels to surround a specific pixel, to let it be marked bad as
well.
--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 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 min and max pixel values will be rejected.
--cmax and --cmin apply to this method.
ADVANCED PARAMETERS
--cpos_rej --cneg_rej --citer see --cmethod=´ksigma´
--cmax --cmin see --cmethod=´min_max´
--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 CATG Type Explanation Required #Frames
------- ----- ----------- -------- -------
FLAT_ON RAW Flatlamp-on exposures Y 1-n
(at least 3 frames recommended)
FLAT_OFF RAW Flatlamp-off exposures Y 1-n
(at least 3 frames recommended)
BADPIXEL_DARK B2D Bad pixel mask Y 1
Output files:
DO CATG Type Explanation
------- ----- -----------
MASTER_FLAT F2D Normalised flat field
(6 extensions: alternating data & noise
BADPIXEL_FLAT B2D Updated bad pixel mask (3 Extensions)
XCAL F2D Calibration frame 1 (3 Extensions)
YCAL F2D Calibration frame 2 (3 Extensions)
FLAT_EDGE F2L Frame containing parameters of fitted
slitlets of all IFUs of all detectors
OPTIONS
--badpix_thresh <long>
The threshold level to mark bad pixels [%]. (long; default: 35). The full name of this option for
the EsoRex configuration file is kmos.kmos_flat.badpix_thresh [default = 35].
--surrounding_pixels <long>
The nb of bad surrounding pix to mark a pixel bad (long; default: 5). The full name of this option
for the EsoRex configuration file is kmos.kmos_flat.surrounding_pixels [default = 5].
--suppress_extension <bool>
Suppress arbitrary filename extension (bool; default: False). The full name of this option for the
EsoRex configuration file is kmos.kmos_flat.suppress_extension [default = False].
--cmethod <str>
Apply "average", "median", "sum", "min_max." or "ksigma". (str; default: ´ksigma´). The full name
of this option for the EsoRex configuration file is kmos.kmos_flat.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.kmos_flat.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.kmos_flat.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.kmos_flat.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.kmos_flat.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.kmos_flat.cmin [default = 1].
--det <long>
Only reduce the specified detector (long; default: 0). The full name of this option for the EsoRex
configuration file is kmos.kmos_flat.detector [default = 0].
--angle <float>
Only reduce the specified angle (float; default: 370.0). The full name of this option for the
EsoRex configuration file is kmos.kmos_flat.angle [default = 370.0].
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_arithmetic(7), kmo_copy(7), kmo_fit_profile(7),
kmo_fits_check(7), kmo_fits_strip(7), kmo_illumination_flat(7), kmo_make_image(7), kmo_noise_map(7),
kmo_rotate(7), kmo_shift(7), kmo_sky_mask(7), kmo_stats(7), kmos_combine(7), kmos_dark(7),
kmos_extract_spec(7), kmos_gen_reflines(7), kmos_illumination(7), kmos_reconstruct(7), kmos_sci_red(7),
kmos_sky_tweak(7), kmos_std_star(7), kmos_test(7), kmos_wave_cal(7)
VERSION
kmos_flat 1.3.17
AUTHOR
Alex Agudo Berbel, Yves Jung <usd-help@eso.org>
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>.
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