Provided by: cpl-plugin-muse-doc_2.8.7+dfsg-3_all 
NAME
muse_flat - Combine several separate flat images into one master flat file, trace slice locations, and
locate dark pixels.
SYNOPSIS
esorex muse_flat [OPTIONS] FILE.sof
DESCRIPTION
This recipe combines several separate flat-field images into one master flat-field file and traces the
location of the slices on the CCD. The master flat contains the combined pixel values of the raw flat
exposures, with respect to the image combination method used, normalized to the mean flux. The trace
table contains polynomials defining the location of the slices on the CCD. Processing trims the raw data
and records the overscan statistics, subtracts the bias (taking account of the overscan, if --overscan is
not "none"), and optionally, the dark from each raw input image, converts them from adu to count, scales
them according to their exposure time, and combines the exposures using input parameters. To trace the
position of the slices on the CCD, their edges are located using a threshold method. The edge detection
is repeated at given intervals thereby tracing the central position (the mean of both edges) and width of
each slit vertically across the CCD. Deviant positions of detections on CCD rows can be detected and
excluded before fitting a polynomial to all positions measured for one slice. The polynomial parameters
for each slice are saved in the output trace table. Finally, the area between the now known slice edges
is searched for dark (and bright) pixels, using statistics in each row of the master flat.
OPTIONS
--nifu <int>
IFU to handle. If set to 0, all IFUs are processed serially. If set to -1, all IFUs are processed
in parallel. (int; default: 0). The full name of this option for the EsoRex configuration file is
muse.muse_flat.nifu [default = 0].
--overscan <str>
If this is "none", stop when detecting discrepant overscan levels (see ovscsigma), for "offset" it
assumes that the mean overscan level represents the real offset in the bias levels of the
exposures involved, and adjusts the data accordingly; for "vpoly", a polynomial is fit to the
vertical overscan and subtracted from the whole quadrant. (str; default: ´vpoly´). The full name
of this option for the EsoRex configuration file is muse.muse_flat.overscan [default = vpoly].
--ovscreject <str>
This influences how values are rejected when computing overscan statistics. Either no rejection at
all ("none"), rejection using the DCR algorithm ("dcr"), or rejection using an iterative constant
fit ("fit"). (str; default: ´dcr´). The full name of this option for the EsoRex configuration file
is muse.muse_flat.ovscreject [default = dcr].
--ovscsigma <float>
If the deviation of mean overscan levels between a raw input image and the reference image is
higher than |ovscsigma x stdev|, stop the processing. If overscan="vpoly", this is used as sigma
rejection level for the iterative polynomial fit (the level comparison is then done afterwards
with |100 x stdev| to guard against incompatible settings). Has no effect for overscan="offset".
(float; default: 30.0). The full name of this option for the EsoRex configuration file is
muse.muse_flat.ovscsigma [default = 30.0].
--ovscignore <int>
The number of pixels of the overscan adjacent to the data section of the CCD that are ignored when
computing statistics or fits. (int; default: 3). The full name of this option for the EsoRex
configuration file is muse.muse_flat.ovscignore [default = 3].
--combine <str>
Type of combination to use (str; default: ´sigclip´). The full name of this option for the EsoRex
configuration file is muse.muse_flat.combine [default = sigclip].
--nlow <int>
Number of minimum pixels to reject with minmax (int; default: 1). The full name of this option for
the EsoRex configuration file is muse.muse_flat.nlow [default = 1].
--nhigh <int>
Number of maximum pixels to reject with minmax (int; default: 1). The full name of this option for
the EsoRex configuration file is muse.muse_flat.nhigh [default = 1].
--nkeep <int>
Number of pixels to keep with minmax (int; default: 1). The full name of this option for the
EsoRex configuration file is muse.muse_flat.nkeep [default = 1].
--lsigma <float>
Low sigma for pixel rejection with sigclip (float; default: 3.0). The full name of this option for
the EsoRex configuration file is muse.muse_flat.lsigma [default = 3.0].
--hsigma <float>
High sigma for pixel rejection with sigclip (float; default: 3.0). The full name of this option
for the EsoRex configuration file is muse.muse_flat.hsigma [default = 3.0].
--scale <bool>
Scale the individual images to a common exposure time before combining them. (bool; default:
True). The full name of this option for the EsoRex configuration file is muse.muse_flat.scale
[default = True].
--normalize <bool>
Normalize the master flat to the average flux (bool; default: True). The full name of this option
for the EsoRex configuration file is muse.muse_flat.normalize [default = True].
--trace <bool>
Trace the position of the slices on the master flat (bool; default: True). The full name of this
option for the EsoRex configuration file is muse.muse_flat.trace [default = True].
--nsum <int>
Number of lines over which to average when tracing (int; default: 32). The full name of this
option for the EsoRex configuration file is muse.muse_flat.nsum [default = 32].
--order <int>
Order of polynomial fit to the trace (int; default: 5). The full name of this option for the
EsoRex configuration file is muse.muse_flat.order [default = 5].
--edgefrac <float>
Fractional change required to identify edge when tracing (float; default: 0.5). The full name of
this option for the EsoRex configuration file is muse.muse_flat.edgefrac [default = 0.5].
--losigmabadpix <float>
Low sigma to find dark pixels in the master flat (float; default: 5.0). The full name of this
option for the EsoRex configuration file is muse.muse_flat.losigmabadpix [default = 5.0].
--hisigmabadpix <float>
High sigma to find bright pixels in the master flat (float; default: 5.0). The full name of this
option for the EsoRex configuration file is muse.muse_flat.hisigmabadpix [default = 5.0].
--samples <bool>
Create a table containing all tracing sample points. (bool; default: False). The full name of this
option for the EsoRex configuration file is muse.muse_flat.samples [default = False].
--merge <bool>
Merge output products from different IFUs into a common file. (bool; default: False). The full
name of this option for the EsoRex configuration file is muse.muse_flat.merge [default = False].
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 muse pipeline can be downloaded as a PDF file using the following URL:
ftp://ftp.eso.org/pub/dfs/pipelines/muse/muse-pipeline-cookbook-2.8.7.pdf
An overview over the existing ESO pipelines can be found on the web page
https://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
https://packages.python.org/python-cpl/index.html for further information.
The other recipes of the muse pipeline are muse_ampl(7), muse_astrometry(7), muse_bias(7),
muse_create_sky(7), muse_dark(7), muse_exp_align(7), muse_exp_combine(7), muse_geometry(7),
muse_illum(7), muse_lingain(7), muse_lsf(7), muse_qi_mask(7), muse_scibasic(7), muse_scipost(7),
muse_scipost_apply_astrometry(7), muse_scipost_calibrate_flux(7), muse_scipost_combine_pixtables(7),
muse_scipost_correct_dar(7), muse_scipost_correct_rv(7), muse_scipost_make_cube(7),
muse_scipost_raman(7), muse_scipost_subtract_sky(7), muse_scipost_subtract_sky_simple(7),
muse_standard(7), muse_twilight(7), muse_wavecal(7)
VERSION
muse_flat 2.8.7
AUTHOR
Peter Weilbacher (based on Joris Gerssen's draft) <https://support.eso.org>
BUG REPORTS
Please report any problems to https://support.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 MUSE Instrument Pipeline Copyright (C) 2005, 2019 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., 51 Franklin St, Fifth Floor, Boston, MA 02111-1307 USA
muse_flat 2.8.7 MUSE_FLAT(7)