muse_flat - Combine several separate flat images into one master
flat file, trace slice locations, and locate dark pixels.
esorex muse_flat [OPTIONS] FILE.sof
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.
- --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.
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)
Peter Weilbacher (based on Joris Gerssen's draft)
<https://support.eso.org>
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>.
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