muse_ampl - Determine the instrumental throughput from exposures
taken with the pico-amplifier / photo diode readings.
esorex muse_ampl [OPTIONS] FILE.sof
This recipe combines several separate amplifier images
(flat-fields with special FITS headers containing pico amplifier
measurements) into one master image file and computes the instrumental
throughput per IFU (and slice). 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 them using input parameters. To compute the
throughput the image is converted into a pixel table, the flux is then
integrated over the given filter band, and the ratio of the expected flux
(FITS header INS.AMPL2.CURR) to measured flux is taken, in the same units.
If a geometry table was given as input, the relative area of the IFUs is
taken into account when computing the flux per unit area. The resulting
ratio is the instrument efficiency (throughput) and saved as QC parameters
for the whole input image and per slice in the output pixel table.
- --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_ampl.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_ampl.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_ampl.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_ampl.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_ampl.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_ampl.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_ampl.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_ampl.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_ampl.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_ampl.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_ampl.hsigma [default = 3.0].
- --fbeam
<float>
- Factor to describe the widening of the beam from the focal plane to photo
diode 2. (float; default: 1.1). The full name of this option for the
EsoRex configuration file is muse.muse_ampl.fbeam [default =
1.1].
- --temp
<float>
- Lamp temperature [K] used to create the black body function. (float;
default: 3200.0). The full name of this option for the EsoRex
configuration file is muse.muse_ampl.temp [default =
3200.0].
- --savemaster
<bool>
- Save the processed and combined master image before any concolution is
done. (bool; default: False). The full name of this option for the EsoRex
configuration file is muse.muse_ampl.savemaster [default =
False].
- --savetable
<bool>
- Save the table with all the processed pixel values. (bool; default:
False). The full name of this option for the EsoRex configuration file is
muse.muse_ampl.savetable [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_ampl.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_astrometry(7), muse_bias(7), muse_create_sky(7),
muse_dark(7), muse_exp_align(7), muse_exp_combine(7),
muse_flat(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 <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,
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