Provided by: cpl-plugin-muse-doc_2.2+dfsg-2_all 
NAME
muse_scibasic - Remove the instrumental signature from the data of each CCD and convert them from an
image into a pixel table.
SYNOPSIS
esorex muse_scibasic [OPTIONS] FILE.sof
DESCRIPTION
Processing handles each raw input image separately: it trims the raw data and records the overscan
statistics, subtracts the bias (taking account of the overscan, if --overscan is not "none"), optionally
detects cosmic rays (note that by default cosmic ray rejection is handled in the post processing recipes
while the data is reformatted into a datacube, so that the default setting is cr="none" here), converts
the images from adu to count, subtracts the dark, divides by the flat-field, and (optionally) propagates
the integrated flux value from the twilight-sky cube. The reduced image is then saved (if
--saveimage=true). The input calibrations geometry table, trace table, and wavelength calibration table
are used to assign 3D coordinates to each CCD-based pixel, thereby creating a pixel table for each
exposure. If --skylines contains one or more wavelengths for (bright and isolated) sky emission lines,
these lines are used to correct the wavelength calibration using an offset. The data is then cut to a
useful wavelength range (if --crop=true). If an ILLUM exposure was given as input, it is then used to
correct the relative illumination between all slices of one IFU. For this, the data of each slice is
multiplied by the normalized median flux of that slice in the ILLUM exposure. As last step, the data is
divided by the normalized twilight cube (if given), using the 3D coordinate of each pixel in the pixel
table to interpolate the twilight correction onto the data. This pre-reduced pixel table for each
exposure is then saved to disk.
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_scibasic.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_scibasic.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_scibasic.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_scibasic.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_scibasic.ovscignore [default = 3].
--crop <bool>
Automatically crop the output pixel tables in wavelength depending on the expected useful
wavelength range of the observation mode used (4750-9350 Angstrom for nominal mode, 4600-9350
Angstrom for extended mode, 4700-9350 Angstrom for nominal AO mode). (bool; default: True). The
full name of this option for the EsoRex configuration file is muse.muse_scibasic.crop [default =
True].
--cr <str>
Type of cosmic ray cleaning to use (for quick-look data processing). (str; default: ´none´). The
full name of this option for the EsoRex configuration file is muse.muse_scibasic.cr [default =
none].
--xbox <int>
Search box size in x. Only used if cr=dcr. (int; default: 15). The full name of this option for
the EsoRex configuration file is muse.muse_scibasic.xbox [default = 15].
--ybox <int>
Search box size in y. Only used if cr=dcr. (int; default: 40). The full name of this option for
the EsoRex configuration file is muse.muse_scibasic.ybox [default = 40].
--passes <int>
Maximum number of cleaning passes. Only used if cr=dcr. (int; default: 2). The full name of this
option for the EsoRex configuration file is muse.muse_scibasic.passes [default = 2].
--thres <float>
Threshold for detection gap in factors of standard deviation. Only used if cr=dcr. (float;
default: 5.8). The full name of this option for the EsoRex configuration file is
muse.muse_scibasic.thres [default = 5.8].
--combine <str>
Type of combination to use. Note that in most cases, science exposures cannot easily be combined
on the CCD level, so this should usually be kept as "none"! This does not pay attention about the
type of input data, and will combine all raw inputs! (str; default: ´none´). The full name of this
option for the EsoRex configuration file is muse.muse_scibasic.combine [default = none].
--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_scibasic.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_scibasic.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_scibasic.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_scibasic.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_scibasic.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_scibasic.scale
[default = True].
--saveimage <bool>
Save the pre-processed CCD-based image of each input exposure before it is transformed into a
pixel table. (bool; default: True). The full name of this option for the EsoRex configuration file
is muse.muse_scibasic.saveimage [default = True].
--skylines <str>
List of wavelengths of sky emission lines (in Angstrom) to use as reference for wavelength offset
correction using a Gaussian fit. It can contain multiple (isolated) lines, as comma-separated
list, individual shifts are then combined into one weighted average offset. Set to "none" to
deactivate. (str; default: ´5577.339,6300.304´). The full name of this option for the EsoRex
configuration file is muse.muse_scibasic.skylines [default = 5577.339,6300.304].
--skyhalfwidth <float>
Half-width of the extraction box (in Angstrom) around each sky emission line. (float; default:
5.0). The full name of this option for the EsoRex configuration file is
muse.muse_scibasic.skyhalfwidth [default = 5.0].
--skybinsize <float>
Size of the bins (in Angstrom per pixel) for the intermediate spectrum to do the Gaussian fit to
each sky emission line. (float; default: 0.1). The full name of this option for the EsoRex
configuration file is muse.muse_scibasic.skybinsize [default = 0.1].
--skyreject <str>
Sigma clipping parameters for the intermediate spectrum to do the Gaussian fit to each sky
emission line. Up to three comma-separated numbers can be given, which are interpreted as high
sigma-clipping limit (float), low limit (float), and number of iterations (integer), respectively.
(str; default: ´15.,15.,1´). The full name of this option for the EsoRex configuration file is
muse.muse_scibasic.skyreject [default = 15.,15.,1].
--resample <bool>
Resample the input science data into 2D spectral images using all supplied calibrations for a
visual check. Note that the image produced will show small wiggles even when the input
calibrations are good and were applied successfully! (bool; default: False). The full name of this
option for the EsoRex configuration file is muse.muse_scibasic.resample [default = False].
--dlambda <float>
Wavelength step (in Angstrom per pixel) to use for resampling. (float; default: 1.25). The full
name of this option for the EsoRex configuration file is muse.muse_scibasic.dlambda [default =
1.25].
--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_scibasic.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-2.2.0.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 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_flat(7), muse_geometry(7),
muse_lingain(7), muse_lsf(7), muse_qi_mask(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_subtract_sky(7),
muse_scipost_subtract_sky_simple(7), muse_standard(7), muse_twilight(7), muse_wavecal(7)
VERSION
muse_scibasic 2.2.0
AUTHOR
Peter Weilbacher <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 MUSE Instrument Pipeline Copyright (C) 2005, 2017 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