Provided by: cpl-plugin-muse-doc_2.8.7+dfsg-3_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 active instrument mode (4750-9350 Angstrom for
nominal mode and NFM, 4700-9350 Angstrom for nominal AO mode, and 4600-9350
Angstrom for the extended modes). (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-2.8.7.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_flat(7),
muse_geometry(7), muse_illum(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_raman(7),
muse_scipost_subtract_sky(7), muse_scipost_subtract_sky_simple(7), muse_standard(7),
muse_twilight(7), muse_wavecal(7)
VERSION
muse_scibasic 2.8.7
AUTHOR
Peter Weilbacher <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