.TH MUSE_SCIBASIC "7" "2.8.7" "muse_scibasic" "muse recipes"
.SH NAME
muse_scibasic \- Remove the instrumental signature from the data of each CCD and convert them from an image into a pixel table.

.SH SYNOPSIS
esorex
.B muse_scibasic
[OPTIONS] FILE.sof

.SH 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.

.SH OPTIONS
.TP
\fB\-\-nifu\fR \fI<int>\fR
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 \fBmuse.muse_scibasic.nifu\fR [default = \fI0\fR].
.TP
\fB\-\-overscan\fR \fI<str>\fR
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 \fBmuse.muse_scibasic.overscan\fR [default = \fIvpoly\fR].
.TP
\fB\-\-ovscreject\fR \fI<str>\fR
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 \fBmuse.muse_scibasic.ovscreject\fR [default = \fIdcr\fR].
.TP
\fB\-\-ovscsigma\fR \fI<float>\fR
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 \fBmuse.muse_scibasic.ovscsigma\fR [default = \fI30.0\fR].
.TP
\fB\-\-ovscignore\fR \fI<int>\fR
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 \fBmuse.muse_scibasic.ovscignore\fR [default = \fI3\fR].
.TP
\fB\-\-crop\fR \fI<bool>\fR
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 \fBmuse.muse_scibasic.crop\fR [default = \fITrue\fR].
.TP
\fB\-\-cr\fR \fI<str>\fR
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 \fBmuse.muse_scibasic.cr\fR [default = \fInone\fR].
.TP
\fB\-\-xbox\fR \fI<int>\fR
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 \fBmuse.muse_scibasic.xbox\fR [default = \fI15\fR].
.TP
\fB\-\-ybox\fR \fI<int>\fR
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 \fBmuse.muse_scibasic.ybox\fR [default = \fI40\fR].
.TP
\fB\-\-passes\fR \fI<int>\fR
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 \fBmuse.muse_scibasic.passes\fR [default = \fI2\fR].
.TP
\fB\-\-thres\fR \fI<float>\fR
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 \fBmuse.muse_scibasic.thres\fR [default = \fI5.8\fR].
.TP
\fB\-\-combine\fR \fI<str>\fR
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 \fBmuse.muse_scibasic.combine\fR [default = \fInone\fR].
.TP
\fB\-\-nlow\fR \fI<int>\fR
Number of minimum pixels to reject with minmax (int; default: 1). The full name of this option for the EsoRex configuration
file is \fBmuse.muse_scibasic.nlow\fR [default = \fI1\fR].
.TP
\fB\-\-nhigh\fR \fI<int>\fR
Number of maximum pixels to reject with minmax (int; default: 1). The full name of this option for the EsoRex configuration
file is \fBmuse.muse_scibasic.nhigh\fR [default = \fI1\fR].
.TP
\fB\-\-nkeep\fR \fI<int>\fR
Number of pixels to keep with minmax (int; default: 1). The full name of this option for the EsoRex configuration
file is \fBmuse.muse_scibasic.nkeep\fR [default = \fI1\fR].
.TP
\fB\-\-lsigma\fR \fI<float>\fR
Low sigma for pixel rejection with sigclip (float; default: 3.0). The full name of this option for the EsoRex configuration
file is \fBmuse.muse_scibasic.lsigma\fR [default = \fI3.0\fR].
.TP
\fB\-\-hsigma\fR \fI<float>\fR
High sigma for pixel rejection with sigclip (float; default: 3.0). The full name of this option for the EsoRex configuration
file is \fBmuse.muse_scibasic.hsigma\fR [default = \fI3.0\fR].
.TP
\fB\-\-scale\fR \fI<bool>\fR
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 \fBmuse.muse_scibasic.scale\fR [default = \fITrue\fR].
.TP
\fB\-\-saveimage\fR \fI<bool>\fR
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 \fBmuse.muse_scibasic.saveimage\fR [default = \fITrue\fR].
.TP
\fB\-\-skylines\fR \fI<str>\fR
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 \fBmuse.muse_scibasic.skylines\fR [default = \fI5577.339,6300.304\fR].
.TP
\fB\-\-skyhalfwidth\fR \fI<float>\fR
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 \fBmuse.muse_scibasic.skyhalfwidth\fR [default = \fI5.0\fR].
.TP
\fB\-\-skybinsize\fR \fI<float>\fR
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 \fBmuse.muse_scibasic.skybinsize\fR [default = \fI0.1\fR].
.TP
\fB\-\-skyreject\fR \fI<str>\fR
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 \fBmuse.muse_scibasic.skyreject\fR [default = \fI15.,15.,1\fR].
.TP
\fB\-\-resample\fR \fI<bool>\fR
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 \fBmuse.muse_scibasic.resample\fR [default = \fIFalse\fR].
.TP
\fB\-\-dlambda\fR \fI<float>\fR
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 \fBmuse.muse_scibasic.dlambda\fR [default = \fI1.25\fR].
.TP
\fB\-\-merge\fR \fI<bool>\fR
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 \fBmuse.muse_scibasic.merge\fR [default = \fIFalse\fR].

.PP
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.

.SH SEE ALSO
The full documentation for the muse pipeline can be downloaded as 
a PDF file using the following URL:
.IP
.B ftp://ftp.eso.org/pub/dfs/pipelines/muse/muse\-pipeline\-cookbook\-2.8.7.pdf
.PP
An overview over the existing ESO pipelines can be found on the web page
\fBhttps://www.eso.org/sci/software/pipelines/\fR.
.PP
Basic documentation about the EsoRex program can be found at the esorex (1) 
man page.
.PP
It is possible to call the pipelines from python using the python\-cpl package.
See \fBhttps://packages.python.org/python\-cpl/index.html\fR for further
information.
.PP
The other recipes of the muse pipeline are
.IR muse_ampl (7),
.IR muse_astrometry (7),
.IR muse_bias (7),
.IR muse_create_sky (7),
.IR muse_dark (7),
.IR muse_exp_align (7),
.IR muse_exp_combine (7),
.IR muse_flat (7),
.IR muse_geometry (7),
.IR muse_illum (7),
.IR muse_lingain (7),
.IR muse_lsf (7),
.IR muse_qi_mask (7),
.IR muse_scipost (7),
.IR muse_scipost_apply_astrometry (7),
.IR muse_scipost_calibrate_flux (7),
.IR muse_scipost_combine_pixtables (7),
.IR muse_scipost_correct_dar (7),
.IR muse_scipost_correct_rv (7),
.IR muse_scipost_make_cube (7),
.IR muse_scipost_raman (7),
.IR muse_scipost_subtract_sky (7),
.IR muse_scipost_subtract_sky_simple (7),
.IR muse_standard (7),
.IR muse_twilight (7),
.IR muse_wavecal (7)

.SH VERSION
muse_scibasic 2.8.7

.SH AUTHOR
Peter Weilbacher <https://support.eso.org>

.SH 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>.

.SH 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