muse_scibasic - Remove the instrumental signature from the data of
each CCD and convert them from an image into a pixel table.
esorex muse_scibasic [OPTIONS] FILE.sof
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.
- --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.
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)
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,
Inc., 51 Franklin St, Fifth Floor, Boston, MA 02111-1307 USA