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muse_dark - Combine several separate dark images into one master dark file and locate hot pixels.
esorex muse_dark [OPTIONS] FILE.sof
This recipe combines several separate dark images into one master dark file. The master dark contains the combined pixel values of the raw dark exposures, with respect to the image combination method used and normalization time specified. Processing trims the raw data and records the overscan statistics, subtracts the bias (taking account of the overscan, if --overscan is not "none") from each raw input image, converts them from adu to count, scales them according to their exposure time, and combines them using input parameters. Hot pixels are then identified using image statistics and marked in the data quality extension. The combined image is normalized to 1 hour exposure time. QC statistics are computed on the output master dark.
--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_dark.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_dark.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_dark.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_dark.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_dark.ovscignore [default = 3]. --combine <str> Type of image combination to use. (str; default: ´sigclip´). The full name of this option for the EsoRex configuration file is muse.muse_dark.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_dark.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_dark.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_dark.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_dark.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_dark.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_dark.scale [default = True]. --normalize <float> Normalize the master dark to this exposure time (in seconds). To disable normalization, set this to a negative value. (float; default: 3600.0). The full name of this option for the EsoRex configuration file is muse.muse_dark.normalize [default = 3600.0]. --hotsigma <float> Sigma level, in terms of median deviation above the median dark level, above which a pixel is detected and marked as ´hot´. (float; default: 5.0). The full name of this option for the EsoRex configuration file is muse.muse_dark.hotsigma [default = 5.0]. --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_dark.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-2.6.2.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_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 <email@example.com>
Please report any problems to firstname.lastname@example.org. Alternatively, you may send a report to the ESO User Support Department <email@example.com>.
This file is part of the MUSE Instrument Pipeline Copyright (C) 2005, 2018 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