Provided by: cpl-plugin-muse-doc_2.6.2+dfsg-1_all
muse_geometry - Compute relative location of the slices within the field of view and measure the instrumental PSF on the detectors.
esorex muse_geometry [OPTIONS] FILE.sof
Processing first works separately on each IFU of the raw input data (in parallel): it trims the raw data and records the overscan statistics, subtracts the bias and converts them from adu to count. Optionally, the dark can be subtracted and the data can be divided by the flat-field. The data of all input mask exposures is then averaged. The averaged image together with the trace table and wavelength calibration as well as the line catalog are used to detect spots. The detection windows are used to measure the spots on all images of the sequence, the result is saved, with information on the measured PSF, in the spots tables. Then properties of all slices are computed, first separately on each IFU to determine the peak position of the mask for each slice and its angle, subsequently the width and horizontal position. Then, the result of all IFUs is analyzed together to produce a refined horizontal position, applying global shifts to each IFU as needed. The vertical position is then determined using the known slice ordering on the sky; the relative peak positions are put into sequence, taking into account the vertical offsets of the pinholes in the mask. The table is then cleaned up from intermediate debug data. If the --smooth parameter is set to a positive value, it is used to do a sigma-clipped smoothing within each slicer stack, for a more regular appearance of the output table. The table is then saved. As a last optional step, additional raw input data is reduced using the newly geometry to produce an image of the field of view. If these exposures contain smooth features, they can be used as a visual check of the quality of the geometrical calibration.
--ifu1 <int> First IFU to analyze. (int; default: 1). The full name of this option for the EsoRex configuration file is muse.muse_geometry.ifu1 [default = 1]. --ifu2 <int> Last IFU to analyze. (int; default: 24). The full name of this option for the EsoRex configuration file is muse.muse_geometry.ifu2 [default = 24]. --sigma <float> Sigma detection level for spot detection, in terms of median deviation above the median. (float; default: 2.2). The full name of this option for the EsoRex configuration file is muse.muse_geometry.sigma [default = 2.2]. --centroid <str> Type of centroiding and FWHM determination to use for all spot measurements: simple barycenter method or using a Gaussian fit. (str; default: ´gaussian´). The full name of this option for the EsoRex configuration file is muse.muse_geometry.centroid [default = gaussian]. --smooth <float> Use this sigma-level cut for smoothing of the output table within each slicer stack. Set to non-positive value to deactivate smoothing. (float; default: 1.5). The full name of this option for the EsoRex configuration file is muse.muse_geometry.smooth [default = 1.5]. --lambdamin <float> When passing any MASK_CHECK frames in the input, use this lower wavelength cut before reconstructing the image. (float; default: 6800.0). The full name of this option for the EsoRex configuration file is muse.muse_geometry.lambdamin [default = 6800.0]. --lambdamax <float> When passing any MASK_CHECK frames in the input, use this upper wavelength cut before reconstructing the image. (float; default: 7200.0). The full name of this option for the EsoRex configuration file is muse.muse_geometry.lambdamax [default = 7200.0]. 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_dark(7), muse_exp_align(7), muse_exp_combine(7), muse_flat(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 <firstname.lastname@example.org>
Please report any problems to email@example.com. Alternatively, you may send a report to the ESO User Support Department <firstname.lastname@example.org>.
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