Extraction of scientific spectra
esorex fors_pmos_extract [OPTIONS] FILE.sof
This recipe is used to reduce scientific spectra using the extraction mask and the products created by the recipe fors_mpol_calib. The spectra are bias subtracted, flat fielded (if a normalised flat field is specified) and remapped eliminating the optical distortions. The wavelength calibration can be optionally upgraded using a number of sky lines: if no sky lines catalog of wavelengths is specified, an internal one is used instead.
If the alignment to the sky lines is performed, the input dispersion coefficients table is upgraded and saved to disk, and a new CCD wavelengths map is created.
This recipe accepts both FORS1 and FORS2 frames. A grism table (typically depending on the instrument mode, and in particular on the grism used) may also be specified: this table contains a default recipe parameter setting to control the way spectra are extracted for a specific instrument mode, as it is used for automatic run of the pipeline on Paranal and in Garching. If this table is specified, it will modify the default recipe parameter setting, with the exception of those parameters which have been explicitly modifyed on the command line. If a grism table is not specified, the input recipe parameters values will always be read from the command line, or from an esorex configuration file if present, or from their generic default values (that are rarely meaningful).
Either a scientific or a standard star exposure can be specified in input.
The acronym SCI on products should be read STD in case of standard stars observations.
Input files:
DO category: Type: Explanation: Required: SCIENCE_PMOS Raw Scientific exposure Y or STANDARD_PMOS Raw Standard star exposure Y MASTER_BIAS Calib Master bias Y GRISM_TABLE Calib Grism table .
MASTER_SKYLINECAT Calib Sky lines catalog .
MASTER_NORM_FLAT_PMOS Calib Normalised flat field .
DISP_COEFF_PMOS Calib Inverse dispersion Y CURV_COEFF_PMOS Calib Spectral curvature Y SLIT_LOCATION_PMOS Calib Slits positions table Y RETARDER_WAVEPLATE_CHROMATISM Calib Chromatism correction .
Output files:
DO category: Data type: Explanation: REDUCED_SCI_PMOS FITS image Extracted scientific spectra REDUCED_SKY_SCI_PMOS FITS image Extracted sky spectra REDUCED_ERROR_SCI_PMOS FITS image Errors on extracted spectra REDUCED_SCI_X_PMOS FITS image X Stokes parameter (and L) REDUCED_ERROR_X_PMOS FITS image Error on X Stokes parameter REDUCED_NUL_X_PMOS FITS image Null parameter for X REDUCED_POL_ANGLE_PMOS FITS image Direction of linear polarization REDUCED_POL_ANGLE_ERROR_PMOS FITS image Error on polarization direction UNMAPPED_SCI_PMOS FITS image Sky subtracted scientific spectra MAPPED_SCI_PMOS FITS image Rectified scientific spectra MAPPED_ALL_SCI_PMOS FITS image Rectified science spectra with sky MAPPED_SKY_SCI_PMOS FITS image Rectified sky spectra UNMAPPED_SKY_SCI_PMOS FITS image Sky on CCD GLOBAL_SKY_SPECTRUM_PMOS FITS table Global sky spectrum OBJECT_TABLE_SCI_PMOS FITS table Positions of detected objects OBJECT_TABLE_POL_SCI_PMOS FITS table Positions of real objects
Only if the sky-alignment of the wavelength solution is requested: DISP_COEFF_SCI_PMOS FITS table Upgraded dispersion coefficients WAVELENGTH_MAP_SCI_PMOS FITS image Upgraded wavelength map
--dispersion <float>
Resampling step (Angstrom/pixel) (float; default: 0.0). The full name of this option for the EsoRex configuration file is fors.fors_pmos_extract.dispersion [default = 0.0].
--skyalign <long>
Polynomial order for sky lines alignment, or -1 to avoid alignment (long; default: 0). The full name of this option for the EsoRex configuration file is fors.fors_pmos_extract.skyalign [default = 0].
--wcolumn <str>
Name of sky line catalog table column with wavelengths (str; default: \'WLEN\'). The full name of this option for the EsoRex configuration file is fors.fors_pmos_extract.wcolumn [default = WLEN].
--startwavelength <float>
Start wavelength in spectral extraction (float; default: 0.0). The full name of this option for the EsoRex configuration file is fors.fors_pmos_extract.startwavelength [default = 0.0].
--endwavelength <float>
End wavelength in spectral extraction (float; default: 0.0). The full name of this option for the EsoRex configuration file is fors.fors_pmos_extract.endwavelength [default = 0.0].
--flux <bool>
Apply flux conservation (bool; default: True). The full name of this option for the EsoRex configuration file is fors.fors_pmos_extract.flux [default = True].
--flatfield <bool>
Apply flat field (bool; default: False). The full name of this option for the EsoRex configuration file is fors.fors_pmos_extract.flatfield [default = False].
--skyglobal <bool>
Subtract global sky spectrum from CCD (bool; default: False). The full name of this option for the EsoRex configuration file is fors.fors_pmos_extract.skyglobal [default = False].
--skymedian <bool>
Sky subtraction from extracted slit spectra (bool; default: False). The full name of this option for the EsoRex configuration file is fors.fors_pmos_extract.skymedian [default = False].
--skylocal <bool>
Sky subtraction from CCD slit spectra (bool; default: True). The full name of this option for the EsoRex configuration file is fors.fors_pmos_extract.skylocal [default = True].
--cosmics <bool>
Eliminate cosmic rays hits (only if global sky subtraction is also requested) (bool; default: False). The full name of this option for the EsoRex configuration file is fors.fors_pmos_extract.cosmics [default = False].
--slit_margin <long>
Number of pixels to exclude at each slit in object detection and extraction (long; default: 3). The full name of this option for the EsoRex configuration file is fors.fors_pmos_extract.slit_margin [default = 3].
--ext_radius <long>
Maximum extraction radius for detected objects (pixel) (long; default: 6). The full name of this option for the EsoRex configuration file is fors.fors_pmos_extract.ext_radius [default = 6].
--cont_radius <long>
Minimum distance at which two objects of equal luminosity do not contaminate each other (pixel) (long; default: 0). The full name of this option for the EsoRex configuration file is fors.fors_pmos_extract.cont_radius [default = 0].
--ext_mode <long>
Object extraction method: 0 = aperture, 1 = Horne optimal extraction (long; default: 1). The full name of this option for the EsoRex configuration file is fors.fors_pmos_extract.ext_mode [default = 1].
--time_normalise <bool>
Normalise output spectra by the exposure time (bool; default: True). The full name of this option for the EsoRex configuration file is fors.fors_pmos_extract.time_normalise [default = True].
--chromatism <bool>
Chromatism correction to polarization angles (bool; default: True). The full name of this option for the EsoRex configuration file is fors.fors_pmos_extract.chromatism [default = True].
--check <bool>
Create intermediate products (bool; default: False). The full name of this option for the EsoRex configuration file is fors.fors_pmos_extract.check [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 fors pipeline can be downloaded as a PDF file using the following URL:
ftp://ftp.eso.org/pub/dfs/pipelines/fors/fors-pipeline-manual-4.9.pdf
An overview over the existing ESO pipelines can be found on the web page http://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 http://packages.python.org/python-cpl/index.html for further information.
The other recipes of the fors pipeline are fors_wave_calib_lss(7), fors_img_sky_flat(7), fors_resample(7), fors_config(7), fors_extract_objects(7), fors_calib(7), fors_wave_calib(7), fors_detect_objects(7), fors_pmos_science(7), fors_extract_slits(7), test_hough(7), fors_img_screen_flat(7), fors_extract(7), fors_remove_bias(7), fors_subtract_sky(7), fors_normalise_flat(7), montecarlo(7), fors_photometry(7), fors_zeropoint(7), fors_dark(7), fors_subtract_sky_lss(7), fors_trace_flat(7), fors_flatfield(7), fors_img_science(7), fors_detect_spectra(7), fors_sumflux(7), fors_align_sky_lss(7), fors_bias(7), fors_align_sky(7), fors_pmos_calib(7), fors_spec_mflat(7), fors_science(7)
fors_pmos_extract 5.0.0
Carlo Izzo <[email protected]>
Please report any problems to [email protected]. Alternatively, you may send a report to the ESO User Support Department <[email protected]>.
This file is currently part of the FORS Instrument Pipeline Copyright (C) 2002-2010 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.
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