The fors_science recipe

fors_science

Synopsis

Extraction of scientific spectra

Description

This recipe is used to reduce scientific spectra using the extraction mask and the products created by the recipe fors_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).

In the table below the MXU acronym can be read alternatively as MOS and LSS, depending on the instrument mode of the input data. The acronym SCI on products should be read STD in case of standard stars observations A CURV_COEFF table is not (yet) expected for LSS data.

Either a scientific or a standard star exposure can be specified in input.

Only in case of a standard star exposure input, the atmospheric extinction table and a table with the physical fluxes of the observed standard star must be specified in input, and a spectro-photometric table is created in output. This table can then be input again to this recipe, always with an atmospheric extinction table, and if a photometric calibration is requested then flux calibrated spectra (in units of erg/cm/cm/s/Angstrom) are also written in output.

Input files

DO category:               Type:       Explanation:         Required:
SCIENCE_MXU                Raw         Scientific exposure      Y
or STANDARD_MXU            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_MXU       Calib       Normalised flat field    .

DISP_COEFF_MXU             Calib       Inverse dispersion       Y
CURV_COEFF_MXU             Calib       Spectral curvature       Y
SLIT_LOCATION_MXU          Calib       Slits positions table    Y
FLAT_SED_MXU               Calib       Slits dispersion profile .


or, in case of LSS-like MOS/MXU data,

MASTER_NORM_FLAT_LONG_MXU  Calib       Normalised flat field    .

DISP_COEFF_LONG_MXU        Calib       Inverse dispersion       Y
SLIT_LOCATION_LONG_MXU     Calib       Slits positions table    Y
GLOBAL_DISTORTION_TABLE    Calib       Global distortion        .


In case STANDARD_MXU is specified in input,

EXTINCT_TABLE              Calib       Atmospheric extinction   Y
STD_FLUX_TABLE             Calib       Standard star flux       Y
TELLURIC_CONTAMINATION     Calib       Telluric regions list    .


The following input files are mandatory if photometric calibrated  spectra are desired:

EXTINCT_TABLE              Calib       Atmospheric extinction   Y
SPECPHOT_TABLE             Calib       Response curves          Y

If requested for standard star data, the SPECPHOT_TABLE can be dropped:
in this case the correction is applied using the SPECPHOT_TABLE produced
in the same run.

Output files

DO category:               Data type:  Explanation:
REDUCED_SCI_MXU            FITS image  Extracted scientific spectra
REDUCED_SKY_SCI_MXU        FITS image  Extracted sky spectra
REDUCED_ERROR_SCI_MXU      FITS image  Errors on extracted spectra
UNMAPPED_SCI_MXU           FITS image  Sky subtracted scientific spectra
MAPPED_SCI_MXU             FITS image  Rectified scientific spectra
MAPPED_ALL_SCI_MXU         FITS image  Rectified science spectra with sky
MAPPED_SKY_SCI_MXU         FITS image  Rectified sky spectra
UNMAPPED_SKY_SCI_MXU       FITS image  Sky on CCD
OBJECT_TABLE_SCI_MXU       FITS table  Positions of detected objects

Only if the global sky subtraction is requested:
GLOBAL_SKY_SPECTRUM_MXU    FITS table  Global sky spectrum

Only if the sky-alignment of the wavelength solution is requested:
SKY_SHIFTS_LONG_SCI_MXU    FITS table  Sky lines offsets (LSS-like data)
or SKY_SHIFTS_SLIT_SCI_MXU FITS table  Sky lines offsets (MOS-like data)
DISP_COEFF_SCI_MXU         FITS table  Upgraded dispersion coefficients
WAVELENGTH_MAP_SCI_MXU     FITS image  Upgraded wavelength map

Only if a STANDARD_MXU is specified in input:
SPECPHOT_TABLE             FITS table  Efficiency and response curves

Only if a photometric calibration was requested:
REDUCED_FLUX_SCI_MXU       FITS image  Flux calibrated scientific spectra
REDUCED_FLUX_ERROR_SCI_MXU FITS image  Errors on flux calibrated spectra
MAPPED_FLUX_SCI_MXU        FITS image  Flux calibrated slit spectra

Constructor

cpl.Recipe("fors_science")

Create an object for the recipe fors_science.

import cpl
fors_science = cpl.Recipe("fors_science")

Parameters

fors_science.param.skyalign

Polynomial order for sky lines alignment, or -1 to avoid alignment (int; default: -1) [default=-1].

fors_science.param.flatfield

Apply flat field (bool; default: True) [default=True].

fors_science.param.skyglobal

Subtract global sky spectrum from CCD (bool; default: False) [default=False].

fors_science.param.skymedian

Sky subtraction from extracted slit spectra (bool; default: False) [default=False].

fors_science.param.skylocal

Sky subtraction from CCD slit spectra (bool; default: True) [default=True].

fors_science.param.cosmics

Eliminate cosmic rays hits, only if either global or local (not for LSS) sky subtraction is also requested. (bool; default: False) [default=False].

fors_science.param.slit_margin

Number of pixels to exclude at each slit in object detection and extraction (int; default: 3) [default=3].

fors_science.param.ext_radius

Maximum extraction radius for detected objects (unbinned pixel) (int; default: 12) [default=12].

fors_science.param.cont_radius

Minimum distance at which two objects of equal luminosity do not contaminate each other (pixel) (int; default: 0) [default=0].

fors_science.param.ext_mode

Object extraction method: 0 = aperture, 1 = Horne optimal extraction (int; default: 1) [default=1].

fors_science.param.resp_fit_nknots

Number of knots in spline fitting of the instrument response. (-1: No fitting. -2: Read from grism table) (int; default: -2) [default=-2].

fors_science.param.resp_fit_degree

Degree of polynomial in fitting of the instrument response. (-1: No fitting. -2: Read from grism table) (int; default: -2) [default=-2].

fors_science.param.resp_ignore_mode

Types of lines/regions to ignore in response. Valid ones are ‘stellar_absorption’, ‘telluric’ and ‘command_line’ (from parameter resp_ignore_lines) (str; default: ‘stellar_absorption,telluric,command_line’) [default=”stellar_absorption,telluric,command_line”].

fors_science.param.resp_ignore_points

Extra lines/regions to ignore in response. Use a comma separated list of values. A range can be specified like 4500.0-4600.0 (str; default: ‘’) [default=””].

fors_science.param.resp_use_flat_sed

Use the flat SED to normalise the observed spectra. Value are true, false, grism_table. (str; default: ‘grism_table’) [default=”grism_table”].

fors_science.param.nonlinear_level

Level above which the detector is not linear (float; default: 60000.0) [default=60000.0].

fors_science.param.generate_idp

Set to TRUE to request IDP generation (bool; default: False) [default=False].

The following code snippet shows the default settings for the available parameters.

import cpl
fors_science = cpl.Recipe("fors_science")

fors_science.param.skyalign = -1
fors_science.param.flatfield = True
fors_science.param.skyglobal = False
fors_science.param.skymedian = False
fors_science.param.skylocal = True
fors_science.param.cosmics = False
fors_science.param.slit_margin = 3
fors_science.param.ext_radius = 12
fors_science.param.cont_radius = 0
fors_science.param.ext_mode = 1
fors_science.param.resp_fit_nknots = -2
fors_science.param.resp_fit_degree = -2
fors_science.param.resp_ignore_mode = "stellar_absorption,telluric,command_line"
fors_science.param.resp_ignore_points = ""
fors_science.param.resp_use_flat_sed = "grism_table"
fors_science.param.nonlinear_level = 60000.0
fors_science.param.generate_idp = False

You may also set or overwrite some or all parameters by the recipe parameter param, as shown in the following example:

import cpl
fors_science = cpl.Recipe("fors_science")
[...]
res = fors_science( ..., param = {"skyalign":-1, "flatfield":True})

See also

cpl.Recipe for more information about the recipe object.

Bug reports

Please report any problems to Carlo Izzo. Alternatively, you may send a report to the ESO User Support Department.