gimasterflat - Create the fiber master flat field and the
localization mask.
esorex gimasterflat [OPTIONS] FILE.sof
For detailed information please refer to the GIRAFFE pipeline user
manual.
It is available at http://www.eso.org/pipelines.
- --fiber-splist
<str>
- Index list of spectra to use for localization (e.g. 2,10,30-40,55). (str;
default: ´´). The full name of this option for the EsoRex
configuration file is giraffe.fibers.spectra [default =
].
- --fiber-nspec
<int>
- Number of spectra to localize. (int; default: 0). The full name of this
option for the EsoRex configuration file is giraffe.fibers.nspectra
[default = 0].
- --remove-bias
<bool>
- Enable bias removal (bool; default: True). The full name of this option
for the EsoRex configuration file is giraffe.biasremoval.remove
[default = True].
- --bsremove-method
<str>
- Bias removal method (str; default: ´PROFILE´). The full name
of this option for the EsoRex configuration file is
giraffe.biasremoval.method [default = PROFILE].
- --bsremove-areas
<str>
- Bias areas to use (Xl0:Xr0:Yl0:Yr0, ... ,Xln:Xrn:Yln:Yrn) (str; default:
´5:40:0:4095´). The full name of this option for the EsoRex
configuration file is giraffe.biasremoval.areas [default =
5:40:0:4095].
- --bsremove-sigma
<float>
- Sigma Clipping: sigma threshold factor (float; default: 2.5). The full
name of this option for the EsoRex configuration file is
giraffe.biasremoval.sigma [default = 2.5].
- --bsremove-niter
<int>
- Sigma Clipping: maximum number of iterations (int; default: 5). The full
name of this option for the EsoRex configuration file is
giraffe.biasremoval.iterations [default = 5].
- --bsremove-mfrac
<float>
- Sigma Clipping: minimum fraction of points accepted/total [0.0..1.0]
(float; default: 0.8). The full name of this option for the EsoRex
configuration file is giraffe.biasremoval.fraction [default =
0.8].
- --bsremove-xorder
<int>
- Order of X polynomial fit (CURVE method only) (int; default: 1). The full
name of this option for the EsoRex configuration file is
giraffe.biasremoval.xorder [default = 1].
- --bsremove-yorder
<int>
- Order of Y polynomial fit (CURVE method only) (int; default: 1). The full
name of this option for the EsoRex configuration file is
giraffe.biasremoval.yorder [default = 1].
- --bsremove-xstep
<int>
- Sampling step along X (CURVE method only) (int; default: 1). The full name
of this option for the EsoRex configuration file is
giraffe.biasremoval.xstep [default = 1].
- --bsremove-ystep
<int>
- Sampling step along Y (CURVE method only) (int; default: 1). The full name
of this option for the EsoRex configuration file is
giraffe.biasremoval.ystep [default = 1].
- --sloc-mode
<str>
- Localization mode: Use all spectra or the 5 SIWC spectra (str; default:
´all´). The full name of this option for the EsoRex
configuration file is giraffe.localization.mode [default =
all].
- --sloc-start
<int>
- Bin along x-axis (int; default: -1). The full name of this option for the
EsoRex configuration file is giraffe.localization.start [default =
-1].
- --sloc-retries
<int>
- Initial localization detection xbin retries. (int; default: 10). The full
name of this option for the EsoRex configuration file is
giraffe.localization.retries [default = 10].
- --sloc-binsize
<int>
- Initial localization detection xbin size. (int; default: -1). The full
name of this option for the EsoRex configuration file is
giraffe.localization.binsize [default = -1].
- --sloc-ewidth
<float>
- Localization detection extra width. (float; default: 1.0). The full name
of this option for the EsoRex configuration file is
giraffe.localization.ewidth [default = 1.0].
- --sloc-ywidth
<int>
- Full width [pxl] of the equilizing filter (distance between two adjacent
fibers). (int; default: -1). The full name of this option for the EsoRex
configuration file is giraffe.localization.ywidth [default =
-1].
- --sloc-center
<str>
- Method used for mask center computation. (str; default:
´centroid´). The full name of this option for the EsoRex
configuration file is giraffe.localization.center [default =
centroid].
- --sloc-norm
<bool>
- Enable spectrum normalization along the dispersion axis. (bool; default:
False). The full name of this option for the EsoRex configuration file is
giraffe.localization.normalize [default = False].
- --sloc-noise
<float>
- Threshold multiplier. (float; default: 7.0). The full name of this option
for the EsoRex configuration file is giraffe.localization.noise
[default = 7.0].
- --sloc-threshold
<str>
- Selects thresholding algorithm: local, row or global (str; default:
´local´). The full name of this option for the EsoRex
configuration file is giraffe.localization.threshold [default =
local].
- --sloc-ron
<float>
- New bias sigma (RON) value for dark subtraction (float; default: -1.0).
The full name of this option for the EsoRex configuration file is
giraffe.localization.ron [default = -1.0].
- --sloc-yorder
<int>
- Order of Chebyshev polynomial fit. (int; default: 4). The full name of
this option for the EsoRex configuration file is
giraffe.localization.yorder [default = 4].
- --sloc-worder
<int>
- Order of Chebyshev 2D polynomial fit. (int; default: 2). The full name of
this option for the EsoRex configuration file is
giraffe.localization.worder [default = 2].
- --sloc-sigma
<float>
- Localization clipping: sigma threshold factor (float; default: 2.5). The
full name of this option for the EsoRex configuration file is
giraffe.localization.sigma [default = 2.5].
- --sloc-niter
<int>
- Localization clipping: number of iterations (int; default: 5). The full
name of this option for the EsoRex configuration file is
giraffe.localization.iterations [default = 5].
- --sloc-mfrac
<float>
- Localization clipping: minimum fraction of points accepted/total. (float;
default: 0.9). The full name of this option for the EsoRex configuration
file is giraffe.localization.fraction [default = 0.9].
- --psf-model
<str>
- PSF profile model: `psfexp´, `psfexp2´ (str; default:
´psfexp2´). The full name of this option for the EsoRex
configuration file is giraffe.psf.model [default =
psfexp2].
- --psf-norm
<bool>
- Use normalized pixel values. (bool; default: False). The full name of this
option for the EsoRex configuration file is giraffe.psf.normalize
[default = False].
- --psf-binsize
<int>
- Size of bin along dispersion axis (int; default: 64). The full name of
this option for the EsoRex configuration file is
giraffe.psf.binsize [default = 64].
- --psf-maxwidth
<float>
- Maximum width of the PSF profile. (float; default: 16.0). The full name of
this option for the EsoRex configuration file is
giraffe.psf.maxwidth [default = 16.0].
- --psf-width
<float>
- Initial width of the PSF profile. (float; default: 0.0). The full name of
this option for the EsoRex configuration file is giraffe.psf.width
[default = 0.0].
- --psf-exponent
<float>
- Exponent of the exponential PSF profile (will not be fitted if > 0).
(float; default: -3.0). The full name of this option for the EsoRex
configuration file is giraffe.psf.exponent [default =
-3.0].
- --psf-pfniter
<int>
- Maximum number of iterations used for the fit of the fiber PSF profile.
(int; default: 120). The full name of this option for the EsoRex
configuration file is giraffe.psf.profile.iterations [default =
120].
- --psf-pfntest
<int>
- Maximum number of tests used for the fit of the fiber PSF profile (int;
default: 7). The full name of this option for the EsoRex configuration
file is giraffe.psf.profile.tests [default = 7].
- --psf-pfdchisq
<float>
- Minimum chi-square difference used for the fit of the fiber PSF profile.
(float; default: 0.001). The full name of this option for the EsoRex
configuration file is giraffe.psf.profile.dchisquare [default =
0.001].
- --psf-prmfit
<bool>
- 2D fit of the PSF profile parameters using a Chebyshev polynomial model.
(bool; default: False). The full name of this option for the EsoRex
configuration file is giraffe.psf.parameters.fit [default =
False].
- --psf-yorder
<int>
- Order of Chebyshev polynomial fit. (int; default: 4). The full name of
this option for the EsoRex configuration file is
giraffe.psf.parameters.yorder [default = 4].
- --psf-worder
<int>
- Order of Chebyshev 2D polynomial fit. (int; default: 4). The full name of
this option for the EsoRex configuration file is
giraffe.psf.parameters.worder [default = 4].
- --psf-sigma
<float>
- PSF parameter fitting: sigma threshold factor (float; default: 3.5). The
full name of this option for the EsoRex configuration file is
giraffe.psf.parameters.sigma [default = 3.5].
- --psf-niter
<int>
- PSF parameter fitting: number of iterations (int; default: 10). The full
name of this option for the EsoRex configuration file is
giraffe.psf.parameters.iterations [default = 10].
- --psf-mfrac
<float>
- PSF parameter fitting: minimum fraction of points accepted/total. (float;
default: 0.8). The full name of this option for the EsoRex configuration
file is giraffe.psf.parameters.fraction [default =
0.8].
- --extr-method
<str>
- Extraction method: ´SUM´, ´HORNE´ or
´OPTIMAL´ (str; default: ´SUM´). The full name
of this option for the EsoRex configuration file is
giraffe.extraction.method [default = SUM].
- --extr-ron
<float>
- New bias sigma (RON) value for bias and dark corrected image (float;
default: -1.0). The full name of this option for the EsoRex configuration
file is giraffe.extraction.ron [default = -1.0].
- --extr-psfmodel
<str>
- PSF profile model: `psfexp´, `psfexp2´ (str; default:
´psfexp2´). The full name of this option for the EsoRex
configuration file is giraffe.extraction.psf.model [default =
psfexp2].
- --extr-psfsigma
<float>
- Sigma clippging threshold used for rejecting data points during PSF
fitting (Horne´s sigma). It is used to reject bad pixels and
cosmics. (float; default: 7.0). The full name of this option for the
EsoRex configuration file is giraffe.extraction.psf.sigma [default
= 7.0].
- --extr-psfniter
<int>
- Maximum number of iterations used for fitting the PSF profile. (int;
default: 2). The full name of this option for the EsoRex configuration
file is giraffe.extraction.psf.iterations [default =
2].
- --extr-hewidth
<int>
- Horne extraction method: Number of extra pixels added to the fiber
half-width. (int; default: 2). The full name of this option for the EsoRex
configuration file is giraffe.extraction.horne.extrawidth [default
= 2].
- --extr-hmingood
<int>
- Horne extraction method: Minimum number of points used for the profile
fit. It sets the lower limit of data points for the pixel rejection. (int;
default: 3). The full name of this option for the EsoRex configuration
file is giraffe.extraction.horne.mingood [default = 3].
- --extr-omfrac
<float>
- Optimal extraction method: Minimum fraction of the data points used for
fitting the fiber profiles. It sets the lower limit for the pixel
rejection. (float; default: 0.9). The full name of this option for the
EsoRex configuration file is giraffe.extraction.optimal.fraction
[default = 0.9].
- --extr-owfactor
<float>
- Optimal extraction method: Factor by which the fiber PSF half width is
multiplied. Adjacent spectra within this area are assumed to affect the
spectrum being extracted. (float; default: 3.0). The full name of this
option for the EsoRex configuration file is
giraffe.extraction.optimal.wfactor [default = 3.0].
- --extr-obkgorder
<int>
- Optimal extraction method: Order of the polynomial background model, which
is fitted for each wavelength bin along the spatial direction. (int;
default: 2). The full name of this option for the EsoRex configuration
file is giraffe.extraction.optimal.bkgorder [default =
2].
- --transmission
<bool>
- Controls the relative fiber transmission computation. (bool; default:
True). The full name of this option for the EsoRex configuration file is
giraffe.masterflat.transmission [default = True].
- --slight
<bool>
- Controls the scattered light model computation. (bool; default: False).
The full name of this option for the EsoRex configuration file is
giraffe.masterflat.slight [default = False].
- --slight-model
<str>
- Name of the scattered light model to use. (str; default:
´polynom´). The full name of this option for the EsoRex
configuration file is giraffe.slight.model.name [default =
polynom].
- --slight-order
<str>
- Scattered light model fit X and Y order. (str; default:
´4,2´). The full name of this option for the EsoRex
configuration file is giraffe.slight.model.order [default =
4,2].
- --slight-xstep
<int>
- Interspectrum region sampling step along the dispersion direction. (int;
default: 10). The full name of this option for the EsoRex configuration
file is giraffe.slight.xstep [default = 10].
- --slight-ystep
<int>
- Interspectrum region sampling step along the spatial direction. (int;
default: 1). The full name of this option for the EsoRex configuration
file is giraffe.slight.ystep [default = 1].
- --slight-xslice
<str>
- Interspectrum region sampling step along the dispersion direction for a
specific region. This overrides ´xstep´ for the given
region. (str; default: ´none´). The full name of this option
for the EsoRex configuration file is giraffe.slight.xslice [default
= none].
- --slight-ewidth
<float>
- Extra width [pixels] added to both sides of a spectrum trace. (float;
default: 0.5). The full name of this option for the EsoRex configuration
file is giraffe.slight.ewidth [default = 0.5].
- --slight-iswidth
<int>
- Minimum width [pixels] required for interspectrum regions. (int; default:
2). The full name of this option for the EsoRex configuration file is
giraffe.slight.iswidth [default = 2].
- --slight-istrim
<bool>
- Turn off using the first and last interspectrum region. (bool; default:
True). The full name of this option for the EsoRex configuration file is
giraffe.slight.istrim [default = True].
- --slight-phff
<bool>
- Use photometric flat field correction. (bool; default: False). The full
name of this option for the EsoRex configuration file is
giraffe.slight.phffcorrection [default = False].
- --slight-remove
<bool>
- Remove scattered light from the input frame. (bool; default: False). The
full name of this option for the EsoRex configuration file is
giraffe.slight.remove [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 giraf pipeline can be downloaded as
a PDF file using the following URL:
- ftp://ftp.eso.org/pub/dfs/pipelines/giraffe/giraf-pipeline-manual-2.11.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 giraf pipeline are
giframestack(7), gimasterbias(7), gimasterdark(7),
giscience(7), gistandard(7), giwavecalibration(7)
Giraffe Pipeline <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 GIRAFFE Instrument Pipeline
Copyright (C) 2002-2014 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 02110-1301 USA