Provided by: cpl-plugin-sinfo-doc_2.4.0+dfsg-3_all 
NAME
sinfo_rec_jitter - Object or STD star or PSF star data reduction
SYNOPSIS
esorex sinfo_rec_jitter [OPTIONS] FILE.sof
DESCRIPTION
This recipe performs science data reduction.
The input files are: science object and sky frames with tags OBJECT_NODDING and
SKY_NODDING or Telluric standard star frames and sky frames with tags STD and SKY_STD or
PSF standard star and sky frames with tags PSF_CALIBRATOR and SKY_PSF_CALIBRATOR and
Master calibration frames: A corresponding (band,preoptics) wavelength map image with tag
WAVE_MAP A corresponding (band,preoptics) master flat field with tag MASTER_FLAT_LAMP A
corresponding (band,preoptics) master bad pixel map with tag MASTER_BP_MAP A corresponding
(band,preoptics) slitlets position frame with tag SLIT_POS A corresponding (band)
distortion table with tag DISTORTION A corresponding (band) slitlet distance table with
tag SLITLETS_DISTANCE The output is an image resulting from the IMA1 op IMA2 where op
indicates A reference table with the position of the first column with tag FIRST_COLUMN
Relevant outputs are: combined cubes (PRO.CATG=x_OBS x=STD,OBJ,PSF) reconstructed cube
(PRO.CATG=COADD_x_OBS x=STD,OBJ,PSF) An average along Z of the reconstructed cube
(PRO.CATG=MED_x_OBS x=STD,OBJ,PSF) The bad pixel map associated to the cube
(PRO.CATG=BP_MAP_COADD_x_OBS x=STD,OBJ,PSF) Information on relevant parameters can be
found with esorex --params sinfo_rec_jitter esorex --help sinfo_rec_jitter
OPTIONS
--gen-overpar <bool>
Overwrite DRS ini parameters: (bool; default: True). The full name of this option
for the EsoRex configuration file is sinfoni.general.overwrite_parameters [default
= True].
--lc_sw <bool>
Correct for bad lines introduced by instrument software: (bool; default: False).
The full name of this option for the EsoRex configuration file is
sinfoni.general.lc_sw [default = False].
--lc_kappa <long>
Kappa sigma value (long; default: 18). The full name of this option for the EsoRex
configuration file is sinfoni.general.lc_kappa [default = 18].
--lc_filt_rad <long>
Filtering radii applied during median filter. Should be small (long; default: 3).
The full name of this option for the EsoRex configuration file is
sinfoni.general.lc_filt_rad [default = 3].
--product-density <long>
Density of pipeline products: 0 (low), 1 (low+skycor), 2 (med-QC), 3
(high-debug+skycor) (long; default: 2). The full name of this option for the EsoRex
configuration file is sinfoni.product.density [default = 2].
--stack-lo_rej <float>
lower rejection (float; default: 0.1). The full name of this option for the EsoRex
configuration file is sinfoni.stacked.low_rejection [default = 0.1].
--stack-hi_rej <float>
higher rejection (float; default: 0.1). The full name of this option for the EsoRex
configuration file is sinfoni.stacked.high_rejection [default = 0.1].
--stack-flat_ind <bool>
Flat Index: (bool; default: True). The full name of this option for the EsoRex
configuration file is sinfoni.stacked.flat_index [default = True].
--stack-mflat_norm_smooth <long>
Normalize master flat to its smoothed value (to remove lamp response curve). 0 (no
smooth). 1 (apply fft filter along y).2 (apply running median filter along y).
(long; default: 0). The full name of this option for the EsoRex configuration file
is sinfoni.stacked.mflat_norm_smooth [default = 0].
--stack-mflat_smooth_rad <long>
Normalization smoothing radii (long; default: 16). The full name of this option
for the EsoRex configuration file is sinfoni.stacked.mflat_smooth_rad [default =
16].
--stack-mask_ind <long>
BP Mask Interpolation Switch: indicates if the bad pixel mask should be applied (1)
or not (0) (long; default: 1). The full name of this option for the EsoRex
configuration file is sinfoni.stacked.mask_index [default = 1].
--stack-ind_ind <bool>
indicates if the bad pixels should be indicated (yes) or interpolated (no) (bool;
default: False). The full name of this option for the EsoRex configuration file is
sinfoni.stacked.ind_index [default = False].
--stack-mask_rad <long>
Max distance bad-good pix: (long; default: 4). The full name of this option for
the EsoRex configuration file is sinfoni.stacked.mask_rad [default = 4].
--stack-gauss_ind <bool>
Gaussian Convolution Switch: (bool; default: False). The full name of this option
for the EsoRex configuration file is sinfoni.stacked.gauss_index [default = False].
--stack-khw <long>
Kernel Half Width (long; default: 2). The full name of this option for the EsoRex
configuration file is sinfoni.stacked.kernel_half_width [default = 2].
--stack-warpfix_ind <bool>
Warp Fix Index: (bool; default: True). The full name of this option for the EsoRex
configuration file is sinfoni.stacked.warpfix_ind [default = True].
--stack-warpfix_kernel <str>
Warpfix kernel: (str; default: ´tanh´). The full name of this option for the
EsoRex configuration file is sinfoni.stacked.warpfix_kernel [default = tanh].
--stack-qc_thresh_min <long>
qc_thresh_min (long; default: 0). The full name of this option for the EsoRex
configuration file is sinfoni.stacked.qc_thresh_min [default = 0].
--stack-qc_thresh_max <long>
qc_thresh_max (long; default: 49000). The full name of this option for the EsoRex
configuration file is sinfoni.stacked.qc_thresh_max [default = 49000].
--stack-sub_raw_sky <bool>
indicates if the raw sky frame should be subtracted (TRUE) or (FALSE) (bool;
default: True). The full name of this option for the EsoRex configuration file is
sinfoni.stacked.sub_raw_sky [default = True].
--objnod-aj_method <long>
Method to reduce autojitter template frames Raw frames are object only exposures.
object-fake_sky pairs are generated. 0: no sky for all objects (long; default: 1).
The full name of this option for the EsoRex configuration file is
sinfoni.objnod.autojitter_method [default = 1].
--objnod-scales_sky <bool>
Spatial median (sky) subtraction from cube: (If autojitter_method==1),indicates if
the spatial median of each plane should be subtracted (TRUE) or not (FALSE) from
each cube plane (bool; default: False). The full name of this option for the EsoRex
configuration file is sinfoni.objnod.scales_sky [default = False].
--objnod-ks_clip <bool>
Kappa-sigma clipping of coadded cube: indicates if a kappa-sigma clipping should be
performed (TRUE) or not (FALSE) on each plane of the coadded cube (bool; default:
True). The full name of this option for the EsoRex configuration file is
sinfoni.objnod.ks_clip [default = True].
--objnod-kappa <float>
kappa value for kappa-sigma clipping of coadded cube (float; default: 2.0). The
full name of this option for the EsoRex configuration file is sinfoni.objnod.kappa
[default = 2.0].
--objnod-size_x <long>
Cube x size: x-pixel size of the final combined data cube,must lie between 64 and
128. If 0 it is computed automatically (long; default: 0). The full name of this
option for the EsoRex configuration file is sinfoni.objnod.size_x [default = 0].
--objnod-size_y <long>
Cube y size: y-pixel size of the final combined data cube,must lie between 64 and
128.If 0 it is computed automatically (long; default: 0). The full name of this
option for the EsoRex configuration file is sinfoni.objnod.size_y [default = 0].
--objnod-no_coeffs <long>
number of coefficients for the polynomial interpolation (long; default: 3). The
full name of this option for the EsoRex configuration file is
sinfoni.objnod.n_coeffs [default = 3].
--objnod-ns_ind <bool>
Nord South Index Switch: indicates if the slitlet distances are determined by a
north-south-test (TRUE) or slitlet edge fits (FALSE) (bool; default: True). The
full name of this option for the EsoRex configuration file is
sinfoni.objnod.nord_south_index [default = True].
--objnod-fine_tune_mtd <str>
Fine Tuning Method: indicator for the shifting method to use (P: polynomial
interpolation, S: cubic spline interpolation) (str; default: ´P´). The full name
of this option for the EsoRex configuration file is
sinfoni.objnod.fine_tuning_method [default = P].
--objnod-order <long>
Fine Tuning polynomial order: order of the polynomial if the polynomial
interpolation shifting method is used. (long; default: 2). The full name of this
option for the EsoRex configuration file is sinfoni.objnod.order [default = 2].
--objnod-lo_rej <float>
lower rejection: percentage of rejected low value pixels for averaging the sky
spectra (float; default: 10.0). The full name of this option for the EsoRex
configuration file is sinfoni.objnod.low_rejection [default = 10.0].
--objnod-hi_rej <float>
higher rejection: percentage of rejected high value pixels for averaging the sky
spectra (float; default: 10.0). The full name of this option for the EsoRex
configuration file is sinfoni.objnod.high_rejection [default = 10.0].
--objnod-tol <long>
Tolerance: pixel tolerance, this distance tolerance to the diagonal dividing line
is not considered for the sky extraction to be sure to have a clean sky due to
positioning tolerance and crossing through pixels (long; default: 2). The full name
of this option for the EsoRex configuration file is sinfoni.objnod.tolerance
[default = 2].
--objnod-jit_ind <bool>
Jitter Index: jitter mode indicator: TRUE: Auto-Jitter, FALSE: user defined
jitterThe size_x size_y kernel_type parameters are only used if jitterInd is set to
yes, that means in auto-jittering mode! (bool; default: True). The full name of
this option for the EsoRex configuration file is sinfoni.objnod.jitter_index
[default = True].
--objnod-kernel_typ <str>
Kernel Type:the name of the interpolation kernel to shift the single cubes to the
correct places inside the big combined cube (str; default: ´tanh´). The full name
of this option for the EsoRex configuration file is sinfoni.objnod.kernel_type
[default = tanh].
--objnod-vllx <long>
Vignetting on llx: pixels vignetted from lower left corner X coordinate of
contributing cubes before coaddition (long; default: 0). The full name of this
option for the EsoRex configuration file is sinfoni.objnod.vllx [default = 0].
--objnod-vlly <long>
Vignetting on lly: pixels vignetted from lower left corner Y coordinate of
contributing cubes before coaddition (long; default: 0). The full name of this
option for the EsoRex configuration file is sinfoni.objnod.vlly [default = 0].
--objnod-vurx <long>
Vignetting on urx: pixels vignetted from upper right corner X coordinate of
contributing cubes before coaddition (long; default: 0). The full name of this
option for the EsoRex configuration file is sinfoni.objnod.vurx [default = 0].
--objnod-vury <long>
Vignetting on ury: pixels vignetted from upper right corner Y coordinate of
contributing cubes before coaddition (long; default: 0). The full name of this
option for the EsoRex configuration file is sinfoni.objnod.vury [default = 0].
--objnod-fcol <float>
First column offset: (float; default: 0.0). The full name of this option for the
EsoRex configuration file is sinfoni.objnod.fcol [default = 0.0].
--objnod-sky_cor <bool>
Sky residuals correction: (bool; default: True). The full name of this option for
the EsoRex configuration file is sinfoni.objnod.sky_cor [default = True].
--objnod-flux_cor <bool>
Apply flux correction after rebinning: (bool; default: True). The full name of
this option for the EsoRex configuration file is sinfoni.objnod.flux_cor [default =
True].
--objnod-mosaic_max_size <long>
Maximum allowed size for cubes mosaic is 100*mosaic_max_size (long; default:
14196). The full name of this option for the EsoRex configuration file is
sinfoni.objnod.mosaic_max_size [default = 14196].
--skycor-mask_ws <float>
Starting wavelength for object-sky cross correlation (float; default: 1.4). The
full name of this option for the EsoRex configuration file is
sinfoni.sinfo_utl_skycor.mask_ws [default = 1.4].
--skycor-mask_we <float>
End wavelength for object-sky cross correlation (float; default: 2.5). The full
name of this option for the EsoRex configuration file is
sinfoni.sinfo_utl_skycor.mask_we [default = 2.5].
--skycor-min_frac <float>
Threshold value for fraction of spatial pixels to be sky (float; default: 0.8). The
full name of this option for the EsoRex configuration file is
sinfoni.sinfo_utl_skycor.min_frac [default = 0.8].
--skycor-sky_bkg_filter_width <long>
Width of sky-thermal background pre filter (to remove emission lines before fitting
a Black Body). (long; default: 12). The full name of this option for the EsoRex
configuration file is sinfoni.sinfo_utl_skycor.sky_bkg_filter_width [default = 12].
--skycor-line_hw <float>
Threshold value for full width in pixels of unresolved emission line. Lines with
FWHM smaller than this value are not considered in the object-sky cross correlation
and in computation of the optimal sky lines scaling factor (float; default: 4.0).
The full name of this option for the EsoRex configuration file is
sinfoni.sinfo_utl_skycor.line_half_width [default = 4.0].
--skycor-scale_method <long>
Optimal sky lines scaling factor computation method: amoeba fit (0), maximum
likelihood (1) (long; default: 1). The full name of this option for the EsoRex
configuration file is sinfoni.sinfo_utl_skycor.scale_method [default = 1].
--skycor-rot_cor <bool>
Computes scaling factor correction due to rotational levels transitions (bool;
default: False). The full name of this option for the EsoRex configuration file is
sinfoni.sinfo_utl_skycor.rot_cor [default = False].
--skycor-fit_obj_noise <bool>
Do Gaussian fit of object noise (bool; default: False). The full name of this
option for the EsoRex configuration file is sinfoni.sinfo_utl_skycor.fit_obj_noise
[default = False].
--skycor-niter <long>
Number of iterations of background fit (long; default: 10). The full name of this
option for the EsoRex configuration file is sinfoni.sinfo_utl_skycor.niter [default
= 10].
--skycor-pshift <float>
Sky spectrum shift towar object (float; default: 0.0). The full name of this option
for the EsoRex configuration file is sinfoni.sinfo_utl_skycor.pshift [default =
0.0].
--skycor-llx <long>
Lower left X defining object spectrum location (long; default: 1). The full name of
this option for the EsoRex configuration file is sinfoni.sinfo_utl_skycor.llx
[default = 1].
--skycor-lly <long>
Lower left Y defining object spectrum location (long; default: 1). The full name of
this option for the EsoRex configuration file is sinfoni.sinfo_utl_skycor.lly
[default = 1].
--skycor-urx <long>
Upper right X defining object spectrum location (long; default: 64). The full name
of this option for the EsoRex configuration file is sinfoni.sinfo_utl_skycor.urx
[default = 64].
--skycor-ury <long>
Upper right Y defining object spectrum location (long; default: 64). The full name
of this option for the EsoRex configuration file is sinfoni.sinfo_utl_skycor.ury
[default = 64].
--skycor-sub_thr_bkg_from_obj <bool>
Subtract thermal background contribute from object spectra. Set it to TRUE if
stack-sub_raw_sky is set to FALSE (bool; default: False). The full name of this
option for the EsoRex configuration file is
sinfoni.sinfo_utl_skycor.sub_thr_bkg_from_obj [default = False].
--std_star-switch <bool>
Switch to activate spectrum extraction (bool; default: True). The full name of this
option for the EsoRex configuration file is sinfoni.std_star.switch [default =
True].
--std_star-lo_rej <float>
lower rejection (float; default: 0.1). The full name of this option for the EsoRex
configuration file is sinfoni.std_star.low_rejection [default = 0.1].
--std_star-hi_rej <float>
high rejection (float; default: 0.1). The full name of this option for the EsoRex
configuration file is sinfoni.std_star.high_rejection [default = 0.1].
--std_star-fwhm_fct <float>
Factor to find 2D-Gauss FWHM. The extraction box is:
halfbox_x=halfbox_y=fwhm_factor*(fwhm_x+fwhm_y)*0.5 (float; default: 5.0). The full
name of this option for the EsoRex configuration file is
sinfoni.std_star.fwhm_factor [default = 5.0].
--std_star-conv_ind <bool>
Intensity Conversion Index: (bool; default: True). The full name of this option
for the EsoRex configuration file is sinfoni.std_star.conversion_index [default =
True].
--std_star-compute_eff <bool>
Compute efficiency: TRUE/FALSE (bool; default: True). The full name of this option
for the EsoRex configuration file is sinfoni.std_star.compute_eff [default = True].
--psf-switch <bool>
Switch to activate PSF-related (Strehl/Encircled energy) computation (bool;
default: True). The full name of this option for the EsoRex configuration file is
sinfoni.psf.switch [default = True].
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.
SEE ALSO
The full documentation for the sinfo pipeline can be downloaded as a PDF file using the
following URL:
ftp://ftp.eso.org/pub/dfs/pipelines/sinfoni/sinfo-pipeline-manual-19.0.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 sinfo pipeline are sinfo_rec_detlin(7), sinfo_rec_wavecal(7),
sinfo_utl_ima_line_corr(7), sinfo_utl_cube_combine(7), sinfo_utl_bp_mask_add(7),
sinfo_utl_cube2spectrum(7), sinfo_utl_cube_create(7), sinfo_rec_distortion(7),
sinfo_utl_spectrum_divide_by_blackbody(7), sinfo_utl_line_oh_select(7),
sinfo_utl_cube2ima(7), sinfo_utl_cube_arith(7), sinfo_rec_pupil(7), sinfo_rec_mflat(7),
sinfo_utl_ima_arith(7), sinfo_utl_skycor(7), sinfo_utl_spectrum_wavelength_shift(7),
sinfo_utl_skymap(7), sinfo_rec_mdark(7)
VERSION
sinfo_rec_jitter 2.4.0
AUTHOR
Andrea Modigliani <Andrea.Mdigliani@eso.org>
BUG REPORTS
Please report any problems to Andrea.Mdigliani@eso.org. Alternatively, you may send a
report to the ESO User Support Department <usd-help@eso.org>.
LICENSE
This file is part of the SINFONI Instrument Pipeline Copyright (C) 2002,2003 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., 59 Temple Place, Suite 330, Boston,
MA 02111-1307 USA