.TH SINFO_REC_PUPIL "7" "3.1.0" "sinfo_rec_pupil" "sinfo recipes" .SH NAME sinfo_rec_pupil \- Pupil data reduction .SH SYNOPSIS esorex .B sinfo_rec_pupil [OPTIONS] FILE.sof .SH DESCRIPTION This recipe performs science data reduction. .PP The input files are science object and sky frames with tags OBJECT_NODDING and SKY_NODDING 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 1st 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) .SH OPTIONS .TP \fB\-\-product\-density\fR \fI\fR Density of pipeline products: 0 (low), 1 (low+skycor), 2 (med\-QC), 3 (high\-debug+skycor) (int; default: 2). The full name of this option for the EsoRex configuration file is \fBsinfoni.product.density\fR [default = \fI2\fR]. .TP \fB\-\-stack\-lo_rej\fR \fI\fR lower rejection (float; default: 0.1). The full name of this option for the EsoRex configuration file is \fBsinfoni.stacked.low_rejection\fR [default = \fI0.1\fR]. .TP \fB\-\-stack\-hi_rej\fR \fI\fR higher rejection (float; default: 0.1). The full name of this option for the EsoRex configuration file is \fBsinfoni.stacked.high_rejection\fR [default = \fI0.1\fR]. .TP \fB\-\-stack\-flat_ind\fR \fI\fR Flat Index: (bool; default: True). The full name of this option for the EsoRex configuration file is \fBsinfoni.stacked.flat_index\fR [default = \fITrue\fR]. .TP \fB\-\-stack\-mflat_norm_smooth\fR \fI\fR 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). (int; default: 0). The full name of this option for the EsoRex configuration file is \fBsinfoni.stacked.mflat_norm_smooth\fR [default = \fI0\fR]. .TP \fB\-\-stack\-mflat_smooth_rad\fR \fI\fR Normalization smoothing radii (int; default: 16). The full name of this option for the EsoRex configuration file is \fBsinfoni.stacked.mflat_smooth_rad\fR [default = \fI16\fR]. .TP \fB\-\-stack\-mask_ind\fR \fI\fR BP Mask Interpolation Switch: indicates if the bad pixel mask should be applied (1) or not (0) (int; default: 1). The full name of this option for the EsoRex configuration file is \fBsinfoni.stacked.mask_index\fR [default = \fI1\fR]. .TP \fB\-\-stack\-ind_ind\fR \fI\fR 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 \fBsinfoni.stacked.ind_index\fR [default = \fIFalse\fR]. .TP \fB\-\-stack\-mask_rad\fR \fI\fR Max distance bad\-good pix: (int; default: 4). The full name of this option for the EsoRex configuration file is \fBsinfoni.stacked.mask_rad\fR [default = \fI4\fR]. .TP \fB\-\-stack\-gauss_ind\fR \fI\fR Gaussian Convolution Switch: (bool; default: False). The full name of this option for the EsoRex configuration file is \fBsinfoni.stacked.gauss_index\fR [default = \fIFalse\fR]. .TP \fB\-\-stack\-khw\fR \fI\fR Kernel Half Width (int; default: 2). The full name of this option for the EsoRex configuration file is \fBsinfoni.stacked.kernel_half_width\fR [default = \fI2\fR]. .TP \fB\-\-stack\-warpfix_ind\fR \fI\fR Warp Fix Index: (bool; default: True). The full name of this option for the EsoRex configuration file is \fBsinfoni.stacked.warpfix_ind\fR [default = \fITrue\fR]. .TP \fB\-\-stack\-warpfix_kernel\fR \fI\fR Warpfix kernel: (str; default: \'tanh\'). The full name of this option for the EsoRex configuration file is \fBsinfoni.stacked.warpfix_kernel\fR [default = \fItanh\fR]. .TP \fB\-\-stack\-qc_thresh_min\fR \fI\fR qc_thresh_min (int; default: 0). The full name of this option for the EsoRex configuration file is \fBsinfoni.stacked.qc_thresh_min\fR [default = \fI0\fR]. .TP \fB\-\-stack\-qc_thresh_max\fR \fI\fR qc_thresh_max (int; default: 49000). The full name of this option for the EsoRex configuration file is \fBsinfoni.stacked.qc_thresh_max\fR [default = \fI49000\fR]. .TP \fB\-\-stack\-sub_raw_sky\fR \fI\fR 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 \fBsinfoni.stacked.sub_raw_sky\fR [default = \fITrue\fR]. .TP \fB\-\-objnod\-aj_method\fR \fI\fR Method to reduce autojitter template frames Raw frames are object only exposures. object\-fake_sky pairs are generated. 0: no sky for all objects (int; default: 1). The full name of this option for the EsoRex configuration file is \fBsinfoni.objnod.autojitter_method\fR [default = \fI1\fR]. .TP \fB\-\-objnod\-scales_sky\fR \fI\fR 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 \fBsinfoni.objnod.scales_sky\fR [default = \fIFalse\fR]. .TP \fB\-\-objnod\-ks_clip\fR \fI\fR 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 \fBsinfoni.objnod.ks_clip\fR [default = \fITrue\fR]. .TP \fB\-\-objnod\-kappa\fR \fI\fR 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 \fBsinfoni.objnod.kappa\fR [default = \fI2.0\fR]. .TP \fB\-\-objnod\-size_x\fR \fI\fR Cube x size: x\-pixel size of the final combined data cube,must lie between 64 and 128. If 0 it is computed automatically (int; default: 0). The full name of this option for the EsoRex configuration file is \fBsinfoni.objnod.size_x\fR [default = \fI0\fR]. .TP \fB\-\-objnod\-size_y\fR \fI\fR Cube y size: y\-pixel size of the final combined data cube,must lie between 64 and 128.If 0 it is computed automatically (int; default: 0). The full name of this option for the EsoRex configuration file is \fBsinfoni.objnod.size_y\fR [default = \fI0\fR]. .TP \fB\-\-objnod\-no_coeffs\fR \fI\fR number of coefficients for the polynomial interpolation (int; default: 3). The full name of this option for the EsoRex configuration file is \fBsinfoni.objnod.n_coeffs\fR [default = \fI3\fR]. .TP \fB\-\-objnod\-ns_ind\fR \fI\fR 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 \fBsinfoni.objnod.nord_south_index\fR [default = \fITrue\fR]. .TP \fB\-\-objnod\-fine_tune_mtd\fR \fI\fR 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 \fBsinfoni.objnod.fine_tuning_method\fR [default = \fIP\fR]. .TP \fB\-\-objnod\-order\fR \fI\fR Fine Tuning polynomial order: order of the polynomial if the polynomial interpolation shifting method is used. (int; default: 2). The full name of this option for the EsoRex configuration file is \fBsinfoni.objnod.order\fR [default = \fI2\fR]. .TP \fB\-\-objnod\-lo_rej\fR \fI\fR 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 \fBsinfoni.objnod.low_rejection\fR [default = \fI10.0\fR]. .TP \fB\-\-objnod\-hi_rej\fR \fI\fR 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 \fBsinfoni.objnod.high_rejection\fR [default = \fI10.0\fR]. .TP \fB\-\-objnod\-tol\fR \fI\fR 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 (int; default: 2). The full name of this option for the EsoRex configuration file is \fBsinfoni.objnod.tolerance\fR [default = \fI2\fR]. .TP \fB\-\-objnod\-jit_ind\fR \fI\fR 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 \fBsinfoni.objnod.jitter_index\fR [default = \fITrue\fR]. .TP \fB\-\-objnod\-kernel_typ\fR \fI\fR 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 \fBsinfoni.objnod.kernel_type\fR [default = \fItanh\fR]. .TP \fB\-\-objnod\-vllx\fR \fI\fR Vignetting on llx: pixels vignetted from lower left corner X coordinate of contributing cubes before coaddition (int; default: 0). The full name of this option for the EsoRex configuration file is \fBsinfoni.objnod.vllx\fR [default = \fI0\fR]. .TP \fB\-\-objnod\-vlly\fR \fI\fR Vignetting on lly: pixels vignetted from lower left corner Y coordinate of contributing cubes before coaddition (int; default: 0). The full name of this option for the EsoRex configuration file is \fBsinfoni.objnod.vlly\fR [default = \fI0\fR]. .TP \fB\-\-objnod\-vurx\fR \fI\fR Vignetting on urx: pixels vignetted from upper right corner X coordinate of contributing cubes before coaddition (int; default: 0). The full name of this option for the EsoRex configuration file is \fBsinfoni.objnod.vurx\fR [default = \fI0\fR]. .TP \fB\-\-objnod\-vury\fR \fI\fR Vignetting on ury: pixels vignetted from upper right corner Y coordinate of contributing cubes before coaddition (int; default: 0). The full name of this option for the EsoRex configuration file is \fBsinfoni.objnod.vury\fR [default = \fI0\fR]. .TP \fB\-\-objnod\-fcol\fR \fI\fR First column offset: (float; default: 0.0). The full name of this option for the EsoRex configuration file is \fBsinfoni.objnod.fcol\fR [default = \fI0.0\fR]. .TP \fB\-\-objnod\-sky_cor\fR \fI\fR Sky residuals correction: (bool; default: True). The full name of this option for the EsoRex configuration file is \fBsinfoni.objnod.sky_cor\fR [default = \fITrue\fR]. .TP \fB\-\-objnod\-flux_cor\fR \fI\fR Apply flux correction after rebinning: (bool; default: True). The full name of this option for the EsoRex configuration file is \fBsinfoni.objnod.flux_cor\fR [default = \fITrue\fR]. .TP \fB\-\-objnod\-mosaic_max_size\fR \fI\fR Maximum allowed size for cubes mosaic is 100*mosaic_max_size (int; default: 14196). The full name of this option for the EsoRex configuration file is \fBsinfoni.objnod.mosaic_max_size\fR [default = \fI14196\fR]. .PP 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. .SH SEE ALSO The full documentation for the sinfo pipeline can be downloaded as a PDF file using the following URL: .IP .B ftp://ftp.eso.org/pub/dfs/pipelines/sinfoni/sinfo\-pipeline\-manual\-19.0.pdf .PP An overview over the existing ESO pipelines can be found on the web page \fBhttps://www.eso.org/sci/software/pipelines/\fR. .PP Basic documentation about the EsoRex program can be found at the esorex (1) man page. .PP It is possible to call the pipelines from python using the python\-cpl package. See \fBhttps://packages.python.org/python\-cpl/index.html\fR for further information. .PP The other recipes of the sinfo pipeline are .IR sinfo_rec_detlin (7), .IR sinfo_rec_distortion (7), .IR sinfo_rec_jitter (7), .IR sinfo_rec_mdark (7), .IR sinfo_rec_mflat (7), .IR sinfo_rec_wavecal (7), .IR sinfo_utl_bp_mask_add (7), .IR sinfo_utl_cube2ima (7), .IR sinfo_utl_cube2spectrum (7), .IR sinfo_utl_cube_arith (7), .IR sinfo_utl_cube_combine (7), .IR sinfo_utl_cube_create (7), .IR sinfo_utl_ima_arith (7), .IR sinfo_utl_ima_line_corr (7), .IR sinfo_utl_line_oh_select (7), .IR sinfo_utl_skycor (7), .IR sinfo_utl_skymap (7), .IR sinfo_utl_spectrum_divide_by_blackbody (7), .IR sinfo_utl_spectrum_wavelength_shift (7) .SH VERSION sinfo_rec_pupil 3.1.0 .SH AUTHOR Andrea Modigliani .SH BUG REPORTS Please report any problems to Andrea.Modigliani@eso.org. Alternatively, you may send a report to the ESO User Support Department . .SH 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