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ESO SINFONI Pipeline, User Manual

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ESO

SINFONI Pipeline User Manual

Doc:

VLT-MAN-ESO-19500-3600

Issue:

Issue 1.0

Date:

Date 2005-10-19

Page:

60 of 88

9.8.1

Input

/path_file_raw/SINFO.2004-08-15T14:02:18.468.fits SKY_NODDING

/path_file_raw/SINFO.2004-08-15T14:01:54.844.fits OBJECT_NODDING

/path_file_raw/SINFO.2004-08-15T14:01:32.741.fits OBJECT_NODDING

/path_file_raw/SINFO.2004-08-15T14:01:09.827.fits SKY_NODDING

/path_file_raw/SINFO.2004-08-15T14:00:41.593.fits SKY_NODDING

/path_file_raw/SINFO.2004-08-15T14:00:19.119.fits OBJECT_NODDING

/path_file_cdb/MASTER_BP_MAP_K_250.fits MASTER_BP_MAP

/path_file_cdb/MASTER_FLAT_LAMP_K_250.fits MASTER_FLAT_LAMP

/path_file_cdb/WAVE_MAP_K_250.fits WAVE_MAP

/path_file_cdb/SLIT_POS_K_250.tfits SLIT_POS

/path_file_cdb/SLITLETS_DISTANCE_K.tfits SLITLETS_DISTANCE

/path_file_cdb/DISTORTION_K.tfits DISTORTION

/path_file_cdb/FIRST_COLUMN.tfits FIRST_COL

9.8.2

Output

default recipe file name

PRO.CATG

short description

sky00.fits

SKY_STACKED_DUMMY

stacked sky frame

out_sky_stack_dist.fits

SKY_STACKED_DIST

stacked sky frame distortion corrected

out_stack_mflat_dist.fits

MFLAT_STACKED_DIST

stacked master flat

distortion corrected

out_stack0.fits

OBJECT_NODDING_STACKED

stacked PSF frames

out_sky_cube.fits

OBS_SKY

sky cube

out_sky_med.fits

SKY_MED

z-median of SKY_CUBE

out_mflat_cube.fits

MFLAT_CUBE

master flat cube

out_mflat_avg.fits

MFLAT_AVG

z-mean of MFLAT_CUBE

out_mflat_med.fits

MFLAT_MED

z-median of MFLAT_CUBE

out_mflat_cube.fits

OBS_OBJ

OBJ cube
(intermediate product, there
might be more than one of those)

out_objnod.fits

COADD_OBJ

coadded OBJ cube

out_med_cube.fits

MED_COADD_OBJ

z-median of COADD_OBJ

out_bpmap_nodding.fits

MASK_COADD_OBJ

COADD_OBJ’s mask

9.8.3

Quality control

Not yet implemented.

9.8.4

Parameters

parameter

alias

default

Summary of Contents for SINFONI Pipeline

Page 1: ...he Organisation f r astronomische Forschung in der s dlichen Hemisph re VERY LARGE TELESCOPE SINFONI Pipeline User Manual VLT MAN ESO 19500 3600 Issue 1 0 Date 2005 10 19 Prepared ESO SINFONI Pipeline...

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Page 3: ...line User Manual Doc VLT MAN ESO 19500 3600 Issue Issue 1 0 Date Date 2005 10 19 Page 3 of 88 Change record Issue Rev Date Section Parag affected Reason Initiation Documents Remarks 1 0 19 10 2005 All...

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Page 5: ...rview 14 4 Quick start 16 4 1 SINFONI pipeline recipes 16 4 2 An introduction to Gasgano and EsoRex 17 4 2 1 Using Gasgano 17 4 2 2 Using EsoRex 22 4 3 Example of data reduction using EsoRex 24 5 Know...

Page 6: ...ty control 45 9 1 4 Parameters 45 9 2 si_rec_mdark 45 9 2 1 Input 45 9 2 2 Output 46 9 2 3 Quality control 46 9 2 4 Parameters 46 9 3 si_rec_mflat 47 9 3 1 Input 47 9 3 2 Output 47 9 3 3 Quality contr...

Page 7: ...4 Parameters 59 9 8 si_rec_objnod 59 9 8 1 Input 60 9 8 2 Output 60 9 8 3 Quality control 60 9 8 4 Parameters 60 9 9 si_utl_skymap 61 9 9 1 Input 61 9 9 2 Output 62 9 9 3 Parameters 62 9 10 si_utl_bp...

Page 8: ...tput 66 9 16 3 Parameters 66 10 Algorithms and recipe details 67 10 1 Algorithms 67 10 1 1 Frame stacking 67 10 1 2 Average with rejection 67 10 1 3 Detector non linearity computation 67 10 1 4 Neares...

Page 9: ...nearity and non linear bad pixel map determination si_rec_detlin 78 10 2 2 Master dark and bad pixel map determination si_rec_mdark 79 10 2 3 Master flat and threshold pixels bad pixel map determinati...

Page 10: ...ESO SINFONI Pipeline User Manual Doc VLT MAN ESO 19500 3600 Issue Issue 1 0 Date Date 2005 10 19 Page 10 of 88...

Page 11: ...providing ESO with a complete and efficient data reduction software and for their help in documenting testing debugging the recipes and the pipeline during several commissioning and science verificati...

Page 12: ...CPL home page http www eso org cpl ESOREX home page http www eso org cpl esorex html SINFONI home page http www eso org instruments sinfoni VLT SINFONI User Manual VLT MAN ESO 14700 3517 http www eso...

Page 13: ...ipelines consist of a set of data processing modules that can be called from the command line from the automatic data management tools available on Paranal or from Gasgano ESO offers two front end app...

Page 14: ...by an adaptive optics module MACAO developed by ESO more details are given in 11 Figure 3 1 0 An inside view of SPIFFI The cryostat cover and the reinforcing structure have been removed to provide a f...

Page 15: ...x0 8 respectively On raw frames each pixel images a rectangular region on the sky 125x250 50x100 or 12 5x25 mas Each SINFONI FOV image slice corresponds to a so called detector slitlet Each one of the...

Page 16: ...optical distortions and slitlets distances si_rec_wavecal for wavelength calibration si_rec_psf for PSF standard data reduction si_rec_stdstar for STD standard data reduction si_rec_objnod for science...

Page 17: ...from the command line In addition Gasgano allows the user to execute directly the pipeline recipes on a set of selected files 4 2 1 Using Gasgano To get familiar with the SINFONI pipeline recipes and...

Page 18: ...ely modified on the Parameters panel on top The window contents might be saved for later use by selecting the Save Current Settings entry from the File menu as shown in figure At this point the recipe...

Page 19: ...ESO SINFONI Pipeline User Manual Doc VLT MAN ESO 19500 3600 Issue Issue 1 0 Date Date 2005 10 19 Page 19 of 88 Figure 4 2 1 The Gasgano main window...

Page 20: ...ESO SINFONI Pipeline User Manual Doc VLT MAN ESO 19500 3600 Issue Issue 1 0 Date Date 2005 10 19 Page 20 of 88 Figure 4 2 2 Selecting files to be processed by a SINFONI pipeline recipe...

Page 21: ...ESO SINFONI Pipeline User Manual Doc VLT MAN ESO 19500 3600 Issue Issue 1 0 Date Date 2005 10 19 Page 21 of 88 Figure 4 2 3 The Gasgano recipe execution window...

Page 22: ...o not verify in any way the correctness of the classification tags specified by the user in the SOF In the above example the recipe si_rec_wavecal will treat the frame file_path SINFO 2004 08 14T10 20...

Page 23: ...the recipe si_rec_wavecal has its EsoRex generated configuration file named si_rec_wavecal rc and is generated with the command esorex create config si_rec_wavecal The definition of one parameter of...

Page 24: ...nfiguration file settings For instance to set the si_rec_wavecal recipe wcal pixel_tol parameter to 3 0 the following should be typed esorex si_rec_wavecal wcal pixel_tol 3 0 si_rec_wavecal sof For mo...

Page 25: ...47 31 008 fits FIBRE_NS path_raw DISTORTION K SINFO 2005 03 14T11 47 49 771 fits FIBRE_NS path_raw DISTORTION K SINFO 2005 03 14T11 52 35 116 fits FIBRE_NS path_raw DISTORTION K SINFO 2005 03 14T11 5...

Page 26: ...f the user would like to run the same recipe several times with EsoRex having standard names for product files This setting allows the pipeline to overwrite previously generated products 8 In the foll...

Page 27: ...ate several files including the non linearity bad pixel map stored in the file out_bp_lin fits mv out_bp_lin fits path_pro BP_MAP_NL_K fits rm rf out fits paf log 3 Then the user may determine the opt...

Page 28: ...5 fits FLAT_LAMP path_cdb REF_BP_MAP fits REF_BP_MAP path_cdb BP_MAP_NL_K fits BP_MAP_NL The command esorex si_rec_mflat mflat_sof generates several frames including the master flat field stored in th...

Page 29: ...d to find information on the efficiency of the detector it is necessary to reduce standard star calibrations This can be done collecting appropriate data in a stdstar_sof file path_raw OBJNOD SINFO 20...

Page 30: ...ed with the present kit release as input of the si_rec_mflat recipe which determines the MASTER_BP_MAP which is input of the si_ref_wavecal recipe si_rec_objnod This recipe is much demanding in term o...

Page 31: ...occurrence may be an indication that the kappa sigma clipping has removed some object point In those cases we suggest to increase the value of kappa si_rec_objnod Some user may have observations taken...

Page 32: ...6 1 Data features In figure 6 1 0 we have represented how a possible observation target is imaged on the detector The 32 input source s slices generated by the two image slicers are imaged on the dete...

Page 33: ...l raw frames with the relevant FITS keywords omitting the prefix HIERARCH ESO needed to classify them and associate to them the required calibration frames Figure 6 2 0 shows the typical appearance of...

Page 34: ...si_rec_detlin Classification keywords Association keywords Fig DPR CATG CALIB INS SETUP ID 6 2 0 b DPR TYPE LINEARITY LAMP DPR TECH IFU Flat field frames to compute distortions DO category FLAT_NS Pr...

Page 35: ...ute optical distortions d an arc lamp on frame e a science frame f a sky frame Arc frames DO category WAVE_LAMP Processed by si_rec_wavecal Classification keywords Association keywords Fig DPR CATG CA...

Page 36: ...star frames DO category STD Processed by si_rec_stdstar Classification keywords Association keywords Fig DPR CATG CALIB INS SETUP ID 6 2 0 e DPR TYPE STD INS OPTI1 NAME DPR TECH IFU Sky frames taken w...

Page 37: ...ssue 1 0 Date Date 2005 10 19 Page 37 of 88 Sky frames taken with science frames DO category SKY_NODDING Processed by si_rec_objnod Classification keywords Association keywords Fig DPR CATG SCIENCE IN...

Page 38: ...cted in a table having PRO CATG DRS_SETUP_WAVE This frame is an input of the recipes si_rec_distortion and si_rec_wavecal band W_START W_DISP1 W_DISP2 W_HW W_FWHM W_MIN_AMP W_LOW_POS W_HI_POS H 1 65 2...

Page 39: ...ector bad pixels one uses a bad pixel map A master bad pixel map resulting from the combination of a set of different bad pixel maps is generated by the master flat recipe First of all as the detector...

Page 40: ...ly one fibre exposure therefore non linearities of the image scale within the 64 pixel of a single slitlets are currently not corrected and could cause minor slice to slit ripples in the reconstructed...

Page 41: ...sky frames are available Slitlet distances to be able to properly reconstruct a cube Slitlets left edge positions to be able to properly reconstruct a cube Wavelength maps to obtain a cube calibrated...

Page 42: ...erved band and used instrument pre optics the user has also to provide in input a DRS_SETUP_WAVE table If the parameter wcal slitpos_bootstrap has value set to FALSE as we suggest for robustness the u...

Page 43: ...NS_SETUP_ID INS OPTI1_NAME none 2 1 3 4 Calibrations Science STD si_rec_ stdstar 3 3 2 3 3 1 2 LINE_ REF static calib table Match keys Comments DARK PSF FLAT si_rec_ wavecal si_rec_ mdark si_rec_ psf...

Page 44: ...t parameters as they appear in the recipe configuration file the corresponding aliases the corresponding names to be eventually set on command line and their default values Also quality control parame...

Page 45: ...e same quantity as described in 10 1 3 The computed coefficients are QC BP MAP LINi MEAN i 0 1 2 Non linear bad pixels The pipeline computes the number of non linear bad pixels Those are given by QC B...

Page 46: ...computed in two regions and is given by the values of QC RON1 and QC RON2 Dark median counts The median and standard deviation of the counts in the master dark frame are monitored by DFO Its value and...

Page 47: ...Input path_file_raw SINFO 2005 02 28T16 27 43 232 fits FLAT_LAMP path_file_raw SINFO 2005 02 28T16 28 05 846 fits FLAT_LAMP path_file_raw SINFO 2005 02 28T16 28 18 820 fits FLAT_LAMP path_file_raw SIN...

Page 48: ...s above the reset anomaly at the same DIT the dark counts since a broad band filter is used for the lamp off frames while the dark frames are taken with two excluding narrow band filters The pipeline...

Page 49: ...mp_flats qc_fpn_xmax1 lamp_flats qc_fpn_xmax1 1536 sinfoni lamp_flats qc_fpn_ymin1 lamp_flats qc_fpn_ymin1 512 sinfoni lamp_flats qc_fpn_ymax1 lamp_flats qc_fpn_ymax1 1536 sinfoni lamp_flats qc_fpn_xm...

Page 50: ...s MASTER_SLIT on off frame multiplied by BP map out_distances tfits SLITLETS_DISTANCE computed slitlet distances 9 4 3 Quality control The recipe si_rec_distortion generates the DISTORTION product tha...

Page 51: ...iterations lamp_flats iterations 8 sinfoni lamp_flats bad_low_rejection lamp_flats bad_lo_rej 10 0 sinfoni lamp_flats bad_high_rejection lamp_flats bad_hi_rej 10 0 sinfoni lamp_flats llx lamp_flats l...

Page 52: ...ix_kernel stack warpfix_kernel tanh sinfoni stack qc_thresh_min stack qc_thresh_min 0 sinfoni stack qc_thresh_max stack qc_thresh_max 64000 sinfoni distortion calib_indicator dist calib_indicator TRUE...

Page 53: ...2 0 sinfoni north_south_test min_diff ns min_diff 1 0 sinfoni north_south_test dev_tol ns dev_tol 20 0 9 5 si_rec_wavecal The recipe si_rec_wavecal is used to determine the wavelength dispersion coeff...

Page 54: ...s SLIT_POS slitlets positions 9 5 3 Quality control The recipe monitors the resolving power the overall wavelength dispersion offset in and pixels the slitlets position in pixels Dispersion solution T...

Page 55: ...ed kernel_half_width stack khw 2 sinfoni stacked warpfix_ind stack warpfix_ind TRUE sinfoni stacked warpfix_kernel stack warpfix_kernel tanh sinfoni stack qc_thresh_min stack qc_thresh_min 0 sinfoni s...

Page 56: ...its SKY_PSF_CALIBRATOR path_file_cdb MASTER_BP_MAP_K_250 fits MASTER_BP_MAP path_file_cdb MASTER_FLAT_LAMP_K_250 fits MASTER_FLAT_LAMP path_file_cdb WAVE_MAP_K_250 fits WAVE_MAP path_file_cdb SLIT_POS...

Page 57: ...d stack warpfix_ind TRUE sinfoni stacked warpfix_kernel stack warpfix_kernel tanh sinfoni stack qc_thresh_min stack qc_thresh_min 0 sinfoni stack qc_thresh_max stack qc_thresh_max 64000 sinfoni objnod...

Page 58: ...path_file_cdb DISTORTION_H tfits DISTORTION path_file_cdb FIRST_COLUMN tfits FIRST_COL 9 7 2 Output default recipe file name PRO CATG short description sky00 fits SKY_STACKED_DUMMY stacked sky frame o...

Page 59: ...size_x objnod size_x 0 sinfoni objnod size_y objnod size_y 0 sinfoni objnod n_coeffs objnod no_coeffs 3 sinfoni objnod nord_south_index objnod ns_ind TRUE sinfoni objnod fine_tuning_method objnod fine...

Page 60: ...ISTORTION_K tfits DISTORTION path_file_cdb FIRST_COLUMN tfits FIRST_COL 9 8 2 Output default recipe file name PRO CATG short description sky00 fits SKY_STACKED_DUMMY stacked sky frame out_sky_stack_di...

Page 61: ...foni objnod scales_sky objnod scales_sky TRUE sinfoni objnod ks_clip objnod ks_clip TRUE sinfoni objnod kappa objnod kappa 2 0 sinfoni objnod n_coeffs objnod no_coeffs 3 sinfoni objnod nord_south_inde...

Page 62: ...300 0 1 30 0 30 J 0 25 300 0 25 50 0 30 H 0 025 300 0 1 50 0 30 H 0 1 300 0 1 50 0 30 H 0 25 300 0 25 100 0 30 K 0 025 300 0 1 70 0 30 K 0 1 300 0 1 70 0 30 K 0 25 300 0 25 200 0 30 H K 0 025 300 0 1...

Page 63: ...IMA op IMA where op indicates the operation to be performed If a numerical value is specified at command line this is subtracted to the first input image 9 11 3 Parameters parameter alias default si_...

Page 64: ...name for the product is out_spec fits 9 13 3 Parameters Possible operations are average clean_mean median sum If the chosen operation is a clean mean one may define its lower and upper threshold cuts...

Page 65: ...ould be respectively CUBE IMA or SPECTRUM The output is a cube PRO CATG CUBE resulting from the operation CUBE op IMA or CUBE op SPECTRUM or CUBE op value where op indicates the operation to be perfor...

Page 66: ...h_shift This recipe shift a spectrum in wavelength according to value of the input parameter method 9 16 1 Input The input file is a spectrum Its associated tag should be SPECTRUM STD_STAR_SPECTRUM fi...

Page 67: ...d are pixels intensities of several images stacked in a cube the mean along the z axis of the cube is computed at each x y pixel after having rejected the intensity values which lie outside an interva...

Page 68: ...inearity 10 1 4 Nearest neighbours bad pixel cleaning This method is applied in the recipes si_rec_mflat and si_rec_distortion to clean the bad pixels of a flat frame The algorithm is controlled by th...

Page 69: ...eter factor is positive 6 6 if 604 6 6 6 else If method_index is 2 the absolute distances 6 of the eight nearest neighbours pixels are computed for each bad pixel as 6 604 where if B else The median d...

Page 70: ...If the parameter factor is positive 6 6 if 6 4 6 6 6 else If method_index is 4 the local clean low_rejection high_rejection standard deviation _ in a box llx lly urx ury is computed Then the differenc...

Page 71: ...master dark flat The factor does not apply 10 1 8 Line position determination The locations of the arc lamp lines are determined on an arc lamp frame input of the recipe si_rec_wavecal or si_rec_dist...

Page 72: ...tting the line position parameter of the fit to zero For each image column a polynomial fit of degree n_a_coefficients and coefficients is performed so as to determine the dispersion relation between...

Page 73: ...If a dispersion relation and a wavelength map are already available one may still want to adjust them to properly match the given arc lamp frame The positions of the slitlets edges are initially deter...

Page 74: ...ossibly due to bad pixels Then the image intensity values of the maxima reached in each slitlet are determined by searching in rectangular boxes centered at each slitlet positions edge j each of size...

Page 75: ...below is executed by recipes si_rec_psf si_rec_stdstar si_rec_objnod Given a source image and a corresponding wavelength calibration file an image is produced in which elements in a given row are asso...

Page 76: ...cube component to properly merge them in the coadded cube In this manual the 3D frame obtained after cube coaddition is often called cube for simplicity Then each contributing cube plane is shifted to...

Page 77: ...ed over an area of five FWHM of the input source PSF to ensure that all the light is included This spectrum is rescaled by a dividing by the DIT b dividing by the surface area A of M1 in cm c multiply...

Page 78: ...be The residual sky background contribution is given by the constant term of a 2D Gaussian fit of the image obtained by averaging the cube along z in a range of factor times the mean FWHM FWHM 0 5 FWH...

Page 79: ...ted from the mean lamp on frame If lamp_flats bad_ind TRUE the intensity tilt of each column is removed the fit of the pixel intensity is subtracted from the pixel intensity considering in this operat...

Page 80: ...side an intensity range set by parameters bp_norm min_cut and bp_norm low_cut are removed from the resulting median image If bp_norm threshold_index TRUE pixels deviating more than bp_norm mean_factor...

Page 81: ...are determined assuming as offset the position found for the first slitlet Finally the fake fibres on fibres off frame is corrected for distortions and the slitlet distances are deter mined again wit...

Page 82: ...wavecal slitpos_bootstrap_switch FALSE and provide an input slitlets positions table for example the corresponding one band preoptics provided in the calibration data available with this release and...

Page 83: ...ed frame by using the information contained in the slitlet position table SLIT_POS The 3D frame is refined using different methods objnod fine_tuning_method Possible values are P polynomial of order o...

Page 84: ...Date 2005 10 19 Page 84 of 88 10 2 8 PSF data reduction si_rec_psf The initial data reduction is the same as the one of a normal science frame Then the main PSF standard parameters the instrument str...

Page 85: ...nstallation of software packages A 1 Supported platforms The utilisation of the GNU build tools should allow to build and install the SINFONI pipeline on a variety of UNIX platforms but it has only be...

Page 86: ...l 1 0 pdf The SINFONI pipeline manual install_pipeline Install script qfits 5 3 1 tar gz QFITS 5 3 1 cpl 2 1 1 tar gz CPL 2 1 1 esorex 3 5 1 tar gz esorex 3 5 1 gasgano 2 2 3 Linux tar gz GASGANO 2 2...

Page 87: ...modules By default the script will install the SINFONI recipes Gasgano EsoRex all the necessary libraries and the static calibration tables into a directory tree rooted at HOME A different path may b...

Page 88: ...low System department DMD Data Management and Operations Division DRS Data Reduction System ESO European Southern Observatory ESOREX ESO Recipe Execution tool FITS Flexible Image Transport System FOV...

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