ESO SINFONI Pipeline User manual

EUROPEAN SOUTHERN OBSERVATORY
Organisation Européenne pour des Recherches Astronomiques dans l’Hémisphère Austral
Europäische Organisation für astronomische Forschung in der südlichen Hemisphäre
VERY LARGE TELESCOPE
SINFONI Pipeline User Manual
VLT-MAN-ESO-19500-3600
Issue 1.0
Date 2005-10-19
Prepared: ESO SINFONI Pipeline Team 2005-10-19
...............................................................................
Name Date Signature
Approved: P.Ballester, M. Peron
...............................................................................
Name Date Signature
Released: P. Quinn
...............................................................................
Name Date Signature

This page was intentionally left blank

ESO SINFONI Pipeline 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 Public release

This page was intentionally left blank

ESO SINFONI Pipeline User Manual
Doc: VLT-MAN-ESO-19500-3600
Issue: Issue 1.0
Date: Date 2005-10-19
Page: 5 of 88
Contents
1 Introduction 11
1.1 Purpose . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
1.2 Acknowledgements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
1.3 Scope . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
1.4 Reference documents . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
2 Overview 13
3 SINFONI Instrument Description 14
3.1 Instrument overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 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 Known problems 30
6 Instrument Data Description 32
6.1 Data features . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
6.2 Raw frames . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
7 Static Calibration Data 38
7.1 Line reference table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38
7.2 DRS setup table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38
7.3 Reference bad pixel map . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38
7.4 First column reference table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38
8 Data Reduction 39
8.1 Data reduction overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39

ESO SINFONI Pipeline User Manual
Doc: VLT-MAN-ESO-19500-3600
Issue: Issue 1.0
Date: Date 2005-10-19
Page: 6 of 88
8.2 Required input data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
8.3 Reduction cascade . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
9 Pipeline Recipes Interfaces 44
9.1 si_rec_detlin . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44
9.1.1 Input . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44
9.1.2 Output . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44
9.1.3 Quality 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 control . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
9.3.4 Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48
9.4 si_rec_distortion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49
9.4.1 Input . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49
9.4.2 Output . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50
9.4.3 Quality control . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50
9.4.4 Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51
9.5 si_rec_wavecal . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53
9.5.1 Input . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53
9.5.2 Output . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54
9.5.3 Quality control . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54
9.5.4 Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55
9.6 si_rec_psf . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56
9.6.1 Input . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56

ESO SINFONI Pipeline User Manual
Doc: VLT-MAN-ESO-19500-3600
Issue: Issue 1.0
Date: Date 2005-10-19
Page: 7 of 88
9.6.2 Output . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56
9.6.3 Quality control . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57
9.6.4 Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57
9.7 si_rec_stdstar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58
9.7.1 Input . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58
9.7.2 Output . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58
9.7.3 Quality control . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58
9.7.4 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_mask_add . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62
9.10.1 Input . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62
9.10.2 Output . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62
9.10.3 Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63
9.11 si_utl_ima_arith . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63
9.11.1 Input . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63
9.11.2 Output . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63
9.11.3 Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63
9.12 si_utl_cube2ima . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63
9.12.1 Input . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63
9.12.2 Output . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63
9.12.3 Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64
9.13 si_utl_cube2spectrum . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64

ESO SINFONI Pipeline User Manual
Doc: VLT-MAN-ESO-19500-3600
Issue: Issue 1.0
Date: Date 2005-10-19
Page: 8 of 88
9.13.1 Input . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64
9.13.2 Output . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64
9.13.3 Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64
9.14 si_utl_cube_arith . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65
9.14.1 Input . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65
9.14.2 Output . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65
9.14.3 Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65
9.15 si_utl_spectrum_divide_by_blackbody . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65
9.15.1 Input . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65
9.15.2 Output . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66
9.15.3 Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66
9.16 si_utl_spectrum_wavelength_shift . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66
9.16.1 Input . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66
9.16.2 Output . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 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 Nearest neighbours bad pixel cleaning . . . . . . . . . . . . . . . . . . . . . . . . . . . 68
10.1.5 Detector gain computation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71
10.1.6 Read Out Noise computation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71
10.1.7 Fixed Pattern Noise computation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71
10.1.8 Line position determination . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71
10.1.9 Dispersion relation and wavelength map determination . . . . . . . . . . . . . . . . . . 72
10.1.10 Line shift computation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73
10.1.11 Dispersion relation adjustment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73
10.1.12 Slitlet position computation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 74
10.1.13 Slitlet distances computation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75

ESO SINFONI Pipeline User Manual
Doc: VLT-MAN-ESO-19500-3600
Issue: Issue 1.0
Date: Date 2005-10-19
Page: 9 of 88
10.1.14 Cube construction: resampling . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75
10.1.15 Cube coaddition . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76
10.1.16 Estimation of the sky from object frames in case the input set is missing sky frames . . . 76
10.1.17 Efficiency computation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77
10.1.18 Strehl computation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 78
10.1.19 Encircled energy computation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 78
10.1.20 Spectrum extraction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 78
10.1.21 Standard star position detection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 78
10.2 Recipes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 78
10.2.1 Detector linearity 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) determination: si_rec_mflat . . . . . . . 79
10.2.4 Optical distortion and slitlet distances determination: si_rec_distortions . . . . . . . . . 80
10.2.5 Wavelength solution determination: si_rec_wavecal . . . . . . . . . . . . . . . . . . . 81
10.2.6 Science observations: si_rec_objnod . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83
10.2.7 STD star data reduction: si_rec_stdstar . . . . . . . . . . . . . . . . . . . . . . . . . . 83
10.2.8 PSF data reduction: si_rec_psf . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 84
A Installation 85
A.1 Supported platforms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85
A.2 Building the SINFONI pipeline . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85
A.2.1 Requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85
A.2.2 Compiling and installing the SINFONI pipeline . . . . . . . . . . . . . . . . . . . . . . 86
B Abbreviations and acronyms 88

ESO SINFONI Pipeline User Manual
Doc: VLT-MAN-ESO-19500-3600
Issue: Issue 1.0
Date: Date 2005-10-19
Page: 10 of 88

ESO SINFONI Pipeline User Manual
Doc: VLT-MAN-ESO-19500-3600
Issue: Issue 1.0
Date: Date 2005-10-19
Page: 11 of 88
1 Introduction
1.1 Purpose
The SINFONI pipeline is a subsystem of the VLT Data Flow System (DFS). Its target user is ESO Data Flow
Operations (DFO) in the generation of master calibration data, in the reduction of scientific exposures, and
in the data quality control. It should also serve as a quick look tool for Paranal Science Operations (PSO).
Additionally, the SINFONIpipeline recipes are made public to the user community, to allow a more personalised
processing of the data from the instrument. The purpose of this document is to describe a typical SINFONI data
reduction sequence with the SINFONI pipeline.
This manual is a complete description of the data reduction recipes implemented by the the SINFONI pipeline,
reflecting the status of the SINFONI pipeline as of Oct 19, 2005 (version 1.2.0).
1.2 Acknowledgements
The SINFONI pipeline is based on the SPIFFI Data Reduction Software developed by the Max-Planck-Institut
für extraterrestrische Physik (MPE). We would like to thank the SPIFFI team for 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 verifications phases. We are particularly grateful to the
MPE responsibles for the data reduction: Jurgen Schreiber, Matthew Horrobin and Roberto Abuter for their
contributions and support.
Release 1.2.0benefited from the feedback provided by the SINFONI SV team and SINFONI instrument opera-
tions team. In particular we would like to thank Wolfgang Hummel and Juha Runanen for extensively testing
and improving the pipeline and documentation, as well as Jochen Liske for proof reading the manual.
1.3 Scope
This document describes the SINFONI pipeline used at ESO-Garching and ESO-Paranal for the purpose of data
assessment and data quality control.
Updated versions of the present document may be found on [1]. For general information about the current
instrument pipelines status we remind the user of [2]. Quality control information are at [3].
Additional information on QFITS, the Common Pipeline Library (CPL) and ESOREX can be found respectively
at [4], [5], [6]. The Gasgano tool is described in [14]. A description of the instrument is in [7]. The SINFONI
instrument user manual is in [8] while results of Science Verifications (SV) are at [9].

ESO SINFONI Pipeline User Manual
Doc: VLT-MAN-ESO-19500-3600
Issue: Issue 1.0
Date: Date 2005-10-19
Page: 12 of 88
1.4 Reference documents

SINFONI Pipeline Users’ Manual VLT-MAN-ESO-19500-3600
http://www.eso.org/projects/dfs/dfs-shared/web/vlt/vlt-instrument-pipelines.html

Current pipeline status http://www.eso.org/observing/dfo/quality/pipeline-status.html

ESO-Data Flow Operation home page http://www.eso.org/observing/dfo/quality/
 
QFITS home page http://www.eso.org/projects/aot/qfits/

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.org/instruments/sinfoni/usermanual.html

SINFONI SV home page http://www.eso.org/science/vltsv/sinfonisv/

VLT Data Flow System Specifications for Pipeline and Quality Control
VLT-SPE-ESO-19600-1233

DFS Pipeline & Quality Control – User Manual VLT-MAN-ESO-19500-1619

ESO DICB – Data Interface Control Document GEN-SPE-ESO-00000-0794

Common Pipeline Library User Manual VLT-MAN-ESO-19500-2720

Gasgano User’s Manual VLT-PRO-ESO-19000-1932

SINFONI Calibration Plan VLT-PLA-ESO-14700-2617

ESO SINFONI Pipeline User Manual
Doc: VLT-MAN-ESO-19500-3600
Issue: Issue 1.0
Date: Date 2005-10-19
Page: 13 of 88
2 Overview
In collaboration with instrument consortia, the Data Flow Systems Department (DFS) of the Data Manage-
ment and Operation Division is implementing data reduction pipelines for the most commonly used VLT/VLTI
instrument modes. These data reduction pipelines have the following three main purposes:
Data quality control: pipelines are used to produce the quantitative information necessary to monitor instru-
ment performance.
Master calibration product creation: pipelines are used to produce master calibration products (e.g., com-
bined bias frames, super-flats, wavelength dispersion solutions).
Science product creation: using pipeline-generated master calibration products, science products are produced
for the supported instrument modes (e.g., combined ISAAC jitter stacks; bias-corrected, flat-fielded FORS
images, wavelength-calibrated UVES spectra). The accuracy of the science products is limited by the
quality of the available master calibration products and by the algorithmic implementation of the pipelines
themselves. In particular, adopted automatic reduction strategies may not be suitable or optimal for all
scientific goals.
Instrument pipelines 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 applications for launching pipeline recipes, Gasgano [14] and EsoRex, both included
in the pipeline distribution (see Appendix A, page 85). These applications can also be downloaded separately
from http://www.eso.org/gasgano and http://www.eso.org/cpl/esorex.html. An il-
lustrated introduction to Gasgano is provided in the "Quick Start" Section of this manual (see page 16).
The SINFONI instrument and the different types of SINFONI raw frames and auxilliary data are described in
Sections 3, 6, and 7.
A brief introduction to the usage of the available reduction recipes using Gasgano or EsoRex is presented
in Section 4. In section 5 we advice the user about known data reduction problems providing also possible
solutions.
An overview of the data reduction, what are the input data, and the recipes involved in the calibration cascade
is provided in section 8.
More details on what are inputs, products, quality control measured quantities, and controlling parameters of
each recipe is given in section 9.
More detailed descriptions of the data reduction algorithms used by the individual pipeline recipes can be found
in Section 10.
In Appendix A the installation of the SINFONI pipeline recipes is described and in Appendix B a list of used
abbreviations and acronyms is given.

ESO SINFONI Pipeline User Manual
Doc: VLT-MAN-ESO-19500-3600
Issue: Issue 1.0
Date: Date 2005-10-19
Page: 14 of 88
3 SINFONI Instrument Description
SINFONI has been developed by ESO and the Max-Planck-Institut für extraterrestrische Physik (MPE) in
Garching.
The instrument has been made available to the community and started operations in Paranal on April
 
, 2005.
In this chapter a brief description of the SINFONI instrument is given. A more complete documentation can be
found in the SINFONI User Manual, downloadable from http://www.eso.org/instruments/sinfoni/
3.1 Instrument overview
SINFONI is a near-infrared (1.05 - 2.45

m) integral field spectrograph (SPIFFI, developed by MPE) fed 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 free view on the opto-mechanical components of SPIFFI. The light enters from the top, and passes
the sky-spider. The pre-optics with a filter-wheel and interchangeable lenses provides three different image
scales. The image slicer re-arranges the two-dimensional field into a pseudo-long slit, which is perpendicular
to the base plate. Three diamond turned mirrors collimate the light onto the gratings. In total, four gratings
are implemented on the grating drive. A multiple-lens system then focuses the spectra on a Rockwell HAWAII
array. The diameter of the instrument is 1.3m.
The spectrograph operates with 4 gratings (J, H, K, H+K) providing a spectral resolution around 2000, 3000,

ESO SINFONI Pipeline User Manual
Doc: VLT-MAN-ESO-19500-3600
Issue: Issue 1.0
Date: Date 2005-10-19
Page: 15 of 88
4000 in J, H, K, respectively, and 1500 in H+K - each wavelength band fitting fully on the 2048 pixels of
the Hawaii 2RG (2kx2k) detector in the dispersion direction. The SINFONI field of view on the sky is sliced
into 32 slices. Pre-optics allow to chose the width of the slices. The choices are 250mas, 100mas and 25mas,
leading to field of views on the sky of 8"x8", 3"x3", or 0.8"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 32 slitlets is imaged onto 64 pixels of the detector.
Thus one obtains 32x64 spectra of the imaged region on the sky.
Figure 3.1.0: SPIFFI image slicer (top): The light enters through the hole in the big slicer. A stack of 32 small
mirrors, the small slicer (also shown in the sub-panel), slices the image and redirects the light towards the 32
mirrors of the big slicer, which re-arranges the slitlets into a 31 cm long pseudo-slit. (bottom). The layout of the
slitlets on a raw SPIFFI frame.

ESO SINFONI Pipeline User Manual
Doc: VLT-MAN-ESO-19500-3600
Issue: Issue 1.0
Date: Date 2005-10-19
Page: 16 of 88
4 Quick start
This section describes the most immediate usage of the SINFONI pipeline recipes.
4.1 SINFONI pipeline recipes
The current SINFONI pipeline is based on a set of 8 stand-alone recipes involved in the data reduction cascade:
si_rec_detlin to evaluate the detector non linearity and generate a corresponding non linear pixel map.
si_rec_mdark to create a master dark and a hot-pixel map.
si_rec_mflat to create a master flat and a map of pixels which have intensities greater than a given threshold.
si_rec_distortion to compute the 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 standard data reduction.
Additional 8 stand-alone recipes are also provided, that perform useful tasks:
si_utl_skymap to flag sky lines as bad pixels in a “sky map” (for Paranal operations, to prepare input data of
the SINFONI Real Time Display).
si_utl_bp_mask_add to coadd bad pixel maps.
si_utl_ima_arith to do image arithmetics.
si_utl_cube2ima to collapse a cube to an image over a given wavelength range.
si_utl_cube2spectrum to extract a spectrum from a cube.
si_utl_cube_arith to perform cube arithmetics.
si_utl_spectrum_divide_by_blackbody to divide a spectrum by a black body spectrum.
si_utl_spectrum_wavelegth_shift to shift in wavelength a spectrum.

ESO SINFONI Pipeline User Manual
Doc: VLT-MAN-ESO-19500-3600
Issue: Issue 1.0
Date: Date 2005-10-19
Page: 17 of 88
4.2 An introduction to Gasgano and EsoRex
Before being able to call pipeline recipes on a set of data, the data must be opportunely classified, and associated
with the appropriate calibrations. The Data Classification consists of tasks such as: "What kind of data am
I?", e.g., BIAS, "to which group do I belong?", e.g., to a particular Observation Block or template. Data
Association is the process of selecting appropriate calibration data for the reduction of a set of raw science
frames. Typically, a set of frames can be associated if they share a number of properties, such as instrument and
detector configuration. As all the required information is stored in the FITS headers, data association is based
on a set of keywords (called "association keywords") and is specific to each type of calibration.
The process of data classification and association is known as data organisation.
An instrument pipeline consists of a set of data processing modules that can be called from different host
applications, either from the command line with Esorex, from the automatic data management tools available
at Paranal, or from the graphical Gasgano tool.
Gasgano is a data management tool that simplifies the data organisation process, offering automatic data clas-
sification and making the data association easier (even if automatic association of frames is not yet provided).
Gasgano determines the classification of a file by applying an instrument specific rule, while users must pro-
vide this information to the recipes when they are executed manually using Esorex 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 their usage, it is advisable to begin with Gasgano,
because it provides a complete graphic interface for data browsing, classification and association, and offers
several other utilities such as easy access to recipes documentation and preferred data display tools.
Gasgano can be started from the system prompt in the following way:
gasgano &
The Gasgano main window will appear. On Figure 4.2.1 (next page), a view on a set of SINFONI IFU data
is shown as an example. Gasgano can be pointed to the directories where the data to be handled are located
using the navigation panels accessible via the Add/Remove Files entry of the File menu (shown on the upper
left of the figure).
The data are hierarchically organised as preferred by the user. After each file name are shown the classification,
the instrument setup id (which indicates the band), the instrument pre-optic (which indicates the camera setting),
the template exposure number and the number of exposures in the template, and the value of the DPR.TYPE.
More information about a single frame can be obtained by clicking on its name: the corresponding FITS file
header will be displayed on the bottom panel, where specific keywords can be opportunely filtered and searched.
Images and tables may be easily displayed using the viewers specified in the appropriate Preferences fields.
Frames can be selected from the main window for being processed by the appropriate recipe: on Figure 4.2.2,
the standard star frame and a sky frame, already produced master bad pixel map and master flat field frames,
together with distortion and slitlet distance tables, and the necessary static calibration tables, are all selected

ESO SINFONI Pipeline User Manual
Doc: VLT-MAN-ESO-19500-3600
Issue: Issue 1.0
Date: Date 2005-10-19
Page: 18 of 88
and sent to the si_rec_stdstar recipe. This will open a Gasgano recipe execution window (see Figure 4.2.3),
having all the specified files listed in its Input Frames panel.
Help about the recipe may be obtained from the Help menu. Before launching the recipe, its configuration may
be opportunely 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 can be launched by pressing the Execute button. Messages from the running recipe will
appear on the Log Messages panel at bottom, and in case of successful completion the products will be listed
on the Output Frames panel, where they can be easily viewed and located back on the Gasgano main window.
Please refer to the Gasgano User’s Manual [7] for a more complete description of the Gasgano interface.

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.

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.