PACS instrument and calibration web pages

Introduction

This page provides up-to-date information, documents, reports, and links about the PACS instrument, from preparing observations, through reducing and calibrating PACS observations, to working with PACS maps and cubes.

Observing with PACS

• The PACS Observer's Manual HTML PDF (11 Mb), version 2.3, 8-June-2011 : the first thing to read before applying for time with PACS (or even before working on PACS data for the first time), as it tells you how the instrument works. This includes:
  • A description of the layout and the components of the PACS photometer and spectrometer
  • A description of the scientific capabilities of the instrument: spectral response functions, sensitivity values, point spread functions, astrometric accuracy, flux calibration information
  • A description of the standard observing templates used to set up PACS observations; here you can also find the various acronyms that are used in the PACS data reduction guides
  • A brief description of PACS data products

• AOT Release Notes: dedicated release notes per AOT (the astronomer's observing template, i.e. the observing time planning).
  • Information about how the various standard observing blocks work
  • Summaries of transmission functions, sensitivity, etc. for use in your observing planning (similar to what you will find in the Observer's Manual)
  • Here you can also find the various acronyms that are used elsewhere in PACS documentation

• The PACS fact sheet

Although we are now in the post-operations phase of the mission, the PACS OM and the AOT release notes can still be useful to read for a background understanding on how PACS data were gathered

The In-flight scientific capabilities of the PACS instrument are also given in this paper: The Photodetector Array Camera and Spectrometer (PACS) on the Herschel Space Observatory (1.5 Mb), Poglitsch et al., 2010, A&A, 518, L2

PACS calibration and performance

• Data processing known issues of standard products for photometry and spectroscopy: Browse quality Level 2/2.5 products are provided in the Herschel Science Archive. This summary page describes typical problems and caveats the observer needs to be familiar when looking at these preview products. Aspects of product quality which can be further optimised by interactive processing are also summarised here. The document refers to the version of data processing pipeline currently being used for processing of incoming Herschel data (version number provided therein).

Photometer calibration in scan maps

• Point Spread Function: PACS Photometer Point Spread function (10 Mb), version 2.0, 4 April 2012. A detailed document of the in-flight observed PSF. The accompanying tarball can be found here (76 Mb).

• Herschel/PACS modelled point spread functions (3.1 Mb) is a related document presenting Zemax modelled point spread functions for both an `ideal' and an 'as built' Herschel telescope model. Tarballs with corresponding broad-band and monochromatic PSFs for these two cases are at http://pacs.ster.kuleuven.ac.be/pubtool/PSF. These are useful in addition to the observed PSFs but cannot replace them, since the models do not capture all effects found in the observed PSFs.

• Point-source photometry: PACS uses 5 stars as primary calibrators with fluxes ranging from 0.6 to 15 Jy, plus fainter stars and asteroids as secondary calibrators. The absolute flux scale accuracy is dominated by the model uncertainties and amounts to 5% in the 3 filter bands. At the same time, the reproducibility for a given non-variable point source is better than 2% for all PACS bands. The flux calibration is described in detail in Balog et al, 2013, Experimental Astronomy and confirmed with asteroids in Müller et al., 2013, Experimental Astronomy.

• Point-source photometry in deep PACS maps/surveys: The effect of the high-pass filter data reduction technique on the PACS Photometer PSF, point-source photometry, and noise has been investigated in depth in this technical note.

• Colour corrections:
  • PACS Photometer Passbands and Colour Correction Factors for various source SEDs (2.5 Mb), PICC-ME-TN-038, version 1.0, 12 April 2011
  • The bandwidth of the PACS photometric system, PICC-CR-TN-044 provides supplementary information on colour corrections with the PACS photometer

• Extended emission photometry: Three technical reports which assess the extended emission (or surface brightness) measured from PACS data and compare that to IRAS and Spitzer/MIPS data:
  • Assessment analysis of the extended emission calibration for the PACS red channel, version 1.0, April 2012: latest results on the comparison of extended emission in the PACS red channel (i.e. 160um) with corresponding data from Spitzer/MIPS 160um
  • Experiments in photometric measurements of extended sources (3.2 Mb), (report SAp-PACS-MS-0718-11, March 18, 2011). This report compares photometry of large extended galaxies (using large apertures) between PACS, IRAS and MIPS
  • Surface brightness comparison of PACS blue array with IRAS and Spitzer/MIPS images (1 Mb), (report PICC-NHSC-TN-029, v1.01, 12 April 2011). This report summarises pixel-to-pixel comparisons between extended emission as measured between PACS, IRAS and MIPS
  • We refer to the paper Common-Resolution Convolution Kernels for Space- and Ground-Based Telescopes, G. Aniano et al. (2011) for kernels and associated routines (IDL) to match spatial resolution between several infrared instruments PSFs (PACS, SPIRE, Spitzer/MIPS, Spitzer/IRAC, WISE) as well as GALEX (UV) and other PSF families (gaussian, bi-gaussian, Moffat)

• Chop/nod observations:
  • Chop/nod observations were not used for scientific observations during the mission, however they were heavily used for the photometry monitoring and well as numerous observations for the pointing accuracy check/monitoring. See Nielbock et al., 2013, Experimental Astronomy for the time dependent flux calibration for the PACS chopped point-source photometry AOT mode.

Photometer map-makers

Three fundamentally different map-makers are offered in Hipe 12 with ipipe scripts, starting from level 1 on pairs of obsids :

• highpass filtering branch, where the bolometer timelines are highpass filtered to remove the 1/f noise at the expense of extended emission. It provides optimum sensitivity to point-sources
• MADmap, a GLS (generalized least square) map-maker, that allows to preserve extended emission at all scale
• JyScanam, a Java-version of the IDL Scanamorphos map-maker

Another two public map-makers, also starting from level 1, widely used and both very easy to use are :

• Scanamorphos, an IDL map-maker from Hélène Roussel (IAP) with an advanced and powerful destriper for PACS maps
• Unimap a light (memory wise) GLS map-maker from Lorenzo Piazzo ('La Sapienza' University of Rome ) under a free Matlab runtime environment, with an advanced pre-processing (drift correction, jump detection) and post-processing stages (bright sources)

A report of the map-making working group compiled by Roberta Paladini is available: PACS map-making tools: analysis and benchmarking, 1 Nov. 2013.

An updated version of that report concentrating on JScanam, MADmap and Unimap in their latest versions is available in PACS Map-making Tools: Update on Analysis and Benchmarking, 30 March 2014.

The optical field distortion is not applied in level 1, as this calibration is applied by the native photProject task. As a result, external map-makers starting from level 1 have a systematic flux overestimate of 6-7% in the red channel and a lower underestimate (~2%) in the blue channel of the flux scale. This is corrected for MADmap in Hipe12 by introducing the new task convertToFixedPixelSize() at the end of level1. The flux difference come from the fact that the mean values of the optical flat are significantly different from 1, in other words it cannot be assumed by external map-makers that the pixel sizes is constant of the field of view at 3.2"/6.4 in the blue/red channel respectively.

Scanamorphos and Unimap are also affected, but not JScanam that makes use of photProject.

PACS spectrometer calibration

• PACS Spectrometer performance and calibration: The PACS Spectrometer Calibration Document v2.4 (16-June-2011) provides details on the calibration accuracy and the necessary information to optimally interpret PACS spectroscopy observations. (Please note, this document refers to the calibration status and performance of pipeline version v8.0. An update compatible with HIPE v12.1 release will be provided soon.) This includes:
  • flux calibration accuracies for chop nod and unchopped observations
  • the beam efficiencies and the PACS integral field footprint
  • spectral leakages and ghosts
  • wavelength calibration, including information on a skew our native line profile develops as a point source moves off the centre of a spaxel
  • table of the point source correction factors for different wavelengths
• The calibration of the spectrometer is based on repeated measurements of planets, asteroids, and stars. The RMS scatter of these measurements are just over 10% within any spectral band, about the same when comparing different spaxels, and similar (but higher in the red) when looking for broad-band features within any band. These calibration certainties are independent, and should be combined when quoting errors in science papers. Read the above-mentioned document for the most up-to-date information.

• PACS spectrometer beams, version 3, can be downloaded here: PCalSpectrometer_Beam_v3.tar.gz. These beams are based on measurements of a raster with step size 2.5" around Neptune. These beams are useful to compare the flux seen in the different IFU spaxels with with a point source, or a certain brightness distribution in the sky. Version 3 has the beam effiencies for all IFU spaxels, and has a drastic improvement wrt version 2 since the spacecraft pointing was reconstructed more accurately. This resulted in a non-equidistant sampling of the beam efficiency in the sky. The beam products offered are equidistantly sampled on a grid of 0.5 arcseconds. The central part of the beam is the Gaussian fit to the measured beam efficiencies. This has been verified to be a very good description on the different raster observations we have of the central spaxels for wavelengths longer than 80 micron. Below 80 micron, the actual beam shows the square detector footprint, and the Gaussian approximation in the beam products v3 overpredicts the real beam efficiency by 1.5 to 2 percent. The outer part of the beams contains the interpolated values of the irregularly sampled measurements. Thanks to the improved data reduction quality, version 3 of the spectrometer beams are sharper than version 2, and shows the ghosts (see also the PACS spectrometer calibration document) more clearly, as well as the three-lobe structure of the Herschel telescope PSF. Each beam is normalised to the fitted peak value of the central spaxel. The WCS associated with the beam is in sky coordinates for position angle 0.
• The raw data from which the PACS spectrometer beams above have been derived, is also made available to the users in tables (y, z offset - signal):
  • SpecSpatial_BeamEfficiency_central_spaxel_tables_v1.tar.gz: Raw measurements PACS beams - central spaxel only. This contains a fits file for each wavelength measured for the CENTRAL SPAXEL only. Raw data of the coarse and fine rasters are combined. The array dimension of the fits file is [3,npoints] where the first column gives the y raster position, the 2nd column the z raster position and the 3rd column the normalised flux measured at this raster position.
  • SpecSpatial_BeamEfficiency_tables_v1.tar.gz: Raw measurements PACS beams - all spaxels, coarse raster measurements only: each fits files corresponds to one wavelength. Each file contains the data for all spaxels of the coarse raster measurement only. Each fits file holds an array of 3x25x25x25 where: (0,25,25,25)=y raster position, (1,25,25,25)=z raster position, (2,25,25,25)=flux normalized to the central spaxel. The second and third dimensions are the raster position indices (y and z) and the last dimension is the module number (=spaxel number).

• Point source observations. We provide a task at the end of the pipeline scripts to extract the spectrum of point sources, corrected for flux losses due to the PSF being larger than the spaxel size, and including a correction for flux losses due to small pointing offsets from the centre of the the central spaxel and pointing jitter. This task (extractCentralSpectrum) is used on cubes of a single pointing (i.e. not those created from combine several raster pointings) and must be run in order to correctly extract the spectrum of point sources. This task uses the beams we refer to above. The pros and cons and how and when to use the task are documented in the spectrometer PDRG (in the pipeline chapters and again in chap. 7).

PACS calibration file versions

• When starting HIPE, you will be informed if new calibration files are available. Clicking on 'show details' will show you the release note of the new calibration set, with details about the changes. This is further explained in the PDRGs (chap. 2). Clicking on 'Install' will install the latest calibration files.
• The history of the calibration files that have been released to the community is provided here: PACS Calibration File History.
• You can inspect the release notes for the calibration sets installed on your machine from within HIPE. Open the Calibration Sets View from the menu Window -> Show Views -> Workbench.
• When reducing your data in HIPE you will normally use the latest version of the calibration tree that you have on disk (this happens by default), but you can chose to use a previous version instead. How to do this is explained in the PDRGs.

Reducing PACS data

A brief introduction to reducing PACS data in HIPE. You can consult the PACS Data Reduction Guides (photometry and spectroscopy; available via HIPE) for more detail.

• PACS data are reduced with pipeline scripts which are a set of command-line tasks that process the data from Level 0 (raw) to Level 2/2.5 (science-ready). There is more than one flavour of pipeline script, tailored to different types of science target, AOT, and observing plan. These 'interactive' pipeline scripts are provided in HIPE and explained in the data reduction guides.
• The data you get from the the HSA will have been processed by the 'SPG' (Standard Product Generator) using one pipeline script flavour per AOT. Which script is used is documented in the PDRG.
• The SPG scripts include all the stable pipeline tasks within those scripts, with task settings that correspond to the most common type of science target for each AOT. But some pipeline tasks still can only be run via the interactive pipeline scripts, and to modify the parameter settings for the important pipeline tasks also requires you re-process the data. The Launch Pads (see below) include a guide to understanding the pipeline scripts and how to decide whether to reprocess your data and if so, with which script.

HIPE, data reduction documentation, and useful links for data issues

• HIPE (Herschel Interactive Processing Environment) is the tool used to inspect, reduce, and analyse Herschel data. The latest User Release HCSS (Herschel common science system) version that you should use for reducing PACS data is HIPE v13.0 It can be downloaded from: http://herschel.esac.esa.int/HIPE_download.shtml. In the CIB (continuous integration build) this version corresponds to Track 13, build 5130. The CIB is the continuously bug-fixed/upgraded/improved version of HIPE, which every few months (in the beginning of the mission) or yearly (in the post-operations phase) becomes a stable User Release.

• Within HIPE you can access all the PACS data reduction documentation and the general HCSS and HIPE user documentation for Track 13 here. The documentation provided via HIPE opens in a web browser, but for those of you who prefer PDF, we include the PACS Data Reduction Guides as PDF files here (note that within the standalone pdf versions, external links will not work):
  • PACS Spectrometer Data Reduction Guide for Hipe 13
  • PACS Photometer Data Reduction Guide for Hipe 13

• The what's new in HIPE 13 page lists the changes in HIPE version 13.x with respect to the 12.x series, and provides a detailed list of updated functionalities, product changes, and calibration aspects.

• The Data products known issues page details issues about the pipelines or the data products that are known about and offers advice for dealing with them. Consult this if you encounter problems with your data to see if it has already been addressed.

• Link to the General HCSS Public Twiki page (with general framework information and updates): http://herschel.esac.esa.int/twiki/bin/view/Public/WebHome

Cookbooks and interactive pipeline scripts

• The various interactive pipeline scripts PACS photometry and spectroscopy provide in HIPE can be seen as cookbooks, since they take you through each pipeline, task by task, explaining briefly what each task does, commenting on the more crucial pipeline tasks, and showing you how to plot, image, visualise and inspect your data as you work through the pipeline. An example public observation is included with each so you can test it out before using it on your data. These data reduction scripts are available in HIPE under the menu: Pipeline --> PACS --> Photometer/Spectrometer.

• The PACS Launch Pad from HIPE 13 for photometry is provided here. The PACS Launch Pad from HIPE 13 for spectroscopy is provided here. These are taken from the first chapters of the respective PDRGs and are a useful quick-start guide to loading your data into HIPE, looking at them, and then what to know and do before you begin reprocessing your data with one of the pipelines. Also included is
  • why we recommend you do re-pipeline your data
  • what you need to pay attention to for different types of astronomical source
  • what the crucial pipeline tasks are
  • what the post-pipeline processing tasks that we provide are

 

Tutorials and scripts

• See the various walkthroughs on the NHSC PACS page.

• The Nasa Herschel Science center (NHSC) has also posted some PACS Data Processing Tutorials.

• HIPE Academy on YouTube: here you can find recordings of various seminars and webinars that the HSC have given on working in HIPE, reducing Herschel data, using various tools to visualise and manipulate data in HIPE, and etc.

• In HIPE there is a Scripts menu in which you can find various "useful scripts" for working with PACS data in HIPE. For example, for spectroscopy there is a script showing how to fit the spectra in cubes and make integrated flux images from them; for photometry we show how to do point source aperture photometry. These are written as scripts which you can open in HIPE and run on a test dataset, and in most cases you can replace the test dataset with your own and take it from there. Please do note that these scripts do not explain how to use the GUI version of the tasks - for this you need to read the PDRGs or the general Data Reduction Guide.

A summary of the PACS instrument for an astronomer

Here we provide a summary of instrumental and calibration details that a data-reducing astronomer often wants know. The summary provides a set of links or information about where to find the information.

Spectroscopy

• Wavelength ranges and limits, band names
  • The blue bands are B2A (blue, second order) and B2B (green, second order), and B3A (blue, third order), and in the red we have R1 (first order)
  • The wavelength ranges and resolutions can be found in Table 4.1 of the PACS Observer's Manual (here for the HTML version)
• The footprint of the integral field unit: text and figures showing the footprint of the PACS IFU, and how that compares to the beam, can be found in the PACS Spectrometer Calibration Document v2.4 (16-June-2011) (sec. 3) where you will also find information about the beam maps (at high spatial resolution and for various wavelengths), beam efficiencies, and the point source loss corrections. This is mentioned again in the 'PACS spectrometer calibration' section below. The same information can be found in the PACS Observer's Manual (sec. 4.6)
• The spatial FWHM of a point source: this information can be found in fig. 4.12 of the PACS Observer's Manual and again in the PACS Spectrometer Calibration Document
• Spectral leaks: there is order leakage in our filters that affects the ends of the blue and red bands. These are documented as figures in sec. 4.1 of the PACS Spectrometer Calibration Document and again in sec. 4.8 of the PACS Observer's Manual . Dealing with this leakage by reducing the data with a particular calibration file is documented in the PACS spectrometer data reduction guide (in the pipeline chapters where the flatfielding task is discussed, and sec. 3.7)
• Ghosts: see sec. 4.2 of the PACS Spectrometer Calibration Document to learn about ghosts - echos of spectral lines from one wavelength to another from one spaxel to another. This is also documented in sec. 4.9 of the PACS Observer's Manual
• Skews for off-centred sources: point sources that are not centrally located in a spaxel will show a skew to their spectral lines (although if the lines are faint this may not be obvious). Some calibration of this has been done and this can be found in sec. 4.7.2 and 4.7.3 of the PACS Observer's Manual and sec. 5.2 of the PACS Spectrometer Calibration Document. Some more information concerning how to tell whether your source's offset should lead to a skew can be found in the PACS spectrometer data reduction guide, sec. 7.5
• Calibration certainties: these are all documented in the beginning of the PACS Spectrometer Calibration Document
• Names of the AOTs and what they mean: can be found in the AOT Release Notes
• Expected signal-to-noise ratios and line sensitivity: this depends on the AOT, this information is also provided in the AOT Release Notes

Photometry

• Filters and bands
  • The blue and green bands are not observed simultaneously, the red is observed simultaneously with each. Transmission functions can be found in the PACS Observer's Manual sec. 3.2.
• PSF and beams: the beams maps as FITS files, and information about then can be found below in the section 'Photometer calibration in scan maps'
• Point source photometry
  • Colour corrections: these are provided below in the section 'Photometer calibration in scan maps'
  • Aperture corrections/eefs (encircled energy fractions) are provided in sec. 8 of the PACS Photometer Point Spread function document
• Effects of nonlinearity, saturation, stray light, crosstalk and ghosts: can be found in sec. 6 of the PACS Photometer Point Spread function document
• Calibration certainty: is discussed below in the section 'Photometer calibration in scan maps' (item 'Point-source photometry'), with links there to two publications. You can also read sec 3.3 of the PACS Observer's Manual
• Names of the AOTs and what they mean: can be found in the AOT Release Notes
• Sensitivity: this depends on the AOT, this information is also provided in the AOT Release Notes

Planned processing and calibration improvements

• The PACS ICC and the HSC calibration scientist teams are currently working on making the following processing and calibration improvements available to the users:
  • Making spectrometer convolution kernels available. These products will be useful to estimate line-ratios in oversampled spectral maps.
  • Improved a-posteriori pointing reconstruction based on guide star positions used for the observation and the gyroscope raw output.
  • Improved correction for systematics affecting the spectral shape of sources and detectability of unresolved lines.

Links

• PACS NHSC homepage
• Key information of PACS on the NHSC web site.
• Scanamorphos by H. Roussel can be used to build maps from scan observations made with bolometer arrays, in particular with the PACS and SPIRE photometers.

• pacs_mapmaking_report14_v2.pdf: PACS Map-making Tools: Update on Analysis and Benchmarking