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PACS instrument and calibration web pages

Introduction

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This page provides up-to-date information about using the PACS instrument: from preparing observations to reducing your data. This includes information on the PACS instrument, PACS data, reducing PACS data in HIPE, and post-pipeline processing, and links to tutorials and scripts that you can run in HIPE. The calibration accuracies and technical information about the spectrometer and photometer of PACS are also provided here, as well as information about what future calibration and processing improvements can be expected.
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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
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    • A brief description of PACS data products (although much more detail is provided in the appendices of the PACS data reduction guides)
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    • 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)
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    • Here you can also find the various acronyms that are used in the PACS data reduction guides
    • We are now at the end of the mission. But these release notes can still be useful to read for a background understanding on how PACS data were gathered - this dictates what you will see as you look at your PACS data while pipeline processing them
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    • Here you can also find the various acronyms that are used elsewhere in PACS documentation
 
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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
 
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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

Reducing PACS data

Brief explanation

A brief introduction to reducing PACS data in HIPE. You can consult the PACS Data Reduction Guides (photometry and spectroscopy) 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 (e.g. mapping or single pointing for spectroscopy). 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), meaning that they are processed with a tailored version of the latest pipeline scripts from the User Release. For example, when HIPE User Release 11.0 was released, soon after all the Herschel data are processed with the SPG pipeline scripts of version 11.0, and so on for each User Release.
  • These SPG scripts are a copy of one flavour of interactive pipeline scripts, differing only on the AOT type. The SPG scripts include all the stable pipeline tasks with settings that correspond to the most common type of science target for each AOT. But some pipeline tasks can only be run via the interactive pipeline scripts, and to modify the important parameter settings for pipeline tasks also requires you re-run the pipeline. The Launch Pads (see below) include a guide to understanding the pipeline scripts and how to decide which to run.
  • The SPG results a good starting point to look at your PACS data, but in most cases you can improve the results at least somewhat by reducing the data yourself.

HIPE and data reduction documentation

  • 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 v12.1 It can be downloaded from: http://herschel.esac.esa.int/HIPE_download.shtml. In the CIB (continuous integration build) this version corresponds to Track 12, build 2765. (The CIB is the continuously bug-fixed/upgraded/improved version of HIPE, which every X months becomes a stable User Release. The CIB has the latest software in it, but it will not be bug-free.)

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  • The full documentation-set provided via HIPE includes the following:
    • The PACS (HIFI and SPIRE) DRGs. The main function of the PACS DRGs (photometry and spectroscopy) is to take you through reducing your data with the interactive pipeline, explaining the steps and the individual tasks in more detail and showing you how to inspect your results. This makes them rather long documents, and they should be read along with the pipeline scripts rather than on their own. They also show you how to quick-look at the SPG products you get from the HSA, what to consider before and after reducing your data, and explain what is contained in the PACS data products you get from the HSA.
    • A guide to using HIPE itself (i.e. HIPE as a GUI rather than a scientific tool).
    • The Data Reduction Guide, which is about working with all Herschel (or any other) data in HIPE: the various data analysis tools and data viewers are explained here.
    • The Scripting Guide: the language of HIPE is 'HIPE's version of jython', and it is a full scripting environment in which you can manipulate data, do mathematics, and view data in various ways. The 'SG' is a guide to scripting in HIPE. It is not necessary, but it does help, if you are already comfortable with scripting before embarking on scripting in HIPE.
    • Reference manuals. For most of the tasks that you can run in HIPE the description of what they do and listings of all the parameters can be found in the 'User's Reference Manual'. To learn more about the various HIPE product classes you can read the JAVA docs (APIs) a.k.a. the 'Developer's Reference Manual'. These tell you e.g. how to manipulate spectra and images directly by querying on the product, rather than using a pre-provided task.

  • The what's new in HIPE 12 page lists the changes in HIPE version 12.x with respect to the 11.x series, provides a detailed lists of updated functionalities and calibration aspects.

Cookbooks and interactive pipeline scripts

  • The various pipeline scripts PACS photometry and spectroscopy provide can be seen as cookbooks, since they take you through each pipeline, task by task (on the command-line), 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 June 2013 for photometry is provided here. The PACS Launch Pad from July 2013 for spectroscopy is provided here. These are taken from the first chapter of the respective PDRG 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 post-pipeline processing tasks are you can, or must, do
 

Tutorials and scripts

  • 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.

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.
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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

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  • 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).
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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.

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  • 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.

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

  • 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:
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    • 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.
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Interest Groups and Scripts

 

Links

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