As for SPIRE FTS spectroscopy, semi-extended sources provide the user with a very special set of problems, as they are sources of a size intermediate between point sources (i.e. unresolved) and extended sources (clearly resolved), for which neither point source reduction techniques, nor extended source techniques work well.

We assume that you have watched the Herschel Science Centre short videotutorial called Starting with PACS Spectroscopy:

https://www.youtube.com/watch?v=rcY487Z9Kyg 

Or, at least, are familiar with the contents of this short videotutorial and its associated documentation. There is a Herschel Science Centre short videotutorial that will guide you through the process of processing and analyzing semi-extended sources. You can find the short videotutorial here:

https://www.youtube.com/watch?v=PNSuxM105UY

A pre-requisite for processing semi-extended sources is to know:

1. The surface brightness distribution.

and

2. The off-set of the source from the centre of the central spaxel.

If you do not have this information, you can still attempt to use these techniques (the short videotutorial will advise you on this), but may have larger errors in your calibration. 

You can find a package of useful support materials for this short videotutorial in the Herschel Explanatory Legacy library (HELL) in the Level 2, Data reduction, PACS spectroscopy section.

This short videotutorial you will be shown how to use the useful script that was developed to deal with semi-extended sources that extracts the spectrum of the central spaxel of a re-binned cube and applies a point source correction to it. It then compares the surface brightness of a point source with the known surface brightness distribution and creates an extended-to-point correction too that is used to generate the semi-extended source correction. It will show you how to apply the models and which data products to use for different observing modes. Finally, you will be shown some examples of PACS data processed with the script.

We recommend, as background information, that you consult the following Herschel Science Centre short videotutorials too:

Point Source Spectroscopy with PACS, https://www.youtube.com/watch?v=nYWTccEQz_M

PACS Cubes in Detail, https://www.youtube.com/watch?v=CxZF9-9D8UM

Or the following guide:

Dealing with extended sources observed with PACS spectroscopy

Extended sources provide the user with a particular set of problems that require special techniques.

We assume that you have watched the Herschel Science Centre short videotutorial called Starting with PACS Spectroscopy:

https://www.youtube.com/watch?v=rcY487Z9Kyg 

You should also watch the Herschel Science Centre short videotutorial called PACS Cubes in Detail:

https://www.youtube.com/watch?v=CxZF9-9D8UM

Or, at least, are familiar with the contents of these short videotutorials and their associated documentation. There is a Herschel Science Centre short videotutorial that will guide you through the process of processing and analyzing extended sources. You can find the short videotutorial here:

https://www.youtube.com/watch?v=j270VI0Ah1g

A pre-requisite for processing extended sources is to be familiar with the different spectroscopy products: cubes and tables that are produced when processing PACS spectroscopy.

We assume here that you have watched the Herschel Science Centre short videotutorial called Starting with PACS Spectroscopy:

https://www.youtube.com/watch?v=rcY487Z9Kyg 

And the Herschel Science Centre short videotutorial Point Source Spectroscopy with PACS:

https://www.youtube.com/watch?v=nYWTccEQz_M

Or, at least, are familiar with the contents of both short videotutorials and their associated documentation. If you have/are, you may find that using the PACS Pointing Off-set Correction Script will improve the quality of you results. There is a Herschel Science Centre short videotutorial that will show you how to use it and teach you the background information that you need to make effective use of it. You can find the short videotutorial here:

https://www.youtube.com/watch?v=f861D8CoYqc

The Pointing Off-set Correction Script will improve the spectra of point sources that suffer from pointing off-sets, or pointing jitter, provided that the off-set is no greater than 10 arcseconds. The script measures the average pointing off-set and its variation with time (the jitter). The script works best for:

1. Sources with a flux of about 10Jy or more.

2. Sources that are off-set by no more than 4 arcseconds.

For these objects you will get a much improved continuum shape and will be able to detect broad features much more reliably.

In contrast, the script will not work for:

• A source located at the edge of the central 3x3 spaxel box.
• Un-chopped spectroscopy.

And it will be unreliable for faint sources.

You can find the Pointing Off-set Correction Script in the HIPE Scripts menu and must be run from Level 0: i.e. with raw data. It is fully described in the PACS Data Reduction Guide. It will produce two spectra from the extractCentralSpectrum task - the so-called c9 and the c129 spectra - of which, the one with the higher flux is the one to use. You will see several examples of spectra of sources with off-sets from 2-6 arcseconds that have been processed with and without the Pointing Off-set Correction Script to illustrate the differences that can be found.

If you are an absolutely beginner with Herschel data and want to learn how to do photometry on PACS observations there are two places to start before working with data.

First, you should look at the Quick Start Guide for Photometry (CSG), otherwise known as the PACS Data Reduction Launchpad: Photometry. This will teach you some of the basics of PACS data analysis. It will also guide you towards more detailed documentation that will explore photometry in more depth.

Second, you should consult the Herschel Science Centre short videotutorial on Starting with PACS Photometry. You can find it here:

https://www.youtube.com/watch?v=yLHLA5Jjtiw

The short videotutorial will talk you through the PACS photometry data products that are available in the Herschel Science Archive (HSA) and which products are best for the analysis of what type of object. You will be shown the structure of a PACS photometry observation when downloaded from the HSA and how the filename structure of a product tells you what type of product it is. You will be shown also what Highly Processed Data Products (HPDPs) - also known as "Expert Reduced Data Products" - are available and how they may be used.

Answer provided by Katrina Exter:

For chop-nod observations, a “Split On-Off” pipeline script in HIPE allows you to create separate off-source and on-source cubes, which you can check for contamination. For un-chopped range scan observations, the Level 2 of the on-source observation contains the non-background subtracted products, which can be compared to the Level 2 products of the off-source observation to look for contamination. For un-chopped line scans, on-source and off-source cubes are created at the end of the pipeline, however only the subtraction of the two is saved to Level 2 of the observation stored in the HSA, hence it is necessary to re-run the pipeline in HIPE to retrieve these cubes.

However, an Highly Processed Data Product called “On-source/Off-source cubes” has been created and the products are available through the HSA. These HPDPs contain separate on-source and off-source cubes for each observation, which can be opened in any cube viewer and inspected for contamination. The comprehensive Release Note accompanying these HPDPs includes a discussion of what to do if your off-source position was “contaminated”.

You can find the Release Note for the On-source/Off-source cubes, here:

http://www.cosmos.esa.int/documents/12133/996891/PACS+Spectrometer+HPDP+-+The+separated+On-source+and+Off-source+cubes

Assuming that you have watched the Herschel Science Centre short videotutorial called Starting with PACS Spectroscopy:

https://www.youtube.com/watch?v=rcY487Z9Kyg 

And the Herschel Science Centre short videotutorial Point Source Spectroscopy with PACS:

https://www.youtube.com/watch?v=nYWTccEQz_M

Or, at least, are familiar with the contents of both short videotutorials and their associated documentation, you will find that the Herschel Science Centre short videotutorial on Point source spectroscopy with PACS: point sources in the central 3x3 spaxels, which you can find here:

https://www.youtube.com/watch?v=v1W5pT9DYUk

will show you how to proceed if your point source is in the central 3x3 spaxels, but not in the central spaxel itself. This case is valid if you have a point source, with a pointed observation, in which the target is centred within one of the eight spaxels surrounding the central spaxel, or for a mapping observation, in which, for one of the raster positions, the point source is centred within one of the eight spaxels surrounding the central spaxel. You will learn to identify cases for which the process may not work well (contamination, poorly centred point sources, ...) You will learn how to identify the spaxel coordinates of a source and which HIPE scripts and tasks to apply in the different possible cases. It will also show you a "last resort" case that you can use if your source is not even centred in the central 3x3 spaxels. You will also be guided towards the other processing and post-processing that may be helpful, such as the Pointing Offset Correction pipeline, or the Extended-to-point Correction.

Before going further, there are two excellent starting points for learning how to use PACS spectroscopy data. We recommend strongly that, if you are unfamiliar with PACS spectroscopy, you start by reading the Quick Start Guide to Spectroscopy (also known as the PACS Data Reduction Launchpad: Spectroscopy), which summarises the PACS spectroscopy observing modes, data products, calibration uncertainties and science-readiness of the different PACS spectroscopy products.

There is also a Herschel Science Centre short videotutorial called Starting with PACS Spectroscopy, which will walk you through the basics of PACS Spectroscopy. You can find the short videotutorial here:

https://www.youtube.com/watch?v=rcY487Z9Kyg

If you are already familiar with these items and are ready to advance to the next stage, there are two further documents that you should read (or, at least, have to hand) that give essential background: The PACS Products Explained and the Product Decision Tree, knowledge of both is implicit in other documents and training materials. These and other interesting documents are in the PACS section of the Herschel Explanatory Legacy Library (HELL).

There is a Herschel Science Centre short videotutorial that will guide you through the basics of the process of working with PACS spectra, giving you the knowledge essential to work with them. You can find it here:

https://www.youtube.com/watch?v=nYWTccEQz_M

The short videotutorial will explain what is meant by point source spectroscopy and the caveats and corrections that need to be applied, showing the footprint of the PACS Integral Field Unit on a typical point source, showing the re-binned and interpolated cubes that are an essential intermediate step in PACS spectroscopy reduction. It will show you the main keywords to look for to know the observing mode and how to determine where the point source is in the field of view for different observing modes, which is essential information for knowing which case to apply in data reduction and which product you need to use. It will then show you how to decide which HIPE task or script to use for different cases, depending on where the target is located in the field of view.

According to the source centering case that you find, you should then continue with one of the two specialist short videotutorials that deal with the different special cases:

Point sources in the central 3x3 spaxels.

Point sources in the central spaxel.

Assuming that you have watched the Herschel Science Centre short videotutorial called Starting with PACS Spectroscopy:

https://www.youtube.com/watch?v=rcY487Z9Kyg 

And the Herschel Science Centre short videotutorial Point Source Spectroscopy with PACS:

https://www.youtube.com/watch?v=nYWTccEQz_M

Or, at least, are familiar with the contents of both short videotutorials and their associated documentation, you will find that the Herschel Science Centre short videotutorial on PACS Cubes in Detail here:

https://www.youtube.com/watch?v=CxZF9-9D8UM

The PACS spectrometer produces five types of data cube and one table as products, although not all types of data have all types of cube. You will learn about each type of cube (re-binned cubes, mosaic cubes - including interpolated, projected, drizzled equidistant mosaic cubes), how and why it is produced and what data it contains, as well as the re-binned cube tables. You will learn also what useful scripts are available to transform cubes to a product of your own personal specifications (e.g. one that has spaxels of a different size).

Answer supplied by Katrina Exter:

All PACS maps are differential maps. In other words, the absolute level is arbitrary as the dominating source in the background is thermal emission from the telescope mirror. The map-making algorithm simply subtracts the background when making the map. This means that negative values are just as valid as positive ones for the background. Hence, negative background values are to be expected and are no issue when calculating photometry and should be used in the same way that the positive values are.

This is addressed in more detail in the PACS Photometer Quick Start Guide (section, “Science readiness of the photometry products”).

You can find more about the background and its effect on PACS photometry in the Herschel Science Centre short videotutorials on:

Starting with PACS photometry - https://www.youtube.com/watch?v=yLHLA5Jjtiw

And

DealingWithPointSources_phot - https://www.youtube.com/watch?v=R5S8VnfbNEI

 

Answer supplied by Katrina Exter:

The size of the spaxels of the so-called “re-binned cubes” are the 9.4" size of the native spaxel of the PACS integral field unit. The size of the spatial pixels of the so-called mosaic cubes (drizzled, interpolated, or projected cubes) depend on the pointing pattern adopted by the observation: the values range from 0.5” to 3”. 

Definitions of the cubes mentioned here, and the decision tree used when the mosaic cubes spatial pixel sizes were set by the SPG pipeline, can be found in the PACS Spectrometer Quick Start Guide (“Data structure for PACS spectrometer”) and the PACS Products Explained document (Sec 3.2 and 3.5). 

The WCS of the mosaic cubes includes the size of the spatial pixel in the WCS (in HIPE this would be print cube.getWcs().getCdelt1()*3600.0 to get the size in arcsecs). Be aware that the re-binned cubes do not have a correct WCS array.

You can find more information on this topic in the useful Herschel Science Centre short videotutorial on PACS Cubes in Detail. You can find this videotutorial, here:

https://www.youtube.com/watch?v=CxZF9-9D8UM

There are two, well-known sources of potential problems:

First, check that you are using the secure "https" protocol and not "http". If you have the latter, the link will fail.

Second, it is possible that the script is searching to the wrong directory because, unfortunately there were some changes to the URL where the on-line kernels were kept that were not within the control of the Herschel Science Centre. In order to fix the directory error, you have to edit the PhotometryConvoloveResolutionKernel.py script and change this line (line #424):

kernelRoot = 'http://www.astro.princeton.edu/~ganiano/Kernels/Ker_2012_May/Kernels_fits_Files/Hi_Resolution/'

With this line:

kernelRoot = 'https://www.astro.princeton.edu/~ganiano/Kernels/Ker_2012/Kernels_fits_Files/Hi_Resolution/'

This should resolve both issues.

There are two, well-known sources of potential problems:

First, check that you are using the secure "https" protocol and not "http". If you have the latter, the link will fail.

Second, it is possible that the script is searching to the wrong directory because, unfortunately there were some changes to the URL where the on-line kernels were kept that were not within the control of the Herschel Science Centre. In order to fix the directory error, you have to edit the SpectroscopyConvolveResolutionKernel.py script and change this line:

kernelRoot = 'http://www.astro.princeton.edu/~ganiano/Kernels/Ker_2012_May/Kernels_fits_Files/Hi_Resolution/'

With this line:

kernelRoot = 'https://www.astro.princeton.edu/~ganiano/Kernels/Ker_2012/Kernels_fits_Files/Hi_Resolution/'

This should resolve both issues.