TWiki> Public Web>SpireCalibrationWeb (revision 89)EditAttach

SPIRE instrument and calibration web pages

Back to main Herschel Public TWiki page

Introduction

This page provides up-to-date information about using the SPIRE instrument: from preparing observations to reducing your data. This page also provides you with the latest calibration accuracies and known SPIRE calibration issues.

Observing with SPIRE

The most up to date information on instrument calibration and performance is given in the SPIRE Observers' Manual. This is the reference document used by all the rest of the SPIRE user guides (eg data reduction guide, cookbooks etc). Sometimes it may happen that outdated values are quoted in some of the documents. In such a case use the values given in the SPIRE Observers' Manual.

AOT release notes

Photometer  
Photometer point source mode SPIRE photometer point source release note (30 April 2010)
Photometer scan map mode SPIRE scan map release note (20 October 2009), ADDENDUM to scan map mode (2 June 2010)
Photometer small scan map mode SPIRE small scan map mode (17 March 2010)

Spectrometer  
FTS point source mode (sparse) Spectrometer point source mode release note (21 May 2010)
FTS mapping mode (intermediate, full) Spectrometer mapping mode release note (30 April 2010))
FTS bright source modes Spectrometer bright source release note (7 September 2010)

Reducing SPIRE data

Software and documentation

  • HIPE (Herschel Interactive Processing Environment): The latest User Release HCSS version that you should use for reducing SPIRE data is HIPE v10.2. It can be downloaded from: http://herschel.esac.esa.int/HIPE_download.shtml.
    • Warning, important Please note that there was a bug in the destriper task included in HIPE 9.0 that may affect your final map, especially if there are bright objects in the observed field. This has been corrected since HIPE 9.1. If your observation falls in the mentioned category, you are strongly advised to update your HIPE installation.

  • We also provide access to the latest stable developer build (latest stable CIB).
    • Beware These developer builds do not undergo the same in-depth testing as the user releases do. The latest developer build can be found here.

  • SPIA: The SPIRE Photometer Interactive Analysis (SPIA) package is available as a plug-in for HIPE. SPIA provides a structured GUI based access to the more intricate parts of the scan map photometer pipeline for SPIRE without the immediate need to resort to scripts. More information can be found in the SDRG or on the SPIA web page

The SPIRE Launch Pads

  • The SPIRE Launch Pads are single sheet quick entries (like a cheat sheet) into SPIRE data reduction and providing quick references to the relevant sections in the SPIRE Data Reduction Guide. There are launch pads for Data Access, SPIRE Photometer and Spectrometer data reduction.

Document Version
SPIRE Data Launch Pad version 1.6
SPIRE Photometer Launch Pad version 1.7
SPIRE Spectrometer Launch Pad version 1.7

Photometer data reduction

Overview
The best source of information for reducing SPIRE Photometer data is the SPIRE Data Reduction Guide available through the HIPE help. This runs through the User Pipeline scripts step by step, describes several other Useful Scripts, and offers advice for specific issues that might be encountered.

New definition of Leve2 products
  • For versions of the HCSS prior to HIPE 10.0, a single point source calibrated (Jy/beam) map was provided in the Level 2 product for each of the PSW, PMW, PLW bands. However, for observations processed with HIPE 10.0 or later, more than one map calibration is made available within the Level 2 product. Maps are provided for the following scenarios for post HIPE 10.0 processing:

Description New Name (HIPE10+) Original (pre-HIPE10) Name
Point Source (standard) Maps psrcPSW PSW
Extended Emission Maps extdPSW -
Solar System Object Maps ssoPSW -
Point Source Destriper Diagnostic psrcPSWdiag pddPSW
Extended Emission Destriper Diagnostic extdPSWdiag -
     

  • psrcPxW are the previous PxW maps, calibrated for point source and in units of Jy/beam. Note that to do aperture photometry on such maps you'll first need to convert them to surface brightness (Jy/pixel, MJy/sr, etc.), although it is suggested to directly use the already extended emission calibrated extdPxW maps. Finally, bear in mind that SPIRE itself cannot measure the absolute sky flux, hence psrcPxW maps have an arbitrary offset having zero median.

  • ssoPxW maps are corrected for SSO proper motion: maps are in Jy/beam and they are subject to the same photometry rules of the psrcPxW maps.

  • extdPxW maps are calibrated for extended emission and provided in units of MJy/sr. These maps are provided with an estimation of the absolute offset via cross-calibration with Planck data.

  • In all cases, SPIRE data is calibrated in the assumption of source having a spectral index equal to -1, i.e. νSν = const. To calibrate your data for other cases or convert to e.g. Jy/sr, please refer to section 5.7 of the SPIRE Data Reduction Guide.

  • The SPIRE Photometer filter transmission curves, also known as Relative Spectral Response Functions (RSRF) are available here. For more details, please read the .readme file in this ftp folder.

Data Processing Issues

The main issues that you might find in your data are: undetected glitches, thermistor or detector jumps, and bad baseline removal.

  • Stripes in PSW, PMW and/or PLW (Level 2) maps
    • All SPIRE photometry pipelines now use the destriper by default, which improves the issue of stripes in Level 2 maps. There should be noticeable improvements in that respect with HIPE version 9. The destriper documentation can be found on the NHSC website

  • De-glitcher masks faint sources
    • For data taken in Parallel Mode in particular (sampling at 10Hz, at high speed 60"/s), the de-glitcher may flag very faint sources as glitches when it is run with standard parameters. Faint sources may have a "delta function" shape due to the low sampling rate, which looks similar to a small glitch. Try modifying the "correlation parameter" to 0.95: this will decrease the number of detected glitches - it may be better to have a limited detection rate in first level deglitching and defer to Level 2 deglitching.

  • Cooler temperature variations (Cooler Burps)
    • The SPIRE cooler is recycled after 48 hours. Between 6 to 7h after the cooler recycle ends, its temperature rises steeply and reaches the stable plateau. Observations taken during such times may exhibit stripes in the final maps. An option to correct for this effect is now available in the User Pipelines (See the SPIRE DRG for details).

  • NaN pixels present in the PSW, PMW and/or PLW (Level 2) maps
    • This effect, related to data masking or poor coverage, is more evident in single fast-scan Parallel Mode maps. To avoid NaNs, increase the pixel size (i.e., decrease the map's resolution).
    • This effect can also occur with destriped maps. In this case check if increasing the sigma parameter or switching off the Level 2 deglitcher helps.

  • WCS in 3-colour images
    • Problems with the wrong WCS in the output RGB images in all observations reduced with HIPE 8 have been fixed in HIPE 9

  • Quality flags in the quality context
    • Currently, the quality flags at the quality context inside the observation context are just meant for HSC/ICC internal evaluation of the quality of the products and not for the users. In case the data had some serious quality problem, the PI of the program has been contacted about it. Otherwise, only information in the quality summary, when available, should concern the observers.

Known Issues in ODs 1304 & 1305
For (yet) unknown reasons, the three detectors PSW-B5, PSW-E9 and PSW-F8 - that use to behave well during the entire mission - were noisy during the two operational days 1304 and 1305. The result are stripes visible in the final PSW map which the current (HIPE 10) pipeline is not able to correct. The solution is to mask and exclude these detectors from the analysis. This could be done in 2 ways:
  1. You can use the SpireMaskEditor GUI as described in sec. 7.4.2 of the SPIRE Data Reduction Guide: write-click on your observation context variable and then select Level1_SpireMaskEditor and set to Master all samples in all scans (listed as BBID) for the detectors mentioned above.
  2. Alternatively, you can use the following line of codes:

##### EDIT MASK SCRIPT BEGINS #####

# List of detectors to be masked
bolos = ['PSWB5', 'PSWE9', 'PSWF8']

# Level1 of your observation, assuming the observation context varible is named 'obs'
level1 = obs.level1

# Create new level 1
new_l1 = Level1Context()

for scan in range(0, level1.getCount()):
   #
   # Load level 1 product, scan by scan
   data = level1.refs[scan].product
   #
   # Change mask for selected detectors in all scans, setting it to MASTER
   for bolo in bolos:
      data['mask'][bolo].data[:] = 1
   #
   new_l1.addProduct(data)

##### EDIT MASK SCRIPT ENDS #####

  • After either of those cases, you must then re-run level 1 to 2 steps on the newly modified level1 product. If your observation has been already re-reduced with HIPE 10, original and new level1s are already destriped, so you can directly run the naive map-maker on the new level1. Otherwise, you must run the destriper step: check the pipeline script for details.

Planck-HFI & Herschel-SPIRE cross calibration: absolute offset re-processing

Herschel-SPIRE detectors are only sensitive to relative variations, as a consequence the absolute brightness of the observed region is unknown and maps are constructed such that they have zero median. Planck-HFI detectors are similar to the SPIRE ones, however its observing strategy allows it to (almost) observe a sky's great circle every minute (having a 1 rpm spinning rate). By comparing the sky brightness as measured by COBE-FIRAS at the galactic poles (where the dust emission is lower), HFI is capable of setting an absolute offset to its maps. SPIRE and HFI share two channels with overlapping wavebands: SPIRE-PMW and HFI-857 have a similar filter profile, while SPIRE-PLW and HFI-545 are shifted by $\sim 10$\%.

As of HCSS 10, a new task named zeroPointCorrection is available: this task calculates the absolute offset for a SPIRE map based on cross-calibration with HFI-545 and HFI-857 maps, colour-correcting HFI to SPIRE wavebands assuming a grey body function with fixed beta. At first, Planck data needed by the task were delivered to HSC under special agreement: as a consequence, Herschel users were not able to re-process the absolute offset calculation. However, Planck data became public in April 2013 and it is now possible to exectue the zeroPointCorrection.

Files needed:

  • Download the HFI-545 and HFI-857 maps from the HSC/SPIRE FTP area. These maps are derived from the ones available in the Planck Legacy Archive, but convolved with an 8 arcmin Gaussian beam in order to circularize the effective maps' beams, plus the maps absolute offset as estimated by the Planck-HFI team via cross-calibration with FIRAS (see Planck Collaboration VIII. 2013, In preparation)
  • Download the colour correction table file SpireHfiColourCorrTab_v1.1

The offsets are computed on extdPxW maps, calibrated for extended emission, with extended gain correction applied and in units of MJy/sr (as explained in the section 5.7 of the SPIRE Data Reduction Guide). Hence, the re-processing will start from a level-1 context (which may be the result of merging multiple observations, see e.g. the Photometry Map Merging scirpt available in HIPE under the menu ScriptsSPIRE Useful script) and then executing the zeroPointCorrection task with one of the following methods:

  1. Run the zeroPointCorr.py script. It assumes that a Level1Context and Level2Context are already defined and named level1 and level2, respectively. It also sets three required properties needed by the zeroPointCorrection task, i.e. the location of two HFI maps and the colour correction table: please modify the PATH_TO_FILE accordingly to your set-up.
  2. Alternatively, run the correction using the SPIA interface (SPIRE Photometer Interactive Analysis). In order to be able to run the zeroPointCorrection task, the user.props file present (by default) in you $HOME/.hcss directory must be modified and the following lines added (please modify the PATH_TO_FILE accordingly to your set-up):
    • spire.spg.hfi.545map = PATH_TO_FILE/DX9_map_545_smooth_8arcmin.fits
    • spire.spg.hfi.857map = PATH_TO_FILE/DX9_map_857_smooth_8arcmin.fits
    • spire.spg.hfi.colorc = PATH_TO_FILE/SpireHfiColourCorrTab_v1.1.fits

A detailed descirption of the algorithm used for the cross-calibration with Planck and implemented in the zeroPointCorrection is described in the attached document and it will be soon in the official HCSS documentation.

Source Extraction and Photometry

  • The current recommended method for photometry sourceExtractorTimeline task (formerly known as the Timeline Fitter) which works on the detector timelines. The Map based algorithm sourceExtractorSussex (SUSSEXtractor) providers good results and is useful on larger maps where the sourceExtractorTimeline will be significantly slower. sourceExtractorDaophot (DAOphot) also provides a reasonable estimate of the source flux but may require an aperture correction.

Spectrometer data reduction

The best source of information for reducing SPIRE Spectrometer data is the SPIRE Data Reduction Guide available through the HIPE help. This runs through the User Pipeline scripts step by step, describes several other Useful Scripts, and offers advice for specific types of sources:

  • Faint (<10 Jy) and medium (<100 Jy) strength sources
  • Bright sources (>500 Jy)
  • Extended sources
  • Observations with few repetitions
  • H+L observations

For faint sources, the subtraction of instrument, telescope and background emission is particularly important. Optimum subtraction can be performed in several ways (read the SPIRE Data Reduction Guide for details):

  1. Subtract the Dark Sky spectrum closest to your observation (use the "Background Subtraction" script in HIPE)
  2. Subtract the spectrum of surrounding detectors (use the "Background Subtraction" script in HIPE)

Dark Sky observations are observed on every SPIRE Spectrometer OD, and are all public in the Archive.

A listing of the available Dark Sky observations can be found here.

Spectral Cube Analysis

Spectral cubes are produced by the Spectrometer pipeline for mapping observations. Some tips, suggestions and examples of spectral cube analysis for SPIRE data are provided here.

Cookbooks

Cookbooks are provided inside the SPIRE Data Reduction Guide (see above).

The standalone "Photometry Cookbook", is no longer maintained - it is being incorporated into the SPIRE DRG - please see the SDRG for photometry cookbook information, and raise a Helpdesk ticket if you find something missing.

SPIRE calibration file versions

The available calibration trees for SPIRE are listed below (with the current operational version at the top).

SPIRE Calibration Tree Applicable HIPE Version Comment
SPIRE_CAL_9_1 HIPE v9 Final v9 cal tree
SPIRE_CAL_8_1 HIPE v8 Final v8 cal tree
SPIRE_CAL_7_0 HIPE v7 Final v7 cal tree.
SPIRE_CAL_6_1 HIPE v6 Final v6 cal tree
(SPIRE_CAL_6_0) HIPE v6 Spec major update
SPIRE_CAL_5_2 HIPE v5 Final v5 cal tree
(SPIRE_CAL_5_1) HIPE v5  
(SPIRE_CAL_5_0) HIPE v5 Phot flux conv. based on Neptune. Spec major update
SPIRE_CAL_4_0 HIPE v4 Spec point source flux conv based on Uranus
SPIRE_CAL_3_2 HIPE v3  
(SPIRE_CAL_3_1) HIPE v3  
(SPIRE_CAL_3_0) HIPE v3  
SPIRE_CAL_2_1 HIPE v2 Spec point source flux conv based on Vesta
(SPIRE_CAL_2_0) HIPE v2  
SPIRE_CAL_10_1 HIPE v10 Calibration tree currently used in operations
SPIRE_CAL_1_2 HIPE v1 Phot flux conv based on Ceres
(SPIRE_CAL_1_1) HIPE v1 Pre-launch dummy values

More details of the changes in each version are given here.

  • Any of the calibration trees can be retrieved in HIPE from the HSA using (e.g.) cal = spireCal(calTree="spire_cal_10_1") etc. The default (applicable to the HIPE version in use) can be obtained with cal = spireCal(calTree="spire_cal"). It can then be saved to a local pool right-clicking on the cal variable and then selecting from the context menu Send To -> Local Pool.
  • Alternatively, the latest calibration tree for SPIRE can be obtained as a jar file from Latest calibration trees. Then, you have to possibilities to read and save:
    1. The jar file can be load directly into HIPE with the command: cal = spireCal(jarFile="PATH_TO_FILE/spire_cal_10_1.jar"). To save it to a local pool, proceed as described above, right-clicking on the cal variable and then selecting from the context menu Send To -> Local Pool.
    2. The jar file can also be saved directly to a local pool without opening HIPE, running the following command in the terminal command line: cal_import PATH_TO_FILE/spire_cal_10_1.jar. Then, to load the calibration tree in HIPE, simply type: cal = spireCal(pool="spire_cal_10_1")

See the SPIRE Data Reduction Guide for more details.

SPIRE calibration and performance

Photometer calibration

  • SPIRE Photometer Calibration:
    Full details of the SPIRE calibration can be found in the SPIRE Observers Manual and in dedicated publications: the calibration scheme is described in Griffin et al. (2013) and the implementation using Neptune as the primary calibration standard, is described in Bendo et al. (2013).
    • Calibration uncertainties, which should be included in addition to the statistical errors of any measurement, are as follows:
      • 4% absolute from Neptune model (this uncertainty is systematic and correlated across the three bands)
      • 1.5% (random) from Neptune photometry
    • Extended emission calibration
      • In addition to the above uncertainties, there is an additional 4% uncertainty due to the current uncertainty in the measured beam area

  • SPIRE Photometer Beams:
    • These are available in the SPIRE calibration context, at the standard map pixel size of (6,10,14) arcsec/pixel for (250,350,500) m bands, and can be accessed in HIPE after a calibration context has been loaded (see above).
    • Tip, idea The observed beams at much finer scale of 1 arcsec/pixel, as well as the theoretical ones, are available from here . Please read the release note for more details.
    • NEW A new more detailed analysis of the SPIRE beam profile data was undertaken in 2012, leading to revised values for beam profile solid angles and derivation of a semi empirical wavelength dependent beam profile model. The results at a scale of 1 arcsec/pixel as well as the data needed for the model are available for download. A detailed description of the analysis is given as well.

  • SPIRE Photometer filter transmission curves:
    • These are also available in the SPIRE calibration context (photRsrf) and can be accessed in HIPE after a calibration context has been loaded (See above).

  • Neptune and Uranus models used for the SPIRE photometer flux calibration:
    • The ESA2 models of the SPIRE calibration, used up to HIPE v10 and spire_cal_10_1, are available here.
    • NEW The ESA4 models of the SPIRE calibration, used from HIPE v11 and spire_cal_11_0, are available here.

Spectrometer calibration

Important FTS information, including details of the calibration, point source and extended source calibration etc, is available in the SPIRE Observers' Manual, Sections 4.2 and 5.3. These two sections are a must-read for anybody processing SPIRE FTS data.

Interest groups and scripts

  • The following interest groups relate to processing of observations taken with SPIRE. The links provided allow subscription to these interest groups.
    • subscribe to the SPIRE Photometer interest group
    • subscribe to the SPIRE and PACS parallel mode large map and point source extraction interest group
    • subscribe to the SPIRE Spectrometer interest group
    • subscribe to the PACS, SPIRE and HIFI spectral maps interest group
  • User contributed scripts: Users are welcome to submit scripts and software that they believe could be of general interest to the community to the Herschel http://herschel.esac.esa.int/esupport/Helpdesk.

Further information

Contact the Helpdesk

Topic attachments
I Attachment History Action Size Date Who Comment
PDFpdf Offset_Estimation_Description.pdf r1 manage 2352.7 K 2013-06-13 - 15:09 LucaConversi  
PDFpdf Phot_Pipeline_Issue7.pdf r1 manage 453.9 K 2011-05-06 - 11:07 LucaConversi  
PDFpdf Pipe_Description_2.1.pdf r1 manage 2078.9 K 2011-05-06 - 11:06 LucaConversi  
PDFpdf SPIRE-BSS-DOC-002966_SPIRE_Spectrometer_pipeline_description_Issue_4_0_1.pdf r1 manage 793.5 K 2012-02-28 - 09:49 EdwardPolehampton  
PDFpdf SPIRE_DataLaunchPad_v1.6.pdf r1 manage 200.4 K 2012-08-24 - 13:57 ChrisPearson SPIRE Data Launch Pad v1.6
PDFpdf SPIRE_Detector_Parameter_Sensitivity_Issue_1_Nov_14_2007.pdf r1 manage 185.0 K 2013-05-21 - 08:17 IvanV Sensitivity of the SPIRE Detectors to Operating Parameters
PDFpdf SPIRE_PhotometerLaunchPad_v1.7.pdf r1 manage 205.4 K 2012-08-24 - 13:58 ChrisPearson SPIRE Photometer Launch Pad v1.7
PDFpdf SPIRE_SpectrometerLaunchPad_v1.7.pdf r1 manage 190.6 K 2012-08-24 - 13:57 ChrisPearson SPIRE Spectrometer Launch Pad v1.7
Unknown file formatfits SpireHfiColourCorrTab_v1.1.fits r1 manage 19.7 K 2013-06-04 - 11:09 LucaConversi  
PDFpdf aa14519-10.pdf r1 manage 1321.5 K 2011-01-24 - 09:51 AnthonyMarston SPIRE A&A paper, Griifin et al 2010
PDFpdf aa14605-10.pdf r1 manage 264.1 K 2011-01-24 - 16:48 IvanV SPIRE in-flight calibration
PDFpdf beam_release_note_v1-1.pdf r1 manage 4044.5 K 2011-05-11 - 09:44 LucaConversi  
Texttxt zeroPointCorr.py.txt r1 manage 2.9 K 2013-06-10 - 08:53 LucaConversi  
Edit | Attach | Watch | Print version | History: r150 | r91 < r90 < r89 < r88 | Backlinks | Raw View | Raw edit | More topic actions...
Topic revision: r89 - 2013-06-13 - LucaConversi
 
This site is powered by the TWiki collaboration platform Powered by Perl