(r58) HifiCalibrationWeb < Public

Public Web>HifiCalibrationWeb (revision 58) (raw view)~~EditAttach~~
---+ HIFI instrument and calibration web pages

%TOC{depth="2"}%

%N% %N% %N% %RED% *Latest updates -- 18 September 2013* %ENDCOLOR% %N% %N% %N%
   * %BLUE%HIPE 11.0%ENDCOLOR% has been released ! 
   * %BLUE%HIPI 2.1%ENDCOLOR% (a library of Hifi Plug-In's) has been released - see Interest Groups and Scripts section
   * %BLUE%New matching technique script%ENDCOLOR% is available in the Expert Version of HIPE - see the "Outstanding calibration issues" section
   * %BLUE%A large amount of calibration data has been released ! %ENDCOLOR% - see the "Observing with HIFI" section
   

---++ Observing with HIFI
   * Useful Documentation
      * The HIFI observer's manual version 2.4 (version for OT-2) [[http://herschel.esac.esa.int/Docs/HIFI/html/hifi_om.html  (HTML)]] or [[http://herschel.esac.esa.int/Docs/HIFI/pdf/hifi_om.pdf PDF (5.7 Mb)]]
      * [[%ATTACHURL%/aa14698-10.pdf The Herschel-Heterodyne Instrument for the Far-Infrared (HIFI) -- PDF (0.8MB)]], de Graauw et al., 2010, A&A, 518, L6, in-flight scientific capabilities of the HIFI instrument.
      * [[http://herschel.esac.esa.int/Docs/Flyers/HIFI_flyer_20May2010.pdf HIFI fact sheet]] A 2-page guide to the HIFI instrument
      * [[%ATTACHURL%/HifiObservingModesPerformance_110926a.pdf    HIFI AOT Observing Mode Release and Performance Notes v3.0 (24 September 2011)]]
      * [[http://herschel.esac.esa.int/Docs/TechnicalNotes/HIFI_Mapping_Modes_note_30Jun2010.pdf Technical note on HIFI mapping modes (30 June 2010)]]
      * [[%ATTACHURL%/Ossenkopf_2008_AllanVariance.pdf A&A paper describing the method used to measure stability performance with HIFI (added 4 Oct 2011)]]

   * HIFI calibration data
      * A significant number of the data taken by HIFI in the framework of the Performance Validation (PV) and routine phase are now publicly available. There are particular caveats that apply to those data. They are described in this [[%ATTACHURL%/HIFI_Calibration_ReleaseNotes.pdf disclaimer]] note 
 
---++ Reducing HIFI data

---+++ Recommended User release
   * [[http://herschel.esac.esa.int/HIPE_download.shtml#HIPE_download HIPE 11.0]]

---+++ Which data would most benefit from being reprocessed in HIPE 11.0?

   * *DBS Observations*
      * A new pipeline step, mkDbsReference, calculates the  differences the chop positions in all DBS observations and after applying the band-pass correction stores them in a product in calibration->pipeline-out called _ReferenceSpectra._  This allows you to check for contamination in chop positions for all types of DBS observations.

   * *Rotated maps*
      * Rotated cubes are now produced in the Level 2.5 product by default for maps carried out with a non-zero position angle, a non-rotated cube is also produced.
 
   * *Improved pointing reconstruction for observations taken between OD 320 and 761*  %BLUE% If you have data processed with < HIPE 9 %ENDCOLOR%
      * The pointing information attached to the data for observations taken between OD 320 and OD761 did not use the most accurate representation of the star tracker focal length. This will be done for the bulk reprocessing with HIPE 9. As a consequence, some observations will experience a shift in astrometry, that can be as high as 8 arcsec. All the details about the consequences for a particular obsid, and recipes to reconstruct yourself the improved pointing can be found at [[http://herschel.esac.esa.int/twiki/bin/view/Public/HowToUseImprovedPointingProducts]] as well as in the [[http://herschel.esac.esa.int/hcss-doc-11.0/index.jsp#hifi_um:what_l0 level0 section]] of the Hifi Data Reduction Guide

   * *Backfilling of observational parameters* %BLUE% If you have data processed with < HIPE 9 %ENDCOLOR%
      * From 9.1 onwards, most of the observational parameters that got optimised in !HSpot will be propagated into the observation context, under a new product called !HifiUplinkProduct (in the auxiliary product branch). Some of these parameters will be used in the pipeline to e.g. estimate the dimension of the cubes in the mapping and have them more representative of how the map was really obtained.

   * *Solar System Object maps* %BLUE% If you have data processed with < HIPE 9 %ENDCOLOR%
      * Cubes for moving targets are now created in the comoving frames in HIPE 9. In order to benefit from that, you should re-pipeline from level 0 up to level 2.5. Note the hifiPipeline task should be called with the option "Aux=True". Please check the [[http://herschel.esac.esa.int/hcss-doc-11.0/index.jsp#hifi_um:runninghifipipeline Pipeline chapter]] of the HIFI Data Reduction Guide for more details about how to do that.

   * *Solar System Object ephemerides* %BLUE% If you have data processed with < HIPE 11 %ENDCOLOR%
      * A bug [[http://herschel.esac.esa.int/twiki/bin/view/Public/HipeKnownIssues#Known_issues_in_HIPE_10_1 (see here)]] was fixed in the calculation of SSO ephemeris positions (ra_centre/dec_centre) that led to offsets of up to ~10".  This bug affected users that use cubes in a co-moving frame (including the standard level 2.5 cubes), use the doOffset task, or make explicit use of ra_centre / dec_centre in their HIPE scripts. The offset is practically constant over a map and could, e.g., make the emission of a comet appear to be off-center when it really isn't.  The fixed bug is in the level 0 pipeline, which users cannot run easily. The issue will be fixed by the HIPE 11 bulk reprocessing.  In the meantime, you can use a HIPE snippet such as the one attached [[%ATTACHURL%/fixSSOephemeris.py.txt here]].

   * *Strong continuum sources* 
      *  An optional step in the pipeline can be used to remove standing waves arising in the loads, this is particularly effective for strong continuum sources.  A report describing the technique can be found [[%ATTACHURL%/calibration_hifi_stdw_2011_v0_1.PDF here]]. Instructions for using this modified passband technique are available in the Standing Wave Removal chapter of the HIFI Data Reduction Guide:
         * _[[http://herschel.esac.esa.int/hcss-doc-11.0/load/hifi_um/html/sw_removal_passb2.html  Modified Passband Technique]]_ 

   <!--* *Calibration of data in bands 2a, 5a and 5b*  %BLUE% If you have data processed with < HIPE 8 %ENDCOLOR%
      * Un-balanced side-band gains will apply for some ranges of these bands (see also the calibration section). Reprocessing data from band 2a is recommended if your data are still processed with HIPE 6. Reprocessing data from band 5a and 5b is recommended if your data are processed with HIPE 8.

   * *Spectral Scan Data in bands 6 and 7* %BLUE% If you have data processed with < HIPE 8 %ENDCOLOR%
      * It is recommended to reprocess spectral scan data taken in band 6 and 7 if they are still processed with HIPE <8. This is not needed in data processed with HIPE 8.
      * Reprocessing with HIPE 9 will create a new level 2.5 product containing a deconvolved single-side-band spectrum for each applicable spectrometer

   * *Maps* %BLUE% If you have data processed with < HIPE 8 %ENDCOLOR%
      *  Spectral cubes from mapping observations after OD 835 gridded using actual scan line and readout used in observation, earlier maps use a better approximation than in HIPE 7.  These improvements are a consequence of changes in the level 0 pipeline to read in information about how the observation was performed and require the pipeline to be re-run after running the _doUplink_ step:

<verbatim>
from herschel.hifi.pipeline.level0 import DoUplink
doUplink=DoUplink()
backend = "WBS-V"
htp=obs.refs["level1"].product.refs[backend].product
htp1=doUplink(htp=htp.copy(), auxiliary=obs.getAuxiliary())
l1=obs.refs["level1"].product
l1.setProduct(backend,htp1)
obs.setProduct("level1",l1)
obs = hifiPipeline( obs=obs, fromLevel=1, upToLevel=2.5,save=0,apids=[backend])
#
# Now repeat replacing backend with "WBS-H", "HRS-H", "HRS-V"
</verbatim> -->


   * See the What's New page for more details of improvements in HIPE 11.0
      * [[http://herschel.esac.esa.int/twiki/bin/view/Public/HipeWhatsNew11x What's New in HIPE 11]]
      
   * Other details about the benefits of reprocessing with HIPE 11.0 are also compiled in the [[http://herschel.esac.esa.int/hcss-doc-11.0/load/hifi_um/html/hum_when_reprocess.html HIFI Data Reduction Guide]] .

---+++ Documentation and Cookbooks
   * The HIFI Launch Pad is intended to help you quickly off the ground with HIFI data reduction
      * [[http://herschel.esac.esa.int/hcss-doc-11.0/load/hifi_um/html/hificookbook.html HIFI Launch Pad]]
 
   * There is a cookbook for point mode DBS observations, other observing mode cookbooks are in progress
      * [[http://herschel.esac.esa.int/hcss-doc-11.0/load/hifi_um/html/hdrg_cookbooks.html#pdbscook HIFI Point Mode DBS Cookbook]]

   * The _HIFI Data Reduction Guide_ and the _HIFI AOT Observing Mode Release and Performance Notes_ contain information you need to know about HIFI data, regardless of the software you use for data reduction
      * [[http://herschel.esac.esa.int/hcss-doc-11.0/index.jsp#hifi_um:hifi-um HIFI Data Reduction Guide]] 
      * [[%ATTACHURL%/HifiObservingModesPerformance_110926a.pdf    HIFI AOT Observing Mode Release and Performance Notes v3.0 (24 September 2011)]]

   *  If you want to know more about the details of the HIFI pipeline, you should look at the _HIFI Pipeline Specification Document_ 
      * [[http://herschel.esac.esa.int/hcss-doc-11.0/load/hifi_pipeline/html/hifi_pipeline.html HIFI Pipeline Specification Document]]

   * If you are working in HIPE, the [[http://herschel.esac.esa.int/hcss-doc-11.0/index.jsp#hifi_um:hifi-um HIFI Data Reduction Guide]] will be your prime resource for all things HIFI but you should also look at the _Herschel Data Analysis Guide_ for information about general tools, such as those for viewing and manipulating spectra and spectral cubes, and for obtaining data from the archive.
      * [[http://herschel.esac.esa.int/hcss-doc-11.0/index.jsp#howtos:dag Herschel Data Analysis Guide]]

   * The full set of online documentation for the current user release also contains detailed information about the HIFI pipeline, information about scripting in HIPE, and reference manuals for command listings. New users of HIPE are recommended to read through the Quick Start Guide and the HIPE Owner's Guide
      * You can create pdfs of each document by clicking on the pdf symbol at the top of the main page. 
      * [[http://herschel.esac.esa.int/hcss-doc-11.0/ online documentation for the current User Release]]

   * The full set of Herschel documentation for the developer track is also available.  This documentation contains revisions and updates to the documentation associated with the current User Release but you should also be aware that it may describe functionality not available in the current User Release
      * [[http://herschel.esac.esa.int/hcss-doc-12.0/  full set of Herschel documentation for the developer track]]  

   * The General HCSS Public Twiki page provides general framework information and updates: 
      * http://herschel.esac.esa.int/twiki/bin/view/Public/WebHome
 


---+++ Typical Data Reduction Workflow
   * _Download data from the HSA_.  If you are downloading several observations it is better to use the tar ball.
      * [[http://herschel.esac.esa.int/hcss-doc-11.0/load/howtos/html/Dag.DataIO.Hsa.html Documentation about downloading data]]

   * _Inspect data quality_. Both point spectra and spectral cubes can be viewed in the !SpectrumExplorer.  In addition to inspecting the quality of your level 2 data,  you should always check the level 1 data for any bad scans.  If data at level 2 appears strange then looking at level 1 data may provide insight to the problem, see the Data Primer chapter of the HIFI Data Reduction Guide for more information about levels of data
      * [[http://herschel.esac.esa.int/hcss-doc-11.0/load/howtos/html/Dag.Sec.SpectrumViewing.html Viewing spectra in Spectrum Explorer]]
      * [[http://herschel.esac.esa.int/hcss-doc-11.0/load/howtos/html/Dag.Sec.CubeSpectrumViewing.html Viewing cubes in Spectrum Explorer]]
      * [[http://herschel.esac.esa.int/hcss-doc-11.0/index.jsp#hifi_um:dataprimer Data Primer]]

   * _Assess whether data should be re-pipelined_. 
      * Look at the section above and also at the  [[http://herschel.esac.esa.int/twiki/bin/view/Public/HipeWhatsNew What's New]] in the latest User Release to decide if you should re-pipeline.  
      * Note that  the ICC recommends that data processing should not be allowed to fall more than one version behind the HIPE version being used.  
      * Everything you need to re-pipeline data is available in the !ObservationContext, and the instructions for using the pipeline, including tips on *re-pipelining using new calibration data* and *customising the pipeline*, can be found in the Pipeline chapter of the Hifi Data Reduction Guide
         * [[http://herschel.esac.esa.int/hcss-doc-11.0/index.jsp#hifi_um:runninghifipipeline Pipeline chapter]]

   * _Flag data_. A new user-friendly task has been developed in order to easily flag your data: !FlagTool. It can be used both as a GUI (similar concept as for the !FitBaseline task) or in command line
      * [[http://herschel.esac.esa.int/hcss-doc-11.0/load/hifi_um/html/hdrg_flags_flagtool.html Flagging data interactively]]

   * _Remove standing waves_. Standing waves are a common problem in HIFI data, particularly in bands 3, 4, 6, and 7.  The HIFI Data Reduction Guide provides some information about typical standing waves in HIFI data and describes how to remove them in HIPE using *fitHifiFringe* and the modified band pass technique
      * [[http://herschel.esac.esa.int/hcss-doc-11.0/index.jsp#hifi_um:sw_removal_hifi2 Standing Wave Removal]] 

   * _Correct baseline drift_. Baselines can be flattened by subtracted, or division in the case of real continuum.  This can be done in HIPE with the *fitBaseline* task
      * [[http://herschel.esac.esa.int/hcss-doc-11.0/index.jsp#hifi_um:hifium_bl1 Baseline Removal]]

   * _Fold frequency switch data_.  Frequency switch data is not folded in the pipeline and can be done with the *doFold* task.
      * [[http://herschel.esac.esa.int/hcss-doc-11.0/index.jsp#hifi_pipeline:dofold doFold documentation]].

   * _Average together H and V polarisation_.  
      * The noise estimates given by HSpot assume that the H and V polarisations are averaged together.   This can be done in HIPE with the *PolarPair* task, which resamples the spectra to the same frequency scale (they are frequency calibrated with different comb measurements) and then averages them.  Alternatively, you can use the *Accumulate* task, which allows you to specify the resampling width if you desire.
         * [[http://herschel.esac.esa.int/hcss-doc-11.0/index.jsp#hifi_um:avhv PolarPair]] 
         * [[http://herschel.esac.esa.int/hcss-doc-11.0/load/howtos/html/Dag.Sec.SpectrumWorking.html#Dag.Sec.SpectrumStats.SEII Accumulate]]
      * Note that differences may be seen in H and V profiles, see the _note on H and V positions_.  If you are particularly interested in the spatial structure of your source you may prefer not to average the H and V polarisations together.
         * [[http://herschel.esac.esa.int/Docs/TechnicalNotes/HIFI_HandVPositions_03Dec2010.zip note on H and V positions]]

   * _Spectral manipulation_. The *Spectral Toolbox* in HIPE allows you to perform typical spectral arithmetic tasks on spectra and spectral cubes  
      * [[http://herschel.esac.esa.int/hcss-doc-11.0/load/howtos/html/Dag.Sec.SpectrumWorking.html Spectral Toolbox documentation for spectra]]
      * [[http://herschel.esac.esa.int/hcss-doc-11.0/load/howtos/html/Dag.Sec.SpectrumWorking.html Spectral Toolbox documentation for spectral cubes]]

   * _Fit lines_. The *SpectrumFitterGUI*, which is also a part of the Spectral Toolbox, can be used to fit line profiles.
      *  [[http://herschel.esac.esa.int/hcss-doc-11.0/load/howtos/html/Dag.Ch.SpectralFitting.SEII.html Spectral Fitting]]

   * _Save modified data_ You can save data to a pool, or  store your session in order to continue working in HIPE.
      * [[http://herschel.esac.esa.int/hcss-doc-11.0/load/howtos/html/Dag.DataIO.SaveEntireObservation.html Saving data to a pool]]
      * [[http://herschel.esac.esa.int/hcss-doc-11.0/load/hipeowner/html/Hipeowner.Sec.SavingRestoring.html Storing your HIPE session]]

   * You may wish to _export data_ as FITS, ASCII or use the *HiClass* task to export data as CLASS readable FITs files.
      * [[http://herschel.esac.esa.int/hcss-doc-11.0/index.jsp#howtos:howto.save.image Saving as FITS]]
      * [[http://herschel.esac.esa.int/hcss-doc-11.0/index.jsp#howtos:Dag.DataIO.Ascii Saving as ASCII]]
      * [[http://herschel.esac.esa.int/hcss-doc-11.0/index.jsp#hifi_um:hiclass HiClass task]].
         * %ICON{"warning"}% %RED% *WARNING!* %ENDCOLOR%  When converting to velocity, CLASS corrects the reference frequency (the frequency at the reference channel) for the Doppler shift, but not the channel width so there is a very small mismatch between the channel width before and after Doppler correction. Lines are shifted from the correct velocity as a consequence, with an increasing shift away from the reference channel..  The ICC recommends that line frequencies are checked in HIPE before exporting to CLASS.


---+++Dedicated data reduction tips for *Spectral Scan* data
   * The data needs to be deconvolved to a single sideband solution.  This can be done with the *doDeconvolution* task, which works with an !ObservationContext. 
      *  [[http://herschel.esac.esa.int/hcss-doc-11.0/index.jsp#hifi_um:decon Deconvolving HIFI data]]

   * It is important to clean the data before deconvolving it, this means removing standing waves, correcting baselines and flagging out any spurs or bad data that the pipeline missed.

   * If you are planning to deconvolve your data with CLASS, please contact the Helpdesk, or Claudia Comito (email:ccomito@mpifr-bonn.mpg.de) if you need further details.

   * Note that deconvolution does not work properly on data take in the Frequency Switching mode (see also the [[http://herschel.esac.esa.int/twiki/bin/view/Public/DpKnownIssues Data Known Issues Page]])

---+++Dedicated data reduction tips for *Mapping* observations
   *  Spectral cubes from all HIFI mapping observations are produced as part of the SPG pipeline (that is, the pipeline run for the HSA) and are now found in the level 2.5 product. However, baseline and standing wave corrections are not done automatically in the pipeline because of the risk of harming the scientific content of the data. This can now be customised in the level 2.5 step and be done prior to the cube creation.

   * *It is strongly recommended that you inspect your level 2 HTPs for baseline drift  and residual standing waves and decide if some, or all, datasets need to be cleaned up before re-running the gridding task.*     

   * Regridding in HIPE > 9 will automatically use the comoving frame for SSOs. See the section above about the benefits from reprocessing with HIPE 11 for more details on how to do that

   *  You can then grid your cleaned data into a spectral cube using the *doGridding* task, you can also use this task to customise the cube creation to best suit your science goals.
      *  [[http://herschel.esac.esa.int/hcss-doc-11.0/index.jsp#hifi_um:otfmapping Creating Spectral Cubes]] 


---++ HIFI performance and calibration

---+++Documentation
   * General: [[%ATTACHURL%/aa15120-10.pdf In-orbit performance of Herschel-HIFI, Roelfsema et al.]]
   * This  [[ftp://ftp.sciops.esa.int/pub/hsc-calibration/HIFI/TSYS_PLOTS/ FTP repository]] of system temperature plots across the IF for each HIFI subband (updated 24 Jan 2011) inform about the variation in system temperature (sensitivity) across the HIFI intermediate frequency band at various frequencies
   * Intensity calibration: [[%ATTACHURL%/calibframework.pdf Intensity Calibration Framework document]] 
   * Beam calibration
      *  [[%ATTACHURL%/spatial_response_framework.pdf Spatial Calibration Framework document]]
      * [[http://herschel.esac.esa.int/Docs/TechnicalNotes/HIFI_Beam_Efficiencies_17Nov2010.pdf Measured beam efficiencies on Mars (17 Nov 2010)]]
      * [[http://herschel.esac.esa.int/Docs/TechnicalNotes/HIFI_HandVPositions_03Dec2010.zip ZIP file containing information and data needed for accessing HIFI H and V beam positions from within an observation context in HIPE (3 Dec 2010)]]
      * [[http://herschel.esac.esa.int/Docs/TechnicalNotes/HIFI_HSpot_BeamEfficiency_15Dec2010.pdf][Effect of beam efficiencies on HSpot time estimates  (15 Dec 2010)]]
   *  Spectral calibration
      *  [[%ATTACHURL%/freq_framework.pdf Spectral Calibration Framework document]]
      *  [[%ATTACHURL%/freq_vel_1.1.pdf HIFI frequency/velocity transform document]]: a document describing the frequency & velocity handling algorithms adopted in the HIFI pipeline
   * Side band ratio
      * [[%ATTACHURL%/HIFI_SBR_Cookbook_V1.0.pdf Side band ratio technical note]]: This note describes the general calibration problem associated with the side-band gain imbalance existing in double-side-band heterodyne systems such as HIFI, and provides some recipes and calibration tables applicable to the particular case of the HIFI mixers.
   
---+++Calibration error budget

*<u>Line Intensity Calibration Accuracy</u>*

The following table provides the percentage flux error associated with each component of the error budget (from Roelfsema et al. 2011).

| *Error source*               | *Bands 1/2*  | *Bands 3/4*  | *Band 5* | *Bands 6/7* |
| Side-band ratio*            | 3-4               |    4-6            |      4-6    |     5-8          |
| Hot load coupling          | < 1               |    < 1        |      < 1   |     < 1       |
| Cold load coupling       | < 1               |    < 1        |      < 1   |     < 1       |
| Hot load temperature    | < 1               |    < 1        |      < 1   |     < 1       |
| Cold load temperature   | < 1               |    < 1        |      < 1   |     < 1       |
| Planetary model error | < 3               |    < 3        |      < 3   |     < 3       |
| Beam efficiency              | < 5               |    < 5        |      < 10   |     < 5       |
| Pointing                         | < 1               |    < 2        |      < 2   |     < 4       |
| Opt. standing waves      | 4               |    4            |      3    |     3          |

**Note that the "side-band gain ratio" convention used in the HIFI pipeline does not correspond to the ratio between the respective side-band gains (equal to 1 for a balanced system), but to the gain in one side-band normalised by the combined gain of the two side-band. Consequently, perfectly-balanced  side-bands will feature a side-band ratio of 0.5* (see also section 5.3.1 of the [[http://herschel.esac.esa.int/Docs/HIFI/html/hifi_om.html Observers' Manual]], and the [[%ATTACHURL%/calibframework.pdf Intensity Calibration Framework document]]).

*<u>Frequency Calibration Accuracy</u>*

| *Spectrometer*                  |  *Resolution Bandwidth (kHz)*  | *Accuracy (kHz)*  |
|HRS (high-res. mode, Hann appodization) |  207 - 364                     | 20                |
|WBS                                     |  1100                          | 100               |

<u>Dominant Contributions</u>:
   * _HRS accuracy_: Master Oscillator accuracy (1 part in 10^8)
   * _HRS resolution_: LO signal frequency profile, as determined by the LO Source Unit mixers; band-dependent
   * _WBS accuracy_: COMB algorithm and interpolation interval
   * _WBS resolution_: optical alignment & thermal expansion effects within spectrometer


---+++Access to the calibration tree:
   * Information about what calibration is found in the HIFI !ObservationContext is found in the [[http://herschel.esac.esa.int/hcss-doc-10.0/index.jsp#hifi_um:hum_tour_cal Data Primer]] of the HIFI Data Reduction Guide

   * Information about how to find what calibration version was used on your data, how to get the latest calibration and reprocess observations with it is found in the [[http://herschel.esac.esa.int/hcss-doc-10.0/index.jsp#hifi_um:pipeline_cal Pipeline]] chapter of the HIFI Data reduction Guide

   * the latest calibration tree pool can be also retrieved directly [[ftp://ftp.sciops.esa.int/pub/hsc-calibration/latest_cal_tree/][here]] (4 Jul 2013)

   *  Updates to the HIFI calibration data are generally concurrent with the release of each major version of the HCSS-HIFI software. However, it is possible to have updates to the calibration data in between major releases of the software as the software and data are independent of each other, in the table below the HIPE or the OD  from which the calibration updates apply are given.  The calibration versions available since HIPE 5 are listed in the table below 


| *Calibration version number* | *Release date*  | *OD*  | *HIPE version* | *Changes* |
| IA_CAL_USER_ or HIFI_CAL_    | dd-mm-yy        |           |                        |                  |
| 2_0                                        | 29-11-10         |           | 5.0                  | Beam efficiency parameters introduced,  updates to spur table |
| 3_0                                        | 11-01-11         |           | 5.1                  | Beam efficiency parameters updated |
| 4_0                                        | 18-02-11         | 645    |                        | Spur table update |
| 5_0                                        | 13-04-11         |           | 6.1                  | Smoothing widths of OFF positions updated |
| 6_0                                        | 21-06-11         | 779    |                        | Sideband ratios in band 2a, addition of strong spur at 1108 GHz in band 5a to spur table |
| 7_0                                        | 12-12-11         |           | 8.0                  | Prevention of unnecessary Quality Flags by correction and addition of units in calibration products and correction of thresholds, addition of Quality Flags when LO multiplier currents are out of limits, improved saturated pixel flagging, addition to spur table, uplink product| 
| 8_0                                        | 03-02-12         | 995    | 8.1                  | Update of a priori table of IF saturations, used in order to flag bad LO data to be discarded in the deconvolution| 
| 9_0                                        | 24-07-12         |          | 9.0                | Sideband ratios in bands 5a and 5b, update of a number of engineering threshold for more accurate quality flagging related to hardware housekeeping, introduction of a list of a priori known corrupted data-frames for dedicated flagging in level0 data | 
| 10_0                                        | 08-11-12         |          | 9.1                | Introduction of a new !HifiUplink product to back-fill most the observational parameters as of !HSpot optimisation back into the Uplink product, update of the list of corrupted data-frames for flagging at Level 0, update of a number of engineering threshold for more accurate quality flagging related to hardware housekeeping  | 
| 11_0                                      | 22-01-13          |          | 10.0               | Update of the list of corrupted data-frames for flagging at Level 0, Quality flags created for SEUs (Singe Event Upsets leading to on-board software corruption) |
| 12_0                                      | 10-05-13          |          | 10.1               | Update of the list of corrupted data-frames for flagging at Level 0, updates to quality flag meta-data and uplink information for mapping modes |
| 13_0                                      | 30-05-13          |          | 11.0              | Update of the list of corrupted data-frames for flagging at Level 0, updates to spur table to account for band 3B purification |
| 14_0                                      | 04-07-13          |          | 11.0              | Update of the list of corrupted data-frames for flagging at Level 0 |

   * The side-band ratio assumed in the pipeline as of the latest calibration tree pool are illustrated in this [[%ATTACHURL%/HIFI_SBR_Summary_V9.0.png plot]]. 

   * Beam efficiencies are derived from Mars maps. Deeper beam maps are currently being taken and analysed, and will result in a possible update of the coupling efficiencies. Those will be posted together with 2D beam map for each of the HIFI bands, which could be of particular interest for the interpretation of extended emission

---+++Outstanding calibration issues
   * An overview of the data product known issues can be found [[http://herschel.esac.esa.int/twiki/bin/view/Public/DpKnownIssues Data Known Issues Page]]

   * _Standing waves_:
      *  there are several standing waves that can affect the HIFI data at various processing levels.  Their nature and impact on the HIFI calibration are described in the Standing Wave technical note and, more briefly, in the Standing Wave removal chapter of the HIFI Data Reduction Guide
         * [[%ATTACHURL%/calibration_hifi_stdw_2011_v0_1.PDF Standing Wave technical note]] 
         * [[http://herschel.esac.esa.int/hcss-doc-11.0/index.jsp#hifi_um:sw_removal_hifi2 Standing Wave Removal]] 
      * There are various techniques currently offered to clean these baseline distortions:
         * Remove sine waves, or combinations of sine waves.  Check the bullet about usage of the *[[http://herschel.esac.esa.int/hcss-doc-11.0/index.jsp#hifi_um:sw_removal_hifi2 fitHifiFringe]]* task in the data reduction section above.
         * *Matching technique*: for the strong IF standing waves seen in bands 6 and 7. 
            * A script is available in the source directory of the 'expert' install of HIPE: scripts/hifi/scripts/users/engineering/HEBStWvCatalogCorrection.py
              It is extensively commented.  Alternatively, the *latest version* can be found [[http://www.sron.rug.nl/~avruch/HEB_baseline/src/HEBStWvCatalogCorrection_latest.py here]]
            * At the HIPE Forum 2012, a demo of a %RED%pre-release version%ENDCOLOR% of the script provided in HIPE 11.0 was given. The presentation, that version of the script, a prepared input catalog for use by the script, and some result plots can be found on the twiki page:
               * [[http://herschel.esac.esa.int/twiki/bin/view/Hcss/Hipe2012HifiHebWave][Matching technique demo at HIPE Forum 2012]]
            * A thorough description of the technique, and the underlying causes, is in Ronan Higgins' thesis:
                [[http://eprints.nuim.ie/2584/1/thesis_ronan_higgins_nuim.pdf _Advanced optical calibration of the Herschel HIFI heterodyne spectrometer_]]
            * Published astronomical results using the technique:
               * attached poster (Sherry, Tchernyshyov and Martin, AAS Meeting #217, #255.07; Bulletin of the American Astronomical Society, Vol. 43, 2011)
                  [[%ATTACHURL%/Sherry_et_al_AAS217_poster.pdf poster]] 
            * for more information please contact Ian Avruch (I.Avruch@sron.nl) at the HIFI ICC. You can also check the progress on this effort in the following internal ICC [[http://www.sron.rug.nl/~wikiman/wikis/HifiIlt/HebBaselineProblem pages]]. 
         *  in case of strong source continuum some standing waves can be enhanced, as described in the Alternative Calibration Scheme report.  Such standing waves can be significantly reduced in amplitude using an alternative pipeline algorithm known as the _Modified Passband Technique_ , which is described in the Standing Wave Removal chapter of the HIFI Data Reduction Guide.  Alternatively, you can run the Level1PipelineAlgo_hc_filtered_v1.py script. <!--Note that in 9.0, a bug still affects the doFilterLoad task in such a way that it will ignore the user-input parameters, resulting in the task always applying the "cubic_spline" method with default parameters - i.e. the "fft" method will not be applied despite being set in the task inputs. This will be fixed in 9.1.-->
            * [[%ATTACHURL%/Alternative_Calibration_Schemes_v1.0.pdf Alternative Calibration Scheme Report]]    
            * [[http://herschel.esac.esa.int/hcss-doc-11.0/load/hifi_um/html/sw_removal_passb2.html Modified Passband Technique]].  
            * [[%ATTACHURL%/Level1PipelineAlgo_hc_filtered_v1.py.txt Level1PipelineAlgo_hc_filtered_v1.py  script]] 

   * _Baseline removal_: imperfect ON-OFF calibration scheme can result in residual baseline distortion (not necessarily standing waves). Check the bullet about usage of the *[[http://herschel.esac.esa.int/hcss-doc-11.0/index.jsp#hifi_um:hifium_bl1 fitBaseline]]* task in the data reduction section above.

   * _Spectral purity_: there are places over the HIFI frequency range where the Local Oscillator does not offer a single frequency tone, so that spurious spectral line may end up in the data, and the calibration of the targeted line gets affected. A dedicated cookbook on the matter is in preparation. In the meantime, we refer to section [[http://herschel.esac.esa.int/Docs/HIFI/html/ch05s04.html#N11370 5.4.6]] of the Observer's Manual, and to the release notes provided above. 

   * _Spurs_: Spurs are reported in HSpot when using the frequency editor and general information is also provided in the HIFI Observer's Manual (see above link). Spurs are also being checked in the pipeline and any detected feature is reported in the [[http://herschel.esac.esa.int/hcss-doc-11.0/load/hifi_um/html/notes_about_the_trendanalysis_context.html TrendAnalysis]] product of an observation context. The list of currently known spurs can be found in section [[http://herschel.esac.esa.int/Docs/HIFI/html/ch05s04.html#N11370 5.4.6]] of the Observer's Manual. However not all possible spurs can be predicted or caught by the data processing, so that Users are invited to inform the [[http://herschel.esac.esa.int/esupport/ Helpdesk]] about any features they found in their data and may not have been properly flagged by the system.

---++ Interest Groups and Scripts

   * %RED%HIPI%ENDCOLOR%: a library of HIFI Plug-In's has been prepared by the NHSC, and is regularly upgraded with new features - check the [[https://nhscsci.ipac.caltech.edu/sc/index.php/Hifi/HIPI][HIPI website]] for more information
   * The following interest groups relate to processing of observations taken with HIFI. The links provided allow subscription to these interest groups.
      * [[http://www.sciops.esa.int/mailman/listinfo/herschel_dp_specmap/ subscribe]] to PACS, SPIRE and HIFI spectral maps interest group
      * [[http://www.sciops.esa.int/mailman/listinfo/herschel_dp_hifi/ subscribe]] to HIFI point source and spectral scan interest group
   * User scripts: Users are welcome to submit scripts they believe could be of general interest to the community to the Herschel [[http://herschel.esac.esa.int/esupport/ Helpdesk]].

---++ Further Information

   * More information -- particularly for US users -- can be found at the HIFI home page at the [[https://nhscsci.ipac.caltech.edu/sc/index.php/Hifi/HomePage NHSC NASA Herschel Science Center]]
   * [[http://www.sron.nl/index.php?option=com_content&task=view&id=1963&Itemid=1795 HIFI science pages]]
   * [[http://www.aanda.org/index.php?option=com_toc&url=/articles/aa/abs/2010/10/contents/contents.html A&A Herschel First Science Result issue (Vol. 518)]] and [[http://www.aanda.org/index.php?option=com_toc&url=/articles/aa/abs/2010/13/contents/contents.html A&A Herschel/HIFI Special issue (Vol. 521)]]
   * Further details about some of the standing waves at play in HIFI and the matching technique can be found in the [[%ATTACHURL%/thesis_ronan_higgins_nuim.pdf thesis of Ronan Higgins (18.5 Mb)]]

-- Main.DavidTeyssier , Main.CarolynMcCoey and Main.SylvieFBeaulieu - 26 July 2013
Attachments
Topic attachments
I	Attachment	History	Action	Size	Date	Who	Comment
pdf	Alternative_Calibration_Schemes_v1.0.pdf	r1	manage	2815.8 K	2011-12-14 - 08:57	DavidTeyssier
pdf	HIFI_Calibration_ReleaseNotes.pdf	r1	manage	174.5 K	2013-01-31 - 12:56	DavidTeyssier
pdf	HIFI_SBR_Cookbook_V1.0.pdf	r1	manage	1440.2 K	2013-06-27 - 13:16	SylvieFBeaulieu	HIFI_SBR_Cookbook_V1.0
png	HIFI_SBR_Summary_V9.0.png	r1	manage	86.0 K	2012-08-23 - 11:18	DavidTeyssier
pdf	HifiObservingModesPerformance_110926a.pdf	r1	manage	4324.4 K	2011-09-30 - 13:26	JeanMatagne
txt	Level1PipelineAlgo_hc_filtered_v1.py.txt	r1	manage	10.6 K	2011-06-09 - 09:08	DavidTeyssier
pdf	Ossenkopf_2008_AllanVariance.pdf	r1	manage	1500.3 K	2011-10-04 - 09:27	DavidTeyssier
pdf	Sherry_et_al_AAS217_poster.pdf	r1	manage	101.6 K	2011-06-26 - 16:00	DavidTeyssier
pdf	aa14698-10.pdf	r1	manage	767.0 K	2011-01-21 - 09:38	AnthonyMarston	de Graauw et al 2010 -- HIFI instrument paper
pdf	aa15120-10.pdf	r1	manage	377.9 K	2011-12-01 - 17:21	DavidTeyssier
pdf	calibframework.pdf	r1	manage	303.5 K	2011-06-08 - 08:18	DavidTeyssier
PDF	calibration_hifi_stdw_2011_v0_1.PDF	r1	manage	2897.1 K	2013-01-10 - 10:58	DavidTeyssier
pdf	calibration_hifi_stdw_2011_v0_1.pdf	r1	manage	4022.0 K	2011-08-10 - 20:47	CarolynMcCoey
pdf	freq_framework.pdf	r1	manage	181.3 K	2011-06-08 - 08:18	DavidTeyssier
pdf	freq_vel_1.1.pdf	r1	manage	255.4 K	2011-06-26 - 17:55	DavidTeyssier
PDF	freq_vel_3.PDF	r1	manage	305.2 K	2011-06-08 - 08:19	DavidTeyssier
pdf	spatial_response_framework.pdf	r1	manage	581.8 K	2011-06-08 - 08:18	DavidTeyssier
pdf	thesis_ronan_higgins_nuim.pdf	r1	manage	18922.3 K	2011-06-26 - 16:10	DavidTeyssier
Topic revision: r58 - 2013-09-18 - DavidTeyssier
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