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What's new in HIPE 8

PDF Version Portrait Landscape

help Interested in what's new for other versions of HIPE? See this page for links to all the What's New documents from HIPE 4.0 onwards.

This document lists the changes in HIPE version 8.0 with respect to the 7.x series. Additional pages list changes between minor versions of the 8.x series.

See also the HIPE known issues and the Data products known issues pages for last-minute information on known problems.

Highlights

HIPE

  • User pool names (pool ID) restrictions: Allowed characters in name: alphanumeric, dash ("-") and underscore ("_"). The pool ID is case-sensitive, must be with less than 255 characters, and "urn" is not allowed as pool ID, and finally the pool ID cannot start with a dash ("-"). Old pools with names that violate those restrictions need to be renamed (at OS level) in order to be used in HIPE.

HIFI

  • Improved spectral cubes: Spectral cubes from mapping observations after OD 835 gridded using actual scan line and readout used in observation, earlier maps use a better approximation.
  • Improved band 6 and 7 Spectral Scan data: Improvements in the level 1 pipeline give noticeably improved noise and baseline quality of Spectral Scan observations performed in bands 6 and 7.
  • Standing waves: For strong continuum sources an optional pipeline step, doFilterLoads, can reduce or eliminate standing waves from the hot and cold loads
  • Calibration version: The calibration version used by the pipeline is now included in the metadata of all calibrated products. You can also select the calibration version to be used by the pipeline (command line only).

PACS

  • PACS Spectroscopy: Several new and improved tasks: flux calibration now includes the calibration block; errors are calculated at the cube level; better transient correction for unchopped observations; improved the flatfielding tasks (line scan and range scan separately).
  • New Spectroscopy pipeline scripts: To combine or bulk process data; to compare off-source (sky) spectra to the on-source spectra; and to experiment with an alternative spectral response method.
  • PACS Photometry: Second-level deglitching more efficient; a companion task to photProject, which is much faster; new cross-talk correction task; updated calibration file for non-linearity.
  • Reprocess PACS photometry with HIPE 8: Only if you have a very bright target of which you want to do the photometry with the non-linearity correction and the crosstalk artefact removal.

SPIRE

  • SPIRE Spectroscopy of bright sources: Big improvements in the processing of bright source mode observations with the SPIRE Spectrometer.
  • Calibration files: Improvements in a number of Spectrometer calibration file
  • FTS spectra: The representation of FTS spectra is now in terms of Frequency in GHz and not in wavenumbers in cm-1.
  • SPIRE Photometry of extended emission: improved destriper; new module and calibration file to correct for relative gains correction for extended emission
  • Astrometry: new astrometry correction module. Given a reference image, it will correct the whole observation conext (level 1 and level 2)

Core system

Jython major upgrade. The version of Jython on which HIPE is based has been upgraded from 2.1 to 2.5.2. You may have to adapt your scripts for them to work with the new version.

ALERT! See this page for details on changes from Jython 2.1 to 2.5.2 that could affect your scripts.

HIPE

Status bar

The maximum memory level reached is indicated with a vertical line in the memory bar. The tooltip shows the actual maximum value, and allows you to reset it.

Editors & Views

Variables View
  • Added contextual menu entry Show contents to show the contents of a variable in the console.
  • Added contextual menu entry Send To --> Text File to save the contents of table datasets to files.
  • Names of variables created from the Product Viewer are more consistent and meaningful.

Dataset Viewer
  • Numeric values in metadata, array datasets or table datasets can be displayed in decimal or hexadecimal format, and dates can be shown in either UTC or TAI. These options are available in the table's contextual menu.

Product Viewer
  • The title (product's description) can be selected and copied.
  • The expanded sections can be resized, for example to show more metadata rows.
  • The summary of the Observation Viewer has been enriched with useful metadata of the observation being shown.
  • Products can be saved directly from the tree with the Send To entry of the popup menu, without creating an intermediate variable.

Jython & Text Editors
  • The supported Jython language has been upgraded from version 2.1 to 2.5.2.
  • Scripts and text files coming with the installation or with plug-ins are now safe to edit without losing the original version.
  • Improved the step by step execution of scripts. See the note on this page for more details.

Help & Debug

  • The Tip of the day contains information on the Console meta commands (those starting with !)
  • If you get temporary (or permanent) freezes in the HIPE GUI, or you have created a custom task dialogue or view in HIPE, you can debug it by enabling the corresponding preference in Edit --> Preferences --> General --> Debug. Any problem found with this debugging can be reported like previously, with the HSC Helpdesk or Give Feedback options of the Help menu.

Plug-ins

  • More protection against problematic plug-ins. You can now disable all plug-ins without having to start HIPE. This can be convenient when you know or suspect that a plug-in causes HIPE not to start. To disable all plug-ins, run the disable_plugins utility located in the bin directory of the installation. You can use the Plug-ins panel (from the Tools menu) to re-enable your plug-ins.
  • More flexible update mechanism. If multiple updates for a plug-in are found, they are now all shown. Previously only the most recent update was shown.
  • Improved user feedback. You now get popup messages when no updates are found for installed plug-ins, and when you install a plug-in incompatible with your version of HIPE.
  • Many improvements to plug-in installation:
    • The installation process is now much faster for large plug-ins, such as those containing data pools.
    • The HIPE interface is no longer unresponsive while installing a plug-in.
    • You can follow the progress of the installation in the progress bar at the bottom of the HIPE window.
  • Fixed a problem with the scanamorphos plug-in, which would not read correctly some scanamorphos output. The plug-in assumed that the PrimaryImage HDU contained a 3-dim array. Output containing a 2-dim array in the PrimaryImage HDU was not read correctly.

Upgrades

If there is a new user release available, HIPE will notify you and offer to install the new version.

Plotting

PlotXY is now able to display images (i.e. 2D data). Look at an advanced example here.

TablePlotter

TablePlotter can now display plot with Date/Time format.

OverPlotter

OverPlotter can now display plot with Date/Time format.

Astronomical utilities

  • Planck class moved from spire_ia_pipeline_spec_util to ia_toolbox_astro. If you are doing an explicit import (it is not needed) you have to change it to (preferred) import herschel.ia.toolbox.astro.Planck or from herschel.ia.toolbox.astro import Planck
  • New task astrometryFix: adjusts the absolute pointing of map data to give the best possible agreement in overall astrometry with some ancillary data. This is done either by cross correlation of the map(s) with ancillary map data, or by stacking the map(s) at a list of known source positions (e.g., from radio observations).

Numeric routines

Wavelet transform

  • Continuous Wavelet Transform synthesis operation now adds low frequencies for a reliable reconstruction.
  • Continuous Wavelet Transform is now able to deal with Complex1d signal.

Deprecations

A number of potentially confusing features have been deprecated for a long time. This release will be the last time these features are still accessible.

As of HCSS 9 we will remove those deprecated functions:

deprecated alternative comment
Uniq.IS_UNIQ Uniq.COUNT_UNIQ_VALUES
UniqSorted.IS_UNIQ UniqSorted.COUNT_UNIQ_VALUES
Normalize.MEAN_FIDUTIAL Normalize.MEAN_FIDUCIAL
Normalize.PEAK_FIDUTIAL Normalize.PEAK_FIDUCIAL
RMS QRMS use as is explained in the User's Reference Manual
POLYNOMIAL Polynomial use as is explained in the User's Reference Manual
RESHAPE Reshape use as is explained in the User's Reference Manual
SHIFT Shift use as is explained in the User's Reference Manual
LOGN LogN use as is explained in the User's Reference Manual
EXPN ExpN use as is explained in the User's Reference Manual
POW Pow use as is explained in the User's Reference Manual
ANY_PRESENT AnyPresent use as is explained in the User's Reference Manual
ALL_PRESENT AllPresent use as is explained in the User's Reference Manual
NOT_PRESENT NotPresent use as is explained in the User's Reference Manual
WeightedMean.error WeightedMean.errorDistr

Source extraction

  • Improvements to handling of pixel coordinates and region of interest in sourceExtractor tasks:
    • Output source list now contains pixel coordinates of source (x, y) = (column, row).
    • Added getWcs and setWcs methods to the SourceListProduct/Dataset.
    • Added roi parameter (region of interest) to tasks.
    • Removed corner* and returnPixelCoordinates parameters from tasks.
  • Non-standard columns are now accepted in a SourceListDataset, e.g., when converting from a TableDataset (an exception will be thrown if there are no standard columns at all).
  • Removed subtractMedianBackground parameter from sourceExtractorSussextractor (it did not do anything).
  • Minor bug fixes and performance improvements.

Images

Display

  • The methods addCircle, addEllipse and addRectangle ae no longer dependent on the zoom factor of the image.

Spectra

Analysis

  • The SpectrumFitter now recognizes a CUBE such that you can give the x,y position of the spectrum. The script as written by the SpectrumFitterGUI also takes the correct spectrum.

  • The avg task now warns if wavescales are not sufficiently aligned to get a good result.

  • Various changes when applying toolbox tasks to cubes, in particular avg, select and extract now allow you to work on several pixels/spaxels within the cube rather than only the entire cube.

  • The resampling task now allows alternative ways to specify the grid for resampling.

Herschel Science Archive

  • HIPE can now store username and password in encrypted form outside of property files. It is recommended to remove HSA username and password from all property files.

Calibration sources

  • All SED models for asteroid observations have been added to the ESAC database.
  • The Calibrators data has been reformatted, so that spectra are now stored as SimpleSpectrum objects, allowing them to be viewed with standard HIPE spectrum tools.

Products and datasets

All products

  • Removed the legacy diff methods from Product and Dataset interfaces. All functionality moved to the ProductDiff class in the utility toolbox (herschel.ia.toolbox.util)

History

A new task historyExtract is available to facilitate retrieving the value of a certain parameter from the product history. For instance, you can use the following command to find out which calibration file was used in a given task of the PACS spectrometer pipeline:

value = historyExtract(product=frames, task='convertSignal2StandardCap', parameter='effectiveCapacitance')

The GUI of this task guides you through the available tasks and parameters: The option lists of the task and parameter parameters only show what is available in the history of the specified product:

Screenshot-HIPE_-_historyExtract.png

Observation context

Product Access Layer

  • A Cache entry has been added to the HIPE Preferences, with an overview of all existing caches on the system. You can clear these caches from this panel.
  • Product Browser: A simplified Observations tab has been added, that allows you to list all observations on local disk, just by pressing the Run button. The data source selector has also been redesigned to be more flexible and intuitive.

Tasks

  • General clean up of tasks:
    • All mandatory parameters must be filled in by users: removed default values from mandatory parameters, warnings issued (detection of programming mistakes)
    • Improved parameter checking and messages on bad data: Validators in primary inputs, they return false on error and log a warning (detection of programming mistakes)
    • All task GUIs and nodes should now show tooltips
  • Added some new user-friendly parameter editors (see For Task developers only below)
  • Default task layout:
    • Parameter name tooltips now show the parameter name (for long names).
    • Big modifiers can occupy a full row.
    • You can move through groups (tabs) with the mouse wheel.
    • Parameters can be reset individually via contextual menu on parameter names (in addition to resetting all parameters with the Clear button)
    • Parameters can list the variables they accept via contextual menu on parameter names, so you can check if you have the proper data to use in a parameter.
  • For Task developers only:
    • Task registration will issue warnings if the task was already registered or the taskname was already used.
    • Command generation: added converters so that arbitrary types can be represented with Jython strings (part of better visibility for defaults)
    • New shared Modifiers (parameter editors):
      • Added Editor for selecting a subset of a list of values (JListModifier, N values of M possible, M >= N)
      • Added a variant of JOptionModifier (Combo box) that returns some values but shows others (example: parameter uses integers but we show strings to users)

Miscellaneous tasks

  • OpenTask parameter names have changed capitalisation to comply with naming conventions.

Data input-output

  • Improved entries in the User's Reference Manual.
  • Task importUFDirToPal renamed to importObservation
  • Task exportPalToUFDir renamed to exportObservation
  • Task simpleAsciiTableReader extended to support all options of asciiTableReader via the Advanced tab.
  • Improved type guessing for table reading (affects (simple)AsciiTableReader): for floating-point data it will detect precision loss and maintain representation. If a floating-point number will lose precision as a float (32-bits) a double (64-bits) will be used instead: up to 17 significant digits but in these case it will use twice the memory.
  • Improved documentation and information provided by getObservation.
  • saveObservation now reports the progress in the status bar and can be interrupted.
  • Added contextual menu option to the Variables view to save tables with asciiTableWriter. Also added a validator to the task that will restrict its applicability to table datasets that can be fit into an ASCII table.

Virtual Observatory

  • Explicit support for DS9 was added. Right-clicking on a product will now show "SAOImage DS9" always, even if it is not running. In previous versions, DS9 had to be running for the menu item to appear. Requires DS9 version 5.3 or greater.
  • Upgrade to JSAMP 1.3, which targets version 1.3 of the SAMP protocol.
  • Improved GUI feedback using the HIPE progress bar when sending and receiving data.
  • The connection to the VO is now automatically established on HIPE start-up, to improve usability.

Installer

  • Sometimes, especially with an unstable internet connection, an installation might fail in such a way that your local repository of hcss libraries gets corrupted. The installer has been modified to give an error if such thing takes place. Moreover, a better error reporting has been implemented to give more information on the cause of the error.
  • The user installer now reports the estimated time of completion.

Documentation

HIFI

HIFI Software Configuration and Properties

HIFI Calibration

  • Updates to Calibration tree (HICAL-30)
    • Spur table (7b).
    • FPU HK Thresholds (5a) (Prevents unnecessary Quality Flags).
    • Units added to columns (Prevents unnecessary Quality Flags).
    • Wbs Bad Pixel (saturated regions) (Causes necessary Quality Flags).
    • QC flags for bad LOU currents (Causes necessary Quality Flags).
    • Uplink auxiliary product parameter filtering (First steps in ensuring information about the way the observation was carried out is put in the metadata).

HIFI Pipeline

hifiPipeline task

  • Can now select calibration version to reprocess data with (command line only).

  • By default the pipeline now runs without saving products. Previously it always wrote output to .hcss/lstore/pipeline-out, which in theory allowed you to access processed observations from that location. This was rarely used and could cause disk space problems.

  • Improvements to tooltips in the Pipeline GUI.

Level 0 Pipeline

  • DoUplink now uses the new uplink auxiliary product to set some observation parameters in the metadata, such as mapReadoutSep and mapLineStep.

  • Suppression of unneeded Quality Flags: Quality check for mixer voltage now accounts for magnet tuning.

Level 1 Pipeline

  • New (optional) pipeline step allowing smooth band pass to eliminate standing waves: doFilterLoads. This is an alternative calibration scheme for strong continuum sources.

  • Substantial refactoring of CheckFrequencyGrid to correct assumptions made about the sequence of on-, off- and hc-datasets. This primarily affected HEB band data and resulted in unnecessary Quality Flags being raised. This correction produces a noticeable improvement in the noise and baseline quality of observations performed in bands 6 and 7.

Level 2 Pipeline

  • Sideband gains coefficients added to metadata.

  • doGridding now uses AOT parameters in the meta data (such as beam size, map size, and - for observations after OD 835 - readout and line separations) to create cubes that reflect how the observation was carried out. In addition a box filter (previously a Gaussian) is automatically used for greater than Nyquist sampled DBS Raster maps.

Note that for the needed meta data to be present, the observation must be pipelined with HIPE 8 after the level 0 pipeline step doUplink has been run on the HTP.

Maps older than OD 835 will not have the readout and line spacings in the the meta data (this will happen with HIPE 9) instead doGridding calculates an approximate pixel size based on other meta data.

HIFI Products

  • Meta data calVersion is applied to all calibrated products and has format HIFI_CAL_version_number

  • Updated browse image for point mode observations.

HIFI Spectrum Toolbox

Spectrum tasks (HIFI specifics)

  • Introduced the flagTool task, which allows you go through every subband of a spectrum dataset and interactively flag spurs, lines, bright lines, and data to ignore. Input data can be an Observation context, a HifiTimelineProduct, or a SpectrumDataset.

  • PolarPair is now a task and can be applied to spectrum datasets.

HIFI Data Processing Tools

Standing Wave Removal

  • Introduced avermask option in FitHifiFringe. It allows a line mask to be calculated using the average of all scans. Makes fringe removal from maps much more efficient.

  • Variable result_sds should no longer be created if FitHifiFringe is run from the GUI with obs_or_htp input.

  • When an Observation Context is supplied standing waves are now automatically removed from both upper and lower sidebands.

Baseline Removal

  • FitBaseline now operates by default in interactive mode.

  • The back-end(s) to be processed can now be selected by clicking in a list.

  • FitBaseline divide option now handles negative signals robustly.

Deconvolution

  • Some output from doDeconvolution is now written to the console as it runs - helpful to know HIPE has not frozen!

  • doDeconvolution now picks up the applied sideband gains from the meta data and "undoes" their effect on the incoming DSB data. Then you can apply gains on or gains off. The pipeline supplied gains can in this way offer an optional starting point for the gain iteration inside the deconvolution.
    • This only has practical application for band 2 data at present.

  • New redundancy product allows you to overplot redundancy on the SSB solution. Helpful to identify where the SSB solution may not be reliable.

  • SSB spectrum now has y-axis labels Antenna Temperature (K), x-axis label changed to Frequency (GHz).

  • When diagnostic mode is turned on, doDeconvolution now produces an interim product in addition to the pop-up plots.

  • The min chi squared and the number of iterations are now included in the meta data of the SSB solution.

  • Bug fix: In doDeconvolution an algorithmic error in binning the input data has been corrected. The fix has stopped the occurrence of two problems: Some band-edge channels had fluxes set to zero and some very narrow lines had their peaks shifted by as much 1/2 MHz.

Spectral Cube creation

  • BeamSize is now taken from the calibration tree if hpbw is in the metadata.
    • If hpbw is not in the metadata, the beam size is calculated in the same way as in convertK2Jy using the rfreq in the metadata.

* Can rotate maps using new parameter, FlyAngle.

  • GUI behaviour modified:
    • Picks up information from metadata to provide better default input parameters.
    • Changes to values in the GUI form now only go in one direction, e.g. changing the PixelSize or the BeamSize results in an update of the Filter Parameters but not vice versa.

HiClass export tool

  • You can now create keywords when exporting to CLASS fits format.

Documentation

  • The HIFI User's Manual changed name to HIFI Data Reduction Guide, chapters rearranged into more logical order, addition of a changelog.
    • Addition of introductory chapter, HIFI Launch Pad.
    • Addition of a DBS Point Mode cookbook.
    • Addition of chapter, How to flag and remove flags from your data.
    • Addition of chapter, Unit Conversion.
    • Updates to chapters on Pipeline, Deconvolution, Creating Spectral Cubes, What was done to my data (clarifying units at each stage of the pipeline).
  • Updates to the examples in the HIFI Pipeline Specification Document.
  • HIFI User Reference Manual (URM) improvements.
    • All HIFI tasks in URM now have a category and show up in the categorised view of commands.
    • The categorised view of commands now is grouped into headers that should be meaningful to astronomers.
    • Many URM entries have been improved so that descriptions are clear and examples are useful.

PACS

Pipeline

Photometry

  • The HIPE menu Pipeline --> PACS has been reorganised and new interactive pipe scripts added.
  • Automatic pipeline scripts save the products at the end in the Observation Context. That mean the scripts can be executed in a sequence without interaction.
  • The less memory intensive task mapDeglitch is now used for deglitching instead of IIndLevelDeglitch
  • The second level glitch mask is now stored in level 1.
  • The new task filterOnScanSpeed now used to select frames at constant speed instead of the BBID selection.
  • The new task photMaskCrosstalk, masking the column 0 of all matrices, is now used in the pipeline too. This is a bit of brute force to avoid negative or positive cross-talk artifact in the level 2 maps, at the expense of getting rid of 1/16th of the data.

Spectroscopy

  • Interactive reduction scripts for all observing modes are now available.
  • Flatfielding is available in the interactive pipeline scripts.
  • Error propagation (and error bars) is implemented in the PACS rebinned cubes (STDDEV dataset).
  • SPG pipeline: the wavelength switching pipeline is merged with the unchopped pipeline and removed.
  • Improved documentation and user friendliness of the pipeline tasks within HIPE.
  • The spectrometer level-2 tasks now produce the specialized sliced products SlicedPacsCube and SlicedPacsRebinnedCube, which offer the same functionality as the SlicedFrames product.

Calibration

  • The calibration sets that are installed on your local system can now be inspected with a 'Calibration Sets Viewer'. The viewer is located in Window --> Show View --> Workbench --> Calibration Sets. Select a version from the available buttons, then you can inspect the release note for that version or the product list with the versions of the individual calibration products.

Photometry

  • A new calibration file is available for non linearity correction required by the task photNonLinearityCorrection.

Spectroscopy

  • Major improvements of the flux calibration:
    • Implementation of the background normalization method for chop/nod observations.
    • It is now based on observations of astronomical standards and the calibration block attached to each observation. The pipeline task specDiffCs computes the detector response of the current observation.
    • Implementation of a correction of transients for unchopped observations.

  • The spectral (pixel) dependency of the spatial calibration is now available for each pixel.

Analysis tools

  • The Preferences windo now contain a Logging panel under the general tab which allows you to increase or decrease the number of logging messages sent to the terminal.
  • The calibration file version is now also shown in the product history.

Photometry

  • MapMonitor got an improved interface and allows to flip north up-or downwards.
  • The PhotProject task got a companion task miProject (MapIndex-Project). If you have a full MapIndex, you may use miProject instead of photProject. It needs frames and the MapIndex as parameters and speeds up projection time by a factor of at least 20. Use as follows: map = miProject(frames, mapindex)
  • A new task has been developed. It deglitches without MapIndex and runs with significantly less memory abuse than the IIndLevelDeglitch task. The name and package is herschel.pacs.spg.phot.deglitching.map.MapDeglitchTask. The HIPE alias is mapDeglitch. It is documented as javadoc, URM and on the online deglitching documentation page.
  • A new task has been implemented which removes crosstalk effects by masking (CrossTalkMask) the first rows of detector arrays: frames = photMaskCrosstalk(frames)
  • Pacs products (for example Frames, Ramps, PacsCube) got a method to rename a Mask: renameMask(String oldname, String newname). Up to now, a mask had to be removed and recreated, if the name had to be changed.
  • photProject, miProject, IIndLevelDeglitching and some other tasks now report their progress in the HIPE progress bar instead of the terminal output.
  • The effects of 2-bit rounding on second level deglitching have been reduced in the pipeline for blue parallel maps.
  • The Pacs MaskViewer has been relocated to a new package: herschel.pacs.gui.maskviewer.MaskViewer. If you manually imported the old location (from herschel.pacs.signal import MaskViewer), the import will fail. Please remove the import, since everything should work automatically. If nevertheless there is a problem, please import the new location: from herschel.pacs.gui.maskviewer import MaskViewer
  • A new task maskFromCatalogue is available, very convenient to mask a list of point sources for high-pass filtering in deep fields.

Spectroscopy

  • There is a new GUI for viewing the footprint of the spectrometer upon an image with WCS: the tool pacsSpectralFootprint. It can be accessed through the Applicable tasks list in the Tasks view.
  • A tool specBaselineEstimator has been made available especially for long-range spectrum baseline removal. The wavelet-based multiresolution engine can also provide automatic line identification, line mask and continuum noise products.
  • The Spectrum Explorer GUI has a new panel for editing PACS masks.
  • Implementation of user friendly viewer for the PACS specific part of the ObservationContext?:
    • Each spectrometer slice now shows after the slice number a short description of its contents.
    • The tooltip of the slice shows the complete list of slice info keywords.

Product changes

Photometry

  • A new level 2.5 product is available combining photProject scan and cross-scan maps.

Spectroscopy

  • Browse products and browse image products are now available in SPG.
  • Red and blue camera spectra can now be combined in a single context in the level-2 processing, therefore, the lineId has changed for the red camera: 100 is added!

Documentation

  • PACS Data Reduction Guide. Chapter 1 is now a collection of Launch Pads: on getting Data into HIPE, doing your PACS Spectroscopy and doing your PACS Photometry. These are quick-start guides to work with your PACS observations. Chapter 2 tells you how to load your data, your pipeline script, and your calibration tree into HIPE, for photometry and spectroscopy. An appendix describes the PACS products in detail and some PACS product viewers.
  • Spectroscopy: the pipeline chapters have been re-organised to follow the new pipeline scripts.
  • Photometry: the pipeline chapters have been re-organised to follow the new pipeline scripts.

SPIRE

Calibration Products

  • Photometer:
    • SCalPhotChanRelGain is a new product to improve extended emission calibration.
    • The SCalPhotChanNoise product has been updated to improve the flux calibration for MadMap (this is only used for MadMap).
  • Spectrometer:
    • The "extended" calibration in SCalSpecTeleRsrf is now derived from a mean of many observations, reducing the noise level in the RSRF. In addition, RSRFs have been added for the Bright Source mode, and the units have been updated to be in GHz.
    • The "point-source" calibration in SCalSpecBeamParam has been updated, Bright Source mode factors added and units updated to GHz. The internal structure of the product has been updated to allow the point-source conversion factors for other off-axis detectors to be added in future, and the "beam area" column has been removed (as this was misleading, and the beam area is better calculated from the diameter, assuming a Gaussian shape).
    • The Instrument RSRF in SCalSpecInstRsrf has been updated, Bright Source mode RSRFs added and units updated to GHz
    • The OPD limits in SCalSpecOpdLimits have been changed such that the interferograms for calibration observations (resolution CR) are cut to have the same limits as high resolution science observations (HR).
    • The spectral band edges in SCalSpecBandEdges have been made slightly narrower to avoid spikes at the edges. They have also been converted to GHz.
    • The spectral limits used for phase correction (used for the polynomial fit method) in SCalSpecPhaseCorrLim have been converted to GHz.
    • Three new calibration products have been added to allow processing of Bright Source mode data:
      • SCalSpecNomPcal contains the weighted mean and standard deviation PCAL level separation for dark sky in Nominal Mode - this is used to compare with the PCAL level separation in Bright Source mode in order to calculate a bright mode gain factor for each detector.
      • SCalSpecBrightGain contains a frequency dependent correction to the PCAL gain factor (the gradient and intercept of a straight line). It is applied in the spectral domain to correct the spectral shape of Bright Mode observations.
      • SCalSpecBolPhase contains the optimum bolometer phases for each detector. These are used in the engineering conversion to correct the voltages for Bright Source mode, where the bolometers are dephased to reduce their responsivity.

Calibration Framework

Engineering Conversion

An additional option to correct the bolometer voltages for phase gain has been added. This is used in the Spectrometer pipeline to process Bright Source mode observations.

Common Pipeline

The default value for the correctionMode parameter in the sigmaKappa deglitcher is changed to "DIRECT".

A new metadata item, calVersion, is added to all pipeline produced products to specity the calibration tree version used.

Photometer Pipeline

Extended Emission Calibration Using the Relative Detector Gains

A new optional module in the User Pipelines that takes into account the fact that the SPIRE detectors do not all have exactly the same beamshape.
  • The Flag applyExtendedEmissionGains needs to be set to True.

Include Turnaround Data for Maps

Extra area / coverage can be obtained by including the scan line turnarounds in the processing.
  • The Flag includeTurnaround needs to be set to True.

Spectrometer Pipeline

Spectral Unit and Unit-Flexibility

The standard spectral unit used in the pipeline is now frequency in GHz rather than wavenumber in cm-1. In addition the band limits have been slightly reduced so that instrumental spikes at the edges are not included.

For interactive processing, it is now possible to specify the desired spectral unit in the Fourier Transform and Phase Correction modules. Both tasks accept an optional spectralUnit string parameter to specify the output spectral unit. For example, if spectralUnit='GHz', then the output spectra will be in units of V/GHz versus GHz (or K/GHz versus GHz for bright mode observations). If no unit is specified, the output spectra will be in units of V/(1/OPD_UNIT) (or K/(1/OPD_UNIT)) versus 1/OPD_UNIT (the OPD unit is typically cm).

To accommodate this new feature, all spectral modules now accept spectra and calibration data products in any unit of wavenumber or frequency. For example, if a module is provided with spectra in units of V/GHz versus GHz and a calibration product in units of cm-1, then the cm-1 calibration product will be converted to GHz, and the output spectra will be in GHz.

Averaging Spectra

The Average Spectra module no longer supports the bandEdge parameter. This parameter was used only for the module's defunct outlier rejection functionality, and so it is no longer needed. Please ensure that your scripts do not use this parameter.

Spectrum Flux Calibration

The Flux Calibration module has been replaced by two modules, the Point Source Flux Calibration module and the Extended Source Flux Calibration module. References to SpecFluxConversionTask should be replaced with SpecPointFluxConversionTask or SpecExtendedFluxConversionTask. Read more in the pipeline specification manual at Spectrum Point Source Flux Calibration and Spectrum Extended Source Flux Calibration.

Bright Source Mode

The pipeline has been adapted so that observations made using Bright Source mode can be calibrated. The processing sequence has several different steps from the Nominal mode: the bolometer voltages are corrected for a phase gain in the engineering conversion, they are converted to bolometer temperature, and two additional modules to correct for the remaining gain factors (due to the reduced responsivity in bright mode) are added:

  • The PCAL Gain module computes the ratio of a measured PCAL flash level separation to the mean PCAL flash separation measured on Dark Sky in Nominal Mode.
  • The Bright Mode Gain module computes and then applies a frequency-dependent gain factor.

Phase Correction

  • The Phase Correction module's interface has been simplified. As before, the module provides three ways of applying phase correction, but executing the module is simpler now:
    1. From the observation data:
      sdi = phaseCorrection(sdi=sdi, avgSdi=avgSdi, spectralUnit= GHz | cm-1) 
    2. From a calibration file:
      sdi = phaseCorrection(sdi=sdi, nonLinPhase=nonLinPhase)
    3. From a polynomial fit to the observation:
      sdi = phaseCorrection(sdi=sdi, sds=dsds, phaseCorrLim=phaseCorrLim,\
            polyDegree=2, pcfSize=64, convolApodName="aNB_15")
            polynomial fit to the observation

  • The Phase Correction module creates four new quality control metadata on the phase-corrected interferogram. These values will be used by the Quality Control module to assess observations:
    • phaseWrapSLW/SSW counts the number of times that in-band phase changes by +/-1.5pi in any of the nominal SLW/SSW detectors.
    • residualPhaseSLW/SSW gives the maximum absolute phase value (in units of degree) inside the phase correction limits in any of the nominal SLW/SSW detectors.

Create SDI from SDS

  • inverseFourierTransform has been created to transform SDS objects into SDI objects by applying the inverse Fourier transform:
    sdi = inverseFourierTransform(sds = sds)
  • inverseFourierTransform is not the inverse of the fourierTransform task because it does not remove zeropadding from the output interferograms. The already existing makeSameOpds can be used to remove zero-padding.

Improved pre-processed cube product

The "preCube" product which contains the collection of spectra to be gridded into the final cube has been improved and now contains a dataset in Spectrum2d format, that can easily be viewed with Herschel viewers.

Convenience task for spectral cube creation

SpireProjectionTask has been created to provide a convenient single API for creating spectral cubes. The task can make spectral cubes using any of the following algorithms:
  • Naive projection (cf. SPIRE photometer).
  • Nearest neighbour projection.
  • Gridding projection (cf. HIFI OTF gridding).

Interactive Analysis and Tools

Useful Scripts

A new menu item, Scripts has been added to HIPE to contain "useful" scripts. Scripts have been added for the Photometer and Spectrometer (see below).

Photometer Destriper
THe Destriper example use is now contained in a new Useful Script accessed from the top Scripts menu within HIPE. The following new features are introduced in HIPE 8:
  • Level 2 deglitching is available through setting l2DeglitchRepeat parameter.
  • The 5 individual output parameters are combined to one ArrayList parameter where each of 5 parameter can be retrieved base on its position.
  • The new diagnostic product is introduced which provides with useful diagnostic information.
  • Both Tod and TodBuffer are acceptable input for the tod parameter.
  • The input parameter array now is MANDATORY.
  • Pixel size can be changed through setting pixelSize parameter.
  • The brightSource parameter is changed to boolean.
  • The boolean fitWithWeight parameter was introduced.
  • Interruption is added so that the destriper can be terminated at your request.
  • Tod files stored in temporary directory are available until HIPE is terminated.
  • The destriper speed increased by 30%.
  • The input parameter name Level1 was changed to level1.
  • The input parameter name Tod was changed to tod.
  • The input parameter name L2DeglitchRepeat was changed to l2DeglitchRepeat.

Photometer Baseline Removal
The Median and Polynomial Baseline Removal example use is now contained in a new script accessed from the top Scripts menu within HIPE.
  • New roi (region of interest) parameter for baselineRemoval* tasks, specifying the region of the sky to be used in estimating the baseline.
  • Removed doInterpolation task parameter. The reason is that this parameter is of such limited use that it is best left as a parameter in the madMapper task.
  • Minor changes and bug fixes (for example, the tasks now do ignore masked data samples when a TodBuffer is used internally).

Photometer Moving Object Correction Script
A new script accessed from the top Scripts menu within HIPE:
  • Takes a SSO observation and corrects the map to be in the moving object frame.
  • For example, target is no longer a streak on a stable background.

Photometer SPIRE Astrometry Alignment
A new script accessed from the top Scripts menu within HIPE:
  • Takes a reference SPIRE map and a SPIRE map to be corrected and aligns the astrometry of the latter to the former.
  • Takes a reference SPIRE map and a list of SPIRE maps to be corrected and aligns the astrometry of the latter to the former.
  • Takes a reference ancillary map and a SPIRE map to be corrected and aligns the astrometry of the latter to the former .
  • Takes a reference source list (as a SourceListProduct) and a SPIRE map to be corrected and aligns the astrometry of the latter to the former.
  • In all cases both the Level 2 map astrometry and Level 1 timelines are corrected.

Spectrometer Array Footprint Plot
A new script accessed from the top Scripts menu within HIPE:
  • Plots the locations of the detectors on top of an image of the source.

Spectrometer Background Subtraction
A new script accessed from the top Scripts menu within HIPE:
  • Provides two methods to subtract residual background from the final spectrum:
    • using the daily dark observation.
    • using off-axis detectors.
This is particularly useful for faint sources.

Spectrometer Line Fitting
A new script accessed from the top Scripts menu within HIPE:
  • Allows simultaneous fitting of lines and continuum in the central detectors using the HIPE SpectrumFitter.
  • CO lines are fitted with a polynomial baseline and results are printed for each line, including the error estimate for the line flux.

Spectrometer Thumbnail Mosaic Plot
A new script accessed from the top Scripts menu within HIPE:
  • Gives several examples of plotting the spectra from each detector as a thumbnail arranged as the detectors appear in the array.

SDI/SDS Explorer

The SDI and SDS Explorer tools have been updated with the following features:
  • Added ability to plot errors as a shaded region on the spectrum.
  • Right click options added for each detector in the array footprint, including Open With, Send To and Create Variable.
  • Zooming is now permitted in the thumbnail view.

Documentation

  • New SPIRE Launch Pads to give you an overview of the SPIRE processing, what's available, and quick link jumps into the documentation.
  • A major revision of the SPIRE Data Reduction Guide for both Photometer and Spectrometer Chapters.
  • SPIRE Data Reduction Guide restructured to be "recipe" orientated.
  • Includes description of new scripts accessed from the Scripts menu in HIPE.
  • SPIRE Data Reduction Guide includes the manual for mapmaking with the SPIRE Photometer Interactive Analysis (SPIA) plug-in.


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