2021A Starlink Release

Starlink Software Collection — 2021A Release Notes

Highlights

• The HDS-V5 data format (which was introduced in the 2018A release and uses HDF5) is
  now the default output format for all NDFs and other HDS files created by Starlink. It
  is still possible to create output files using the old HDS-V4 format by setting the
  environmental variable HDS_VERSION to 4 before running the command to create the file.
  The HDS-V5 format is described in Jenness 2015.

• Perl updated to Version 5.32.0.

• SCUBA-2 calibration parameters (opacity relationships and FCFs) have been updated as per
  the new SCUBA-2 calibration paper Mairs et al. 2021.

• SCUBA-2 beam parameters also updated: 10--15% change in calibration when using
  matched filter (see also this blog post).

Changes to Applications

ATOOLS (ascl:1708.001)

• New wrappers for AST functions: astdecompose, astmoc, astaddpixelmask, astaddregion,
  astgetregdisc
• ATOOLS commands can now read and write FrameSet objects in STScI ASDF format.
• New tool astviewer provides a GUI that allows interactive exploration of Mappings and Frames
  within FrameSets.

CUPID (ascl:1311.007)

• All CUPID commands now support NDFs containing more than 2^31 pixels.
• Some parts of the code have been multi-threaded to improve execution speed.
• The FINDCLUMPS command has a new configuration parameter called GaussClumps.AllowEdge.
  It controls whether clumps found by the GaussClumps algorithm that touch the edge of the
  array are retained or not.
• The FINDCLUMPS command has a new option, "Ellipse3", for the SHAPE parameter (which
  determines the shape of the clump outlines stored in the output catalogue). It provides
  a more-robust alternative to the older options "Ellipse" and "Ellipse2".
• Several bugs have been fixed.

GAIA (ascl:1403.024)

• The cubehelix0 colourmap has been added to the quick lookups in the main panel.
• A new toolbox to display IVOA MOCs over images has been added. MOCs can also be exported
  from the Image regions toolbox.
• Various bugs in the display of ARD regions have been fixed.

KAPPA (ascl:1403.022)

• Various bugs have been fixed.
• The following commands can now handle NDFs containing over 2^31 pixels (some have been
  multi-threaded too for increased speed): ADD, CADD, CDIV, CHANMAP, CMULT, COLLAPSE,
  CSUB, DIV, FITSURFACE, MFITTREND, MSTATS, MULT, NDFCOPY, NDFTRACE, NUMB,
  PERMAXES, STATS, SUB, SURFIT, and WCSALIGN.
• A new command COMPLEX was added to manipulate complex NDFs, e.g. to extract the real
  and imaginary parts, compute the modulus and argument or to combine these parts into a new
  complex NDF.
• New command MOCGEN generates a MOC covering pixels in a two-dimensional NDF.
• New command PIXBIN performs generalised rebinning of an NDF by reading destination
  coordinates for each pixel from a set of associated NDFs.
• ARDMASK can now process complex data.
• HISCOM has a new parameter called APPNAME that specifies the application name
  to be stored in the new history record (previously, "HISCOM" was always used).
• LINPLOT Parameter XMAP has a new option called "LRLinear", which forces the X axis
  to be annotated linearly increasing from left to right.
• LISTSHOW can now display NDF data values at the positions in the supplied positions list.
• NDFCOMPRESS Parameter METHOD can now be set to "BOTH", causing the NDF to be
  compressed twice, once using Method SCALED and then again using Method DELTA.
• REMQUAL has new Parameter CLEAR, which allows the quality bits corresponding to the
  removed quality names to be cleared.
• SCATTER can now display a symmetric linear fit to the points in the scatter plot.
• SQORST has new Parameter CENTRE, which allow the centre of the squash or stretch to be
  specified.
• SUBSTITUTE has a new parameter called LUT, which allows multiple values to be changed
  simultaneously.

ORAC-DR (ascl:1310.001)

See the ORAC-DR change log.

POLPACK (ascl:1405.014)

• POLSELECT now aligns the supplied mask and catalogue in sky coordinates rather than pixel
  coordinates.
• The output catalogue column values stored by POLVEC for pixels that have negattive total
  intensity have been changed. Previously all output values were set bad at such pixels. Now only
  P (percentage polarisation) is set bad.
• A new option has been added to POLVEC and POLBIN that allows P and PI (polarised intensity)
  values to be debiased using the "modified asymptotic estimator". See Section 2.5 of Montier et al.
• A new command POLEDIT has been added, which allows an existing vector catalogue
  to be changed in various ways. These include changing column values, adding new columns,
  changing the debiasing method and recalculating all columns derived from I, Q, and U.
• The POLPLOT command can now draw all vectors with a constant specified fixed length.

SMURF (ascl:1310.007)

• Various bugs have been fixed.

• The SCUBA-2 opacity relations have been updated as described in the new SCUBA-2 calibration
  paper (Mairs et al. 2021).

• New command MATCHBEAM MATCHBEAM smooths a 450 um SCUBA-2 map so that it has the
  resolution of an 850 um map.

• New command POL2NOISE can verify or re-model the error values in a vector catalogue created
  by POL2MAP.

• New command GAU2FIT determines a two-component Gaussian PSF from a map of a compact
  source of known diameter (e.g. a planet).

• CALCQU:

  • The half-wave plate origin given by Configuration Parameter PaOff now has separate
    default values for 450 um and 850 um, which differ by about 4 degrees.
  • Fix a bug that could result in sources being smeared out in the output time-stream data.

• CONFIGMELD:

  • New Parameter APP allows the application from which the configuration should be read to be
    specified. Previously this was fixed at "Makemap", but now for instance it can be set to
    "skyloop" or "calcqu".

• MAKECUBE:

  • A new parameter called POINTING allows pointing corrections to be applied as the data are
    gridded into a cube.

• MAKEMAP::

  • If an error occurs, attempt to create maps from any remaining chunks before quitting.
    Previously, any remaining chunks were ignored.
  • A new add-on dimmconfig file called "dimmconfig_pca.lis" allows removal of multiple
    common modes using principal-component analysis. This can produce maps with flatter
    backgrounds.
  • Improvements to diagnostics system.

• POLMAP:

  • All the above CALCQU and MAKEMAP changes are also incorporated into POL2MAP.
  • The default Instrumental Polarisation (IP) model has been changed from JAN2018 to
    AUG2019.
  • New Parameter WEIGHTLIM specifies the lowest weight for usable observations, in
    the range 0.0 to 1.0 (default 0.05).
  • A HISTORY record describing the invocation of POL2MAP is now added to all output NDFs.
  • Do not include lists of input NDFs in the log file by default.
  • New Parameter TRIM to trim noisy edges off the output coadded maps.
  • Allow user control of the S/N levels used to define the AST and PCA masks.
  • New Parameter SMOOTH450 causes 450 um data to be smoothed to 850 um resolution.
  • Debiasing may now be performed using the "modified asymptotic estimator". See Section 2.5
    of Montier et al.
  • A new column called AST has been added to the output vector catalogues. It indicates
    which island within the AST mask (if any) contains each vector.
  • If the total intensity map comes from a non-POL2 observation, degrade it by a factor of
    1.35 before using it to take account of losses within POL-2.
  • An error is now reported if any map supplied as input to POL2MAP has a pixel size that is
    different from the value specified by Parameter PIXSIZE.

• SKYLOOP:

  • All the above MAKEMAP changes are also incorporated into SKYLOOP.
  • Shortmaps and bolomaps are now created if they are requested via Parameter CONFIG.
  • New Parameter INITIALSKY allows an initial guess at the sky map to be supplied.
  • Now honours the Ast.Mapspike_Freeze configuration parameter.

• UNMAKEMAP:

  • Accept raw data as input (previously input data needed to have been flatfielded first).

SOURCEPLOT

• The included JCMT source catalog has been updated.

SPLAT (ascl:1402.007)

• A bug extracting the lines from two-dimensional input data has been fixed. Previously this was
  completely broken and only the first line was extracted and repeated for each other line.
• Support for SDSS spectra.
• SAMP:
  • It is now also possible to send coordinates to SPLAT SSAP or ObsCore browsers.
  • Option to receive result tables.
  • Option to overwrite all SAMP spectra in one plot.
• Option to collapse/extract two-- and three-dimensional spectra coming from SSAP or ObsCore.
• Improved Datalink and time-series processing.
• Minor bug fixes.

STILTS (ascl:1105.001)

• Updated to Version 3.4-2.

See the STILTS version history.

TOPCAT (ascl:1101.010)

• Updated to Version v4.8-2.

See the TOPCAT version history

Changes to Libraries

AST (ascl:1404.016)

• Various bugs have been fixed.
• An alternative API has been added that uses 8-byte integers for functions that receive or return
  integer pixel indices or pixel counts.
• A new class called YamlChan has been added, which can be used to transform WCS information
  between AST and ASDF format.
• The Plot class has a new attribute TextGapType, which adds extra control over how the axis
  labels and title are positioned.
• New Moc and MocChart classes, which represents regions using the IVOA MOC format.
• The Region class has a new method, astGetRegionDisc, which returns a bounding disc for a region.
• The Region class has a new method, astPointInRegion, which tests if a single point is inside a Region.
• The FitsChan class has a new attribute, AltAxes, that can be used to control when to write out FITS
  headers describing FITS-WCS alternate axis descriptions).
• The FitsChan class will now return a FrameSet from a FITS-WCS header that contains only alternate
  axis descriptions (i.e. no primary axis descriptions).
• The KeyMap class now supports entries holding 8-byte integer values.
• The structure of the distributed source directory has been changed.
• Simplification of compound Mappings that include linear atomic Mappings has been improved.

CVG

• File extensions are now retained in CADC style provenance headers.

HDS

• HDS-V5 is now the default output format.
• An alternative API has been added that uses 8-byte (rather than 4-byte) integers to hold pixel
  counts and indices, thus allowing HDS arrays with more than 2^31 pixels to be accessed by
  application code

NDF

• The Fortran NDF library has been completely re-written in C.
• An alternative API has been added that uses 8-byte (rather than 4-byte) integers to hold pixel
  counts and indices, thus allowing NDFs with more than 2^31 pixels to be accessed by
  application code.
• New tuning parameters FIXDT and FIXSW allow date/time and software path within new history
  records to be fixed at specified values (useful for regression testing purposes).
• Support tilde ("~") expansion when using HDF_V5.

PCS

• Extra routines added to support ADAM parameters with 8-byte integer type.

STIL

• Updated to Version 4.0-4.

See the STIL version history

CFITSIO

• Updated to v3.450.

Changes to Cookbooks and Guides

• SC/20
  • Now includes information relating to the Namakanui instrument
  • Uses a new jiggle graphic.
  • New appendix about the removal of off-position lines appended.
  • Updated classified recipe parameters, log files, and PICARD recipe options.
  • Added how to access a list of the available receptors in an observation or the good receptors
    used by MAKECUBE.
  • Removed description of withdrawn Group Type for CADC searches.
  • More information on the identification of telluric lines added.
• SC/21
  • There is more on the various FCFs, calibrations and extinction corrections derived in Mairs
    et al 2021. This includes new graphics and an appendix FCFs by Time of Night. The
    FCFs by Reduction Date appendix was rewritten.
  • Added advice on whether to use a PONG or a 15-arcmin PONG,
  • Links to online tutorials included.
  • Section on the new dimmconfig_pca.lis added.
  • Tips and footnotes added.
• SC/22
  • The Advanced Data Reduction chapter is much expanded, notably new sections
    addressing the remodelling of error estimates and the de-biasing of POL-2 vector
    catalogues, the smoothing of 450-micron POL-2 maps to 850-micron resolution,
    controlling the masks used by pol2map, checking for convergence in pol2map log files,
    and combining multiple POL-2 fields.
  • New section on SKYLOOP added.
  • Documented the new pol2map catalogue fields AST and PCA.
  • The CALQU subsection was re-written.
  • Replaced CURSA usage with polselect from POLPACK.

Known issues

• There is a known threading problem that prevents the Java application Treeview from working
  on HDS Version 5 (HDF5) files.