Starlink Software Collection - Hokulei Release Notes

General Changes

• All HDS files are now created in 64-bit by default.

Changes to Applications

• KAPPA

  • COLLAPSE was modified to reduce its dependency on an inverse WCS transformation, and to reduce its memory usage in certain cases. Variance information can now be ignored if desired.
  • DISPLAY can now show rectangular pixels as rectangles rather than squares.
  • MLINPLOT now understands SpecFrames and FluxFrames.
  • PSF now reports the position of the first fitted star to the screen and to an output parameter (previously it only wrote the position to the log file).
  • ROTATE can now re-orient planes of three-dimensional NDFs.
  • Allow positions lists (such as generated by smurf:makecube) to have a textual label associated with each position.
  • Modified some graphics apps in order to allow temporary (i.e. non-sticky) changes to the plotting style.
  • Produced a perl script to strip "Dut1" and/or AlignSideBand values from an NDFs WCS FrameSet.
  • Various documentation improvements, such as the PSF fitting algorithm and WCSMOSAIC transformation requirements.

• GAIA

  • Spectra can now be sent to other PLASTIC-enabled applications.
  • Extracted spectra can now be saved to NDF and FITS files.
  • Extracted spectra may now contain additional meta-data about the extraction position (used by SPLAT-VO synopsis).
  • An animated GIF of a range of image slices can now be created.
  • A Go menu has been added that selects only cubes.
  • New controls for rebinning a cube.
  • New controls for filtering image planes of a cube.
  • It is now possible to display the variance and quality components.
  • It is now possible to view the FITS headers of a cube.
  • The grid overlay and celestial coordinate system toolboxes now support Horizon (AZEL) coordinates.
  • Images with any dimension of size 1 should now be accepted and handled as other images.
  • Cubes with trivial first and second dimensions are now loaded.
  • Timeseries cubes can now be switched between different time scales.
  • The default cube axis is now selected to be the spectral one.
  • The "send to SPLAT" option is extended to allow replacement or comparison.
  • Ranges used to extract spectra and control other operations are now preserved, when possible.
  • Channel maps now have a marker drawn to display the same position in each tile. The average spectral coordinate is also displayed.
  • The XY profile toolbox can now be activated using control-e.
  • The direction compass is now always a fixed size.
  • The behaviour of the spectral plot window can now be changed so that it no longer remains above the main window.
  • Bug Fixes:
    • The coordinate system of a channel map is now matched to that of the current cube, so that any displayed coordinates are in the correct context.
    • When a cube is collapsed the result image is now in the same coordinates as the current ones in use by the toolbox. This gives the correct units for any integrated intensity measurements.
    • The distance ruler now measures to the middle of the final pixel to the top and right of the display.
    • FITS headers are now shown out to 80 characters, not 79.
    • The precession facility of the positions toolbox should now correctly transform the current list of coordinates, rather than a single position.
    • The handling of broken WCS components in NDFs should now result in the display of an image/cube, without a WCS rather than an unrelated error report about a missing data component.
    • The initial order of baseline subtraction is now shown with the correct value (previously this was incorrect until the value was modified).
    • A bug causing a double free core dump when saving modified world coordinate systems for NDF data has been fixed.
    • A fatal bug when reading FITS headers from multiple NDFs in a container has been fixed.
    • SkyRef can now be set to Origin (previously was ignored)

• CONVERT

  • FITS2NDF and NDF2FITS support a "native" mode where scaled arrays may be converted without loss of compression.

• CUPID

  • Provide an option to suppress the removal of the instrument beam width from the reported clump sizes.
  • Provide option to include Gaussian FWHM values and other GaussClumps parameters as columns in the output catalogue when using the GaussClumps method to identify clumps.
  • Provide an option to produce catalogue columns containing values in the current WCS Frame rather than in pixel coordinates.
  • Provide a command to outline a specific clump within a 2D image.
  • The values of ADAM and configuration parameters used to create a catalogue are now stored as history information within the catalogue.
  • There is now an option to create a textual log file containing most of the information in the output catalogue.

• SPLAT

  • A synopsis of the current spectrum (name, exposure, extraction position system temperature, etc.) can now be shown in a plot.
  • The use of file type "guessing" has been extended beyond the File->Browse dialogue. This can now be selected from the command-line, or from the File->Open dialogue.
  • SPLAT has also been extended so that it can now interoperate with other VO-enabled desktop tools using the PLASTIC protocol.
  • The SSAP query has been remodelled so that all queries are performed concurrently. This means that a failing service will not block access to all the others.
  • The quick change of units has been extended to allow a change in standard of rest. A option has been added that controls how dual sideband spectra are aligned, by default this remains in the same sideband.
  • The FWHM value is now reported for all line profiles.
  • The rendering of line identifier labels has been improved to remove the trailing _lines from all names and replace any underscores with spaces. The positioning of the vertical lines has been improved so that it doesn't intersect the labels.
  • Usability improvements:
    • New keyboard interactions:
      • All menus are now accessible using keyboard mnemonics.
      • Keyboard accelerators have also been assigned to some more useful menu items.
      • Some one character accelerators have been assigned to plot actions.
    • Add new controls for replacing displayed spectrum (rather than adding to) with processed version in the polynomial, filter and interpolate toolboxes.
    • UI defaults are now saved for many more toolboxes. Filter, Polynomial fitting
    • When defining ranges the associated plot window is now brought forward and the cursor is changed.
    • Ranges can now be created without any graphical interaction.
    • The set of automatically chosen colours are now dimmed slightly so that they are always distinguishable from overlay graphics elements.
  • An integrated flux option has been added to the statistics toolbox.
  • It is now possible to define a spectral origin. This allows the plotting of offset coordinates.
  • The axes of a plot should now always be drawn on on the edges, unless the option to plot them in the plot interior is selected.
  • The splatdisp command now has a new argument that forces the clearing of the plot, so that the new spectrum replaces the existing one.
  • A filter that rebins a spectrum to reduce its resolution has been added.
  • The percentile autocut now just applies to the data within the X range, when the X range is not being autoranged. When autoranged it applies to all the data.
  • Bug Fixes:
    • The statistics toolbox had an off-by-one difference between the selected stats and the individual region stats, giving slighty different results.
    • A bug when reading text files that use whitespace column separators, other than simple spaces, has been fixed and the previous behaviour should be restored
    • When native NDF support is not available spectra are now opened as NDXs.
    • NDF/NDX spectra can now also be saved to NDF using NDX support.
    • When fitting spectral lines of spectra whose coordinate systems run high to low, rather than low to high, the widths etc. are now correctly reported as positive values.
    • When deleting spectra in the global list the selection now remains set at the next spectrum in the list (rather than selecting the first spectrum).
    • Aligning line identifiers to spectra with non-trivial observer rest frames should now work correctly.

• ORAC-DR

  • Added support for ACSIS.
  • Various minor improvements and bug fixes.

New Applications

• SMURF

  SMURF (Sub-Millimetre User Reduction Facility) has been released to allow ACSIS raw time series to be processed into data cubes. SMURF is the same software that will be used to process SCUBA-2 data. Functionality includes:

  • Implemented a system for automatic determination of optimal WCS grid parameters in makecube.
  • Allow makecube to generate a cube from a subset of the available detectors.
  • Allow makecube to generate an output catalogue containing all used detector positions.
  • Allow use of other rebinning methods in addition to "nearest neighbour".
  • Allow creation of output cubes from randomly positioned ("sparse") input spectra.
  • Make some components of the output cube optional, in order to reduce the size of the output cube.
  • Add option to restrict the spectral range of the output cube, in order to reduce the size of the output cube.
  • Allow output variances to be created from the input TSYS values.

Changes to Libraries

It is recommended that all applications that use any libraries be rebuilt from source.

• AST

  • Modifications:
    • Allow spectral positions to be described as an offset from a specified spectral origin.
    • Introduced a Dut1 attribute to the AST Frame class that allows conversion between UTC and UT1.
    • Provided an option to ignore sidebands when aligning two DSBSpecFrames
    • Allow Source velocity to be specified as a redshift.
    • Allow an instance of a basic Frame class (e.g. a SkyFrame, SpecFrame, TimeFrame, etc) to be used as a template when searching a compound Frame (CmpFrame) of higher dimensionality.
  • Bug Fixes:
    • Correct use of time origin when displaying offsets from a given time.
    • Corrected use of MJD-AVG and MJD-OBS FITS keywords.
    • Fixed bug that could prevent the ZSOURCE FITS-WCS keyword from being created when writing out WCS information.
    • Fixed a bug which could prevent ndf2fits from creating FITS-WCS headers from the NDF WCS component in certain border-line cases.
    • Fixed bug that could cause AST to go into an infinite loop when simplifying MathMaps.
    • Fixed bug in the handling or WcsMap projection parameters.
    • Fixed bug in SpecFrame so that (by default) account is taken of any difference in rest frequency when aligning two SpecFrames which both represent some form of velocity.

• ESP

  • Bug Fixes:
    • Reported FWHM in GAUFIT was too small by sqrt(2).

• HDSTOOLS

  • Bug Fixes:
    • Fix locator leak in hcopy command.

STARJAVA

The STARJAVA applications and libraries were built using Java version 1.4.2. A version of the Java runtime environment of at least this level is required to make use of them.

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