= Starlink Software Collection - Puana Release Notes =

== General Changes ==

  * Sourceplot is now included.
  * NDF sections can now be specified using WCS coordinates.
  * The Starlink software can now be built using gfortran (GCC 4.3 only).
  * Successful build of Starlink software on intel solaris 10 with studio 11 compiler suite
  * The Skycat package is now unbundled from GAIA and is part of the thirdparty.
  * The imcopy, fitscopy and listhead utilities of CFITSIO are now built and installed.
  * Successful build using the full intel compiler suite (previously had only tried intel fortran + gcc)

== New Applications ==

  * Sourceplot allows you to plot astronomical objects in azimuth and elevation for a specific point on Earth. This is useful for planning observing strategies.

== Changes to Applications ==

=== CONVERT ===
    * NDF2FITS can now create either a PC matrix or a CD matrix when using FITS-WCS encoding.
    * NDF2FITS writes CHECKSUM and DATASUM keywords at the end of each HDU when new parameter CHECKSUMS is TRUE.
    * NDF2FITS can now convert in-line compressed images (RICE, GZIP and PLIO) directly into NDFs.
    * Bug fixes:
      * Form online help dynamically.
      * Restored FITS-CLASS documentation.
=== GAIA ===
    * The version of Skycat that GAIA is based on has been updated to version 3.0-1. Major changes to the GAIA infrastructure.
    * When merging FITS headers from the primary data unit into those of an extensions the INHERIT keyword is now checked.
    * Inline compressed images (RICE) are now extracted more efficiently using built-in methods, rather than an external filter. The primary headers are now merged into such images as needed.
    * Reading FITS catalogues is now also handled using built-in methods. This should be more efficient.
    * FITS catalogues can now have 64 bit integer columns ('K' type).
    * Compressed NDFs can now be opened directly in the cube toolbox.
    * Very small images now fill the zoom window. Previously small images did not show correctly.
    * The rotatable box graphics item can now be used as a catalogue symbol.
    * The spectrum can now be re-extracted by pressing a simple button, as well as by clicking on the image.
    * The data range used to display the extracted spectrum can now be defined explicitly.
    * The spectral cube window will now retain some settings between sessions.
    * FITS spectra now have the extraction meta-data added to their headers.
    * The default on-line catalogue list has been updated. Fixes a problem with NED CADC access and includes some new CADC catalogues and the JCMT archive.
    * The "gaiadisp" command has been extended to accept a percentile cut as a command-line option.
    * The SMURF extension data are now ignored in their dimensions do not match the cube. This probably means the cube has had addition processing that makes the extension data invalid (or at least misleading).
    * Bug fixes:
      * Re-opening modified cubes now works (via File->Re-open and gaiadisp).
      * The spectral offsets from the centre of the observation of cube now preserve the sense of the direction by including a sign.
      * A bug when writing an extracted spectrum to NDF and FITS files has been corrected. Previously the coordinates were incorrect by a single channel.
      * Data values are now only reported when moving over part of the image. Previously reports continued for an additional pixel to the bottom and left.
      * When the first pixel has a NaN or blank value and has less than 10 pixels the lower value is now correctly set, rather than being left at the bad pixel value.
      * The various bounds for extracting spectra etc. should now work correctly when the lower bound is greater than the upper bound.
      * Increased the output length of a TST catalogue line to 4096 characters from 1024.
      * The rebin cube tools now correctly use "mean" as the combination method. Previously "sum" was used until either "mean" or "sum" was explicitly selected.
      * FITS images that contain NaN values should now contour correctly.
      * A bug that caused image region circles to be drawn at the wrong scale has been fixed.
      * A bug extracting a TSYS value when cubes have greater image dimensions than expected has been fixed.
=== KAPPA ===
    * New task BEAMFIT for fitting up to five Gaussians to beam features, with various fixed and relative constraints.
    * ADD and SUB propagate units if it is the same in both input NDFs.
    * ARDPLOT can now draw outlines around AST regions through a new REGION parameter.
    * COLLAPSE now has a new parameter (TRIM) that will retain the collapsed axis as a single pixel with size corresponding to the original axis extent.
    * Two invocations of COLLAPSE can now be used to collapse along the two spatial axes of a spectral cube to produce a single spectrum.
    * DIV and MULT propagate units combining to a normalised form.
    * FITSURFACE now writes PIXEL or AXIS values to the SURFACEFIT.COSYS component to bring it into line with AST usage.
    * HISTAT and STATS have new output parameters (MAXWCS & MINWCS) that hold formatted WCS co-ordinates of the maximum- and minimum-valued pixels. MAXCOORD and MINCOORD hold the numerical equivalents.
    * HISTAT has new parameters METHOD and NUMBIN that permit other ways to obtain the mode including the peak bin of an optimally binned histogram.
    * LINPLOT can now align new plots with old plots in any suitable co-ordinate system, specified using a new parameter called ALIGNSYS.
    * MAKESURFACE recognises GRID, PIXEL, and AXIS values for the SURFACEFIT.COSYS component.
    * MFITTREND can now cope without an inverse WCS transformation.
    * NDFTRACE now reports a nominal pixel scale and writes it to parameter FPIXSCALE. There is a new output parameter, FPIXSCALE, to store the nominal pixel scale or each axis in the current WCS Frame.
    * SQORST has a new PixelScale mode and corresponding PIXSCALE and AXIS parameters. These allow the WCS scales per pixel to be modified. So for example, it can resample a spectral cube into a cube with a specified channel width.
    * STATS reports formatted or numeric WCS co-ordinates of the maximum and minimum values, and stores them in output parameters including the new MAXWCS and MINWCS. It had previously returned AXIS co-ordinates, and continues to do so if the NDF does not have a WCS FrameSet.
    * SURFIT writes a SURFACEFIT extension like FITSURFACE for a polynomial fit.
    * WCSMOSAIC now has a parameter (VARIANCE) that allows input variances to be used as weights. New output parameters FLBND and FUBND record the WCS bounds of the output NDF.
    * Bug fixes:
      * COLLAPSE can now correctly collapse along an RA or Dec axis.
      * MFITTREND modified so that it can manage without an inverse WCS transformation.
      * ROTATE can again rotate a two-dimensional array with a dimension of one element, or a cube with two single-element dimensions.
      * LINPLOT sometimes choose wrong default for XMAP, resulting in a logarithmic X axis when linear would have been more appropriate.
      * WCSALIGN now only propagates the restfreq and IF values from the reference NDF to the output NDFs if alignment is not performed in velocity.
=== HDSTOOLS ===
    * Bug fixes:
      * Now works properly on 64-bit.
=== SMURF ===
    * MAKECUBE now uses input variances as weights when combining input data.
    * Add BADMASK parameter to MAKECUBE.
    * Bug fixes:
      * Fix non-nearest neighbour gridding in the presence of bad values
      * Spectra with no good data are now ignored.
=== SPLAT ===
    * TSYS can now be calculated for regions of a spectrum if the exposure time is known.
    * When opening 2 or 3D data, spectra that do not have valid data limits are now automatically removed by default.
    * Statistics of variance component can now be reported
    * Spectral coordinate searching can now be disabled so that non-spectral coordinates can be displayed.
    * Generated spectra how inherit some of the properties of the parent spectrum (line and plotting style).
    * Rebinned spectra are now displayed with a histogram style.
    * The alignment of sidebands is now not done by default.
    * An Interop menu has been added to the SSAP query results controls. This allows a table to be transmitted to other applications for further analysis.
    * The plot spectrum synopsis now includes the number of channels (points in the spectrum).
    * When changing the DSB sideband the labels now include which sideband is the observed and which the image.
    * Data units which dimensionally match one of the preset flux values will now be identified and shown as the standardised value.
    * Controls have been added to the statistics toolbox so that the TSYS related parameters can be set and inspected.
    * The FITS headers of all selected spectra can now be viewed and printed.
    * The builtin sub-millimetre line identifiers have been updated to match the latest ones used at the JAC.
    * Experimental support for the SSAP version 1 protocol has been added.
    * A new rest frequency can now be selecting using the plot units toolbox. The new frequency can be selected by clicking on a position in the plot, or a line identifier.
    * The TSYS value is now derived from the median effective exposure time when a better estimate is not available.
    * Bug fixes:
      * The readout of the spectral coordinate in a plot should now always have sufficient precision so that adjacent values can be distinguished.
      * Problems displaying spectra sent from GAIA when the plot synopsis is enabled (which came out at the wrong size and with the synopsis misplaced) should be resolved.
      * The synopsis should now be placed at the top-left hand corner of the axis for all plot aspect ratios.
      * FITS headers are now preserved when creating derived spectra.
=== SURF ===
    * CHANGE_POINTING now accepts POLMAP observations

== Changes to Libraries ==

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

=== ARD ===
    * ARD regions can now refer to regions within time or spectral coordinate systems.
=== AST ===
    * Add support for healpix (-HPX) projections
    * Allow astRebinSeq to use input variances as weights
    * AlignSideband now defaults to false
    * DSBCentre now refers to the reference pixel in a spectrum
    * Bug fixes:
      * DSBSpecFrame AlignSideband no longer is forced to a value when the DSBSpecFrame is created
      * FitsChan now interprets IMAGFREQ correctly within headers that describe velocity axes. Previously, the IF deduced from the IMAGFREQ value was incorrect for velocity axes.
      * Correction to approximation for LST used when the Epoch of a SkyFrame is changed by a small amount.
      * astRebinSeq - correct a flaw in the calculation of output variances based on the spread of input values.
=== HDS ===
    * Bug fixes:
      * Double precision numbers are now reported at full precision when converting to character strings.
      * A bug that stopped HDS_CLOSE from executing under certain error conditions has been fixed.

== 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.

TOPCAT has been upgraded to v3.0, which includes major graphics enhancements. For further information, see [[http://www.star.bristol.ac.uk/~mbt/topcat/sun253/versions.html|the TOPCAT version history page]].

STILTS has been upgraded to v1.3-2, which includes minor enhancements and bugfixes. For further information, see [[http://www.star.bristol.ac.uk/~mbt/stilts/sun256/versions.html|the STILTS version history page]].