Starlink Software Collection - Humu Release Notes

General Changes

• It is now possible to relocate a binary release to a directory (other than /star) using the STARLINK_DIR environment variable. This variable must be set.

• A copy of the GNU scientific library, Visualisation Toolkit, FFTW fourier transform library, and the Mesa 3D library have been incorporated into the build system to avoid external dependencies.

• The dvi2bitmap package has been relocated into the thirdparty section. This is now supported in a SourceForge project.

• Many documents not associated with a specific package, such as the SSN and SGP series, are now built.
• This will be the last supported OS X PPC release.
• This will be the last supported OS X 10.4 (Tiger) release.
• This may be the last supported CentOS 4 release, depending on operational requirements of the Joint Astronomy Centre.

New Applications

• A new KAPPA application PLUCK for extracting interpolated slices at selected WCS co-ordinates not corresponding to pixel centres. For instance, it can obtain a spectrum at given equatorial co-ordinates from a spectral cube
• A new KAPPA application called PROVSHOW has been added that displays the provenance information stored within a given NDF.
• A new KAPPA application called PROVADD has been added that stores information about a parent NDF within the provenance information of a child NDF.
• A new SMURF application called TIMESORT can re-order time slices in a raw data cube into increasing time.

Changes to Applications

CONVERT

• NDF2FITS now makes special provision for the JCMT SMURF-package extension. It treats the extension contents as NDFs rather than arbitrary HDS structures.
• NDF2FITS has a new DUPLEX parameter. When set TRUE (and PROFITS is also TRUE), it permits the FITS-airlock headers to appear also in the IMAGE extensions for the VARIANCE and QUALITY arrays as required.
• Bug Fixes:
  • The channel width in the SPECX2NDF WCS has been fixed.
  • NDF2FITS writes the correct BUNIT keyword value in the IMAGE extension storing the VARIANCE component. The BUNIT keyword is absent for a QUALITY array.

CUPID

• FINDCLUMPS can now find clumps in each spectrum indpendently of the other spectra.
• Bug Fixes:

  • A bug that caused the ClumpFind algorithm to ignore the top contour level has been fixed.

  • The FellWalker algorithm used to reject small clumps before merging neighbouring clumps together, resulting in more data being rejected than was necessary. It now merges neighbouring clumps first and then rejects small clumps.

CCDPACK

• Each CCDPACK command can now store provenance information in its output NDF describing the input NDFs (this includes the provenance for each input NDF).

DAOPHOT

• Bug Fixes:
  • A non-portable format call has been fixed (this was causing a runtime exception).

EXTRACTOR

• SExtractor user guide updated to latest version and dummies guide URL updated.

FIGARO

• Bug Fixes:
  • Corrected pointer handling for 64-bit addressing that caused crashes of EMLT (with SYNTH or CALIB options) and IXSMOOTH.

GAIA

• New volume visualisation extension. New facilities for visualising data cubes have been developed for GAIA. These include the facility to display 3D iso-surfaces and also to do volume rendering. The current slice and spectral point extraction can also be rendered into the scene, and there are also facilities for drawing annotated axes and direction vectors. The scene is fully interactive and can be manipulated to view regions of interest, as well as move the current slice and spectrum. Readout of the celestial and spectral coordinates are also available (these work in the plane of the visualised slice). Finally it is also possible to display iso-surfaces of other cubes into the same scene for intercomparison purposes.

• A new command-line option "-autoscale" has been added. This enables the option to scale the image to fit the main window. Also available as a persistent startup option. The "Auto scale" feature now includes any off-image graphics that have been drawn, so these now remain visible.

• A new command-line option "-autofit" and menu item "View->Auto fit" menu item has been added. This arranges for newly loaded images to fit the main window (unlike "Auto scale" this happens just once and control of the zoom remains active). Also available as a persistent startup option.

• A cube toolbox can now couple the position of its slice and spectral extraction to another toolbox so that cubes of the same size can be inspected concurrently.
• The mouse wheel will now scroll the main image (and some other components). Using it in combination with the control and shift keys gives horizontal scrolling (also available for horizontal wheels) and zooming.
• The cube toolbox can now read an ARD region from a file and use a pre-defined shape for extracting a spectrum.
• When saving an image with a new WCS the strategy for removing redundant information from FITS headers has been improved.

• Temporary files created by GAIA can now be placed into a named directory by defining the GAIA_TEMP_DIR environment variable.

• The display of cubes in MEFs is now possible using the -hdu or file.fits[hdu] forms on the command line, or by using the file.fits[hdu] form as the file name in the cube toolbox.

• The Tycho-2 catalogue has been added to the default list.
• The major fonts used in the interface may now be changed as startup options.
• Inline compressed images (e.g. RICE) can now have more than 2 dimensions.
• The scale factor used in the pick object zoom window is now a command-line and startup option.

• A -geometry command-line option is now available. This uses the standard X11 syntax, widthxheight+xoffset+yoffset.

• Other new command-line options, -blank_color, -image_background and -ident, which set the blank pixel colour and the background colour of the main window. -ident adds a string to the window title so that different instances of GAIA may be distinguished.

• Bug Fixes:
  • A problem displaying cubes using the gaiadisp command has been fixed (reported an invalid NDF identifier when the cube spectral axis changed from that of the previous cube).
  • A bug reading four byte integer FITS cubes has been fixed. This could result in blank data values not being ignored.
  • It should now be possible to read NDF byte data cubes. Previously these were handled incorrectly.

  • The -hdu command-line option will now work again. This allows the selection of a extension when displaying an MEF.

  • FITS images containing floating point values will now assign any NaN values to the BLANK pixel colour.
  • A memory leak when contouring external images over the displayed image has been fixed.

  • A bug in the gaia_tcl program caused the gaiadisp command to fail under OS X. This has been fixed.

  • When extracting spectra from ACSIS sparse cubes, the offset from the source position should now be correctly determined.
  • A problem in the ROSAT catalogue query URL has been fixed.
  • A problem opening NDFs with the same basename as a directory, in the same directory, has been fixed.
  • A bug open FITS cubes with sizes greater than 2Gb has been fixed. Previously these could be reported as having no dimensions.
  • The time needed to open some NDFs with very large lookup tables in their WCS has been significantly decreased.
  • A bug saving graphics that included contour lines to a disk file has been fixed.

KAPPA

• New application PLUCK for extracting interpolated slices at selected WCS co-ordinates not corresponding to pixel centres. For instance, it can obtain a spectrum at given equatorial co-ordinates from a spectral cube.
• A new application called PROVADD has been added that stores information about a parent NDF within the provenance information of a child NDF.
• A new application called PROVSHOW has been added that displays the provenance information stored within a given NDF.
• Each KAPPA command can now store provenance information in its output NDF describing the input NDFs (this includes the provenance for each input NDF).
• ARDMASK has a new option to use WCS co-ordinates in the input NDF as the default co-ordinate system for the supplied ARD description. It can now use a two-dimensional ARD description to mask each plane in a three-dimensional NDF.
• COLLAPSE now issues a warning whenever any output values are set bad because there are too few contributing data values. This reports the fraction of flagged output data in comparison with the WLIM parameter.
• FILLBAD is no longer limited to two-dimensional data. The scale lengths may be different along each pixel axis, and can be disabled along axes so spectra in a cube may have their bad pixels replaced independently.
• MAKESURFACE parameter VARIANCE set to TRUE now writes a uniform VARIANCE component to the output NDF. Since the constant variance is the mean squared residual of the fit, variance information can be created for a spline fit.
• MFITTREND has three methods for automatic feature exclusion, including one where each trend line is analysed independently. For this Single method the created feature mask may be saved to an NDF. In other modes the reported fitting ranges are now given in the current current co-ordinate system.
• SURFIT has a new parameter GENVAR to enable creation of a uniform VARIANCE component in the output NDF. The constant variance is the mean squared residual of the fit.
• Graphics tasks that draw over an existing plot, such as LINPLOT, no longer store WCS information in the graphics database when the device is not cleared. This makes overplotting of data progressively faster as more plots are added, and it avoids the graphics database growing rapidly.
• PSF has new TOTAL output parameter recording the total flux of the fitted profile.
• Bug Fixes:
  • Prevent segmentation violations after an abort is supplied to a parameter in BLOCK and GAUSMOOTH.

  • BEAMFIT generates correct widths for data converted from AzEl to an equatorial system.

  • Integrate estimator in COLLAPSE now uses the correct widths.
  • Fixed propagation of quality arrays by WCSALIGN.

ORAC-DR

• A new command-line option -grptrans can be used when Groups are not re-used during processing. This option will help conserve memory, and is the default for all current UKIRT instruments (CGS4, UFTI, UIST, and WFCAM).

• A new command-line option -recsuffix allows a suffix to be added to the recipe name. For example, putting -recsuffix CADC on the command-line will cause all recipes used by ORAC-DR (as determined from file headers) to have the _CADC suffix appended.

• UIST IFU slices are handled properly, depending on the rotation of the array inside the cryostat.
• Bad-pixel masks are used for WFCAM.
• New flats are available for WFCAM.
• Large ACSIS rasters are now split into multiple spatial tiles.
• When collapsing an ACSIS cube around a central line, the line width is looked up in the JCMT pointing catalogue to determine the region to collapse over.
• Frame and Group infrastructure has been simplified.
• The recipe parser has been rewritten, allowing for reading of primitives on demand and caching primitives until they have been changed on disk. This should give some minor speed improvements when parsing recipes.

• A new command orac_carp is available for ORAC-DR developers, which will allow for easier debugging of primitives.

• Bug Fixes:
  • Multi-cycle imaging was using an incorrect flat field for all cycles after the first. This has been fixed.
  • Unknown wavebands when doing aperture photometry are handled more gracefully.
  • IFU pair reduction now falls back to telescope offsets if the pipeline is unable to determine which observation is on source and which is off source.
  • IRIS2 multi-cycle groups are now properly handled.

PERIOD

• Bug Fixes:
  • Memory handling bugs in the clean procedure have been fixed.

PHOTOM

• AUTOPHOTOM has new extended error messages when parsing bad input catalogues (previously unspecific error reports where made). The input description file may now contain tab character between the various fields
• Bug Fixes:
  • A memory fault in the optimal photometry code when stars where close to the edges of the image has been fixed. Various initialisation issues have also been fixed.

SPLAT

• Standard IR spectral lines from UKIRT have been added to the built-in line identifiers.
• Line identifier labels in text files can now be quoted using single or double quotes.

• Two new command-line options have been added, --hub and --exthub. These start an internal PLASTIC hub and an external one respectively.

• Bug Fixes:
  • When displaying a dual-sideband spectrum with the observed band set to LSB the axes coordinates for the USB sideband were shown incorrectly.
  • A bug converting the epoch into UTC, in the absence of a DATE-OBS, has been fixed in the synopsis. Previously times were reported in TAI.

SMURF

• A new application called TIMESORT can re-order time slices in a raw data cube into increasing time.
• The output cube from MAKECUBE can be divided up into tiles of a given spatial size.
• Polarisation data can now be handled by MAKECUBE, producing separate output cubes for data in different analyser angle ranges.
• The output cube from MAKECUBE can now be aligned with a reference cube, image or spectrum.

• The output NDFs from MAKECUBE now contain provenance information in a form that can be displayed using KAPPA:PROVSHOW.

• Input data for MAKECUBE can now optionally be aligned in the celestial coordinate system of the output cube, whatever it may be, instead of ICRS.
• The list of detectors to use by MAKECUBE can now be specified by exclusion as well as inclusion.
• The extent of the output cube from MAKECUBE can now be specified in pixel indices.
• The default spectral range for the output cube from MAKECUBE can now be either the union or the intersection of the input spectral ranges.

Changes to Libraries

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

AST

• A correction for diurnal aberration is now included when converting between AZEL and other celestial coordinate systems.
• A new class called Plot3D has been added that provides facilities for producing 3-dimensional annotated coordinate grids.

• Searching of hash tables (i.e. AstKeyMaps) has been made much faster.

• Bug Fixes:
  • Various bugs fixed that could prevent correct alignment of co-ordinate systems.
  • Some of the issues that caused difficulties when using FITS-CLASS encodings have been fixed.
  • A flaw in the calculation of output variances by astRebinSeq has been fixed.
  • Formatted angles given as decimal degrees may now include an exponent.
  • The testing of NDF WCS components to see if they can be represented in FITS-WCS form has been improved.
  • Alignment between two dual-sideband spectral frames now always occurs in the observed sideband (whether USB or LSB). It used to occur always in USB.

  • A bug has been fixed that prevented a LutMap cancelling with its own inverse.

HDS

• Bug Fixes:
  • When existing files are overwritten they appear corrupted to any other processes that have the file open. To avoid this existing files are now unlinked before creating a new file with the same name.

KAPLIBS

• A new routine has been added that smoothes an N-d array using a generalised 1D kernel. This opens the way for Hann and Hamming smoothing.

NDF

• It is now possible to specify external handler routines that are to be called whenever an NDF is opened or closed.
• Bug Fixes:
  • Various bugs have been fixed regarding the interpretation of NDF section specifiers that include WCS values.

NDG

• New routines have been added that allow the saving and retrieval of provenance information within an NDF.

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.