Global changes

The main changes from a user perspective were as follows.

• Updated and expanded documentation, particularly the description of the primitives and lists the main primitives used at each stage, mention of xoracdr, and many more hyperlinks.

• Introduction of environment variable ORAC_KEEP to retain intermediate frames.

• Environment variables ORAC_DATA_IN and ORAC_DATA_OUT can define paths relative to the current working directory.

• xoracdr now knows the default calibrations for all instruments. A bug which prevented xoracdr operating on non-networked computers is fixed.

• Calibration reference offset added for off-centre nod patterns. This and the baseshift offset used array references. Arrays of values in a -calib can be comma separated.
• A bug affecting ORACTIME in calibrations for Michelle fixed; it was previously set to 0 in all cases.

• Cater for early Michelle data which had missing metadata affecting six headers. Allow for missing, undefined, or malformed RA_BASE and DEC_BASE headers in UFTI data.

• Allow for old UFTI data with CTYPE1 header set erroneously to 'Detector Rows' to create WCS.
• For IRIS2, modify the header translations for filter name and observation mode; correct the airmass calculation; and allow alternate frames to have alternate files, but still be members of the same group by using different headers for group membership checks.

• There is no longer the assumption of a right-handed world co-ordinate system in co-ordinate transformations benefitting UIST and future instruments with an extra reflection in the optical train.

• There are additional checks for significantly negative frame means after dark subtraction. Depending on the severity this may stop the pipeline, or merely issue a warning. This is to ensure that valid darks are observed.

• The broadened mean method has been reinstated for combining frames into a flat. This avoids the artefact in self-flat fielding where in an n-point jitter pattern, 1/n pixels divide by themselves giving rise to a false peak at the normalisation factor in the histogram of values in a flat-fielded frame.

• A possible cause of cause of a negative mode in is given in the warning announnced by _NORMALISE_TO_MODE_.
• _GENERATE_OFFSETS_EXTENDED_ now uses the 98 percentile, the same as the other _GENERATE_OFFSETS_ primitives.
• Centroiding now has a default smoothing option to make object location more robust for fainter sources.

• A double-pass median filtering of bad pixels now occurs just prior to the near-infra-red photometry to reduce bias from unmeasured flux. It particulalry helps the flat-fielded images, as the mosaics almost invariably lose their bad pixels in the region of interest during their formation.
• If variance information is available, the aperture photometry uses it to estimate photometric errors.

• Tidying correctly erases NDF components within HDS container files. Allow for _bc files in relevant _TIDY_ primitives.

• Support added to remove electronic ghosting, correct residual bias, and resample for field distortion, all initially for ISAAC.

The main changes from a programmer perspective were as follows.

• Calibration index files permit user header (uhdr) to be in expressions for bias, dark, flat, and sky.

• Infrastructure uses perl modules Astro::FITS::Header for access to FITS headers, and Starlink::HDSPACK for manipulation of HDS components.

• Add the internal headers ORAC_TELESCOPE, ORAC_X_REFERENCE_PIXEL, and ORAC_Y_REFERENCE_PIXEL.

• There is a $Grp->memberindex( $Frm ) method which returns the position the supplied frame has in the group, starting from 0. This is useful in batch-mode processing where the groups are pre-populated.

• _CLIPPED_STATS_ has new NUMBER argument returning the number of good pixels.

• _DIVIDE_BY_FLAT_CHOP_SKY_ and _DIVIDE_BY_FLAT_EXTENDED_ permit flat-fielding of sky frames via a new argument FLATSKY.

• There are some new primitives including _GET_FILTER_PARAMETERS_ to encapsulate filter attributes, and _FORM_SKY_LEVELS_ to determine the modal sky level for the sky frames after flat-fielding.

• Script nongeneric_imaging.csh is moved from the etc/ to the new admin/ directory.

• Lexical handles rather than global variables are used for accessing files.