p3d full changelog

New functionality and bug fixes
- The spectrum viewer now handles image (files) that contain a second
image in the extension BSW_DATA; this second image could contain
so-called laser offset, or beam-switched, spectra that are offset from
the regular spectra. The user can select between the regular spectra,
the [laser] offset spectra, the difference between the two, and a,
so-called, laser normalized difference between the two using the new
droplist widget on the Extra control panel or using the new menu entries
in the "Image View" menu. Two additional widgets allow the offset BSW
data to be multiplied with a factor before the offset spectra are
subtracted from the nominal spectra; the default multiplication factor
is 1.0.
- Add File menu entries to look at the FITS file headers of the BSW_DATA
and BSW_ERR extensions, when they are present.

All tools that combine raw-data images:
· Major bug fix - When I optimized the C routine of the image combination routine I introduced a serious bug. This bug is present in revisions 2753-2779 of p3d_cimcom.c, and is fixed with revision >=2780

C routines:
· Optimization - Optimized the C routines p3d_cpixex.c and p3d_cmpd.c

All tools that combine raw-data images:
· Major bug fix - When I optimized the C routine of the image combination routine I introduced a serious bug. This bug is present in revisions 2753-2779 of p3d_cimcom.c, and is fixed with revision >=2780

C routines:
· Optimization - Optimized the C routines p3d_cpixex.c and p3d_cmpd.c

Combining multiple files with extracted data (p3d_cexposure):
· New functionality.
· Added a new tool that combines mutliple extracted exposures that are
· taken illuminating the exact same field on the sky. The supplied data
· are at first checked for consistency in image size and equal values on
· the wavelength calibration parameters CRVAL and CDELT. Thereafter the
· files are either averaged, weighting with the exposure time of the
· individual exposures. Alternatively, setting the /SATURATED keyword it
· is expected that all files have a different exposure time. In this case
· the longest exposure is used as reference. Portions of individual
· spectra, where a mask indicates that a pixel was saturated, are then
· replaced with scaled data of the same spectrum and portion of a file
· using a shorter exposure time. The routine accepts any number of files.
· The routine produces one output file with merged data, and a file with

Correction for differential atmospheric refraction (p3d_darc):
· Added a new tool that corrects extracted science images for differential
· atmospheric refraction. The new tool works out-of-the-box with all the
· IFUs that use square-shaped spatial elements (VIMOS, FLAMES, PMAS/Larr,
· MPFS, and SPIRAL). In some cases the required physical properties are
· unavailable in the data header. In that case they must be entered by
· hand.
· The routine allows the user to choose between three implemented
· approaches to calculate the offsets. The results of all three approaches
· are collected in a plot, which allows the user to choose the most
· accurate method as he or she believes is more correct.
· The offsets are calculated using the wavelength-dependent
· refractive-index equation of Ciddor (1996; as well as Edlén 1966).
· A second approach uses a height-integrating approach to calculate the
· refractive-index that comes from the Starlink project. The routine

· Corrected a problem that occasionally would prevent the spectra from being properly traced.
The story is:
· The first part of the tracing procedure locates peaks in the data. The routine (p3d_tracing_findspec0) tries to find a reasonable value on what is a minimum value in non-peak areas.
· It could fail if the bias level varies across the image, as it does with the PMAS 4kx4k CCD. Consequently the master-bias image is now subtracted from the continuum image, before the latter one is used to trace the spectra. This solution seems to work.
· This is a problem that is more likely to occur with a multi-file instrument such as PMAS using the 4kx4k CCD; because, the bias level differs across the files.
The VIMOS extracted-images combination routine; p3d_cvimos_combine:
· Corrected a serious bug that would prevent the correct use of an input
· renormalization correction-array file (the keyword CORRFFILE). Also replaced the calculation of a mean telluric-line flux with a median.

Regarding the instrument support for VIMOS:
· Added a new feature to the combination routine (p3d_cvimos_combine).
· Flux-calibrated data are now re-normalized using a telluric line. This final normalization corrects for smaller inaccuracies in the data that are left after the flux calibration (which is performed using, e.g., IRAF). This new re-normalization can be switched off, and the telluric line that is used can be chosen freely (or automatically). The re-normalization can be done both per spectrum and per quadrant.
· The telluric-line fits are now illustrated in a plot that includes the raw data and the fit. One plot is created for each spectrum and each detector. The file is compressed automatically to save space.

Modified the implementation:
VLT/UT3/VIMOS (/VIMOS, /NVIMOS, /MVIMOS, /MNVIMOS):
· Data using the high (medium) resolution grism (HR [MR]) are now selected
· using the /VIMOS and /NVIMOS (/MVIMOS and /MNVIMOS) keywords. Data from
· before (after) the instrument reburbish in May-August 2010 must now use
· the /VIMOS and /MVIMOS (/NVIMOS and /MNVIMOS) keywords.

The IDL VM scripts:
· Made some minor corrections to how the code is executed using the IDL VM.
· The routine scripts (p3d_c*_vm.sh) would have returned an error regarding
· a missing environmental variable quot;pathquot;, which is never set, or used, in
· these routines. Removed the statement quot;cd $pathquot;. The script quot;p3d_vm.shquot;
· has prevented a correct use of the data output directory. The script no
· more changes directory to ${p3d_path} before launching the p3d GUI; this
· allows a correct use of the /CWD keyword.
· These scripts contain a large number of additional improvements.