Release Notes for HEAsoft 5.3.1

May 20, 2004


HEASOFT 5.3.1 is a software suite consisting of FTOOLS 5.3.1, FV 4.1.2,
XIMAGE 4.2.1, XRONOS 5.21, XSPEC 11.3.1, and XSTAR 2.1k. This document
contains notes about significant changes made since the last major
release of each.  All this software shares common build, installation
and initialization procedures.  Please see the files README.Q-AND-A,

For each of the HEASOFT subpackages below are listed tools and/or
features which are new in version 5.3.1. More information on FTOOLS,
XIMAGE, XRONOS, XSPEC, and XSTAR 2.1k can be obtained using the fhelp
utility.  Type "fhelp ftools" to obtain a full listing of all the tools
available, or "fhelp <sub-package-name>" to list all of the tools in a
particular subpackage, e.g., "fhelp asca".  Finally, type "fhelp <toolname>"
for more detailed help on a particular tool.  FV, XIMAGE, and XSPEC all
have online help available from within the program.  In addition, XIMAGE,
XSPEC, and XSTAR have TeX formatted manuals for their usage.


- genrsp: Fixed some minor TFORM and HDUVERS1 problems that triggered
  errors under fitsverify.

- dmprmf: Fixed bug which caused dmprmf to crash with a segmentation fault
  if the specified input file did not exist.


- modified the disk file driver (drvrfile.c) so that if an output
  file is specified when opening an ordinary file (e.g. with the syntax
  'myfile.fits(outputfile.fits)' then it will make a copy of the file,
  close the original file and open the copy.  Previously, the specified
  output file would be ignored unless the file was compressed.

- modified f77_wrap.h and f77_wrap3.c to support the Fortran wrappers
  on 64-bit AMD Opteron machines

- new group.c file from the INTEGRAL Science Data Center.  It fixes
  a problem when you attach a child to a parent and they are both
  is the same file, but, that parent contains groups in other files.
  In certain cases the attach would not happen because it seemed that
  the new child was already in the parent group.

- fixed bug in fits_calculator_rng when performing a calculation
  on a range of rows in a table, so that it does not reset the
  value in all the other rows that are not in the range = 0.

- modified the filename parser so that it accepts extension names
  that begin with digits, as in 'myfile.fits[123TEST]'.  In this
  case CFITSIO will try to open the extension with EXTNAME = '123TEST'
  instead of trying to move to the 123rd extension in the file.

- the template keyword parser now preserves the comments on the
  the mandatory FITS keywords if present, otherwise a standard
  default comment is provided.

- modified the ftp driver file (drvrnet.c) to overcome a timeout
  or hangup problem caused by some firewall software at the user's
  end (Thanks to Bruce O'Neel for this fix).

- modified iraffits.c to incorporate Doug Mink's latest changes to
  his wcstools library routines.  The biggest change is that now
  the actual image dimensions, rather than the physically stored
  dimensions, are used when converting an IRAF file to FITS.

- If a cfitsio calculator expression was imported from a text file
  (e.g. using the extended filename syntax 'file.fits[col @file.calc]')
  and if any individual lines in that text file were greater than
  255 characters long, then a space character would be inserted
  after the 255th character.  This could corrupt the line if the space
  was inserted within a column name or keyword name token.


- fmaskfilt: Set default value for ecrval, ecrpix, ecdelt when there are
  no wcs keywords in the event file (e.g. for INTEGRAL fits files).
  Enhanced to handle mask region which is smaller than that of the event
  list.  Fixed uninitialized status variable which generated the error
  "fmaskfilt2.2f : Error reading mask file" under Linux.


- fverify: Fixed error that caused it to list 'XTENSION' instead of 'EXTNAME'
  as the name of a keyword that should not be included in a primary array

- fimgcreate: Fixed a bug which caused fimgcreate to ignore input datafile
  parameters which start with the letter 'n' or 'N' (it assumed you were
  using "datafile=none" and fills the image with 0s instead). 

- fdiff: Fixed error in output NAXIS index

- spibkg_init: Added capability to use an additional source as input to
  initialize the SPI background models (previously only 3 were allowed, now 4).
  Made minor improvement to the SPIBACK option. This leads to template spectra
  which will usually be a slightly better representation of the actual detector
  background data.

- fstruct: modified to read the TLMINn and TLMAXn keywords as doubles instead
  of integers in case the values are greater than the range of a 32 bit
  integer.  Prints values in exponential notation if they are very large.

                                  FV / POW

FV version 4.1.2:

Changes to FV and POW since FV 4.0 (in the HEASOFT 5.3 release):


- Added support for Cartesian projection. 

- Added record capability for profile of FITS image. 

- Enhanced capabilities for printing and saving FITS image or plot, including
  the ability to preview the image before printing. 

- A row selection function was added to fv. User can select/de-select row(s)
  by clicking on the row index in the table with the mouse's left button (or
  clicking left button then right button to select row range). Row(s) also can
  be selected using selection condition and expression.  fv's plot, calculator,
  histogram and statistics tools now can perform on the selected rows. 

- Export command can export the selected rows and columns from a table to
  fits file or text file. 

- Delete command will now delete the selected rows and cols. 

- Added short cut on the selection panel to allow users access fv preference

- Enhanced support for ds9 image display. User can choose to display images
  or plots using either DS9 or POW as the primary display tool. 

- Added more XPA scripting commands for controlling fv from external processes,
  including create (create an image or table file or extension), export
  (export hdu to a Fits file or a text file), opentool (open skyview, catalog,
  vizier or ftools dialog panel) and preference (set up FV preferences). 

- Function buttons incorporated into the File Summary window to provide short
  cuts to common operations: 'Hist' (displays a histogram image of 1 or 2
  columns in a table), 'Plot' (plots table columns), 'Table All' and 'Table
  Select' (The first button displays all the columns in a table, whereas the
  second button allows the user to select which columns to display). 

- When displaying Hierarchical grouping tables, a new 'OPEN' button is
  available at the beginning of each row which can be used to open the
  corresponding group member file. 

- Can display and edit images that are compressed with the new FITS 'Tile
  Compression' algorithm. 


- Enhanced Print and Save capability on Pow image. 

- Added support for Cartesian Projection. 

- Allow user to save the image in POW display to one of these formats:
  bmp, jpeg postscript (default), png, pnm or tiff. 

- Allow user to reverse the functionality of the left and right mouse
  buttons within the POW display via POW's Preferences settings.
        left mouse button - control zoom
        right mouse button - control brightness/contrast

- Support new DS9 region file format. 

- Measure the distance between two points on a graph using the Ruler tool. 

- Flux and centroid values for a region of an image can be calculated with
  the Probe tool. 

- Plot an image cross-section with the Profile tool. 


- bcmppha: Corrected bug which cause bcmppha to segfault when input files
  containing  more than 350 spectra were used. These are typically the
  "MER" data, which may have ~10^3 spectra in the case of long, bright bursts.

- bodfluxhis: The BATSE Earth-occultation flux history files (with suffix
  "NHIS"), contain many (very nearly) duplicate points.  Previously, these
  were all over-plotted. Now, only one entry for each overlapping set of
  points is selected for output.

- bod2pha: Increased array sizes for all quantities read in from input fits
  file data from 1000 to 300000 to accommodate mission long and single step
  files.  Increased precision in tjd1 and tjd2 (times read in from the FITS
  file) to real*8.  Added selection of data using manual flags. These flags
  were set by the BATSE team to indicate problem data. Such flags can also
  be set by users if desired.

- bod2rmf: Added code that corrects the response for attenuation effects
  from the HEXEL window (as described in Harmon et al. 2002, ApJS, 138,149).

- vp_list.fits:  Modified to include more accurate viewing-period start and
  stop times.


- extractor:

  Fixed a few minor problems when the image coordinates are in detector space.If
  the region file is in detector coordinates then the PIXSIZE and NPIXSOU
  keywords are not set in the WMAP. The region extension has columns X, Y but
  they should be DETX, DETY since this is what the DM keywords claim are in use.

  Fixed inconsistency that arose when using a region filter at the same time
  as cuts in image coordinates specified as arguments to the input filename.
  The correct counts would be extracted but the attempt to write an image
  would fail.

  Fixed bug that showed up with XMM when using region files in detector
  coordinates.  The problem only arose if using set image detector and a
  region file for an instrument whose detector coordinates do not start at 1.

  Changed the defaults if no WCS keywords are given in the input event file.
  Now consistent with the FITS WCS paper.

  Used the value of TIMEUNIT for the units in lightcurves and GTIs. If the
  input file has no TIMEUNIT then look for the TUNIT keyword of the TIME column.

  Added more diagnostic keywords to the output WMAP. These relate the
  WMAP coordinates to sky coordinates in the case when these are different.
  The keywords may be helpful for downstream software.

- addspec: Updated help and default errmeth parameter for a change made some
  time ago to mathpha to allow the case of not calculating the error and just
  setting POISSERR=T in the resulting file. This should be the default because
  it is the option required for most modern spectra.

- grppha & rbnpha: Updated to search for SPECTRUM extension using 'HDUCLASn'
  keyword in addition to EXTNAME.  This allows grppha and rbnpha to work with
  INTEGRAL FITS files without explicitly specifying the extension.


- pcexpmap: Fixed bug in pcexpmap which caused it to generate an invalid
  exposure map under certain conditions (i.e. when an aspect time is
  accepted within a GTI [at time=t1, for example] and the aspect time
  just before this entry [which occurred at a time t0] occurred more
  than 1 second before the aspect time within the GTI [i.e. t1-t0 > 1 sec]).
  In most cases such large gaps do not exist between t1 and t0, i.e. good
  aspect times will start prior to the start of the GTI, but, for example,
  in rp800105n00 the good aspect time occurs at the start of the GTI. 



For full documentation on XIMAGE, refer to:

   * Swift XRT PSF problems corrected
   * Output from detect/fitsdet now conforms to fverify specifications
   * New options
      + centroid
         -> pixboxrad - Specify size of box in detector pixels
      + skyview
         -> size - Specify output image size
         -> fov - Specify output image field of view
         -> ra/dec - Specify output image center

For complete change history of XIMAGE see:



Minor upgrades:
   * The 'veN' file option now selects a GTI extension for use as
     exposure if the input file is an event list.
   * Maximum number of files that can be in a single series
     increased from 50 to 1000.

For complete change history of XRONOS see:


- Fixed segmentation fault under Mac OS X 10.3 (Panther).

- Increased accuracy of the binsize in the label written for light curve plots.

- Added support for Integral.


XSPEC 11.3.1 release notes:

Commands :

fakeit   - the randomization algorithm has been modified to use Gaussian
           instead of Poisson random numbers where appropriate for the

tclout   - added the cosmo and lumin options. The flux and lumin options
           write the error ranges if they were calculated

The output of show rate and tclout rate has been fixed so that the error is 
the correct uncertainty on rate. Previously, this error had been inflated if
there were channels with no counts.

Changes to models :

compbb   - The range of validity has been extended (from 0.1-70 keV) although
           the high energy thermal cut-off is not calculated so the spectrum
           may not be realistic at higher energies.

v(apec)  - options have been added (xset APECTHERMAL and xset APECVELOCITY)
           to set thermal and velocity broadening of lines.

New models :

b(v)apec - A version of the (v)apec model with velocity broadening as a free
           parameter. Thermal line broadening is automatically included.

gabs     - A multiplicative gaussian absorption line.

kerrd    - An optically thick extreme-Kerr disk model.

Markov-Chain Monte Carlo :

The MCMC code has been reworked so that chains are written to ascii files
as they are calculated. Previously calculated chains can be reloaded into
xspec. See the chain command for details.

The margin command uses the currently loaded chains to write out a multi-
dimensional probability distribution which can be plotted (in 1- or 2-D)
using plot margin.

Bug fixes :

Fixes to 11.3.0a - 11.3.0y are included with the exception of 11.3.0l, which
still requires a workaround.


Xstar Version 2.1k contains the following changes to v2.1j:

1) Added prinouts of level opacitites, and level populations to
   final printout if the print switch is set to 2.

2) Added a column to the printout of the file xout_detail.fits
   for the upp level index of each line.

3) Repaired and streamlined the printing of the file xout_detail.fits.

4) Added more informative statement when the code stops because
   the rate matrix overflows (ipmat too large).

5) Added rate type 42: Auger decay

6) Fixed arithmetic error which affected recombonation rate calculation
   when kT >> E_th

7) Added new data type (85) for photoionization resonances below threshold,
   along with new subroutine to calculate cross section (PEXS.f).

8) Streamlined the photoionization rate calculation (phint53)

9) Changed treatment of line damping, Voigt profiles.

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