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RELEASE NOTES FOR HEASOFT 6.27
March 26, 2020
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The HEASoft 6.27 release is driven primarily by updates to mission-
specific data analysis software (MAXI, NICER, NuSTAR, Swift, XTE et al.),
but includes many other enhancements and fixes.
As before, configuration-related changes throughout the package mean that
users who already have HEASoft installed will need to completely replace
their software installation; there is no clean way to simply overlay
this new release or to update an existing installation.
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CFITSIO
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Version 3.48:
- Now can handle parentheses in path names rather than automatically
interpreting them as output file specifiers.
- Fixed bug in imcompress.c that wasn't properly handling conversion
between float and double types when reading from a gzip compressed
float or double image.
- Fixed bug that was preventing use of bracket and parentheses symbols
in pathnames when opening multiple READWRITE files, even when
requesting no-extended-syntax usage. *This fix necessitates a
library interface version number change.
- Fixed bug in ffmnhd / fits_movnam_hdu to properly handle wildcard
syntax.
- Fixed bug in fits_open_extlist to handle filename[EXT] syntax
properly. The hdutype parameter may now be null. More documentaion
for this function is in cfitsio.tex.
- Added new function fits_copy_hdutab to create a new table with the same
structure as an existing table.
- fits_copy_col / ffcpcl handles long long integer data types more
natively to prevent precision loss.
- histo.c routines now recognize integer columns that have been scaled by
TSCALn keywords and may be closer to floating point type.
- Added backward compatibility for very old Rice compressed files which
were not using the ZVAL2 keyword in the way that later became standard.
- Change made to cfitsio.pc.in to prevent forcing downstream libraries
to link against cfitsio's dependencies when using pkgconfig.
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CCFITS
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- Converted all cases of catching std::bad_cast exceptions from
by-value to by-reference.
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HEASP
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General:
Made arf, pha, and rmf classes a bit more tolerant by allowing
reading of files where extensions are identified only by HDUCLAS*
keywords.
Replaced deprecated auto_ptr by unique_ptr.
Added SPneedVecCol routine to check whether a column should be vector
or scalar.
Changed SPcopyKeys so it only copies keywords that do not already
exist in the target extension. This prevents overwriting keyword
values that have been set by the tool calling the routine.
grouping:
Changed the grouping class to include separate grouping and quality
vectors instead of combining them in a single flag vector. Made
corresponding changes to methods.
Fixed bug which was incorrectly rejecting binning factors of -1 in a
binning text file.
pha:
Fixed a bug in convertUnits() which prevented the conversion working
in the case of input fluxes in ph/cm^2/s/keV
In rebinChannels set the grouping identically to 0 rather than 1 for
consistency with the standard since a GROUPING keyword will be
written.
Changed setting of output quality to be bad if either any input
channel making the bin is bad or if phafile grouping is being used
any channel in the grouping pha is bad.
arf:
Added handy routines to return the extension numbers of SPECRESP
extensions in a file and the type of an extension.
arfII:
Made recognition of arf extensions more flexible in NumberofARFs.
rmf:
When writing output files change N_GRP and CHANNEL to J format if required.
Fixed out-of-bounds writes in cases when the F_CHAN and N_CHAN
vector columns are longer than N_GRP.
Modified rmf::read so that the EBOUNDS data is first read into a
separate rmf object so it can test for consistency between MATRIX and
EBOUNDS keywords such as CHANTYPE and INSTRUME. If inconsistencies are
found then messages are written to SPreportError so the calling program
can check for them. The keywords from MATRIX take priority over
those from EBOUNDS.
Add handy functions to return vectors of extension numbers of
EBOUNDS and MATRIX extensions.
Changed rmf compression criterion to only include elements with
values > LO_THRES instead of >= LO_THRES.
Write EBOUNDS and MATRIX energy columns as D instead of E to avoid
precision issues with high-resolution optical/UV spectra.
table:
Changed ENERGIES columns from single to double precision.
Fixed a bug in convertUnits() which prevented the conversion working
in the case of input fluxes in ph/cm^2/s/keV
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ATTITUDE
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- prefilter:
Updated to support POSITION and VELOCITY inputs; accepts units of
m and km (m/s and km/s)
Incorporated the new magnetic field model of IGRF v13 (released
December 2019); going back to the year 2000, use full degree-13
precision of published model instead of degree-10 truncation;
differences expected to be less than 0.01%
Prepared for configurable columns=ALLV4 without losing backward
compatibility
Added XYZMAGAUX subroutine which computes extra magnetic quantities
Added new derived columns relating to magnetic field, view directions
and earth viewing; these are optionally produced if columns=ALLV4
(however, compatibility with prefilter v3 is maintained by default):
MAGFIELD MAGFIELD_MIN MAGVECT MAGVECT_POL ZENITH_ANGLE EAST_ANGLE
NORTH_ANGLE BEARING_ANGLE EARTHPNT_LAT EARTHPNT_LON EARTHPNT_RANGE
Fixed bug in dependency ordering which led to segfault; now
derived->coordquat is initialized with pointing instead of RA/DEC/ROLL
Added MAG_ANGLE = angle between pointing direction and magnetic field
Added more powerful ability to include or exclude columns from the
selected list
Support for attfile == NONE for HaloSat (ATT in .orb file)
Addition of LOCAL_TIME derived column
- geomagterp (new task): New tool for interpolating geomagnetic
quantities; the CALDB portion is not ready yet, so for now it's
basically a glorified finterp
- tristarid: Updated TDISP keywords for rates in source catalog
- Updated tasks to allow longer filenames
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FIMAGE
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- flst2im: (v1.4.1) Added support for columns scaled with non-integer
TSCALn keywords
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FUTILS
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- fdiff: Added support for TLONGLONG 64-bit integers
- finterp:
Check for TLONGLONG type
'sortkey2' parameter can be an expression
Improved error output and documentation
Fixed bug in handling of new sortkey1=(expr) function with tcheck=YES;
tcheck is now disabled when expressions are used
Relaxed requirements upon matching input and output column properties
when they are not needed; removed restrictions on how FITS filenames are
specified; the extension number is no longer required if the 'first
table extension' is acceptable; added ability to rename and/or change
data type of source column names, as documented in the help; preserves
compatibilty with existing usage
Added more checking of output columns and make sure any T<col>n
properties of existing columns aren't accidentally preserved;
Fixed bug in 'copyall' case when writing existing file
Fixed bug when column exists in output but is not last column
Fixed bug in which column number is used for backward compatibility;
allow copyall=COPYBEFORE and copyall=COPYAFTER for more flexibility
in transferring input file to output
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FV
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- Fixed crash when plotting image tables
- Fixed crash stemming from incorrect WCS initialization
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HEAGEN
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- barycorr:
In the case where TSTART & TSTOP are not in the header, set
tstart=tstop=TIMENULLVAL to prevent trying to write these keywords.
This problem was triggered on macOS 10.15 when using a non-Xcode
compiler suite (MacPorts, Homebrew).
(heautils library) HDget_frac_time(): Initialize valuei & valuef
to avoid returning an undefined value (to e.g. barycorr) when
TSTART & TSTOP are missing
Handle Swift UVOT event files and Swift MAGHIST files (output of
uvotevtlc)
Document (and warn) about .gz input and output files
- ftadjustgti: Now uses fits_open_extlist()
- xrtraytrace: Fixed bug that used back-side mirror reflectivity
in place of precollimator reflectivity in two places; fixed
bug that retrieved MINENERG and MAXENERG keywords redundantly
after FITS file was closed; fixed bug that truncated at 7 the
number of interactions per photon path written to the PATHCODE
column in the output events file; this number is now 8, as
intended.
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HEASARC
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- extractor: Fixed trap of no xcolf/ycolf in w_events. Moved
correction of time for TIMEPIXR to after the time filtering.
This may make small differences for missions which do not use
TIMEPIXR values of 0.5 but does make the filtering consistent
with that from ftselect.
- fadmap: Path/filename corrections to COS-B/SAS-2 CALDB; corrected date
errors introduced by Y2K updates
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HEASPTOOLS
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- Fixed all heasptools so that output files starting with an exclamation
mark are handled correctly.
- ftgcorrmf, ftmarfrmf, ftrgsrmfsmooth, ftrsp2rmfarf, ftstripnegchan:
Use SPcopyKeys for the EBOUNDS extension as well as the MATRIX
extension.
- ftmkrsp: Trapped case of an input energy bin with no response groups.
- ftsdss2xsp: Fixed check of PLATEID keyword - it is in the primary
header, not the COADD extension.
- genrsp (wrapper to ftgenrsp): Fixed conditional parameter prompts
- rbnrmf (wrapper to ftrbnrmf): If a binfile has been specified set
cmpmode=binfile; revised to reflect ftrbnrmf prompting behavior
(also ftrbnrmf help file): always prompt for cmpmode, and use it
to determine prompting for binfile & nchan; if an ebinfile is
specified, pass ecmpmode=ebinfile; otherwise pass ecmpmode=linear
and the ebfact value.
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HEATOOLS
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- ftdiff: Check for TLONGLONG data type
- ftimgcalc: Use fit_get_eqcoltype to more accurately reflect
data type of image (could be 'float-like' if BSCAL is used)
- ftmgtime: Now uses fits_open_extlist(); added compatibility layer to
support mgtime's idiosyncracies for future mgtime wrapper to ftmgtime
- ftsort: Handle TLONGLONG 64-bit integers in input columns; work with
non-integer TSCALn values; relocated fits_copy_hdutab to CFITSIO;
fixed case of outfile=infile where the specified column doesn't exist
- ftleapsec: Factored out leap second retrieval code into its own Perl
library (see above)
- fitsverify (standalone ftverify variant): Use fits_open_diskfile (via
ifdef) rather than fits_open_file per a user request. This allows for
file paths with special characters (e.g. brackets) that would otherwise
fail; note that this also necessitates omitting the call to
fits_parse_rootname (via ifdef).
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XRONOS
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- All tasks updated to fix memory faults occurring under recent Debian-
based systems (e.g. Ubuntu 18.10 and newer)
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XSELECT
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- Fixed bug in cpd command which could cause a confusing error message
if immediately preceded by some other set command.
- (xsl_filter_intensity) Considerable simplification due to using (new)
premax and postmax parameters for maketime.
- Minor rearrangement for some variables which were in the wrong common
blocks; changed to initialize all global variables with some
rearrangement to match up with common block order in xselvar.inc;
Removed unnecessary include of xselect.h and added one of cfortran.h;
added missing Common_AppInit prototype; replaced call of close by the
(correct) call of fclose; changed the READ logical to EVREAD for
clarity; these changes fix an error restoring saved sessions.
- Added support for HaloSat event files.
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XSPEC
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HEASoft 6.27 includes Xspec 12.11:
New Models:
ismdust - Extinction due to silicate and graphite grains.
olivineabs - Extinction due to olivine grains.
agnslim - AGN super-Eddington accretion model.
zkerrbb - Redshifted version of kerrbb.
thcomp - Thermally comptonized continuum convolution model.
logconst - Convert normalization to log units.
log10con - Convert normalization to log10 units.
Updated Models:
Using the new 201 tabulated temperatures v3.0.9 AtomDB files
for apec models. These CEI files reduce potential interpolation
problems (see http://atomdb.org/interpolation/index.php).
The interpolation scheme can be switched between log and linear
interpolation using xset APECLOGINTERP. Another option to reduce
interpolation errors is provided by xset APECUSENEI which
switches all calculation of CEI spectra through the NEI
code. This is slower but can be used to check calculations. To
recover the older v3.0.9 files use xset APECROOT 3.0.9_51. If
you do this and also want to use NEI models then you also need
to use xset NEIAPECROOT 3.0.9.
The diskline, rdblur, kdblur, kdblur2, laor, laor2, kerrconv,
kerrdisk have all been sped up using a new FFT-based convolution
routine.
The xscat model has been updated to extend the range of the Rext
parameter for MRN and ZDABAS options from 0-199 arcsec to 0-236 arcsec.
Major overhaul to code calculating statistics. Main visible
change is that each spectrum can have a different fit statistic
but there is only a single test statistic.
Added support for responses which have been split into parts
with different resolution. This is very effective for responses
which have high resolution but long tails down to low energies. In
the case of the XRISM Resolve instrument this will provide speed
increases of up to an order of magnitude. Note that if a file
contains multiple response extensions then XSPEC will read and use
them all unless a response extension is specified using e.g. resp.rsp{n}.
PyXspec v2.0.3:
- Plot values can now be retrieved from the individual additive
components within a model, using the new Plot.addComp() method.
- Added Fit.nVarPars attribute to perform the equivalent of standard
Xspec's "tclout varpar".
- Added access to standard Xspec's "rerror" command (for running the
"error" command on response parameters. This is now available by
passing a second (bool) argument to the Fit.error() method.
See also:
https://heasarc.gsfc.nasa.gov/lheasoft/xanadu/xspec/issues/issues.html
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XSTAR
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Xstar v2.54a:
- New in xstar version 2.54a is the inclusion of radiative excitation.
The rate of radiative excitation for all bound-bound transitions are
calculated and then multiplied by a factor of 1-cfrac. So, if cfrac=1 the
effective rate is zero and results from previous versions are recovered.
The effects of Thomson scattering as an attenuation process in the continuum
have now also been included, and the same 1-cfrac multiplier is used so that
previous results can be recovered.
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ASCA
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- ascaarf, ascaexpo, ascalin, fmosaic, gisrti, sispi: Updated to use
GSL/FGSL random number generator
- cleansis, faintdfe: Updated to use GSL/FGSL gamma function and auxiliary
routines
- ofaintdfe: Removed this deprecated task
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EXOSAT
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- tkexomerge: Altered window parenting to make children windows visible
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MAXI
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- mxdownload_wget: Added new ATT data types to downloadable products;
force gmtime() to use four-digit year
- mxextract: Avoid writing repeats of STDGTI rows; replaced printf with
headas_printf output
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NICER
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NICERDAS v007:
- nicerl2:
Fixed crash when mkfile is specified but gzipped version does
not exist; also changed check for missing $indir, previously
reported as a missing file
Added parameter 'niprefilter' which re-runs niprefilter task
if set to YES (additional new parameters orbfile, attfile,
prefilter_columns)
- nicerpi, nicertimecal, nicertimeconv, nimaketime, niprefilter,
niprefilter2:
Changes to fix the timegm() Y2020 "trap": This affects routines
that use Perl's Time::LocalTime::timegm() function:
http://blogs.perl.org/users/grinnz/2019/07/the-timelocal-trap.html
For NICER, which uses timegm() for the year 1970, this would cause
problems after the year 2020, as timegm() treats the year entry of
"70" as meaning 2070 instead of 1970, when the run date is after
the year 2020.
- nicerpi: Bubble pigain and pioffset parameters up to 'nicerpi' level
- nicertimeconv: Use HeaSoftLeapSec library version of NicerTime.pm;
fixed bug in output of GPS time (offset of ~20 sec); better handle
leap second transitions; output of MJD
- nimpumerge: Pass history parameter to subtasks
- niprefilter: When writing NULL columns (missing APID) use same
column-ordering as normal; Added ability to re-run prefilter
and update .mkf file in place using RUNMODE=UPDATE;
Fixed fatal bug in handling of global start/stop time from MPU
housekeeping; Fixed bug in handling of vehiclefile=NONE;
Be more careful about preserving other extensions of infile;
Fixed bug of copying keyword comments when runmode=UPDATE
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NUSTAR
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NuSTARDAS V1.9.0:
- This is primarily a quality-of-life upgrade for the NuSTARDAS.
The two main additions are: (1) Add the ability to save the
barycenter-corrected event files in the output directory when
barycorr=yes. Previously the user had to use cleanup=no to retail the
barycenter-corrected event file, which also stored a number of other
intermediate files. This allows for a more streamlined analysis
approach for timing observations; (2) The "PRIOR" column is now
preserved by default when producing the cleaned event files. This
column is useful for recovering the time-dependent livetime on
sub-second timescales and for high-rate observations. Please see
the NuSTAR Software User's Guide for more details.
There are also several minor bug fixes and other improvements:
- nupipeline: 1) when barycorr=yes and existage=3: updated the
'nuproducts' run setting the orbit file to the "attorb" file;
2) updated the 'nuproducts' run with `write_baryevtfile=no'.
- nuproducts: 1) added new input parameter `write_baryevtfile' to
optionally save the barycenter-corrected event file when barycorr=yes;
2) added an internal check to make sure that pilow, pihigh, pilowarf,
pihigharf, grppibadhigh, grppibadlow are integer numbers; 3) added an
internal gunzip of input mastaspectfile (to speed-up processing).
- nuscreen: added the "PRIOR" column to the list of columns that are
preserved by default when the cleaned event files are created.
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ROSAT
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- detect: Updated to use GSL/FGSL gamma function and auxiliary routines
- pcecor, pctcor, pcpicor, pcsasscor: Retired these deprecated tasks;
no longer needed since ROSAT data has been reprocessed using the
necessary corrections (i.e. with SASS version SASS7_8)
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SUZAKU
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- xisarfgen: Updated to support PHAFILE==NONE
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SWIFT
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BAT:
- batdetmask, bat-burst-advocate, batsurvey, batsurvey-detmask:
Changes to fix the timegm() Y2020 "trap": This affects routines
that use Perl's Time::LocalTime::timegm() function:
http://blogs.perl.org/users/grinnz/2019/07/the-timelocal-trap.html
- batcelldetect:
MPFIT: Bug fixes for two-sided derivative mode (buffer overflow
avoidance as well as correct two-sided calculation)
UVOT:
- uvotmaghist, uvotproduct, uvotsource: Improved region validation
for UVOT photometry/light curves.
- uvotproduct: Install uvotproduct ds9 v7 grid file in REFDATA
XRT:
- xrtgrblc: Modified XRT pipeline with correct settings to match
revisions to nH code
- xrtgrblc, xrtgrblcspec: Added support for high resolution HI4PI
all-sky nH map with nhmap=2
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XTE
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- hxtrsp, pcarsp: Updated to call ftrbnrmf instead of rbnrmf
(rbnrmf is merely a wrapper to ftrbnrmf)
- pcaextspect2:
Changes to fix the timegm() Y2020 "trap": This affects routines
that use Perl's Time::LocalTime::timegm() function:
http://blogs.perl.org/users/grinnz/2019/07/the-timelocal-trap.html
Also: bug fix for C-preprocessor macro expansion error
- trans2fits: New wrtparm=O option to create OGIP-compatible event
files (mostly cribbed from xenon2fits work several eyars ago);
further mods to simplify code and to write new output columns that
counts various interesting flags
- addshots, addsine, fakelc: Updated to use GSL/FGSL random number generator
- xenon2fits: (O)GIP output format now agrees with trans2fits
- Removed buggy and erroneous clause meant to deal with empty GTI
entries, and other overzealous GTI checking
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MISC.
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- Dropped support for Cygwin in favor of Windows Subsystem for Linux (WSL)
- Fixed bugs in the DESTDIR mechanism
- HEASoft now includes the GSL & FGSL libraries, and therefore GNU Fortran
compilers older than v5.x are unsupported.
- PGPLOT:
Updated PGPLOT dynamic library build to link in PNG library (if
available); this aids external packages (e.g. ISIS) using our libpgplot
by allowing the PNG dependency to be inherited.
SVG driver: improved support for Microsoft Edge SVG implementation
- Fixed history keyword writing for long (>72 char) lines;
some characters were being lost using the previous algorithm