Solar abundances in xspec

Jeremy Sanders provided Solar abundances from Asplund, Grevesse & Sauval (2005) which I have added to abundances.dat in the develop version of xspec.

Update 9/8/09: Martin Asplund supplied values from his 2009 ARAA paper so I used them instead for the aspl abundance option.

light curves with extractor

Alex requested a way of better controlling the start time of a light curve created using extractor. I've added a new parameter lcstart which sets the time of the first bin (in spacecraft time units). This is checked into the development version as extractor v5.12.

cleansis

We have seen a few cases of observations of bright sources using Suzaku where running cleansis creates a hole in the image. Part of the problem is running with too high a log probability parameter but there is also a subtle error when iterating. Pixels which are already identified as bad and have their counts set to zero are still included when calculating the local background. This artificially lowers the estimated background hence increases the probability that a pixel will be flagged as bad.

I changed the algorithm so that pixels flagged as bad in previous iterations are ignored when calculating the local background. This change has been checked into the development version.

New release

HEAsoft 6.7 is now available. This includes XSPEC v12.5.1. The biggest change is in gain fitting which has been reworked as the preliminary step towards allowing the creation of response models. Response models will be created analogously to spectral models and will be used to either replace or augment response matrices.

This release is also the first which does not include XSPEC v11. This version has in practice not been supported for some time and it is getting increasingly difficult to ensure that it builds and runs on all systems.

XSPEC bug fixes update

12.5.0af	The zredden multiplicative model component is calling the same function as redden, and therefore its redshift parameter has no effect. Our thanks to Brian Refsdal for pointing this out. Report added on May 05, 2009.
12.5.0ag	When in setplot wave mode and the user's Xspec.init file entry for WAVE_PLOT_UNITS is set to angstrom, plot efficiency and plot icounts don't display due to a missing plot label error. Our thanks to Maurice Leutenegger for pointing this out. Report added on May 08, 2009.
12.5.0ah	Fix to sqrt(2) error in the definition of the thermal broadening used in APEC models. Our thanks to Irina Zhuravleva for pointing this out. Report added on May 21, 2009.
12.5.0ai	This adds a new C-callable function to provide access to the version string for users linking the XSPEC models library into their own programs. The function is declared in src/XSUtil/FunctionUtils/xsFortran.h, and has the prototype: int xs_getVersion(char* buffer, int buffSize); Report added on May 22, 2009.
12.5.0aj	The model command fails to parse expressions that are explicitly of the form: M(M1(A1)+M2(A2)+M3(A3)). Our thanks to Jeremy Sanders for pointing this out. Report added on May 22, 2009.
12.5.0ak	When soft limits are in use during fitting, the pegged parameter test should be comparing the actual value against the hard limits, not the adjusted value. Otherwise the parameter may in some cases peg too soon. Report added on June 08, 2009.
12.5.0al	The same sqrt(2) fix mentioned in patch 12.5.0ah is needed when thermal broadening is turned on for v2.0 NEI models. Our thanks to Richard Sturm for pointing this out. Report added on June 08, 2009.

xselect cleansis

Fixed a bug spotted by Ed Cackett that the iterate_clean parameter is not recognized. Just needed to add it to the xselect.key file.

Note that there are issues turning up using the probabilistic sisclean tool for bright Suzaku sources. There is a tendency for the core of the PSF to be removed. Suggested fixes are either to change the critical probability or turn the iteration off.

self-irradiated funnel

Pavel Abolmasov sent in his self-irradiated funnel model (Abolmasov et al. 2009) and I added an entry to the new models web page.

addascaspec

The perl script addascapec, which is actually useful for other missions in addition to ASCA, had a couple of problems which I've fixed. The default errmeth should have been POISS-0 instead of POISS-1 and this parameter was not being used when summing background spectra.

Lexicon of handy statistical methods

Andrew Gelman's statistical lexicon.

bug in thermal broadening

Irina Zhuravleva at MPE pointed out that the thermal broadening option in the xspec apec model gives a sigma which is a factor of sqrt(2) too large. Fortunately, I don't think has any science implications since there have been no observations capable of measuring this broadening.

update on 6/8/09: Richard Sturm points out there is the same error in the NEI code.

panda/epanda/bpanda regions

I've added support to cfitsio region filtering for the panda/epanda/bpanda regions produced by ds9. Note that this assumes only one azimuthal region and one annulus although the region specification itself allows multiple for both. Made corresponding changes in extractor though note that the FITS region extension written in this case is not covered by the standard which does not include these shapes.

Spectral file format standard document

I updated the PHA file standard document to try to make it clearer. I fixed an error in the type II example which had HDUCLAS3 and HDUCLAS4 inverted.

XSPEC bug fixes update

Here are the bug fixes from the last month. They can be found in the usual place.

12.5.0w	A new tclout option has been added to make it easier to retrieve the fit parameters' sigma values. The syntax for this option is: tclout sigma [<>:]n where n is the parameter number. If it is not a variable parameter or if the fit was unable to calculate its sigma, a value of -1.0 is returned. Report added on Mar 06, 2009.
12.5.0x	The model.dat entry for the vequil model is missing the parameter for Ar abundance, causing the vequil parameters which follow it to be misinterpreted in the code. (This bug does not affect the equil model.) Report added on Mar 06, 2009.
12.5.0y	The kerrconv convolution model code is still using the xspec11-only LMODDIR environment variable for locating the kerrtable.dat model data file. This should be modified for usage in xspec12, where LMODDIR doesn't exist. Report added on Mar 11, 2009.
12.5.0z	This removes an ambiguous reference build error specific to gcc-4.1.1 on the Solaris-2.9 platform. Our thanks to Dacheng Lin for pointing this out. Report added on Mar 26, 2009.
12.5.0aa	The diskir model goes to infinity when its rirr parameter = 1.0, which is also the default value of rirr's lower limit. Our thanks to Brian Refsdal for pointing this out. Report added on Mar 26, 2009.
12.5.0ab	The nsmax model function is only able to find its auxiliary files when it is run directly from XSPEC's model data directory (heasoft-6.x/spectral/modelData). Our thanks to Stephen Doe for pointing this out. Report added on Mar 31, 2009.
12.5.0ac	Fixes to a couple of obscure cases of gain parameter usage: If a gain parameter belongs to a response temporarily replaced by a dummy response, or a gain parameter is indirectly removed through the data command erasing its associated spectrum and response, the gain shift may still be applied to a response occupying its former spectrum and source number. This patch also improves the show response output. Report added on Apr 06, 2009.
12.5.0ad	The nthcomp model has an uninitialized variable for the case of input energies less than kT_bb/10^4, which may cause a crash to occur. Our thanks to Gulab Dewangan for pointing this out. Report added on Apr 14, 2009.
12.5.0ae	For those linking the models library into their own programs, the swind1 model crashes when outputing a warning message as it indirectly accesses a variable intended for use only in XSPEC. Our thanks to Stephen Doe for pointing this out. Report added on Apr 14, 2009.

Notes on using SWIG to import C++ in Python

As a test case using my heasp library which is being converted from C to C++. Created heasp.i file to define interface. Basically a concatenation of the heasp.h, PHA.h and PHAII.h files with the following at the top. Adding additional classes will just require cat'ing their *.h file to the end and adding the appropriate #include at the top. Note the %include of "std_string.i" which is required to make the string arguments work. Similar %include specifications will be required if other STL classes are arguments for methods.

%module heasp

%include "std_string.i"

%{
#include
#include
#include
#include
#include
#include
#include
#include
#include
#include
#include
#include

#include

#include "heasp.h"
#include "PHA.h"
#include "PHAII.h"
%}

The interface file is then converted to C++ using

swig -python -c++ -classic heasp.i

which creates heasp_wrap.cxx and heasp.py. These must then be combined with the *.o files to build a shareable library called _heasp.so (note that the _ prefix and .so suffix are required). Compiling heasp_wrap.cxx will require include files from python. On my mac the relevant flag is
-I/Library/Frameworks/Python.framework/Versions/Current/include/python2.5
and on the lab Linux network
-I/usr1/local/include/python2.5

On the mac the command to make the shareable library is
ld -bundle -flat_namespace -undefined suppress -o _heasp.so ${OFILES} heasp_wrap.o -L${HEADAS}/lib -lCCfits_2.1 -lcfitsio_3.12
and on Linux
$(CXX) -shared -o _heasp.so ${OFILES} heasp_wrap.o -L${HEADAS}/lib -lCCfits_2.1 -lcfi
tsio_3.13

The module is loaded into python by
>>> import heasp
On the mac this generates an undefined symbol ___eprintf. This may require an update of Xcode to fix. On linux (running python2.5) there are no problems. Example use is

>>> import heasp
>>> spectrum = heasp.PHA()
>>> spectrum.read('file1.pha',1,1)
>>> spectrum.disp()
>>> spectrum.write('test.pha')

chkarf

Updated and much simplified chkarf so it actually lists the correct keywords as mandatory. This tool really should just be a perl script - the current program is overkill.

using openMP in gcc

I'm testing out parallelization using openMP on an 8-core Linux box. To build xspec to support openMP options requires the hmakerc to be edited to add -fopenmp to CFLAGS, FFLAGS, and CXXFLAGS and -lgomp to be added to F77LIBS4C (I added it immediately before -lgfortran).

First test is in sumape.f to parallelize over the individual elements when interpolating the continuum and pseudo-continuum...

C$OMP PARALLEL PRIVATE(ien,limdown,limup,ihigh,energy)

C$OMP DO SCHEDULE(DYNAMIC)

DO ielt = 1, nmelt

...


ENDDO

C$OMP END DO

C$OMP END PARALLEL

The variables defined as private are to avoid threads overwriting variables being set and used by other threads.

Timing tests show that parallelization doesn't win enough in this case. Including the parallel directives slows a newpar down from 0.02 seconds to 0.4 seconds due to the overhead.

Computing with GPUs

There is web site all about using GPUs for general purpose computing. One particularly useful looking article goes into some of the options and issues of coding for GPUs.

problem with extractor5.09

In the course of Suzaku pipeline testing Lorella spotted a problem I introduced during the attempted speed-up of the fixwmp routine. Pixels with non-zero counts show up even within the part of the region which is supposed to be set to -1.

The particular case of Suzaku demonstrated a conceptual issue here. Those pixels showing up within the supposed excluded region are real events. What is happening is that the region is defined in sky coordinates but the WMAP is written in detector coordinates. I calculate a conversion to determine which WMAP pixels are within the image region however it is a time-averaged solution. In the pre-5.09 version the satellite attitude wobble results in some events being incorrectly excluded from the WMAP. It was these events that the 5.09 version actually included however they are potentially confusing to users.

The fix is checked in as v5.10.

xselect and Chandra grating data

Jane Turner reported that the current version of xselect fails to read Chandra HETG evt2 data. This is due to a bug in xsel_mdb.f which I think only matters for Chandra grating files.

XSPEC units for setplot wave

In v12.5 we switched the y-axis units under setplot wave to per Hz instead of per Angstrom. Since this has not been universally popular we have added an initialization option to decide between the two cases. This is available as patch 12.5.0t. That and other recent patches can be obtained from the usual place and are summarized below

12.5.0r	Fix needed for all etable model calculations. Our thanks to Roderick Johnstone for pointing this out. Report added on Feb 12, 2009.
12.5.0s	When the both the absori and pexriv models are loaded during the same XSPEC session, whichever model is loaded second will not work properly. Note: this bug originated in version 12.5.0. Report added on Feb 13, 2009.
12.5.0t	This adds an option for choosing Y-axis units when plotting in setplot wave mode. The selection is made by the WAVE_PLOT_UNITS entry, which has been added to the new version of the Xspec.init file. The units may now be specified in Hz (the default for version 12.5.0), or angstroms as they were prior to 12.5.0. This applies to plots of data, counts, and all variants of model and ufspec plots. Report added on Feb 19, 2009.
12.5.0u	Minor code changes mostly to clean up the messages reported when running XSPEC under the valgrind software tool. Report added on Feb 19, 2009.
12.5.0v	Multiplicative model components which are created with the mdefine command should not be multiplied by the energy bin widths. Our thanks to Roderick Johnstone for pointing this out. Report added on Feb 19, 2009.