Synopsis
Convert a XSPEC save file to Sherpa commands *experimental*
Syntax
convert_xspec_script infile outfile Unlike most CIAO contributed scripts, there is no parameter file. If infile or outfile are - then stdin or stdout are used, respectively. The supported command-line flags can be found using -h/--help: --clean if the script should start with a call to clean --clobber will overwrite existing files --verbose will change the amount of screen output --version prints the script version --copyright prints the script copyright
Description
The convert_xspec_script tool will attempt to convert a XSPEC save file (often ending in .xcm) into Sherpa commands. The resulting file can then be run from sherpa or modified for further analysis.
This script is *experimental* and will not work for all XSPEC commands or datasets. The results should be considered as the start of a Sherpa analysis, as further work may be needed. Please contact the CXC HelpDesk if you find there are scripts which this tool will not convert.
Examples
Example 1
unix% convert_xspec_script savespec.xcm example.py model phabs*powerlaw
The script displays each model line it processes. With an input file (savexspec.xcm) containing:
method leven 10 0.01
abund angr
xsect vern
cosmo 70 0 0.73
xset delta 0.01
systematic 0
model phabs*powerlaw
0.0115491 0.001 0 0 100000 1e+06
1.98713 0.01 -3 -2 9 10
0.000185474 0.01 0 0 1e+20 1e+24
bayes off
then the script will produce:
from sherpa.astro.ui import *
set_method('levmar')
set_xsabund('angr')
set_xsxsect('vern')
set_xscosmo(70, 0, 0.73)
# model phabs*powerlaw
m1 = create_model_component('xsphabs', 'm1')
m2 = create_model_component('xspowerlaw', 'm2')
set_par(m1.nH, 0.0115491)
set_par(m2.PhoIndex, 1.98713)
set_par(m2.norm, 0.000185474, max=1e+20)
# Set up the model expressions
#
set_source(1, m1 * m2)
Example 2
unix% convert_xspec_script bestfit.xcm bestfit.py model phabs*apec unix% sherpa ... sherpa In [1]: %run bestfit sherpa In [2]: plot_fit(1, ylog=True, alpha=0.5) sherpa In [2]: plot_fit(2, overplot=True, alpha=0.5)
The example above shows how the converted script can be used in Sherpa. In this particular case the XSPEC save file was:
unix% cat bestfit.xcm
statistic chi
data 1:1 obs1.pi
data 1:2 obs2.pi
ignore 1:1-3,76-301 2:1-2,110-376
method leven 10 0.01
abund angr
xsect vern
cosmo 70 0 0.73
xset delta 0.01
systematic 0
model phabs*apec
0.252632 0.001 0 0 100000 1e+06
0.85796 0.01 0.008 0.008 64 64
0.359129 0.001 0 0 5 5
0.0175 -0.01 -0.999 -0.999 10 10
0.000618978 0.01 0 0 1e+20 1e+24
bayes off
and the converted file is
unix% cat bestfit.py
from sherpa.astro.ui import *
from sherpa_contrib.xspec import xcm
set_stat('chi2datavar')
load_pha(1, 'obs1.pi', use_errors=True)
load_pha(2, 'obs2.pi', use_errors=True)
xcm.ignore(1, 1, 3)
xcm.ignore(1, 76, 301)
xcm.ignore(2, 1, 2)
xcm.ignore(2, 110, 376)
set_method('levmar')
set_xsabund('angr')
set_xsxsect('vern')
set_xscosmo(70, 0, 0.73)
xcm.subtract(1)
xcm.subtract(2)
# model phabs*apec
m1 = create_model_component('xsphabs', 'm1')
m2 = create_model_component('xsapec', 'm2')
set_par(m1.nH, 0.252632)
set_par(m2.kT, 0.85796)
set_par(m2.Abundanc, 0.359129)
set_par(m2.redshift, 0.0175, frozen=True)
set_par(m2.norm, 0.000618978, max=1e+20)
# Set up the model expressions
#
set_source(1, m1 * m2)
set_source(2, m1 * m2)
Note that the conversion uses several routines from sherpa_contrib.xspec.xcm, which provide some Sherpa-like functions which simplify the conversion of the XSPEC script.
Example 3
CIAO 4.13 adds support for XSPEC convolution models, so the model expression
model phabs*cflux*powerlaw
will be converted to
# model phabs*cflux*powerlaw
m1 = create_model_component('xsphabs', 'm1')
m2 = create_model_component('xscflux', 'm2')
m3 = create_model_component('xspowerlaw', 'm3')
# Set up the model expressions
#
set_source(1, m1 * m2(m3))
and
model cflux*phabs*powerlaw
will create
# model cflux*phabs*powerlaw
m1 = create_model_component('xscflux', 'm1')
m2 = create_model_component('xsphabs', 'm2')
m3 = create_model_component('xspowerlaw', 'm3')
# Set up the model expressions
#
set_source(1, m1(m2 * m3))
Example 4
unix% echo "model phabs(apec)" | convert_xspec_script - -
model phabs(apec)
Unable to find parameter value for nH - skipping other parameters
from sherpa.astro.ui import *
# model phabs(apec)
m1 = create_model_component('xsphabs', 'm1')
m2 = create_model_component('xsapec', 'm2')
# Set up the model expressions
#
set_source(1, m1 * (m2))Convert the input from stdin - in this case the string "model phabs(apec)" - and write the output to stdin.
Known Problems
This script is intended to simplify analysis in Sherpa, but is not guaranteed to produce the same results. In part this is due to missing functionality, but other differences include
- differences in how Sherpa and XSPEC work,
- possible differences in your ~/.xspec/Xspec.init file (as of CIAO 4.12 Sherpa now uses this file),
- and differences between the XSPEC version and that of CIAO (12.12.1c for CIAO 4.15).
The script is also designed to parse the output of the SAVE command from XSPEC. It can handle hand-edited files but it is more likely to fail or work incorrectly.
Tied parameters
Comlplicated tie expressions, in particular those involving functions, are not guaranteed to be converted correctly.
Unsupported models
Only additive, multiplicative, and convolution models are recognized. Only models included in XSPEC 12.12.1c (used in CIAO 4.15) are available.
Unsupported commands
Some commands are ignored by the script, but others will cause the message
SKIPPING '...'
to be displayed while converting the file.
Multiple files
There is currently no support for files containing multiple data sets (e.g. PHA-II format files). In particular the {} syntax is not support for commands like DATA and RESPONSE.
Further help
Please contact the CXC HelpDesk if you have a problem with the script.
Changes in the scripts 4.15.1 (January 2023) release
Better handling of un-supported models. Please contact the CXC HelpDesk if you have XCM files with this problem. The script should once again be able to handle multiple groups (creating a model instance for each group).
Changes in the scripts 4.14.0 (December 2021) release
Updated for changes in Sherpa. Support XSPEC table models using atable, mtable, and etable expressions. Input and output can no be taken from stdin and stdout respectively by using the "-" name. Added the --verbose flag.
Changes in the scripts 4.13.0 (December 2020) release
The script is new in this release.
Notes
This script is not an official part of the CIAO release but is made available as "contributed" software via the CIAO scripts page. Please see the installation instructions page for help on installing the package.