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Intro

Sherpa is a modeling and fitting application for Python. It contains a powerful language for combining simple models into complex expressions that can be fit to the data using a variety of statistics and optimization methods. It is easily extensible to include user models, statistics and optimization methods.

What can you do with Sherpa?

  • Fit 1D (multiple) data including: spectra, surface brightness profiles, light curves, general ASCII arrays
  • Fit 2D images/surfaces in Poisson/Gaussian regime
  • Build complex model expressions
  • Import and use your own models
  • Use appropriate statistics for modeling Poisson or Gaussian data
  • Import new statistics, with priors if required by analysis
  • Visualize a parameter space with simulations or using 1D/2D cuts of the parameter space
  • Calculate confidence levels on the best fit model parameters
  • Choose a robust optimization method for the fit: Levenberg-Marquardt [lm], Nelder-Mead Simplex [nm] or Monte Carlo/Differential Evolution [mc].

Documentation

For detailed documentation see:

http://cxc.cfa.harvard.edu/sherpa

New Features in Version 4.5.1

No new features in Sherpa 4.5.1. This is a bug fix release. Please refer to the Sherpa 4.5.0 release notes for details on current features. Sherpa 4.5.1 provides a small number of bug fixes allowing Sherpa to build on newer systems.
  • Sherpa can now be built with the GCC 4.7 and 4.8 compiler suites.

  • Sherpa can now be built with clang on OS X.

  • Added library path and installation instructions for Macports.

  • Updated version number to 4.5.1 for this patch.

These bug fixes were contributed by Tim van Werkhoven of Leiden University. See the release notes NOTES

New Features in Version 4.5.0

  • Many updates for dynamic grouping functions.

  • The Sersic2d model has been added. This model is a generalization of the de Vaucouleurs profile (i.e., the exponent is allowed to be values other than 4).

  • A new function, sample_flux(), has been added to calculate the unabsorbed energy flux due to a Sherpa model. It returns a sample of parameters with a corresponding flux and a flux uncertainty for a model component or a combination of model components. The model components have to be previously defined and used in the fit. The samples are generated from the multi-variate normal distributions with the scales defined by covariance (if at the best fit) or supplied (as “scales”). The flux is calculated for each set of new parameters. The returned flux value is given by a sample’s median with the lower and upper quantiles defined by the confidence level supplied to the function.

  • To simulate X-ray spectra, the function fake_pha() has been updated to include background counts at the user’s discretion. If the user chooses to include background counts that had been read in with a previous PHA file, then the background counts are appropriately scaled, a Poisson draw is taken of the scaled background counts, and then that is added to the simulated source counts. (If there are multiple backgrounds, then the average of the backgrounds is added to the simulated source counts.)

  • Several corrections were made to formulas in the following sherpa.astro.optical models:

    AbsorptionEdge AbsorptionGaussian AbsorptionVoigt EmissionGaussian EmissionLorentz EmissionVoigt OpticalGaussian

  • See the release notes NOTES

Dependencies

The new Sherpa can be downloaded, built, installed, and used independently of CIAO. I/O support and plotting can be supplemented using PyFITS and matplotlib. The current (Sherpa 4.5.1) source tarball has the following prerequisites:

Compilers:

  • GCC compilers with gfortran, versions 3.4.5 or later

  • Sun Studio with f95 WS 10 or later

  • Xcode with gfortran 4.2.3 or later (disk images of gfortran for Mac can be found at http://r.research.att.com/tools/)

    • Mac OSX 10.8 Mountain Lion, Xcode 4.0 or later
    • Mac OSX 10.7 Lion, Xcode 4.0 or later
    • Mac OSX 10.6 Snow Leopard, Xcode 3.2 or later
    • Mac OSX 10.5 Leopard, Xcode 3.1, 3.1.1, 3.1.2, or 3.1.3 (Intel processors preferred)

Required:

Python 2.6 or 2.7 [py]:
 Python is an interpreted, interactive, object-oriented, extensible programming language.
NumPy 1.5.1 or later [np]:
 Powerful N-dimensional array object for Python.
FFTW 3.3 or later [fftw]:
 Fast fourier transform library speeds up Sherpa PSF model convolution. Be sure to build with “–enable-float” also.

Optional:

CIAO dmRegion Library 4.4 [reg]:
 The Sherpa region module accepts CIAO region filtering syntax parsed by the dmRegion library. Regions are two dimensional filters that can be used to include or exclude data points in a 2D data set.
DS9 5.6 or later [ds9]:
 DS9 is the SAO imager used for astronomical imaging and data visualization.
IPython 0.13 [ipy]:
 IPython provides a nicer interpreter interface with readline support compared to regular Python.
matplotlib 1.0.0 or later preferred [mpl]:
 Sherpa can use matplotlib for line and contour plotting and image visualization. For smooth behavior in Sherpa, set the configuration switch “interactive=True” in ~/.matplotlib/matplotlibrc.
PyFITS 2.3.1 or later preferred [pyfits]:
 Sherpa uses PyFITS as a FITS file reader backend.
WCS 3.7.0 or later [wcs]:
 The World Coordinate System library provides the transforms necessary to support the physical and world coordinate systems found in FITS file headers. Sherpa builds against the wcssub library http://tdc-www.harvard.edu/software/wcstools/wcssubs-3.8.7.tar.gz. (N.B. On some systems this will require the user to set the CFLAGS environment variable before building wcssub: "setenv CFLAGS -fPIC" in C shell, or "export CFLAGS=-fPIC" in the Bourne shell.)
XPA 2.1.9 or later [xpa]:
 Sherpa uses XPA applications (e.g. xpaset, xpaget) to communicate with DS9.
XSPEC 12.7.1 [xspec]:
 The XSPEC spectral models are available in Sherpa by linking to certain dynamic libraries found in an XSPEC installation.

Download

Current version 4.5.1 July 9, 2013

source tarball sherpa-4.5.1.tar.gz
Release Notes 4.5.1 NOTES
Release Notes 4.5.0 NOTES

For previous versions see downloads

Build and Install

To build and install the package, do the following

$ tar xzf sherpa-4.5.1.tar.gz
$ cd sherpa-4.5.1
$ python setup.py [config-vars] install --prefix=<dest-dir>

config-vars is an optional list of arguments in the format var=value that specifies where to find prerequisites required at build time. The following variables can be set

Variable Default
fftw_library_dir /usr/lib (only needed if in alternate location, e.g. /usr/lib64)
fftw_include_dir /usr/include (only needed if in alternate location)
wcs_library_dir None (if not given, World Coordinate System, WCS, module is not built)
wcs_include_dir None (if not given, World Coordinate System, WCS, module is not built)
reg_library_dir None (if not given, Region 2D filtering module is not built)
reg_include_dir None (if not given, Region 2D filtering module is not built)
fortran_library_dir None (may be needed to find libgfortran.so or libf95.a depending on how XSPEC was built)
fortran_lib None (‘gfortran’, or ‘f95’ depending on fcompiler )
xspec_library_dir None (if not given, XSPEC module is not built)
cfitsio_lib cfitsio (or ‘cfitsio_3.25’ depending on version found in XSPEC installation)
cfitsio_library_dir <xspec_library_dir>

NOTE: The version of gfortran used to compile XSPEC and Sherpa must be identical. This issue with gfortran has been known to cause compiler errors.

For example, to use the FFTW in /soft/fftw and the XSPEC library in /opt/local/headas/lib, the command to install Sherpa would be

$ python setup.py \
   fftw_library_dir=/soft/fftw/lib \
   fftw_include_dir=/soft/fftw/include \
   xspec_library_dir=/opt/local/headas/lib \
   cfitsio_library_dir=/opt/local/headas/lib \
   install ...

The setup.py script distributed with Sherpa uses the standard Python distutils package. For more information on using it, see Installing Python Modules.

Platforms

Notes about building Sherpa from source on various platforms

  • Mac OSX 10.6 Snow Leopard

    On Mac 10.6, there are various different flavors of Python.

    • The Python 2.6 that comes with the installation of OSX 10.6 is typically called Apple Python, located here

      /System/Library/Frameworks/Python.framework/Versions/Current

      This version is built as a three-way binary: i386, x86_64, and ppc.

    • The Python 2.6 disk image from www.python.org for OSX 10.6 is typically called python.org Python. It installs here

      /Library/Frameworks/Python.framework/Versions/Current

      This version is built as a two-way binary: i386 and ppc. Using this disk image of Python 2.6 can be problematic when building Sherpa from source on 10.6 because the default Mach-O architecture is x86_64.

    Apple Python or a Python installation built from source are the recommended options for building 64-bit Sherpa from source on Mac 10.6. The version of Apple Python is usually out-of-date, so a source build of Python + NumPy is preferred. Users are always free to investigate building fat binaries. It can be done!

  • Mac OSX 10.5 Leopard

    On Mac 10.5, there are again different flavors of Python.

    • The Python 2.5 that comes with the installation of OSX 10.5 is typically called Apple Python, located here

      /System/Library/Frameworks/Python.framework/Versions/Current

      This version is built as a two-way binary: i386 and ppc.

    • The Python 2.6 disk image from www.python.org for OSX 10.5 is typically called python.org Python. It installs here

      /Library/Frameworks/Python.framework/Versions/Current

      This version is built as a two-way binary: i386 and ppc.

    The default Mach-O architecture is i386, so a python.org Python installation or a Python installation from source are the recommended options.

Configuration Files

Sherpa comes with a configuration file “sherpa.rc”. This file is located in <dest-dir>/lib/python2.X/site-packages/sherpa/sherpa.rc. For a stand-alone installation, this file should be copied from source in to the home directory as “~/.sherpa.rc”. Be sure to indicate the IO and Plotting back-ends as “pyfits” and “pylab” depending on configuration.

matplotlib comes with a configuration file “matplotlibrc”. For smooth behavior with Sherpa, be sure to indicate “interactive=True” in ~/.matplotlib/matplotlibrc.

Environment Variables

If Sherpa is installed in a non-standard location, be sure to update the following variables accordingly.

PYTHONPATH

HEADAS (for XSPEC spectral tables) e.g. export HEADAS=<xspec_install>/spectral

References

[ds9]http://hea-www.harvard.edu/RD/ds9
[fftw]http://www.fftw.org
[ipy]http://ipython.scipy.org
[lm]Lecture Notes in Mathematics 630: Numerical Analysis, G.A. Watson (Ed.), Springer-Verlag: Berlin, 1978, pp. 105-116
[mc]Differential Evolution: A Simple and Efficient Adaptive Scheme for Global Optimization over Continuous Spaces, J. Global Optimization 11, Storn, R. and Price, K., 1997, pp. 341-359 http://www.icsi.berkeley.edu/~storn/code.html
[mpl]Hunter, JD (2007). Matplotlib: A 2D graphics environment. Computing in Science and Engineering. 9: 90-95. http://matplotlib.sourceforge.net.
[nm]Computer Journal, J.A. Nelder and R. Mead, 1965, vol 7, pp. 308-313. Jeffrey C. Lagarias, James A. Reeds, Margaret H. Wright, Paul E. Wright “Convergence Properties of the Nelder-Mead Simplex Algorithm in Low Dimensions”, SIAM Journal on Optimization,Vol. 9, No. 1 (1998), pp. 112-147. http://citeseer.ist.psu.edu/3996.html. Wright, M. H. (1996) “Direct Search Methods: Once Scorned, Now Respectable” in Numerical Analysis 1995 (Proceedings of the 1995 Dundee Biennial Conference in Numerical Analysis) (D.F. Griffiths and G.A. Watson, eds.), 191-208, Addison Wesley Longman, Harlow, United Kingdom. http://citeseer.ist.psu.edu/155516.html
[np]http://numpy.scipy.org
[py]http://www.python.org
[pyfits]http://www.stsci.edu/resources/software_hardware/pyfits
[reg]http://cxc.harvard.edu/ciao
[wcs]http://tdc-www.harvard.edu/wcstools
[xpa]http://hea-www.harvard.edu/saord/xpa
[xspec]http://heasarc.gsfc.nasa.gov/docs/xanadu/xspec