xspec_emcee

emcee

emcee is a pure-Python implementation of Goodman & Weare’s Affine Invariant Markov chain Monte Carlo (MCMC) Ensemble sampler.

xspec

xspec is an X-Ray Spectral Fitting Package, distributed as part of the high energy astrophysics software package, HEAsoft from NASA.

xspec has its own implementation of the GW algorithm, but I find it somewhat difficult to use, so I created my own implementation, which gives more control over the chains.

INSTALL:

Quick Start

The recommended way to install the patched MCMC functions is to install the conda package available in the releases page. Download .conda file relevant for you operating system and install it using:

# use conda or mamba and run from a folder that contains the .conda file
mamba create -n xspec_env xspec -c ./ -c conda-forge
conda activate xspec_env

See the HEASoft conda page for more details on installing heasoft from conda.

The Following is more version-specific on how to install it, including patching the xspec source code.

Versions >= 6.35

For HEASoft >= 6.35, both heasoft and xspec are available as conda packages, and therefore modifying some files in the source tree is not possible. The MCMC patch is also available as a conda package:

Installing HEASoft from source

If you are installing heasoft from source, follow the steps similar to versions #Versions<6.35 below, but before running hmake, ensure to apply the patches by running the following in side the relevant folders for each file: patch -b < name.patch, then run hmake as described below.

Versions < 6.35

Prior to HEASoft 6.35, this repo stored the patched xspec source files. There are five of them. To install them follow these instructions: Choose the files relevant to your HEAsoft version by selecting the appropriate branch (master is the latest). Here I will work with v6.30.

• Download all updated 5 files: Chain.cxx, Chain.h, ChainManager.cxx, ChainManager.h, xsChain.cxx
• Place them in the right place inside the xspec source structure and recompile the relevant code:
  • Chain.cxx, Chain.h, ChainManager.cxx, ChainManager.h inside: heasoft-6.30/Xspec/src/XSFit/MCMC, and then inside heasoft-6.30/Xspec/src/XSFit, run: hmake and hmake install. Ensure that HEAsoft is initialized in the standard way before doing this. See their documentation.
  • xsChain.cxx inside: heasoft-6.30/Xspec/src/XSUser/Handler, then inside heasoft-6.30/Xspec/src/XSUser, run: hmake and hmake install
• Run the GW chain in the usual way.

Example:

Assuming the spectra and model have been setup and an initial fit is found, we do:

chain len 10000
chain burn 10000
chain walker 100
para walk 30
chain run mcmc.fits

This will run the chain, printing progress along the way:

• The chains are initialized using 0.5*sigma from the fit covariance, so a valid fit is needed.
• The progress prints:
  • percentage progress:
  • best statistic in the current run.
  • acceptance fraction. It should be around ~0.2-0.3
  • The last number is the adjustable a parameter in the GW algorithm (see the algorithm paper for details). It can be adjusted to drive the acceptance fraction towards a desired value. If the acceptance fraction is too small, a can be reduced (using chain temperature 1.5 for example) to increase the acceptance fraction.

* Initializing: Using the 0.5* Covariance **

** Done initializaing **
         5%  498.871    0.313333       2
        10%  498.868       0.307       2
        15%  498.869       0.342       2
        20%  498.866       0.342       2
        25%  498.868       0.328       2
        30%  498.865       0.308       2
        35%  498.872       0.327       2
        40%  498.866       0.324       2
        45%  498.866       0.346       2
        50%  498.87       0.331       2
        55%  498.871       0.285       2
        60%  498.868       0.252       2
        65%  498.867       0.301       2
        70%  498.867        0.33       2
        75%  498.869       0.308       2
        80%  498.869       0.317       2
        85%  498.866       0.321       2
        90%  498.873       0.312       2
        95%  498.868       0.318       2
       100%  498.867       0.299       2
  New chain tmp.fits is now loaded.