Skip to content
Branch: master
Go to file
Code

Latest commit

Files

Permalink
Failed to load latest commit information.
Type
Name
Latest commit message
Commit time
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 

README.md

psfMC

MCMC 2D surface brightness modeling for quasar / host galaxy decompositions

Usage is provided in docstrings, and an example model is provided in the examples directory. My Ph.D. thesis contains a more detailed discussion of the problem (simultaneous modeling of quasar point sources and host galaxies) and why I have made specific design decisions. My dissertation is available open-access at the following URL:

[Markov Chain Monte Carlo Modeling of High-Redshift Quasar Host Galaxies in Hubble Space Telescope Imaging] (http://repository.asu.edu/attachments/126037/content/Mechtley_asu_0010E_13571.pdf)

A journal article is forthcoming, but if you use psfMC in the meantime, please cite:

[Mechtley, M. 2014, PhD Thesis, Arizona State Univ.] (https://ui.adsabs.harvard.edu/#abs/2014PhDT.........1M)

Recent Changes and Notes

The current master branch is a beta release (until I finalize formal unit tests). I've used it myself extensively, but please be aware that there may still be bugs lurking around.

Beta release 2.0b1 is a backwards-incompatible release that switches to emcee for sampling (and is compatible with Python3). The pymc requirement has dropped entirely, as I now also store trace databases as a FITS table and handle the priors myself in a more lightweight manner. Note that because priors in psfMC.distributions now wrap scipy.stats distributions directly, some parameter names have changed (e.g., Normal now expects loc= and scale= instead of mu= and tau=).

The rationale behind such a large change is that the Affine-Invariant ensemble sampler used by emcee is much more efficient for this particular problem (high-dimensional parameter space, reasonably convex single-mode posterior). Traditional Metropolis-Hastings chains required 50,000 samples or more of burn-in each to approach convergence, severely limiting the number of chains that could be used, and thus our confidence in the final result. The sampler now reliably approaches convergence with a similar number of total burn-in samples (e.g., iterations=250 * nwalkers=200 = 50000), but the ensemble sampler means this only has to be run once, rather than once for each chain. The large number of walkers replaces the primary purpose of multiple independent chains in the previous implementation: to improve our confidence in convergence.

As a side effect, the sampling is now overall faster (takes less time to run the same number of samples), since emcee is a lightweight sampler only and doesn't attempt clever caching / lazy evaluation like pymc (which the previous pymc implementation was not taking advtange of anyway).

Beta release 1.0b5 adds a new analysis submodule. FITS image production has been moved there, and various statistical and plotting methods have been added for analyzing posterior chains. This includes MCMC covariance corner plots via Dan Foreman-Mackey's corner.py module. Also includes two new command line scripts: corner_plot and plot_chain to generate these plots from a terminal.

Dependencies

The software depends on the numpy, scipy, emcee, astropy, and six (for Python 2 backward compatibility) modules. Additionally the matplotlib and corner modules are required for posterior analysis plots.

The pyregion module is optional but strongly recommended for ease of masking out foreground or background objects unrelated to the quasar being modeled.

The numexpr module is also optional, and is used to parallelize certain calculations (generating Sersic profiles), providing a slight increase in overall speed.

Installation

I only test/support Anaconda, use other Python distributions at your own risk. Note: everything else is included with the default Anaconda distribution. conda install --channel astropy emcee pyregion corner pip install git+https://github.com/mmechtley/psfMC.git

About

MCMC 2D surface brightness fitting for quasar host galaxies

Resources

License

Languages

You can’t perform that action at this time.