Some of the codes that I have developed over the years are published in my github site. I am publishing them for the sake of reproducibility of the published research, and also that someone may find them useful.

Documentations of the codes is usually embedded within the code. From time to time, I write short posts to highlight useful features:

  • aztools: A collection of python tools for spectral/timing of X-ray data.
  • fqlag: A python library for modeling time series (light curves) to measure the Fourier frequency-dependent power and time lags using Gaussian Porcesses.
  • xspec_emcee: Affine Invariant Markov chain Monte Carlo (MCMC) Ensemble sampler in XSPEC
  • azTcl: Spectral modeling scripts in tcl to run inside xspec
  • gr: Ray tracing code in the curved space-time of for General Relativity

aztools

This is a collection of python tools that I have been using over the years in the analysis of Astronomical time series and X-ray telescope data. It handles light curves from X-ray satellites, calculated power and cross/spectra, phase/time lags and related products.

Some of the functionality in aztools.data_tools can be useful in reducing and calibrating X-ray data from common X-ray telescopes. They organize calls to heasoft functionality and allows for reducing multiple datasets in parallel for example.

Examples of using the aztools package can be found in the relevant posts, and in the notebooks associated with published papers.

fqlag

fqlag is a python library to characterize the variability in the frequency domain of light curves that are not continuously sampled. This supersedes the plag library, with a different implementation that is more stable during the calculations.

Both libraries implement the method presented in Zoghbi et. al. (2013) paper (Astrophysical Journal; 2013. 777. 24) to calculate periodogram and time/phase lags in the frequency domain from unevenly-sampled light curves.

The following are two examples of using fqlag:

xspec_emcee

This is an implementation of the Goodman & Weare’s Affine Invariant Markov chain Monte Carlo (MCMC) Ensemble sampler in XSPEC, which 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 difficult to use, and sometimes fails to converge, so I created my own implementation, which gives more control on the MCMC chains.

azTcl

This repository contains a collection of scripts written in tcl to be used within XSPEC, the X-ray spectral modeling package. It contains several useful functions that streamlines some of the xspec functionality. Examples of the functions include:

  • az_scan_en_norm and az_sim_dchi2: which can be used for scanning fit residuals for spectral emission or absorption lines and assessing their significance.
  • az_calc_errors: Calculate the uncertainties on the fit parameters, making sure to restart if a new fit is found, save progress, and save the final results in clean manner.
  • az_rand_pars: randomize the parameters given the covariance from the best fit, or give a loaded MCMC chain.
  • az_rand_plot: Plot a set of models whose parameters are randomly-selected from the best fit parameters and their covariance.
  • az_save_pars: return a string ($res) that has the current parameters, so that they can be loaded again quickly by doing newpar $res.
  • az_best_chain_pars: return a string ($res) of the best parameters from a loaded chain. These parameters can be applied to the model by doing: newpar $res.
  • az_plot_unfold: a clean and easy function to plot the unfoled data, model and their residual and ratio to a veusz-ready file.
  • az_free_params: returns a list of free parameters.

gr

A ray tracing code for simulating light rays around a black hole implemented in C++ using gsl. This solves the partial differential equations of the motion of a photon in curved space-time to track how the photons move from around the black hole to the detecting telescope.