pyXsis

Python X-ray Spectral Interpretation System

Toy python code for manipulating high resolution X-ray spectra

Acknowledgements: This python library owes it's inspiration to the Interactive Spectral Interpretation System written by J. Houck and J. Davis (creator of S-lang), as well as long-time users and contributors M. Nowak, J. Wilms, and the group at Remeis Observatory. Thank you also to the entire Chandra HETG group at MIT for personal help throughout the years with interpreting high resolution X-ray spectra.

Install instructions

You must have Astropy and Specutils installed.

I have a pending pull request to add the XraySpectrum1D object to specutils. For now, you will need to install my development version of specutils to run this version of pyXsis.

After installing Astropy, go to you favorite folder for storing development code and run the following:

mkdir specutils-dev
cd specutils-dev

git clone https://github.com/eblur/specutils.git .
python setup.py develop

git fetch origin
git checkout xrayspectrum_loaders

cd ..

Next download and install from the pyXsis repository:

git clone https://github.com/eblur/pyxsis.git
cd pyxsis
python setup.py install

Testing the installation

To run the test notebooks in pyxsis/tests/notebooks, you will need to download the test HETG data.

First, download the tar ball from https://doi.org/10.5281/zenodo.2528474

Next, copy the downloaded file to your pyxsis folder and unpack the tar ball:

tar -xvf pyxsis_test_data.tar

You're now ready to run the notebooks!

Dependencies

• Numpy Version 1.1 or later
• Astropy Version 3.0 or later
• Specutils development version from eblur

Quick start

import pyxsis
my_spectrum = pyxsis.XBinSpectrum.load('my_Chandra_HETG_file.pha')

import matplotlib.pyplot as plt
ax = plt.subplot(111)
pyxsis.plot_counts(ax, my_spectrum, xunit='keV')

Installing a development version of pyXsis

These instructions teach you how to create an Anaconda environment for pyXsis development.

conda create -n pyxsis-dev python=3
source activate pyxsis-dev
conda install numpy scipy matplotlib astropy

Go to the folder where you would like to keep your libraries. Then re-install specutils, as above.

mkdir specutils-dev
cd specutils-dev

git clone https://github.com/eblur/specutils.git .
python setup.py develop

git fetch origin
git checkout xrayspectrum_loaders

cd ..

Now clone and install pyXsis.

git clone https://github.com/eblur/pyxsis.git
cd pyxsis
python setup.py develop

If you use Jupyter notebooks, you can install the conda environment as a separate kernel, using the ipykernel package.

conda install ipykernel
python -m ipykernel install --user --name pyxsis-dev --display-name "pyxsis-dev"

When you are done playing with pyXsis, you can exit out the conda environment with:

source deactivate