PyFstat

This is a python package providing an interface to perform F-statistic based continuous gravitational wave (CW) searches.

For documentation, please use the wiki.

In the examples, we have a number of scripts demonstrating different use cases.

Installation

python installation

This package works best with python3.5+, with higher versions to be required soon. While many systems come with a system wide python installation, it can often be easier to manage a user-specific python installation. This way one does not require root access to install or remove modules. One method to do this, is to use the conda system, either through the stripped down miniconda installation, or the full-featured anaconda (these are essentially the same, but the anaconda version installs a variety of useful packages such as numpy and scipy by default).

The fastest/easiest method is to follow your OS instructions here which will install Miniconda.

For the rest of this tutorial, we will make use of pip to install modules ( not all packages can be installed with conda and for those using alternatives to conda, pip is more universal).

This can be installed with

conda install pip

install PyFstat the easy way

Currently, the easiest way to install PyFstat is to point pip to this git repository, which will give you the latest master version:

pip install git+https://gitlab.aei.uni-hannover.de/GregAshton/PyFstat

or, if you have an ssh key installed in this gitlab instance:

pip install git+ssh://git@gitlab.aei.uni-hannover.de/GregAshton/PyFstat

(The release on Zenodo is outdated and might not even install depending on your python version. New Zenodo and/or PyPi releases are on our to-do list.)

See further down for installing manually from a local git clone.

Dependencies

PyFstat uses the following external python modules, which should all be pulled in automatically if you use pip:

• numpy
• matplotlib >= 1.4
• scipy
• ptemcee
• corner
• dill
• peakutils
• pathos
• tqdm
• bashplotlib
• lalsuite

Optional

• pycuda, required for the tCWFstatMapVersion=pycuda option of the TransientGridSearch class. (Note: 'pip install pycuda' requires a working nvcc compiler in your path.)

In case the automatic install doesn't properly pull in all dependencies, to install all of these modules manually, you can also run

pip install -r /PATH/TO/THIS/DIRECTORY/requirements.txt

For a general introduction to installing modules, see here.

If you prefer to make your own LALSuite installation https://git.ligo.org/lscsoft/lalsuite/, make sure it is swig-enabled and contains at least the lalpulsar package. A minimal confuration line to use would be e.g.:

./configure --prefix=${HOME}/lalsuite-install --disable-all-lal --enable-lalpulsar --enable-lalapps --enable-swig

PyFstat installation from source

In a terminal, clone the directory:

git clone https://gitlab.aei.uni-hannover.de/GregAshton/PyFstat.git

The module and associated scripts can be installed system wide (or to the currently active venv), assuming you are in the source directory, via

python setup.py install

As a developer, alternatively

python setup.py develop

can be useful so you can directly see any changes you make in action. Alternatively, add the source directory directly to your python path.

To check that the installation was successful, run

python -c 'import pyfstat'

if no error message is output, then you have installed pyfstat. Note that the module will be installed to whichever python executable you call it from.

Ephemerides installation

PyFstat requires paths to earth and sun ephemerides files in order to use the lalpulsar.ComputeFstat module and various lalapps tools.

If you have done pip install lalsuite, you need to manually download at least these two files:

• earth00-40-DE405.dat.gz
• sun00-40-DE405.dat.gz

(Other ephemerides versions exist, but these should be sufficient for most applications.) You then need to tell PyFstat where to find these files, by either setting an environment variable $LALPULSAR_DATADIR or by creating a ~/.pyfstat.conf file as described further below. If you are working with a virtual environment, you should be able to get a full working ephemerides installation with these commands:

mkdir $VIRTUAL_ENV/share/lalpulsar
wget https://git.ligo.org/lscsoft/lalsuite/raw/master/lalpulsar/lib/earth00-40-DE405.dat.gz -P $VIRTUAL_ENV/share/lalpulsar
wget https://git.ligo.org/lscsoft/lalsuite/raw/master/lalpulsar/lib/sun00-40-DE405.dat.gz -P $VIRTUAL_ENV/share/lalpulsar
echo 'export LALPULSAR_DATADIR=$VIRTUAL_ENV/share/lalpulsar' >> ${VIRTUAL_ENV}/bin/activate
deactivate
source path/to/venv/bin/activate

If instead you have built and installed lalsuite from source, and set your path up properly through something like source $MYLALPATH/etc/lalsuite-user-env.sh, then the ephemerides path should be automatically picked up from the $LALPULSAR_DATADIR environment variable. Alternatively, you can place a file ~/.pyfstat.conf into your home directory which looks like

earth_ephem = '/home/<USER>/lalsuite-install/share/lalpulsar/earth00-19-DE421.dat.gz'
sun_ephem = '/home/<USER>/lalsuite-install/share/lalpulsar/sun00-19-DE421.dat.gz'

Paths set in this way will take precedence over the environment variable.

Finally, you can manually specify ephemerides files when initialising each PyFstat search (as one of the arguments).

Contributors

• Greg Ashton
• David Keitel
• Reinhard Prix
• Karl Wette
• Sylvia Zhu

This project is open to development, please feel free to contact us for advice or just jump in and submit a pull request.

Citing this work

If you use PyFstat in a publication we would appreciate if you cite the original paper introducing the code, the ADS page can be found here and the version release:

@misc{pyfstat,
  author       = {{Ashton}, G. and {Keitel}, D.},
  title        = {{PyFstat-v1.2}},
  month        = may,
  year         = 2018,
  doi          = {10.5281/zenodo.1243931},
  url          = {https://doi.org/10.5281/zenodo.1243931},
  note= {\url{https://doi.org/10.5281/zenodo.1243931}}
}