PEXOpy v0.2 Beta

A python wrapper for PEXO software.

NOTE : this is an early alpha and is under development.

Requirements

• Python 3.6 or higher. It should work with 2.7, but it is not recommended.
• numpy
• rpy2
• PEXO and its dependencies, see documentation for installation guidance.

Installation

Install the dependencies and set an environment variable $PEXODIR to a path to the PEXO repository. Add export PEXODIR=/example/path/to/pexo to your ~/.bashrc or ~/.bash_profile if you’re using bash, or setenv PEXODIR /example/path/to/pexoto ~/.tcshrc if you’re using tcsh.

from this repository

git clone https://github.com/timberhill/pexopy.git
cd pexopy
python setup.py install

or

pip install git+https://github.com/timberhill/pexopy.git -U

uninstall

pip uninstall pexopy

Usage

PEXO needs to run in a pexo environment (see readme).

The package contains a python class Pexo that is used to run PEXO. Optional arguments:

Rscript: path to Rscript executable (uses output of which Rscript if None)

pexodir: path to PEXO directory (uses PEXODIR environment variable if None)

verbose: whether to show the PEXO stdout (default: True)

The function to start PEXO is Pexo().run(). The arguments are consistent with the command line arguments of PEXO (see documentation).

Examples

Emulation

from pexopy import Pexo

output = Pexo(verbose=False).run(
    mode="emulate",
    primary="HD128621",
    ins="HARPS",
    time="2450000 2453000 10"
)

Here, output is a type of EmulationOutput:

output.contents contains a numpy.ndarray with the output results

output.path is a PEXO output file path

output.saveto(path=...) saves the output table to the specified path

Fitting

from pexopy import Pexo

output = Pexo(verbose=False).run(
    primary="HD239960",
    mode="fit",
    N=100,
    ncore=4,
    C=1,
    o="HD239960-fit.Robj"
)

Here, output is a type of FitOutput:

output.contents contains a rpy2 object with all the fitting results

output.path is a PEXO output file path

output.saveto(path=...) saves the output Robj file to the specified path

output.parstat contains the fit parameters, their values, and some key statistical parameters of the MCMC fit, e.g. output.raOff.mean and output.raOff.sd being the mean value and standard deviation of the right ascension offset

output.mc contains the markov chains of each of the parameters.

output.data is a table of data points with columns utc,V1,eV1,V2,eV2,star,type,instrument,wavelength

output.model is the same table, but with the fitted model values