JOSE: An Open-Source Python Optimal Spectrum Extraction Package

We present John and Joe’s Optimal Spectrum Extraction (JOSE), a new, open-source Python package for data processing, correction and spectrum extraction from reduced spectrograph data frames. JOSE uses and improves upon Horne’s optimal extraction algorithm while featuring interactive, real-time plotting and highly configurable parameter controls. Along with the base procedure of background fitting, profile estimation, cosmic-ray masking and spectrum extraction, JOSE includes the additional capabilities of Gaussian and running-average-fit profile construction and optional data-trace-straightening. Should the built-in fitting and straightening functions be insufficient, JOSE offers the ability to include user-written adjustment functions in the processing workflow. Running on native Python and the NumPy and SciPy packages for optimization, JOSE has a low dependency overhead in environments already running astronomical data pipelines. For data visualization, JOSE leverages the speed of the PyQtGraph package, allowing for not just the display of, but interaction with data during processing. Interactive graphics can also be disabled for batch processing. We present the development of this package along with a demonstration of its capabilities by performing spectral extraction on simulated spectrograph frames featuring noisy sky backgrounds, bad pixels, cosmic-ray strikes, and curved data traces. This work was supported by NASA Exoplanets Research Program grant NNX17AB62G.