  The Gemini Planet Imager (GPI) is a new facility instrument for the Gemini
Observatory designed to provide direct detection and characterization of
planets and debris disks around stars in the solar neighborhood. In addition to
its extreme adaptive optics and corona graphic systems which give access to
high angular resolution and high-contrast imaging capabilities, GPI contains an
integral field spectrograph providing low resolution spectroscopy across five
bands between 0.95 and 2.5 $\mu$m. This paper describes the sequence of
processing steps required for the spectro-photometric calibration of GPI
science data, and the necessary calibration files. Based on calibration
observations of the white dwarf HD 8049B we estimate that the systematic error
in spectra extracted from GPI observations is less than 5%. The flux ratio of
the occulted star and fiducial satellite spots within coronagraphic GPI
observations, required to estimate the magnitude difference between a target
and any resolved companions, was measured in the $H$-band to be $\Delta m =
9.23\pm0.06$ in laboratory measurements and $\Delta m = 9.39\pm 0.11$ using
on-sky observations. Laboratory measurements for the $Y$, $J$, $K1$ and $K2$
filters are also presented. The total throughput of GPI, Gemini South and the
atmosphere of the Earth was also measured in each photometric passband, with a
typical throughput in $H$-band of 18% in the non-coronagraphic mode, with some
variation observed over the six-month period for which observations were
available. We also report ongoing development and improvement of the data cube
extraction algorithm.

Instrumentation and Methods for Astrophysics;Earth and Planetary Astrophysics