The Balloon Experimental Twin Telescope for Infrared Interferometry (BETTII) is an 8-meter interferometer which operates on a high-altitude balloon. BETTII had its first successful engineering flight in June 2017. In this paper we discuss the design of the control system for BETTII, which includes the coarse pointing loop and the estimator controls algorithm (Extended Kalman Filter) implemented in FPGA. We will also discuss the different system modes that we defined in the controls system loop, which are used in different phases of the flight and are activated in order to acquire a target star in the science detector. The pointing loop uses different sensors and actuators in each phase to keep pointing at the desired target. The main sensors aregyroscopes, star cameras, and auxiliary sensors such as high-altitude GPS and magnetometers. The azimuth control is achieved with Compensated Controlled Moment Gyros (CCMG) and a Momentum Dump motor. For the elevation control, high-precision motors are used, which change the elevation of the siderostat mirrors. The combination of these instruments keep the baseline oriented within few arcseconds from the target star.In this paper, we will also present the software architecture relevant to the control system. This includes the description of the two flight computers present on the payload and the different control loops that are executed on them. Similarly, we will explain the importance of synchronization between all the sensors and actuators, which have to be referenced to a single master clock in order to obtain science data.
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