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This paper builds a traffic state estimation system based on fusion of the information of the Geographic Information Systems for Transportation (GIS-T) and Global Positioning System (GPS). In this system, a new method is presented to construct the GIS-T digital map more accurately and efficiently. By this means, the system can perform better in estimation of traffic state with the information provided by the GPS probe vehicles. In addition, a fast affine algorithm is applied in the system to transform the GPS coordinates to the GIS-T coordinates. Finally, the experiments with the real GPS traffic data of Shanghai verify that the proposed method can improve the performance of the system in traffic state estimation.