In this paper, we consider signals with intra-wave frequency modulation. To handle this kind of signals effectively, we generalize our data-driven time-frequency analysis by using a shape function to describe the intra-wave frequency modulation. The idea of using a shape function in time-frequency analysis was first proposed by Wu. A shape function could be any periodic function. Based on this model, we propose to solve an optimization problem to extract the shape function. By exploring the fact that s is a periodic function, we can identify certain low rank structure of the signal. This structure enables us to extract the shape function from the signal. To test the robustness of our method, we apply our method on several synthetic and real signals. The results are very encouraging.