Height is a key factor in monitoring the growth status and rate of crops. Compared with large-scale satellite remote sensing images and high-cost LiDAR point cloud, the point cloud generated by the Structure from Motion (SfM) algorithm based on UAV images can quickly estimate crop height in the target area at a lower cost. However, crop leaves gradually start to cover the ground from the beginning of the stem elongation stage, making more and more ground points below the canopy disappear in the data. The terrain undulations and outliers will seriously affect the height estimation accuracy. This paper proposed a ground point fitting method to estimate the height of winter wheat based on the UAV SfM point cloud. A canopy slice filter was designed to reduce the interference of middle canopy points and outliers. Random Sample Consensus (RANSAC) was applied to obtain the ground points from the valid filtered point cloud. Then, the missing ground points were fitted according to the known ground points. Furthermore, we achieved crop height monitoring at the stem elongation stage with an R2 of 0.90. The relative root mean squared error (RRMSE) of height estimation was 5.9%, and the relative mean absolute error (RMAE) was 4.6% at the stem elongation stage. This paper proposed the canopy slice filter and fitting missing ground points. It was concluded that the canopy slice filter successfully optimized the extraction of ground points and removed outliers. Fitting the missing ground points simulated the terrain undulations effectively and improved the accuracy.
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