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Refer to the predict.py the function of decoder reveals the network predicts the offsets to the grid cell , while in the loss.py we can find that box1_xyxy and the box2_xyxy they are not the truely center_x and center_y for the image size, they are the offsets to the specific grid cell, and they need to add the location of the grid cell, but here we want to compute the iou for the predicted box and the target box,so we can treat them as a shift transformation of the center_x and center_y and the final iou won't change.
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