Use backpropagation to identify the pixel contributing the strongest to the activation and put a reasonable threshold to identify which pixels belong to the object.
The default algorithm does this then computes an axis-aligned bounding box of the selected pixels (because it's really simple). You need to run another bounding box algorithm that allows for arbitrary orientation. Wikipedia has some ideas ( link ).
For how to get the interesting pixels you can look inside the tensorflow code to figure it out.
Oriented bounding boxes is a very interesting topic and it has been kind of ignored by the deep learning based object detection approaches and it's hard to find datasets.
A recent paper/dataset/challenge wich I found very interesting (specially because they pay attention to oriented boxes) can be found here:
http://captain.whu.edu.cn/DOTAweb/index.html
They don't share the code (nor give much details in the paper) of their modification of Fater-RCNN to work with oriented bounding boxes but the dataset by itself and the representation discussion are quite usefull.
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