I've been photographing church windows and have had the problem of getting the sides of the windows vertical after having to take the images from below the windows' horizontal plane.
I've tried PTLens with little success and also warping in Photoshop, but I can see it's not right even if no one else can.
I'm afraid I haven't found anything better than Lightroom's manual correction for straightening single images.
I ended up splitting each window into two and stitching in AutopanoPro. The vertical tool nailed it in seconds.
David