Despite all my efforts to defeat this problem, it continues to be a bug in my workflow for photogrammetry. To get a good lens calibration in Photoscan, you shoot calibration images by rotating the camera -90 and +90 degrees along with the horizontal images in a sequence of overlapping positions.
I've set my camera not to rotate pictures, so the calibration shots should appear as normal horizontal images, with the top of the object in the image facing right or left, depending on the camera rotation. However, the camera exif data apparently still records the image orientation and when I import the images into Lightroom, they're all rotated vertically so the top of the object is pointing up and the images are in portrait orientation, not landscape. Lightroom 4 doesn't allow you to set a preference to ignore image orientation during import, so it automatically rotates the images whether you like it or not. When you export the images as TIFFs or JPEGs, they're all rotated so the object appears oriented right-side-up.
I've tried using Photoshop CS6 to open the same DNGs that were imported into Lightroom, after I set PS6 preferences to ignore image orientation, but it still rotates them into portrait mode.
Photoscan has a pair of buttons that allow you to rotate the images right or left 90 degrees after they're uploaded to the workspace window, but this doesn't affect how Photoscan uses the images for calibration--Photoscan still thinks the sensor has portrait dimensions with the shorter side at the bottom, instead of the longer side. Therefore, Photoscan groups all the vertically oriented images into a separate calibration instead of using them to refine the calibration for the horizontal images.
This is a maddening problem because once you've created masks for your images, the masks have to have the same orientation as the images or Photoscan won't allow you to apply the same masks that you created using rotated images to the unrotated images. If you un-rotate the original images, you also have to remove rotation information for the masks to allow them to align properly, or Photoscan won't let you re-import the masks.
I've heard that some use Windows Explorer to remove image orientation data, but I don't have Windows on all my Macs, and I've heard there are also problems with Windows applying lossy compression to JPEGs when it rotates them--very bad behavior!
How do I defeat the image rotation problem? This gets very time consuming for projects with hundreds of images.