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I'm using a Canon PowerShot G12 camera to take photos for vegetation analysis. The camera is looking straight down at the vegetation - or at least CLOSE to straight down. The autorotation function on this model of PowerShot cannot be turned off. Because the camera on the pole we carry through the field may be slightly tipped in any direction, the images are autorotated in all directions. We're saving RAW images.

Is there a program that can read the EXIF and orient all the images so bottom of the camera is the bottom of the image?

I can take up to hundreds of photos on a day, so I don't want to rotate image by image in Digital Photo Professional. And the powers-that-be are hesitant to use a CHDK.

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Any metadata editing tool can do this. For simple cases with JPEG files, I recommend jhead, a free and open source program available for Linux, Mac OS, and Windows.

jhead --norot *.jpg will clear the rotation flag from all *.jpg images in the current directory.

Since you're using RAW, I recommend eitherExifTool or exiv2 (also free, cross-platform, and open source).

So, for all the cr2 files in a directory, either:

exiftool -Orientation=1 -n *.cr2

or

exiv -M'del Exif.Image.Orientation' *.cr2

(Setting Orientation to 1 means "no rotation"; deleting the tag as in the second example should have the same effect.)

It's also possible that the camera writes this flag to more than one metadata group in the file. If this doesn't work, there's some flags which can be added to get the others (but I think that probably won't be needed).

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