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Not solved directly, but I found a solution. The pgm file can be read correctly by MATLAB. You can use MATLAB functions to flip the image to normal direction and write to other file format.
When export the scan to pgm file format, the result depth map is flipped up side down.
By the way, is there any way to export pgm by binary rather than ascii? I found photoshop cannot import the ascii pgm format correctly.
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