RAW images are generally linear but not always. I worked through an issue with Adobe earlier this year to update their RAW converter software to address some of the non-linearities introduced by certain Canon SLR modes. Since Hugin doesn't work with RAW files, images you feed it will almost certainly be non-linear as they have already been RAW converted. Canon DPP software has an option to output linear luminance images. You'll know if you used it because all the images will be very dark and it will be hard to see any content in them. Good luck manually aligning a panorama with such images.
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