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How to setup Panomatic 0.9.3 to be used with PTGui ?

Goto Tools > Options :

I want to use fisheye images but this does not work very well...

1. Try increasing ransac distance (50, 100, 150 pixels). But potentially you will get false matches.

How to control the number of output points per image pair ?

Play with second sieve parameters. At maximum you will get height x width x size matches per image pair.

What is linear matching ?

By default (All pairs), if you have 4 images A B C D, matches will be detected between A-B, A-C, A-D, B-C, B-D, C-D.
If you have a single row panorama you can enable this option. This will lead to detect matches between A-B, B-C, C-D.
You can increase the linear match size. With a value of 2, matches will be detected in those pairs : A-B, A-C, B-C, B-D, C-D.