tbepler/topaz

Radius for `topaz train`

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train command accepts radius as an optional argument, and in most places it's set to either 1, 2, or 3 (default), regardless of what actual radius in pix is. For example, this is the radius description in train script:

training.add_argument('-r', '--radius', default=3, type=int, help='pixel radius around particle centers to consider positive (default: 3)')

However, the actual positive area particle center is usually larger (8 and more, even with downscaling). Even extract command reflects radius boundaries (for tuning) between 5 and 100.

When I tried to increase the radius for training, I got worse results than with a smaller radius. Why the radius for training don't seem to correspond to an actual radius of particles?