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It seems to me that the topas_scale variable in topasdiff.py calculated from the manual user input of the TOPAS scale factor is too large by a factor of 10. If you do not enter a scale factor manually, the approximated scale factor is 10x less. I'm not sure why this is happening - perhaps there was a TOPAS update in how the TOPAS scale factor is worked into the intensity calculation in TOPAS?
Regardless, this is an easy fix:
if topas_scale: scale = float(topas_scale) ** 0.5/10
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