The script timelessFixGSOutput is part of the TIMEleSS tools.

Sometimes, GrainSpotter does not work properly and produces grains with 0 assigned peaks. This utility can be used to generate a new output file with those bogus grains removed.

You also have an option in timelessGrainSpotterMerge and timelessRemoveUsedGVE that allows ignoring those grains.

timelessFixGSOutput -h
usage: timelessFixGSOutput [options] file

Cleans output from GrainSpotter indexings. In particular, removes grains with
no assigned peaks that occur from time to time. Generates a new output file
with no such grain. This is part of the TIMEleSS project
http://timeless.texture.rocks

positional arguments:
  files                 grainSpotter output file

optional arguments:
  -h, --help            show this help message and exit
  -o OUTPUT, --output OUTPUT
                        Name of output file. Default is clean.log