#!/bin/bash

module purge
module use MX unstable
module load crystfel/0.10.2-rhel8

# add path to images
# add output stream name
# add path to cell
# change threshold to 3000 if at Alvra

indexamajig -i <path-to-images> \
  -o <output.steam> \
  --geometry=<path-to-geom> \
  --pdb=<path-to-cell> \
  --indexing=xgandalf-latt-cell \
  --peaks=peakfinder8 \
  --integration=rings-nograd-nocen \
  --tolerance=10.0,10.0,10.0,2,3,2 \
  --threshold=10 \
  --min-snr=5 \
  --int-radius=5,5,9 \
  -j 32 \
  --multi \
  --retry \
  --check-peaks \
  --max-res=3000 \
  --min-pix-count=2 \
  --local-bg-radius=4 \
  --min-res=85