MicroED scripts

list.sh

#!/bin/bash

JOB=$1

for f in */$1/dials.scale.log; do
    DIR=`dirname $f | cut -d/ -f1,2`
    awk '/cc_ano/ {f=1; b=999; next}
         f==1 && $13 > 0.3 {b = $2;}
         f==1 && $13 <= 0.3 {printf FILENAME" "b" "; exit}' $f
    grep "Best sol" $DIR/dials.cosym.log| tr -d '\n'
    grep Unit $DIR/dials.integrate.log
done | grep scale

process_P1.sh

#!/bin/bash

# The list of files is created by:
#     ls images/| cut -d_ -f 3,4  |tee LIST
# Then this script is executed in parallel:
#     parallel -P8 --ungroup bash process_P1.sh < LIST

if [ -e $1/P1 ]; then
    echo $1 has been already processed
    exit
fi

mkdir -p $1/P1
cd $1/P1
rm -fr {indexed,refined,integrated,symmetrized,scaled}.{expt,refl} image.emd
ln -sf "../../images/Camera_Ceta_"*"$1_670_mm.emd" image.emd
dials.import image.emd mask=../../pixels.mask panel.pedestal=-40 distance=618 fast_slow_beam_centre=1050,1002 # image_range=$2
dials.find_spots imported.expt gain=0.1 max_separation=4 nproc=4
#dials.search_beam_position imported.expt strong.refl
#dials.find_rotation_axis optimised.expt strong.refl # just for check

if [ ! -f optimised.expt ]; then
    cp imported.expt optimised.expt
fi
dials.index optimised.expt strong.refl detector.fix=distance #space_group=P2 # unit_cell=5,10,20,90,90,90
if [ ! -f indexed.expt ]; then
    dials.index optimised.expt strong.refl detector.fix=distance indexing.method=fft1d #space_group=P2 # unit_cell=5,10,20,90,90,90
fi
#if [ ! -f indexed.expt ]; then
#    dials.index imported.expt strong.refl detector.fix=distance indexing.method=real_space_grid_search #space_group=P2 # unit_cell=5,10,20,90,90,90 
#fi
if [ ! -f indexed.expt ]; then
    exit
fi
dials.refine indexed.expt indexed.refl scan_varying=False detector.fix=distance
dials.refine refined.expt refined.refl scan_varying=True detector.fix=distance

dials.integrate refined.expt refined.refl prediction.d_min=0.8 nproc=4
if [ ! -f integrated.expt ]; then
    exit
fi
dials.check_indexing_symmetry integrated.{expt,refl} d_min=1.2 d_max=6 grid=2
dials.cosym integrated.expt integrated.refl
dials.scale integrated.expt integrated.refl d_min=0.9 json=scaled.json
cd ..

repack_emd.sh

#!/bin/sh

# Our data layout is:
# PROJECT_NAME/
#              navigator items, montage files
#              crystal images
#              raw/ <--- Verlox writes here (uncompressed EMDs)
#              compressed <--- This scripts writes compressed EMDs here
#
# This script is called as:
#    while true; do find -name '*.emd*' -mmin +3 | parallel -P16 bash ~/prog/scripts/repack_emd.sh {} ../compressed/\`echo {} \| sed -e 's,\ ,_,g'\`; sleep 10; done& 
# -mmin +3 is to prevent processing files being recorded.
# But this might not be necessary, because Verlox locks files anyway...
#
# The compressed files are then retrieved by the processing node.
#    while true; do rsync -avuP --exclude raw --exclude '*.tmp' talos-otf:/mnt/falcon/USER/PROJECT_NAME . ; sleep 90; done&

if [ "$#" -ne 2 ]; then
        echo "Usage: repack_emd input.emd output.emd"
        exit
fi

if [ -f "$2" ]; then
        echo "Output file $2 already exists."
        exit
fi

rm -fr "$2.tmp"
/home/talos_admin/.local/dials-v3-9-2/conda_base/bin/h5repack -f SHUF -f GZIP=4 "$1" "$2.tmp"
mv "$2.tmp" "$2"

Please note that further updates to these scripts will be posted to https://github.com/GKLabIPR/MicroED.