SSX and XFEL-PReSTO

MASTERFILE=$1
OUTPUT=$2
  QX=`h5dump -d "/entry/instrument/detector/x_pixel_size" $MASTERFILE | awk '/\(0\): [0-9]/{print $2*1000}'`
  QY=`h5dump -d "/entry/instrument/detector/y_pixel_size" $MASTERFILE | awk '/\(0\): [0-9]/{print $2*1000}'`

  echo Data from a Eiger hdf5
  SENSOR_THICKNESS=`h5dump -d "/entry/instrument/detector/sensor_thickness" $MASTERFILE | awk '/\(0\): [0-9]/{print $2*1000}'`
  X_RAY_WAVELENGTH=`h5dump -d "/entry/instrument/beam/incident_wavelength" $MASTERFILE | awk '/\(0\): [0-9]/{print $2}'`
  photon_energy=$(bc -l <<<"12398/${X_RAY_WAVELENGTH}")

  NX=`h5dump -d "/entry/instrument/detector/detectorSpecific/x_pixels_in_detector" $MASTERFILE | awk '/\(0\): [0-9]/{print $2}'`
  NY=`h5dump -d "/entry/instrument/detector/detectorSpecific/y_pixels_in_detector" $MASTERFILE | awk '/\(0\): [0-9]/{print $2}'`

  # find ORGX and ORGY:
  ORGX=`h5dump -d "/entry/instrument/detector/beam_center_x" $MASTERFILE | awk '/\(0\): [0-9]/{print $2}'`
  ORGY=`h5dump -d "/entry/instrument/detector/beam_center_y" $MASTERFILE | awk '/\(0\): [0-9]/{print $2}'`

  # find DETECTOR_DISTANCE and OSCILLATION_RANGE:
  DETECTOR_DISTANCE=`h5dump -d "/entry/instrument/detector/detector_distance" $MASTERFILE | awk '/\(0\): [0-9]/{print $2*1000}'`

cat >> $OUTPUT << eof
; Camera length (in m) and photon energy
clen            = $(bc -l <<<"${DETECTOR_DISTANCE}/1000")
photon_energy   = $photon_energy

; adu_per_photon needs a relatively recent CrystFEL version.  If your version is
; older, change it to adu_per_eV and set it to one over the photon energy in eV
adu_per_photon = 1 
res             = 13333.3 

; These lines describe the data layout for the Eiger native multi-event files
dim0 = %
dim1 = ss
dim2 = fs
data = /entry/data/data

; Uncomment these lines if you have a separate bad pixel map (recommended!)
mask = /entry/instrument/detector/detectorSpecific/pixel_mask
mask_file = $1
mask_good = 0x0
mask_bad  = 0xFFFFFFFF

; corner_{x,y} set the position of the corner of the detector (in pixels)
; relative to the beam
p0/min_fs        = 0
p0/max_fs        = `expr $NX - 1`
p0/min_ss        = 0
p0/max_ss        = `expr $NY - 1`
p0/corner_x      = -$ORGX
p0/corner_y      = -$ORGY
p0/fs            = x
p0/ss            = y

; used by geoptimiser
;rigid_group_g0 = p0
;rigid_group_collection_c0 = g0
eof

#!/bin/sh
# Split a large indexing job into many small tasks and submit using SLURM
# Copyright © 2016-2017 Deutsches Elektronen-Synchrotron DESY,
#                       a research centre of the Helmholtz Association.
# Authors:
#   2016      Steve Aplin <steve.aplin@desy.de>
#   2016-2017 Thomas White <taw@physics.org>
#   2017 Modified by Oskar Aurelius <oskar.aurelius@dbb.su.se>


LAUNCH=TRUE # Launch jobs directly if 'TRUE'. Otherwise just write each script file

MULTI_EVENT_FILES=FALSE #If using multi-event ("CXI") files, should be 'TRUE'
INPUT=files.lst # List of frames to be processed
RUN=trial_run1 # Name of run
GEOM=5HT2B-Liu-2013.geom # Geometry file
STREAMDIR=output # Directory for output. No trailing /
PARAM="--peaks=hdf5 --int-radius=3,4,5 --indexing=mosflm-axes-latt -p 5ht2b.cell" # Parameters for indexamajig

NPROC=16 # Number of CPU cores to use per job
MAX_TIME=01:00:00 # Maximum usage time of one node. hh:mm:ss
SPLIT=1000  # Number of frames per job/node

CRY_V=CrystFEL/0.6.3-PReSTO # Version (module name) of CrystFEL to use
CCP4_V=CCP4/7.0.045-SHELX-ARP-7.6-PReSTO # Version (module name) of CCP4. Needed for mosflm
XDS_V=XDS/20170923-PReSTO # Version (module name) of XDS
L_BIN=/home/x_user/local_bin # Path to extra executables. mosflm

PROPOSAL=snic2017-1-xxx # SNIC proposal for compute time usage
MAIL=name.surname@lu.se  # Email address for SLURM notifications

################################################################################################################

if [[ $MULTI_EVENT_FILES == TRUE ]]; then
   module load $CRY_V
   list_events -i $INPUT -g $GEOM -o events-${RUN}.lst
   if [[ $? != 0 ]]; then
      echo "list_events failed"
      exit 1
   fi
elif [[ $MULTI_EVENT_FILES == FALSE ]]; then
   cp $INPUT events-${RUN}.lst
else
   echo "Have to pick if MULTI_EVEN_FILES is TRUE or FALSE"
   exit 1
fi

# Count total number of events
wc -l events-${RUN}.lst

# Split the events up, will create files with $SPLIT lines
split -a 3 -d -l $SPLIT events-${RUN}.lst split-events-${RUN}.lst

# Clean up
rm -f events-${RUN}.lst

# Loop over the event list files, and submit a batch job for each of them
for FILE in split-events-${RUN}.lst*; do

    # Stream file is the output of crystfel
    STREAM=`echo $FILE | sed -e "s/split-events-${RUN}.lst/${RUN}.stream/"`

    # Job name
    NAME=`echo $FILE | sed -e "s/split-events-${RUN}.lst/${RUN}-/"`
 
    echo "$NAME: $FILE  --->  $STREAM"

    SLURMFILE="${NAME}.sh"

    echo "#!/bin/sh" > $SLURMFILE
    echo >> $SLURMFILE

    echo "#SBATCH --account   $PROPOSAL" >>$SLURMFILE
    echo >> $SLURMFILE

    echo "#SBATCH --time=$MAX_TIME" >> $SLURMFILE
    echo "#SBATCH --nodes=1 --exclusive" >> $SLURMFILE
    echo >> $SLURMFILE

    echo "#SBATCH --workdir   $PWD" >> $SLURMFILE
    echo "#SBATCH --job-name  $NAME" >> $SLURMFILE
    echo "#SBATCH --output    $NAME.out" >> $SLURMFILE
    echo >> $SLURMFILE

    echo "#SBATCH --mail-type ALL" >> $SLURMFILE
    echo "#SBATCH --mail-user $MAIL" >> $SLURMFILE
    echo >> $SLURMFILE

    echo "module load $CRY_V" >> $SLURMFILE  # Load CrystFEL
    echo "module load $CCP4_V" >> $SLURMFILE  # Load CCP4
    echo "module load $XDS_V" >> $SLURMFILE  # Load XDS
    echo "PATH=\$PATH:$L_BIN" >> $SLURMFILE  # Add path with extra executables
    echo >> $SLURMFILE

    command="indexamajig -i $FILE -o $STREAMDIR/$STREAM"
    command="$command -j $NPROC -g $GEOM"
    command="$command $PARAM"  # Indexing and other parameters added here

    echo $command >> $SLURMFILE

    if [ $LAUNCH == TRUE ]; then
      sbatch $SLURMFILE
    fi

done