diff options
Diffstat (limited to 'scripts')
| -rw-r--r-- | scripts/Rsplit_surface.py | 16 | ||||
| -rwxr-xr-x | scripts/add-beam-params | 14 | ||||
| -rwxr-xr-x | scripts/ave-resolution | 15 | ||||
| -rw-r--r-- | scripts/clean-stream.py | 4 | ||||
| -rwxr-xr-x | scripts/crystal-frame-number | 13 | ||||
| -rwxr-xr-x | scripts/detector-shift | 16 | ||||
| -rwxr-xr-x | scripts/find-pairs | 37 | ||||
| -rwxr-xr-x | scripts/gaincal-to-saturation-map | 9 | ||||
| -rwxr-xr-x | scripts/move-entire-detector | 16 | ||||
| -rwxr-xr-x | scripts/peak-intensity | 16 | ||||
| -rwxr-xr-x | scripts/peakogram-stream | 8 | ||||
| -rwxr-xr-x | scripts/split-by-mask | 12 | ||||
| -rwxr-xr-x | scripts/sum-peaks | 47 | ||||
| -rwxr-xr-x | scripts/truncate-stream | 14 | ||||
| -rw-r--r-- | scripts/turbo-index-lsf (renamed from scripts/turbo-index) | 5 | ||||
| -rwxr-xr-x | scripts/turbo-index-slurm | 85 |
16 files changed, 235 insertions, 92 deletions
diff --git a/scripts/Rsplit_surface.py b/scripts/Rsplit_surface.py index ca68a92e..63a72cd8 100644 --- a/scripts/Rsplit_surface.py +++ b/scripts/Rsplit_surface.py @@ -1,13 +1,5 @@ #!/usr/bin/python -# coding=utf-8 - -from __future__ import division -from array import array -from numpy import * - -import matplotlib - -# Rsplit_surface.py +# -*- coding: utf-8 -*- # # Plot Rsplit as a contour map # @@ -32,6 +24,12 @@ import matplotlib # along with CrystFEL. If not, see <http://www.gnu.org/licenses/>. +from __future__ import division +from array import array +from numpy import * + +import matplotlib + """there could be problems with dependencies, in this case, """ #matplotlib.use('PS') diff --git a/scripts/add-beam-params b/scripts/add-beam-params index 23c9caaf..e4e38f70 100755 --- a/scripts/add-beam-params +++ b/scripts/add-beam-params @@ -1,13 +1,13 @@ #!/usr/bin/env python - +# -*- coding: utf-8 -*- # # Add beam parameters to stream # -# Copyright (c) 2014 Deutsches Elektronen-Synchrotron DESY, -# a research centre of the Helmholtz Association. +# Copyright © 2014-2017 Deutsches Elektronen-Synchrotron DESY, +# a research centre of the Helmholtz Association. # # Author: -# 2014 Thomas White <taw@physics.org> +# 2014,2017 Thomas White <taw@physics.org> # import sys @@ -66,7 +66,7 @@ def count_crystals(f, g, start_after, stop_after): in_crystal = 0 need_end_chunk = 1 - print "Wrote %i crystals to %s" % (n_crystals_written, opt.ofn) + print("Wrote {} crystals to {}".format(n_crystals_written, opt.ofn)) def count_chunks(f, g, start_after, stop_after): n_chunks_seen = 0 @@ -95,7 +95,7 @@ def count_chunks(f, g, start_after, stop_after): if n_chunks_written == stop_after: break - print "Wrote %i chunks to %s" % (n_chunks_written, opt.ofn) + print("Wrote {} chunks to {}".format(n_chunks_written, opt.ofn)) op = optparse.OptionParser() op.add_option('', '--input', action='store', type='string', dest='ifn', @@ -111,7 +111,7 @@ op.add_option('', '--chunks', action='store_true', dest='chunks', opt,arg = op.parse_args(sys.argv) if not (opt.ifn and opt.ofn): - print "You need at least --input and --output" + print("You need at least --input and --output") exit(1) f = open(opt.ifn, 'r') diff --git a/scripts/ave-resolution b/scripts/ave-resolution index a69c456e..69c21195 100755 --- a/scripts/ave-resolution +++ b/scripts/ave-resolution @@ -1,14 +1,13 @@ #!/usr/bin/env python # -*- coding: utf-8 -*- - # # Find mean diffracting resolution # -# Copyright © 2014-2015 Deutsches Elektronen-Synchrotron DESY, +# Copyright © 2014-2017 Deutsches Elektronen-Synchrotron DESY, # a research centre of the Helmholtz Association. # # Author: -# 2014-2015 Thomas White <taw@physics.org> +# 2014-2017 Thomas White <taw@physics.org> # import sys @@ -24,16 +23,16 @@ while True: break if fline.find("diffraction_resolution_limit") != -1: res = float(fline.split('= ')[1].split(' ')[0].rstrip("\r\n")) - a.append(res) + a.append(res) continue f.close() b = numpy.array(a) -print " Mean: %.2f nm^-1 = %.2f A" % (numpy.mean(b),10.0/numpy.mean(b)) -print " Best: %.2f nm^-1 = %.2f A" % (numpy.max(b),10.0/numpy.max(b)) -print "Worst: %.2f nm^-1 = %.2f A" % (numpy.min(b),10.0/numpy.min(b)) -print "Std deviation: %.2f nm^-1" % (numpy.std(b)) +print(" Mean: {:.2} nm^-1 = {:.2} A".format(numpy.mean(b),10.0/numpy.mean(b))) +print(" Best: {:.2} nm^-1 = {:.2} A".format(numpy.max(b),10.0/numpy.max(b))) +print("Worst: {:.2} nm^-1 = {:.2} A".format(numpy.min(b),10.0/numpy.min(b))) +print("Std deviation: {:.2} nm^-1".format(numpy.std(b))) plt.hist(a,bins=30) plt.title('Resolution based on indexing results') diff --git a/scripts/clean-stream.py b/scripts/clean-stream.py index 1e906e54..57c0ed93 100644 --- a/scripts/clean-stream.py +++ b/scripts/clean-stream.py @@ -1,6 +1,6 @@ #!/usr/bin/python # coding=utf-8 - +# # clean-stream.py # # Remove non-indexed frames from a stream @@ -86,5 +86,5 @@ while (line != ''): line = infile_1.readline() -print '%d suited of %d patterns have been extracted and saved as %s' % (num_suited, n_patt, sys.argv[2]) +print('%d suited of %d patterns have been extracted and saved as %s' % (num_suited, n_patt, sys.argv[2])) Nfile.write('%d' % num_suited) diff --git a/scripts/crystal-frame-number b/scripts/crystal-frame-number index b3ed3f1f..883abb81 100755 --- a/scripts/crystal-frame-number +++ b/scripts/crystal-frame-number @@ -1,6 +1,13 @@ #!/usr/bin/env python # -*- coding: utf-8 -*- - +# +# Show sequence numbers of crystals and frames +# +# Copyright © 2015-2017 Deutsches Elektronen-Synchrotron DESY, +# a research centre of the Helmholtz Association. +# +# Author: +# 2015-2017 Thomas White <taw@physics.org> import sys @@ -16,9 +23,9 @@ while True: if fline.find("Image filename") != -1: frame_number += 1 fn = fline.split(': ')[1].split(' ')[0].rstrip("\r\n") - print 'Frame %i: %s' % (frame_number, fn) + print('Frame {}: {}'.format(frame_number, fn)) if fline.find("diffraction_resolution_limit") != -1: crystal_number += 1 - print ' Crystal %i: %s' % (crystal_number, fline.rstrip("\r\n")) + print(' Crystal {}: {}'.format(crystal_number, fline.rstrip("\r\n"))) f.close() diff --git a/scripts/detector-shift b/scripts/detector-shift index a348e3c9..24cbb504 100755 --- a/scripts/detector-shift +++ b/scripts/detector-shift @@ -1,13 +1,13 @@ #!/usr/bin/env python - +# -*- coding: utf-8 -*- # # Determine mean detector shift based on prediction refinement results # -# Copyright (c) 2015-2016 Deutsches Elektronen-Synchrotron DESY, -# a research centre of the Helmholtz Association. +# Copyright © 2015-2017 Deutsches Elektronen-Synchrotron DESY, +# a research centre of the Helmholtz Association. # # Author: -# 2015-2016 Thomas White <taw@physics.org> +# 2015-2017 Thomas White <taw@physics.org> # 2016 Marmoru Suzuki <mamoru.suzuki@protein.osaka-u.ac.jp> # @@ -54,13 +54,13 @@ f.close() mean_x = sum(x_shifts) / len(x_shifts) mean_y = sum(y_shifts) / len(y_shifts) -print 'Mean shifts: dx = %.2f mm, dy = %.2f mm' % (mean_x,mean_y) +print('Mean shifts: dx = {:.2} mm, dy = {:.2} mm'.format(mean_x,mean_y)) # Apply shifts to geometry if have_geom: out = os.path.splitext(geom)[0]+'-predrefine.geom' - print 'Applying corrections to %s, output filename %s' % (geom,out) + print('Applying corrections to {}, output filename {}'.format(geom,out)) g = open(geom, 'r') h = open(out, 'w') panel_resolutions = {} @@ -99,7 +99,7 @@ if have_geom: res = panel_resolutions[panel] else: res = default_res - print 'Using default resolution (%f px/m) for panel %s' % (res, panel) + print('Using default resolution ({} px/m) for panel {}'.format(res, panel)) h.write('%s/corner_x = %f\n' % (panel,panel_cnx+(mean_x*res*1e-3))) continue @@ -111,7 +111,7 @@ if have_geom: res = panel_resolutions[panel] else: res = default_res - print 'Using default resolution (%f px/m) for panel %s' % (res, panel) + print('Using default resolution ({} px/m) for panel {}'.format(res, panel)) h.write('%s/corner_y = %f\n' % (panel,panel_cny+(mean_y*res*1e-3))) continue diff --git a/scripts/find-pairs b/scripts/find-pairs index 4629767d..8c3b69d0 100755 --- a/scripts/find-pairs +++ b/scripts/find-pairs @@ -1,14 +1,13 @@ #!/usr/bin/env python # -*- coding: utf-8 -*- - # # Find pairs of observations from the same pattern # -# Copyright © 2014 Deutsches Elektronen-Synchrotron DESY, -# a research centre of the Helmholtz Association. +# Copyright © 2014-2017 Deutsches Elektronen-Synchrotron DESY, +# a research centre of the Helmholtz Association. # # Author: -# 2014 Thomas White <taw@physics.org> +# 2014-2017 Thomas White <taw@physics.org> # import re as regexp @@ -41,33 +40,33 @@ def find_405(f): f = open(fn1, 'r') flines = find_405(f) -print len(flines),"measurements in",fn1 +print("{} measurements in {}".format(len(flines),fn1)) g = open(fn2, 'r') glines = find_405(g) -print len(glines),"measurements in",fn2 +print("{} measurements in {}".format(len(glines),fn2)) -print "\nThe common measurements:\n" +print("\nThe common measurements:\n") for fn in flines.keys(): if fn in glines: - print fn - print flines[fn].rstrip("\r\n") - print glines[fn] - print + print(fn) + print(flines[fn].rstrip("\r\n")) + print(glines[fn]) + print() del flines[fn] del glines[fn] -print "\nThe measurements only in",fn1,":\n" +print("\nThe measurements only in {}:\n".format(fn1)) for fn in flines.keys(): - print fn - print flines[fn].rstrip("\r\n") - print + print(fn) + print(flines[fn].rstrip("\r\n")) + print() -print "\nThe measurements only in",fn2,":\n" +print("\nThe measurements only in {}:\n".format(fn2)) for fn in glines.keys(): - print fn - print glines[fn].rstrip("\r\n") - print + print(fn) + print(glines[fn].rstrip("\r\n")) + print("") diff --git a/scripts/gaincal-to-saturation-map b/scripts/gaincal-to-saturation-map index 8a803526..eac8883c 100755 --- a/scripts/gaincal-to-saturation-map +++ b/scripts/gaincal-to-saturation-map @@ -1,4 +1,13 @@ #!/usr/bin/env python +# -*- coding: utf-8 -*- +# +# Convert gain map to saturation map +# +# Copyright © 2016-2017 Deutsches Elektronen-Synchrotron DESY, +# a research centre of the Helmholtz Association. +# +# Author: +# 2016-2017 Thomas White <taw@physics.org> import numpy as np import h5py diff --git a/scripts/move-entire-detector b/scripts/move-entire-detector index 79ce5a5c..3d06c408 100755 --- a/scripts/move-entire-detector +++ b/scripts/move-entire-detector @@ -1,13 +1,13 @@ #!/usr/bin/env python - +# -*- coding: utf-8 -*- # # Shift the detector by a given amount # -# Copyright (c) 2016 Deutsches Elektronen-Synchrotron DESY, -# a research centre of the Helmholtz Association. +# Copyright © 2016-2017 Deutsches Elektronen-Synchrotron DESY, +# a research centre of the Helmholtz Association. # # Author: -# 2016 Thomas White <taw@physics.org> +# 2016-2017 Thomas White <taw@physics.org> # import sys @@ -58,8 +58,8 @@ if args.beam: else: bm = 'detector' -print 'Input filename %s\nOutput filename %s' % (args.ifn,out) -print 'Shifting %s by %f,%f %s' % (bm, args.xshift, args.yshift, units) +print('Input filename {}\nOutput filename {}'.format(args.ifn,out)) +print('Shifting {} by {},{} {}'.format(bm, args.xshift, args.yshift, units)) if args.beam: args.xshift = -args.xshift @@ -104,7 +104,7 @@ while True: else: res = default_res if not args.px: - print 'Using default resolution (%f px/m) for panel %s' % (res, panel) + print('Using default resolution ({} px/m) for panel {}'.format(res, panel)) if args.px: h.write('%s/corner_x = %f\n' % (panel,panel_cnx+args.xshift)) else: @@ -120,7 +120,7 @@ while True: else: res = default_res if not args.px: - print 'Using default resolution (%f px/m) for panel %s' % (res, panel) + print('Using default resolution ({} px/m) for panel {}'.format(res, panel)) if args.px: h.write('%s/corner_y = %f\n' % (panel,panel_cny+args.yshift)) else: diff --git a/scripts/peak-intensity b/scripts/peak-intensity index 53610b73..65e066cf 100755 --- a/scripts/peak-intensity +++ b/scripts/peak-intensity @@ -1,13 +1,13 @@ #!/usr/bin/env python - +# -*- coding: utf-8 -*- # # Quantify peak intensities # -# Copyright (c) 2015 Deutsches Elektronen-Synchrotron DESY, -# a research centre of the Helmholtz Association. +# Copyright © 2015-2017 Deutsches Elektronen-Synchrotron DESY, +# a research centre of the Helmholtz Association. # # Author: -# 2015 Thomas White <taw@physics.org> +# 2015-2017 Thomas White <taw@physics.org> # import sys @@ -40,8 +40,8 @@ while True: f.close() -print '%i patterns, %i peaks' % (n_patt,n_peaks) -print 'Mean %.2f peaks per pattern' % (n_peaks/n_patt) -print 'Mean %.2f ADU per peak' % (total_intens/n_peaks) -print 'Mean %.2f ADU total per pattern' % (total_intens/n_patt) +print('{} patterns, %i peaks'.format(n_patt,n_peaks)) +print('Mean {:.2f} peaks per pattern'.format(n_peaks/float(n_patt))) +print('Mean {:.2f} ADU per peak'.format(total_intens/float(n_peaks))) +print('Mean {:.2f} ADU total per pattern'.format(total_intens/n_patt)) diff --git a/scripts/peakogram-stream b/scripts/peakogram-stream index 209e7e95..1f67b39c 100755 --- a/scripts/peakogram-stream +++ b/scripts/peakogram-stream @@ -1,16 +1,14 @@ #!/usr/bin/env python # -*- coding: utf-8 -*- - -# peakogram-stream # # Check a stream for saturation # -# Copyright © 2016 Deutsches Elektronen-Synchrotron DESY, +# Copyright © 2016-2017 Deutsches Elektronen-Synchrotron DESY, # a research centre of the Helmholtz Association. # Copyright © 2016 The Research Foundation for SUNY # # Authors: -# 2016 Thomas White <taw@physics.org> +# 2016-2017 Thomas White <taw@physics.org> # 2014-2016 Thomas Grant <tgrant@hwi.buffalo.edu> # # This file is part of CrystFEL. @@ -120,7 +118,7 @@ data = np.asarray(data,dtype=float) sys.stdout.write("\r%i peaks found" % n) sys.stdout.flush() -print "" +print("") x = data[:,0] y = data[:,1] diff --git a/scripts/split-by-mask b/scripts/split-by-mask index aede3f43..18b672e4 100755 --- a/scripts/split-by-mask +++ b/scripts/split-by-mask @@ -1,13 +1,13 @@ #!/usr/bin/env python - +# -*- coding: utf-8 -*- # # Split stream according to an external mask # -# Copyright (c) 2014-2016 Deutsches Elektronen-Synchrotron DESY, -# a research centre of the Helmholtz Association. +# Copyright © 2014-2017 Deutsches Elektronen-Synchrotron DESY, +# a research centre of the Helmholtz Association. # # Author: -# 2014-2016 Thomas White <taw@physics.org> +# 2014-2017 Thomas White <taw@physics.org> # import sys @@ -21,7 +21,7 @@ prog = re.compile("^\s+([\d-]+)\s+([\d-]+)\s+([\d-]+)\s+[\d\.\-]+\s+[\d\.\-]+\s+ def process_refln(fline, g, h, mask): match = prog.match(fline) if not match: - print 'Line not understood, WTF? %s' % fline + print('Line not understood, WTF? {}'.format(fline)) return fs = int(round(float(match.group(4)))) ss = int(round(float(match.group(5)))) @@ -48,7 +48,7 @@ op.add_option('', '--mask', action='store', type='string', dest='mask_fn', opt,arg = op.parse_args(sys.argv) if not opt.ifn: - print "You need at least --input" + print("You need at least --input") exit(1) f = open(opt.ifn, 'r') diff --git a/scripts/sum-peaks b/scripts/sum-peaks new file mode 100755 index 00000000..eccb9fc6 --- /dev/null +++ b/scripts/sum-peaks @@ -0,0 +1,47 @@ +#!/usr/bin/env python +# -*- coding: utf-8 -*- +# +# Generate "peak powder" from CrystFEL stream +# +# Copyright © 2017 Deutsches Elektronen-Synchrotron DESY, +# a research centre of the Helmholtz Association. +# +# Author: +# 2017 Thomas White <taw@physics.org> +# + +import numpy as np +import h5py +import sys +import re + +f = open(sys.argv[1], 'r') +powder = np.zeros((512,1024), dtype=float) +peaks = [] + +prog1 = re.compile("^\s*([\d\-\.]+)\s+([\d\-\.]+)\s+[\d\-\.]+\s+([\d\-\.]+)\s+\S+$") + +while True: + + fline = f.readline() + if not fline: + break + + if fline == '----- End chunk -----\n': + if len(peaks) > 10: + for p in peaks: + powder[p[1],p[0]] += p[2] + peaks = [] + + match = prog1.match(fline) + if match: + fs = int(float(match.group(1))) + ss = int(float(match.group(2))) + intensity = float(match.group(3)) + peaks.append((fs,ss,intensity)) + +f.close() + +fh = h5py.File("summed-peaks.h5", "w") +fh.create_dataset("/data", (512,1024), data=powder) +fh.close() diff --git a/scripts/truncate-stream b/scripts/truncate-stream index 1725082a..60679d30 100755 --- a/scripts/truncate-stream +++ b/scripts/truncate-stream @@ -1,13 +1,13 @@ #!/usr/bin/env python - +# -*- coding: utf-8 -*- # # Chop chunks or crystals from one or both ends of a stream # -# Copyright (c) 2014 Deutsches Elektronen-Synchrotron DESY, -# a research centre of the Helmholtz Association. +# Copyright © 2014-2017 Deutsches Elektronen-Synchrotron DESY, +# a research centre of the Helmholtz Association. # # Author: -# 2014 Thomas White <taw@physics.org> +# 2014-2017 Thomas White <taw@physics.org> # import sys @@ -66,7 +66,7 @@ def count_crystals(f, g, start_after, stop_after): in_crystal = 0 need_end_chunk = 1 - print "Wrote %i crystals to %s" % (n_crystals_written, opt.ofn) + print("Wrote {} crystals to {}".format(n_crystals_written, opt.ofn)) def count_chunks(f, g, start_after, stop_after): n_chunks_seen = 0 @@ -95,7 +95,7 @@ def count_chunks(f, g, start_after, stop_after): if n_chunks_written == stop_after: break - print "Wrote %i chunks to %s" % (n_chunks_written, opt.ofn) + print("Wrote {} chunks to {}".format(n_chunks_written, opt.ofn)) op = optparse.OptionParser() op.add_option('', '--input', action='store', type='string', dest='ifn', @@ -111,7 +111,7 @@ op.add_option('', '--chunks', action='store_true', dest='chunks', opt,arg = op.parse_args(sys.argv) if not (opt.ifn and opt.ofn): - print "You need at least --input and --output" + print("You need at least --input and --output") exit(1) f = open(opt.ifn, 'r') diff --git a/scripts/turbo-index b/scripts/turbo-index-lsf index c11f521e..00e4ec15 100644 --- a/scripts/turbo-index +++ b/scripts/turbo-index-lsf @@ -3,9 +3,9 @@ RUN=$1 NOSAMPLE=`echo $RUN | sed -e 's/\-.*$//'` -GEOM=<name of geometry file> +GEOM=my.geom # Name of your geometry file -find <path to CXI files>/$RUN -name '*.cxi' > files-${RUN}.lst +find /path/to/CXI/files/$RUN -name '*.cxi' > files-${RUN}.lst # Set location of files list_events -i files-${RUN}.lst -g $GEOM -o events-${RUN}.lst wc -l events-${RUN}.lst rm -f split-events-${RUN}.lst files-${RUN}.lst @@ -18,6 +18,7 @@ for FILE in split-events-${RUN}.lst*; do NAME=`echo $FILE | sed -e "s/split-events-${RUN}.lst/${NOSAMPLE}-/"` echo "$NAME: $FILE ---> $STREAM" + # Set indexing parameters here bsub -q psanaq -o $NAME.log -J $NAME -n 12 -R "span[hosts=1]" \ indexamajig \ -i $FILE -o $STREAM -j 32 -g $GEOM --peaks=cxi diff --git a/scripts/turbo-index-slurm b/scripts/turbo-index-slurm new file mode 100755 index 00000000..a0f1bec5 --- /dev/null +++ b/scripts/turbo-index-slurm @@ -0,0 +1,85 @@ +#!/bin/sh + +# Split a large indexing job into many small tasks and submit using SLURM + +# ./turbo-index my-files.lst label my.geom /location/for/streams + +# 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> + +SPLIT=1000 # Size of job chunks +MAIL=you@example.org # Email address for SLURM notifications + +INPUT=$1 +RUN=$2 +GEOM=$3 +STREAMDIR=$4 + +# Set up environment here if necessary +#source /path/to/crystfel/setup.sh + +# Generate event list from file above +list_events -i $INPUT -g $GEOM -o events-${RUN}.lst +if [ $? != 0 ]; then + echo "list_events failed" + exit 1 +fi +# If you are using single-event files instead of multi-event ("CXI") ones, +# comment out the above lines and uncomment the following one: +#cp $INPUT events-${RUN}.lst + +# 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 --partition=mypartition" >> $SLURMFILE # Set your partition here + echo "#SBATCH --time=01:00:00" >> $SLURMFILE + echo "#SBATCH --nodes=1" >> $SLURMFILE + echo "#SBATCH --nice=100" >> $SLURMFILE # Set priority very low to allow other jobs through + echo >> $SLURMFILE + + echo "#SBATCH --workdir $PWD" >> $SLURMFILE + echo "#SBATCH --job-name $NAME" >> $SLURMFILE + echo "#SBATCH --output $NAME-%N-%j.out" >> $SLURMFILE + echo "#SBATCH --error $NAME-%N-%j.err" >> $SLURMFILE + echo "#SBATCH --mail-type END" >> $SLURMFILE + echo "#SBATCH --mail-user $MAIL" >> $SLURMFILE + echo >> $SLURMFILE + + echo "#source /path/to/crystfel/setup.sh" >> $SLURMFILE # Set up environment here (again) if necessary + echo >> $SLURMFILE + + command="indexamajig -i $FILE -o $STREAMDIR/$STREAM" + command="$command -j \`nproc\` -g $GEOM" + #command="$command --peaks=zaef" # Indexing parameters here + + echo $command >> $SLURMFILE + + sbatch $SLURMFILE + +done |