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-rw-r--r--scripts/Rsplit_surface.py16
-rwxr-xr-xscripts/add-beam-params14
-rwxr-xr-xscripts/ave-resolution15
-rw-r--r--scripts/clean-stream.py4
-rwxr-xr-xscripts/crystal-frame-number13
-rwxr-xr-xscripts/detector-shift16
-rwxr-xr-xscripts/find-pairs37
-rwxr-xr-xscripts/gaincal-to-saturation-map9
-rwxr-xr-xscripts/move-entire-detector16
-rwxr-xr-xscripts/peak-intensity16
-rwxr-xr-xscripts/peakogram-stream8
-rwxr-xr-xscripts/split-by-mask12
-rwxr-xr-xscripts/truncate-stream14
13 files changed, 100 insertions, 90 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/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')