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#!/usr/bin/env python
#
# Split stream according to an external mask
#
# Copyright (c) 2014-2016 Deutsches Elektronen-Synchrotron DESY,
# a research centre of the Helmholtz Association.
#
# Author:
# 2014-2016 Thomas White <taw@physics.org>
#
import sys
import optparse
from collections import deque
import h5py
import re
prog = re.compile("^\s+([\d-]+)\s+([\d-]+)\s+([\d-]+)\s+[\d\.\-]+\s+[\d\.\-]+\s+[\d\.\-]+\s+[\d\.\-]+\s+([\d\.]+)\s+([\d\.]+)")
def process_refln(fline, g, h, mask):
match = prog.match(fline)
if not match:
print 'Line not understood, WTF? %s' % fline
return
fs = int(round(float(match.group(4))))
ss = int(round(float(match.group(5))))
m = mask[ss][fs]
if m:
g.write(fline)
else:
h.write(fline)
op = optparse.OptionParser()
op.add_option('', '--input', action='store', type='string', dest='ifn',
help="Input stream")
op.add_option('', '--output1', action='store', type='string', dest='ofn1',
help="Output stream", default='mask-split.stream1')
op.add_option('', '--output2', action='store', type='string', dest='ofn2',
help="Output stream", default='mask-split.stream2')
op.add_option('', '--mask', action='store', type='string', dest='mask_fn',
help="Filename of mask", default='mask.h5')
opt,arg = op.parse_args(sys.argv)
if not opt.ifn:
print "You need at least --input"
exit(1)
f = open(opt.ifn, 'r')
g = open(opt.ofn1, 'w')
h = open(opt.ofn2, 'w')
fh = h5py.File(opt.mask_fn, 'r')
mask = fh['/data/data'].value
fh.close()
in_refl = 0
while True:
fline = f.readline()
if not fline:
break
if fline.find("End of reflections") != -1:
in_refl = 0
if in_refl == 1:
process_refln(fline, g, h, mask)
else:
g.write(fline)
h.write(fline)
if in_refl == 2:
in_refl = 1
if fline.find("Reflections measured after indexing") != -1:
in_refl = 2
f.close()
g.close()
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