Add Rsplit_surface and clean-stream.py

1 files changed, 87 insertions, 0 deletions

diff --git a/scripts/clean-stream.py b/scripts/clean-stream.py
new file mode 100644
index 00000000..0982f455
--- /dev/null
+++ b/scripts/clean-stream.py
@@ -0,0 +1,87 @@
+#!/usr/bin/python
+# coding=utf-8
+
+# clean-stream.py
+#
+# Remove non-indexed frames from a stream
+#
+# Copyright © 2013 Fedor Chervinskii
+#
+# Authors:
+#   2013 Fedor Chervinskii <fedor.chervinskii@gmail.com>
+#
+# This file is part of CrystFEL.
+#
+# CrystFEL is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# CrystFEL is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with CrystFEL.  If not, see <http://www.gnu.org/licenses/>.
+
+
+from __future__ import division
+from itertools import islice
+import sys
+import re
+
+
+infile_1 = open (sys.argv[1],'r')
+infile_2 = open (sys.argv[1],'r')
+outfile = open (sys.argv[2],'w')
+Nfile = open ('N.dat','w')
+
+suited = False
+counter1 = -1
+counter2 = 0
+start_index = 0
+n_patt = 0
+num_peaks = 0
+indexed = False
+num_suited = 0
+
+line = infile_1.readline()
+
+reg0 = re.compile('----- Begin chunk')
+reg1 = re.compile('----- End chunk')
+reg6 = re.compile('^indexed_by')
+reg7 = re.compile('none')
+
+while  (line != ''):
+
+	counter1 += 1
+
+	if (reg6.match(line)):
+		indexed = ( False if reg7.search(line) else True)
+
+	if (reg0.match(line)):
+		if (start_index == 0) :
+			while (counter2 < counter1) :
+				outline = infile_2.readline()
+				outfile.write(outline)
+				counter2 += 1
+		start_index = counter1
+
+	if (reg1.match(line)):
+		n_patt += 1
+		if indexed :
+			suited = True		
+		if suited :
+			num_suited += 1 
+		while (counter2 <= counter1) :
+			outline = infile_2.readline()
+			if suited :	
+				outfile.write(outline)
+			counter2 += 1
+		suited = False 
+
+	line = infile_1.readline()	
+	
+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)