lopez suffix array extractor with copyrighted david chiang code excised

1 files changed, 148 insertions, 0 deletions

diff --git a/sa-extract/compile_bin.py b/sa-extract/compile_bin.py
new file mode 100755
index 00000000..0196e552
--- /dev/null
+++ b/sa-extract/compile_bin.py
@@ -0,0 +1,148 @@
+#!/usr/bin/env python
+
+'''This program compiles/decompiles binary data objects used
+by the decoder'''
+
+import sys
+import cdat
+import calignment
+import csuf
+import clex
+import precomputation
+#import parse
+import monitor
+import optparse
+
+def main(argv=None):
+	'''Call this from the command-line to create a 
+	pre-computed binary data array for later use'''
+	if argv is None:
+		argv = sys.argv
+
+	parser = optparse.OptionParser(usage="Usage: %prog [-s|-d|-a|-p] <input file> <output file>"+
+								"\n\nNote: -d,-s,-a, and -p are mutually exclusive")
+	parser.add_option("-d", "--data-array", 
+					action="store_true", default=False,
+					dest="da", help="Compile file into data array (default)")
+	parser.add_option("-s", "--suffix-array", 
+					action="store_true", default=False,
+					dest="sa", help="Compile file into suffix array")
+	parser.add_option("-a", "--alignment", 
+					action="store_true", default=False,
+					dest="a", help="Compile file into alignment")
+	parser.add_option("-l", "--lexical", 
+					action="store_true", default=False,
+					dest="l", help="Compile file into lex file")
+	parser.add_option("-x", "--compute_lexical", action="store", nargs=2,
+					dest="lex_args", help="Compute lex file from data",
+					metavar="<f file> <e file>")
+	parser.add_option("-p", "--parse", 
+					action="store_true", default=False,
+					dest="p", help="Compile file into parse")
+	parser.add_option("-b", "--binary-infile", 
+					action="store_true", default=False,
+					dest="bin", help="Input file is binary (default: text)")
+	parser.add_option("-t", "--text-outfile", 
+					action="store_true", default=False,
+					dest="text", help="Output file is text (default: binary)")
+	parser.add_option("-e", "--enhanced-outfile", 
+					action="store_true", default=False,
+					dest="enhanced", help="Output file is enhanced text (default: binary)")
+	parser.add_option("-r", action="store", nargs=7,
+					dest="precomp_args", help="Precompute collocations (Hiero only)", 
+					metavar="max-len=<INT> max-nt=<INT> max-size=<INT> min-gap=<INT> rank1=<INT> rank2=<INT> sa=<FILE>")
+	(options, args) = parser.parse_args()
+
+	filetype_opts =  [options.da, options.sa, options.a, options.p]
+
+	if (len(filter(lambda x: x, filetype_opts))) > 1 or len(args) != 2:
+		parser.print_help()
+		sys.exit(1)
+
+	(infilename, outfilename) = args
+	if options.bin:
+		bin = " binary"
+	else:
+		bin = ""
+
+	start_time = monitor.cpu()
+	if options.precomp_args:
+		if options.bin:
+			obj = precomputation.Precomputation(infilename, from_binary=True)
+		else:
+			keys = set(["max-len", "max-nt", "max-size", "min-gap", "rank1", "rank2", "sa"])
+			precomp_opts = {} 
+			sys.stderr.write("Precomputing statistics for list %s\n" % infilename)
+			for pair in options.precomp_args:
+				(key, val) = pair.split("=")
+				if key in keys:
+					keys.remove(key)
+					if key != "sa":
+						val = int(val)
+					precomp_opts[key] = val
+				else:
+					sys.stderr.write("Unknown keyword arg %s for -r (must be one of: max-len, max-nt, max-size, min-gap, rank1, rank2)\n" % key)
+					return 1
+			sa = csuf.SuffixArray(precomp_opts["sa"], True)
+			obj = precomputation.Precomputation(infilename, sa, 
+				precompute_rank=precomp_opts["rank1"], 
+				precompute_secondary_rank=precomp_opts["rank2"], 
+				max_length=precomp_opts["max-len"], 
+				max_nonterminals=precomp_opts["max-nt"], 
+				train_max_initial_size=precomp_opts["max-size"], 
+				train_min_gap_size=precomp_opts["min-gap"])
+	elif options.sa:
+		sys.stderr.write("Reading %s as%s suffix array...\n" % (infilename, bin))
+		obj = csuf.SuffixArray(infilename, options.bin)
+	elif options.a:
+		sys.stderr.write("Reading %s as%s alignment array...\n" % (infilename, bin))
+		obj = calignment.Alignment(infilename, options.bin)
+	elif options.p:
+		sys.stderr.write("Reading %s as%s parse array...\n" % (infilename, bin))
+		obj = parse.ParseArray(infilename, options.bin)
+	elif options.l:
+		sys.stderr.write("Reading %s as%s lex array...\n" % (infilename, bin))
+		obj = clex.CLex(infilename, options.bin)
+	elif options.lex_args:
+		ffile = options.lex_args[0]
+		efile = options.lex_args[1]
+		sys.stderr.write("Computing lex array from:\n A=%s\n F=%s\n E=%s\n" % (infilename, ffile, efile))
+		fsarray = csuf.SuffixArray(ffile, True)
+		earray = cdat.DataArray(efile, True)
+		aarray = calignment.Alignment(infilename, True)
+		obj = clex.CLex(aarray, from_data=True, earray=earray, fsarray=fsarray)
+	else:
+		sys.stderr.write("Reading %s as%s data array...\n" % (infilename, bin))
+		obj = cdat.DataArray(infilename, options.bin)
+
+	sys.stderr.write("  Total time for read: %f\n" % (monitor.cpu() - start_time))
+	start_time = monitor.cpu()
+	if options.text:
+		sys.stderr.write("Writing text file %s...\n" % outfilename)
+		obj.write_text(outfilename)
+	elif options.enhanced:
+		sys.stderr.write("Writing enhanced text file %s...\n" % outfilename)
+		obj.write_enhanced(outfilename)
+	else:
+		sys.stderr.write("Writing binary file %s...\n" % outfilename)
+		obj.write_binary(outfilename)
+	sys.stderr.write("Finished.\n")
+	sys.stderr.write("  Total time for write: %f\n" % (monitor.cpu() - start_time))
+
+	mem_use = float(monitor.memory())
+	metric = "B"
+	if mem_use / 1000 > 1:
+		mem_use /= 1000
+		metric = "KB"
+	if mem_use / 1000 > 1:
+		mem_use /= 1000
+		metric = "MB"
+	if mem_use / 1000 > 1:
+		mem_use /= 1000
+		metric = "GB"
+	sys.stderr.write("  Memory usage: %.1f%s\n" % (mem_use, metric))
+
+
+
+if __name__ == "__main__":
+	sys.exit(main(sys.argv))