1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
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))
|
