Merge branch 'master' of https://github.com/redpony/cdec

3 files changed, 25 insertions, 355 deletions

diff --git a/python/pkg/cdec/sa/extract.py b/python/pkg/cdec/sa/extract.py
index dc72c18c..b6502c52 100644
--- a/python/pkg/cdec/sa/extract.py
+++ b/python/pkg/cdec/sa/extract.py
@@ -1,23 +1,26 @@
 #!/usr/bin/env python
 import sys
 import os
+import re
+import gzip
 import argparse
 import logging
-import re
-import multiprocessing as mp
 import signal
+import multiprocessing as mp
 import cdec.sa
 from cdec.sa._sa import monitor_cpu
 
 extractor, prefix = None, None
-online = False
+online, compress = False, False
 
-def make_extractor(config, grammars, features):
-    global extractor, prefix, online
+def make_extractor(args):
+    global extractor, prefix, online, compress
     signal.signal(signal.SIGINT, signal.SIG_IGN) # Let parent process catch Ctrl+C
-    load_features(features)
-    extractor = cdec.sa.GrammarExtractor(config, online)
-    prefix = grammars
+    load_features(args.features)
+    extractor = cdec.sa.GrammarExtractor(args.config, online)
+    prefix = args.grammars
+    online = args.online
+    compress = args.compress
 
 def load_features(features):
     for featdef in features:
@@ -28,7 +31,7 @@ def load_features(features):
         sys.path.remove(prefix)
 
 def extract(inp):
-    global extractor, prefix, online
+    global extractor, prefix, online, compress
     i, sentence = inp
     sentence = sentence[:-1]
     fields = re.split('\s*\|\|\|\s*', sentence)
@@ -37,7 +40,7 @@ def extract(inp):
     if online:
         if len(fields) < 3:
             sys.stderr.write('Error: online mode requires references and alignments.'
-                    '  Not adding sentence to training data: {0}\n'.format(sentence))
+                    '  Not adding sentence to training data: {}\n'.format(sentence))
             sentence = fields[0]
         else:
             sentence, reference, alignment = fields[0:3]
@@ -47,15 +50,17 @@ def extract(inp):
         if len(fields) > 1:
             sentence = fields[0]
             suffix = ' ||| ' + ' ||| '.join(fields[1:])
-    grammar_file = os.path.join(prefix, 'grammar.{0}'.format(i))
-    with open(grammar_file, 'w') as output:
+
+    grammar_file = os.path.join(prefix, 'grammar.'+str(i))
+    if compress: grammar_file += '.gz'
+    with (gzip.open if compress else open)(grammar_file, 'w') as output:
         for rule in extractor.grammar(sentence):
             output.write(str(rule)+'\n')
     # Add training instance _after_ extracting grammars
     if online:
         extractor.add_instance(sentence, reference, alignment)
     grammar_file = os.path.abspath(grammar_file)
-    return '<seg grammar="{0}" id="{1}"> {2} </seg>{3}'.format(grammar_file, i, sentence, suffix)
+    return '<seg grammar="{}" id="{}">{}</seg>{}'.format(grammar_file, i, sentence, suffix)
 
 def main():
     global online
@@ -71,15 +76,17 @@ def main():
                         help='number of sentences / chunk')
     parser.add_argument('-f', '--features', nargs='*', default=[],
                         help='additional feature definitions')
-    parser.add_argument('-o', '--online', action='store_true', default=False,
+    parser.add_argument('-o', '--online', action='store_true',
                         help='online grammar extraction')
+    parser.add_argument('-z', '--compress', action='store_true',
+                        help='compress grammars with gzip')
     args = parser.parse_args()
 
     if not os.path.exists(args.grammars):
         os.mkdir(args.grammars)
     for featdef in args.features:
         if not featdef.endswith('.py'):
-            sys.stderr.write('Error: feature definition file <{0}>'
+            sys.stderr.write('Error: feature definition file <{}>'
                     ' should be a python module\n'.format(featdef))
             sys.exit(1)
 
@@ -88,14 +95,14 @@ def main():
     start_time = monitor_cpu()
     if args.jobs > 1:
         logging.info('Starting %d workers; chunk size: %d', args.jobs, args.chunksize)
-        pool = mp.Pool(args.jobs, make_extractor, (args.config, args.grammars, args.features))
+        pool = mp.Pool(args.jobs, make_extractor, (args,))
         try:
             for output in pool.imap(extract, enumerate(sys.stdin), args.chunksize):
                 print(output)
         except KeyboardInterrupt:
             pool.terminate()
     else:
-        make_extractor(args.config, args.grammars, args.features)
+        make_extractor(args)
         for output in map(extract, enumerate(sys.stdin)):
             print(output)
 
diff --git a/python/pkg/cdec/sa/online_extractor.py b/python/pkg/cdec/sa/online_extractor.py
deleted file mode 100755
index 03a46b3b..00000000
--- a/python/pkg/cdec/sa/online_extractor.py
+++ /dev/null
@@ -1,337 +0,0 @@
-#!/usr/bin/env python
-
-import collections, sys
-
-import cdec.configobj
-
-CAT = '[X]'  # Default non-terminal
-MAX_SIZE = 15  # Max span of a grammar rule (source)
-MAX_LEN = 5  # Max number of terminals and non-terminals in a rule (source)
-MAX_NT = 2  # Max number of non-terminals in a rule
-MIN_GAP = 1  # Min number of terminals between non-terminals (source)
-
-# Spans are _inclusive_ on both ends [i, j]
-# TODO: Replace all of this with bit vectors?
-def span_check(vec, i, j):
-    k = i
-    while k <= j:
-        if vec[k]:
-            return False
-        k += 1
-    return True
-
-def span_flip(vec, i, j):
-    k = i
-    while k <= j:
-        vec[k] = ~vec[k]
-        k += 1
-
-# Next non-terminal
-def next_nt(nt):
-     if not nt:
-         return 1
-     return nt[-1][0] + 1
-
-class NonTerminal:
-    def __init__(self, index):
-        self.index = index
-    def __str__(self):
-        return '[X,{0}]'.format(self.index)
-
-def fmt_rule(f_sym, e_sym, links):
-    a_str = ' '.join('{0}-{1}'.format(i, j) for (i, j) in links)
-    return '[X] ||| {0} ||| {1} ||| {2}'.format(' '.join(str(sym) for sym in f_sym),
-                                                ' '.join(str(sym) for sym in e_sym),
-                                                a_str)
-
-class OnlineGrammarExtractor:
-
-    def __init__(self, config=None):
-        if isinstance(config, str) or isinstance(config, unicode):
-            if not os.path.exists(config):
-                raise IOError('cannot read configuration from {0}'.format(config))
-            config = cdec.configobj.ConfigObj(config, unrepr=True)
-        elif not config:
-            config = collections.defaultdict(lambda: None)
-        self.category = CAT
-        self.max_size = MAX_SIZE
-        self.max_length = config['max_len'] or MAX_LEN
-        self.max_nonterminals = config['max_nt'] or MAX_NT
-        self.min_gap_size = MIN_GAP
-        # Hard coded: require at least one aligned word
-        # Hard coded: require tight phrases
-
-        # Phrase counts
-        self.phrases_f = collections.defaultdict(lambda: 0)
-        self.phrases_e = collections.defaultdict(lambda: 0)
-        self.phrases_fe = collections.defaultdict(lambda: collections.defaultdict(lambda: 0))
-
-        # Bilexical counts
-        self.bilex_f = collections.defaultdict(lambda: 0)
-        self.bilex_e = collections.defaultdict(lambda: 0)
-        self.bilex_fe = collections.defaultdict(lambda: collections.defaultdict(lambda: 0))
-
-    # Aggregate bilexical counts
-    def aggr_bilex(self, f_words, e_words):
-
-        for e_w in e_words:
-            self.bilex_e[e_w] += 1
-
-        for f_w in f_words:
-            self.bilex_f[f_w] += 1
-            for e_w in e_words:
-                self.bilex_fe[f_w][e_w] += 1
-
-    # Aggregate stats from a training instance:
-    # Extract hierarchical phrase pairs
-    # Update bilexical counts
-    def add_instance(self, f_words, e_words, alignment):
-
-        # Bilexical counts
-        self.aggr_bilex(f_words, e_words)
-
-        # Phrase pairs extracted from this instance
-        phrases = set()
-
-        f_len = len(f_words)
-        e_len = len(e_words)
-
-        # Pre-compute alignment info
-        al = [[] for i in range(f_len)]
-        al_span = [[f_len + 1, -1] for i in range(f_len)]
-        for (f, e) in alignment:
-            al[f].append(e)
-            al_span[f][0] = min(al_span[f][0], e)
-            al_span[f][1] = max(al_span[f][1], e)
-
-        # Target side word coverage
-        # TODO: Does Cython do bit vectors?
-        cover = [0] * e_len
-
-        # Extract all possible hierarchical phrases starting at a source index
-        # f_ i and j are current, e_ i and j are previous
-        def extract(f_i, f_j, e_i, e_j, wc, links, nt, nt_open):
-            # Phrase extraction limits
-            if wc + len(nt) > self.max_length or (f_j + 1) > f_len or \
-                    (f_j - f_i) + 1 > self.max_size:
-                return
-            # Unaligned word
-            if not al[f_j]:
-                # Open non-terminal: extend
-                if nt_open:
-                    nt[-1][2] += 1
-                    extract(f_i, f_j + 1, e_i, e_j, wc, links, nt, True)
-                    nt[-1][2] -= 1
-                # No open non-terminal: extend with word
-                else:
-                    extract(f_i, f_j + 1, e_i, e_j, wc + 1, links, nt, False)
-                return
-            # Aligned word
-            link_i = al_span[f_j][0]
-            link_j = al_span[f_j][1]
-            new_e_i = min(link_i, e_i)
-            new_e_j = max(link_j, e_j)
-            # Open non-terminal: close, extract, extend
-            if nt_open:
-                # Close non-terminal, checking for collisions
-                old_last_nt = nt[-1][:]
-                nt[-1][2] = f_j
-                if link_i < nt[-1][3]:
-                    if not span_check(cover, link_i, nt[-1][3] - 1):
-                        nt[-1] = old_last_nt
-                        return
-                    span_flip(cover, link_i, nt[-1][3] - 1)
-                    nt[-1][3] = link_i
-                if link_j > nt[-1][4]:
-                    if not span_check(cover, nt[-1][4] + 1, link_j):
-                        nt[-1] = old_last_nt
-                        return
-                    span_flip(cover, nt[-1][4] + 1, link_j)
-                    nt[-1][4] = link_j
-                for rule in self.form_rules(f_i, new_e_i, f_words[f_i:f_j + 1], e_words[new_e_i:new_e_j + 1], nt, links):
-                    phrases.add(rule)
-                extract(f_i, f_j + 1, new_e_i, new_e_j, wc, links, nt, False)
-                nt[-1] = old_last_nt
-                if link_i < nt[-1][3]:
-                    span_flip(cover, link_i, nt[-1][3] - 1)
-                if link_j > nt[-1][4]:
-                    span_flip(cover, nt[-1][4] + 1, link_j)
-                return
-            # No open non-terminal
-            # Extract, extend with word
-            collision = False
-            for link in al[f_j]:
-                if cover[link]:
-                    collision = True
-            # Collisions block extraction and extension, but may be okay for
-            # continuing non-terminals
-            if not collision:
-                plus_links = []
-                for link in al[f_j]:
-                    plus_links.append((f_j, link))
-                    cover[link] = ~cover[link]
-                links.append(plus_links)
-                for rule in self.form_rules(f_i, new_e_i, f_words[f_i:f_j + 1], e_words[new_e_i:new_e_j + 1], nt, links):
-                    phrases.add(rule)
-                extract(f_i, f_j + 1, new_e_i, new_e_j, wc + 1, links, nt, False)
-                links.pop()
-                for link in al[f_j]:
-                    cover[link] = ~cover[link]
-            # Try to add a word to a (closed) non-terminal, extract, extend
-            if nt and nt[-1][2] == f_j - 1:
-                # Add to non-terminal, checking for collisions
-                old_last_nt = nt[-1][:]
-                nt[-1][2] = f_j
-                if link_i < nt[-1][3]:
-                    if not span_check(cover, link_i, nt[-1][3] - 1):
-                        nt[-1] = old_last_nt
-                        return
-                    span_flip(cover, link_i, nt[-1][3] - 1)
-                    nt[-1][3] = link_i
-                if link_j > nt[-1][4]:
-                    if not span_check(cover, nt[-1][4] + 1, link_j):
-                        nt[-1] = old_last_nt
-                        return
-                    span_flip(cover, nt[-1][4] + 1, link_j)
-                    nt[-1][4] = link_j
-                # Require at least one word in phrase
-                if links:
-                    for rule in self.form_rules(f_i, new_e_i, f_words[f_i:f_j + 1], e_words[new_e_i:new_e_j + 1], nt, links):
-                        phrases.add(rule)
-                extract(f_i, f_j + 1, new_e_i, new_e_j, wc, links, nt, False)
-                nt[-1] = old_last_nt
-                if new_e_i < nt[-1][3]:
-                    span_flip(cover, link_i, nt[-1][3] - 1)
-                if link_j > nt[-1][4]:
-                    span_flip(cover, nt[-1][4] + 1, link_j)
-            # Try to start a new non-terminal, extract, extend
-            if (not nt or f_j - nt[-1][2] > 1) and len(nt) < self.max_nonterminals:
-                # Check for collisions
-                if not span_check(cover, link_i, link_j):
-                    return
-                span_flip(cover, link_i, link_j)
-                nt.append([next_nt(nt), f_j, f_j, link_i, link_j])
-                # Require at least one word in phrase
-                if links:
-                    for rule in self.form_rules(f_i, new_e_i, f_words[f_i:f_j + 1], e_words[new_e_i:new_e_j + 1], nt, links):
-                        phrases.add(rule)
-                extract(f_i, f_j + 1, new_e_i, new_e_j, wc, links, nt, False)
-                nt.pop()
-                span_flip(cover, link_i, link_j)
-            # TODO: try adding NT to start, end, both
-            # check: one aligned word on boundary that is not part of a NT
-
-        # Try to extract phrases from every f index
-        f_i = 0
-        while f_i < f_len:
-            # Skip if phrases won't be tight on left side
-            if not al[f_i]:
-                f_i += 1
-                continue
-            extract(f_i, f_i, f_len + 1, -1, 1, [], [], False)
-            f_i += 1
-
-        for rule in sorted(phrases):
-            print rule
-
-    # Create a rule from source, target, non-terminals, and alignments
-    def form_rules(self, f_i, e_i, f_span, e_span, nt, al):
-    
-        # This could be more efficient but is unlikely to be the bottleneck
-    
-        rules = []
-    
-        nt_inv = sorted(nt, cmp=lambda x, y: cmp(x[3], y[3]))
-    
-        f_sym = f_span[:]
-        off = f_i
-        for next_nt in nt:
-            nt_len = (next_nt[2] - next_nt[1]) + 1
-            i = 0
-            while i < nt_len:
-                f_sym.pop(next_nt[1] - off)
-                i += 1
-            f_sym.insert(next_nt[1] - off, NonTerminal(next_nt[0]))
-            off += (nt_len - 1)
-    
-        e_sym = e_span[:]
-        off = e_i
-        for next_nt in nt_inv:
-            nt_len = (next_nt[4] - next_nt[3]) + 1
-            i = 0
-            while i < nt_len:
-                e_sym.pop(next_nt[3] - off)
-                i += 1
-            e_sym.insert(next_nt[3] - off, NonTerminal(next_nt[0]))
-            off += (nt_len - 1)
-    
-        # Adjusting alignment links takes some doing
-        links = [list(link) for sub in al for link in sub]
-        links_len = len(links)
-        nt_len = len(nt)
-        nt_i = 0
-        off = f_i
-        i = 0
-        while i < links_len:
-            while nt_i < nt_len and links[i][0] > nt[nt_i][1]:
-                off += (nt[nt_i][2] - nt[nt_i][1])
-                nt_i += 1
-            links[i][0] -= off
-            i += 1
-        nt_i = 0
-        off = e_i
-        i = 0
-        while i < links_len:
-            while nt_i < nt_len and links[i][1] > nt_inv[nt_i][3]:
-                off += (nt_inv[nt_i][4] - nt_inv[nt_i][3])
-                nt_i += 1
-            links[i][1] -= off
-            i += 1
-    
-        # Rule
-        rules.append(fmt_rule(f_sym, e_sym, links))
-        if len(f_sym) >= self.max_length or len(nt) >= self.max_nonterminals:
-            return rules
-        last_index = nt[-1][0] if nt else 0
-        # Rule [X]
-        if not nt or not isinstance(f_sym[-1], NonTerminal):
-            f_sym.append(NonTerminal(last_index + 1))
-            e_sym.append(NonTerminal(last_index + 1))
-            rules.append(fmt_rule(f_sym, e_sym, links))
-            f_sym.pop()
-            e_sym.pop()
-        # [X] Rule
-        if not nt or not isinstance(f_sym[0], NonTerminal):
-            for sym in f_sym:
-                if isinstance(sym, NonTerminal):
-                    sym.index += 1
-            for sym in e_sym:
-                if isinstance(sym, NonTerminal):
-                    sym.index += 1
-            for link in links:
-                link[0] += 1
-                link[1] += 1
-            f_sym.insert(0, NonTerminal(1))
-            e_sym.insert(0, NonTerminal(1))
-            rules.append(fmt_rule(f_sym, e_sym, links))
-        if len(f_sym) >= self.max_length or len(nt) + 1 >= self.max_nonterminals:
-            return rules
-        # [X] Rule [X]
-        if not nt or not isinstance(f_sym[-1], NonTerminal):
-            f_sym.append(NonTerminal(last_index + 2))
-            e_sym.append(NonTerminal(last_index + 2))
-            rules.append(fmt_rule(f_sym, e_sym, links))
-        return rules
-
-def main(argv):
-
-    extractor = OnlineGrammarExtractor()
-
-    for line in sys.stdin:
-        print >> sys.stderr, line.strip()
-        f_words, e_words, a_str = (x.split() for x in line.split('|||'))
-        alignment = sorted(tuple(int(y) for y in x.split('-')) for x in a_str)
-        extractor.add_instance(f_words, e_words, alignment)
-
-if __name__ == '__main__':
-    main(sys.argv)
diff --git a/python/pkg/cdec/score.py b/python/pkg/cdec/score.py
index 22257774..829dfdfd 100644
--- a/python/pkg/cdec/score.py
+++ b/python/pkg/cdec/score.py
@@ -1 +1 @@
-from _cdec import BLEU, TER, CER, Metric
+from _cdec import BLEU, TER, CER, SSK, QCRI, Metric