Fixes duplicate outcomes when removes_duplicates=True (#148)

* enforces unique outcomes in preprocess.py; bumps version number

* adds test for remove_duplicates in test_preprocess.py

Author: kuchenrolle

pyndl/__init__.py

@@ -17,7 +17,7 @@
 __author__ = ('Konstantin Sering, Marc Weitz, '
               'David-Elias Künstle, Lennard Schneider')
 __author_email__ = '[email protected]'
-__version__ = '0.5.0'
+__version__ = '0.5.1'
 __license__ = 'MIT'
 __description__ = ('Naive discriminative learning implements learning and '
                    'classification models based on the Rescorla-Wagner '

pyndl/preprocess.py

@@ -100,9 +100,9 @@ def ngrams_to_word(occurrences, n_chars, outfile, remove_duplicates=True):
         if not ngrams or not occurrence:
             continue
         if remove_duplicates:
-            outfile.write("{}\t{}\n".format("_".join(set(ngrams)), occurrence))
-        else:
-            outfile.write("{}\t{}\n".format("_".join(ngrams), occurrence))
+            ngrams = set(ngrams)
+            occurrence = "_".join(set(occurrence.split("_")))
+        outfile.write("{}\t{}\n".format("_".join(ngrams), occurrence))
 
 
 def process_occurrences(occurrences, outfile, *,
@@ -132,9 +132,9 @@ def process_occurrences(occurrences, outfile, *,
             if not cues:
                 continue
             if remove_duplicates:
-                outfile.write("{}\t{}\n".format("_".join(set(cues.split("_"))), outcomes))
-            else:
-                outfile.write("{}\t{}\n".format(cues, outcomes))
+                cues = "_".join(set(cues.split("_")))
+                outcomes = "_".join(set(outcomes.split("_")))
+            outfile.write("{}\t{}\n".format(cues, outcomes))
     else:
         raise NotImplementedError('cue_structure=%s is not implemented yet.' % cue_structure)
 
@@ -245,19 +245,16 @@ def gen_occurrences(words):
         """
         if event_structure == 'consecutive_words':
             occurrences = list()
-            cur_words = list()
-            ii = 0
-            while True:
-                if ii < len(words):
-                    cur_words.append(words[ii])
-                if ii >= len(words) or ii >= number_of_words:
-                    # remove the first word
-                    cur_words = cur_words[1:]
+            # can't have more consecutive words than total words
+            length = min(number_of_words, len(words))
+            # slide window over list of words
+            for ii in range(1 - length, len(words)):
+                # no consecutive words before first word
+                start = max(ii, 0)
+                # no consecutive words after last word
+                end = min(ii + length, len(words))
                 # append (cues, outcomes) with empty outcomes
-                occurrences.append(("_".join(cur_words), ''))
-                ii += 1
-                if not cur_words:
-                    break
+                occurrences.append(("_".join(words[start:end]), ""))
             return occurrences
         # for words = (A, B, C, D); before = 2, after = 1
         # make: (B, A), (A_C, B), (A_B_D, C), (B_C, D)
@@ -274,6 +271,8 @@ def gen_occurrences(words):
         elif event_structure == 'line':
             # (cues, outcomes) with empty outcomes
             return [('_'.join(words), ''), ]
+        else:
+            raise ValueError('gen_occurrences should be one of {"consecutive_words", "word_to_word", "line"}')
 
     def process_line(line):
         """processes one line of text."""

setup.cfg

@@ -4,7 +4,7 @@ max-line-length = 120
 
 [pylint]
 max-line-length = 120
-good-names = nn, ii, _
+good-names = nn, ii, _, jj
 extension-pkg-whitelist=numpy,pyndl.ndl_parallel
 ignore=pyndl/ndl_parallel
 disable=E1101

tests/reference/event_file_bigrams_to_word.tab.gz

@@ -109,6 +109,53 @@ def test_bigrams_to_word():
     os.remove(event_file)
 
 
+def test_remove_duplicates():
+    event_file_noduplicates = os.path.join(TEST_ROOT, "temp/event_file_bigrams_to_word_noduplicates.tab.gz")
+    event_file_duplicates = os.path.join(TEST_ROOT, "temp/event_file_bigrams_to_word_duplicates.tab.gz")
+    create_event_file(RESOURCE_FILE, event_file_duplicates,
+                      context_structure="document",
+                      event_structure="consecutive_words",
+                      event_options=(3, ),
+                      cue_structure="bigrams_to_word",
+                      remove_duplicates=False)
+    create_event_file(RESOURCE_FILE, event_file_noduplicates,
+                      context_structure="document",
+                      event_structure="consecutive_words",
+                      event_options=(3, ),
+                      cue_structure="bigrams_to_word",
+                      remove_duplicates=True)
+
+    with gzip.open(event_file_noduplicates, "rt") as new_file:
+        lines_new = new_file.readlines()
+    with gzip.open(event_file_duplicates, "rt") as reference:
+        lines_reference = reference.readlines()
+    assert len(lines_new) == len(lines_reference)
+    n_cues_unequal = 0
+    n_outcomes_unequal = 0
+    for ii, line in enumerate(lines_new):
+        cues, outcomes = line.strip().split('\t')
+        cues = sorted(cues.split('_'))
+        outcomes = sorted(outcomes.split('_'))
+        ref_cues, ref_outcomes = lines_reference[ii].strip().split('\t')
+        ref_cues = sorted(ref_cues.split('_'))
+        ref_outcomes = sorted(ref_outcomes.split('_'))
+        if len(cues) != len(ref_cues):
+            n_cues_unequal += 1
+        if len(outcomes) != len(ref_outcomes):
+            n_outcomes_unequal += 1
+        # there should be no duplicates in (noduplicates)
+        assert len(cues) == len(set(cues))
+        assert len(outcomes) == len(set(outcomes))
+        # after making each list unique it should be the same
+        assert set(cues) == set(ref_cues)
+        assert set(outcomes) == set(ref_outcomes)
+    assert n_cues_unequal == 1098
+    assert n_outcomes_unequal == 66
+
+    os.remove(event_file_noduplicates)
+    os.remove(event_file_duplicates)
+
+
 def test_word_to_word():
     event_file = os.path.join(TEST_ROOT, "temp/event_file_word_to_word.tab.gz")
     reference_file = os.path.join(TEST_ROOT, "reference/event_file_word_to_word.tab.gz")