class Tests(WithTempDir):
def setUp(self):
WithTempDir.setUp(self)
self.lex = LexStat(test_data('KSL.qlc'))
self.part = Partial(test_data('partial_cognates.tsv'),
segments='segments')
self.part.add_entries('pid1', 'partial_cognate_sets', lambda x: x)
self.part.add_entries('pid2', 'partialids2',
lambda x: [int(y) for y in x.split(' ')])
def test_bcubes(self):
res = bcubes(self.lex, test='cogid', pprint=False)
self.assertAlmostEquals(res, (1.0, 1.0, 1.0))
_ = bcubes(self.lex, 'cogid', 'cogid', pprint=True, per_concept=True)
def test_partial_bcubes(self):
res = partial_bcubes(self.part, 'pid1', 'pid2', pprint=False)
assert [round(x, 2) for x in res] == [0.92, 0.98, 0.95]
_ = partial_bcubes(self.part, 'pid1', 'pid2', pprint=True)
def test_pairs(self):
res = pairs(self.lex, test='cogid', pprint=False)
self.assertAlmostEquals(res, (1.0, 1.0, 1.0))
def test_diff(self):
res = diff(self.lex, test='cogid', tofile=False, pprint=False)
self.assertAlmostEquals(res, ((1.0, 1.0, 1.0), (1.0, 1.0, 1.0)))
self.lex.add_entries('cugid', 'cogid',
lambda x: x + 1 if x % 2 else x * x)
_ = diff(self.lex, gold='cogid', test='cogid',
filename='%s' % self.tmp_path('test_acd'), pprint=False)
d2 = diff(self.lex, gold='cugid', test='cogid',
filename='%s' % self.tmp_path('test_acd'),
pprint=False, tofile=False)
_ = diff(self.lex, gold='cugid', test='cogid',
filename='%s' % self.tmp_path('test_acd'),
pprint=False, tofile=True)
assert d2[0] != 1
def test_random_cognates(self):
random_cognates(self.lex, ref='randomid')
assert 'randomid' in self.lex.header
def test_extreme_cognates(self):
extreme_cognates(self.lex, ref="lumperid", bias='lumper')
assert self.lex[1, 'lumperid'] == self.lex[2, 'lumperid']
extreme_cognates(self.lex, ref='splitterid', bias='splitter')
assert self.lex[1, 'splitterid'] != self.lex[2, 'splitterid']
assert_raises(ValueError, extreme_cognates, self.lex, bias='')
def setUp(self):
WithTempDir.setUp(self)
self.lex = LexStat(test_data('KSL.qlc'))
self.part = Partial(test_data('partial_cognates.tsv'),
segments='segments')
self.part.add_entries('pid1', 'partial_cognate_sets', lambda x: x)
self.part.add_entries('pid2', 'partialids2', lambda x: [int(y)
for y in x.split(' ')])
class Tests(WithTempDir):
def setUp(self):
WithTempDir.setUp(self)
self.lex = LexStat(test_data('KSL.qlc'))
self.part = Partial(test_data('partial_cognates.tsv'),
segments='segments')
self.part.add_entries('pid1', 'partial_cognate_sets', lambda x: x)
self.part.add_entries('pid2', 'partialids2', lambda x: [int(y)
for y in x.split(' ')])
def test_bcubes(self):
from lingpy.evaluate.acd import bcubes
res = bcubes(self.lex, test='cogid', pprint=False)
self.assertAlmostEquals(res, (1.0, 1.0, 1.0))
res = bcubes(self.lex, 'cogid', 'cogid', pprint=True,
per_concept=True)
def test_partial_bcubes(self):
from lingpy.evaluate.acd import partial_bcubes
res = partial_bcubes(self.part, 'pid1', 'pid2', pprint=False)
assert [round(x, 2) for x in res] == [0.92, 0.98, 0.95]
res = partial_bcubes(self.part, 'pid1', 'pid2', pprint=True)
def test_pairs(self):
from lingpy.evaluate.acd import pairs
res = pairs(self.lex, test='cogid', pprint=False)
self.assertAlmostEquals(res, (1.0, 1.0, 1.0))
def test_diff(self):
from lingpy.evaluate.acd import diff
res = diff(self.lex, test='cogid', tofile=False, pprint=False)
self.assertAlmostEquals(res, ((1.0, 1.0, 1.0), (1.0, 1.0, 1.0)))
self.lex.add_entries('cugid', 'cogid', lambda x: x+1 if x % 2 else x*x)
d1 = diff(self.lex, gold='cogid', test='cogid', filename='%s' % self.tmp_path('test_acd'), pprint=False)
d2 = diff(self.lex, gold='cugid', test='cogid', filename='%s' %
self.tmp_path('test_acd'), pprint=False, tofile=False)
d3 = diff(self.lex, gold='cugid', test='cogid', filename='%s' %
self.tmp_path('test_acd'), pprint=False, tofile=True)
assert d2[0] != 1
def writeToFile():
print("LOAD TEST WORDLIST")
pathToAnnotatedWordList = "Data/IELex/output/IELex-2016.tsv"
print("LOAD WORDLIST")
#pathToAnnotatedWordList = "Data/mattis_new/output/ObUgrian-110-21.tsv.asjp"
languages,words,global_ids,cognate_classes = loadAnnotatedWordList(pathToAnnotatedWordList)
print(len(set(global_ids)))
stoplist = {221 , 646 ,1333 ,1224 , 778 ,1402, 1411, 1232, 1203, 1292}
languages,words,global_ids,cognate_classes = getRidOfValidationSet(languages,words,global_ids,cognate_classes,stoplist)
print(len(set(global_ids)))
with codecs.open("lexstat_wordlist.txt","w",encoding="UTF-8") as f:
f.write("CONCEPT\tIPA\tDOCULECT\tCOGID\n")
for l,w,gi,cog in zip(languages,words,global_ids,cognate_classes):
f.write(str(gi)+"\t"+w+"\t"+l+"\t"+cog+"\n")
wl =get_wordlist("lexstat_wordlist.txt",delimiter="\t")
print(wl.get_dict(concept="730",entry="IPA"))
print("initializing lexstat")
lex = LexStat(wl)
print("getting scorer")
lex.get_scorer()
print("clustering")
lex.cluster(method="lexstat", threshold=0.6, ref="cognate_class_pred")
print("output")
lex.output('tsv', filename="lexstat_ielex")
from lingpy.evaluate.acd import bcubes, diff
bcubes(lex, "cognate_class", "COGID")
print(bcubes(lex, "cognate_class", "cognate_class_pred"))
def test_correctness(self):
lex = LexStat({
0: ['ID', 'doculect', 'concept', 'IPA'],
1: ['1', 'deu', 'hand', 'hand'],
2: ['2', 'eng', 'hand', 'hand'],
3: ['3', 'xyz', 'hand', 'xyz']})
lex.get_scorer(**self.get_scorer_kw)
lex.cluster(ref='cogid')
self.assertEquals(lex.get_entries('cogid'), [[1, 1, 3]])
lex = LexStat({
0: ['ID', 'concept', 'ipa', 'doculect'],
1: ['5424', 'Abend::N', 'swar', 'FRA'],
2: ['5425', 'Abend::N', 'sware', 'FRA'],
3: ['5426', 'Abend::N', 'sear3', 'RON'],
4: ['5427', 'Abend::N', 'ivniN', 'ENG'],
5: ['5428', 'Abend::N', 'noyt3', 'POR'],
6: ['5429', 'Abend::N', 'tardi5a', 'POR'],
7: ['5430', 'Abend::N', 'afd3n', 'DAN'],
})
lex.get_scorer()
lex.cluster(method='lexstat', threshold=0.8, ref='cogid')
self.assertEquals(lex.get_entries('cogid'), [[1, 2, 3, 4, 5], [0, 0, 3, 3, 0]])
def setUp(self):
WithTempDir.setUp(self)
self.lex = LexStat(test_data('KSL.qlc'))
self.log = get_log()
self.get_scorer_kw = dict(runs=10, rands=10, limit=100)
class TestLexStat(WithTempDir):
def setUp(self):
WithTempDir.setUp(self)
self.lex = LexStat(test_data('KSL.qlc'))
self.log = get_log()
self.get_scorer_kw = dict(runs=10, rands=10, limit=100)
def test_init(self):
LexStat({0: ['ID', 'doculect', 'concept', 'IPA']}, model='sca')
ls = LexStat({0: ['ID', 'doculect', 'concept', 'IPA']})
self.assertIn('lexstat', repr(ls))
LexStat(ls)
LexStat({0: ['ID', 'doculect', 'concept', 'tokens']})
self.assertRaises(AssertionError, LexStat, {0: ['ID', 'doculect', 'concept']})
LexStat(test_data('phybo.qlc'), check=True)
with patch('lingpy.compare.lexstat.log', self.log):
LexStat(test_data('KSL.qlc'), check=True)
assert self.log.info.called
error_log = self.tmp_path('errors')
with patch('lingpy.util.confirm', Mock(return_value=True)):
lex = LexStat({
0: ['ID', 'doculect', 'concept', 'IPA', 'tokens'],
1: ['1', 'deu', 'hand', 'hand', ['']],
2: ['2', 'eng', 'hand', 'hand', ['abc']],
3: ['3', 'xyz', 'hand', 'hund', 'h u n d'],
}, check=True, errors='%s' % error_log)
assert error_log.exists()
self.assertEquals(len(lex._meta['errors']), 2)
def test_init2(self):
freqs = self.lex.freqs['Hawaiian']
for char, n in {'5.W.C': 19, '5.I.V': 87, '5.Y.V': 75, '5.U.V': 87}.items():
self.assertEquals(freqs[char], n)
self.assertEquals(len(self.lex.chars), 187)
self.assertEquals(len(self.lex.rchars), 35)
self.maxDiff = None
for name in 'bscorer rscorer pairs'.split():
obj = jsonload(test_data('KSL.%s.json' % name))
if name != 'pairs':
self.assertEquals(getattr(self.lex, name).matrix, obj)
else:
for key, values in self.lex.pairs.items():
values = set(values)
ovalues = set(tuple(v) for v in obj['---'.join(key)])
if 'TRAVIS' not in os.environ and sys.version_info < (3, 5):
# For some reason this assertion fails when run on travis-ci with
# python 3.3
self.assertEquals(values, ovalues)
def test_getitem(self):
self.assertIsNone(self.lex['xyz'])
def test_get_scorer(self):
self.lex.get_scorer(**self.get_scorer_kw)
assert hasattr(self.lex, "cscorer")
with patch('lingpy.compare.lexstat.log', self.log):
self.lex.get_scorer(**self.get_scorer_kw)
assert self.log.warn.called
del self.lex.cscorer
self.lex.get_scorer(**self.get_scorer_kw)
self.lex.get_scorer(method='markov', **self.get_scorer_kw)
def test_cluster(self):
self.lex.get_scorer(**self.get_scorer_kw)
self.lex.cluster(method="lexstat", threshold=0.7)
self.lex.cluster(method="edit-dist", threshold=0.7)
self.lex.cluster(method="turchin", threshold=0.7)
self.assertRaises(ValueError, self.lex.cluster, method="fuzzy")
with patch('lingpy.basic.parser.input', Mock(return_value='y')):
self.lex.cluster(method="sca", guess_threshold=True, gt_mode='nulld')
assert 'scaid' in self.lex.header \
and 'lexstatid' in self.lex.header \
and 'editid' in self.lex.header \
and 'turchinid' in self.lex.header
def test_align_pairs(self):
self.lex.align_pairs('English', 'German', method='sca')
def test_get_subset(self):
self.lex.get_subset([])
self.assertEquals([v for v in self.lex.subsets.values() if v], [])
pairs = jsonload(test_data('KSL.pairs.json'))
self.assertEquals(
sorted('---'.join(k) for k in self.lex.subsets.keys()),
sorted(pairs.keys()))
def test_get_distances(self):
self.lex.get_scorer(**self.get_scorer_kw)
self.lex.get_random_distances()
self.lex.get_distances()
self.lex.get_distances(method='turchin')
self.lex.get_distances(aggregate=False)
def test_get_frequencies(self):
f = self.lex.get_frequencies('sounds')
assert len(f) == self.lex.width
f = self.lex.get_frequencies('sounds', aggregated=True)
tokens = []
for k in self.lex:
for t in self.lex[k, 'tokens']:
tokens += [t]
assert len(f) == len(set(tokens))
d = self.lex.get_frequencies('diversity', ref='cogid')
assert isinstance(d, float)
w = self.lex.get_frequencies('wordlength')
assert len(w) == self.lex.width
w = self.lex.get_frequencies('wordlength', aggregated=True)
assert isinstance(w, float)
def test_output(self):
self.lex.output('csv', filename='%s' % self.tmp_path('test_lexstat'))
self.lex.output('scorer', filename='%s' % self.tmp_path('test_lexstat'))
def test_correctness(self):
lex = LexStat({
0: ['ID', 'doculect', 'concept', 'IPA'],
1: ['1', 'deu', 'hand', 'hand'],
2: ['2', 'eng', 'hand', 'hand'],
3: ['3', 'xyz', 'hand', 'xyz']})
lex.get_scorer(**self.get_scorer_kw)
lex.cluster(ref='cogid')
self.assertEquals(lex.get_entries('cogid'), [[1, 1, 3]])
lex = LexStat({
0: ['ID', 'concept', 'ipa', 'doculect'],
1: ['5424', 'Abend::N', 'swar', 'FRA'],
2: ['5425', 'Abend::N', 'sware', 'FRA'],
3: ['5426', 'Abend::N', 'sear3', 'RON'],
4: ['5427', 'Abend::N', 'ivniN', 'ENG'],
5: ['5428', 'Abend::N', 'noyt3', 'POR'],
6: ['5429', 'Abend::N', 'tardi5a', 'POR'],
7: ['5430', 'Abend::N', 'afd3n', 'DAN'],
})
lex.get_scorer()
lex.cluster(method='lexstat', threshold=0.8, ref='cogid')
self.assertEquals(lex.get_entries('cogid'), [[1, 2, 3, 4, 5], [0, 0, 3, 3, 0]])
def make(*args, **kw):
kw.setdefault('errors', str(tmppath / 'errors.log'))
return LexStat(*args, **kw)
def setUp(self):
self.lex = LexStat(test_data('KSL.qlc'))
class TestLexStat(unittest.TestCase):
def setUp(self):
self.lex = LexStat(test_data('KSL.qlc'))
def test_get_scorer(self):
self.lex.get_scorer()
assert hasattr(self.lex,"cscorer") == True
def test_cluster(self):
self.lex.get_scorer()
self.lex.cluster(method="lexstat", threshold=0.7)
self.lex.cluster(method="edit-dist", threshold=0.7)
self.lex.cluster(method="turchin", threshold=0.7)
assert ('scaid' in self.lex.header and 'lexstatid' in self.lex.header \
and 'editid' in self.lex.header and 'turchinid' in \
self.lex.header) == True
def test_align_pairs(self):
self.lex.align_pairs('English', 'German', method='sca')
def _make_one(self, *args, **kw):
kw.setdefault('errors', self.tmp_path('errors.log').as_posix())
return LexStat(*args, **kw)
class Tests(WithTempDir):
def setUp(self):
WithTempDir.setUp(self)
self.lex = LexStat(test_data('KSL.qlc'))
self.part = Partial(test_data('partial_cognates.tsv'),
segments='segments')
self.part.add_entries('pid1', 'partial_cognate_sets', lambda x: x)
self.part.add_entries('pid2', 'partialids2',
lambda x: [int(y) for y in x.split(' ')])
def test_bcubes(self):
res = bcubes(self.lex, test='cogid', pprint=False)
self.assertAlmostEquals(res, (1.0, 1.0, 1.0))
_ = bcubes(self.lex, 'cogid', 'cogid', pprint=True, per_concept=True)
def test_partial_bcubes(self):
res = partial_bcubes(self.part, 'pid1', 'pid2', pprint=False)
assert [round(x, 2) for x in res] == [0.92, 0.98, 0.95]
_ = partial_bcubes(self.part, 'pid1', 'pid2', pprint=True)
def test_pairs(self):
res = pairs(self.lex, test='cogid', pprint=False)
self.assertAlmostEquals(res, (1.0, 1.0, 1.0))
def test_diff(self):
res = diff(self.lex, test='cogid', tofile=False, pprint=False)
self.assertAlmostEquals(res, ((1.0, 1.0, 1.0), (1.0, 1.0, 1.0)))
self.lex.add_entries('cugid', 'cogid', lambda x: x + 1
if x % 2 else x * x)
_ = diff(self.lex,
gold='cogid',
test='cogid',
filename='%s' % self.tmp_path('test_acd'),
pprint=False)
d2 = diff(self.lex,
gold='cugid',
test='cogid',
filename='%s' % self.tmp_path('test_acd'),
pprint=False,
tofile=False)
_ = diff(self.lex,
gold='cugid',
test='cogid',
filename='%s' % self.tmp_path('test_acd'),
pprint=False,
tofile=True)
assert d2[0] != 1
def test_random_cognates(self):
random_cognates(self.lex, ref='randomid')
assert 'randomid' in self.lex.header
def test_extreme_cognates(self):
extreme_cognates(self.lex, ref="lumperid", bias='lumper')
assert self.lex[1, 'lumperid'] == self.lex[2, 'lumperid']
extreme_cognates(self.lex, ref='splitterid', bias='splitter')
assert self.lex[1, 'splitterid'] != self.lex[2, 'splitterid']
assert_raises(ValueError, extreme_cognates, self.lex, bias='')
def main():
results = []
"""for i in range(20):
lex = LexStat("../PIE_scored_{}_og.csv".format(i))
# lex.get_scorer()
# lex.cluster(method="lexstat", threshold=0.6, ref="cognates")
print(".", end="", flush=True)
results.append( (
i,
bcubes(
lex,
"cogid",
"newcogid",
pprint=False,
modify_ref=lambda x: abs(int(x)),
),
)
)
:
print()
print("OG")
for r in results:
print(r)
"""
records = []
f_names = [
"SLV", "GER", "ROM", "OUG", "KSL", "BAI", "JAP", "PIE", "IEL", "PAN"
]
for name in f_names:
print(name)
for n in range(1, 7):
results = []
for i in [50]:
lex = LexStat("../{}_updating_{}_{}.csv".format(name, i, n))
# lex.get_scorer()
# lex.cluster(method="lexstat", threshold=0.6, ref="cognates")
precision, recall, f_score = bcubes(
lex,
"cogid",
"newcogid",
pprint=False,
modify_ref=lambda x: abs(int(x)),
)
records.append([name, n, precision, recall, f_score])
for r in results:
print(r)
print()
f, axes = plt.subplots(1, 2, figsize=(20, 8))
# markers = {i: "${}$".format(i) for i in range(1, 7)}
df = pd.DataFrame.from_records(
records,
columns=["Partition", "Iteration", "Precision", "Recall", "F-score"])
sns.lineplot(x="Recall",
y="Precision",
hue="Partition",
data=df,
marker="o",
ax=axes[0])
# plt.subplots_adjust(right=0.7)
# plt.legend(bbox_to_anchor=(1.02, 1.02), loc="upper left")
for _, i, precision, recall, _ in records:
if i == 1 or i == 6:
axes[0].annotate(str(i), (recall, precision))
# markers = {i: "${}$".format(i) for i in range(1, 7)}
df = pd.DataFrame.from_records(
records,
columns=["Partition", "Iteration", "Precision", "Recall", "F-score"])
sns.lineplot(x="Iteration",
y="F-score",
hue="Partition",
data=df,
ax=axes[1])
# plt.subplots_adjust(right=0.7)
axes[0].get_legend().remove()
lgd = plt.legend(bbox_to_anchor=(1.02, 1.00), loc="upper left")
plt.savefig("bbb.png", bbox_extra_artists=[lgd], bbox_inches="tight")
def setUp(self):
self.lex = LexStat(test_data('KSL.qlc'))
class TestLexStat(unittest.TestCase):
def setUp(self):
self.lex = LexStat(test_data('KSL.qlc'))
def test_get_scorer(self):
self.lex.get_scorer()
assert hasattr(self.lex, "cscorer") == True
def test_cluster(self):
self.lex.get_scorer()
self.lex.cluster(method="lexstat", threshold=0.7)
self.lex.cluster(method="edit-dist", threshold=0.7)
self.lex.cluster(method="turchin", threshold=0.7)
assert ('scaid' in self.lex.header and 'lexstatid' in self.lex.header \
and 'editid' in self.lex.header and 'turchinid' in \
self.lex.header) == True
def test_align_pairs(self):
self.lex.align_pairs('English', 'German', method='sca')