def run(args):
ds = Dataset()
try:
part = Partial(
ds.dir.joinpath('workflow', 'D_Chen_partial.bin.tsv').as_posix())
except:
part = Partial(ds.dir.joinpath('workflow',
'D_Chen_subset.tsv').as_posix(),
segments='tokens')
part.get_partial_scorer(runs=10000)
part.output('tsv',
filename=ds.dir.joinpath('workflow',
'D_Chen_partial.bin').as_posix(),
ignore=[],
prettify=False)
args.log.info('[i] saved the scorer')
finally:
part.partial_cluster(method='lexstat',
threshold=0.55,
ref='cogids',
mode='global',
gop=-2,
cluster_method='infomap')
part.output('tsv',
filename=ds.dir.joinpath('workflow',
'D_Chen_partial').as_posix(),
prettify=False)
from lingpy import *
from lingpy.compare.partial import Partial
try:
part = Partial('hm-111-17.bin.tsv', segments='segments')
except:
part = Partial('hm-111-17.tsv', segments='segments')
part.get_scorer(runs=10000)
part.output('tsv', filename='hm-111-17.bin')
# manually correct error in data
part.partial_cluster(method='lexstat',
cluster_method='infomap',
threshold=0.6,
ref='cogids')
part.add_entries('note', 'cogid', lambda x: '')
part.add_entries('morphemes', 'cogid', lambda x: '')
part.output('tsv', filename='hm-111-17-t06', ignore='all', prettify=False)
from lingpy import *
from lingpy.compare.partial import Partial
from lingpy.evaluate.acd import partial_bcubes
try:
lexx = LexStat('hm-jerry-scored.bin.tsv', segments='segments')
lex = Partial('../hm-111-17_16feb.tsv', segments='segments')
lex.cscorer = lexx.cscorer
except:
lex = Partial('../hm-111-17_16feb.tsv', segments='segments')
lex.get_scorer(runs=10000)
lex.output('tsv', filename='hm-jerry-scored.bin')
# we test several thresholds
for i in range(2, 8):
lex.partial_cluster(method='lexstat',
cluster_method='infomap',
threshold=i * 0.1,
ref='t' + str(i))
a, b, c = partial_bcubes(lex, 'cogids', 't' + str(i), pprint=False)
print('{0:2} {1:.2f} {2:.2f} {3:.2f}'.format(i, a, b, c))
f, mode, ts, p, r, fs))
methods = ['sca', 'lexstat']
cluster_methods = ['infomap', 'mcl', 'upgma']
measures = ['partial', 'strict', 'loose']
for f in infiles:
try:
lex = Partial(pcd_path('data', 'BIN_'+f+'.tsv'))
except IOError:
lex = Partial(pcd_path('data', f+'.tsv'))
lex.get_scorer(
preprocessing=False,
runs=10000,
)
lex.output('tsv', filename=pcd_path('data', 'BIN_'+f[2:]))
# create new reference ids for cogantes from partial cognates
if not 'strict_cogid' in lex.header:
lex.add_cognate_ids('partialids', 'strict_cogid', 'strict')
if not 'loose_cogid' in lex.header:
lex.add_cognate_ids('partialids', 'loose_cogid', 'loose')
for i in range(1,20):
print("Analyzing {0} with t={1}...".format(f, i))
t = 0.05 * i
ts = '{0:.2f}'.format(t).replace('0.','')
for m in methods:
msf = 'f_'+m
for cm in cluster_methods:
def prepare(ds):
# steps:
# parse characters (numbers, zeros)
# check for number
# recreate partial cognate identifiers
# create strict cognate identifieres
# code everything as CLDF-like file
con = Concepticon()
beida = con.conceptlists['BeijingDaxue-1964-905']
inv = ds.sounds
words = Wordlist(ds.raw('chars-corrected-2017-06-18.tsv'))
partialids, pidc = {}, {}
pidx = 1
concepts = {}
for idx, chars, tks, doculect, glossid in iter_rows(
words, 'benzi', 'segments', 'doculect', 'beida_id'):
tokens = tokens2morphemes(tks)
benzi = parse_chars(chars, doculect, tokens)
if len(tokens) != len(benzi):
print(doculect, glossid, benzi, tokens)
pids = []
for char in benzi:
if char == '囗':
pids += [str(pidx)]
pidx += 1
else:
if char not in partialids:
partialids[char] = str(pidx)
pidx += 1
pids += [partialids[char]]
words[idx, 'cogids'] = ' '.join(pids)
words[idx, 'benzi'] = ' '.join(benzi)
# retrieve correct concept
bidx = 'BeijingDaxue-1964-905-' + glossid
concept = beida.concepts[bidx]
concepts[idx] = [
concept.concepticon_id, concept.attributes['chinese'],
concept.attributes['pageno'], concept.attributes['pinyin']
]
words[idx, 'concept'] = concept.gloss + ' (' + concept.attributes[
'pinyin'] + ' ' + concept.attributes['chinese'] + ')'
for i, entry in enumerate(['concepticon_id', 'chinese', 'page', 'pinyin']):
words.add_entries(entry, concepts, lambda x: x[i])
words.add_entries('benzi_in_source', 'hanzi', lambda x: x)
words.add_entries('source', 'ipa', lambda x: 'BeijingDaxue1964')
words.add_entries('value', 'ipa', lambda x: x)
words.add_entries('form', 'ipa', lambda x: x)
words.add_entries('glottolog', 'doculect',
lambda x: ds.languages[x]['glottolog'])
words.add_entries('iso', 'doculect', lambda x: ds.languages[x]['iso'])
# determine order of entries
order = {}
for d in words.cols:
entries = words.get_list(col=d, flat=True)
concept, oid = '', 1
for idx in sorted(entries):
new_concept = words[idx, 'concept']
if new_concept == concept:
oid += 1
else:
concept = new_concept
oid = 1
order[idx] = oid
words.add_entries('order', order, lambda x: str(x))
words.output('tsv', filename=ds.raw('tmp-2017-06-18'))
print('first run on words')
part = Partial(ds.raw('tmp-2017-06-18.tsv'), segments='segments')
part.add_cognate_ids('cogids', 'cogid')
part.output('tsv', filename=ds.raw('tmp-2017-06-18'))
print('created cognate ids')
alm = Alignments(ds.raw('tmp-2017-06-18.tsv'),
segments='segments',
ref='cogids',
alignment='alignments')
alm.align()
alm.output('tsv',
filename=ds.raw('tmp-2017-06-18-finalized'),
subset=True,
cols=[
'doculect', 'glottolog', 'iso', 'concept', 'concepticon_id',
'chinese', 'pinyin', 'benzi', 'benzi_in_source', 'value',
'form', 'segments', 'cogid', 'cogids', 'note', 'source',
'beida_id', 'page', 'order', 'alignments'
])
words = Wordlist(ds.raw('tmp-2017-06-18-finalized.tsv'))
ds.write_wordlist(words)
with open('cldf/beijingdaxue1964.csv', 'w') as f:
f.write(','.join([
'ID', 'Language_name', 'Language_ID', 'Language_iso',
'Parameter_ID', 'Parameter_name', 'Source', 'Comment',
'Parameter_Chinese', 'Parameter_Pinyin', 'Value', 'Form',
'Segments', 'Cognate_Set', 'Cognate_Sets', 'Alignments', 'Order',
'Beida_ID', 'Page', 'Benzi', 'Benzi_in_source'
]) + '\n')
for idx in words:
out = [str(idx)]
for entry in [
'doculect', 'glottolog', 'iso', 'concepticon_id',
'concept', 'source', 'note', 'chinese', 'pinyin', 'value',
'form', 'segments', 'cogid', 'cogids', 'alignments',
'order', 'beida_id', 'page', 'benzi', 'benzi_in_source'
]:
value = words[idx, entry]
if isinstance(value, list):
value = ' '.join([str(x) for x in value])
else:
value = str(value)
if '"' in value:
value = value.replace('"', '""')
if ',' in value:
value = '"' + value + '"'
out += [value]
f.write(','.join(out) + '\n')
from lingpy.compare.partial import Partial
from lingpy.convert.plot import plot_tree
from sys import argv
from clldutils.text import strip_brackets, split_text
from collections import defaultdict
from lingpy import basictypes
if 'all' in argv:
fname='../output/A_Deepadung_'
else:
fname='../output/D_Deepadung_'
part = Partial(fname+'crossids.tsv')
part.add_cognate_ids('crossids', 'crossid', idtype='strict')
part.add_entries('cog', 'crossid,concept', lambda x, y: str(x[y[0]])+x[y[1]])
part.renumber('cog')
part.calculate('distance', ref='cogid')
part.calculate('tree', tree_calc='neighbor')
part.output('dst', filename=fname+'distance')
part.output('tre', filename=fname+'tree')
if 'plot' in argv:
plot_tree(str(part.tree), degree=350, filename=fname+'tree')
from lingpy import *
from lingpy.compare.partial import Partial
from sys import argv
if 'all' in argv:
fname='A_Chen_'
else:
fname='D_Chen_'
try:
part = Partial(fname+'partial.bin.tsv')
except:
part = Partial(fname+'subset.tsv', segments='tokens')
print('[i] loaded the file')
part.get_partial_scorer(runs=10000)
part.output('tsv', filename=fname+'partial.bin', ignore=[], prettify=False)
print('[i] saved the scorer')
finally:
part.partial_cluster(
method='lexstat',
threshold=0.55,
ref='cogids',
mode='global',
gop=-2,
cluster_method='infomap'
)
part.output('tsv', filename=fname+'partial', prettify=False)
methods = ['sca', 'lexstat']
cluster_methods = ['infomap', 'mcl', 'upgma']
measures = ['partial', 'strict', 'loose']
for f in infiles:
try:
lex = Partial(pcd_path('data', 'BIN_' + f + '.tsv'))
except IOError:
lex = Partial(pcd_path('data', f + '.tsv'))
lex.get_scorer(
preprocessing=False,
runs=10000,
)
lex.output('tsv', filename=pcd_path('data', 'BIN_' + f[2:]))
# create new reference ids for cogantes from partial cognates
if not 'strict_cogid' in lex.header:
lex.add_cognate_ids('partialids', 'strict_cogid', 'strict')
if not 'loose_cogid' in lex.header:
lex.add_cognate_ids('partialids', 'loose_cogid', 'loose')
for i in range(1, 20):
print("Analyzing {0} with t={1}...".format(f, i))
t = 0.05 * i
ts = '{0:.2f}'.format(t).replace('0.', '')
for m in methods:
msf = 'f_' + m
for cm in cluster_methods:
# create a new column by cog column. The new column assign
wl.renumber('cog')
print('Saving full cognate file...')
wl.output('tsv',
filename='{0}-{1}'.format(sys.argv[3], 'cognate'),
prettify=False,
ignore='all')
## get partical cognate
try:
part = Partial('{0}-{1}-{2}.tsv'.format(sys.argv[3], 'partial', 'temp'),
segments='segments')
except:
part = Partial(wl, segments='segments')
part.get_scorer(runs=10000)
part.output('tsv',
filename='{0}-{1}-{2}'.format(sys.argv[3], 'partial', 'temp'))
## manually correct error in data
part.partial_cluster(method='lexstat',
cluster_method='infomap',
threshold=0.6,
ref='cogids')
part.add_entries('note', 'cogid', lambda x: '')
part.add_entries('morphemes', 'cogid', lambda x: '')
print('Saving partial cognate file')
part.output('tsv',
filename='{0}-{1}-{2}'.format(sys.argv[3], 'partial', 'final'),
ignore='all',
prettify=False)