def main():
my_format_string='%(asctime)s %(levelname)s %(module)s.' \
'%(funcName)s: %(message)s'
logging.basicConfig(level=logging.INFO, format=my_format_string)
chunkmap = chunkmap_factory(
pickle.load(bz2.BZ2File('test_data/5th.chunkmap.bz2')))
semrep_reader = SemrepOutput(bz2.BZ2File('test_data/5th.semrep.out.bz2'),
DEFAULT_LINES_TO_IGNORE, chunkmap)
tfidf = TF_IDF(file_mode="c")
tfidf.build_tf_from_file(semrep_reader)
semrep_reader.rewind()
semrep_grapher = SemrepCooccurrenceGraphBuilder(
node_weight_threshold=0.001,
link_weight_threshold=0.003,
tf_idf_provider=tfidf)
eval_params = EvaluationParameters()
eval_params.alpha = 0.65
work = myWorkflow(semrep_reader, semrep_grapher, TextRanker(), eval_params,
PAGERANK_CUTOFF, MESH_TREE_FILE, SAVCC_MATRIX_FILE,
lambda x: 1.0 / math.exp(x) if x >= 0 and x < 5 else 0.0,
UMLS_CONVERTER_DATA, UMLS_CONCEPT_DATA,
open(OUTPUT_FILE, 'w'))
work.run()
def main():
logging.basicConfig(level=logging.INFO,
format='%(asctime)s %(levelname)s %(message)s')
chunkmap=chunkmap_factory(pickle.load(
bz2.BZ2File('test_data/5th.chunkmap.bz2')))
setupstart=time.clock()
semrep_reader=SemrepOutput(bz2.BZ2File('test_data/5th.semrep.out.bz2'),
["semrep wrapper error"],
chunkmap)
semrep_grapher=SemrepGraphBuilder()
pr_algorithm=PageRanker()
count=0
parsestart=time.clock()
for article in semrep_reader:
print "Read article", article.set_id,
graph=semrep_grapher.create_graph(article.lines)
print "graphed it",
matrixed=graph.as_mapped_link_matrix()
print "matrixed it,",
fake_e_vector=[0.0] * len(matrixed)
if fake_e_vector==[]:
print "didn't pagerank because it was empty."
else:
ranked=pr_algorithm.evaluate(matrixed, fake_e_vector)
print "pageranked it. Stats:", pr_algorithm.stats
count+=1
endparse=time.clock()
print "Total time elapsed: %1.3f seconds (%1.7f seconds were setup) for "\
"%d total articles, for a grand total of %1.3f compressed "\
"articles/second turned into semantic graphs, link matrices," \
" and finally pageranked." % (
endparse-setupstart, parsestart-setupstart, count,
float(count)/(endparse-setupstart))
def main():
my_format_string='%(asctime)s %(levelname)s %(module)s.' \
'%(funcName)s: %(message)s'
logging.basicConfig(level=logging.INFO,
format=my_format_string)
chunkmap=chunkmap_factory(pickle.load(
bz2.BZ2File('test_data/5th.chunkmap.bz2')))
semrep_reader=SemrepOutput(bz2.BZ2File('test_data/5th.semrep.out.bz2'),
DEFAULT_LINES_TO_IGNORE,
chunkmap)
tfidf=TF_IDF(file_mode="c")
tfidf.build_tf_from_file(semrep_reader)
semrep_reader.rewind()
semrep_grapher=SemrepCooccurrenceGraphBuilder(node_weight_threshold=0.001,
link_weight_threshold=0.003,
tf_idf_provider=tfidf
)
eval_params=EvaluationParameters()
eval_params.alpha=0.65
work=myWorkflow(semrep_reader, semrep_grapher, TextRanker(), eval_params,
PAGERANK_CUTOFF, MESH_TREE_FILE, SAVCC_MATRIX_FILE,
lambda x: 1.0/math.exp(x) if x>=0 and x<5 else 0.0,
UMLS_CONVERTER_DATA, UMLS_CONCEPT_DATA,
open(OUTPUT_FILE, 'w'))
work.run()
def main():
logging.basicConfig(level=logging.INFO,
format='%(asctime)s %(levelname)s %(message)s')
chunkmap = chunkmap_factory(
pickle.load(bz2.BZ2File('test_data/5th.chunkmap.bz2')))
setupstart = time.clock()
semrep_reader = SemrepOutput(bz2.BZ2File('test_data/5th.semrep.out.bz2'),
["semrep wrapper error"], chunkmap)
semrep_grapher = SemrepGraphBuilder()
pr_algorithm = PageRanker()
count = 0
parsestart = time.clock()
for article in semrep_reader:
print "Read article", article.set_id,
graph = semrep_grapher.create_graph(article.lines)
print "graphed it",
matrixed = graph.as_mapped_link_matrix()
print "matrixed it,",
fake_e_vector = [0.0] * len(matrixed)
if fake_e_vector == []:
print "didn't pagerank because it was empty."
else:
ranked = pr_algorithm.evaluate(matrixed, fake_e_vector)
print "pageranked it. Stats:", pr_algorithm.stats
count += 1
endparse = time.clock()
print "Total time elapsed: %1.3f seconds (%1.7f seconds were setup) for "\
"%d total articles, for a grand total of %1.3f compressed "\
"articles/second turned into semantic graphs, link matrices," \
" and finally pageranked." % (
endparse-setupstart, parsestart-setupstart, count,
float(count)/(endparse-setupstart))
def main():
my_format_string='%(asctime)s %(levelname)s %(module)s.' \
'%(funcName)s: %(message)s'
logging.basicConfig(level=logging.DEBUG, format=my_format_string)
chunkmap = chunkmap_factory(
pickle.load(bz2.BZ2File('test_data/all_abstracts.mti_chunkmap.bz2')))
reader = MtiOutput(
bz2.BZ2File('test_data/all_abstracts.mti.just_metamap.out.bz2'),
DEFAULT_LINES_TO_IGNORE, chunkmap)
eval_params = EvaluationParameters()
eval_params.alpha = 0.65
work = MtiWorkflow(
reader, None, None, eval_params, PAGERANK_CUTOFF, MESH_TREE_FILE,
SAVCC_MATRIX_FILE, lambda x: 1.0 / math.exp(x)
if x >= 0 and x < 5 else 0.0, UMLS_CONVERTER_DATA, UMLS_CONCEPT_DATA,
open(OUTPUT_FILE, 'w'))
work.run()
def main():
logging.basicConfig(level=logging.INFO,
format='%(asctime)s %(levelname)s %(message)s')
chunkmap=chunkmap_factory(pickle.load(
bz2.BZ2File(
'test_data/metamap.chunkmap.bz2')))
setupstart=time.clock()
metamap_reader=MetamapOutput(bz2.BZ2File(
'test_data/metamap.out.bz2'),
DEFAULT_LINES_TO_IGNORE,
chunkmap)
grapher=MetamapCoccurrenceGraphBuilder()
# PageRank is not the correct algorithm for a matrix of adirectional nodes
# but it'll do for now, to exercise the system
# pr_algorithm=PageRanker()
# TextRanker now written
pr_algorithm=MappedRanker(TextRanker())
count=0
parsestart=time.clock()
for article in metamap_reader:
print "Read article", article.set_id,
graph=grapher.create_graph(article.lines)
print "graphed it",
matrix=graph.as_mapped_link_matrix()
print "turned it into a", matrix,
#fake_e_vector=[0.0] * len(matrix)
if len(matrix)==0:
print "didn't pagerank because it was empty."
else:
ranked=pr_algorithm.evaluate(matrix)
print "TextRanked it. First results: %r Stats:" % \
[x for x in ranked][:5], pr_algorithm.stats
count+=1
endparse=time.clock()
print "Total time elapsed: %1.3f seconds (%1.7f seconds were setup) "\
"for %d total articles, for a grand total of %1.3f compressed "\
"articles/second read, turned into link matrices, and " \
" pageranked." \
% (endparse-setupstart, parsestart-setupstart, count,
float(count)/(endparse-setupstart))
count+=1
def main():
my_format_string='%(asctime)s %(levelname)s %(module)s.' \
'%(funcName)s: %(message)s'
logging.basicConfig(level=logging.DEBUG,
format=my_format_string)
chunkmap=chunkmap_factory(pickle.load(
bz2.BZ2File('test_data/all_abstracts.mti_chunkmap.bz2')))
reader=MtiOutput(bz2.BZ2File('test_data/all_abstracts.mti.just_metamap.out.bz2'),
DEFAULT_LINES_TO_IGNORE,
chunkmap)
eval_params=EvaluationParameters()
eval_params.alpha=0.65
work=MtiWorkflow(reader, None, None, eval_params,
PAGERANK_CUTOFF, MESH_TREE_FILE, SAVCC_MATRIX_FILE,
lambda x: 1.0/math.exp(x) if x>=0 and x<5 else 0.0,
UMLS_CONVERTER_DATA, UMLS_CONCEPT_DATA,
open(OUTPUT_FILE, 'w'))
work.run()
def main():
logging.basicConfig(level=logging.INFO,
format='%(asctime)s %(levelname)s %(message)s')
chunkmap = chunkmap_factory(
pickle.load(bz2.BZ2File('test_data/metamap.chunkmap.bz2')))
setupstart = time.clock()
metamap_reader = MetamapOutput(bz2.BZ2File('test_data/metamap.out.bz2'),
DEFAULT_LINES_TO_IGNORE, chunkmap)
grapher = MetamapCoccurrenceGraphBuilder()
# PageRank is not the correct algorithm for a matrix of adirectional nodes
# but it'll do for now, to exercise the system
# pr_algorithm=PageRanker()
# TextRanker now written
pr_algorithm = MappedRanker(TextRanker())
count = 0
parsestart = time.clock()
for article in metamap_reader:
print "Read article", article.set_id,
graph = grapher.create_graph(article.lines)
print "graphed it",
matrix = graph.as_mapped_link_matrix()
print "turned it into a", matrix,
#fake_e_vector=[0.0] * len(matrix)
if len(matrix) == 0:
print "didn't pagerank because it was empty."
else:
ranked = pr_algorithm.evaluate(matrix)
print "TextRanked it. First results: %r Stats:" % \
[x for x in ranked][:5], pr_algorithm.stats
count += 1
endparse = time.clock()
print "Total time elapsed: %1.3f seconds (%1.7f seconds were setup) "\
"for %d total articles, for a grand total of %1.3f compressed "\
"articles/second read, turned into link matrices, and " \
" pageranked." \
% (endparse-setupstart, parsestart-setupstart, count,
float(count)/(endparse-setupstart))
count += 1
