def run_annotator():
parser = argparse.ArgumentParser(description='')
parser.add_argument('--source-files',
dest='source_files',
type=str,
nargs='+',
help='')
args = parser.parse_args()
anno = Annotator()
anno.annotate(args.source_files)
def start_loop(stream_name=None,
network='s3fd',
redis_host='localhost',
redis_port=6379):
"""
Starts the processing loop
"""
killer = GracefulKiller()
LOG.info('Initializing Redis cache...')
cache = redis.StrictRedis(host=redis_host, port=redis_port, db=0)
LOG.info('Initializing annotator...')
annotator = Annotator(network=network)
LOG.info('Starting processing loop...')
while True:
# Get next available frame from the cache
image_bytes = cache.get('{}_raw'.format(stream_name))
if image_bytes is None:
continue
# Annotate with bounding boxes
# TODO: Get size from feed configs
image = Image.frombytes('RGB', (1920, 1080), image_bytes)
image = annotator.annotate(image)
# Save frame to cache as raw bytes
cache.set('{}_annotated'.format(stream_name), image.tobytes())
# Capture kill signals and terminate loop
if killer.kill_now:
LOG.info('Shutting down gracefully...')
break
def generate_annotator(self, event):
annotation = Annotator(self.channel_fnames, self.probability_table,
self.output_dir)
new_table = annotation.annotate([self.x0, self.y0], [self.x1, self.y1])
# add the new table to the groundtruth table
self.groundtruth_table.loc[
new_table.index,
self.column_names] = new_table.loc[:, self.column_names]
class Caption(Resource):
"""REST end point for the captioning service.
Accepts images (via HTTP POST requests) and returns corresponding captions.
"""
def __init__(self):
self.annotator = Annotator()
def post(self):
"""Create caption for an image.
The POST request should include either an image or a url pointing to an image.
Parameters
----------
image
Image data send with the request.
url
URL of the image to be processed.
"""
parser = reqparse.RequestParser()
parser.add_argument("image",
type=datastructures.FileStorage,
location='files')
parser.add_argument("url")
args = parser.parse_args()
if args.image:
image = Image.open(args.image)
else:
ssl._create_default_https_context = ssl._create_unverified_context
with urllib.request.urlopen(args.url) as url:
f = io.BytesIO(url.read())
image = Image.open(f)
annotation = self.annotator.annotate(image)
data = {
"annotation": annotation,
}
return data, 201
def test(nlp,
src,
gen,
bert=False,
print_annotations=False,
print_latex=False,
verbose=False):
if print_annotations:
print("source:", src_line[:50])
print("summary:", gen_line[:50])
src = nlp(src)
gen = nlp(gen)
if verbose:
print("clusters:", src._.coref_clusters, gen._.coref_clusters)
ce = CompoundEquivalency()
spe = SpeakerPronounEquivalency()
spe.register(src)
spe.register(gen)
kg = KnowledgeGraph(nlp,
use_bert=bert,
equivalencies=[ce, spe],
verbose=verbose)
if print_annotations:
annotator = Annotator(src, gen, latex=print_latex)
kg.add_document(src)
contained = 0
contained_bert = 0
missing = 0
missing_verb = 0
missing_actors = 0
missing_acteds = 0
contradiction = 0
contradiction_bert = 0
invalid_simplification = 0
total = 0
for token in gen:
if token.pos_ == "VERB":
total += 1
relation = kg.get_relation(token)
r = kg.query_relation(relation)
if r[0] == KnowledgeGraph.entailment:
if print_annotations:
print(util.format("contained", "blue", latex=print_latex),
"|", relation, "|", r[1])
contained += 1
if r[0] == KnowledgeGraph.entailment_bert:
if print_annotations:
print(
util.format("contained (BERT)",
"blue",
latex=print_latex), "|", relation, "|",
r[1])
contained_bert += 1
if r[0] == KnowledgeGraph.contradiction_bert:
if print_annotations:
print(
util.format("contradiction (BERT)",
"red",
latex=print_latex), "|", relation, "|",
r[1])
contradiction_bert += 1
elif r[0] == KnowledgeGraph.missing_dependencies:
missing += 1
if print_annotations:
print(
util.format("generic missing dependency",
"yellow",
latex=print_latex), "|", relation, "|",
r[1])
elif r[0] == KnowledgeGraph.missing_actors:
missing_actors += 1
if print_annotations:
print(
util.format("missing actors",
"magenta",
latex=print_latex), "|", relation, "|",
r[1])
elif r[0] == KnowledgeGraph.missing_acteds:
missing_acteds += 1
if print_annotations:
print(
util.format("missing acteds",
"magenta",
latex=print_latex), "|", relation, "|",
r[1])
elif r[0] == KnowledgeGraph.missing_verb:
missing_verb += 1
if print_annotations:
print(
util.format("missing verb",
"magenta",
latex=print_latex), "|", relation, "|",
r[1])
elif r[0] == KnowledgeGraph.invalid_simplification:
invalid_simplification += 1
if print_annotations:
print(
util.format("invalid simplification",
"magenta",
latex=print_latex), "|", relation, "|",
r[1])
elif r[0] == KnowledgeGraph.contradiction:
contradiction += 1
if print_annotations:
print(
util.format("contradiction", "red", latex=print_latex),
"|", relation, "|", r[1])
if print_annotations:
annotator.annotate(relation, r)
if print_annotations:
annotated_document, annotated_summary = annotator.annotated()
print("Document:", " ".join(annotated_document))
print("Summary:", " ".join(annotated_summary))
if total == 0:
return 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
return 100.0 * contained / total, \
100.0 * contained_bert / total, \
100.0 * missing / total, \
100.0 * missing_verb / total, \
100.0 * missing_actors / total, \
100.0 * missing_acteds / total, \
100.0 * contradiction / total, \
100.0 * contradiction_bert / total, \
100.0 * invalid_simplification / total
#Testing of the Annotator script from annotator import Annotator #Example region that has all features annotator = Annotator() region = dict() region['chromosome'] = 'chr1' region['chromosome2'] = 'chr1' region['start'] = '3541566' region['end'] = '3541586' annotator.annotate(region)
""" Input: tab-delimited file with variants (or simply, regions). Required format: columns chr 1, s1, e1, chr2, s2, e2, somatic (yes/no) per region on the rows. Output: null Functionality: starting point of the annotation pipeline. Sorts the input file and starts the annotation process. TODO: - Update input data format """ ### Imports ### import sys import numpy as np from inputDataParser import InputDataParser from annotator import Annotator ### Code ### #1. Initialize annotator = Annotator() #2. Read input data inFile = sys.argv[1] inputDataParser = InputDataParser() inputData = inputDataParser.parseInputData(inFile) #3. Prepare input data, including sorting for speed preparedInputData = inputDataParser.prepareInputData(inputData) #4. Do the annotation annotator.annotate(preparedInputData)
