def test_ann_conversions(self):
"""Tests converting and un-converting a valid Annotations object to an ANN file."""
annotations = Annotations(self.ann_file_path_one, annotation_type='ann')
annotations.to_ann(write_location=join(self.test_dir,"intermediary.ann"))
annotations2 = Annotations(join(self.test_dir, "intermediary.ann"), annotation_type='ann')
self.assertEqual(annotations.get_entity_annotations(return_dictionary=True),
annotations2.get_entity_annotations(return_dictionary=True)
)
def test_intersection(self):
annotations1 = Annotations(join(self.dataset.get_data_directory(),
self.ann_files[0]),
annotation_type='ann')
annotations2 = Annotations(join(self.dataset.get_data_directory(),
self.ann_files[1]),
annotation_type='ann')
annotations1.add_entity(*annotations2.get_entity_annotations()[0])
annotations1.add_entity(*annotations2.get_entity_annotations()[1])
self.assertEqual(
annotations1.intersection(annotations2),
set([
annotations2.get_entity_annotations()[0],
annotations2.get_entity_annotations()[1]
]))
def test_get_entity_annotations_dict(self):
"""
Tests the validity of the annotation dict
:return:
"""
annotations = Annotations(join(self.dataset.get_data_directory(), self.ann_files[0]), annotation_type='ann')
self.assertIsInstance(annotations.get_entity_annotations(return_dictionary=True), dict)
def test_init_from_ann_file(self):
"""
Tests initialization from valid ann file
:return:
"""
annotations = Annotations(join(self.dataset.get_data_directory(), self.ann_files[0]), annotation_type='ann')
self.assertIsNotNone(annotations.get_entity_annotations())
def test_confusion_matrix(self):
annotations1 = Annotations(join(self.dataset.get_data_directory(), self.ann_files[0]), annotation_type='ann')
annotations2 = Annotations(join(self.dataset.get_data_directory(), self.ann_files[1]), annotation_type='ann')
annotations1.add_entity(*annotations2.get_entity_annotations()[0])
self.assertEqual(len(annotations1.compute_confusion_matrix(annotations2, self.entities)[0]), len(self.entities))
self.assertEqual(len(annotations1.compute_confusion_matrix(annotations2, self.entities)), len(self.entities))
def test_get_entity_annotations_list(self):
"""
Tests the validity of annotation list
:return:
"""
annotations = Annotations(join(self.dataset.get_data_directory(), self.ann_files[0]), annotation_type='ann')
self.assertIsInstance(annotations.get_entity_annotations(), list)
def test_good_con_data(self):
"""Tests to see if valid con data can be used to instantiate an Annotations object."""
with open(join(self.test_dir, "test_con.con"), 'w+') as c,\
open(join(self.test_dir, "test_con_text.txt"), 'w+') as t:
c.write(con_text)
t.write(con_source_text)
annotations = Annotations(c.name, annotation_type='con', source_text_path=t.name)
self.assertIsInstance(annotations.get_entity_annotations(), list)
def test_compute_ambiguity(self):
annotations1 = Annotations(join(self.dataset.get_data_directory(),
self.ann_files[0]),
annotation_type='ann')
annotations2 = Annotations(join(self.dataset.get_data_directory(),
self.ann_files[0]),
annotation_type='ann')
label, start, end, text = annotations2.get_entity_annotations()[0]
annotations2.add_entity('incorrect_label', start, end, text)
self.assertEqual(len(annotations1.compute_ambiguity(annotations2)), 1)
def get_training_data(self, data_format='spacy'):
"""
Get training data in a specified format.
:param data_format: The specified format as a string.
:return: The requested data in the requested format.
"""
# Only spaCy format is currently supported.
if data_format != 'spacy':
raise TypeError("Format %s not supported" % format)
training_data = []
# Add each entry in dataset with annotation to train_data
for data_file in self.all_data_files:
txt_path = data_file.get_text_path()
ann_path = data_file.get_annotation_path()
annotations = Annotations(ann_path, source_text_path=txt_path)
training_data.append(
annotations.get_entity_annotations(format='spacy'))
return training_data
def __call__(self, doc):
nlp = self.nlp
if hasattr(doc._, 'file_name'):
logging.debug("%s: Called GoldAnnotator Component",
doc._.file_name)
if logging.getLogger().getEffectiveLevel(
) == logging.DEBUG: #print document tokenization
for token in doc:
logging.debug(str(token))
#check if gold annotation file path has been set.
if not hasattr(doc._, 'gold_annotation_file'):
raise ValueError(
"No extension doc._.gold_annotation_file is present.")
gold_annotations = Annotations(doc._.gold_annotation_file,
annotation_type='ann')
# for label in set([label for _,_,label in [gold['entities'][key] for key in gold['entities']]]):
# for token in doc:
# print(token.text, token.idx)
for e_label, e_start, e_end, _ in gold_annotations.get_entity_annotations(
):
#print(e_label, e_start, e_end)
if e_start > e_end:
logging.critical(
"%s: Broken annotation - start is greater than end: (%i,%i,%s)",
doc._.file_name, e_start, e_end, e_label)
continue
span = doc.char_span(e_start, e_end)
if span is None:
self.failed_overlay_count += 1
self.failed_identifying_span_count += 1
logging.warning(
"%s: Number of failed annotation overlays with current tokenizer: %i (%i,%i,%s)",
doc._.file_name, self.failed_overlay_count, e_start, e_end,
e_label)
fixed_span = self.find_span(e_start, e_end, e_label, span, doc)
if fixed_span is not None:
if span is None:
logging.warning("%s: Fixed span (%i,%i,%s) into: %s",
doc._.file_name, e_start, e_end, e_label,
fixed_span.text)
self.failed_identifying_span_count -= 1
for token in fixed_span:
if e_label in self.labels or not self.labels:
token._.set('gold_label', e_label)
else: #annotation was not able to be fixed, it will be ignored - this is bad in evaluation.
logging.warning("%s: Could not fix annotation: (%i,%i,%s)",
doc._.file_name, e_start, e_end, e_label)
logging.warning("%s: Total Failed Annotations: %i",
doc._.file_name,
self.failed_identifying_span_count)
if self.failed_overlay_count > .3 * len(
gold_annotations.get_entity_annotations()):
logging.warning(
"%s: Annotations may mis-aligned as more than 30 percent failed to overlay: %s",
doc._.file_name, doc._.gold_annotation_file)
return doc
def test_init_from_ann_file(self):
"""Tests initialization from valid ann file"""
annotations = Annotations(self.ann_file_path_one, annotation_type='ann')
self.assertIsNotNone(annotations.get_entity_annotations())
def test_get_entity_annotations_list(self):
"""Tests the validity of annotation list"""
annotations = Annotations(self.ann_file_path_one, annotation_type='ann')
self.assertIsInstance(annotations.get_entity_annotations(), list)
def test_get_entity_annotations_dict(self):
"""Tests the validity of the annotation dict."""
annotations = Annotations(self.ann_file_path_one, annotation_type='ann')
self.assertIsInstance(annotations.get_entity_annotations(return_dictionary=True), dict)
