def prepare_conll_lines(self, gold_corefs, sys_corefs, gold_mention_table, system_mention_table,
gold_2_system_one_2_one_mapping, threshold=1.0):
"""
Convert to ConLL style lines
:param gold_corefs: gold coreference chain
:param sys_corefs: system coreferenc chain
:param gold_mention_table: gold mention table
:param system_mention_table: system mention table
:param gold_2_system_one_2_one_mapping: a mapping between gold and system
:param threshold: To what extent we treat two mention can be aligned, default 1 for exact match
:return:
"""
aligned_gold_table, aligned_system_table = self.create_aligned_tables(gold_2_system_one_2_one_mapping,
gold_mention_table,
system_mention_table,
threshold)
logger.debug("Preparing CoNLL files using mapping threhold %.2f" % threshold)
gold_conll_lines = self.prepare_lines(gold_corefs, aligned_gold_table,
self.extract_token_map(gold_mention_table), self.gold_id_2_text)
sys_conll_lines = self.prepare_lines(sys_corefs, aligned_system_table,
self.extract_token_map(system_mention_table), self.sys_id_2_text)
if not gold_conll_lines:
utils.terminate_with_error("Gold standard has data problem for doc [%s], please refer to log. Quitting..."
% self.doc_id)
if not sys_conll_lines:
utils.terminate_with_error("System has data problem for doc [%s], please refer to log. Quitting..."
% self.doc_id)
return gold_conll_lines, sys_conll_lines
def parse_line(l, invisible_ids):
"""
Parse the line, get the token ids, remove invisible ones.
:param l: A line in the tbf file.
:param invisible_ids: Set of invisible ids to remove.
"""
fields = l.split("\t")
num_attributes = len(Config.attribute_names)
if len(fields) < 5 + num_attributes:
utils.terminate_with_error(
"System line has too few fields:\n ---> %s" % l)
if MutableConfig.eval_mode == EvalMethod.Token:
spans, original_spans = parse_token_ids(fields[3], invisible_ids)
if len(spans) == 0:
logger.warn(
"Find mention with only invisible words, will not be mapped to anything"
)
else:
# There is no filtering thing in the character mode.
spans = parse_characters(fields[3])
original_spans = spans
attributes = [canonicalize_string(a) for a in fields[5:5 + num_attributes]]
if EvalState.white_listed_types:
if attributes[0] not in EvalState.white_listed_types:
return None
event_id = fields[2]
text = fields[4]
# span_id = fields[script_column] if len(fields) > script_column else None
return spans, attributes, event_id, original_spans, text
def prepare_conll_lines(self, gold_corefs, sys_corefs, gold_mention_table, system_mention_table,
gold_2_system_one_2_one_mapping, threshold=1.0):
"""
Convert to ConLL style lines
:param gold_corefs: gold coreference chain
:param sys_corefs: system coreferenc chain
:param gold_mention_table: gold mention table
:param system_mention_table: system mention table
:param gold_2_system_one_2_one_mapping: a mapping between gold and system
:param threshold: To what extent we treat two mention can be aligned, default 1 for exact match
:return:
"""
aligned_gold_table, aligned_system_table = self.create_aligned_tables(gold_2_system_one_2_one_mapping,
gold_mention_table,
system_mention_table,
threshold)
logger.debug("Preparing CoNLL files using mapping threhold %.2f" % threshold)
gold_conll_lines = self.prepare_lines(gold_corefs, aligned_gold_table, self.gold_id_2_text)
sys_conll_lines = self.prepare_lines(sys_corefs, aligned_system_table, self.sys_id_2_text)
if not gold_conll_lines:
utils.terminate_with_error("Gold standard has data problem for doc [%s], please refer to log. Quitting..."
% self.doc_id)
if not sys_conll_lines:
utils.terminate_with_error("System has data problem for doc [%s], please refer to log. Quitting..."
% self.doc_id)
return gold_conll_lines, sys_conll_lines
def parse_line(l, invisible_ids):
"""
Parse the line, get the token ids, remove invisible ones.
:param l: A line in the tbf file.
:param invisible_ids: Set of invisible ids to remove.
"""
fields = l.split("\t")
num_attributes = len(Config.attribute_names)
if len(fields) < 5 + num_attributes:
utils.terminate_with_error("System line has too few fields:\n ---> %s" % l)
if MutableConfig.eval_mode == EvalMethod.Token:
spans, original_spans = parse_token_ids(fields[3], invisible_ids)
if len(spans) == 0:
logger.warn("Find mention with only invisible words, will not be mapped to anything")
else:
spans = parse_characters(fields[3])
original_spans = spans
attributes = [canonicalize_string(a) for a in fields[5:5 + num_attributes]]
if EvalState.white_listed_types:
if attributes[0] not in EvalState.white_listed_types:
return None
# The temporal column is after the last attribute.
temporal_column = 5 + num_attributes
event_id = fields[2]
text = fields[4]
# span_id = fields[temporal_column] if len(fields) > temporal_column else None
return spans, attributes, event_id, original_spans, text
def main():
parser = argparse.ArgumentParser(
description=
"Event mention scorer, provides support to Event Nugget scoring, Event Coreference and Event "
"Sequencing scoring.")
parser.add_argument("-g", "--gold", help="Golden Standard", required=True)
parser.add_argument("-s", "--system", help="System output", required=True)
parser.add_argument("-d",
"--comparison_output",
help="Compare and help show the difference between "
"system and gold")
parser.add_argument(
"-o",
"--output",
help="Optional evaluation result redirects, put eval result to file")
parser.add_argument(
"-c",
"--coref",
help="Eval Coreference result output, need to put the reference"
"conll coref scorer in the same folder with this scorer")
parser.add_argument(
"-a",
"--sequencing",
help="Eval Event sequencing result output (After and Subevent)")
parser.add_argument("-nv",
"--no_script_validation",
help="Whether to turn off script validation",
action="store_true")
parser.add_argument(
"-t",
"--token_path",
help=
"Path to the directory containing the token mappings file, only used in token mode."
)
parser.add_argument(
"-m",
"--coref_mapping",
help="Which mapping will be used to perform coreference mapping.",
type=int)
parser.add_argument(
"-of",
"--offset_field",
help="A pair of integer indicates which column we should "
"read the offset in the token mapping file, index starts"
"at 0, default value will be %s" % Config.default_token_offset_fields)
parser.add_argument(
"-te",
"--token_table_extension",
help=
"any extension appended after docid of token table files. Default is [%s], only used in token mode."
% Config.default_token_file_ext)
parser.add_argument("-ct",
"--coreference_threshold",
type=float,
help="Threshold for coreference mention mapping")
parser.add_argument("-b",
"--debug",
help="turn debug mode on",
action="store_true")
# parser.add_argument("--eval_mode", choices=["char", "token"], default="char",
# help="Use Span or Token mode. The Span mode will take a span as range [start:end], while the "
# "Token mode consider each token is provided as a single id.")
parser.add_argument(
"-wl",
"--type_white_list",
type=argparse.FileType('r'),
help=
"Provide a file, where each line list a mention type subtype pair to be evaluated. Types "
"that are out of this white list will be ignored.")
parser.add_argument("-dn",
"--doc_id_to_eval",
help="Provide one single doc id to evaluate.")
parser.set_defaults(debug=False)
args = parser.parse_args()
if args.debug:
stream_handler.setLevel(logging.DEBUG)
logger.setLevel(logging.DEBUG)
logger.debug("Entered debug mode.")
else:
stream_handler.setLevel(logging.INFO)
logger.setLevel(logging.INFO)
if args.type_white_list is not None:
logger.info(
"Only the following types in the white list will be evaluated.")
EvalState.white_listed_types = set()
for line in args.type_white_list:
logger.info(line.strip())
EvalState.white_listed_types.add(canonicalize_string(line))
if args.output is not None:
out_path = args.output
utils.create_parent_dir(out_path)
mention_eval_out = open(out_path, 'w')
logger.info("Evaluation output will be saved at %s" % out_path)
else:
mention_eval_out = sys.stdout
logger.info("Evaluation output at standard out.")
if os.path.isfile(args.gold):
gf = open(args.gold)
else:
logger.error("Cannot find gold standard file at " + args.gold)
sys.exit(1)
if args.coref is not None:
Config.conll_out = args.coref
Config.conll_gold_file = args.coref + "_gold.conll"
Config.conll_sys_file = args.coref + "_sys.conll"
logger.info("CoNLL script output will be output at " +
Config.conll_out)
logger.info("Gold and system conll files will generated at " +
Config.conll_gold_file + " and " + Config.conll_sys_file)
if args.sequencing is not None:
Config.script_result_dir = args.sequencing
logger.info("Temporal files will be output at " +
Config.script_result_dir)
utils.supermakedirs(Config.script_result_dir)
logger.info("Will evaluate link type: %s." %
",".join(Config.script_types))
for t in Config.script_types:
utils.supermakedirs(os.path.join(Config.script_result_dir, t))
utils.remove_file_by_extension(Config.script_result_dir, ".tml")
utils.remove_file_by_extension(Config.script_result_dir, ".tml")
if args.no_script_validation:
Config.no_script_validation = True
if os.path.isfile(args.system):
sf = open(args.system)
else:
logger.error("Cannot find system file at " + args.system)
sys.exit(1)
if args.coref_mapping is not None:
if args.coref_mapping < 4:
Config.coref_criteria = Config.possible_coref_mapping[
args.coref_mapping]
else:
logger.error(
"Possible mapping : 0: Span only 1: Mention Type 2: Realis 3 Type and Realis"
)
utils.terminate_with_error("Must provide a mapping between 0 to 3")
else:
Config.coref_criteria = Config.possible_coref_mapping[1]
diff_out = None
if args.comparison_output is not None:
diff_out_path = args.comparison_output
utils.create_parent_dir(diff_out_path)
diff_out = open(diff_out_path, 'w')
token_dir = "."
if args.token_path is not None:
MutableConfig.eval_mode = EvalMethod.Token
logger.info("Eval mode is set to token.")
if os.path.isdir(args.token_path):
logger.debug("Will search token files in " + args.token_path)
token_dir = args.token_path
else:
logger.debug("Cannot find given token directory at [%s], "
"will try search for current directory" %
args.token_path)
else:
MutableConfig.eval_mode = EvalMethod.Char
token_offset_fields = Config.default_token_offset_fields
if args.offset_field is not None:
try:
token_offset_fields = [
int(x) for x in args.offset_field.split(",")
]
except ValueError as _:
logger.error(
"Token offset argument should be two integer with comma in between, i.e. 2,3"
)
if args.coreference_threshold is not None:
MutableConfig.coref_mention_threshold = args.coreference_threshold
# Read all documents.
read_all_doc(gf, sf, args.doc_id_to_eval)
# Take all attribute combinations, which will be used to produce scores.
attribute_comb = get_attr_combinations(Config.attribute_names)
logger.info("Coreference mentions need to match %s before consideration" %
Config.coref_criteria[0][1])
while True:
print('dir is:', token_dir)
if not evaluate(token_dir, args.coref, attribute_comb,
token_offset_fields, args.token_table_extension,
diff_out):
break
# Run the CoNLL script on the combined files, which is concatenated from the best alignment of all documents.
if args.coref is not None:
logger.debug("Running coreference script for the final scores.")
ConllEvaluator.run_conll_script(Config.conll_gold_file,
Config.conll_sys_file,
Config.conll_out)
# Get the CoNLL scores from output
EvalState.overall_coref_scores = ConllEvaluator.get_conll_scores(
Config.conll_out)
# Run the TimeML evaluation script.
if Config.script_result_dir:
TemporalEval.eval_time_ml()
print_eval_results(mention_eval_out, attribute_comb)
# Clean up, close files.
close_if_not_none(diff_out)
logger.info("Evaluation Done.")
return 0
def main():
parser = argparse.ArgumentParser(
description="Event mention scorer, which conducts token based "
"scoring, system and gold standard files should follows "
"the token-based format.")
parser.add_argument("-g", "--gold", help="Golden Standard", required=True)
parser.add_argument("-s", "--system", help="System output", required=True)
parser.add_argument("-d", "--comparison_output",
help="Compare and help show the difference between "
"system and gold")
parser.add_argument(
"-o", "--output", help="Optional evaluation result redirects, put eval result to file")
parser.add_argument(
"-c", "--coref", help="Eval Coreference result output, need to put the reference"
"conll coref scorer in the same folder with this scorer")
parser.add_argument(
"-a", "--sequencing", help="Eval Event sequencing result output (After and Subevent)"
)
parser.add_argument(
"-t", "--token_path", help="Path to the directory containing the "
"token mappings file")
parser.add_argument(
"-m", "--coref_mapping", help="Which mapping will be used to perform coreference mapping.", type=int
)
parser.add_argument(
"-of", "--offset_field", help="A pair of integer indicates which column we should "
"read the offset in the token mapping file, index starts"
"at 0, default value will be %s" % Config.default_token_offset_fields
)
parser.add_argument(
"-te", "--token_table_extension",
help="any extension appended after docid of token table files. "
"Default is [%s]" % Config.default_token_file_ext)
parser.add_argument("-ct", "--coreference_threshold", type=float, help="Threshold for coreference mention mapping")
parser.add_argument(
"-b", "--debug", help="turn debug mode on", action="store_true")
parser.add_argument("--eval_mode", choices=["char", "token"], default="char",
help="Use Span Overlap or Token Overlap mode. The Span Overlap mode will take a span as range "
"[start:end], while the Token Overlap mode consider each token is provided as a single "
"id.")
parser.add_argument("-wl", "--type_white_list", type=argparse.FileType('r'),
help="Provide a file, where each line list a mention type subtype pair to be evaluated. Types "
"that are out of this white list will be ignored.")
parser.add_argument(
"-dn", "--doc_id_to_eval", help="Provide one single doc id to evaluate."
)
parser.set_defaults(debug=False)
args = parser.parse_args()
if args.debug:
stream_handler.setLevel(logging.DEBUG)
logger.setLevel(logging.DEBUG)
logger.debug("Entered debug mode.")
else:
stream_handler.setLevel(logging.INFO)
logger.setLevel(logging.INFO)
if args.type_white_list is not None:
logger.info("Only the following types in the white list will be evaluated.")
EvalState.white_listed_types = set()
for line in args.type_white_list:
logger.info(line.strip())
EvalState.white_listed_types.add(canonicalize_string(line))
if args.eval_mode == "char":
MutableConfig.eval_mode = EvalMethod.Char
else:
MutableConfig.eval_mode = EvalMethod.Token
if args.output is not None:
out_path = args.output
utils.create_parent_dir(out_path)
mention_eval_out = open(out_path, 'w')
logger.info("Evaluation output will be saved at %s" % out_path)
else:
mention_eval_out = sys.stdout
logger.info("Evaluation output at standard out.")
if os.path.isfile(args.gold):
gf = open(args.gold)
else:
logger.error("Cannot find gold standard file at " + args.gold)
sys.exit(1)
if args.coref is not None:
Config.conll_out = args.coref
Config.conll_gold_file = args.coref + "_gold.conll"
Config.conll_sys_file = args.coref + "_sys.conll"
logger.info("CoNLL script output will be output at " + Config.conll_out)
logger.info(
"Gold and system conll files will generated at " + Config.conll_gold_file + " and " + Config.conll_sys_file)
# if os.path.exists(Config.conll_tmp_marker):
# # Clean up the directory to avoid scoring errors.
# remove_conll_tmp()
# supermakedirs(Config.conll_tmp_marker)
if args.sequencing is not None:
Config.temporal_result_dir = args.sequencing
utils.supermakedirs(os.path.join(Config.temporal_result_dir, Config.temporal_gold_dir))
utils.supermakedirs(os.path.join(Config.temporal_result_dir, Config.temporal_sys_dir))
if os.path.isfile(args.system):
sf = open(args.system)
else:
logger.error("Cannot find system file at " + args.system)
sys.exit(1)
if args.coref_mapping is not None:
if args.coref_mapping < 4:
Config.coref_criteria = Config.possible_coref_mapping[args.coref_mapping]
else:
logger.error("Possible mapping : 0: Span only 1: Mention Type 2: Realis 3 Type and Realis")
utils.terminate_with_error("Must provide a mapping between 0 to 3")
else:
Config.coref_criteria = Config.possible_coref_mapping[1]
diff_out = None
if args.comparison_output is not None:
diff_out_path = args.comparison_output
utils.create_parent_dir(diff_out_path)
diff_out = open(diff_out_path, 'w')
token_dir = "."
if args.token_path is not None:
if args.eval_mode == EvalMethod.Token:
utils.terminate_with_error("Token table (-t) must be provided in token mode")
if os.path.isdir(args.token_path):
logger.debug("Will search token files in " + args.token_path)
token_dir = args.token_path
else:
logger.debug("Cannot find given token directory at [%s], "
"will try search for current directory" % args.token_path)
token_offset_fields = Config.default_token_offset_fields
if args.offset_field is not None:
try:
token_offset_fields = [int(x) for x in args.offset_field.split(",")]
except ValueError as _:
logger.error("Token offset argument should be two integer with comma in between, i.e. 2,3")
if args.coreference_threshold is not None:
MutableConfig.coref_mention_threshold = args.coreference_threshold
# Read all documents.
read_all_doc(gf, sf, args.doc_id_to_eval)
# Take all attribute combinations, which will be used to produce scores.
attribute_comb = get_attr_combinations(Config.attribute_names)
logger.info("Coreference mentions need to match %s before consideration" % Config.coref_criteria[0][1])
while True:
if not evaluate(token_dir, args.coref, attribute_comb,
token_offset_fields, args.token_table_extension,
diff_out):
break
# Run the CoNLL script on the combined files, which is concatenated from the best alignment of all documents.
if args.coref is not None:
logger.debug("Running coreference script for the final scores.")
ConllEvaluator.run_conll_script(Config.conll_gold_file, Config.conll_sys_file, Config.conll_out)
# Get the CoNLL scores from output
EvalState.overall_coref_scores = ConllEvaluator.get_conll_scores(Config.conll_out)
# Run the TimeML evaluation script.
TemporalEval.eval_time_ml()
print_eval_results(mention_eval_out, attribute_comb)
# Clean up, close files.
close_if_not_none(diff_out)
logger.info("Evaluation Done.")
