# Overlap Filter
from joblib import delayed, Parallel
from six import iteritems
import pandas as pd
import pyprind
from py_stringsimjoin.filter.filter import Filter
from py_stringsimjoin.index.inverted_index import InvertedIndex
from py_stringsimjoin.utils.generic_helper import convert_dataframe_to_array, \
find_output_attribute_indices, get_attrs_to_project, \
get_num_processes_to_launch, get_output_header_from_tables, \
get_output_row_from_tables, remove_redundant_attrs, split_table, COMP_OP_MAP
from py_stringsimjoin.utils.missing_value_handler import \
get_pairs_with_missing_value
from py_stringsimjoin.utils.simfunctions import overlap
from py_stringsimjoin.utils.validation import validate_attr, \
validate_attr_type, validate_comp_op_for_sim_measure, validate_key_attr, \
validate_input_table, validate_threshold, validate_tokenizer, \
validate_output_attrs
[docs]class OverlapFilter(Filter):
"""Finds candidate matching pairs of strings using overlap filtering
technique.
A string pair is output by overlap filter only if the number of common
tokens in the strings satisfy the condition on overlap size threshold. For
example, if the comparison operator is '>=', a string pair is output if the
number of common tokens is greater than or equal to the overlap size
threshold, as specified by "overlap_size".
Args:
tokenizer (Tokenizer): tokenizer to be used.
overlap_size (int): overlap threshold to be used by the filter.
comp_op (string): comparison operator. Supported values are '>=', '>'
and '=' (defaults to '>=').
allow_missing (boolean): A flag to indicate whether pairs containing
missing value should survive the filter (defaults to False).
Attributes:
tokenizer (Tokenizer): An attribute to store the tokenizer.
overlap_size (int): An attribute to store the overlap threshold value.
comp_op (string): An attribute to store the comparison operator.
allow_missing (boolean): An attribute to store the value of the flag
allow_missing.
"""
def __init__(self, tokenizer, overlap_size=1, comp_op='>=',
allow_missing=False):
# check if the input tokenizer is valid
validate_tokenizer(tokenizer)
# check if the overlap size is valid
validate_threshold(overlap_size, 'OVERLAP')
# check if the comparison operator is valid
validate_comp_op_for_sim_measure(comp_op, 'OVERLAP')
self.tokenizer = tokenizer
self.overlap_size = overlap_size
self.comp_op = comp_op
super(self.__class__, self).__init__(allow_missing)
[docs] def filter_pair(self, lstring, rstring):
"""Checks if the input strings get dropped by the overlap filter.
Args:
lstring,rstring (string): input strings
Returns:
A flag indicating whether the string pair is dropped (boolean).
"""
# If one of the inputs is missing, then check the allow_missing flag.
# If it is set to True, then pass the pair. Else drop the pair.
if pd.isnull(lstring) or pd.isnull(rstring):
return (not self.allow_missing)
# check for empty string
if (not lstring) or (not rstring):
return True
# tokenize input strings
ltokens = self.tokenizer.tokenize(lstring)
rtokens = self.tokenizer.tokenize(rstring)
num_overlap = overlap(ltokens, rtokens)
if COMP_OP_MAP[self.comp_op](num_overlap, self.overlap_size):
return False
else:
return True
[docs] def filter_tables(self, ltable, rtable,
l_key_attr, r_key_attr,
l_filter_attr, r_filter_attr,
l_out_attrs=None, r_out_attrs=None,
l_out_prefix='l_', r_out_prefix='r_',
out_sim_score=False, n_jobs=1, show_progress=True):
"""Finds candidate matching pairs of strings from the input tables using
overlap filtering technique.
Args:
ltable (DataFrame): left input table.
rtable (DataFrame): right input table.
l_key_attr (string): key attribute in left table.
r_key_attr (string): key attribute in right table.
l_filter_attr (string): attribute in left table on which the filter
should be applied.
r_filter_attr (string): attribute in right table on which the filter
should be applied.
l_out_attrs (list): list of attribute names from the left table to
be included in the output table (defaults to None).
r_out_attrs (list): list of attribute names from the right table to
be included in the output table (defaults to None).
l_out_prefix (string): prefix to be used for the attribute names
coming from the left table, in the output table
(defaults to 'l\_').
r_out_prefix (string): prefix to be used for the attribute names
coming from the right table, in the output table
(defaults to 'r\_').
out_sim_score (boolean): flag to indicate whether the overlap score
should be included in the output table (defaults to True).
Setting this flag to True will add a column named '_sim_score'
in the output table. This column will contain the overlap scores
for the tuple pairs in the output.
n_jobs (int): number of parallel jobs to use for the computation
(defaults to 1). If -1 is given, all CPUs are used. If 1 is
given, no parallel computing code is used at all, which is
useful for debugging. For n_jobs below -1,
(n_cpus + 1 + n_jobs) are used (where n_cpus is the total
number of CPUs in the machine). Thus for n_jobs = -2, all CPUs
but one are used. If (n_cpus + 1 + n_jobs) becomes less than 1,
then no parallel computing code will be used (i.e., equivalent
to the default).
show_progress (boolean): flag to indicate whether task progress
should be displayed to the user (defaults to True).
Returns:
An output table containing tuple pairs that survive the filter
(DataFrame).
"""
# check if the input tables are dataframes
validate_input_table(ltable, 'left table')
validate_input_table(rtable, 'right table')
# check if the key attributes and filter attributes exist
validate_attr(l_key_attr, ltable.columns,
'key attribute', 'left table')
validate_attr(r_key_attr, rtable.columns,
'key attribute', 'right table')
validate_attr(l_filter_attr, ltable.columns,
'attribute', 'left table')
validate_attr(r_filter_attr, rtable.columns,
'attribute', 'right table')
# check if the filter attributes are not of numeric type
validate_attr_type(l_filter_attr, ltable[l_filter_attr].dtype,
'attribute', 'left table')
validate_attr_type(r_filter_attr, rtable[r_filter_attr].dtype,
'attribute', 'right table')
# check if the output attributes exist
validate_output_attrs(l_out_attrs, ltable.columns,
r_out_attrs, rtable.columns)
# check if the key attributes are unique and do not contain
# missing values
validate_key_attr(l_key_attr, ltable, 'left table')
validate_key_attr(r_key_attr, rtable, 'right table')
# remove redundant attrs from output attrs.
l_out_attrs = remove_redundant_attrs(l_out_attrs, l_key_attr)
r_out_attrs = remove_redundant_attrs(r_out_attrs, r_key_attr)
# get attributes to project.
l_proj_attrs = get_attrs_to_project(l_out_attrs,
l_key_attr, l_filter_attr)
r_proj_attrs = get_attrs_to_project(r_out_attrs,
r_key_attr, r_filter_attr)
# Do a projection on the input dataframes to keep only the required
# attributes. Then, remove rows with missing value in filter attribute
# from the input dataframes. Then, convert the resulting dataframes
# into ndarray.
ltable_array = convert_dataframe_to_array(ltable, l_proj_attrs,
l_filter_attr)
rtable_array = convert_dataframe_to_array(rtable, r_proj_attrs,
r_filter_attr)
# computes the actual number of jobs to launch.
n_jobs = min(get_num_processes_to_launch(n_jobs), len(rtable_array))
if n_jobs <= 1:
# if n_jobs is 1, do not use any parallel code.
output_table = _filter_tables_split(
ltable_array, rtable_array,
l_proj_attrs, r_proj_attrs,
l_key_attr, r_key_attr,
l_filter_attr, r_filter_attr,
self,
l_out_attrs, r_out_attrs,
l_out_prefix, r_out_prefix,
out_sim_score, show_progress)
else:
# if n_jobs is above 1, split the right table into n_jobs splits and
# filter each right table split with the whole of left table in a
# separate process.
r_splits = split_table(rtable_array, n_jobs)
results = Parallel(n_jobs=n_jobs)(delayed(_filter_tables_split)(
ltable_array, r_splits[job_index],
l_proj_attrs, r_proj_attrs,
l_key_attr, r_key_attr,
l_filter_attr, r_filter_attr,
self,
l_out_attrs, r_out_attrs,
l_out_prefix, r_out_prefix,
out_sim_score,
(show_progress and (job_index==n_jobs-1)))
for job_index in range(n_jobs))
output_table = pd.concat(results)
# If allow_missing flag is set, then compute all pairs with missing
# value in at least one of the filter attributes and then add it to the
# output obtained from applying the filter.
if self.allow_missing:
missing_pairs = get_pairs_with_missing_value(
ltable, rtable,
l_key_attr, r_key_attr,
l_filter_attr, r_filter_attr,
l_out_attrs, r_out_attrs,
l_out_prefix, r_out_prefix,
out_sim_score, show_progress)
output_table = pd.concat([output_table, missing_pairs])
# add an id column named '_id' to the output table.
output_table.insert(0, '_id', range(0, len(output_table)))
return output_table
def find_candidates(self, probe_tokens, inverted_index):
candidate_overlap = {}
if not inverted_index.index:
return candidate_overlap
for token in probe_tokens:
for cand in inverted_index.probe(token):
candidate_overlap[cand] = candidate_overlap.get(cand, 0) + 1
return candidate_overlap
def _filter_tables_split(ltable, rtable,
l_columns, r_columns,
l_key_attr, r_key_attr,
l_filter_attr, r_filter_attr,
overlap_filter,
l_out_attrs, r_out_attrs,
l_out_prefix, r_out_prefix,
out_sim_score, show_progress):
# Find column indices of key attr, filter attr and output attrs in ltable
l_key_attr_index = l_columns.index(l_key_attr)
l_filter_attr_index = l_columns.index(l_filter_attr)
l_out_attrs_indices = []
l_out_attrs_indices = find_output_attribute_indices(l_columns, l_out_attrs)
# Find column indices of key attr, filter attr and output attrs in rtable
r_key_attr_index = r_columns.index(r_key_attr)
r_filter_attr_index = r_columns.index(r_filter_attr)
r_out_attrs_indices = find_output_attribute_indices(r_columns, r_out_attrs)
# Build inverted index over ltable
inverted_index = InvertedIndex(ltable, l_filter_attr_index,
overlap_filter.tokenizer)
inverted_index.build(False)
comp_fn = COMP_OP_MAP[overlap_filter.comp_op]
output_rows = []
has_output_attributes = (l_out_attrs is not None or
r_out_attrs is not None)
if show_progress:
prog_bar = pyprind.ProgBar(len(rtable))
for r_row in rtable:
r_string = r_row[r_filter_attr_index]
r_filter_attr_tokens = overlap_filter.tokenizer.tokenize(r_string)
# probe inverted index and find overlap of candidates
candidate_overlap = overlap_filter.find_candidates(
r_filter_attr_tokens, inverted_index)
for cand, overlap in iteritems(candidate_overlap):
if comp_fn(overlap, overlap_filter.overlap_size):
if has_output_attributes:
output_row = get_output_row_from_tables(
ltable[cand], r_row,
l_key_attr_index, r_key_attr_index,
l_out_attrs_indices, r_out_attrs_indices)
else:
output_row = [ltable[cand][l_key_attr_index],
r_row[r_key_attr_index]]
if out_sim_score:
output_row.append(overlap)
output_rows.append(output_row)
if show_progress:
prog_bar.update()
output_header = get_output_header_from_tables(l_key_attr, r_key_attr,
l_out_attrs, r_out_attrs,
l_out_prefix, r_out_prefix)
if out_sim_score:
output_header.append("_sim_score")
output_table = pd.DataFrame(output_rows, columns=output_header)
return output_table