from __future__ import division
import os
import logging
import numpy as np
import pandas as pd
from .base import BaseParser
from ..core import Table
from ..utils import (text_in_bbox, get_table_index, compute_accuracy,
compute_whitespace, setup_logging, encode_)
logger = setup_logging(__name__)
class Stream(BaseParser):
"""Stream method of parsing looks for spaces between text
to form a table.
If you want to specify columns when specifying multiple table
areas, make sure that the length of both lists are equal.
Parameters
----------
table_area : list, optional (default: None)
List of table areas to analyze as strings of the form
x1,y1,x2,y2 where (x1, y1) -> left-top and
(x2, y2) -> right-bottom in pdf coordinate space.
columns : list, optional (default: None)
List of column x-coordinates as strings where the coordinates
are comma-separated.
split_text : bool, optional (default: False)
Whether or not to split a text line if it spans across
multiple cells.
flag_size : bool, optional (default: False)
Whether or not to highlight a substring using
if its size is different from rest of the string. (Useful for
super and subscripts)
row_close_tol : int, optional (default: 2)
Rows will be formed by combining text vertically
within this tolerance.
col_close_tol : int, optional (default: 0)
Columns will be formed by combining text horizontally
within this tolerance.
margins : tuple, optional (default: (1.0, 0.5, 0.1))
PDFMiner margins. (char_margin, line_margin, word_margin)
For more information, refer `PDFMiner docs `_.
"""
def __init__(self, table_area=None, columns=None, split_text=False,
flag_size=False, row_close_tol=2, col_close_tol=0,
margins=(1.0, 0.5, 0.1)):
self.table_area = table_area
self.columns = columns
self._validate_columns()
self.split_text = split_text
self.flag_size = flag_size
self.row_close_tol = row_close_tol
self.col_close_tol = col_close_tol
self.char_margin, self.line_margin, self.word_margin = margins
@staticmethod
def _text_bbox(t_bbox):
"""Returns bounding box for the text present on a page.
Parameters
----------
t_bbox : dict
Dict with two keys 'horizontal' and 'vertical' with lists of
LTTextLineHorizontals and LTTextLineVerticals respectively.
Returns
-------
text_bbox : tuple
Tuple (x0, y0, x1, y1) in pdf coordinate space.
"""
xmin = min([t.x0 for direction in t_bbox for t in t_bbox[direction]])
ymin = min([t.y0 for direction in t_bbox for t in t_bbox[direction]])
xmax = max([t.x1 for direction in t_bbox for t in t_bbox[direction]])
ymax = max([t.y1 for direction in t_bbox for t in t_bbox[direction]])
text_bbox = (xmin, ymin, xmax, ymax)
return text_bbox
@staticmethod
def _group_rows(text, row_close_tol=2):
"""Groups PDFMiner text objects into rows vertically
within a tolerance.
Parameters
----------
text : list
List of PDFMiner text objects.
row_close_tol : int, optional (default: 2)
Returns
-------
rows : list
Two-dimensional list of text objects grouped into rows.
"""
row_y = 0
rows = []
temp = []
for t in text:
# is checking for upright necessary?
# if t.get_text().strip() and all([obj.upright for obj in t._objs if
# type(obj) is LTChar]):
if t.get_text().strip():
if not np.isclose(row_y, t.y0, atol=row_close_tol):
rows.append(sorted(temp, key=lambda t: t.x0))
temp = []
row_y = t.y0
temp.append(t)
rows.append(sorted(temp, key=lambda t: t.x0))
__ = rows.pop(0) # hacky
return rows
@staticmethod
def _merge_columns(l, col_close_tol=0):
"""Merges column boundaries horizontally if they overlap
or lie within a tolerance.
Parameters
----------
l : list
List of column x-coordinate tuples.
col_close_tol : int, optional (default: 0)
Returns
-------
merged : list
List of merged column x-coordinate tuples.
"""
merged = []
for higher in l:
if not merged:
merged.append(higher)
else:
lower = merged[-1]
if col_close_tol >= 0:
if (higher[0] <= lower[1] or
np.isclose(higher[0], lower[1], atol=col_close_tol)):
upper_bound = max(lower[1], higher[1])
lower_bound = min(lower[0], higher[0])
merged[-1] = (lower_bound, upper_bound)
else:
merged.append(higher)
elif col_close_tol < 0:
if higher[0] <= lower[1]:
if np.isclose(higher[0], lower[1], atol=abs(col_close_tol)):
merged.append(higher)
else:
upper_bound = max(lower[1], higher[1])
lower_bound = min(lower[0], higher[0])
merged[-1] = (lower_bound, upper_bound)
else:
merged.append(higher)
return merged
@staticmethod
def _join_rows(rows_grouped, text_y_max, text_y_min):
"""Makes row coordinates continuous.
Parameters
----------
rows_grouped : list
Two-dimensional list of text objects grouped into rows.
text_y_max : int
text_y_min : int
Returns
-------
rows : list
List of continuous row y-coordinate tuples.
"""
row_mids = [sum([(t.y0 + t.y1) / 2 for t in r]) / len(r)
if len(r) > 0 else 0 for r in rows_grouped]
rows = [(row_mids[i] + row_mids[i - 1]) / 2 for i in range(1, len(row_mids))]
rows.insert(0, text_y_max)
rows.append(text_y_min)
rows = [(rows[i], rows[i + 1])
for i in range(0, len(rows) - 1)]
return rows
@staticmethod
def _add_columns(cols, text, row_close_tol):
"""Adds columns to existing list by taking into account
the text that lies outside the current column x-coordinates.
Parameters
----------
cols : list
List of column x-coordinate tuples.
text : list
List of PDFMiner text objects.
ytol : int
Returns
-------
cols : list
Updated list of column x-coordinate tuples.
"""
if text:
text = Stream._group_rows(text, row_close_tol=row_close_tol)
elements = [len(r) for r in text]
new_cols = [(t.x0, t.x1)
for r in text if len(r) == max(elements) for t in r]
cols.extend(Stream._merge_columns(sorted(new_cols)))
return cols
@staticmethod
def _join_columns(cols, text_x_min, text_x_max):
"""Makes column coordinates continuous.
Parameters
----------
cols : list
List of column x-coordinate tuples.
text_x_min : int
text_y_max : int
Returns
-------
cols : list
Updated list of column x-coordinate tuples.
"""
cols = sorted(cols)
cols = [(cols[i][0] + cols[i - 1][1]) / 2 for i in range(1, len(cols))]
cols.insert(0, text_x_min)
cols.append(text_x_max)
cols = [(cols[i], cols[i + 1])
for i in range(0, len(cols) - 1)]
return cols
def _validate_columns(self):
if self.table_area is not None and self.columns is not None:
if len(self.table_area) != len(self.columns):
raise ValueError("Length of table_area and columns"
" should be equal")
def _generate_table_bbox(self):
if self.table_area is not None:
table_bbox = {}
for area in self.table_area:
x1, y1, x2, y2 = area.split(",")
x1 = float(x1)
y1 = float(y1)
x2 = float(x2)
y2 = float(y2)
table_bbox[(x1, y2, x2, y1)] = None
else:
table_bbox = {(0, 0, self.pdf_width, self.pdf_height): None}
self.table_bbox = table_bbox
def _generate_columns_and_rows(self, table_idx, tk):
# select elements which lie within table_bbox
t_bbox = {}
t_bbox['horizontal'] = text_in_bbox(tk, self.horizontal_text)
t_bbox['vertical'] = text_in_bbox(tk, self.vertical_text)
self.t_bbox = t_bbox
for direction in self.t_bbox:
self.t_bbox[direction].sort(key=lambda x: (-x.y0, x.x0))
text_x_min, text_y_min, text_x_max, text_y_max = self._text_bbox(self.t_bbox)
rows_grouped = self._group_rows(self.t_bbox['horizontal'], row_close_tol=self.row_close_tol)
rows = self._join_rows(rows_grouped, text_y_max, text_y_min)
elements = [len(r) for r in rows_grouped]
if self.columns is not None and self.columns[table_idx] != "":
# user has to input boundary columns too
# take (0, pdf_width) by default
# similar to else condition
# len can't be 1
cols = self.columns[table_idx].split(',')
cols = [float(c) for c in cols]
cols.insert(0, text_x_min)
cols.append(text_x_max)
cols = [(cols[i], cols[i + 1]) for i in range(0, len(cols) - 1)]
else:
ncols = max(set(elements), key=elements.count)
if ncols == 1:
logger.info("No tables found on {}".format(
os.path.basename(self.rootname)))
cols = [(t.x0, t.x1) for r in rows_grouped if len(r) == ncols for t in r]
cols = self._merge_columns(sorted(cols), col_close_tol=self.col_close_tol)
inner_text = []
for i in range(1, len(cols)):
left = cols[i - 1][1]
right = cols[i][0]
inner_text.extend([t for direction in self.t_bbox
for t in self.t_bbox[direction]
if t.x0 > left and t.x1 < right])
outer_text = [t for direction in self.t_bbox
for t in self.t_bbox[direction]
if t.x0 > cols[-1][1] or t.x1 < cols[0][0]]
inner_text.extend(outer_text)
cols = self._add_columns(cols, inner_text, self.row_close_tol)
cols = self._join_columns(cols, text_x_min, text_x_max)
return cols, rows
def _generate_table(self, table_idx, cols, rows, **kwargs):
table = Table(cols, rows)
table = table.set_all_edges()
pos_errors = []
for direction in self.t_bbox:
for t in self.t_bbox[direction]:
indices, error = get_table_index(
table, t, direction, split_text=self.split_text,
flag_size=self.flag_size)
if indices[:2] != (-1, -1):
pos_errors.append(error)
for r_idx, c_idx, text in indices:
table.cells[r_idx][c_idx].text = text
accuracy = compute_accuracy([[100, pos_errors]])
data = table.data
data = encode_(data)
table.df = pd.DataFrame(data)
table.shape = table.df.shape
whitespace = compute_whitespace(data)
table.flavor = 'stream'
table.accuracy = accuracy
table.whitespace = whitespace
table.order = table_idx + 1
table.page = int(os.path.basename(self.rootname).replace('page-', ''))
# for plotting
_text = []
_text.extend([(t.x0, t.y0, t.x1, t.y1) for t in self.horizontal_text])
_text.extend([(t.x0, t.y0, t.x1, t.y1) for t in self.vertical_text])
table._text = _text
table._image = None
table._segments = None
return table
def extract_tables(self, filename):
logger.info('Processing {}'.format(os.path.basename(filename)))
self._generate_layout(filename)
if not self.horizontal_text:
logger.info("No tables found on {}".format(
os.path.basename(self.rootname)))
return []
self._generate_table_bbox()
_tables = []
# sort tables based on y-coord
for table_idx, tk in enumerate(sorted(self.table_bbox.keys(),
key=lambda x: x[1], reverse=True)):
cols, rows = self._generate_columns_and_rows(table_idx, tk)
table = self._generate_table(table_idx, cols, rows)
_tables.append(table)
return _tables