498 lines
19 KiB
Python
498 lines
19 KiB
Python
from __future__ import division
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import os
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import sys
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import copy
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import types
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import logging
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import copy_reg
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import warnings
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import subprocess
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import numpy as np
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import pandas as pd
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from .core import Table, Geometry
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from .image_processing import (adaptive_threshold, find_lines, find_table_contours,
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find_table_joints)
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from .utils import (scale_to_pdf, scale_to_image, segments_bbox, text_in_bbox,
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merge_close_values, get_table_index, compute_accuracy, count_empty,
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get_text_objects, get_page_layout, encode_)
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__all__ = ['Stream', 'Lattice']
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logger = logging.getLogger('app_logger')
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def _reduce_method(m):
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if m.im_self is None:
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return getattr, (m.im_class, m.im_func.func_name)
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else:
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return getattr, (m.im_self, m.im_func.func_name)
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copy_reg.pickle(types.MethodType, _reduce_method)
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class Stream:
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"""
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"""
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def __init__(self, table_area=None, columns=None, ytol=[2], mtol=[0],
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margins=(1.0, 0.5, 0.1), split_text=False, flag_size=True,
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debug=False):
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self.method = 'stream'
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self.table_area = table_area
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self.columns = columns
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self.ytol = ytol
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self.mtol = mtol
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self.char_margin, self.line_margin, self.word_margin = margins
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self.split_text = split_text
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self.flag_size = flag_size
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self.debug = debug
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@staticmethod
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def _text_bbox(t_bbox):
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xmin = min([t.x0 for direction in t_bbox for t in t_bbox[direction]])
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ymin = min([t.y0 for direction in t_bbox for t in t_bbox[direction]])
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xmax = max([t.x1 for direction in t_bbox for t in t_bbox[direction]])
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ymax = max([t.y1 for direction in t_bbox for t in t_bbox[direction]])
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text_bbox = (xmin, ymin, xmax, ymax)
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return text_bbox
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@staticmethod
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def _group_rows(text, ytol=2):
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row_y = 0
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rows = []
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temp = []
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for t in text:
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# is checking for upright necessary?
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# if t.get_text().strip() and all([obj.upright for obj in t._objs if
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# type(obj) is LTChar]):
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if t.get_text().strip():
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if not np.isclose(row_y, t.y0, atol=ytol):
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rows.append(sorted(temp, key=lambda t: t.x0))
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temp = []
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row_y = t.y0
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temp.append(t)
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rows.append(sorted(temp, key=lambda t: t.x0))
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__ = rows.pop(0) # hacky
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return rows
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@staticmethod
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def _merge_columns(l, mtol=0):
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merged = []
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for higher in l:
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if not merged:
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merged.append(higher)
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else:
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lower = merged[-1]
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if mtol >= 0:
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if (higher[0] <= lower[1] or
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np.isclose(higher[0], lower[1], atol=mtol)):
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upper_bound = max(lower[1], higher[1])
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lower_bound = min(lower[0], higher[0])
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merged[-1] = (lower_bound, upper_bound)
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else:
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merged.append(higher)
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elif mtol < 0:
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if higher[0] <= lower[1]:
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if np.isclose(higher[0], lower[1], atol=abs(mtol)):
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merged.append(higher)
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else:
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upper_bound = max(lower[1], higher[1])
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lower_bound = min(lower[0], higher[0])
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merged[-1] = (lower_bound, upper_bound)
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else:
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merged.append(higher)
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return merged
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@staticmethod
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def _join_rows(rows_grouped, text_y_max, text_y_min):
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row_mids = [sum([(t.y0 + t.y1) / 2 for t in r]) / len(r)
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if len(r) > 0 else 0 for r in rows_grouped]
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rows = [(row_mids[i] + row_mids[i - 1]) / 2 for i in range(1, len(row_mids))]
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rows.insert(0, text_y_max)
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rows.append(text_y_min)
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rows = [(rows[i], rows[i + 1])
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for i in range(0, len(rows) - 1)]
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return rows
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@staticmethod
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def _add_columns(cols, text, ytol):
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if text:
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text = Stream._group_rows(text, ytol=ytol)
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elements = [len(r) for r in text]
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new_cols = [(t.x0, t.x1)
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for r in text if len(r) == max(elements) for t in r]
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cols.extend(Stream._merge_columns(sorted(new_cols)))
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return cols
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@staticmethod
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def _join_columns(cols, text_x_min, text_x_max):
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cols = sorted(cols)
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cols = [(cols[i][0] + cols[i - 1][1]) / 2 for i in range(1, len(cols))]
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cols.insert(0, text_x_min)
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cols.append(text_x_max)
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cols = [(cols[i], cols[i + 1])
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for i in range(0, len(cols) - 1)]
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return cols
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def extract_tables(self, pdfname):
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"""
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Parameters
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----------
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pdfname
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Returns
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-------
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"""
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layout, dim = get_page_layout(pdfname, char_margin=self.char_margin,
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line_margin=self.line_margin, word_margin=self.word_margin)
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lttextlh = get_text_objects(layout, ltype="lh")
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lttextlv = get_text_objects(layout, ltype="lv")
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ltchar = get_text_objects(layout, ltype="char")
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width, height = dim
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bname, __ = os.path.splitext(pdfname)
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logger.info('Processing {0}.'.format(os.path.basename(bname)))
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if not lttextlh:
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warnings.warn("{0}: Page contains no text.".format(
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os.path.basename(bname)))
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return {os.path.basename(bname): None}
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g = Geometry()
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if self.debug:
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text = []
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text.extend([(t.x0, t.y0, t.x1, t.y1) for t in lttextlh])
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text.extend([(t.x0, t.y0, t.x1, t.y1) for t in lttextlv])
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g.text = text
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if self.table_area is not None:
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if self.columns is not None:
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if len(self.table_area) != len(self.columns):
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raise ValueError("{0}: Length of table area and columns"
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" should be equal.".format(os.path.basename(bname)))
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table_bbox = {}
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for area in self.table_area:
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x1, y1, x2, y2 = area.split(",")
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x1 = float(x1)
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y1 = float(y1)
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x2 = float(x2)
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y2 = float(y2)
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table_bbox[(x1, y2, x2, y1)] = None
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else:
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table_bbox = {(0, 0, width, height): None}
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if len(self.ytol) == 1 and self.ytol[0] == 2:
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ytolerance = copy.deepcopy(self.ytol) * len(table_bbox)
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else:
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ytolerance = copy.deepcopy(self.ytol)
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if len(self.mtol) == 1 and self.mtol[0] == 0:
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mtolerance = copy.deepcopy(self.mtol) * len(table_bbox)
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else:
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mtolerance = copy.deepcopy(self.mtol)
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_tables = []
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# sort tables based on y-coord
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for table_no, k in enumerate(sorted(table_bbox.keys(), key=lambda x: x[1], reverse=True)):
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# select elements which lie within table_bbox
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t_bbox = {}
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t_bbox['horizontal'] = text_in_bbox(k, lttextlh)
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t_bbox['vertical'] = text_in_bbox(k, lttextlv)
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for direction in t_bbox:
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t_bbox[direction].sort(key=lambda x: (-x.y0, x.x0))
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text_x_min, text_y_min, text_x_max, text_y_max = self._text_bbox(t_bbox)
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rows_grouped = self._group_rows(t_bbox['horizontal'], ytol=ytolerance[table_no])
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rows = self._join_rows(rows_grouped, text_y_max, text_y_min)
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elements = [len(r) for r in rows_grouped]
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guess = False
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if self.columns is not None and self.columns[table_no] != "":
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# user has to input boundary columns too
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# take (0, width) by default
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# similar to else condition
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# len can't be 1
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cols = self.columns[table_no].split(',')
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cols = [float(c) for c in cols]
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cols.insert(0, text_x_min)
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cols.append(text_x_max)
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cols = [(cols[i], cols[i + 1]) for i in range(0, len(cols) - 1)]
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else:
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guess = True
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ncols = max(set(elements), key=elements.count)
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len_non_mode = len(filter(lambda x: x != ncols, elements))
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if ncols == 1:
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# no tables detected
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warnings.warn("{0}: Page contains no tables.".format(
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os.path.basename(bname)))
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cols = [(t.x0, t.x1)
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for r in rows_grouped if len(r) == ncols for t in r]
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cols = self._merge_columns(sorted(cols), mtol=mtolerance[table_no])
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inner_text = []
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for i in range(1, len(cols)):
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left = cols[i - 1][1]
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right = cols[i][0]
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inner_text.extend([t for direction in t_bbox
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for t in t_bbox[direction]
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if t.x0 > left and t.x1 < right])
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outer_text = [t for direction in t_bbox
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for t in t_bbox[direction]
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if t.x0 > cols[-1][1] or t.x1 < cols[0][0]]
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inner_text.extend(outer_text)
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cols = self._add_columns(cols, inner_text, ytolerance[table_no])
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cols = self._join_columns(cols, text_x_min, text_x_max)
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table = Table(cols, rows)
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table = table.set_all_edges()
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pos_errors = []
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for direction in t_bbox:
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for t in t_bbox[direction]:
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indices, error = get_table_index(
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table, t, direction, split_text=self.split_text,
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flag_size=self.flag_size)
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if indices[:2] != (-1, -1):
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pos_errors.append(error)
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for r_idx, c_idx, text in indices:
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table.cells[r_idx][c_idx].add_text(text)
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if guess:
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accuracy = compute_accuracy([[66, pos_errors], [34, [len_non_mode / len(elements)]]])
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else:
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accuracy = compute_accuracy([[100, pos_errors]])
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data = table.data
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data = encode_(data)
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table.df = pd.DataFrame(data)
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table.shape = table.df.shape
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whitespace, __, __ = count_empty(data)
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table.accuracy = accuracy
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table.whitespace = whitespace
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table.order = table_no + 1
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table.page = int(os.path.basename(bname).replace('page-', ''))
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_tables.append(table)
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return _tables, g
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class Lattice:
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"""
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"""
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def __init__(self, table_area=None, fill=None, mtol=[2], jtol=[2],
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blocksize=15, threshold_constant=-2, scale=15, iterations=0,
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invert=False, margins=(1.0, 0.5, 0.1), split_text=False,
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flag_size=True, shift_text=['l', 't'], debug=None):
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self.method = 'lattice'
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self.table_area = table_area
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self.fill = fill
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self.mtol = mtol
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self.jtol = jtol
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self.blocksize = blocksize
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self.threshold_constant = threshold_constant
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self.scale = scale
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self.iterations = iterations
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self.invert = invert
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self.char_margin, self.line_margin, self.word_margin = margins
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self.split_text = split_text
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self.flag_size = flag_size
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self.shift_text = shift_text
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self.debug = debug
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@staticmethod
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def _reduce_index(t, idx, shift_text):
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indices = []
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for r_idx, c_idx, text in idx:
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for d in shift_text:
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if d == 'l':
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if t.cells[r_idx][c_idx].spanning_h:
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while not t.cells[r_idx][c_idx].left:
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c_idx -= 1
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if d == 'r':
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if t.cells[r_idx][c_idx].spanning_h:
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while not t.cells[r_idx][c_idx].right:
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c_idx += 1
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if d == 't':
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if t.cells[r_idx][c_idx].spanning_v:
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while not t.cells[r_idx][c_idx].top:
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r_idx -= 1
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if d == 'b':
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if t.cells[r_idx][c_idx].spanning_v:
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while not t.cells[r_idx][c_idx].bottom:
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r_idx += 1
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indices.append((r_idx, c_idx, text))
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return indices
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def _fill_spanning(t, fill=None):
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for f in fill:
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if f == "h":
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for i in range(len(t.cells)):
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for j in range(len(t.cells[i])):
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if t.cells[i][j].get_text().strip() == '':
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if t.cells[i][j].spanning_h and not t.cells[i][j].left:
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t.cells[i][j].add_text(t.cells[i][j - 1].get_text())
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elif f == "v":
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for i in range(len(t.cells)):
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for j in range(len(t.cells[i])):
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if t.cells[i][j].get_text().strip() == '':
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if t.cells[i][j].spanning_v and not t.cells[i][j].top:
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t.cells[i][j].add_text(t.cells[i - 1][j].get_text())
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return t
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def extract_tables(self, pdfname):
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"""
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Parameters
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----------
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pdfname
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Returns
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-------
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"""
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layout, dim = get_page_layout(pdfname, char_margin=self.char_margin,
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line_margin=self.line_margin, word_margin=self.word_margin)
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lttextlh = get_text_objects(layout, ltype="lh")
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lttextlv = get_text_objects(layout, ltype="lv")
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ltchar = get_text_objects(layout, ltype="char")
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width, height = dim
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bname, __ = os.path.splitext(pdfname)
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logger.info('Processing {0}.'.format(os.path.basename(bname)))
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if not ltchar:
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warnings.warn("{0}: Page contains no text.".format(
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os.path.basename(bname)))
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return {os.path.basename(bname): None}
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imagename = ''.join([bname, '.png'])
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gs_call = [
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"-q", "-sDEVICE=png16m", "-o", imagename, "-r600", pdfname
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]
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if "ghostscript" in subprocess.check_output(["gs", "-version"]).lower():
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gs_call.insert(0, "gs")
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else:
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gs_call.insert(0, "gsc")
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subprocess.call(gs_call, stdout=open(os.devnull, 'w'),
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stderr=subprocess.STDOUT)
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img, threshold = adaptive_threshold(imagename, invert=self.invert,
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blocksize=self.blocksize, c=self.threshold_constant)
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pdf_x = width
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pdf_y = height
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img_x = img.shape[1]
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img_y = img.shape[0]
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sc_x_image = img_x / float(pdf_x)
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sc_y_image = img_y / float(pdf_y)
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sc_x_pdf = pdf_x / float(img_x)
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sc_y_pdf = pdf_y / float(img_y)
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factors_image = (sc_x_image, sc_y_image, pdf_y)
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factors_pdf = (sc_x_pdf, sc_y_pdf, img_y)
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vmask, v_segments = find_lines(threshold, direction='vertical',
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scale=self.scale, iterations=self.iterations)
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hmask, h_segments = find_lines(threshold, direction='horizontal',
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scale=self.scale, iterations=self.iterations)
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if self.table_area is not None:
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areas = []
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for area in self.table_area:
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x1, y1, x2, y2 = area.split(",")
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x1 = float(x1)
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y1 = float(y1)
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x2 = float(x2)
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y2 = float(y2)
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x1, y1, x2, y2 = scale_to_image((x1, y1, x2, y2), factors_image)
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areas.append((x1, y1, abs(x2 - x1), abs(y2 - y1)))
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table_bbox = find_table_joints(areas, vmask, hmask)
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else:
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contours = find_table_contours(vmask, hmask)
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table_bbox = find_table_joints(contours, vmask, hmask)
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if len(self.mtol) == 1 and self.mtol[0] == 2:
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mtolerance = copy.deepcopy(self.mtol) * len(table_bbox)
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else:
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mtolerance = copy.deepcopy(self.mtol)
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if len(self.jtol) == 1 and self.jtol[0] == 2:
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jtolerance = copy.deepcopy(self.jtol) * len(table_bbox)
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else:
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jtolerance = copy.deepcopy(self.jtol)
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g = Geometry()
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if self.debug:
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g.images = (img, table_bbox)
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table_bbox, v_segments, h_segments = scale_to_pdf(table_bbox, v_segments,
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h_segments, factors_pdf)
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if self.debug:
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g.segments = (v_segments, h_segments)
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_tables = []
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# sort tables based on y-coord
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for table_no, k in enumerate(sorted(table_bbox.keys(), key=lambda x: x[1], reverse=True)):
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# select elements which lie within table_bbox
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t_bbox = {}
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v_s, h_s = segments_bbox(k, v_segments, h_segments)
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t_bbox['horizontal'] = text_in_bbox(k, lttextlh)
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t_bbox['vertical'] = text_in_bbox(k, lttextlv)
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for direction in t_bbox:
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t_bbox[direction].sort(key=lambda x: (-x.y0, x.x0))
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cols, rows = zip(*table_bbox[k])
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cols, rows = list(cols), list(rows)
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cols.extend([k[0], k[2]])
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rows.extend([k[1], k[3]])
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# sort horizontal and vertical segments
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cols = merge_close_values(sorted(cols), mtol=mtolerance[table_no])
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|
rows = merge_close_values(
|
|
sorted(rows, reverse=True), mtol=mtolerance[table_no])
|
|
# make grid using x and y coord of shortlisted rows and cols
|
|
cols = [(cols[i], cols[i + 1])
|
|
for i in range(0, len(cols) - 1)]
|
|
rows = [(rows[i], rows[i + 1])
|
|
for i in range(0, len(rows) - 1)]
|
|
|
|
table = Table(cols, rows)
|
|
# set table edges to True using ver+hor lines
|
|
table = table.set_edges(v_s, h_s, jtol=jtolerance[table_no])
|
|
# set spanning cells to True
|
|
table = table.set_spanning()
|
|
# set table border edges to True
|
|
table = table.set_border_edges()
|
|
|
|
pos_errors = []
|
|
for direction in ['vertical', 'horizontal']:
|
|
for t in 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)
|
|
indices = self._reduce_index(table, indices, shift_text=self.shift_text)
|
|
for r_idx, c_idx, text in indices:
|
|
table.cells[r_idx][c_idx].add_text(text)
|
|
accuracy = compute_accuracy([[100, pos_errors]])
|
|
|
|
if self.fill is not None:
|
|
table = self._fill_spanning(table, fill=self.fill)
|
|
|
|
data = table.data
|
|
data = encode_(data)
|
|
table.df = pd.DataFrame(data)
|
|
table.shape = table.df.shape
|
|
|
|
whitespace, __, __ = count_empty(data)
|
|
table.accuracy = accuracy
|
|
table.whitespace = whitespace
|
|
table.order = table_no + 1
|
|
table.page = int(os.path.basename(bname).replace('page-', ''))
|
|
|
|
_tables.append(table)
|
|
|
|
if self.debug:
|
|
g.tables = _tables
|
|
|
|
return _tables, g |