Source code for camelot.parsers.stream

# -*- coding: utf-8 -*-

import os
import logging
import warnings

import numpy as np
import pandas as pd

from .base import BaseParser
from ..core import TextEdges, Table
from ..utils import text_in_bbox, get_table_index, compute_accuracy, compute_whitespace


logger = logging.getLogger("camelot")


[docs]class Stream(BaseParser): """Stream method of parsing looks for spaces between text to parse the table. If you want to specify columns when specifying multiple table areas, make sure that the length of both lists are equal. Parameters ---------- table_regions : list, optional (default: None) List of page regions that may contain tables of the form x1,y1,x2,y2 where (x1, y1) -> left-top and (x2, y2) -> right-bottom in PDF coordinate space. table_areas : list, optional (default: None) List of table area 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 strings where the coordinates are comma-separated. split_text : bool, optional (default: False) Split text that spans across multiple cells. flag_size : bool, optional (default: False) Flag text based on font size. Useful to detect super/subscripts. Adds <s></s> around flagged text. strip_text : str, optional (default: '') Characters that should be stripped from a string before assigning it to a cell. edge_tol : int, optional (default: 50) Tolerance parameter for extending textedges vertically. row_tol : int, optional (default: 2) Tolerance parameter used to combine text vertically, to generate rows. column_tol : int, optional (default: 0) Tolerance parameter used to combine text horizontally, to generate columns. """ def __init__( self, table_regions=None, table_areas=None, columns=None, split_text=False, flag_size=False, strip_text="", edge_tol=50, row_tol=2, column_tol=0, **kwargs ): self.table_regions = table_regions self.table_areas = table_areas self.columns = columns self._validate_columns() self.split_text = split_text self.flag_size = flag_size self.strip_text = strip_text self.edge_tol = edge_tol self.row_tol = row_tol self.column_tol = column_tol @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_tol=2): """Groups PDFMiner text objects into rows vertically within a tolerance. Parameters ---------- text : list List of PDFMiner text objects. row_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_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) # TODO: hacky return rows @staticmethod def _merge_columns(l, column_tol=0): """Merges column boundaries horizontally if they overlap or lie within a tolerance. Parameters ---------- l : list List of column x-coordinate tuples. column_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 column_tol >= 0: if higher[0] <= lower[1] or np.isclose( higher[0], lower[1], atol=column_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 column_tol < 0: if higher[0] <= lower[1]: if np.isclose(higher[0], lower[1], atol=abs(column_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_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_tol=row_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_areas is not None and self.columns is not None: if len(self.table_areas) != len(self.columns): raise ValueError("Length of table_areas and columns" " should be equal") def _nurminen_table_detection(self, textlines): """A general implementation of the table detection algorithm described by Anssi Nurminen's master's thesis. Link: https://dspace.cc.tut.fi/dpub/bitstream/handle/123456789/21520/Nurminen.pdf?sequence=3 Assumes that tables are situated relatively far apart vertically. """ # TODO: add support for arabic text #141 # sort textlines in reading order textlines.sort(key=lambda x: (-x.y0, x.x0)) textedges = TextEdges(edge_tol=self.edge_tol) # generate left, middle and right textedges textedges.generate(textlines) # select relevant edges relevant_textedges = textedges.get_relevant() self.textedges.extend(relevant_textedges) # guess table areas using textlines and relevant edges table_bbox = textedges.get_table_areas(textlines, relevant_textedges) # treat whole page as table area if no table areas found if not len(table_bbox): table_bbox = {(0, 0, self.pdf_width, self.pdf_height): None} return table_bbox def _generate_table_bbox(self): self.textedges = [] if self.table_areas is None: hor_text = self.horizontal_text if self.table_regions is not None: # filter horizontal text hor_text = [] for region in self.table_regions: x1, y1, x2, y2 = region.split(",") x1 = float(x1) y1 = float(y1) x2 = float(x2) y2 = float(y2) region_text = text_in_bbox((x1, y2, x2, y1), self.horizontal_text) hor_text.extend(region_text) # find tables based on nurminen's detection algorithm table_bbox = self._nurminen_table_detection(hor_text) else: table_bbox = {} for area in self.table_areas: 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 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) t_bbox["horizontal"].sort(key=lambda x: (-x.y0, x.x0)) t_bbox["vertical"].sort(key=lambda x: (x.x0, -x.y0)) self.t_bbox = t_bbox 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_tol=self.row_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: # calculate mode of the list of number of elements in # each row to guess the number of columns ncols = max(set(elements), key=elements.count) if ncols == 1: # if mode is 1, the page usually contains not tables # but there can be cases where the list can be skewed, # try to remove all 1s from list in this case and # see if the list contains elements, if yes, then use # the mode after removing 1s elements = list(filter(lambda x: x != 1, elements)) if len(elements): ncols = max(set(elements), key=elements.count) else: warnings.warn( f"No tables found in table area {table_idx + 1}" ) cols = [(t.x0, t.x1) for r in rows_grouped if len(r) == ncols for t in r] cols = self._merge_columns(sorted(cols), column_tol=self.column_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_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 = [] # TODO: have a single list in place of two directional ones? # sorted on x-coordinate based on reading order i.e. LTR or RTL for direction in ["vertical", "horizontal"]: 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, strip_text=self.strip_text, ) 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 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 table._textedges = self.textedges return table def extract_tables(self, filename, suppress_stdout=False, layout_kwargs={}): self._generate_layout(filename, layout_kwargs) base_filename = os.path.basename(self.rootname) if not suppress_stdout: logger.info(f"Processing {base_filename}") if not self.horizontal_text: if self.images: warnings.warn( f"{base_filename} is image-based, camelot only works on" " text-based pages." ) else: warnings.warn(f"No tables found on {base_filename}") 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) table._bbox = tk _tables.append(table) return _tables