#!/usr/bin/env python3 import csv import logging import os import re import warnings import sys from xml.dom.expatbuilder import Namespaces from lxml import etree as ET from itertools import groupby from operator import attrgetter from typing import List from collections.abc import MutableMapping, Sequence import click import pandas as pd import numpy as np from tqdm import tqdm from .lib import TagGroup, sorted_groupby, flatten, ns logger = logging.getLogger('alto4pandas') def alto_to_dict(alto, raise_errors=True): """Convert ALTO metadata to a nested dictionary""" value = {} # Iterate through each group of tags for tag, group in sorted_groupby(alto, key=attrgetter('tag')): group = list(group) localname = ET.QName(tag).localname alto_namespace = ET.QName(tag).namespace namespaces={"alto": alto_namespace} if localname == 'Description': value[localname] = TagGroup(tag, group).is_singleton().has_no_attributes().descend(raise_errors) elif localname == 'MeasurementUnit': value[localname] = TagGroup(tag, group).is_singleton().has_no_attributes().text() elif localname == 'OCRProcessing': value[localname] = TagGroup(tag, group).is_singleton().descend(raise_errors) elif localname == 'Processing': # TODO This enumerated descent is used more than once, DRY! for n, e in enumerate(group): value[f'{localname}{n}'] = alto_to_dict(e, raise_errors) elif localname == 'ocrProcessingStep': for n, e in enumerate(group): value[f'{localname}{n}'] = alto_to_dict(e, raise_errors) elif localname == 'preProcessingStep': for n, e in enumerate(group): value[f'{localname}{n}'] = alto_to_dict(e, raise_errors) elif localname == 'processingDateTime': value[localname] = TagGroup(tag, group).is_singleton().has_no_attributes().text() elif localname == 'processingSoftware': value[localname] = TagGroup(tag, group).is_singleton().descend(raise_errors) elif localname == 'processingAgency': value[localname] = TagGroup(tag, group).is_singleton().has_no_attributes().text() elif localname == 'processingStepDescription': value[localname] = TagGroup(tag, group).is_singleton().has_no_attributes().text() elif localname == 'processingStepSettings': value[localname] = TagGroup(tag, group).is_singleton().has_no_attributes().text() elif localname == 'softwareCreator': value[localname] = TagGroup(tag, group).is_singleton().has_no_attributes().text() elif localname == 'softwareName': value[localname] = TagGroup(tag, group).is_singleton().has_no_attributes().text() elif localname == 'softwareVersion': value[localname] = TagGroup(tag, group).is_singleton().has_no_attributes().text() elif localname == 'sourceImageInformation': value[localname] = TagGroup(tag, group).is_singleton().has_no_attributes().descend(raise_errors) elif localname == 'fileName': value[localname] = TagGroup(tag, group).is_singleton().has_no_attributes().text() elif localname == 'Layout': value[localname] = TagGroup(tag, group).is_singleton().has_no_attributes().descend(raise_errors) elif localname == 'Page': value[localname] = {} value[localname].update(TagGroup(tag, group).is_singleton().attributes()) value[localname].update(TagGroup(tag, group).subelement_counts()) value[localname].update(TagGroup(tag, group).xpath_statistics("//alto:String/@WC", namespaces)) # Count all alto:String elements with TAGREFS attribute value[localname].update(TagGroup(tag, group).xpath_count("//alto:String[@TAGREFS]", namespaces)) elif localname == 'Styles': pass elif localname == 'Tags': value[localname] = {} value[localname].update(TagGroup(tag, group).subelement_counts()) else: if raise_errors: print(value) raise ValueError('Unknown tag "{}"'.format(tag)) else: pass return value def walk(m): # XXX do this in mods4pandas, too if os.path.isdir(m): tqdm.write(f'Scanning directory {m}') for f in tqdm(os.scandir(m), leave=False): if f.is_file() and not f.name.startswith('.'): yield f.path elif f.is_dir(): try: yield from walk(f.path) except PermissionError: warnings.warn(f"Error walking {f.path}") else: yield m.path @click.command() @click.argument('alto_files', type=click.Path(exists=True), required=True, nargs=-1) @click.option('--output', '-o', 'output_file', type=click.Path(), help='Output pickle file', default='alto_info_df.pkl', show_default=True) @click.option('--output-csv', type=click.Path(), help='Output CSV file') @click.option('--output-xlsx', type=click.Path(), help='Output Excel .xlsx file') def process(alto_files: List[str], output_file: str, output_csv: str, output_xlsx: str): """ A tool to convert the ALTO metadata in INPUT to a pandas DataFrame. INPUT is assumed to be a ALTO document. INPUT may optionally be a directory. The tool then reads all files in the directory. alto4pandas writes two output files: A pickled pandas DataFrame and a CSV file with all conversion warnings. """ # Extend file list if directories are given alto_files_real = [] for m in alto_files: for x in walk(m): alto_files_real.append(x) # Process ALTO files with open(output_file + '.warnings.csv', 'w') as csvfile: csvwriter = csv.writer(csvfile) alto_info = [] logger.info('Processing ALTO files') for alto_file in tqdm(alto_files_real, leave=False): try: root = ET.parse(alto_file).getroot() alto = root # XXX .find('alto:alto', ns) does not work here with warnings.catch_warnings(record=True) as caught_warnings: warnings.simplefilter('always') # do NOT filter double occurrences # ALTO d = flatten(alto_to_dict(alto, raise_errors=True)) # "meta" d['alto_file'] = alto_file d['alto_xmlns'] = ET.QName(alto).namespace alto_info.append(d) if caught_warnings: # PyCharm thinks caught_warnings is not Iterable: # noinspection PyTypeChecker for caught_warning in caught_warnings: csvwriter.writerow([alto_file, caught_warning.message]) except Exception as e: logger.error('Exception in {}: {}'.format(alto_file, e)) import traceback; traceback.print_exc() # Convert the alto_info List[Dict] to a pandas DataFrame columns = [] for m in alto_info: for c in m.keys(): if c not in columns: columns.append(c) data = [[m.get(c) for c in columns] for m in alto_info] index = [m['alto_file'] for m in alto_info] # TODO use ppn + page? alto_info_df = pd.DataFrame(data=data, index=index, columns=columns) # Pickle the DataFrame logger.info('Writing DataFrame to {}'.format(output_file)) alto_info_df.to_pickle(output_file) if output_csv: logger.info('Writing CSV to {}'.format(output_csv)) alto_info_df.to_csv(output_csv) if output_xlsx: logger.info('Writing Excel .xlsx to {}'.format(output_xlsx)) alto_info_df.to_excel(output_xlsx) def main(): logging.basicConfig(level=logging.INFO) for prefix, uri in ns.items(): ET.register_namespace(prefix, uri) process() if __name__ == '__main__': main()