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Python

#!/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()