mirror of
https://gitlab.ub.uni-bielefeld.de/sfb1288inf/ocr.git
synced 2025-10-31 21:33:15 +00:00
Correct order for output files.
This commit is contained in:
Patrick Jentsch
20
Dockerfile
20
Dockerfile
@@ -1,6 +1,6 @@
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FROM debian:stretch-slim
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MAINTAINER Patrick Jentsch <p.jentsch@uni-bielefeld.de>
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LABEL maintainer="inf_sfb1288@lists.uni-bielefeld.de"
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ENV DEBIAN_FRONTEND=noninteractive
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ENV LANG=C.UTF-8
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@@ -11,34 +11,31 @@ RUN apt-get update && \
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ca-certificates \
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gnupg2 \
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imagemagick \
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pdftk \
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poppler-utils \
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python2.7 \
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python3.5 \
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python-numpy \
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wget
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WORKDIR /root
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# Install ocropy
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ENV OCROPY_VERSION 1.3.3
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RUN wget -nv https://github.com/tmbdev/ocropy/archive/v"$OCROPY_VERSION".tar.gz && \
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tar -xzf v"$OCROPY_VERSION".tar.gz && \
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rm v"$OCROPY_VERSION".tar.gz && \
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cd ocropy-"$OCROPY_VERSION" && \
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apt-get install -y --no-install-recommends $(cat PACKAGES) python-pil python-tk && \
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wget -nv http://www.tmbdev.net/en-default.pyrnn.gz -P models/ && \
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python2.7 setup.py install && \
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cd ..
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cd .. && \
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rm -r v"$OCROPY_VERSION".tar.gz ocropy-"$OCROPY_VERSION"
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# Install pyFlow
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ENV PYFLOW_VERSION 1.1.20
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RUN wget -nv https://github.com/Illumina/pyflow/releases/download/v"$PYFLOW_VERSION"/pyflow-"$PYFLOW_VERSION".tar.gz && \
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tar -xzf pyflow-"$PYFLOW_VERSION".tar.gz && \
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rm pyflow-"$PYFLOW_VERSION".tar.gz && \
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cd pyflow-"$PYFLOW_VERSION" && \
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python2.7 setup.py build install && \
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cd ..
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cd .. && \
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rm -r pyflow-"$PYFLOW_VERSION".tar.gz pyflow-"$PYFLOW_VERSION"
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# Install Tesseract OCR and Data Files
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RUN echo "deb https://notesalexp.org/tesseract-ocr/stretch/ stretch main" >> /etc/apt/sources.list && \
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@@ -52,11 +49,12 @@ RUN echo "deb https://notesalexp.org/tesseract-ocr/stretch/ stretch main" >> /et
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wget -nv https://github.com/tesseract-ocr/tessdata_best/raw/master/enm.traineddata -P /usr/share/tesseract-ocr/4.00/tessdata && \
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wget -nv https://github.com/tesseract-ocr/tessdata_best/raw/master/fra.traineddata -P /usr/share/tesseract-ocr/4.00/tessdata && \
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wget -nv https://github.com/tesseract-ocr/tessdata_best/raw/master/frm.traineddata -P /usr/share/tesseract-ocr/4.00/tessdata && \
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wget -nv https://github.com/tesseract-ocr/tessdata_best/raw/master/por.traineddata -P /usr/share/tesseract-ocr/4.00/tessdata && \
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wget -nv https://github.com/tesseract-ocr/tessdata_best/raw/master/ita.traineddata -P /usr/share/tesseract-ocr/4.00/tessdata && \
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wget -nv https://github.com/tesseract-ocr/tessdata_best/raw/master/por.traineddata -P /usr/share/tesseract-ocr/4.00/tessdata && \
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wget -nv https://github.com/tesseract-ocr/tessdata_best/raw/master/spa.traineddata -P /usr/share/tesseract-ocr/4.00/tessdata
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COPY ocr /usr/local/bin
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COPY hocrtotei /usr/local/bin
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COPY ocr /usr/local/bin
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CMD ["/bin/bash"]
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ENTRYPOINT ["ocr"]
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CMD ["--help"]
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45
hocrtotei
45
hocrtotei
@@ -7,22 +7,31 @@ import os
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import re
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import sys
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input_files = filter(lambda x: x.endswith(".hocr"), sorted(os.listdir(sys.argv[1])))
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input_files = sorted(
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filter(
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lambda x: x.endswith(".hocr"),
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os.listdir(sys.argv[1])
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),
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key=lambda x: int(re.search(r'\d+', x).group(0))
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)
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# "page-1.hocr" -> "1"
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output_file = open(sys.argv[2], "w")
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output_file.write('<?xml version="1.0" encoding="UTF-8"?>\n' +
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'<TEI xmlns="http://www.tei-c.org/ns/1.0" xml:id="dtabf">\n' +
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' <teiHeader>\n' +
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' <fileDesc>\n' +
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' <titleStmt/>\n' +
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' <publicationStmt/>\n' +
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' <sourceDesc/>\n' +
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' </fileDesc>\n' +
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' <encodingDesc/>\n' +
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' <profileDesc/>\n' +
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' </teiHeader>\n' +
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' <text>\n' +
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' <body>\n')
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output_file.write(
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'<?xml version="1.0" encoding="UTF-8"?>\n'
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+ '<TEI xmlns="http://www.tei-c.org/ns/1.0" xml:id="dtabf">\n'
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+ ' <teiHeader>\n'
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+ ' <fileDesc>\n'
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+ ' <titleStmt/>\n'
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+ ' <publicationStmt/>\n'
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+ ' <sourceDesc/>\n'
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+ ' </fileDesc>\n'
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+ ' <encodingDesc/>\n'
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+ ' <profileDesc/>\n'
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+ ' </teiHeader>\n'
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+ ' <text>\n'
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+ ' <body>\n'
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)
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for input_file in input_files:
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tree = ET.parse(os.path.join(sys.argv[1], input_file))
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@@ -40,7 +49,9 @@ for input_file in input_files:
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output_file.write('<lb/>\n')
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output_file.write(' </p>\n')
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output_file.write(' </body>\n' +
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' </text>\n' +
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'</TEI>')
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output_file.write(
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' </body>\n'
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+ ' </text>\n'
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+ '</TEI>')
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output_file.close()
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189
ocr
189
ocr
@@ -19,32 +19,27 @@ from pyflow import WorkflowRunner
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''' TODO:
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' Implement --end-page: Last page to ocr
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' Implement --memMb: Total amount of memory (RAM) available for this workflow. Default: 2048 * nCores
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' Implement --memMb: Total amount of memory (RAM) available for this workflow.
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' Default: 2048 * nCores
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' Implement --rotate: Rotate pages from input (90, 180, 270)
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' Implement --split-pages: Split pages in half after possible rotation
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' Implement --start-page: First page to ocr
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'''
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def parse_arguments():
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parser = argparse.ArgumentParser(
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"Performs OCR of (historical) documents utilizing OCRopus for \
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preprocessing and Tesseract OCR for OCR. Available outputs are HOCR, \
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PDF, shrinked PDF, and simple DTAbf (TEI P5 compliant). Software \
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requirements: imagemagick, ocropus, pdftk, pdftoppm, poppler-utils, \
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pyflow, python2.7, tesseract"
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pyflow, python2.7, python3.5, tesseract"
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)
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parser.add_argument("-i",
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dest="inputDir",
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help="Input directory.",
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required=True)
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parser.add_argument("-l",
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dest='lang',
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help="Language for OCR",
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required=True)
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parser.add_argument("-o",
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dest="outputDir",
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help="Output directory.",
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required=True)
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parser.add_argument("--skip-binarization",
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action='store_true',
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default=False,
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@@ -67,14 +62,16 @@ def parse_arguments():
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class OCRWorkflow(WorkflowRunner):
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def __init__(self, jobs, skipBinarization, keepIntermediates, lang, nCores):
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self.jobs = jobs
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self.skipBinarization = skipBinarization
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self.keepIntermediates = keepIntermediates
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self.lang = lang
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self.nCores = nCores
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self.defaultNCores = min(nCores, max(1, int(nCores / len(jobs))))
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def __init__(self, args):
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self.jobs = analyze_jobs()
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self.skipBinarization = args.skipBinarization
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self.keepIntermediates = args.keepIntermediates
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self.lang = args.lang
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self.nCores = args.nCores
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self.defaultNCores = min(
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self.nCores,
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max(1, int(self.nCores / len(self.jobs)))
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)
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def workflow(self):
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###
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@@ -93,10 +90,17 @@ class OCRWorkflow(WorkflowRunner):
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)
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if not self.skipBinarization:
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cmd += ' "%s" "%s"' % (
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os.path.join(job["output_dir"], "tmp", "binarized_png"),
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os.path.join(job["output_dir"], "tmp", "normalized_png"),
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os.path.join(job["output_dir"], "tmp", "bin.png"),
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os.path.join(job["output_dir"], "tmp", "nrm.png"),
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)
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create_output_directories_jobs.append(
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self.addTask(
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command=cmd,
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label="create_output_directories_job_-_%i" % (
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create_output_directories_job_number
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),
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nCores=self.defaultNCores)
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)
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create_output_directories_jobs.append(self.addTask(label="create_output_directories_job_-_%i" % (create_output_directories_job_number), command=cmd, nCores=self.defaultNCores))
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###
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# Task "split_job": split input file into one tiff file per page
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@@ -116,7 +120,14 @@ class OCRWorkflow(WorkflowRunner):
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job["path"],
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os.path.join(job["output_dir"], "tmp", "page")
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)
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split_jobs.append(self.addTask(label="split_job_-_%i" % (split_job_number), command=cmd, dependencies=create_output_directories_jobs, nCores=self.defaultNCores))
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split_jobs.append(
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self.addTask(
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command=cmd,
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dependencies=create_output_directories_jobs,
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label="split_job_-_%i" % (split_job_number),
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nCores=self.defaultNCores
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)
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)
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###
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# Task "ocropus_nlbin_job": binarize tiff files from previous split
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@@ -132,12 +143,21 @@ class OCRWorkflow(WorkflowRunner):
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if not self.skipBinarization:
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for job in self.jobs:
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binarization_job_number += 1
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cmd = 'ocropus-nlbin --output "%s" --parallel "%i" $(ls "%s"/*.tif | sort -V)' % (
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cmd = 'ocropus-nlbin --output "%s" --parallel "%i" $(ls --quoting-style=shell-escape -v "%s"/*.tif)' % (
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os.path.join(job["output_dir"], "tmp"),
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binarization_job_nCores,
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os.path.join(job["output_dir"], "tmp")
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)
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binarization_jobs.append(self.addTask(label="binarization_job_-_%i" % (binarization_job_number), command=cmd, dependencies=split_jobs, nCores=binarization_job_nCores))
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binarization_jobs.append(
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self.addTask(
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command=cmd,
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dependencies=split_jobs,
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label="binarization_job_-_%i" % (
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binarization_job_number
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),
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nCores=binarization_job_nCores
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)
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)
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###
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# Task "post_binarization_job": Normalize file names from binarization
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@@ -152,9 +172,21 @@ class OCRWorkflow(WorkflowRunner):
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post_binarization_job_number += 1
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cmd = 'mv "%s" "%s"' % (
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os.path.join(job["output_dir"], "tmp", file),
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os.path.join(job["output_dir"], "tmp", "page-%i.%s" % (int(file.split(".", 1)[0]), file.split(".", 1)[1])),
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os.path.join(job["output_dir"], "tmp", "page-%i.%s" % (
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int(file.split(".", 1)[0]),
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file.split(".", 1)[1])
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),
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)
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post_binarization_jobs.append(
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self.addTask(
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command=cmd,
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dependencies=binarization_jobs,
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label="post_binarization_job_-_%i" % (
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post_binarization_job_number
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),
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nCores=self.defaultNCores
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)
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)
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post_binarization_jobs.append(self.addTask(label="post_binarization_job_-_%i" % (post_binarization_job_number), command=cmd, dependencies=binarization_jobs, nCores=self.defaultNCores))
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###
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# Task "ocr_job": perform OCR
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@@ -165,8 +197,8 @@ class OCRWorkflow(WorkflowRunner):
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ocr_job_number = 0
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'''
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' Tesseract runs fastest with four cores. So we run it with either four
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' or, if there are less then four cores available for this workflow, the
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' available core number.
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' or, if there are less then four cores available for this workflow,
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' the available core number.
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'''
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ocr_job_nCores = min(4, self.nCores)
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'''
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@@ -183,7 +215,14 @@ class OCRWorkflow(WorkflowRunner):
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os.path.join(job["output_dir"], "tmp", file.rsplit(".", 1 if self.skipBinarization else 2)[0]),
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self.lang
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)
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ocr_jobs.append(self.addTask(label="ocr_job_-_%i" % (ocr_job_number), command=cmd, dependencies=post_binarization_jobs, nCores=ocr_job_nCores))
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ocr_jobs.append(
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self.addTask(
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command=cmd,
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dependencies=post_binarization_jobs,
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label="ocr_job_-_%i" % (ocr_job_number),
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nCores=ocr_job_nCores
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)
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)
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###
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# Task "hocr_to_tei_job": create TEI P5 file from hocr files
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@@ -197,7 +236,14 @@ class OCRWorkflow(WorkflowRunner):
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os.path.join(job["output_dir"], "tmp"),
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os.path.join(job["output_dir"], job["filename"].rsplit(".", 1)[0] + ".xml")
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)
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hocr_to_tei_jobs.append(self.addTask(label="hocr_to_tei_job_-_%i" % (hocr_to_tei_job_number), command=cmd, dependencies=ocr_jobs, nCores=self.defaultNCores))
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hocr_to_tei_jobs.append(
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self.addTask(
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command=cmd,
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dependencies=ocr_jobs,
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label="hocr_to_tei_job_-_%i" % (hocr_to_tei_job_number),
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nCores=self.defaultNCores
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)
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)
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###
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# Task "pdf_merge_job": Merge PDF files
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@@ -207,11 +253,18 @@ class OCRWorkflow(WorkflowRunner):
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pdf_merge_job_number = 0
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for job in self.jobs:
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pdf_merge_job_number += 1
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cmd = 'pdftk $(ls "%s"/*.pdf | sort -V) cat output "%s"' % (
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cmd = '(ls --quoting-style=shell-escape -v "%s"/*.pdf && echo "\'%s\'") | xargs pdfunite' % (
|
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os.path.join(job["output_dir"], "tmp"),
|
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os.path.join(job["output_dir"], job["filename"].rsplit(".", 1)[0] + ".pdf")
|
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)
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pdf_merge_jobs.append(self.addTask(label="pdf_merge_job_-_%i" % (pdf_merge_job_number), command=cmd, dependencies=ocr_jobs, nCores=self.defaultNCores))
|
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pdf_merge_jobs.append(
|
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self.addTask(
|
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command=cmd,
|
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dependencies=ocr_jobs,
|
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label="pdf_merge_job_-_%i" % (pdf_merge_job_number),
|
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nCores=self.defaultNCores
|
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)
|
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)
|
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|
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###
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# Task "txt_merge_job": Merge .txt files
|
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@@ -221,11 +274,18 @@ class OCRWorkflow(WorkflowRunner):
|
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txt_merge_job_number = 0
|
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for job in self.jobs:
|
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txt_merge_job_number += 1
|
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cmd = 'cat $(ls "%s"/*.txt | sort -V) > "%s"' % (
|
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cmd = 'ls --quoting-style=shell-escape -v "%s"/*.txt | xargs cat > "%s"' % (
|
||||
os.path.join(job["output_dir"], "tmp"),
|
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os.path.join(job["output_dir"], job["filename"].rsplit(".", 1)[0] + ".txt")
|
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)
|
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txt_merge_jobs.append(self.addTask(label="txt_merge_job_-_%i" % (txt_merge_job_number), command=cmd, dependencies=ocr_jobs, nCores=self.defaultNCores))
|
||||
txt_merge_jobs.append(
|
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self.addTask(
|
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command=cmd,
|
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dependencies=ocr_jobs,
|
||||
label="txt_merge_job_-_%i" % (txt_merge_job_number),
|
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nCores=self.defaultNCores
|
||||
)
|
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)
|
||||
|
||||
###
|
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# Task "cleanup_job": remove temporary files
|
||||
@@ -236,35 +296,59 @@ class OCRWorkflow(WorkflowRunner):
|
||||
if self.keepIntermediates:
|
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for job in self.jobs:
|
||||
cleanup_job_counter += 1
|
||||
cmd = 'mv "%s"/*.hocr "%s" && mv "%s"/*.pdf "%s" && mv "%s"/*.tif "%s" && mv "%s"/*.txt "%s"' % (
|
||||
cmd = 'mv "%s"/*.hocr "%s"' % (
|
||||
os.path.join(job["output_dir"], "tmp"),
|
||||
os.path.join(job["output_dir"], "tmp", "hocr"),
|
||||
)
|
||||
cmd += ' && mv "%s"/*.pdf "%s"' % (
|
||||
os.path.join(job["output_dir"], "tmp"),
|
||||
os.path.join(job["output_dir"], "tmp", "pdf"),
|
||||
)
|
||||
cmd += ' && mv "%s"/*.tif "%s"' % (
|
||||
os.path.join(job["output_dir"], "tmp"),
|
||||
os.path.join(job["output_dir"], "tmp", "tiff"),
|
||||
)
|
||||
cmd += ' && mv "%s"/*.txt "%s"' % (
|
||||
os.path.join(job["output_dir"], "tmp"),
|
||||
os.path.join(job["output_dir"], "tmp", "txt")
|
||||
os.path.join(job["output_dir"], "tmp", "txt"),
|
||||
)
|
||||
if not self.skipBinarization:
|
||||
cmd += ' && mv "%s"/*.bin.png "%s" && mv "%s"/*.nrm.png "%s"' % (
|
||||
cmd += ' && mv "%s"/*.bin.png "%s"' % (
|
||||
os.path.join(job["output_dir"], "tmp"),
|
||||
os.path.join(job["output_dir"], "tmp", "binarized_png"),
|
||||
os.path.join(job["output_dir"], "tmp"),
|
||||
os.path.join(job["output_dir"], "tmp", "normalized_png"),
|
||||
os.path.join(job["output_dir"], "tmp", "bin.png"),
|
||||
)
|
||||
cleanup_jobs.append(self.addTask(label="cleanup_job_-_%i" % (cleanup_job_counter), command=cmd, dependencies=hocr_to_tei_jobs + pdf_merge_jobs + txt_merge_jobs, nCores=self.defaultNCores))
|
||||
cmd += ' && mv "%s"/*.nrm.png "%s"' % (
|
||||
os.path.join(job["output_dir"], "tmp"),
|
||||
os.path.join(job["output_dir"], "tmp", "nrm.png"),
|
||||
)
|
||||
cleanup_jobs.append(
|
||||
self.addTask(
|
||||
command=cmd,
|
||||
dependencies=hocr_to_tei_jobs + pdf_merge_jobs + txt_merge_jobs,
|
||||
label="cleanup_job_-_%i" % (cleanup_job_counter),
|
||||
nCores=self.defaultNCores
|
||||
)
|
||||
)
|
||||
else:
|
||||
for job in self.jobs:
|
||||
cleanup_job_counter += 1
|
||||
cmd = 'rm -r "%s"' % (
|
||||
os.path.join(job["output_dir"], "tmp")
|
||||
)
|
||||
cleanup_jobs.append(self.addTask(label="cleanup_job_-_%i" % (cleanup_job_counter), command=cmd, dependencies=hocr_to_tei_jobs + pdf_merge_jobs + txt_merge_jobs), nCores=self.defaultNCores)
|
||||
cleanup_jobs.append(
|
||||
self.addTask(
|
||||
label="cleanup_job_-_%i" % (cleanup_job_counter),
|
||||
command=cmd,
|
||||
dependencies=hocr_to_tei_jobs + pdf_merge_jobs + txt_merge_jobs,
|
||||
nCores=self.defaultNCores
|
||||
)
|
||||
)
|
||||
|
||||
|
||||
def analyze_jobs(inputDir, outputDir):
|
||||
def analyze_jobs():
|
||||
inputDir = "/files_for_ocr"
|
||||
jobs = []
|
||||
outputDir = "/files_from_ocr"
|
||||
|
||||
for file in os.listdir(inputDir):
|
||||
if os.path.isdir(os.path.join(inputDir, file)):
|
||||
@@ -273,7 +357,13 @@ def analyze_jobs(inputDir, outputDir):
|
||||
os.path.join(outputDir, file)
|
||||
)
|
||||
elif file.endswith((".pdf", ".tif", ".tiff")):
|
||||
jobs.append({"filename": file, "output_dir": os.path.join(outputDir, file), "path": os.path.join(inputDir, file)})
|
||||
jobs.append(
|
||||
{
|
||||
"filename": file,
|
||||
"output_dir": os.path.join(outputDir, file),
|
||||
"path": os.path.join(inputDir, file)
|
||||
}
|
||||
)
|
||||
|
||||
return jobs
|
||||
|
||||
@@ -281,15 +371,10 @@ def analyze_jobs(inputDir, outputDir):
|
||||
def main():
|
||||
args = parse_arguments()
|
||||
|
||||
wflow = OCRWorkflow(
|
||||
analyze_jobs(args.inputDir, args.outputDir),
|
||||
args.skipBinarization,
|
||||
args.keepIntermediates,
|
||||
args.lang,
|
||||
args.nCores
|
||||
)
|
||||
wflow = OCRWorkflow(args)
|
||||
|
||||
retval = wflow.run(dataDirRoot="/files_from_ocr", nCores=args.nCores)
|
||||
|
||||
retval = wflow.run(nCores=args.nCores)
|
||||
sys.exit(retval)
|
||||
|
||||
|
||||
|
||||
Reference in New Issue
Block a user