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ocr/ocr_pyflow
Patrick Jentsch aa48ea6ed2 Initial commit
2018-10-09 14:43:23 +02:00

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#!/usr/bin/env python2.7
# coding=utf-8
"""
ocr_pyflow.py
Date: 01/04/2018
Usage: For usage instructions run with option --help
Author: Madis Rumming <mrumming@uni-bielefeld.de>
"""
__author__ = "Madis Rumming <mrumming@uni-bielefeld.de>"
__copyright__ = "Copyright 2018, Data Infrastructure and Digital Humanities,\
SFB 1288, Bielefeld University"
__version__ = "0.6"
__maintainer__ = "Madis Rumming"
__email__ = "mrumming@uni-bielefeld.de"
__status__ = "Development"
import argparse
import os
import sys
# from string import maketrans
# from lxml import html
from pyflow import WorkflowRunner
ocropusnlbin_bin = "/usr/local/bin/ocropus-nlbin"
def parse_arguments():
parser = argparse.ArgumentParser(
"Performs OCR of (historical) documents utilizing ocropy for preprocessing and tesseract \
for final OCR. Available outputs are HOCR, PDF, shrinked PDF, and simple DTAbf \
(TEI P5 compliant). Software requirements: python2.7, pyflow, pdftoppm, ocropus, \
tesseract, ghostscript, imagick, ")
parser.add_argument("-i", "--input-directory",
dest="input_dir",
help="Input directory with input images/PDFs. For each PDF an OCR-Run is \
instantiated and output is created. If images reside in the directory, a \
single OCR run is performed. For each subdirectory containing images, a \
particular OCR run is instantiated.",
required=True)
parser.add_argument("-o", "--output-directory",
dest="output_dir",
help="Directory, where output directories are created if necessary. \
Default: %s" % (os.path.curdir),
required=False,
default=os.path.curdir)
parser.add_argument("--image-suffix",
dest="suffix",
help="Input images suffix. Case-sensitive! tiff!=TIFF!=Tiff Default: tif.",
default="tif",
required=False)
parser.add_argument("--skip-pdf-processing",
dest="skip_pdf",
help="Skip detection of PDFs as input.",
default=False,
action='store_true',
required=False)
parser.add_argument("--skip-image-processing",
dest="skip_images",
help="Skip detection of images as input.",
default=False,
action='store_true',
required=False)
parser.add_argument("--skip_binarization",
dest="skip_bin",
help="skip binarizaiton pre-processing.",
default=False,
action="store_true",
required=False)
parser.add_argument("--start-page",
dest='startp',
default=-1, help="First page to ocr.",
required=False, type=int)
parser.add_argument("--end-page",
dest='endp',
default=-1,
help="Last page to ocr.",
required=False, type=int)
parser.add_argument("-r", "--rotate-pages",
dest='rotate',
default='norotation',
help="Rotate pages from input. Values: clockwise, counterclockwise, \
upsidedown. Default: norotation",
required=False,
choices=['clockwise', 'counterclockwise', 'upsidedown', 'norotation'])
parser.add_argument("-s", "--split-pages",
dest='split',
default=False,
help="Split pages in half after possible rotation. Default: Not performed.",
required=False,
action='store_true')
parser.add_argument("--ppi-import",
dest="ppi_in", help="Down-/Scaling for input images. Default: 300 ppi.",
default=300,
required=False,
type=int)
parser.add_argument("-l", "--language",
dest='lang',
help="Language for OCR",
required=True,
type=str)
parser.add_argument("-p", "--create-pdf",
dest='pdf',
default=False,
action='store_true',
required=False)
parser.add_argument("-c", "--compress-pdf",
dest='comp',
default=False,
action='store_true',
required=False)
parser.add_argument("--ppi-export",
dest="ppi_out",
help="Down-/Scaling for output images in PDF. Default: 150 ppi.",
default=150,
required=False,
type=int)
parser.add_argument("-t", "--temp-directory",
dest="temp",
help="Location of intermediate files. Defaults to tmp in output directory.",
default="",
required=False,
type=str)
parser.add_argument("-k", "--keep-intermediate",
dest="intermediate",
help="Keep intermediate files. Default: True",
default=False,
action='store_true')
parser.add_argument("--cores",
dest='nCores',
help="Amount of CPUs to use for parallel jobs. Default: %i" % (4),
default=4,
required=False,
type=int)
parser.add_argument("--is-continued", dest='continued',
help="Enables continuing an erroneous or paused workflow. MUST use the \
same dataDirRoot as before.",
default=False,
required=False,
action='store_true')
parser.add_argument("--is-dry-run",
dest='dry_run',
help="Check workflow without execution.",
default=False,
action='store_true',
required=False)
parser.add_argument("--memory",
dest='mem',
help="Total amount of memory (RAM) available for this workflow. \
Default: %i" % (8192),
default=8192,
required=False,
type=int)
args = parser.parse_args()
return (args)
class PureOCR(WorkflowRunner):
def __init__(self, input_path, output_path):
self.input_path = input_path
self.output_path = output_path
def workflow(self):
pass
class OCRWorkflow(WorkflowRunner):
def __init__(self, pdfImageJobs, inputDir, outputDir, suffix, lang, pdf, intermediate, skip_bin,
nCores, memMb, dry_run):
self.pdfImageJobs = pdfImageJobs
self.outputDir = outputDir
self.inputDir = inputDir
self.suffix = suffix
self.lang = lang
self.pdf = pdf
self.intermediate = intermediate
self.skip_bin = skip_bin
self.nCores = nCores
self.memMb = memMb
self.dry_run = dry_run
def workflow(self):
cmd = None
print(self.outputDir)
if os.path.isabs(self.outputDir):
if not os.path.exists(self.outputDir):
cmd = "mkdir -p %s" % (self.outputDir)
else:
self.outputDir = os.path.join(os.path.abspath(self.inputDir), self.outputDir)
if not os.path.exists(self.outputDir):
cmd = "mkdir -p %s" % (self.outputDir)
self.addTask(label="mkdir_outputdir", command=cmd, isForceLocal=True)
deps = []
if self.pdfImageJobs["pdf"]:
cmd = "mkdir %s" % (os.path.join(self.outputDir, "pdf"))
deps.append("mkdir_pdf")
self.addTask(label="mkdir_pdf", command=cmd, isForceLocal=True,
dependencies="mkdir_outputdir")
if self.pdfImageJobs["images"]:
cmd = "mkdir %s" % (os.path.join(self.outputDir, "images"))
deps.append("mkdir_images")
self.addTask(label="mkdir_images", command=cmd, isForceLocal=True,
dependencies="mkdir_outputdir")
###
# Generate directories
###
deps_dirs = []
if self.pdfImageJobs["pdf"]:
i = 0
for k in self.pdfImageJobs["pdf"]:
cmd = "mkdir -p %s %s %s %s %s" % (
os.path.join(os.path.abspath(self.outputDir), "pdf", k, "tmp", "tiff"),
os.path.join(os.path.abspath(self.outputDir), "pdf", k, "tmp", "tesseract"),
os.path.join(os.path.abspath(self.outputDir), "pdf", k, "tmp", "ocropy"),
os.path.join(os.path.abspath(self.outputDir), "pdf", k, "tmp", "gs"),
os.path.join(os.path.abspath(self.outputDir), "pdf", k, "HOCR"))
deps_dirs.append("mkdir_pdf_%i" % (i))
self.addTask(label="mkdir_pdf_%i" % (i), command=cmd, isForceLocal=True,
dependencies=deps)
i += 1
if self.pdfImageJobs["images"]:
i = 0
for k in self.pdfImageJobs["images"]:
cmd = "mkdir -p %s %s %s %s" % (
os.path.join(os.path.abspath(self.outputDir), "images", k, "tmp", "tesseract"),
os.path.join(os.path.abspath(self.outputDir), "images", k, "tmp", "ocropy"),
os.path.join(os.path.abspath(self.outputDir), "images", k, "tmp", "gs"),
os.path.join(os.path.abspath(self.outputDir), "images", k, "HOCR"))
deps_dirs.append("mkdir_images_%i" % (i))
self.addTask(label="mkdir_images_%i" % (i), command=cmd, isForceLocal=True,
dependencies=deps)
i += 1
###
# Extract images from PDF input files
###
pdf_counter = 0
deps_ppm = []
for pdf in self.pdfImageJobs["pdf"]:
cmd = "pdftoppm %s %s -tiff -r 300 -tiffcompression lzw -cropbox" % (self.pdfImageJobs["pdf"][pdf],
os.path.join(
os.path.abspath(self.outputDir),
"pdf", pdf, "tmp",
"tiff", "interm"))
self.addTask(label="pdftoppm_%i" % (pdf_counter), command=cmd, isForceLocal=True,
dependencies=deps_dirs, nCores=1, memMb=1024)
deps_ppm.append("pdftoppm_%i" % (pdf_counter))
pdf_counter += 1
###
# Perform image binarization if not skipped
###
self.waitForTasks()
ocropus_counter = 0
deps_ocropus = []
if not self.skip_bin:
for pdf in self.pdfImageJobs["pdf"]:
cmd = "%s -Q %i -o %s %s" % (ocropusnlbin_bin, self.nCores,
os.path.join(os.path.abspath(self.outputDir), "pdf", pdf, "tmp", "ocropy"),
os.path.join(os.path.abspath(self.outputDir), "pdf", pdf, "tmp", "tiff",
"interm-*"))
self.addTask(label="ocropusnlbin_%i" % (ocropus_counter), command=cmd, isForceLocal=True,
dependencies=deps_ppm,
nCores=self.nCores, memMb=self.memMb)
deps_ocropus.append("ocropusnlbin_%i" % (ocropus_counter))
ocropus_counter += 1
for img in self.pdfImageJobs["images"]:
cmd = "%s -Q %i -o %s %s" % (ocropusnlbin_bin, self.nCores,
os.path.join(os.path.abspath(self.outputDir), "images", img, "tmp",
"ocropy"),
os.path.join(self.pdfImageJobs["images"][img], "*.%s" % (self.suffix)))
self.addTask(label="ocropusnlbin_%i" % (ocropus_counter), command=cmd, isForceLocal=True,
dependencies=deps_ppm,
nCores=self.nCores, memMb=self.memMb)
deps_ocropus.append("ocropusnlbin_%i" % (ocropus_counter))
ocropus_counter += 1
###
# Perform OCR, HOCR as default output, PDF only optional
###
self.waitForTasks()
pdf_counter = 0
for pdf in self.pdfImageJobs["pdf"]:
if self.skip_bin:
inp_images = sorted(os.listdir(
os.path.join(os.path.abspath(self.outputDir), "pdf", pdf, "tmp", "tiff")))
else:
inp_images = sorted(filter(lambda x: ".bin." in x, os.listdir(
os.path.join(os.path.abspath(self.outputDir), "pdf", pdf, "tmp",
"ocropy"))))
deps_ocr_pdf = []
for image in inp_images:
cmd = "tesseract %s %s -l %s hocr %s" % (
os.path.join(os.path.abspath(self.outputDir), "pdf", pdf, "tmp",
"tiff" if self.skip_bin else "ocropy", image),
os.path.join(self.outputDir, "pdf", pdf, "tmp", "tesseract",
"%04i" % int(image.split(".")[0].split("-")[1]) if self.skip_bin else image.split(".")[
0]),
self.lang, "pdf" if self.pdf else "")
self.addTask(label="ocr_%i_%s" % (pdf_counter, image.split(".")[0]), command=cmd, isForceLocal=True,
dependencies=deps_ocropus, nCores=1, memMb=2048)
deps_ocr_pdf.append("ocr_%i_%s" % (pdf_counter, image.split(".")[0]))
pdf_counter += 1
for img in self.pdfImageJobs["images"]:
if self.skip_bin:
images = sorted(
list(filter(lambda x: x.endswith(self.suffix), os.listdir(self.pdfImageJobs["images"][img]))))
else:
images = sorted(
list(filter(lambda x: ".bin." in x, os.listdir(
os.path.join(os.path.abspath(self.outputDir), "images", img, "tmp", "ocropy")))))
deps_ocr = []
for image in images:
if self.skip_bin:
cmd = "tesseract %s %s -l %s hocr %s" % (
os.path.join(self.pdfImageJobs["images"][img], image),
os.path.join(self.outputDir, "images", img, "tmp", "tesseract", image.split(".")[0]),
self.lang, "pdf" if self.pdf else "")
else:
cmd = "tesseract %s %s -l %s hocr %s" % (
os.path.join(os.path.abspath(self.outputDir), "images", img, "tmp", "ocropy", image),
os.path.join(self.outputDir, "images", img, "tmp", "tesseract", image.split(".")[0]),
self.lang, "pdf" if self.pdf else "")
print(cmd)
self.addTask(label="ocr_%s_%s" % (img, image.split(".")[0]), command=cmd, isForceLocal=True,
dependencies=deps_ocropus, nCores=1, memMb=2048)
deps_ocr.append("ocr_%s_%s" % (img, image.split(".")[0]))
pdftk_jobs = []
###
# Creation of PDF output
###
if self.pdf:
pdf_counter_conv = 0
for img in self.pdfImageJobs["images"]:
if self.skip_bin:
images = sorted(
list(filter(lambda x: x.endswith(self.suffix), os.listdir(self.pdfImageJobs["images"][img]))))
else:
images = sorted(
list(filter(lambda x: ".bin." in x, os.listdir(
os.path.join(os.path.abspath(self.outputDir), "images", img, "tmp", "ocropy")))))
deps_tiffpdf = []
for image in images:
if self.skip_bin:
cmd = "tiff2pdf -o %s.pdf %s" % (
os.path.join(self.outputDir, "images", img, "tmp", "gs", image.split(".")[0]),
os.path.join(self.pdfImageJobs["images"][img], image))
self.addTask(label="tiffpdf_%s_%s" % (img, image.split(".")[0]), command=cmd, isForceLocal=True,
dependencies=deps_dirs, nCores=1, memMb=256)
deps_tiffpdf.append("tiffpdf_%s_%s" % (img, image.split(".")[0]))
else:
cmd = "convert %s %s.pdf" % (
os.path.join(os.path.abspath(self.outputDir), "images", img, "tmp", "ocropy", image),
os.path.join(self.outputDir, "images", img, "tmp", "gs", image.split(".")[0]))
self.addTask(label="tiffpdf_%s_%s" % (img, image.split(".")[0]), command=cmd, isForceLocal=True,
dependencies=deps_ocropus, nCores=1, memMb=256)
deps_tiffpdf.append("tiffpdf_%s_%s" % (img, image.split(".")[0]))
cmd = "gs -dBATCH -dNOPAUSE -q -r150 -dPDFSETTINGS=/ebook -sDEVICE=pdfwrite -sOutputFile=%s %s" % (
os.path.join(self.outputDir, "images", img, "tmp", "gs", "image.pdf"),
os.path.join(self.outputDir, "images", img, "tmp", "gs", "*.pdf"))
self.addTask(label="gs_image_%s" % (img), command=cmd, isForceLocal=True,
dependencies=deps_tiffpdf, nCores=1, memMb=4096)
deps_ocr.append("gs_image_%s" % (img))
cmd = "gs -dBATCH -dNOPAUSE -q -r150 -dPDFSETTINGS=/ebook -dFILTERIMAGE -sDEVICE=pdfwrite -sOutputFile=%s %s" % (
os.path.join(self.outputDir, "images", img, "tmp", "gs", "text.pdf"),
os.path.join(self.outputDir, "images", img, "tmp", "tesseract", "*.pdf"))
self.addTask(label="gs_layer_%s" % (img), command=cmd, isForceLocal=True,
dependencies=deps_ocr, nCores=1, memMb=4096)
cmd = "pdftk %s multistamp %s output %s" % (
os.path.join(self.outputDir, "images", img, "tmp", "gs", "text.pdf"),
os.path.join(self.outputDir, "images", img, "tmp", "gs", "image.pdf"),
os.path.join(self.outputDir, "images", img, "%s.pdf" % (img)))
self.addTask(label="pdftk_%s" % (img), command=cmd, isForceLocal=True,
dependencies="gs_layer_%s" % (img), nCores=1, memMb=4096)
pdftk_jobs.append("pdftk_%s" % (img))
for pdf in self.pdfImageJobs["pdf"]:
pdf_counter_conv += 1
if self.skip_bin:
inp_images = sorted(os.listdir(
os.path.join(os.path.abspath(self.outputDir), "pdf", pdf, "tmp", "tiff")))
else:
inp_images = sorted(filter(lambda x: ".bin." in x, os.listdir(
os.path.join(os.path.abspath(self.outputDir), "pdf", pdf, "tmp",
"ocropy"))))
deps_pdf_tiffpdf = []
for image in inp_images:
if self.skip_bin:
cmd = "tiff2pdf -o %s.pdf %s" % (
os.path.join(self.outputDir, "pdf", pdf, "tmp", "gs", image.split(".")[0]),
os.path.join(os.path.abspath(self.outputDir), "pdf", pdf, "tmp", "tiff", image))
self.addTask(label="tiffpdf_pdf%i_%s" % (pdf_counter_conv, image.split(".")[0]), command=cmd,
isForceLocal=True,
dependencies=deps_dirs, nCores=1, memMb=256)
deps_pdf_tiffpdf.append("tiffpdf_pdf%i_%s" % (pdf_counter_conv, image.split(".")[0]))
else:
cmd = "convert %s %s.pdf" % (
os.path.join(os.path.abspath(self.outputDir), "pdf", pdf, "tmp", "ocropy", image),
os.path.join(self.outputDir, "pdf", pdf, "tmp", "gs", image.split(".")[0]))
self.addTask(label="tiffpdf_pdf%i_%s" % (pdf_counter_conv, image.split(".")[0]), command=cmd,
isForceLocal=True,
dependencies=deps_ocropus, nCores=1, memMb=256)
deps_pdf_tiffpdf.append("tiffpdf_pdf%i_%s" % (pdf_counter_conv, image.split(".")[0]))
cmd = "gs -dBATCH -dNOPAUSE -q -r150 -dPDFSETTINGS=/ebook -sDEVICE=pdfwrite -sOutputFile=%s %s" % (
os.path.join(self.outputDir, "pdf", pdf, "tmp", "gs", "image.pdf"),
os.path.join(self.outputDir, "pdf", pdf, "tmp", "gs", "*.pdf"))
self.addTask(label="gs_image_pdf%i" % (pdf_counter_conv), command=cmd, isForceLocal=True,
dependencies=deps_pdf_tiffpdf, nCores=1, memMb=4096)
deps_ocr.append("gs_image_pdf%i" % (pdf_counter_conv))
cmd = "gs -dBATCH -dNOPAUSE -q -r150 -dPDFSETTINGS=/ebook -dFILTERIMAGE -sDEVICE=pdfwrite -sOutputFile=%s %s" % (
os.path.join(self.outputDir, "pdf", pdf, "tmp", "gs", "text.pdf"),
os.path.join(self.outputDir, "pdf", pdf, "tmp", "tesseract", "*.pdf"))
self.addTask(label="gs_layer_pdf%i" % (pdf_counter_conv), command=cmd, isForceLocal=True,
dependencies=deps_ocr, nCores=1, memMb=4096)
cmd = "pdftk %s multistamp %s output %s" % (
os.path.join(self.outputDir, "pdf", pdf, "tmp", "gs", "text.pdf"),
os.path.join(self.outputDir, "pdf", pdf, "tmp", "gs", "image.pdf"),
os.path.join(self.outputDir, "pdf", pdf, "%s.pdf" % (pdf)))
self.addTask(label="pdftk_pdf%i" % (pdf_counter_conv), command=cmd, isForceLocal=True,
dependencies="gs_layer_pdf%i" % (pdf_counter_conv), nCores=1, memMb=4096)
pdftk_jobs.append("pdftk_pdf%i" % (pdf_counter_conv))
else:
self.addTask(label="pdftk_", command=None, dependencies=deps_ocr)
pdftk_jobs.append("pdftk_")
###
# Merging and cleanup
###
self.waitForTasks()
for img in self.pdfImageJobs["images"]:
cmd = "mv %s %s" % (os.path.join(self.outputDir, "images", img, "tmp", "tesseract", "*.hocr"),
os.path.join(os.path.abspath(self.outputDir), "images", img, "HOCR"))
self.addTask(label="mv_%s" % (img), command=cmd, isForceLocal=True,
dependencies=pdftk_jobs, nCores=1, memMb=32)
cmd = "parse_hocr %s %s" % (
os.path.join(os.path.abspath(self.outputDir), "images", img, "HOCR"),
os.path.join(os.path.abspath(self.outputDir), "images", img, "%s.xml" % (img)))
self.addTask(label="generate_hocr_%s" % (img), command=cmd, isForceLocal=True,
dependencies="mv_%s" % (img), nCores=1, memMb=250)
if not self.intermediate:
cmd = "rm -rf %s" % (os.path.join(self.outputDir, "images", img, "tmp"))
self.addTask(label="cleanup_%s" % (img), command=cmd, isForceLocal=True,
dependencies="mv_%s" % (img), nCores=1, memMb=32)
pdf_counter = 0
for pdf in self.pdfImageJobs["pdf"]:
pdf_counter += 1
cmd = "mv %s %s" % (os.path.join(self.outputDir, "pdf", pdf, "tmp", "tesseract", "*.hocr"),
os.path.join(os.path.abspath(self.outputDir), "pdf", pdf, "HOCR"))
self.addTask(label="mv_%i" % (pdf_counter), command=cmd, isForceLocal=True,
dependencies=pdftk_jobs, nCores=1, memMb=32)
cmd = "parse_hocr %s %s" % (
os.path.join(os.path.abspath(self.outputDir), "pdf", pdf, "HOCR"),
os.path.join(os.path.abspath(self.outputDir), "pdf", pdf, "%s.xml" % (pdf)))
self.addTask(label="generate_hocr_%i" % (pdf_counter), command=cmd, isForceLocal=True,
dependencies="mv_%i" % (pdf_counter), nCores=1, memMb=250)
if not self.intermediate:
cmd = "rm -rf %s" % (os.path.join(self.outputDir, "pdf", pdf, "tmp"))
self.addTask(label="cleanup_%i" % (pdf_counter), command=cmd, isForceLocal=True,
dependencies="mv_%i" % (pdf_counter), nCores=1, memMb=32)
def strip_files_of_spaces(current_path, old_path):
"""Strips inputfiles of spaces to avoid bugs and also for better usage and readability."""
os.chdir(current_path)
for f in os.listdir("."):
r = f.replace(" ", "_")
if(r != f):
os.rename(f, r)
os.chdir(old_path)
def analyze_jobs(input_dir, image_suffix="tiff", skip_pdf=False, skip_images=False):
pdfs = {}
images = {}
files = os.listdir(os.path.abspath(input_dir))
dirs = list(filter(lambda x: os.path.isdir(os.path.join(os.path.abspath(input_dir), x)), files))
# Scan root input dir
if not skip_pdf:
pdfs_ = list(filter(lambda x: x.endswith(".pdf"), files))
pdfs = {".".join(k.split(".")[:-1]): os.path.join(os.path.abspath(input_dir), k) for k in pdfs_}
if not skip_images:
print("sdf")
if list(filter(lambda x: x.endswith(".%s" % (image_suffix)), files)):
images["input_root"] = os.path.abspath(input_dir)
# Scan subdirectories for inputs if available
for d in dirs:
strip_files_of_spaces(os.path.join(input_dir, d), os.getcwd())
files = os.listdir(os.path.join(input_dir, d))
if not skip_pdf:
for p in list(filter(lambda x: x.endswith(".pdf"), files)):
pdfs[".".join(p.split(".")[:-1])] = os.path.join(os.path.abspath(input_dir), d, p)
if not skip_images:
if sorted(list(filter(lambda x: x.endswith(".%s" % (image_suffix)), files))):
images[d] = os.path.join(os.path.abspath(input_dir), d)
return {"pdf": pdfs, "images": images}
def main():
args = parse_arguments()
# DICT{DICT}
# 'pdf' :: {name: path}
# 'images' :: {name: path}
current_path = os.getcwd()
strip_files_of_spaces(args.input_dir, current_path)
jobs = analyze_jobs(args.input_dir, image_suffix=args.suffix, skip_pdf=args.skip_pdf, skip_images=args.skip_images)
wflow = OCRWorkflow(jobs, args.input_dir, args.output_dir, args.suffix, args.lang, args.pdf, args.intermediate,
args.skip_bin,
args.nCores, args.mem,
args.dry_run)
retval = wflow.run(mode="local", nCores=args.nCores, memMb=args.mem, isDryRun=args.dry_run)
sys.exit(retval)
if __name__ == "__main__":
main()
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