def process_paper_tar(paper_tarname: str) -> None:
parts = paper_tarname.split('/')
partition_name = parts[-2]
paper_name = os.path.splitext(parts[-1])[0]
result_path = os.path.join(ARXIV_FIGURE_JSON_DIR, partition_name,
paper_name + '.json')
paper_dir = os.path.join(ARXIV_SRC_DIR, partition_name, paper_name)
if os.path.isfile(result_path):
return
print('.', end='', flush=True)
try:
file_util.extract_tarfile(paper_tarname, paper_dir)
except tarfile.ReadError:
logging.debug('File %s is not a tar' % paper_tarname)
return
diffs = generate_diffs(paper_dir)
if diffs is None:
return
figures_by_page = dict()
for diff in diffs:
figures = consume_diff_generate_figures(diff)
if figures is None:
continue
page_name = os.path.dirname(
diff) + '/' + diff[diff.find('black.pdf-'):]
figures_by_page[page_name] = figures
file_util.safe_makedirs(os.path.dirname(result_path))
file_util.write_json_atomic(
result_path,
config.JsonSerializable.serialize(figures_by_page),
sort_keys=True)
def extract_figures_json(pdf_path, page_image_paths, pdffigures_output,
output_directory):
"""Extract information about figures to JSON and save to disk.
:param str pdf_path: path to the PDF from which to extract
figures.
:returns: path to the JSON file containing the detection results.
"""
page_images_array = np.array(
[imread(page_image_path) for page_image_path in page_image_paths])
detector = get_detector()
figure_boxes_by_page = detector.get_detections(page_images_array)
pdffigures_captions = pdffigures_wrapper.get_captions(
pdffigures_output=pdffigures_output,
target_dpi=settings.DEFAULT_INFERENCE_DPI)
figures_by_page = []
for page_num in range(len(page_image_paths)):
figure_boxes = figure_boxes_by_page[page_num]
pf_page_captions = [
caption for caption in pdffigures_captions
if caption.page == page_num
]
caption_boxes = [
caption.caption_boundary for caption in pf_page_captions
]
figure_indices, caption_indices = figure_utils.pair_boxes(
figure_boxes, caption_boxes)
page_image = page_images_array[page_num]
pad_pixels = PAD_FACTOR * min(page_image.shape[:2])
for (figure_idx, caption_idx) in zip(figure_indices, caption_indices):
figures_by_page.append(
Figure(figure_boundary=figure_boxes[figure_idx].expand_box(
pad_pixels).crop_to_page(
page_image.shape).crop_whitespace_edges(page_image),
caption_boundary=caption_boxes[caption_idx],
caption_text=pf_page_captions[caption_idx].caption_text,
name=pf_page_captions[caption_idx].name,
figure_type=pf_page_captions[caption_idx].figure_type,
page=page_num))
pdf_detection_result = PdfDetectionResult(
pdf=pdf_path,
figures=figures_by_page,
dpi=settings.DEFAULT_INFERENCE_DPI,
raw_detected_boxes=figure_boxes_by_page,
raw_pdffigures_output=pdffigures_output)
output_path = os.path.join(
output_directory,
os.path.basename(pdf_path)[:-4] + 'deepfigures-results.json')
file_util.write_json_atomic(output_path,
pdf_detection_result.to_dict(),
indent=2,
sort_keys=True)
return output_path
def process_paper_tar(self):
print("------Processing paper_tarname : {}--------".format(
self.paper_tarname))
parts = self.paper_tarname.split('/')
partition_name = parts[-2]
paper_name = os.path.splitext(parts[-1])[0]
result_path = os.path.join(self.ARXIV_FIGURE_JSON_DIR, partition_name,
paper_name + '.json')
paper_dir = os.path.join(self.ARXIV_SRC_DIR, partition_name,
paper_name)
if os.path.isfile(result_path):
return
print('.', end='', flush=True)
try:
file_util.extract_tarfile(self.paper_tarname, paper_dir)
except tarfile.ReadError:
logging.debug('File %s is not a tar' % self.paper_tarname)
return
try:
diffs, black_ims_paths = self.generate_diffs(paper_dir)
except TypeError:
return
if diffs is None:
return
figures_by_page = dict()
for idx, diff in enumerate(diffs):
figures = self.consume_diff_generate_figures(diff)
if figures is None:
continue
try:
figures = self.augment_images(black_ims_paths[idx], figures)
except Exception as e:
print(
"Error augmenting images for image path: {}. Exception message: {}"
.format(black_ims_paths[idx], e))
page_name = os.path.dirname(
diff) + '/' + diff[diff.find('black.pdf-'):]
figures_by_page[page_name] = figures
file_util.safe_makedirs(os.path.dirname(result_path))
file_util.write_json_atomic(
result_path,
config.JsonSerializable.serialize(figures_by_page),
sort_keys=True)
figure_boundaries, caption_boundaries = transform_figure_json(
result_path, self.ignore_pages_with_no_figures)
return result_path, figure_boundaries, caption_boundaries
def run_full_pipeline(
tarpath: str, skip_done: bool=True, save_intermediate: bool=False
) -> None:
foldername = str(os.path.basename(tarpath).split('.')[0])
result_path = LOCAL_FIGURE_JSON_DIR + get_bin(
tarpath
) + foldername + '.json'
if skip_done and file_util.exists(result_path):
return
d = LOCAL_INTERMEDIATE_DIR + get_bin(tarpath)
while True:
try:
file_util.extract_tarfile(tarpath, d, streaming=False)
# botocore.vendored.requests.packages.urllib3.exceptions.ReadTimeoutError can't be caught because it doesn't
# inherit from BaseException, so don't use streaming
break
except FileNotFoundError as e:
logging.exception('Failure reading %s, retrying' % tarpath)
except ReadTimeout as e:
logging.exception('Timeout reading %s, retrying' % tarpath)
pdfs = glob.glob(d + foldername + '/' + '*.pdf')
res = dict()
for pdf in pdfs:
sha1sum = file_util.compute_sha1(pdf)
with open(pdf + '.sha1', 'w') as f:
print(sha1sum, file=f)
paper_figures = match_figures(pdf)
if paper_figures is not None:
res.update(paper_figures)
if save_intermediate:
intermediate_path = PUBMED_INTERMEDIATE_DIR + get_bin(
tarpath
) + foldername + '/'
for file in glob.glob(d + '/' + foldername + '/' + '*'):
file_util.copy(file, intermediate_path + os.path.basename(file))
file_util.safe_makedirs(os.path.dirname(result_path))
file_util.write_json_atomic(
result_path,
config.JsonSerializable.serialize(res),
indent=2,
sort_keys=True
)
