zzh99 commited on
Commit
d3c9981
1 Parent(s): 167f152

upload pmc_oa

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Files changed (4) hide show
  1. .gitattributes +2 -0
  2. pmc_oa.jsonl +3 -0
  3. pmc_oa.py +99 -44
  4. pmc_oa_beta.jsonl +3 -0
.gitattributes CHANGED
@@ -55,3 +55,5 @@ saved_model/**/* filter=lfs diff=lfs merge=lfs -text
55
  test.jsonl filter=lfs diff=lfs merge=lfs -text
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  train.jsonl filter=lfs diff=lfs merge=lfs -text
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  valid.jsonl filter=lfs diff=lfs merge=lfs -text
 
 
 
55
  test.jsonl filter=lfs diff=lfs merge=lfs -text
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  train.jsonl filter=lfs diff=lfs merge=lfs -text
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  valid.jsonl filter=lfs diff=lfs merge=lfs -text
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+ pmc_oa_beta.jsonl filter=lfs diff=lfs merge=lfs -text
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+ pmc_oa.jsonl filter=lfs diff=lfs merge=lfs -text
pmc_oa.jsonl ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:05702cd5fb41ebf55a7226ca3c53e68edff4b4455224d7e6ff9d01157f5aaf23
3
+ size 454568741
pmc_oa.py CHANGED
@@ -5,10 +5,8 @@ import jsonlines
5
 
6
  import datasets
7
 
8
-
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  logger = datasets.logging.get_logger(__name__)
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11
-
12
  _CITATION = """\
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  @article{lin2023pmc,
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  title={PMC-CLIP: Contrastive Language-Image Pre-training using Biomedical Documents},
@@ -28,57 +26,114 @@ including image-text retrieval on ROCO, MedMNIST image classification, Medical V
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  _HOMEPAGE = "https://weixionglin.github.io/PMC-CLIP/"
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- _URL = "https://huggingface.co/datasets/axiong/pmc_oa/resolve/main/"
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- _URLS = {
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- "images": _URL + "images.zip",
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- "train": _URL + "train.jsonl",
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- "valid": _URL + "valid.jsonl",
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- "test": _URL + "test.jsonl"
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  }
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39
 
 
 
 
 
 
 
 
 
 
 
 
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  class PMC_OA(datasets.GeneratorBasedBuilder):
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- """PMC_OA Dataset."""
 
 
 
 
 
 
 
 
 
 
 
 
42
 
43
  def _info(self):
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- return datasets.DatasetInfo(
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- description=_DESCRIPTION,
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- features=datasets.Features(
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- {
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- "image": datasets.Image(),
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- "caption": datasets.Value("string"),
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- }
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- ),
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- supervised_keys=None,
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- homepage=_HOMEPAGE,
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- citation=_CITATION,
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- )
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
56
 
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  def _split_generators(self, dl_manager):
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- data_dir = dl_manager.download_and_extract(_URLS)
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-
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- return [
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- datasets.SplitGenerator(name=datasets.Split.TRAIN, gen_kwargs={"filepath": data_dir['train'], "image_dir": data_dir['images']}),
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- datasets.SplitGenerator(name=datasets.Split.VALIDATION, gen_kwargs={"filepath": data_dir['valid'], "image_dir": data_dir['images']}),
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- datasets.SplitGenerator(name=datasets.Split.TEST, gen_kwargs={"filepath": data_dir['test'], "image_dir": data_dir['images']}),
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- ]
 
 
 
 
 
 
 
65
 
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  def _generate_examples(self, filepath, image_dir):
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- """This function returns the examples in the raw (text) form."""
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  logger.info("generating examples from = %s", filepath)
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-
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  with jsonlines.open(filepath) as reader:
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- _id = 0
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- for obj in reader:
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- relative_image_path = obj['image']
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- image_path = os.path.join(image_dir, "caption_T060_filtered_top4_sep_v0_subfigures", relative_image_path)
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- caption = obj['caption']
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- yield _id, {
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- "image": {
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- "path": image_path,
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- "bytes": open(image_path, "rb").read(),
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- },
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- "caption": caption,
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- }
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- _id += 1
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-
 
 
 
 
 
 
 
 
 
 
 
 
 
 
5
 
6
  import datasets
7
 
 
8
  logger = datasets.logging.get_logger(__name__)
9
 
 
10
  _CITATION = """\
11
  @article{lin2023pmc,
12
  title={PMC-CLIP: Contrastive Language-Image Pre-training using Biomedical Documents},
 
26
 
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  _HOMEPAGE = "https://weixionglin.github.io/PMC-CLIP/"
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+ _URLs = {
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+ "images": "https://huggingface.co/datasets/axiong/pmc_oa/resolve/main/images.zip",
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+ "pmc_oa_beta": "https://huggingface.co/datasets/axiong/pmc_oa/resolve/main/pmc_oa_beta.jsonl",
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+ "pmc_oa": "https://huggingface.co/datasets/axiong/pmc_oa/resolve/main/pmc_oa.jsonl",
 
 
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  }
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+ class PMC_OA_Config(datasets.BuilderConfig):
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+ """BuilderConfig for PMC_OA"""
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+
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+ def __init__(self, **kwargs):
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+ """
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+ Args:
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+ **kwargs: keyword arguments forwarded to super.
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+ """
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+ super(PMC_OA_Config, self).__init__(version=datasets.Version("1.0.0", ""), **kwargs)
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+
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+
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  class PMC_OA(datasets.GeneratorBasedBuilder):
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+ """PMC_OA Dataset"""
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+
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+ VERSION = datasets.Version("1.0.0")
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+ BUILDER_CONFIGS = [
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+ PMC_OA_Config(
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+ name="pmc_oa_beta",
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+ description="<subfigure, caption> pairs. Subfigures detected by a DETR model.",
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+ ),
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+ PMC_OA_Config(
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+ name="pmc_oa",
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+ description="<subfigure, subcaption> pairs. Subfigures detected by a DETR model. Subcaptions detected by ChatGPT and aligned with subfigures.",
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+ ),
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+ ]
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62
  def _info(self):
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+ if self.config.name == "pmc_oa_beta":
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+ return datasets.DatasetInfo(
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+ description=_DESCRIPTION,
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+ features=datasets.Features(
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+ {
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+ "image": datasets.Value("string"),
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+ "caption": datasets.Value("string"),
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+ }
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+ ),
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+ supervised_keys=None,
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+ citation=_CITATION,
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+ homepage=_HOMEPAGE,
75
+ )
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+ elif self.config.name == "pmc_oa":
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+ return datasets.DatasetInfo(
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+ description=_DESCRIPTION,
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+ features=datasets.Features(
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+ {
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+ "image": datasets.Value("string"),
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+ "caption": datasets.Value("string"),
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+ "alignment_type": datasets.Value("string"),
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+ "alignment_score": datasets.Value("float"),
85
+ }
86
+ ),
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+ supervised_keys=None,
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+ citation=_CITATION,
89
+ homepage=_HOMEPAGE,
90
+ )
91
 
92
  def _split_generators(self, dl_manager):
93
+ """Returns SplitGenerators."""
94
+ downloaded_files = dl_manager.download_and_extract(_URLs)
95
+ if self.config.name == "pmc_oa_beta":
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+ return [
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+ datasets.SplitGenerator(
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+ name=datasets.Split.TRAIN, gen_kwargs={"filepath": downloaded_files["pmc_oa_beta"], "image_dir": downloaded_files['images']}
99
+ )
100
+ ]
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+ elif self.config.name == "pmc_oa":
102
+ return [
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+ datasets.SplitGenerator(
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+ name=datasets.Split.TRAIN, gen_kwargs={"filepath": downloaded_files["pmc_oa"], "image_dir": downloaded_files['images']}
105
+ )
106
+ ]
107
 
108
  def _generate_examples(self, filepath, image_dir):
109
+ """Yields examples."""
110
  logger.info("generating examples from = %s", filepath)
111
+
112
  with jsonlines.open(filepath) as reader:
113
+ for _id, obj in enumerate(reader):
114
+ if self.config.name == "pmc_oa_beta":
115
+ relative_image_path = obj['image']
116
+ image_path = os.path.join(image_dir, "caption_T060_filtered_top4_sep_v0_subfigures", relative_image_path)
117
+ caption = obj['caption']
118
+ yield _id, {
119
+ "image": {
120
+ "path": image_path,
121
+ "bytes": open(image_path, "rb").read(),
122
+ },
123
+ "caption": caption,
124
+ }
125
+ elif self.config.name == "pmc_oa":
126
+ relative_image_path = obj['image']
127
+ image_path = os.path.join(image_dir, "caption_T060_filtered_top4_sep_v0_subfigures", relative_image_path)
128
+ caption = obj['caption']
129
+ alignment_type = obj['alignment_type']
130
+ alignment_score = obj['alignment_score']
131
+ yield _id, {
132
+ "image": {
133
+ "path": image_path,
134
+ "bytes": open(image_path, "rb").read(),
135
+ },
136
+ "caption": caption,
137
+ "alignment_type": alignment_type,
138
+ "alignment_score": alignment_score,
139
+ }
pmc_oa_beta.jsonl ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:0b2d7178ac8b329edad198a6ad25bc86c212fd2c1373d626f6767ede61cfa2ae
3
+ size 1302951005