axiong zzh99 commited on
Commit
d42b8f9
1 Parent(s): 167f152

upload pmc_oa (#4)

Browse files

- upload pmc_oa (d3c99812a696878a30bf5b1cf779f10c8bae0f66)


Co-authored-by: Ziheng Zhao <[email protected]>

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
-
9
  logger = datasets.logging.get_logger(__name__)
10
 
11
-
12
  _CITATION = """\
13
  @article{lin2023pmc,
14
  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
28
 
29
  _HOMEPAGE = "https://weixionglin.github.io/PMC-CLIP/"
30
 
31
- _URL = "https://huggingface.co/datasets/axiong/pmc_oa/resolve/main/"
32
- _URLS = {
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- "images": _URL + "images.zip",
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- "train": _URL + "train.jsonl",
35
- "valid": _URL + "valid.jsonl",
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- "test": _URL + "test.jsonl"
37
  }
38
 
39
 
 
 
 
 
 
 
 
 
 
 
 
40
  class PMC_OA(datasets.GeneratorBasedBuilder):
41
- """PMC_OA Dataset."""
 
 
 
 
 
 
 
 
 
 
 
 
42
 
43
  def _info(self):
44
- return datasets.DatasetInfo(
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- description=_DESCRIPTION,
46
- features=datasets.Features(
47
- {
48
- "image": datasets.Image(),
49
- "caption": datasets.Value("string"),
50
- }
51
- ),
52
- supervised_keys=None,
53
- homepage=_HOMEPAGE,
54
- citation=_CITATION,
55
- )
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
56
 
57
  def _split_generators(self, dl_manager):
58
- data_dir = dl_manager.download_and_extract(_URLS)
59
-
60
- return [
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- datasets.SplitGenerator(name=datasets.Split.TRAIN, gen_kwargs={"filepath": data_dir['train'], "image_dir": data_dir['images']}),
62
- datasets.SplitGenerator(name=datasets.Split.VALIDATION, gen_kwargs={"filepath": data_dir['valid'], "image_dir": data_dir['images']}),
63
- datasets.SplitGenerator(name=datasets.Split.TEST, gen_kwargs={"filepath": data_dir['test'], "image_dir": data_dir['images']}),
64
- ]
 
 
 
 
 
 
 
65
 
66
  def _generate_examples(self, filepath, image_dir):
67
- """This function returns the examples in the raw (text) form."""
68
  logger.info("generating examples from = %s", filepath)
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-
70
  with jsonlines.open(filepath) as reader:
71
- _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(),
80
- },
81
- "caption": caption,
82
- }
83
- _id += 1
84
-
 
 
 
 
 
 
 
 
 
 
 
 
 
 
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
 
27
  _HOMEPAGE = "https://weixionglin.github.io/PMC-CLIP/"
28
 
29
+ _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",
 
 
33
  }
34
 
35
 
36
+ class PMC_OA_Config(datasets.BuilderConfig):
37
+ """BuilderConfig for PMC_OA"""
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+
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+ def __init__(self, **kwargs):
40
+ """
41
+ Args:
42
+ **kwargs: keyword arguments forwarded to super.
43
+ """
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+ super(PMC_OA_Config, self).__init__(version=datasets.Version("1.0.0", ""), **kwargs)
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+
46
+
47
  class PMC_OA(datasets.GeneratorBasedBuilder):
48
+ """PMC_OA Dataset"""
49
+
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+ VERSION = datasets.Version("1.0.0")
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+ BUILDER_CONFIGS = [
52
+ PMC_OA_Config(
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+ name="pmc_oa_beta",
54
+ description="<subfigure, caption> pairs. Subfigures detected by a DETR model.",
55
+ ),
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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.",
59
+ ),
60
+ ]
61
 
62
  def _info(self):
63
+ if self.config.name == "pmc_oa_beta":
64
+ return datasets.DatasetInfo(
65
+ description=_DESCRIPTION,
66
+ features=datasets.Features(
67
+ {
68
+ "image": datasets.Value("string"),
69
+ "caption": datasets.Value("string"),
70
+ }
71
+ ),
72
+ supervised_keys=None,
73
+ citation=_CITATION,
74
+ homepage=_HOMEPAGE,
75
+ )
76
+ elif self.config.name == "pmc_oa":
77
+ return datasets.DatasetInfo(
78
+ description=_DESCRIPTION,
79
+ features=datasets.Features(
80
+ {
81
+ "image": datasets.Value("string"),
82
+ "caption": datasets.Value("string"),
83
+ "alignment_type": datasets.Value("string"),
84
+ "alignment_score": datasets.Value("float"),
85
+ }
86
+ ),
87
+ supervised_keys=None,
88
+ 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":
96
+ return [
97
+ datasets.SplitGenerator(
98
+ name=datasets.Split.TRAIN, gen_kwargs={"filepath": downloaded_files["pmc_oa_beta"], "image_dir": downloaded_files['images']}
99
+ )
100
+ ]
101
+ elif self.config.name == "pmc_oa":
102
+ return [
103
+ datasets.SplitGenerator(
104
+ 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