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rsna-atd

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ziq commited on
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5328cf0
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1 Parent(s): f3a9409

Update rsna-atd.py

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  1. rsna-atd.py +68 -68
rsna-atd.py CHANGED
@@ -32,27 +32,27 @@ class RSNAATD(datasets.GeneratorBasedBuilder):
32
  description=_DESCRIPTION,
33
  features=datasets.Features(
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  {
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- "test": datasets.Value("string")
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- # "patient_id": datasets.Value("int64"),
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- # "series_id": datasets.Value("int64"),
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- # "image": datasets.Array3D(shape=(None, 512, 512), dtype="uint8"),
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- # "mask": datasets.Array3D(shape=(None, 512, 512), dtype="uint8"),
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- # "aortic_hu": datasets.Value("float64"),
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- # "incomplete_organ": datasets.Value("int64"),
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- # "bowel_healthy": datasets.Value("int64"),
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- # "bowel_injury": datasets.Value("int64"),
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- # "extravasation_healthy": datasets.Value("int64"),
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- # "extravasation_injury": datasets.Value("int64"),
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- # "kidney_healthy": datasets.Value("int64"),
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- # "kidney_low": datasets.Value("int64"),
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- # "kidney_high": datasets.Value("int64"),
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- # "liver_healthy": datasets.Value("int64"),
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- # "liver_low": datasets.Value("int64"),
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- # "liver_high": datasets.Value("int64"),
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- # "spleen_healthy": datasets.Value("int64"),
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- # "spleen_low": datasets.Value("int64"),
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- # "spleen_high": datasets.Value("int64"),
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- # "any_injury": datasets.Value("int64"),
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  }
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  ),
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  supervised_keys=None,
@@ -81,53 +81,53 @@ class RSNAATD(datasets.GeneratorBasedBuilder):
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  def _generate_examples(self, images, masks, metadata):
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  df = pd.read_csv(metadata)
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- for i, image in enumerate(images):
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- yield i, {
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- "test": image
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- }
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- return
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- for idx, data in enumerate(df.to_numpy()):
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- # image, mask = [hkl.load(f"images/{data[0]}")], [hkl.load(f"masks/{data[0]}")]
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- # (
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- # patient_id,
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- # series_id,
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- # aortic_hu,
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- # incomplete_organ,
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- # bowel_healthy,
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- # bowel_injury,
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- # extravasation_healthy,
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- # extravasation_injury,
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- # kidney_healthy,
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- # kidney_low,
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- # kidney_high,
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- # liver_healthy,
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- # liver_low,
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- # liver_high,
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- # spleen_healthy,
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- # spleen_low,
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- # spleen_high,
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- # any_injury,
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- # ) = data[1:]
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  yield idx, {
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- # "patient_id": patient_id,
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- # "series_id": series_id,
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- # "image": image,
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- # "mask": mask,
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- # "aortic_hu": aortic_hu,
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- # "incomplete_organ": incomplete_organ,
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- # "bowel_healthy": bowel_healthy,
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- # "bowel_injury": bowel_injury,
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- # "extravasation_healthy": extravasation_healthy,
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- # "extravasation_injury": extravasation_injury,
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- # "kidney_healthy": kidney_healthy,
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- # "kidney_low": kidney_low,
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- # "kidney_high": kidney_high,
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- # "liver_healthy": liver_healthy,
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- # "liver_low": liver_low,
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- # "liver_high": liver_high,
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- # "spleen_healthy": spleen_healthy,
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- # "spleen_low": spleen_low,
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- # "spleen_high": spleen_high,
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- # "any_injury": any_injury,
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  }
 
32
  description=_DESCRIPTION,
33
  features=datasets.Features(
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  {
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+ # "test": datasets.Value("string")
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+ "patient_id": datasets.Value("int64"),
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+ "series_id": datasets.Value("int64"),
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+ "image": datasets.Array3D(shape=(None, 512, 512), dtype="uint8"),
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+ "mask": datasets.Array3D(shape=(None, 512, 512), dtype="uint8"),
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+ "aortic_hu": datasets.Value("float64"),
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+ "incomplete_organ": datasets.Value("int64"),
42
+ "bowel_healthy": datasets.Value("int64"),
43
+ "bowel_injury": datasets.Value("int64"),
44
+ "extravasation_healthy": datasets.Value("int64"),
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+ "extravasation_injury": datasets.Value("int64"),
46
+ "kidney_healthy": datasets.Value("int64"),
47
+ "kidney_low": datasets.Value("int64"),
48
+ "kidney_high": datasets.Value("int64"),
49
+ "liver_healthy": datasets.Value("int64"),
50
+ "liver_low": datasets.Value("int64"),
51
+ "liver_high": datasets.Value("int64"),
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+ "spleen_healthy": datasets.Value("int64"),
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+ "spleen_low": datasets.Value("int64"),
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+ "spleen_high": datasets.Value("int64"),
55
+ "any_injury": datasets.Value("int64"),
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  }
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  ),
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  supervised_keys=None,
 
81
 
82
  def _generate_examples(self, images, masks, metadata):
83
  df = pd.read_csv(metadata)
84
+ # for i, image in enumerate(images):
85
+ # yield i, {
86
+ # "test": image
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+ # }
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+ # return
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+ for idx, (data, (image_path, image_obj), (mask_path, mask_obj)) in enumerate(zip(df.to_numpy(), images, masks)):
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+ image, mask = [hkl.load(image_obj)], [hkl.load(mask_obj)]
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+ (
92
+ patient_id,
93
+ series_id,
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+ aortic_hu,
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+ incomplete_organ,
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+ bowel_healthy,
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+ bowel_injury,
98
+ extravasation_healthy,
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+ extravasation_injury,
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+ kidney_healthy,
101
+ kidney_low,
102
+ kidney_high,
103
+ liver_healthy,
104
+ liver_low,
105
+ liver_high,
106
+ spleen_healthy,
107
+ spleen_low,
108
+ spleen_high,
109
+ any_injury,
110
+ ) = data[1:]
111
 
112
  yield idx, {
113
+ "patient_id": patient_id,
114
+ "series_id": series_id,
115
+ "image": image,
116
+ "mask": mask,
117
+ "aortic_hu": aortic_hu,
118
+ "incomplete_organ": incomplete_organ,
119
+ "bowel_healthy": bowel_healthy,
120
+ "bowel_injury": bowel_injury,
121
+ "extravasation_healthy": extravasation_healthy,
122
+ "extravasation_injury": extravasation_injury,
123
+ "kidney_healthy": kidney_healthy,
124
+ "kidney_low": kidney_low,
125
+ "kidney_high": kidney_high,
126
+ "liver_healthy": liver_healthy,
127
+ "liver_low": liver_low,
128
+ "liver_high": liver_high,
129
+ "spleen_healthy": spleen_healthy,
130
+ "spleen_low": spleen_low,
131
+ "spleen_high": spleen_high,
132
+ "any_injury": any_injury,
133
  }