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rsna-atd

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1 Parent(s): cd70113

Update rsna-atd.py

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  1. rsna-atd.py +65 -62
rsna-atd.py CHANGED
@@ -32,27 +32,27 @@ class RSNAATD(datasets.GeneratorBasedBuilder):
32
  description=_DESCRIPTION,
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  features=datasets.Features(
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  {
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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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- # datasets.Sequence(feature=datasets.Array2D(shape=(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,
@@ -81,48 +81,51 @@ 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 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,
121
- "liver_healthy": liver_healthy,
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- "liver_low": liver_low,
123
- "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"),
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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"),
46
+ # "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
 
82
  def _generate_examples(self, images, masks, metadata):
83
  df = pd.read_csv(metadata)
84
+ yield 0, {
85
+ "test": images
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+ }
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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,
102
+ # liver_low,
103
+ # liver_high,
104
+ # spleen_healthy,
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+ # spleen_low,
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+ # spleen_high,
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+ # any_injury,
108
+ # ) = data[1:]
109
 
110
  yield idx, {
111
+ # "patient_id": patient_id,
112
+ # "series_id": series_id,
113
+ # "image": image,
114
+ # "mask": mask,
115
+ # "aortic_hu": aortic_hu,
116
+ # "incomplete_organ": incomplete_organ,
117
+ # "bowel_healthy": bowel_healthy,
118
+ # "bowel_injury": bowel_injury,
119
+ # "extravasation_healthy": extravasation_healthy,
120
+ # "extravasation_injury": extravasation_injury,
121
+ # "kidney_healthy": kidney_healthy,
122
+ # "kidney_low": kidney_low,
123
+ # "kidney_high": kidney_high,
124
+ # "liver_healthy": liver_healthy,
125
+ # "liver_low": liver_low,
126
+ # "liver_high": liver_high,
127
+ # "spleen_healthy": spleen_healthy,
128
+ # "spleen_low": spleen_low,
129
+ # "spleen_high": spleen_high,
130
+ # "any_injury": any_injury,
131
  }