Update rsna-atd.py
Browse files- rsna-atd.py +61 -22
rsna-atd.py
CHANGED
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@@ -32,26 +32,26 @@ class RSNAATD(datasets.GeneratorBasedBuilder):
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description=_DESCRIPTION,
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features=datasets.Features(
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{
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"image": datasets.Array3D(shape=(None, 512, 512), dtype=np.uint8),
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"mask": datasets.Array3D(shape=(None, 512, 512), dtype=np.uint8),
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}
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),
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supervised_keys=None,
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@@ -81,9 +81,48 @@ 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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yield idx, {
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# for idx, ((image_path), (mask_path)) in enumerate(zip(images, masks)):
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# # row = df.loc[df["path"] == image_path.lower().replace("images/", "")]
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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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"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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# "image": datasets.Array3D(shape=(None, 512, 512), dtype=np.uint8),
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# "mask": datasets.Array3D(shape=(None, 512, 512), dtype=np.uint8),
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}
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),
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supervised_keys=None,
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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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"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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}
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# for idx, ((image_path), (mask_path)) in enumerate(zip(images, masks)):
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# # row = df.loc[df["path"] == image_path.lower().replace("images/", "")]
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