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import datasets
import numpy as np
import pandas as pd
import hickle as hkl
from pathlib import Path
_CITATION = """\
@InProceedings{huggingface:dataset,
title = {rsna-atd},
author = {Yeow Zi Qin},
year = {2023}
}
"""
_DESCRIPTION = """\
The dataset is the processed version of Kaggle Competition: RSNA 2023 Abdominal Trauma Detection.
It comprises of segmentation of 205 series of CT scans with 5 classes (liver, spleen, right_kidney,
left_kidney, bowel).
"""
_NAME = "rsna-atd"
_HOMEPAGE = f"https://huggingface.co/datasets/ziq/{_NAME}"
_LICENSE = "MIT"
_DATA = f"https://huggingface.co/datasets/ziq/{_NAME}/resolve/main/data/"
class RSNAATD(datasets.GeneratorBasedBuilder):
def _info(self):
return datasets.DatasetInfo(
description=_DESCRIPTION,
features=datasets.Features(
{
# "test": datasets.Value("string"),
"patient_id": datasets.Value("int64"),
"series_id": datasets.Value("int64"),
"image_path": datasets.Value("string"),
"mask_path": datasets.Value("string"),
# "image": datasets.Array3D(shape=(None, 512, 512), dtype="uint8"),
# "mask": datasets.Array3D(shape=(None, 512, 512), dtype="uint8"),
"aortic_hu": datasets.Value("float64"),
"incomplete_organ": datasets.Value("int64"),
"bowel_healthy": datasets.Value("int64"),
"bowel_injury": datasets.Value("int64"),
"extravasation_healthy": datasets.Value("int64"),
"extravasation_injury": datasets.Value("int64"),
"kidney_healthy": datasets.Value("int64"),
"kidney_low": datasets.Value("int64"),
"kidney_high": datasets.Value("int64"),
"liver_healthy": datasets.Value("int64"),
"liver_low": datasets.Value("int64"),
"liver_high": datasets.Value("int64"),
"spleen_healthy": datasets.Value("int64"),
"spleen_low": datasets.Value("int64"),
"spleen_high": datasets.Value("int64"),
"any_injury": datasets.Value("int64"),
}
),
supervised_keys=None,
homepage=_HOMEPAGE,
citation=_CITATION,
)
def _split_generators(self, dl_manager):
train_images = dl_manager.download_and_extract(f"{_DATA}images.zip")
train_masks = dl_manager.download_and_extract(f"{_DATA}masks.zip")
metadata = dl_manager.download(f"{_DATA}metadata.csv")
train_images = dl_manager.iter_files(train_images)
train_masks = dl_manager.iter_files(train_masks)
return [
datasets.SplitGenerator(
name=datasets.Split.TRAIN,
gen_kwargs={
"images": train_images,
"masks": train_masks,
"metadata": metadata,
},
),
]
def _generate_examples(self, images, masks, metadata):
df = pd.read_csv(metadata)
# yield 0, {
# "test": images
# }
# return
# for i, image in enumerate(images):
# # image_path = Path(image).name
# # test = hkl.load(image_path)
# yield i, {
# "test": image
# }
# return
for idx, (image_path, mask_path) in enumerate(zip(sorted(images), sorted(masks))):
data = df.loc[df["path"] == Path(image_path).name].to_numpy()[0]
# image, mask = [hkl.load(image_path)], [hkl.load(mask_path)]
(
patient_id,
series_id,
aortic_hu,
incomplete_organ,
bowel_healthy,
bowel_injury,
extravasation_healthy,
extravasation_injury,
kidney_healthy,
kidney_low,
kidney_high,
liver_healthy,
liver_low,
liver_high,
spleen_healthy,
spleen_low,
spleen_high,
any_injury,
) = data[1:]
yield idx, {
"patient_id": patient_id,
"series_id": series_id,
"image_path": image_path,
"mask_path": mask_path,
"aortic_hu": aortic_hu,
"incomplete_organ": incomplete_organ,
"bowel_healthy": bowel_healthy,
"bowel_injury": bowel_injury,
"extravasation_healthy": extravasation_healthy,
"extravasation_injury": extravasation_injury,
"kidney_healthy": kidney_healthy,
"kidney_low": kidney_low,
"kidney_high": kidney_high,
"liver_healthy": liver_healthy,
"liver_low": liver_low,
"liver_high": liver_high,
"spleen_healthy": spleen_healthy,
"spleen_low": spleen_low,
"spleen_high": spleen_high,
"any_injury": any_injury,
}
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